diff --git a/.travis.yml b/.travis.yml
index ff283fa8346bc0eb139a8eb436105fc5a101d96c..8061a78164bfcaf90341ed297a5f72fdbee51b7f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -29,7 +29,7 @@ matrix:
- os: linux
dist: trusty
sudo: required
- env: CPPCHECK=yes CPPCHECK_VERSION=1.85
+ env: CPPCHECK=yes CPPCHECK_VERSION=1.86
# test using external blas with internal lapack
- os: linux
if: branch =~ ^test- OR type IN(pull_request)
diff --git a/CHANGES/v2.3.md b/CHANGES/v2.3.md
index 7bc6c9831c39f6f270d07a0c584d425a0fcb5e97..7bea09c6a5be64a47edc61359017e07605a480a8 100644
--- a/CHANGES/v2.3.md
+++ b/CHANGES/v2.3.md
@@ -261,6 +261,8 @@ For users:
For users:
- Fixed some openMP regression (some related to the whole codes and some specifics for Coordination and Multicolvar), this were compiler dependent so not all users may have experienced them
- Fixed an issue with \ref CS2BACKBONE when more than 2 chains were used
+- Fixed memory leak in \ref RDC.
+- Fixed segmentation fault with more than two CVs in reweighting \ref METAD (see \issue{399}, thanks to fiskissimo).
For developers:
- Small fix in LDFLAGS when enabling coverage.
diff --git a/CHANGES/v2.4.md b/CHANGES/v2.4.md
index 5e92dd979ba56aa3442eb942780709d0e8be245c..da6025dd115718e7c37f2c9887cdcd65e3e226d4 100644
--- a/CHANGES/v2.4.md
+++ b/CHANGES/v2.4.md
@@ -208,6 +208,8 @@ For users:
- Updated NAMD patches to version 2.12 and 2.13. Old patches have been removed.
- GROMACS patch for gromacs-2018.4.
- Fixed a bug in CS2BACKBONE when using more than 2 chains
+ - Fixed a threadsafety issue using forces on histograms
+ - Fixed error message suggesting wrong actions (see \issue{421}).
For developers:
- All fixed done in version 2.3.8
diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md
index bd29ab92d193e013ec9d62610b67798036f67d45..c134e580a2203fbfefa467ac76b87e8c6307c51c 100644
--- a/CHANGES/v2.5.md
+++ b/CHANGES/v2.5.md
@@ -94,13 +94,32 @@ Changes from version 2.4 which are relevant for developers:
in the core parts of the code have been eliminated.
- Exceptions cannot be disabled (`--disable-cxx-exceptions` option has been removed from `./configure`).
- Every exception thrown in PLUMED now also writes its message on PLUMED log.
+- Runtime loader in `Plumed.c` now works also when linked without `-rdynamic` (that is,
+ its names are not exported). Notice that all the combinations are expected to
+ work, that is: `Plumed.c` from <=2.4 or >=2.5 combined with libplumedKernel
+ from <=2.4 or >=2.5. In order to achieve this the following changes are implemented:
+ - libplumedKernel does not depend anymore on `Plumed.c`. This allows loading it even
+ in cases where names in the loader are not visible. The relevant function needed
+ to be compatible with `Plumed.c` <=2.4 are found using `dlsym`.
+ - `Plumed.c` does not need anymore libplumedKernel to register itself, but rather
+ searches the relevant functions using `dlsym`. In addition, if it is not able to
+ load `libplumedKernel` since the latter is <=2.4 and needs `Plumed.c` to be visible,
+ it just uses as a fallback `libplumed`, which should load properly.
+- In addition to the capability mentioned above, the MD-code interface has been significantly
+ improved and allows for:
+ - Translation of exception (allowing to mix PLUMED and an MD-code linked against a different C++ library).
+ - Possibility to choose the path to the PLUMED kernel while instantiating a Plumed object.
+ See the developer documentation for more information.
- The installation layout of shared libraries has been modified. In particular,
both `libplumed.so` and `plumed` links to `libplumedKernel.so`.
This reduces considerably the size of the installed package. In addition, it allows
using two-level namespace on OSX. Notice that this implies that on Linux one should
always set the `LD_LIBRARY_PATH` flag to have a working executable.
+- A smaller number of header files is installed. In particular, all the files that were historically generated in subdirectories
+ (such as `plumed/core/tools/Vector.h', just including `plumed/tools/Vector.h`) are not installed and the related include
+ statements are fixed. This makes the installed package smaller.
- List of preferred compilers (used when `CXX` or `CC` are not set) has been changed. On OSX, `./configure` will try `clang++/clang` as first choices.
-- Added `--enable-static-archive` to `./configure` to build a `libplumed.a` static library.
+- Added `--enable-static-archive` to `./configure` to build a `libplumed.a` static library (yes by default).
- Stop setting `DYLD_LIBRARY_PATH` in `sourceme.sh` and in modulefile. Notice that as of PLUMED v2.3.3
it should not be needed.
- Coverage scan is not anymore contained in developer manual. It can be found in a separate repository
@@ -109,21 +128,9 @@ Changes from version 2.4 which are relevant for developers:
- It is not possible anymore to use `make install prefix=/path`. Prefix can only be changed during `./configure` (see \issue{332}).
- Exception class has been rewritten to allow more extensive messages. Now also function name is shown.
- On linux, library is linked with `-Bsymbolic`.
-- A small number of header files is installed
-- When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearance is the effective one.
+- When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearence is the effective one.
- Internal BLAS and LAPACK libraries updated to gromacs 2018.
- Choosing `./configure --prefix=$PWD` does not lead anymore to deletion of all header files.
-- Runtime loader in `Plumed.c` now works also when linked without `-rdynamic` (that is,
- its names are not exported). Notice that all the combinations are expected to
- work, that is: `Plumed.c` from <=2.4 or >=2.5 combined with libplumedKernel
- from <=2.4 or >=2.5. In order to achieve this the following changes are implemented:
- - libplumedKernel does not depend anymore on `Plumed.c`. This allows loading it even
- in cases where names in the loader are not visible. The relevant function needed
- to be compatible with `Plumed.c` <=2.4 are found using `dlsym`.
- - `Plumed.c` does not need anymore libplumedKernel to register itself, but rather
- searches the relevant functions using `dlsym`. In addition, if it is not able to
- load `libplumedKernel` since the latter is <=2.4 and needs `Plumed.c` to be visible,
- it just uses as a fallback `libplumed`, which should load properly.
- A copy of `plumed-runtime` is installed in `prefix/lib/plumed` and can be used for testing.
- Absolute/relative soname/install_name can be configured on linux/OSX. This feature is only
for testing, the default choice is the typical one used on the respective operating system.
@@ -134,6 +141,7 @@ Fixes done after beta (this list will be merged to the one above):
- (users) added API to set the number of used openMP threads from the linked code, updated gromacs 2018.3 patch to use it
- (users) Fixed sign in Cartesian components of \ref PUCKERING with 6 membered rings (thanks to Carol Simoes and Javi Iglesias).
- (users) LAMMPS patch has been finally removed. Notice that LAMMPS natively supports PLUMED now.
+- (users) AMBER patch has been finally removed. Notice that AMBER (sander module) natively supports PLUMED starting with version 15.
- (developers) plumed can be compiled with arrayfire to enable for gpu code. \ref SAXS collective variable is available as part of the isdb module to provide an example of a gpu implementation for a CV
diff --git a/patches/amber14.config b/patches/amber14.config
deleted file mode 100644
index f8539419a562ec0643248bb9497fb5de62a3faf2..0000000000000000000000000000000000000000
--- a/patches/amber14.config
+++ /dev/null
@@ -1,32 +0,0 @@
-
-
-function plumed_preliminary_test(){
-# check if the README contains the word AMBER and if amber has been already configured
- grep -q Amber README 1>/dev/null 2>/dev/null
-}
-
-function plumed_patch_info(){
-cat << EOF
-
-PLUMED can be incorporated into amber (sander module) using the standard patching procedure.
-Patching must be done in the root directory of amber _before_
-compilation.
-
-To enable PLUMED in a sander simulation one should use
-add to the cntrl input namelist these two fields:
-
-plumed=1 , plumedfile='plumed.dat'
-
-The first is switching PLUMED on, the second is specifying the name of the PLUMED
-input file.
-
-This patch is compatible with the MPI version of sander and supports
-multisander. However, replica exchange is not supported.
-Multisander can thus only be used for multiple walkers
-metadynamics or for ensemble restraints.
-
-For more information on amber you should visit http://ambermd.org
-
-EOF
-}
-
diff --git a/patches/amber14.diff/AmberTools/src/sander/Makefile b/patches/amber14.diff/AmberTools/src/sander/Makefile
deleted file mode 100644
index 03d5dc447e9e76712195e4fef0d32d930134f8f4..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/Makefile
+++ /dev/null
@@ -1,423 +0,0 @@
-#
-#************************************************************************
-# AMBER **
-# **
-# Copyright (c) 1986, 1991, 1995, 1997, 1999 **
-# Regents of the University of California **
-# All Rights Reserved. **
-# **
-# This software provided pursuant to a license agreement containing **
-# restrictions on its disclosure, duplication, and use. This software **
-# contains confidential and proprietary information, and may not be **
-# extracted or distributed, in whole or in part, for any purpose **
-# whatsoever, without the express written permission of the authors. **
-# This notice, and the associated author list, must be attached to **
-# all copies, or extracts, of this software. Any additional **
-# restrictions set forth in the license agreement also apply to this **
-# software. **
-#************************************************************************
-#
-# Makefile for Amber 14 SANDER
-#
-include ../config.h
-include ../../../Plumed.inc
-
-CONFIG_FILE=../config.h
-CONFIG_COMMAND=configure
-PARALLEL_TOKEN=DMPI
-
-# Sander Fortran source files are free format
-# Add also search paths for .mod files
-LOCALFLAGS = $(FREEFORMAT_FLAG) -I../pbsa -I../sqm -I../rism -I../../../include
-
-SHELL=/bin/sh
-VPATH=
-
-EMILOBJ= \
- emil.o mdin_emil_dat.o
-
-NCSU_OBJECTS = \
- ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o \
- ncsu-colvar.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o \
- ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o \
- ncsu-cv-COM_DISTANCE.o ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o \
- ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.o \
- ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o \
- ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o \
- ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o \
- ncsu-cv-PCA.o ncsu-read-pca.o \
- ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o
-
-EVB_BASE = evb_vars.o evb_mathf.o evb_init.o evb_bcast.o \
- evb_dealloc.o check_input.o evb_io.o evb_keywrd.o \
- exchange_gauss.o exchange_warshel.o react_flux_init.o \
- react_path.o react_flux.o kappa_keck.o \
- schlegel_dg.o schlegel_full.o schlegel_diis.o schlegel_gmres.o \
- schlegel_gbasis.o schlegel_pgbasis.o \
- bnd_strtch.o ang_bend.o dihed_tors.o torinternal.o \
- evb_gfchk.o bmat_inv.o bmat_grad.o \
- unitv.o crossv.o cart2internal.o wdc_bmat.o select_coord.o \
- schlegel_uff.o schlegel_dihed.o schlegel_angle.o \
- schlegel_poh_uff.o schlegel_poh_irc.o schlegel_hcn_cart.o \
- schlegel_hcn_int_irc.o schlegel_hcn_cart_irc.o evb_outoptions.o
-
-EVB_DEBUG = evb_2stdebug.o egap_umb_2stdebug.o dg_debug.o \
- evb_io_debug.o bmat_debug.o bmat_inv_debug.o evb_io_debug2.o \
- morse_anal2num.o xwarshel_anal2num.o xgauss_anal2num.o \
- vdw_anal2num.o rcdbonds_anal2num.o rcbond_anal2num.o \
- dg_grad_anal2num.o
-
-EVBOBJ = $(EVB_BASE) $(EVB_DEBUG) evb_input.o evb_alloc.o evb_matrix.o \
- morsify.o mod_vdw.o evb_ntrfc.o evb_force.o out_evb.o \
- dbonds_anal2num.o bond_anal2num.o evb_umb.o evb_umb_primitive.o
-
-EVBPIMD = $(EVB_BASE) $(EVB_DEBUG) evb_input.LES.o evb_alloc.LES.o evb_matrix.LES.o \
- morsify.LES.o mod_vdw.LES.o evb_ntrfc.LES.o evb_force.LES.o \
- evb_pimd_init.LES.o out_evb.LES.o dbonds_anal2num.o bond_anal2num.o \
- evb_umb.LES.o evb_umb_primitive.LES.o
-
-AMOEBAOBJ= \
- amoeba_valence.o amoeba_multipoles.o amoeba_recip.o amoeba_interface.o\
- amoeba_direct.o amoeba_mdin.o amoeba_adjust.o amoeba_self.o\
- amoeba_vdw.o amoeba_induced.o amoeba_runmd.o
-
-APBSOBJ= \
- file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o \
- constants.o state.o memory_module.o stack.o \
- nose_hoover.o nose_hoover_init.o \
- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
- icosasurf.o egb.o remd.o findmask.o \
- relax_mat.o nmr.o multitmd.o \
- multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.APBS.o runmin.o rdparm.o \
- mdread.APBS.o locmem.o runmd.o getcor.o degcnt.o decnvh.o \
- fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o \
- set.o dynlib.APBS.o mdfil.o nmlsrc.o \
- ew_force.o ew_setup.o ew_box.o ew_bspline.o\
- ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o \
- rfree.o rgroup.o amopen.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.o new_time.o extra_pts.o thermo_int.o \
- matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o \
- $(AMOEBAOBJ) $(SANDER_RISM_INTERFACE) AmberNetcdf.o bintraj.o binrestart.o \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o \
- charmm.o crg_reloc.o sander_lib.o amd.o scaledMD.o barostats.o $(EMILOBJ)
-
-QMOBJ= \
- abfqmmm_module.o qm_mm.o qm_ewald.o qmmm_vsolv.o \
- qm2_extern_util_module.o qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o \
- ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o \
- qm2_extern_orc_module.o qm2_extern_nw_module.o qm2_extern_genmpi_module.o \
- qmmm_adaptive_module.o prn_qmmm_dipole.o
-
-ifdef LIOLIBS
-QMOBJ += qm2_extern_lio_module.o
-endif
-
-SEBOMDOBJ = \
- sebomd_module.o sebomd_arrays.o
-
-SEBOMDLIB = ../sebomd/sebomd.a
-
-MMOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \
- nose_hoover.o nose_hoover_init.o \
- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
- icosasurf.o egb.o remd.o findmask.o \
- relax_mat.o nmr.o multitmd.o \
- multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.o runmin.o rdparm.o sander_lib.o \
- mdread.o locmem.o runmd.o getcor.o degcnt.o decnvh.o \
- fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o \
- set.o dynlib.o mdfil.o nmlsrc.o \
- ew_force.o ew_setup.o ew_box.o ew_bspline.o\
- ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o \
- rfree.o rgroup.o amopen.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.o new_time.o extra_pts.o thermo_int.o \
- matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o\
- $(EMILOBJ) $(AMOEBAOBJ) $(SANDER_RISM_INTERFACE) AmberNetcdf.o bintraj.o binrestart.o \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o \
- charmm.o crg_reloc.o amd.o scaledMD.o barostats.o
-
-FULLPIMDOBJ = pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o
-
-PARTPIMDOBJ = pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix.LES.o
-
-PUPILOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \
- nose_hoover.o nose_hoover_init.o \
- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
- pupildata.o icosasurf.o egb.o findmask.o \
- relax_mat.o nmr.o multitmd.o \
- multisander.o sander.PUPIL.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.PUPIL.o runmin.o force.PUPIL.o rdparm.o \
- mdread.PUPIL.o locmem.o runmd.o getcor.o degcnt.o decnvh.o \
- fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o \
- set.o dynlib.PUPIL.o mdfil.PUPIL.o nmlsrc.o \
- ew_force.o ew_setup.o ew_box.o ew_bspline.o\
- ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o \
- rfree.o rgroup.o amopen.o sander_lib.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.PUPIL.o new_time.o extra_pts.o thermo_int.o \
- matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o \
- $(EMILOBJ) $(AMOEBAOBJ) $(SANDER_RISM_INTERFACE) AmberNetcdf.o bintraj.o binrestart.o \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o \
- putvalues.o fixport.o dssp.o charmm.o crg_reloc.o amd.o scaledMD.o \
- barostats.o
-
-LSCIVROBJ = lscivr_vars.o lsc_init.o lsc_xp.o
-
-LESOBJ= memory_module.o stack.o file_io_dat.o \
- constants.o state.o nose_hoover.o nose_hoover_init_LES.o \
- trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \
- egb.LES.o remd.LES.o findmask.o \
- relax_mat.o nmr.LES.o multitmd.o \
- multisander.LES.o sander.LES.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.o runmin.o nonbond_list.LES.o force.LES.o rdparm.LES.o \
- mdread.LES.o locmem.LES.o runmd.LES.o degcnt.LES.o decnvh.o \
- fastwt.o parallel.LES.o shake.o ene.LES.o \
- dynlib.LES.o nmlsrc.o \
- ew_force.LES.o ew_setup.LES.o ew_bspline.o\
- ew_fft.o short_ene.LES.o ew_recip.LES.o pcshift.o \
- align.o csa.o rfree.o rgroup.o \
- amopen.o sander_lib.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.o new_time.o extra_pts.LES.o thermo_int.o matinv.o assert.o \
- mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o \
- $(AMOEBAOBJ) $(EMILOBJ) $(SANDER_RISM_INTERFACE) \
- $(SEBOMDOBJ) \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o \
- charmm.o crg_reloc.o barostats.o \
- qm_ewald.o qmmm_vsolv.o \
- qm2_extern_util_module.o qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o \
- ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o \
- qm2_extern_orc_module.o qm2_extern_nw_module.o qm2_extern_genmpi_module.o \
- qmmm_adaptive_module.o abfqmmm_module.o prn_qmmm_dipole.o \
- AmberNetcdf.o bintraj.LES.o binrestart.LES.o getcor.LES.o mdfil.LES.o mdwrit.LES.o \
- lmod.LES.o trajene.LES.o ew_box.LES.o minrit.LES.o set.LES.o qm_mm.LES.o amd.o scaledMD.o
-ifdef LIOLIBS
-LESOBJ += qm2_extern_lio_module.o
-endif
-
-# Xray sources are incomplete, but should not interfere with normal SANDER function.
-# Add the following to ../config.h to build new X-ray sources:
-#
-# AMBERBUILDFLAGS=-D_XRAY
-# XRAY_OBJS = \
-# xray_fftpack.o xray_fourier.o xray_globals.o xray_interface.o \
-# xray_real_space.o xray_reciprocal_space.o xray_utils.o
-
-.PHONY: configured configured-serial configured_parallel serial parallel
-
-install: serial
-
-SERIALPROGS = $(BINDIR)/sander$(SFX) $(BINDIR)/sander.LES$(SFX) $(BINDIR)/ambmask$(SFX)
-
-.NOTPARALLEL: $(SERIALPROGS)
-
-serial: configured_serial $(SERIALPROGS)
-
-PARALLELPROGS = $(BINDIR)/sander.MPI$(SFX) $(BINDIR)/sander.LES.MPI$(SFX)
-
-.NOTPARALLEL: $(PARALLELPROGS)
-
-parallel: configured_parallel $(PARALLELPROGS)
-
-all_serial_programs: $(SERIALPROGS)
- $(MAKE) $(BINDIR)/sander.PUPIL$(SFX)
- $(MAKE) $(BINDIR)/sander.APBS$(SFX)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(SEBOMDOBJ) sebomd \
- $(LSCIVROBJ) force.o syslib \
- ../lib/nxtsec.o netlib configured_serial \
- $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- $(FULLPIMDOBJ) $(LSCIVROBJ) force.o -L$(LIBDIR) -lsqm \
- $(NCSU_OBJECTS) $(XRAY_OBJS) \
- -lFpbsa ../lib/nxtsec.o $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/sys.a $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(LSCIVROBJ) $(EVBOBJ) force.o \
- $(SEBOMDOBJ) sebomd \
- syslib ../lib/nxtsec.o netlib libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS)
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- $(FULLPIMDOBJ) $(LSCIVROBJ) $(EVBOBJ) force.o \
- -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD)
-
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(LSCIVROBJ) syslib \
- $(SEBOMDOBJ) sebomd \
- ../lib/nxtsec.o netlib libpbsa librism configured_serial $(NCSU_OBJECTS)
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(PUPILOBJ) $(QMOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) \
- $(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o $(EMILLIB) ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(PUPILLIBS) $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \
- ../lib/nxtsec.o netlib \
- $(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \
- libpbsa librism $(EMIL) sebomd
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(PARTPIMDOBJ) $(LSCIVROBJ) \
- $(XRAY_OBJS) -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.LES.MPI$(SFX): libsqm $(LESOBJ) $(EVBPIMD) \
- $(PARTPIMDOBJ) syslib ../lib/nxtsec.o \
- netlib libpbsa librism_mpi $(EMIL) \
- $(LSCIVROBJ) $(NCSU_OBJECTS) sebomd configured_parallel
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(EVBPIMD) \
- $(PARTPIMDOBJ) $(LSCIVROBJ) \
- -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.APBS$(SFX): libsqm $(APBSOBJ) $(QMOBJ) \
- $(LSCIVROBJ) $(FULLPIMDOBJ) $(NCSU_OBJECTS) \
- force.APBS.o syslib librism $(EMIL) \
- $(SEBOMDOBJ) sebomd \
- ../lib/nxtsec.o netlib configured_serial
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(APBSOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- $(FULLPIMDOBJ) $(LSCIVROBJ) force.APBS.o \
- -L$(APBS_LIBDIR) $(APBS_LIBS) \
- -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/ambmask$(SFX): ambmask.o findmask.o amopen.o parms.o \
- memory_module.o mexit.o ../lib/nxtsec.o
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ ambmask.o findmask.o \
- amopen.o mexit.o ../lib/nxtsec.o constants.o memory_module.o parms.o \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-
-#-----------LIBS
-
-EMIL:
- $(MAKE) -C ../emil install
-
-syslib:
- cd ../lib && $(MAKE) sys.a
-
-netlib:
- cd ../blas && $(MAKE) $(BLAS)
- cd ../lapack && $(MAKE) $(LAPACK)
- cd ../arpack && $(MAKE) install
-
-sebomd: $(SEBOMDOBJ)
- cd ../sebomd && $(MAKE) sebomd.a
-
-../lib/nxtsec.o: ../lib/nxtsec.F
- cd ../lib && $(MAKE) nxtsec.o
-
-pmemd_clib:
- cd ../pmemd/src && $(CC) -c $(CPPFLAGS) $(CNOOPTFLAGS) \
- $(CFLAGS) $(AMBERCFLAGS) pmemd_clib.c
-
-../lib/mexit.o: ../lib/mexit.F
- cd ../lib && $(MAKE) mexit.o
-
-rand2.o: ../sff/rand2.c
- $(CC) -c $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- -o rand2.o ../sff/rand2.c
-
-lmodC.o: ../sff/lmodC.c
- $(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- -o lmodC.o ../sff/lmodC.c
-
-xminC.o: ../sff/xminC.c
- $(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- -o xminC.o ../sff/xminC.c
-
-libsqm:
- cd ../sqm && $(MAKE) $@
-
-librism librism_mpi:
- if [ -n "$(RISMSANDER)" ]; then \
- cd ../rism && $(MAKE) $@; \
- fi
-
-libpbsa: decomp.o
- cd ../pbsa && $(MAKE) libFpbsa.a
-
-clean:
- -/bin/rm -f sander.PUPIL$(SFX)
- -/bin/rm -f sander.APBS$(SFX)
- /bin/rm -f *.o
- /bin/rm -f
- /bin/rm -f *.mod
- /bin/rm -f *.d
- /bin/rm -f *nbflag
-
-uninstall.serial:
- -rm -f $(BINDIR)/mopac.sh
- -for file in $(SERIALPROGS) ; do \
- rm -f $${file} ; \
- done
-
-uninstall.parallel:
- -for file in $(PARALLELPROGS) ; do \
- rm -f $${file} ; \
- done
-
-uninstall: uninstall.serial uninstall.parallel
-
-depend::
- ./makedepend > depend
-
-configured:
- @(if [ ! -f $(CONFIG_FILE) ] ; then \
- echo "Error: $(CONFIG_COMMAND) must be executed before $(MAKE) !" ;\
- exit 2 ;\ # $(CONFIG_COMMAND) ;\
- fi ;\
- )
-
-configured_serial: configured
- @(if grep $(PARALLEL_TOKEN) $(CONFIG_FILE) > /dev/null ; then \
- echo "Error: $(CONFIG_FILE) is of type parallel, not serial !" ;\
- echo " Rerun $(CONFIG_COMMAND) and do NOT specify -mpi." ;\
- exit 2 ;\
- fi ;\
- )
-
-configured_parallel: configured
- @(grep $(PARALLEL_TOKEN) $(CONFIG_FILE) > /dev/null || \
- { echo "Error: $(CONFIG_FILE) is of type serial, not parallel !" ;\
- echo " Rerun $(CONFIG_COMMAND) and specify an MPI implementation." ;\
- exit 2 ;\
- } ;\
- )
-
-
-#----------HEADER DEPENDENCIES (constructed from ./makedepend > depend)
-include depend
-# DO NOT DELETE
diff --git a/patches/amber14.diff/AmberTools/src/sander/Makefile.preplumed b/patches/amber14.diff/AmberTools/src/sander/Makefile.preplumed
deleted file mode 100644
index ec1f1f90daebec308e03d1ef8319c5a40b62089e..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/Makefile.preplumed
+++ /dev/null
@@ -1,422 +0,0 @@
-#
-#************************************************************************
-# AMBER **
-# **
-# Copyright (c) 1986, 1991, 1995, 1997, 1999 **
-# Regents of the University of California **
-# All Rights Reserved. **
-# **
-# This software provided pursuant to a license agreement containing **
-# restrictions on its disclosure, duplication, and use. This software **
-# contains confidential and proprietary information, and may not be **
-# extracted or distributed, in whole or in part, for any purpose **
-# whatsoever, without the express written permission of the authors. **
-# This notice, and the associated author list, must be attached to **
-# all copies, or extracts, of this software. Any additional **
-# restrictions set forth in the license agreement also apply to this **
-# software. **
-#************************************************************************
-#
-# Makefile for Amber 14 SANDER
-#
-include ../config.h
-
-CONFIG_FILE=../config.h
-CONFIG_COMMAND=configure
-PARALLEL_TOKEN=DMPI
-
-# Sander Fortran source files are free format
-# Add also search paths for .mod files
-LOCALFLAGS = $(FREEFORMAT_FLAG) -I../pbsa -I../sqm -I../rism -I../../../include
-
-SHELL=/bin/sh
-VPATH=
-
-EMILOBJ= \
- emil.o mdin_emil_dat.o
-
-NCSU_OBJECTS = \
- ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o \
- ncsu-colvar.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o \
- ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o \
- ncsu-cv-COM_DISTANCE.o ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o \
- ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.o \
- ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o \
- ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o \
- ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o \
- ncsu-cv-PCA.o ncsu-read-pca.o \
- ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o
-
-EVB_BASE = evb_vars.o evb_mathf.o evb_init.o evb_bcast.o \
- evb_dealloc.o check_input.o evb_io.o evb_keywrd.o \
- exchange_gauss.o exchange_warshel.o react_flux_init.o \
- react_path.o react_flux.o kappa_keck.o \
- schlegel_dg.o schlegel_full.o schlegel_diis.o schlegel_gmres.o \
- schlegel_gbasis.o schlegel_pgbasis.o \
- bnd_strtch.o ang_bend.o dihed_tors.o torinternal.o \
- evb_gfchk.o bmat_inv.o bmat_grad.o \
- unitv.o crossv.o cart2internal.o wdc_bmat.o select_coord.o \
- schlegel_uff.o schlegel_dihed.o schlegel_angle.o \
- schlegel_poh_uff.o schlegel_poh_irc.o schlegel_hcn_cart.o \
- schlegel_hcn_int_irc.o schlegel_hcn_cart_irc.o evb_outoptions.o
-
-EVB_DEBUG = evb_2stdebug.o egap_umb_2stdebug.o dg_debug.o \
- evb_io_debug.o bmat_debug.o bmat_inv_debug.o evb_io_debug2.o \
- morse_anal2num.o xwarshel_anal2num.o xgauss_anal2num.o \
- vdw_anal2num.o rcdbonds_anal2num.o rcbond_anal2num.o \
- dg_grad_anal2num.o
-
-EVBOBJ = $(EVB_BASE) $(EVB_DEBUG) evb_input.o evb_alloc.o evb_matrix.o \
- morsify.o mod_vdw.o evb_ntrfc.o evb_force.o out_evb.o \
- dbonds_anal2num.o bond_anal2num.o evb_umb.o evb_umb_primitive.o
-
-EVBPIMD = $(EVB_BASE) $(EVB_DEBUG) evb_input.LES.o evb_alloc.LES.o evb_matrix.LES.o \
- morsify.LES.o mod_vdw.LES.o evb_ntrfc.LES.o evb_force.LES.o \
- evb_pimd_init.LES.o out_evb.LES.o dbonds_anal2num.o bond_anal2num.o \
- evb_umb.LES.o evb_umb_primitive.LES.o
-
-AMOEBAOBJ= \
- amoeba_valence.o amoeba_multipoles.o amoeba_recip.o amoeba_interface.o\
- amoeba_direct.o amoeba_mdin.o amoeba_adjust.o amoeba_self.o\
- amoeba_vdw.o amoeba_induced.o amoeba_runmd.o
-
-APBSOBJ= \
- file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o \
- constants.o state.o memory_module.o stack.o \
- nose_hoover.o nose_hoover_init.o \
- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
- icosasurf.o egb.o remd.o findmask.o \
- relax_mat.o nmr.o multitmd.o \
- multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.APBS.o runmin.o rdparm.o \
- mdread.APBS.o locmem.o runmd.o getcor.o degcnt.o decnvh.o \
- fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o \
- set.o dynlib.APBS.o mdfil.o nmlsrc.o \
- ew_force.o ew_setup.o ew_box.o ew_bspline.o\
- ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o \
- rfree.o rgroup.o amopen.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.o new_time.o extra_pts.o thermo_int.o \
- matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o \
- $(AMOEBAOBJ) $(SANDER_RISM_INTERFACE) AmberNetcdf.o bintraj.o binrestart.o \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o \
- charmm.o crg_reloc.o sander_lib.o amd.o scaledMD.o barostats.o $(EMILOBJ)
-
-QMOBJ= \
- abfqmmm_module.o qm_mm.o qm_ewald.o qmmm_vsolv.o \
- qm2_extern_util_module.o qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o \
- ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o \
- qm2_extern_orc_module.o qm2_extern_nw_module.o qm2_extern_genmpi_module.o \
- qmmm_adaptive_module.o prn_qmmm_dipole.o
-
-ifdef LIOLIBS
-QMOBJ += qm2_extern_lio_module.o
-endif
-
-SEBOMDOBJ = \
- sebomd_module.o sebomd_arrays.o
-
-SEBOMDLIB = ../sebomd/sebomd.a
-
-MMOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \
- nose_hoover.o nose_hoover_init.o \
- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
- icosasurf.o egb.o remd.o findmask.o \
- relax_mat.o nmr.o multitmd.o \
- multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.o runmin.o rdparm.o sander_lib.o \
- mdread.o locmem.o runmd.o getcor.o degcnt.o decnvh.o \
- fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o \
- set.o dynlib.o mdfil.o nmlsrc.o \
- ew_force.o ew_setup.o ew_box.o ew_bspline.o\
- ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o \
- rfree.o rgroup.o amopen.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.o new_time.o extra_pts.o thermo_int.o \
- matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o\
- $(EMILOBJ) $(AMOEBAOBJ) $(SANDER_RISM_INTERFACE) AmberNetcdf.o bintraj.o binrestart.o \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o \
- charmm.o crg_reloc.o amd.o scaledMD.o barostats.o
-
-FULLPIMDOBJ = pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o
-
-PARTPIMDOBJ = pimd_vars.o pimd_force.LES.o pimd_init.LES.o cmd_vars.o cmd_matrix.LES.o
-
-PUPILOBJ= file_io_dat.o constants.o state.o memory_module.o stack.o \
- nose_hoover.o nose_hoover_init.o \
- trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o \
- pupildata.o icosasurf.o egb.o findmask.o \
- relax_mat.o nmr.o multitmd.o \
- multisander.o sander.PUPIL.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.PUPIL.o runmin.o force.PUPIL.o rdparm.o \
- mdread.PUPIL.o locmem.o runmd.o getcor.o degcnt.o decnvh.o \
- fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o \
- set.o dynlib.PUPIL.o mdfil.PUPIL.o nmlsrc.o \
- ew_force.o ew_setup.o ew_box.o ew_bspline.o\
- ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o \
- rfree.o rgroup.o amopen.o sander_lib.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.PUPIL.o new_time.o extra_pts.o thermo_int.o \
- matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o \
- $(EMILOBJ) $(AMOEBAOBJ) $(SANDER_RISM_INTERFACE) AmberNetcdf.o bintraj.o binrestart.o \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o \
- putvalues.o fixport.o dssp.o charmm.o crg_reloc.o amd.o scaledMD.o \
- barostats.o
-
-LSCIVROBJ = lscivr_vars.o lsc_init.o lsc_xp.o
-
-LESOBJ= memory_module.o stack.o file_io_dat.o \
- constants.o state.o nose_hoover.o nose_hoover_init_LES.o \
- trace.o rmsgrd.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o \
- egb.LES.o remd.LES.o findmask.o \
- relax_mat.o nmr.LES.o multitmd.o \
- multisander.LES.o sander.LES.o cshf.o nmrcal.o mtmdcall.o pearsn.o \
- printe.o runmin.o nonbond_list.LES.o force.LES.o rdparm.LES.o \
- mdread.LES.o locmem.LES.o runmd.LES.o degcnt.LES.o decnvh.o \
- fastwt.o parallel.LES.o shake.o ene.LES.o \
- dynlib.LES.o nmlsrc.o \
- ew_force.LES.o ew_setup.LES.o ew_bspline.o\
- ew_fft.o short_ene.LES.o ew_recip.LES.o pcshift.o \
- align.o csa.o rfree.o rgroup.o \
- amopen.o sander_lib.o \
- debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o \
- mexit.o new_time.o extra_pts.LES.o thermo_int.o matinv.o assert.o \
- mmtsb.o mmtsb_client.o erfcfun.o \
- constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o \
- $(AMOEBAOBJ) $(EMILOBJ) $(SANDER_RISM_INTERFACE) \
- $(SEBOMDOBJ) \
- spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o \
- charmm.o crg_reloc.o barostats.o \
- qm_ewald.o qmmm_vsolv.o \
- qm2_extern_util_module.o qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o \
- ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o \
- qm2_extern_orc_module.o qm2_extern_nw_module.o qm2_extern_genmpi_module.o \
- qmmm_adaptive_module.o abfqmmm_module.o prn_qmmm_dipole.o \
- AmberNetcdf.o bintraj.LES.o binrestart.LES.o getcor.LES.o mdfil.LES.o mdwrit.LES.o \
- lmod.LES.o trajene.LES.o ew_box.LES.o minrit.LES.o set.LES.o qm_mm.LES.o amd.o scaledMD.o
-ifdef LIOLIBS
-LESOBJ += qm2_extern_lio_module.o
-endif
-
-# Xray sources are incomplete, but should not interfere with normal SANDER function.
-# Add the following to ../config.h to build new X-ray sources:
-#
-# AMBERBUILDFLAGS=-D_XRAY
-# XRAY_OBJS = \
-# xray_fftpack.o xray_fourier.o xray_globals.o xray_interface.o \
-# xray_real_space.o xray_reciprocal_space.o xray_utils.o
-
-.PHONY: configured configured-serial configured_parallel serial parallel
-
-install: serial
-
-SERIALPROGS = $(BINDIR)/sander$(SFX) $(BINDIR)/sander.LES$(SFX) $(BINDIR)/ambmask$(SFX)
-
-.NOTPARALLEL: $(SERIALPROGS)
-
-serial: configured_serial $(SERIALPROGS)
-
-PARALLELPROGS = $(BINDIR)/sander.MPI$(SFX) $(BINDIR)/sander.LES.MPI$(SFX)
-
-.NOTPARALLEL: $(PARALLELPROGS)
-
-parallel: configured_parallel $(PARALLELPROGS)
-
-all_serial_programs: $(SERIALPROGS)
- $(MAKE) $(BINDIR)/sander.PUPIL$(SFX)
- $(MAKE) $(BINDIR)/sander.APBS$(SFX)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(SEBOMDOBJ) sebomd \
- $(LSCIVROBJ) force.o syslib \
- ../lib/nxtsec.o netlib configured_serial \
- $(NCSU_OBJECTS) $(XRAY_OBJS) libpbsa librism
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- $(FULLPIMDOBJ) $(LSCIVROBJ) force.o -L$(LIBDIR) -lsqm \
- $(NCSU_OBJECTS) $(XRAY_OBJS) \
- -lFpbsa ../lib/nxtsec.o $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/sys.a $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.MPI$(SFX): libsqm $(MMOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(LSCIVROBJ) $(EVBOBJ) force.o \
- $(SEBOMDOBJ) sebomd \
- syslib ../lib/nxtsec.o netlib libpbsa librism_mpi configured_parallel $(NCSU_OBJECTS)
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(MMOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- $(FULLPIMDOBJ) $(LSCIVROBJ) $(EVBOBJ) force.o \
- -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.PUPIL$(SFX): libsqm $(PUPILOBJ) $(QMOBJ) $(FULLPIMDOBJ) $(EMIL) \
- $(LSCIVROBJ) syslib \
- $(SEBOMDOBJ) sebomd \
- ../lib/nxtsec.o netlib libpbsa librism configured_serial $(NCSU_OBJECTS)
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(PUPILOBJ) $(QMOBJ) $(SEBOMDOBJ) $(FULLPIMDOBJ) \
- $(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o $(EMILLIB) ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(PUPILLIBS) $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.LES$(SFX): libsqm $(LESOBJ) $(PARTPIMDOBJ) syslib \
- ../lib/nxtsec.o netlib \
- $(LSCIVROBJ) $(NCSU_OBJECTS) $(XRAY_OBJS) configured_serial \
- libpbsa librism $(EMIL) sebomd
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(PARTPIMDOBJ) $(LSCIVROBJ) \
- $(XRAY_OBJS) -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.LES.MPI$(SFX): libsqm $(LESOBJ) $(EVBPIMD) \
- $(PARTPIMDOBJ) syslib ../lib/nxtsec.o \
- netlib libpbsa librism_mpi $(EMIL) \
- $(LSCIVROBJ) $(NCSU_OBJECTS) sebomd configured_parallel
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(LESOBJ) $(EVBPIMD) \
- $(PARTPIMDOBJ) $(LSCIVROBJ) \
- -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/sander.APBS$(SFX): libsqm $(APBSOBJ) $(QMOBJ) \
- $(LSCIVROBJ) $(FULLPIMDOBJ) $(NCSU_OBJECTS) \
- force.APBS.o syslib librism $(EMIL) \
- $(SEBOMDOBJ) sebomd \
- ../lib/nxtsec.o netlib configured_serial
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $(APBSOBJ) $(QMOBJ) $(SEBOMDOBJ) \
- $(FULLPIMDOBJ) $(LSCIVROBJ) force.APBS.o \
- -L$(APBS_LIBDIR) $(APBS_LIBS) \
- -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \
- $(SEBOMDLIB) \
- ../lib/nxtsec.o ../lib/sys.a $(NCSU_OBJECTS) $(NETCDFLIBF) \
- $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-#---------------------------------------------------------------------------
-$(BINDIR)/ambmask$(SFX): ambmask.o findmask.o amopen.o parms.o \
- memory_module.o mexit.o ../lib/nxtsec.o
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ ambmask.o findmask.o \
- amopen.o mexit.o ../lib/nxtsec.o constants.o memory_module.o parms.o \
- $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS)
-
-
-#-----------LIBS
-
-EMIL:
- $(MAKE) -C ../emil install
-
-syslib:
- cd ../lib && $(MAKE) sys.a
-
-netlib:
- cd ../blas && $(MAKE) $(BLAS)
- cd ../lapack && $(MAKE) $(LAPACK)
- cd ../arpack && $(MAKE) install
-
-sebomd: $(SEBOMDOBJ)
- cd ../sebomd && $(MAKE) sebomd.a
-
-../lib/nxtsec.o: ../lib/nxtsec.F
- cd ../lib && $(MAKE) nxtsec.o
-
-pmemd_clib:
- cd ../pmemd/src && $(CC) -c $(CPPFLAGS) $(CNOOPTFLAGS) \
- $(CFLAGS) $(AMBERCFLAGS) pmemd_clib.c
-
-../lib/mexit.o: ../lib/mexit.F
- cd ../lib && $(MAKE) mexit.o
-
-rand2.o: ../sff/rand2.c
- $(CC) -c $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- -o rand2.o ../sff/rand2.c
-
-lmodC.o: ../sff/lmodC.c
- $(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- -o lmodC.o ../sff/lmodC.c
-
-xminC.o: ../sff/xminC.c
- $(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
- -o xminC.o ../sff/xminC.c
-
-libsqm:
- cd ../sqm && $(MAKE) $@
-
-librism librism_mpi:
- if [ -n "$(RISMSANDER)" ]; then \
- cd ../rism && $(MAKE) $@; \
- fi
-
-libpbsa: decomp.o
- cd ../pbsa && $(MAKE) libFpbsa.a
-
-clean:
- -/bin/rm -f sander.PUPIL$(SFX)
- -/bin/rm -f sander.APBS$(SFX)
- /bin/rm -f *.o
- /bin/rm -f
- /bin/rm -f *.mod
- /bin/rm -f *.d
- /bin/rm -f *nbflag
-
-uninstall.serial:
- -rm -f $(BINDIR)/mopac.sh
- -for file in $(SERIALPROGS) ; do \
- rm -f $${file} ; \
- done
-
-uninstall.parallel:
- -for file in $(PARALLELPROGS) ; do \
- rm -f $${file} ; \
- done
-
-uninstall: uninstall.serial uninstall.parallel
-
-depend::
- ./makedepend > depend
-
-configured:
- @(if [ ! -f $(CONFIG_FILE) ] ; then \
- echo "Error: $(CONFIG_COMMAND) must be executed before $(MAKE) !" ;\
- exit 2 ;\ # $(CONFIG_COMMAND) ;\
- fi ;\
- )
-
-configured_serial: configured
- @(if grep $(PARALLEL_TOKEN) $(CONFIG_FILE) > /dev/null ; then \
- echo "Error: $(CONFIG_FILE) is of type parallel, not serial !" ;\
- echo " Rerun $(CONFIG_COMMAND) and do NOT specify -mpi." ;\
- exit 2 ;\
- fi ;\
- )
-
-configured_parallel: configured
- @(grep $(PARALLEL_TOKEN) $(CONFIG_FILE) > /dev/null || \
- { echo "Error: $(CONFIG_FILE) is of type serial, not parallel !" ;\
- echo " Rerun $(CONFIG_COMMAND) and specify an MPI implementation." ;\
- exit 2 ;\
- } ;\
- )
-
-
-#----------HEADER DEPENDENCIES (constructed from ./makedepend > depend)
-include depend
-# DO NOT DELETE
diff --git a/patches/amber14.diff/AmberTools/src/sander/constants.F90 b/patches/amber14.diff/AmberTools/src/sander/constants.F90
deleted file mode 100644
index 50dfb223025e578f144b22581da0809909b979ef..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/constants.F90
+++ /dev/null
@@ -1,270 +0,0 @@
-! <compile=optimized>
-#include "copyright.h"
-#include "../include/dprec.fh"
-
-!+++++++++++++++++++++++++++++++++++++++
-!This module contains various parameters
-!and constants used by the different
-!routines that make up sander.
-!
-!If you want to use one of the constants
-!in your routine you should include the
-!line:
-!
-!use constants, only : xxx, yyy, zzz
-!
-!where xxx,yyy,zzz are the constants you plan
-!to use in your routine.
-!This line needs to go before the
-!implicit none declaration.
-!
-! Based on constants.h, a pre Fortran 90 version, by Scott Brozell
-! and Dave Case (TSRI, 2002)
-! Converted into a Fortran 90 module by: Ross Walker (TSRI, 2005)
-! Expanded by others including: Matthew Clark, Andreas Goetz,
-!
-!++++++++++++++++++++++++++++++++++++++++
-
-module constants
-
- implicit none
-
- ! by default everything in this module is public
- public
-
- !------------------------------------------------------------
- ! Generic Floating Point Constants
- _REAL_, parameter :: TEN_TO_MINUS2 = 1.0d-2
- _REAL_, parameter :: TEN_TO_MINUS3 = 1.0d-3
- _REAL_, parameter :: TEN_TO_MINUS4 = 1.0d-4
- _REAL_, parameter :: TEN_TO_MINUS5 = 1.0d-5
- _REAL_, parameter :: TEN_TO_MINUS6 = 1.0d-6
- _REAL_, parameter :: TEN_TO_MINUS8 = 1.0d-8
- _REAL_, parameter :: TEN_TO_MINUS10 = 1.0d-10
- _REAL_, parameter :: TEN_TO_MINUS25 = 1.0d-25
- _REAL_, parameter :: TEN_TO_PLUS3 = 1.0d+3
- _REAL_, parameter :: TEN_TO_PLUS10 = 1.0d+10
-
- _REAL_, parameter :: zero = 0.0d0
- _REAL_, parameter :: one = 1.0d0
- _REAL_, parameter :: two = 2.0d0
- _REAL_, parameter :: three = 3.0d0
- _REAL_, parameter :: four = 4.0d0
- _REAL_, parameter :: five = 5.0d0
- _REAL_, parameter :: six = 6.0d0
- _REAL_, parameter :: seven = 7.0d0
- _REAL_, parameter :: eight = 8.0d0
- _REAL_, parameter :: nine = 9.0d0
- _REAL_, parameter :: ten = 10.0d0
- _REAL_, parameter :: eleven = 11.0d0
- _REAL_, parameter :: twelve = 12.0d0
- _REAL_, parameter :: sixteen = 16.0d0
- _REAL_, parameter :: twenty = 20.0d0
- _REAL_, parameter :: thirtytwo = 32.0d0
- _REAL_, parameter :: sixtyfour = 64.0d0
-
- _REAL_, parameter :: half = one/two
- _REAL_, parameter :: third = one/three
- _REAL_, parameter :: fourth = one/four
- _REAL_, parameter :: fifth = one/five
- _REAL_, parameter :: sixth = one/six
- _REAL_, parameter :: seventh = one/seven
- _REAL_, parameter :: eighth = one/eight
- _REAL_, parameter :: ninth = one/nine
- _REAL_, parameter :: tenth = one/ten
- _REAL_, parameter :: eleventh = one/eleven
- _REAL_, parameter :: twelfth = one/twelve
- _REAL_, parameter :: sixteenth = one/sixteen
- _REAL_, parameter :: thirtysecond = one/thirtytwo
- _REAL_, parameter :: sixtyfourth = one/sixtyfour
-
- _REAL_, parameter :: thirtieth = one/30.0d0
-
- !------------------------------------------------------------
- ! THE ARRAY FC(I) CONTAINS THE FACTORIALS OF (I-1).
-
- _REAL_, parameter :: FC(1:17) =&
- (/ 1.0D0,1.0D0, 2.0D0, 6.0D0, 24.0D0, 120.0D0, 720.0D0, 5040.0D0, &
- 40320.0D0, 362880.0D0, 3628800.0D0, 39916800.0D0, &
- 4.790016D+08, 6.2270208D+09, 8.71782912D+10, &
- 1.307674368D+12, 2.092278989D+13 /)
-
- _REAL_, parameter :: logFC(1:17) = (/ 0.0D0, 0.0D0, 0.6931471805599D0, &
- & 1.7917594692281D0, 3.1780538303479D0, 4.7874917427820D0, &
- & 6.5792512120101D0, 8.5251613610654D0, 10.6046029027453D0, &
- & 12.8018274800815D0, 15.1044125730755D0, 17.5023078458739D0, &
- & 19.9872144956619D0, 22.5521638531234D0, 25.1912211827387D0, &
- & 27.8992713838409D0, 30.6718601061763D0 /)
-
- ! DEFINE C COEFFICIENTS FOR ASSOCIATE LEGENDRE POLYNOMIALS.
- _REAL_, parameter::CC(1:21,1:3) = reshape ( (/ &
- 8.0D0, 8.0D0, 4.0D0, -4.0D0, 4.0D0, &
- 4.0D0, -12.0D0, -6.0D0, 20.0D0, 5.0D0, &
- 3.0D0, -30.0D0, -10.0D0, 35.0D0, 7.0D0, &
- 15.0D0, 7.5D0, -70.0D0, -17.5D0, 63.0D0, &
- 10.5D0, &
- 0.0D0, 0.0D0, 0.0D0, 12.0D0, 0.0D0, &
- 0.0D0, 20.0D0, 30.0D0, 0.0D0, 0.0D0, &
- -30.0D0, 70.0D0, 70.0D0, 0.0D0, 0.0D0, &
- -70.0D0, -105.D0, 210.0D0, 157.5D0, 0.0D0, &
- 0.0D0, &
- 0.0D0, 0.0D0, 0.0D0, 0.0D0, 0.0D0, &
- 0.0D0, 0.0D0, 0.0D0, 0.0D0, 0.0D0, &
- 35.0D0, 0.0D0, 0.0D0, 0.0D0, 0.0D0, &
- 63.0D0, 157.5D0, 0.0D0, 0.0D0, 0.0D0, &
- 0.0D0/), (/ 21, 3 /) )
-
- !------------------------------------------------------------
- ! Physical Constants
- _REAL_, parameter :: LIGHT_SPEED = 2.997924d08
- _REAL_, parameter :: HBAR = 627.509d0 * 0.0241888d-3 * 20.455d0 !Planck's constant in internal units
- _REAL_, parameter :: J_PER_CAL = 4.184d0 ! This is defined as the thermochemical calorie
- _REAL_, parameter :: JPKC = J_PER_CAL * 1000.0d0 !kilocalories per joule
- _REAL_, parameter :: BOLTZMANN = 1.380658d-23 !Boltzmann's constant in J/K
- _REAL_, parameter :: AVOGADRO = 6.0221367d+23 !Avogadro's number
- _REAL_, parameter :: KB = (BOLTZMANN * AVOGADRO) / JPKC !Boltzmann's constant in internal units
- _REAL_, parameter :: AMBER_ELECTROSTATIC = 18.2223d0
- _REAL_, parameter :: AMBER_ELECTROSTATIC2 = AMBER_ELECTROSTATIC * AMBER_ELECTROSTATIC
- !Ratio by which to scale amber charges to get electron charges - amberchg * oneqscale = electron charges
- ! = 1.0 / 18.2223d0
- _REAL_, parameter :: INV_AMBER_ELECTROSTATIC = 1.0d0/AMBER_ELECTROSTATIC
- _REAL_, parameter :: INV_AMBER_ELECTROSTATIC2 = 1.0d0/AMBER_ELECTROSTATIC2
-
- _REAL_, parameter :: CHARGE_ON_ELEC = 1.60217733d-19 !Charge on an electron in Coulombs
- _REAL_, parameter :: BOHR_RADIUS = 52.9177249d-12 ! in meter
- _REAL_, parameter :: BOHRS_TO_A = 0.529177249D0 ! Bohrs * this = angstroms - Same constants as used in dynamo v2.
- !_REAL_, parameter :: BOHRS_TO_A = 0.52917706D0 ! Bohrs * this = angstroms - Same constants as used in Gaussian 98
- !_REAL_, parameter :: BOHRS_TO_A = 0.529177D0 ! Bohrs * this = angstroms - Same constants as used in Mopac6 hcore.f
- !_REAL_, parameter :: BOHRS_TO_A = 0.529167D0 ! as used in Mopac6 repp.f
- _REAL_, parameter :: A_TO_BOHRS = 1.0d0 / BOHRS_TO_A
- !_REAL_, parameter :: A_TO_BOHRS = 1.88976D0 !Same constants as used in Mopac6 gover.f
- _REAL_, parameter :: A2_TO_BOHRS2 = A_TO_BOHRS * A_TO_BOHRS !Mopac6 uses 3.5711928576D0 in gover.f for this.
- _REAL_, parameter :: A3_TO_BOHRS3 = A2_TO_BOHRS2 * A_TO_BOHRS
- _REAL_, parameter :: A4_TO_BOHRS4 = A2_TO_BOHRS2 * A2_TO_BOHRS2
-
- _REAL_, parameter :: ONE_AU = 27.2113962d0 !One atomic unit of energy in eV.
- _REAL_, parameter :: HARTREE_TO_JOULE = ONE_AU * CHARGE_ON_ELEC !conversion from hartrees to joules
- _REAL_, parameter :: HART_BOHR_TO_JOULE_A = HARTREE_TO_JOULE * BOHRS_TO_A !hartree*bohrs to joules*angstroms
- _REAL_, parameter :: COULOMB_CONST_E = HART_BOHR_TO_JOULE_A*AVOGADRO/JPKC
- !Coulomb's constant for charges in units of e
- !This is the same as AMBER_ELECTROSTATIC2 but to higher precision
- !_REAL_, parameter :: AU_TO_EV = ONE_AU !Conversion from AU to EV - not used because we match dynamo v2 below.
- _REAL_, parameter :: AU_TO_EV = 27.21d0 !Conversion from AU to EV - Same as dynamo v2 uses and Gaussian 98
- !Note (RCW+MC): more precise would be: 1 a.u. 27.211396 eV
- !Mopac6 uses 27.21D0 in calpar.f, delri.f and repp.f but in
- !ffhpol.f it uses 27.2107 and in the manual it quotes 27.211
- _REAL_, parameter :: HALF_AU_TO_EV = AU_TO_EV * half
- _REAL_, parameter :: FOURTH_AU_TO_EV = AU_TO_EV * fourth
- _REAL_, parameter :: EIGHTH_AU_TO_EV = AU_TO_EV * eighth
- _REAL_, parameter :: SXNTH_AU_TO_EV = EIGHTH_AU_TO_EV * half
- _REAL_, parameter :: A2_TO_BOHRS2xAU_TO_EV = A2_TO_BOHRS2*AU_TO_EV
-
- !_REAL_, parameter :: EV_TO_KCAL = 23.060362D0 !Conversion from EV to KCAL/MOL
- !Dynamo parameter
- _REAL_, parameter :: EV_TO_KCAL = 23.061d0 !Dynamo's conversion
- !Mopac6 uses 23.061 in ffhpol.f analyt.f compfg.f datin.f dcart.f
- ! delri1.f delri2.f deritr.f interp.f iter.f
- ! moldat.f mopac.f
- _REAL_, parameter :: KCAL_TO_EV = one / EV_TO_KCAL
-
- _REAL_, parameter :: AU_TO_KCAL = AU_TO_EV*EV_TO_KCAL !1 hartree.
-
-
- ! The following are updated constants from Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730.
- !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
- ! NAME REFERENCE VALUE UNITS !
- !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
- ! Avogadro constant (Table XLVIII, p.708) 6.0221417930E23 mol^-1 !
- ! Bohr radius (Table XLIX, p. 710) 0.5291772085936E-10 m !
- ! a.u. of energy (Table LII, p. 717) 4.3597439422E-18 J !
- ! speed of light (vacuum) (Table I, p.637) 299 792 458 m*s^−1 !
- ! a.u. of charge (Table LIII, p. 717) 1.60217648740E-19 C !
- !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
- _REAL_, parameter :: CODATA08_AVOGADRO = 6.0221417930d23 ! Avogadro's number
- _REAL_, parameter :: CODATA08_BOHR_RADIUS = 0.5291772085936d-10
- _REAL_, parameter :: CODATA08_ONE_AU = 4.3597439422d-18 ! Atomic unit of energy in joules
- _REAL_, parameter :: CODATA08_LIGHT_SPEED = 2.99792458d08
- _REAL_, parameter :: CODATA08_CHARGE_ON_ELEC = 1.60217648740d-19
- ! Derived values
- _REAL_, parameter :: CODATA08_A_TO_BOHRS = 1d-10 / CODATA08_BOHR_RADIUS
- _REAL_, parameter :: CODATA08_AU_TO_KCAL = CODATA08_ONE_AU / J_PER_CAL / 1000 * CODATA08_AVOGADRO
- _REAL_, parameter :: CODATA08_AU_TO_DEBYE = &
- CODATA08_LIGHT_SPEED * CODATA08_CHARGE_ON_ELEC * CODATA08_BOHR_RADIUS / 1d-21
- !_REAL_, parameter :: AU_TO_DEBYE = 1.0d0/0.393430 ! from http://cccbdb.nist.gov/debye.asp (April 12 2011)
-
- !------------------------------------------------------------
- !Numeric Constants
- _REAL_, parameter :: PI = 3.1415926535897932384626433832795d0
-
- !The BOOK says :
- !
- !2Chronicles 4:2 reads thus, 'Also he made a molten sea of ten cubits
- !from brim to brim, round in compass, and five cubits the height thereof;
- !and a line of thirty cubits did compass it round about.'
- !
- !Hence, Pi is exactly equal to three and there is nothing more to discuss!
- !
- !If you want to use the value of PI defined by 'the BOOK' then uncomment
- !the following line and comment out the definition above...
- !_REAL_, parameter :: PI = 3.0d0
-
- _REAL_, parameter :: PI2 = PI*PI
- _REAL_, parameter :: HALFPI = PI * 0.5d0
- _REAL_, parameter :: TWOPI = 2.0d0 * PI
- _REAL_, parameter :: FOURPI = 4.0d0 * PI
- _REAL_, parameter :: INVPI = 1.0d0 / PI
- _REAL_, parameter :: SQRTPI = 1.77245385090551602729816748334d0 !sqrt(PI)
- _REAL_, parameter :: INVSQRTPI = 1.0d0 / SQRTPI
- _REAL_, parameter :: DEG_TO_RAD = PI / 180.0d0
- _REAL_, parameter :: RAD_TO_DEG = 180.0d0 / PI
- _REAL_, parameter :: LN_TO_LOG = 2.30258509299404568402d0 ! log(1.0d1)
-
- _REAL_, parameter :: SQRT2 = 1.4142135623730950488016887242097d0
- _REAL_, parameter :: INVSQRT2 = 1.0d0 / SQRT2
-
- !------------------------------------------------------------
- !Generalised Born Constants
- _REAL_, parameter :: alpb_alpha = 0.571412d0 !Alpha prefactor for alpb_alpha
-
- !------------------------------------------------------------
- ! Unusual Constants
- integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit palindromic prime
- integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
- _REAL_, parameter :: NO_INPUT_VALUE_FLOAT = 12344321.d0
-
- integer :: plumed
- character(256) :: plumedfile
-
-contains
-
- function BinomialCoefficient(m, n) result (bioCoeff)
-
- integer, intent(in)::m,n
- _REAL_::bioCoeff
-
- integer, parameter::size=30
- integer, save::bc(size,size)=0
- logical, save::initialized=.false.;
-
- integer::i,j,k
-
- if (.not.initialized) then
- do i=1,size
- bc(i,1)=one
- bc(i,2:size)=zero
- end do
- do i=2, size
- do j=2, i
- bc(i,j)=bc(i-1,j-1)+bc(i-1,j)
- end do
- end do
-
- initialized=.true.
- end if
-
- bioCoeff=one*bc(m,n)
-
- end function BinomialCoefficient
-
-end module constants
-
diff --git a/patches/amber14.diff/AmberTools/src/sander/constants.F90.preplumed b/patches/amber14.diff/AmberTools/src/sander/constants.F90.preplumed
deleted file mode 100644
index c9aeeb8812eb98e8b0cfc2bfa7f4afe04f495899..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/constants.F90.preplumed
+++ /dev/null
@@ -1,267 +0,0 @@
-! <compile=optimized>
-#include "copyright.h"
-#include "../include/dprec.fh"
-
-!+++++++++++++++++++++++++++++++++++++++
-!This module contains various parameters
-!and constants used by the different
-!routines that make up sander.
-!
-!If you want to use one of the constants
-!in your routine you should include the
-!line:
-!
-!use constants, only : xxx, yyy, zzz
-!
-!where xxx,yyy,zzz are the constants you plan
-!to use in your routine.
-!This line needs to go before the
-!implicit none declaration.
-!
-! Based on constants.h, a pre Fortran 90 version, by Scott Brozell
-! and Dave Case (TSRI, 2002)
-! Converted into a Fortran 90 module by: Ross Walker (TSRI, 2005)
-! Expanded by others including: Matthew Clark, Andreas Goetz,
-!
-!++++++++++++++++++++++++++++++++++++++++
-
-module constants
-
- implicit none
-
- ! by default everything in this module is public
- public
-
- !------------------------------------------------------------
- ! Generic Floating Point Constants
- _REAL_, parameter :: TEN_TO_MINUS2 = 1.0d-2
- _REAL_, parameter :: TEN_TO_MINUS3 = 1.0d-3
- _REAL_, parameter :: TEN_TO_MINUS4 = 1.0d-4
- _REAL_, parameter :: TEN_TO_MINUS5 = 1.0d-5
- _REAL_, parameter :: TEN_TO_MINUS6 = 1.0d-6
- _REAL_, parameter :: TEN_TO_MINUS8 = 1.0d-8
- _REAL_, parameter :: TEN_TO_MINUS10 = 1.0d-10
- _REAL_, parameter :: TEN_TO_MINUS25 = 1.0d-25
- _REAL_, parameter :: TEN_TO_PLUS3 = 1.0d+3
- _REAL_, parameter :: TEN_TO_PLUS10 = 1.0d+10
-
- _REAL_, parameter :: zero = 0.0d0
- _REAL_, parameter :: one = 1.0d0
- _REAL_, parameter :: two = 2.0d0
- _REAL_, parameter :: three = 3.0d0
- _REAL_, parameter :: four = 4.0d0
- _REAL_, parameter :: five = 5.0d0
- _REAL_, parameter :: six = 6.0d0
- _REAL_, parameter :: seven = 7.0d0
- _REAL_, parameter :: eight = 8.0d0
- _REAL_, parameter :: nine = 9.0d0
- _REAL_, parameter :: ten = 10.0d0
- _REAL_, parameter :: eleven = 11.0d0
- _REAL_, parameter :: twelve = 12.0d0
- _REAL_, parameter :: sixteen = 16.0d0
- _REAL_, parameter :: twenty = 20.0d0
- _REAL_, parameter :: thirtytwo = 32.0d0
- _REAL_, parameter :: sixtyfour = 64.0d0
-
- _REAL_, parameter :: half = one/two
- _REAL_, parameter :: third = one/three
- _REAL_, parameter :: fourth = one/four
- _REAL_, parameter :: fifth = one/five
- _REAL_, parameter :: sixth = one/six
- _REAL_, parameter :: seventh = one/seven
- _REAL_, parameter :: eighth = one/eight
- _REAL_, parameter :: ninth = one/nine
- _REAL_, parameter :: tenth = one/ten
- _REAL_, parameter :: eleventh = one/eleven
- _REAL_, parameter :: twelfth = one/twelve
- _REAL_, parameter :: sixteenth = one/sixteen
- _REAL_, parameter :: thirtysecond = one/thirtytwo
- _REAL_, parameter :: sixtyfourth = one/sixtyfour
-
- _REAL_, parameter :: thirtieth = one/30.0d0
-
- !------------------------------------------------------------
- ! THE ARRAY FC(I) CONTAINS THE FACTORIALS OF (I-1).
-
- _REAL_, parameter :: FC(1:17) =&
- (/ 1.0D0,1.0D0, 2.0D0, 6.0D0, 24.0D0, 120.0D0, 720.0D0, 5040.0D0, &
- 40320.0D0, 362880.0D0, 3628800.0D0, 39916800.0D0, &
- 4.790016D+08, 6.2270208D+09, 8.71782912D+10, &
- 1.307674368D+12, 2.092278989D+13 /)
-
- _REAL_, parameter :: logFC(1:17) = (/ 0.0D0, 0.0D0, 0.6931471805599D0, &
- & 1.7917594692281D0, 3.1780538303479D0, 4.7874917427820D0, &
- & 6.5792512120101D0, 8.5251613610654D0, 10.6046029027453D0, &
- & 12.8018274800815D0, 15.1044125730755D0, 17.5023078458739D0, &
- & 19.9872144956619D0, 22.5521638531234D0, 25.1912211827387D0, &
- & 27.8992713838409D0, 30.6718601061763D0 /)
-
- ! DEFINE C COEFFICIENTS FOR ASSOCIATE LEGENDRE POLYNOMIALS.
- _REAL_, parameter::CC(1:21,1:3) = reshape ( (/ &
- 8.0D0, 8.0D0, 4.0D0, -4.0D0, 4.0D0, &
- 4.0D0, -12.0D0, -6.0D0, 20.0D0, 5.0D0, &
- 3.0D0, -30.0D0, -10.0D0, 35.0D0, 7.0D0, &
- 15.0D0, 7.5D0, -70.0D0, -17.5D0, 63.0D0, &
- 10.5D0, &
- 0.0D0, 0.0D0, 0.0D0, 12.0D0, 0.0D0, &
- 0.0D0, 20.0D0, 30.0D0, 0.0D0, 0.0D0, &
- -30.0D0, 70.0D0, 70.0D0, 0.0D0, 0.0D0, &
- -70.0D0, -105.D0, 210.0D0, 157.5D0, 0.0D0, &
- 0.0D0, &
- 0.0D0, 0.0D0, 0.0D0, 0.0D0, 0.0D0, &
- 0.0D0, 0.0D0, 0.0D0, 0.0D0, 0.0D0, &
- 35.0D0, 0.0D0, 0.0D0, 0.0D0, 0.0D0, &
- 63.0D0, 157.5D0, 0.0D0, 0.0D0, 0.0D0, &
- 0.0D0/), (/ 21, 3 /) )
-
- !------------------------------------------------------------
- ! Physical Constants
- _REAL_, parameter :: LIGHT_SPEED = 2.997924d08
- _REAL_, parameter :: HBAR = 627.509d0 * 0.0241888d-3 * 20.455d0 !Planck's constant in internal units
- _REAL_, parameter :: J_PER_CAL = 4.184d0 ! This is defined as the thermochemical calorie
- _REAL_, parameter :: JPKC = J_PER_CAL * 1000.0d0 !kilocalories per joule
- _REAL_, parameter :: BOLTZMANN = 1.380658d-23 !Boltzmann's constant in J/K
- _REAL_, parameter :: AVOGADRO = 6.0221367d+23 !Avogadro's number
- _REAL_, parameter :: KB = (BOLTZMANN * AVOGADRO) / JPKC !Boltzmann's constant in internal units
- _REAL_, parameter :: AMBER_ELECTROSTATIC = 18.2223d0
- _REAL_, parameter :: AMBER_ELECTROSTATIC2 = AMBER_ELECTROSTATIC * AMBER_ELECTROSTATIC
- !Ratio by which to scale amber charges to get electron charges - amberchg * oneqscale = electron charges
- ! = 1.0 / 18.2223d0
- _REAL_, parameter :: INV_AMBER_ELECTROSTATIC = 1.0d0/AMBER_ELECTROSTATIC
- _REAL_, parameter :: INV_AMBER_ELECTROSTATIC2 = 1.0d0/AMBER_ELECTROSTATIC2
-
- _REAL_, parameter :: CHARGE_ON_ELEC = 1.60217733d-19 !Charge on an electron in Coulombs
- _REAL_, parameter :: BOHR_RADIUS = 52.9177249d-12 ! in meter
- _REAL_, parameter :: BOHRS_TO_A = 0.529177249D0 ! Bohrs * this = angstroms - Same constants as used in dynamo v2.
- !_REAL_, parameter :: BOHRS_TO_A = 0.52917706D0 ! Bohrs * this = angstroms - Same constants as used in Gaussian 98
- !_REAL_, parameter :: BOHRS_TO_A = 0.529177D0 ! Bohrs * this = angstroms - Same constants as used in Mopac6 hcore.f
- !_REAL_, parameter :: BOHRS_TO_A = 0.529167D0 ! as used in Mopac6 repp.f
- _REAL_, parameter :: A_TO_BOHRS = 1.0d0 / BOHRS_TO_A
- !_REAL_, parameter :: A_TO_BOHRS = 1.88976D0 !Same constants as used in Mopac6 gover.f
- _REAL_, parameter :: A2_TO_BOHRS2 = A_TO_BOHRS * A_TO_BOHRS !Mopac6 uses 3.5711928576D0 in gover.f for this.
- _REAL_, parameter :: A3_TO_BOHRS3 = A2_TO_BOHRS2 * A_TO_BOHRS
- _REAL_, parameter :: A4_TO_BOHRS4 = A2_TO_BOHRS2 * A2_TO_BOHRS2
-
- _REAL_, parameter :: ONE_AU = 27.2113962d0 !One atomic unit of energy in eV.
- _REAL_, parameter :: HARTREE_TO_JOULE = ONE_AU * CHARGE_ON_ELEC !conversion from hartrees to joules
- _REAL_, parameter :: HART_BOHR_TO_JOULE_A = HARTREE_TO_JOULE * BOHRS_TO_A !hartree*bohrs to joules*angstroms
- _REAL_, parameter :: COULOMB_CONST_E = HART_BOHR_TO_JOULE_A*AVOGADRO/JPKC
- !Coulomb's constant for charges in units of e
- !This is the same as AMBER_ELECTROSTATIC2 but to higher precision
- !_REAL_, parameter :: AU_TO_EV = ONE_AU !Conversion from AU to EV - not used because we match dynamo v2 below.
- _REAL_, parameter :: AU_TO_EV = 27.21d0 !Conversion from AU to EV - Same as dynamo v2 uses and Gaussian 98
- !Note (RCW+MC): more precise would be: 1 a.u. 27.211396 eV
- !Mopac6 uses 27.21D0 in calpar.f, delri.f and repp.f but in
- !ffhpol.f it uses 27.2107 and in the manual it quotes 27.211
- _REAL_, parameter :: HALF_AU_TO_EV = AU_TO_EV * half
- _REAL_, parameter :: FOURTH_AU_TO_EV = AU_TO_EV * fourth
- _REAL_, parameter :: EIGHTH_AU_TO_EV = AU_TO_EV * eighth
- _REAL_, parameter :: SXNTH_AU_TO_EV = EIGHTH_AU_TO_EV * half
- _REAL_, parameter :: A2_TO_BOHRS2xAU_TO_EV = A2_TO_BOHRS2*AU_TO_EV
-
- !_REAL_, parameter :: EV_TO_KCAL = 23.060362D0 !Conversion from EV to KCAL/MOL
- !Dynamo parameter
- _REAL_, parameter :: EV_TO_KCAL = 23.061d0 !Dynamo's conversion
- !Mopac6 uses 23.061 in ffhpol.f analyt.f compfg.f datin.f dcart.f
- ! delri1.f delri2.f deritr.f interp.f iter.f
- ! moldat.f mopac.f
- _REAL_, parameter :: KCAL_TO_EV = one / EV_TO_KCAL
-
- _REAL_, parameter :: AU_TO_KCAL = AU_TO_EV*EV_TO_KCAL !1 hartree.
-
-
- ! The following are updated constants from Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730.
- !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
- ! NAME REFERENCE VALUE UNITS !
- !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
- ! Avogadro constant (Table XLVIII, p.708) 6.0221417930E23 mol^-1 !
- ! Bohr radius (Table XLIX, p. 710) 0.5291772085936E-10 m !
- ! a.u. of energy (Table LII, p. 717) 4.3597439422E-18 J !
- ! speed of light (vacuum) (Table I, p.637) 299 792 458 m*s^−1 !
- ! a.u. of charge (Table LIII, p. 717) 1.60217648740E-19 C !
- !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
- _REAL_, parameter :: CODATA08_AVOGADRO = 6.0221417930d23 ! Avogadro's number
- _REAL_, parameter :: CODATA08_BOHR_RADIUS = 0.5291772085936d-10
- _REAL_, parameter :: CODATA08_ONE_AU = 4.3597439422d-18 ! Atomic unit of energy in joules
- _REAL_, parameter :: CODATA08_LIGHT_SPEED = 2.99792458d08
- _REAL_, parameter :: CODATA08_CHARGE_ON_ELEC = 1.60217648740d-19
- ! Derived values
- _REAL_, parameter :: CODATA08_A_TO_BOHRS = 1d-10 / CODATA08_BOHR_RADIUS
- _REAL_, parameter :: CODATA08_AU_TO_KCAL = CODATA08_ONE_AU / J_PER_CAL / 1000 * CODATA08_AVOGADRO
- _REAL_, parameter :: CODATA08_AU_TO_DEBYE = &
- CODATA08_LIGHT_SPEED * CODATA08_CHARGE_ON_ELEC * CODATA08_BOHR_RADIUS / 1d-21
- !_REAL_, parameter :: AU_TO_DEBYE = 1.0d0/0.393430 ! from http://cccbdb.nist.gov/debye.asp (April 12 2011)
-
- !------------------------------------------------------------
- !Numeric Constants
- _REAL_, parameter :: PI = 3.1415926535897932384626433832795d0
-
- !The BOOK says :
- !
- !2Chronicles 4:2 reads thus, 'Also he made a molten sea of ten cubits
- !from brim to brim, round in compass, and five cubits the height thereof;
- !and a line of thirty cubits did compass it round about.'
- !
- !Hence, Pi is exactly equal to three and there is nothing more to discuss!
- !
- !If you want to use the value of PI defined by 'the BOOK' then uncomment
- !the following line and comment out the definition above...
- !_REAL_, parameter :: PI = 3.0d0
-
- _REAL_, parameter :: PI2 = PI*PI
- _REAL_, parameter :: HALFPI = PI * 0.5d0
- _REAL_, parameter :: TWOPI = 2.0d0 * PI
- _REAL_, parameter :: FOURPI = 4.0d0 * PI
- _REAL_, parameter :: INVPI = 1.0d0 / PI
- _REAL_, parameter :: SQRTPI = 1.77245385090551602729816748334d0 !sqrt(PI)
- _REAL_, parameter :: INVSQRTPI = 1.0d0 / SQRTPI
- _REAL_, parameter :: DEG_TO_RAD = PI / 180.0d0
- _REAL_, parameter :: RAD_TO_DEG = 180.0d0 / PI
- _REAL_, parameter :: LN_TO_LOG = 2.30258509299404568402d0 ! log(1.0d1)
-
- _REAL_, parameter :: SQRT2 = 1.4142135623730950488016887242097d0
- _REAL_, parameter :: INVSQRT2 = 1.0d0 / SQRT2
-
- !------------------------------------------------------------
- !Generalised Born Constants
- _REAL_, parameter :: alpb_alpha = 0.571412d0 !Alpha prefactor for alpb_alpha
-
- !------------------------------------------------------------
- ! Unusual Constants
- integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit palindromic prime
- integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
- _REAL_, parameter :: NO_INPUT_VALUE_FLOAT = 12344321.d0
-
-contains
-
- function BinomialCoefficient(m, n) result (bioCoeff)
-
- integer, intent(in)::m,n
- _REAL_::bioCoeff
-
- integer, parameter::size=30
- integer, save::bc(size,size)=0
- logical, save::initialized=.false.;
-
- integer::i,j,k
-
- if (.not.initialized) then
- do i=1,size
- bc(i,1)=one
- bc(i,2:size)=zero
- end do
- do i=2, size
- do j=2, i
- bc(i,j)=bc(i-1,j-1)+bc(i-1,j)
- end do
- end do
-
- initialized=.true.
- end if
-
- bioCoeff=one*bc(m,n)
-
- end function BinomialCoefficient
-
-end module constants
-
diff --git a/patches/amber14.diff/AmberTools/src/sander/mdread.F90 b/patches/amber14.diff/AmberTools/src/sander/mdread.F90
deleted file mode 100644
index d0365a01fa3ab5cd98acfdc0b5cc0f123fde413b..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/mdread.F90
+++ /dev/null
@@ -1,3856 +0,0 @@
-#include "copyright.h"
-#include "../include/dprec.fh"
-#include "ncsu-config.h"
-#include "../include/assert.fh"
-#ifndef PBSA
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Open input files and read cntrl namelist.
-subroutine mdread1()
-
- use file_io_dat
- use lmod_driver, only : read_lmod_namelist
- use qmmm_module, only : qmmm_nml,qmmm_struct, qm_gb
- use constants, only : RETIRED_INPUT_OPTION, zero, one, two, three, seven, &
- eight, NO_INPUT_VALUE_FLOAT, NO_INPUT_VALUE, &
- plumed, plumedfile
- use constantph, only : mccycles
- use amoeba_mdin, only: AMOEBA_read_mdin, iamoeba
- use nose_hoover_module, only: nchain ! APJ
- use lscivr_vars, only: ilscivr, icorf_lsc
- use pimd_vars, only: ipimd,itimass
- use neb_vars, only: ineb
- use cmd_vars, only: restart_cmd, eq_cmd, adiab_param
- use stack, only: lastist,lastrst
- use nmr, only: echoin
- use crg_reloc, only: ifcr, cropt, crcut, crskin, crin, crprintcharges
- use sgld, only : isgld, isgsta,isgend,fixcom, &
- tsgavg,sgft,sgff,sgfd,tempsg,treflf,tsgavp
- use amd_mod, only: iamd,iamdlag,EthreshD,alphaD,EthreshP,alphaP, &
- w_amd,EthreshD_w,alphaD_w,EthreshP_w,alphaP_w
- use scaledMD_mod, only: scaledMD,scaledMD_lambda
- use nbips, only: ips,teips,tvips,teaips,tvaips,raips,mipsx,mipsy,mipsz, &
- mipso,gridips,dvbips
- use emap,only: temap,gammamap
-#ifdef DSSP
- use dssp, only: idssp
-#endif /* DSSP */
-
- use emil_mod, only : emil_do_calc
- use mdin_emil_dat_mod, only : error_hdr
-
-#if !defined(DISABLE_NCSU) && defined(MPI)
- use ncsu_sander_hooks, only : ncsu_on_mdread1 => on_mdread1
-#endif /* ! DISABLE_NCSU && MPI */
-#ifdef _XRAY
- use xray_interface_module, only: xray_active, xray_read_mdin
-#endif /* _XRAY */
-#ifdef MPI /* SOFT CORE */
- use softcore, only : scalpha,scbeta,ifsc,scmask,logdvdl,dvdl_norest,dynlmb, &
- sceeorder, tishake, emil_sc
- use mbar, only : ifmbar, bar_intervall, bar_l_min, bar_l_max, bar_l_incr
- use remd, only : rem
-#endif /* MPI */
- ! Parameter for LIE module
- use linear_response, only: ilrt, lrt_interval, lrtmask
-#ifdef RISMSANDER
- use sander_rism_interface, only: rismprm,xvvfile, guvfile, huvfile, cuvfile,&
- uuvfile, asympfile, quvFile, chgDistFile
-#endif /*RISMSANDER*/
-#ifdef APBS
- use apbs
-#endif /* APBS */
- use sebomd_module, only: read_sebomd_namelist, sebomd_namelist_default
- implicit none
-# include "box.h"
-# include "def_time.h"
-# include "ew_cntrl.h"
-# include "ew_pme_recip.h"
-# include "../include/md.h"
-# include "../include/memory.h"
-# include "mmtsb.h"
-# include "nmr.h"
-# include "tgtmd.h"
-# include "multitmd.h"
-# include "ew_erfc_spline.h"
-#ifdef LES
-# include "les.h"
-#else
- _REAL_ temp0les
-#endif
-
- character(len=4) watdef(4),watnam,owtnm,hwtnm1,hwtnm2
-
- _REAL_ dele
- integer ierr
- integer ifind
- integer imcdo
- integer itotst
- integer jn
- integer inerr
- logical mdin_cntrl, mdin_lmod, mdin_qmmm ! true if namelists are in mdin
- logical mdin_sebomd
- integer :: ifqnt ! local here --> put into qmmm_nml%ifqnt after read here
- integer mxgrp
- integer iemap
- character(len=8) date
- character(len=10) time
- character(len=512) :: char_tmp_512
- _REAL_ dtemp ! retired
- _REAL_ dxm ! retired
- _REAL_ heat ! retired
- _REAL_ timlim ! retired
-
-#ifdef RISMSANDER
- integer irism
-#endif /*RISMSANDER*/
-
- namelist /cntrl/ irest,ibelly, &
- ntx,ntxo,ntcx,ig,tempi, &
- ntb,ntt,nchain,temp0,tautp, &
- ntp,pres0,comp,taup,barostat,mcbarint, &
- nscm,nstlim,t,dt, &
- ntc,ntcc,nconp,tol,ntf,ntn,nsnb, &
- cut,dielc, &
- ntpr,ntwx,ntwv,ntwe,ntwf,ntave,ntpp,ioutfm, &
- ntr,nrc,ntrx,taur,nmropt, &
- ivcap,cutcap,xcap,ycap,zcap,fcap, &
- xlorth,ylorth,zlorth,xorth,yorth,zorth,forth, &
- imin,drms,dele,dx0, &
- pencut,ipnlty,iscale,scalm,noeskp, &
- maxcyc,ncyc,ntmin,vlimit, &
- mxsub,ipol,jfastw,watnam,owtnm,hwtnm1,hwtnm2, iesp, &
- skmin, skmax, vv,vfac, tmode, ips, &
- mipsx,mipsy,mipsz,mipso,gridips,raips,dvbips, &
- iamd,iamdlag,EthreshD,alphaD,EthreshP,alphaP, &
- w_amd,EthreshD_w,alphaD_w,EthreshP_w,alphaP_w, &
- scaledMD,scaledMD_lambda, &
- iemap,gammamap, &
- isgld,isgsta,isgend,fixcom,tsgavg,sgft,sgff,sgfd,tempsg,treflf,tsgavp,&
- jar, iamoeba, &
- numexchg, repcrd, numwatkeep, hybridgb, &
- ntwprt,tausw, &
- ntwr,iyammp,imcdo, &
- igb,alpb,Arad,rgbmax,saltcon,offset,gbsa,vrand, &
- surften,iwrap,nrespa,nrespai,gamma_ln,extdiel,intdiel, &
- cut_inner,icfe,clambda,klambda, rbornstat,lastrst,lastist, &
- itgtmd,tgtrmsd,tgtmdfrc,tgtfitmask,tgtrmsmask, dec_verbose, &
- idecomp,temp0les,restraintmask,restraint_wt,bellymask, &
- noshakemask,crgmask, iwrap_mask,mmtsb_switch,mmtsb_iterations, &
- rdt,icnstph,solvph,ntcnstph,ntrelax, mccycles, &
- ifqnt,ievb, ipimd, itimass, ineb,profile_mpi, ilscivr, icorf_lsc, &
- ipb, inp, plumed,plumedfile, &
- gbneckscale, &
- gbalphaH,gbbetaH,gbgammaH, &
- gbalphaC,gbbetaC,gbgammaC, &
- gbalphaN,gbbetaN,gbgammaN, &
- gbalphaOS,gbbetaOS,gbgammaOS, &
- gbalphaP,gbbetaP,gbgammaP, &
- Sh,Sc,Sn,So,Ss,Sp, &
- lj1264, &
- ifcr, cropt, crcut, crskin, crin, crprintcharges, &
- csurften, ninterface, gamma_ten, &
-#ifdef MPI /* SOFT CORE */
- scalpha, scbeta, ifsc, scmask, logdvdl, dvdl_norest, dynlmb, &
- sceeorder, &
- ifmbar, bar_intervall, bar_l_min, bar_l_max, bar_l_incr, tishake, &
- emil_sc, &
-#endif
- ilrt, lrt_interval, lrtmask, &
-#ifdef DSSP
- idssp, &
-#endif
-#ifdef RISMSANDER
- irism,&
-#endif /*RISMSANDER*/
- emil_do_calc, &
- restart_cmd, eq_cmd, adiab_param, &
- vdwmodel, & ! mjhsieh - the model used for van der Waals
- dtemp, heat, timlim !all retired
-
- ! Define default water residue name and the names of water oxygen & hydrogens
-
- data watdef/'WAT ','O ','H1 ','H2 '/
-
- ! ----- READ THE CONTROL DATA AND OPEN DIFFERENT FILES -----
-
- if (mdout /= "stdout" ) &
- call amopen(6,mdout,owrite,'F','W')
- call amopen(5,mdin,'O','F','R')
- write(6,9308)
- call date_and_time( DATE=date, TIME=time )
- write(6,'(12(a))') '| Run on ', date(5:6), '/', date(7:8), '/', &
- date(1:4), ' at ', time(1:2), ':', time(3:4), ':', time(5:6)
-
- ! Write the path of the current executable and working directory
- call get_command_argument(0, char_tmp_512)
- write(6,'(/,a,a)') '| Executable path: ', trim(char_tmp_512)
- call getcwd(char_tmp_512)
- write(6,'(a,a)') '| Working directory: ', trim(char_tmp_512)
-! Write the hostname if we can get it from environment variable
-! Note: get_environment_variable is part of the F2003 standard but seems
-! to be supported by GNU, Intel, IBM and Portland (2010+) compilers
- call get_environment_variable("HOSTNAME", char_tmp_512, inerr)
- if (inerr .eq. 0) then
- write(6,'(a,a,/)') '| Hostname: Unknown'
- else
- write(6,'(a,a,/)') '| Hostname: ', trim(char_tmp_512)
- end if
-
- if (owrite /= 'N') write(6, '(2x,a)') '[-O]verwriting output'
-
- ! Echo the file assignments to the user:
-
- write(6,9700) 'MDIN' ,mdin(1:70) , 'MDOUT' ,mdout(1:70) , &
- 'INPCRD' ,inpcrd(1:70), 'PARM' ,parm(1:70) , &
- 'RESTRT',restrt(1:70) , 'REFC' ,refc(1:70) , &
- 'MDVEL' ,mdvel(1:70) , 'MDFRC' ,mdfrc(1:70) , &
- 'MDEN' ,mden(1:70) , &
- 'MDCRD' ,mdcrd(1:70) , 'MDINFO' ,mdinfo(1:70), &
- 'MTMD' ,mtmd(1:70) , 'INPDIP', inpdip(1:70), &
- 'RSTDIP', rstdip(1:70), 'INPTRAJ', inptraj(1:70)
-# ifdef MPI
- write(6,9702) 'REMLOG', trim(remlog), &
- 'REMTYPE', trim(remtype), &
- 'REMSTRIP', trim(remstripcoord), &
- 'SAVEENE', trim(saveenefile), &
- 'CLUSTERINF', trim(clusterinfofile), &
- 'RESERVOIR', trim(reservoirname), &
- 'REMDDIM', trim(remd_dimension_file)
-# endif
-#ifdef RISMSANDER
- if(len_trim(xvvfile) > 0)&
- write(6,9701) 'Xvv',trim(xvvfile)
- if(len_trim(guvfile) > 0)&
- write(6,9701) 'Guv',trim(Guvfile)
- if(len_trim(huvfile) > 0)&
- write(6,9701) 'Huv',trim(Huvfile)
- if(len_trim(cuvfile) > 0)&
- write(6,9701) 'Cuv',trim(Cuvfile)
- if(len_trim(uuvfile) > 0)&
- write(6,9701) 'Uuv',trim(Uuvfile)
- if(len_trim(asympfile) > 0)&
- write(6,9701) 'Asymptotics',trim(asympfile)
- if(len_trim(quvfile) > 0)&
- write(6,9701) 'Quv',trim(Quvfile)
- if(len_trim(chgDistfile) > 0)&
- write(6,9701) 'ChgDist',trim(chgDistfile)
-#endif /*RISMSANDER*/
-
- ! Echo the input file to the user:
- call echoin(5,6)
- ! ----- READ DATA CHARACTERIZING THE MD-RUN -----
- read(5,'(a80)') title
- ! ----read input in namelist format, first setting up defaults
-
- dtemp = RETIRED_INPUT_OPTION
- dxm = RETIRED_INPUT_OPTION
- heat = RETIRED_INPUT_OPTION
- timlim = RETIRED_INPUT_OPTION
- irest = 0
- ibelly = 0
- ipol = RETIRED_INPUT_OPTION
- iesp = 0
- ntx = 1
- ntxo = NO_INPUT_VALUE
- ig = 71277
- tempi = ZERO
- ntb = NO_INPUT_VALUE
- ntt = 0
- nchain = 1
- temp0 = 300.0d0
- plumed = 0
- plumedfile = 'plumed.dat'
-
-#ifdef LES
- ! alternate temp for LES copies, if negative then use single bath
- ! single bath not the same as 2 baths with same target T
- temp0les = -ONE
- rdt = ZERO
-#endif
- ipimd =0
- itimass = 0 ! Default = no TI w.r.t. mass.
- ineb =0
-
- tautp = ONE
- ntp = 0
- barostat = 1
- mcbarint = 100
- pres0 = ONE
- comp = 44.6d0
- taup = ONE
- npscal = 1
- nscm = 1000
- nstlim = 1
- t = ZERO
- dt = 0.001d0
- ntc = 1
- tol = 0.00001
- ntf = 1
- nsnb = 25
- cut = NO_INPUT_VALUE_FLOAT
- dielc = ONE
- ntpr = 50
- ntwr = 500
- ntwx = 0
- ntwv = 0
- ntwf = 0
- ntwe = 0
- ipb = 0
- inp = 2
-
-#ifdef RISMSANDER
- irism = 0
-#endif /*RISMSANDER*/
-
- ntave = 0
- ioutfm = 0
- ntr = 0
- ntrx = 1
- ivcap = 0
- natcap = 0
- fcap = 1.5d0
- cutcap = 0.0d0
- xcap = 0.0d0
- ycap = 0.0d0
- zcap = 0.0d0
- forth = 1.5d0
- xlorth = -1.0d0
- ylorth = -1.0d0
- zlorth = -1.0d0
- xorth = 47114711.0d0
- yorth = 47114711.0d0
- zorth = 47114711.0d0
- numexchg = 0
- repcrd = 1
- lj1264 = 0
-
- profile_mpi = 0 !whether to write profile_mpi timing file - default = 0 (NO).
-
- ! number of waters to keep for hybrid model,
- ! numwatkeep: the number of closest
- ! waters to keep. close is defined as close to non-water.
- ! for simulations with ions, ions should be stripped too
- ! or at least ignored in the "closest" calculation. this
- ! is not currently done.
-
- ! if it stays at -1 then we keep all waters
- ! 0 would mean to strip them all
-
- numwatkeep=-1
-
- ! hybridgb: gb model to use with hybrid REMD.
- hybridgb=0
-
- ! carlos targeted MD, like ntr
-
- itgtmd=0
- tgtrmsd=0.
- tgtmdfrc=0.
- tgtfitmask=''
- tgtrmsmask=''
-
- pencut = 0.1d0
- taumet = 0.0001d0
- omega = 500.0d0
- ipnlty = 1
- scalm = 100.0d0
- iscale = 0
- noeskp = 1
- nmropt = 0
- jar = 0
- tausw = 0.1d0
- imin = 0
- isftrp = 0
- rwell = ONE
- maxcyc = 1
- ncyc = 10
- ntmin = 1
- dx0 = 0.01d0
- drms = 1.0d-4
- vlimit = 20.0d0
- mxsub = 1
- jfastw = 0
- watnam = ' '
- owtnm = ' '
- hwtnm1 = ' '
- hwtnm2 = ' '
- ntwprt = 0
- igb = 0
- alpb = 0
- Arad = 15.0d0
- rgbmax = 25.d0
- saltcon = ZERO
-
- ! default offset depends on igb value, and users need to
- ! be able to modify it, so we need to set a dummy value. if it's still the
- ! dummy after we read the namelist, we set the default based on igb. if not,
- ! we leave it at what the user set.
- ! best solution would be to create a GB namelist.
- offset = -999999.d0
- gbneckscale = -999999.d0
-
- iyammp = 0
- imcdo = -1
- gbsa = 0
- vrand=1000
- surften = 0.005d0
- iwrap = 0
- nrespa = 1
- nrespai = 1
- irespa = 1
- gamma_ln = ZERO
- extdiel = 78.5d0
- intdiel = ONE
- gbgamma = ZERO
- gbbeta = ZERO
- gbalpha = ONE
-
- !Hai Nguyen: set default parameters for igb = 8
- ! NOTE THAT NONE OF THESE ARE USED UNLESS IGB=8, SO USERS SHOULD NOT EVEN SET
- ! THEM
- gbalphaH = 0.788440d0
- gbbetaH = 0.798699d0
- gbgammaH = 0.437334d0
- gbalphaC = 0.733756d0
- gbbetaC = 0.506378d0
- gbgammaC = 0.205844d0
- gbalphaN = 0.503364d0
- gbbetaN = 0.316828d0
- gbgammaN = 0.192915d0
- gbalphaOS = 0.867814d0
- gbbetaOS = 0.876635d0
- gbgammaOS = 0.387882d0
- gbalphaP = 1.0d0 !P parameters are not optimized yet
- gbbetaP = 0.8d0 !P parameters are not optimized yet
- gbgammaP = 4.85d0 !P parameters are not optimized yet
- !scaling parameters below will only be used for igb=8.
- ! the actual code does not use these variables, it uses X(l96)
- ! if igb=8, we will use these to set the X(l96) array.
- Sh = 1.425952d0
- Sc = 1.058554d0
- Sn = 0.733599d0
- So = 1.061039d0
- Ss = -0.703469d0
- Sp = 0.5d0 !P parameters are not optimized yet
- !End Hai Nguyen
-
- iconstreff = 0
- cut_inner = EIGHT
- icfe = 0
- clambda = ZERO
- klambda = 1
- ievb = 0
- rbornstat = 0
- idecomp = 0
- ! added a flag to control output of BDC/SDC synonymous with MMPBSA.py's
- ! version of the same variable.
- dec_verbose = 3
- lastrst = 1
- lastist = 1
- restraintmask=''
- restraint_wt = ZERO
- bellymask=''
- noshakemask=''
- iwrap_mask='' ! GMS: mask to wrap around if iwrap == 2
- crgmask=''
- mmtsb_switch = mmtsb_off ! MMTSB Replica Exchange Off by Default
- mmtsb_iterations = 100 ! MMTSB Replica Exchange Frequency in Iterations
-
- icnstph = 0
- solvph = SEVEN
- ntcnstph = 10
- ntrelax = 500 ! how long to let waters relax
- mccycles = 1 ! How many cycles of Monte Carlo steps to run
- skmin = 50 !used by neb calculation
- skmax = 100 !used by neb calculation
- vv = 0 !velocity verlet -- off if vv/=1
- vfac = 0 !velocity verlet scaling factor, 0 by default
- tmode = 1 !default tangent mode for NEB calculation
-
- ifqnt = NO_INPUT_VALUE
-
- ifcr = 0 ! no charge relocation
- cropt = 0 ! 1-4 EEL is calculated with the original charges
- crcut = 3.0
- crskin = 2.0
- crin = ''
- crprintcharges = 0
-
- ips = 0 ! no isotropic periodic sum
- raips=-1.0d0 ! automatically determined
- mipsx=-1 ! number of grids in x direction, <0 for automatically determined
- mipsy=-1 ! number of grids in y direction, <0 for automatically determined
- mipsz=-1 ! number of grids in z direction, <0 for automatically determined
- mipso=4 ! default 4th order b-spline
- gridips=2 ! grid size. used to determine grid number if not defined
- dvbips=1.0d-8 ! Volume change tolerance. aips will be done when change more than dvbips
-
- iamd = 0 ! No accelerated MD used
- iamdlag = 0 !frequency of boosting in steps
- EthreshD = 0.d0
- alphaD = 0.d0
- EthreshP = 0.d0
- alphaP = 0.d0
- w_amd = 0 ! windowed amd
- EthreshD_w = 0.d0
- alphaD_w = 0.d0
- EthreshP_w = 0.d0
- alphaP_w = 0.d0
-
- scaledMD = 0 ! No scaled MD used
- scaledMD_lambda = 0.d0
-
- iemap=0 ! no emap constraint
- gammamap=1 ! default friction constant for map motion, 1/ps
- isgld = 0 ! no self-guiding
- isgsta=1 ! Begining index of SGLD range
- isgend=0 ! Ending index of SGLD range
- fixcom=-1 ! fix center of mass in SGLD simulation
- tsgavg=0.2d0 ! Local averaging time of SGLD simulation
- sgft=-1.0d3 ! Guiding factor of SGLD simulation
- sgff=-1.0d3 ! Guiding factor of SGLD simulation
- sgfd=-1.0d3 ! Guiding factor of SGLD simulation
- tempsg=0.0d0 ! Guiding temperature of SGLD simulation
- treflf=0.0d0 ! Reference low frequency temperature of SGLD simulation
- tsgavp=2.0d0 ! Convergency time of SGLD simulation
-
- ! Check to see if "cntrl" namelist has been defined.
- mdin_cntrl=.false.
- mdin_qmmm = .false.
- mdin_ewald=.false.
- mdin_pb=.false.
-#ifdef APBS
- mdin_apbs = .false.
-#endif /* APBS */
- mdin_lmod=.false.
- mdin_amoeba=.false.
- mdin_sebomd=.false.
- iamoeba = 0
-#ifdef MPI /* SOFT CORE */
- scalpha=0.5
- scbeta=12.0
- sceeorder=2
- ifsc=0
- logdvdl=0
- dvdl_norest=0
- dynlmb=0.0
- ifmbar=0
- bar_intervall=100
- bar_l_min=0.1
- bar_l_max=0.9
- bar_l_incr=0.1
- tishake = 0
- emil_sc = 0
-#endif
- ilrt = 0
- lrt_interval = 50
- lrtmask=''
-#ifdef DSSP
- idssp = 0
-#endif
- emil_do_calc = 0
-
-! Constant Surface Tension
- csurften = 0 !constant surface tension off (valid options are 0,1,2,3)
- gamma_ten = 0.0d0 !0.0 dyne/cm - default used in charmm. Ignored for csurften=0
- ninterface = 2 !Number of interfaces in the surface tension (Must be greater than 2)
-
- call nmlsrc('cntrl',5,ifind)
- if (ifind /= 0) mdin_cntrl=.true.
-
- call nmlsrc('ewald',5,ifind)
- if (ifind /= 0) mdin_ewald=.true.
-
- call nmlsrc('pb',5,ifind)
- if (ifind /= 0) mdin_pb=.true.
-
- call nmlsrc('qmmm', 5, ifind)
- if (ifind /= 0) mdin_qmmm = .true.
-
-#ifdef APBS
- call nmlsrc('apbs',5,ifind)
- if (ifind /= 0) mdin_apbs=.true.
-#endif /* APBS */
-
- call nmlsrc('lmod',5,ifind)
- if (ifind /= 0) mdin_lmod=.true.
-
- call nmlsrc('amoeba',5,ifind)
- if (ifind /= 0) mdin_amoeba=.true.
-
- call nmlsrc('sebomd',5,ifind)
- if (ifind /= 0) mdin_sebomd=.true.
-
-#ifdef _XRAY
- call nmlsrc('xray',5,ifind)
- xray_active = (ifind /= 0)
-#endif
-
- rewind 5
- if ( mdin_cntrl ) then
- read(5,nml=cntrl,err=999)
- else
- write(6, '(1x,a,/)') 'Could not find cntrl namelist'
- call mexit(6,1)
- end if
-
- if ( igb == 10 .and. ipb == 0 ) ipb = 2
- if ( igb == 0 .and. ipb /= 0 ) igb = 10
-
- if (plumed.eq.1) then
- write(6, '(1x,a,/)') 'PLUMED is on'
- write(6, '(1x,a,a,/)') 'PLUMEDfile is ',plumedfile
- endif
-
- if (ifqnt == NO_INPUT_VALUE) then
- ifqnt = 0 ! default value
- if (mdin_qmmm) then
- write(6, '(1x,a,/)') &
- '| WARNING qmmm namelist found, but ifqnt was not set! QMMM NOT &
- &active.'
- end if
- end if
-
- ! Now that we've read the input file, set up the defaults for variables
- ! whose values depend on other input values (ntb, cut)
- if (ntb == NO_INPUT_VALUE) then
- if (ntp > 0) then
- ntb = 2
- else if (igb > 0) then
- ntb = 0
- else
- ntb = 1
- end if
- end if
-
- if (ntxo == NO_INPUT_VALUE) then
-#ifdef MPI
- if (rem < 0) then
- ntxo = 2
- else
- ntxo = 1
- end if
-#else
- ntxo = 1
-#endif
- end if
-
- if (cut == NO_INPUT_VALUE_FLOAT) then
- if (igb == 0) then
- cut = EIGHT
- else
- cut = 9999.d0
- end if
- end if
-
-#ifdef RISMSANDER
- !force igb=6 to get vacuum electrostatics. This must be done ASAP to ensure SANDER's
- !electrostatics are initialized properly
- rismprm%irism=irism
- if(irism/=0) then
- write(6,'(a)') "|3D-RISM Forcing igb=6"
- igb=6
- end if
-#endif /*RISMSANDER*/
-
-
- if (ifqnt>0) then
- qmmm_nml%ifqnt = .true.
- if (saltcon /= 0.0d0) then
- qm_gb%saltcon_on = .true.
- else
- qm_gb%saltcon_on = .false.
- end if
- if (alpb == 1) then
- qm_gb%alpb_on = .true.
- else
- qm_gb%alpb_on = .false.
- end if
- if (igb == 10 .or. ipb /= 0) then
- write(6, '(1x,a,/)') 'QMMM is not compatible with Poisson Boltzmann (igb=10 or ipb/=0).'
- call mexit(6,1)
- end if
- else
- qmmm_nml%ifqnt = .false.
- end if
-
- if ( mdin_lmod ) then
- rewind 5
- call read_lmod_namelist()
- end if
-
- !--------------------------------------------------------------------
- ! --- vars have been read ---
- !--------------------------------------------------------------------
-
- write(6,9309)
-
- ! emit warnings for retired cntrl namelist variables
-
- if ( dtemp /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: dtemp has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- end if
- if ( dxm /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: dxm has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- ! ' The step length will be unlimited.'
- end if
- if ( heat /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: heat has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- end if
-
- if ( timlim /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: timlim has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- end if
-
-! Constant surface tension valid options
- if (csurften > 0) then
- if (csurften < 0 .or. csurften > 3) then
- write(6,'(/2x,a)') &
- 'Invalid csurften value. csurften must be between 0 and 3'
- call mexit(6,1)
- end if
- if (ntb /= 2) then
- write(6,'(/2x,a)') &
- 'ntb invalid. ntb must be 2 for constant surface tension.'
- call mexit(6,1)
- end if
- if (ntp < 2) then
- write(6,'(/2x,a)') &
- 'ntp invalid. ntp must be 2 or 3 for constant surface tension.'
- call mexit(6,1)
- end if
- if (ninterface < 2) then
- write(6,'(/2x,a)') &
- 'ninterface must be greater than 2 for constant surface tension.'
- call mexit(6,1)
- end if
-
- if (iamoeba > 0 ) then
- write(6,'(/2x,a)') &
- 'Constant Surface Tension is not compatible with Amoeba Runs.'
- call mexit(6,1)
- end if
-
- if (ipimd > 0 ) then
- write(6,'(/2x,a)') &
- 'Constant Surface Tension is not compatible with PIMD Runs.'
- call mexit(6,1)
- end if
-
- end if
-
-! MC Barostat valid options. Some of these may work, but disable them until they
-! are fully tested.
-
- if (ntp > 0 .and. barostat == 2) then
- inerr = 0
- if (ievb /= 0) then
- write(6, '(/2x,a)') 'AMOEBA is not compatible with the MC Barostat'
- inerr = 1
- end if
- if (ipimd /= 0) then
- write(6, '(/2x,a)') 'PIMD is not compatible with the MC Barostat'
- inerr = 1
- end if
- if (icfe /= 0) then
- write(6, '(/2x,a)') 'TI is not compatible with the MC Barostat'
- inerr = 1
- end if
-#ifdef LES
- write(6, '(/2x,a)') 'LES is not compatible with the MC Barostat'
- inerr = 1
-#endif
- ! Any others? Hopefully most or all of the above can be made compatible.
- if (inerr == 1) &
- call mexit(6, 1)
- end if
-
- call printflags()
-
- !--------------------------------------------------------------------
- ! If user has requested ewald electrostatics, read some more input
- !--------------------------------------------------------------------
-
- if( igb == 0 .and. ipb == 0 ) call load_ewald_info(parm,inpcrd,ntp)
-
- !--------------------------------------------------------------------
- ! parameters for IPS and for SGLD:
- ! ips=1 3D IPS for electrostatic and Lennard-Jones potentials
- ! ips=2 3D IPS for electrostatic potential only
- ! ips=3 3D IPS for Lennard-Jones potential only
- ! ips=4 3D IPS/DFFT for electrostatic and Lennard-Jones potentials
- ! ips=5 3D IPS/DFFT for electrostatic potential only
- ! ips=6 3D IPS/DFFT for Lennard-Jones potential only
- !--------------------------------------------------------------------
-
- teips=.false.
- tvips=.false.
- teaips=.false.
- tvaips=.false.
- if((ips-4)*(ips-6) == 0 )tvaips =.true.
- if ( (ips-4)*(ips-5) == 0 )teaips =.true.
- if( tvaips.OR.( (ips -1)*(ips-3) == 0 ))tvips =.true.
- if( teaips.OR.((ips -1)*(ips-2) == 0 ))teips =.true.
- if( teips ) then
- use_pme = 0
- eedmeth = 6
- end if
- if( tvips ) then
- vdwmeth = 2
- if(use_pme/=0.and.tvaips)then
- mipsx=nfft1 ! number of grids in x direction, <0 for automatically determined
- mipsy=nfft2 ! number of grids in y direction, <0 for automatically determined
- mipsz=nfft3 ! number of grids in z direction, <0 for automatically determined
- mipso=order ! default 6th order b-spline
- endif
- end if
- temap=iemap>0
- ishake = 0
- if (ntc > 1) ishake = 1
-
- !--------------------------------------------------------------------
- ! Set up some parameters for AMD simulations:
- ! AMD initialization
- ! iamd=0 no boost is used, 1 boost on the total energy,
- ! 2 boost on the dohedrals, 3 boost on dihedrals and total energy
- !--------------------------------------------------------------------
- if(iamd.gt.0)then
- if(iamd.eq.1)then !only total potential energy will be boosted
- EthreshD=0.d0
- alphaD=0.d0
- else if(iamd.eq.2)then !only dihedral energy will be boosted
- EthreshP=0.d0
- alphaP=0.d0
- endif
- if(w_amd.gt.0)then
- if(iamd.eq.1)then !only total potential energy will be boosted
- EthreshD_w=0.d0
- alphaD_w=0.d0
- else if(iamd.eq.2)then !only dihedral energy will be boosted
- EthreshP_w=0.d0
- alphaP_w=0.d0
- endif
- write(6,'(a,i3)')'| Using Windowed Accelerated MD (wAMD) &
- &LOWERING BARRIERS to enhance sampling w_amd =', w_amd
- write(6,'(a,2f22.12)')'| AMD boost to total energy: EthreshP,alphaP',&
- EthreshP, alphaP
- write(6,'(a,2f22.12)')'| AMD boost to dihedrals: EthreshD,alphaD',&
- EthreshD,alphaD
- write(6,'(a,2f22.12)')'| AMD extra parameters boost to total energy: &
- &EthreshP_w,alphaP_w', EthreshP_w, alphaP_w
- write(6,'(a,2f22.12)')'| AMD extra parameters boost to dihedrals: &
- &EthreshD_w,alphaD_w', EthreshD_w, alphaD_w
- else
- write(6,'(a,i3)')'| Using Accelerated MD (AMD) RASING VALLEYS to &
- &enhance sampling iamd =',iamd
- write(6,'(a,2f22.12)')'| AMD boost to total energy: EthreshP,alphaP', &
- EthreshP, alphaP
- write(6,'(a,2f22.12)')'| AMD boost to dihedrals: EthreshD,alphaD', &
- EthreshD, alphaD
- endif
- endif
-
-
- !--------------------------------------------------------------------
- ! Set up some parameters for scaledMD simulations:
- ! scaledMD initialization
- ! scaledMD=0 no scaling is used, 1 scale the potential energy
- !--------------------------------------------------------------------
- if(scaledMD.gt.0)then
- write(6,'(a,i3)')'| Using Scaled MD to enhance sampling scaledMD =',&
- scaledMD
- write(6,'(a,f22.12)')'| scaledMD scaling factor lambda: ',scaledMD_lambda
- endif
-
-
-
-
- !--------------------------------------------------------------------
- ! Set up some parameters for GB simulations:
- !--------------------------------------------------------------------
- !Hai Nguyen: update offset = 0.09d0 for igb /= 8
- !I add this step because I want to use different offset value as default value
- !for igb = 8
-
- if ( igb == 8 ) then
- if (offset == -999999.d0) then
- offset = 0.195141d0 !set to default for igb=8
- end if
- if (gbneckscale == -999999.d0) then
- gbneckscale = 0.826836d0
- end if
- else
- ! not igb=8, use old defaults
- if (offset == -999999.d0) then
- offset = 0.09d0
- end if
- if (gbneckscale == -999999.d0) then
- gbneckscale = 0.361825d0
- end if
- endif
-
- if( igb == 2 .or. hybridgb == 2 ) then
- ! --- use our best guesses for Onufriev/Case GB (GB^OBC I)
-
- gbgamma = 2.90912499999d0 ! (the "99999" to force roundoff on print)
- gbbeta = ZERO
- gbalpha = 0.8d0
- end if
-
- if( igb == 5 .or. hybridgb == 5 ) then
-
- ! --- use our second best guesses for Onufriev/Case GB (GB^OBC II)
-
- gbgamma = 4.850d0
- gbbeta = 0.8d0
- gbalpha = ONE
- end if
-
- if( igb == 7 ) then
-
- ! --- use parameters for Mongan et al. CFA GBNECK
-
- gbgamma = 2.50798245d0
- gbbeta = 1.90792938d0
- gbalpha = 1.09511284d0
- end if
-
- !--------------------------------------------------------------------
- ! If user has requested PB electrostatics, read some more input
- !--------------------------------------------------------------------
-
- if ( igb == 10 .or. ipb /= 0 ) then
-#ifdef MPI
- write(6,'(a)') "PBSA currently doesn't work with MPI inside SANDER."
- call mexit(6,1)
-#endif /*MPI*/
- call pb_read
- end if
-
-#ifdef APBS
- if ( mdin_apbs ) then
- call apbs_read
- end if
-#endif /* APBS */
-
-#ifdef _XRAY
- call xray_read_mdin(mdin_lun=5)
-#endif
-
- call sebomd_namelist_default
- if (mdin_sebomd) then
- rewind 5
- call read_sebomd_namelist
- endif
-
- if( iamoeba == 1 ) then
- if( mdin_amoeba ) then
- call AMOEBA_read_mdin(5)
- else
- write(6,*) ' iamoeba is set but the &amoeba namelist was not found'
- call mexit(6,1)
- end if
- end if
-
- ! -------------------------------------------------------------------
- ! If the user has requested NMR restraints, do a cursory read of the
- ! restraints file(s) now to determine the amount of memory necessary
- ! for these restraints:
- ! -------------------------------------------------------------------
-
- if (jar == 1 ) nmropt = 1
- intreq = 0
- irlreq = 0
- if (nmropt > 0) then
- mxgrp = 0
- itotst = 1
-
- ! Set ITOTST to 0 if IMIN equals 1 (i.e. if minimization, not dynamics)
- ! This will cause any "time-averaged" requests to be over-ridden.
-
- if (imin == 1) then
- itotst = 0
- end if
- ! CALL AMOPEN(31,NMR,'O','F','R')
- call restlx(5,itotst,mxgrp,dt,6,ierr)
- ! CLOSE(31)
- end if
-
- ! -------------------------------------------------------------------
- ! If EMIL was requested, make sure it was compiled in, and validate.
- ! -------------------------------------------------------------------
- if( emil_do_calc .gt. 0 ) then
-#ifdef EMIL
- if( ntc .ne. 1 ) then
- write (6, '(a,a)') error_hdr, 'emil_do_calc == 1,'
- write (6, '(a)') ' and ntc != 1.'
- write (6, '(a)') ' Current thinking is that SHAKE and '
- write (6, '(a)') ' EMIL do not mix well, consider setting ntc = 1, ntf = 1,'
- write (6, '(a)') ' and dt = 0.001.'
- call mexit(6,1)
- end if
-#else
- write (6, '(a,a)') error_hdr, 'emil_do_calc = 1,'
- write (6, '(a)') ' but AMBER was compiled with EMIL switched out.'
- write (6, '(a)') ' Run $AMBERHOME/configure --help for more info.'
- call mexit(6,1)
-#endif
- end if
-
-
- ! Set the definition of the water molecule. The default definition is in
- ! WATDEF(4).
-
- read(watdef(1),'(A4)') iwtnm
- read(watdef(2),'(A4)') iowtnm
- read(watdef(3),'(A4)') ihwtnm(1)
- read(watdef(4),'(A4)') ihwtnm(2)
- if (watnam /= ' ') read(watnam,'(A4)') iwtnm
- if (owtnm /= ' ') read(owtnm, '(A4)') iowtnm
- if (hwtnm1 /= ' ') read(hwtnm1,'(A4)') ihwtnm(1)
- if (hwtnm2 /= ' ') read(hwtnm2,'(A4)') ihwtnm(2)
-
-#if !defined(DISABLE_NCSU) && defined(MPI)
- call ncsu_on_mdread1()
-#endif
-
- return
- 999 continue ! bad cntrl read
- write(6,*) 'error in reading namelist cntrl'
- call mexit(6,1)
-
- ! --- input file polar opts read err trapping:
-
- 9308 format(/10x,55('-'),/10x, &
- 'Amber 14 SANDER 2014', &
- /10x,55('-')/)
- 9309 format(/80('-')/' 1. RESOURCE USE: ',/80('-')/)
- 9700 format(/,'File Assignments:',/,15('|',a6,': ',a,/))
- 9701 format('|',a6,': ',a)
- 9702 format(7('|',a10,': ',a,/))
-end subroutine mdread1
-#endif /*ifndef PBSA*/
-
-#ifndef PBSA
-!======================================================================
-! MDREAD2
-!======================================================================
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Initialize to defaults and print the inputable variables.
-subroutine mdread2(x,ix,ih,ipairs)
-
- use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms
- use lmod_driver, only : LMOD_NTMIN_LMOD, LMOD_NTMIN_XMIN, write_lmod_namelist
- use decomp, only : jgroup, indx, irespw
- use findmask
- use qmmm_module, only : qmmm_nml,qmmm_struct, qm2_struct, qm2_rij_eqns, qm_gb, qmmm_vsolv
- use qmmm_vsolv_module, only : print
- use constants, only : ZERO, ONE, TWO
- use parms, only: req
- use nbips, only: ips
- use amd_mod, only: iamd,iamdlag,EthreshD,alphaD,EthreshP,alphaP, &
- w_amd,EthreshD_w,alphaD_w,EthreshP_w,alphaP_w
- use scaledMD_mod, only: scaledMD
- use nblist, only: a,b,c,alpha,beta,gamma,nbflag,skinnb,sphere,nbtell,cutoffnb
- use amoeba_mdin, only : iamoeba,beeman_integrator
- use amoeba_runmd, only : AM_RUNMD_get_coords
- use nose_hoover_module, only: nchain ! APJ
- use pimd_vars, only: ipimd, itimass
- use neb_vars, only: last_neb_atom, ineb
- use cmd_vars, only: restart_cmd, eq_cmd, adiab_param
- use constantph, only: cnstphread, cnstph_zero, cph_igb, mccycles
- use file_io_dat
- use sander_lib, only: upper
-
- use emap,only: temap,emap_options
-
- use qmmm_module, only: get_atomic_number
-
- use sebomd_module, only: sebomd_obj, sebomd_write_info, sebomd_write_options
-
-#ifdef APBS
- use apbs
-#endif /* APBS */
-#ifdef EMIL
- use emil_mod, only : emil_do_calc
- use mdin_emil_dat_mod, only : error_hdr, init_emil_dat
-#endif /* EMIL */
-#ifdef _XRAY
- use xray_interface_module, only: xray_write_options
-#endif /* _XRAY */
-#if defined(LES) && defined(MPI)
- use evb_pimd, only: evb_pimd_init
-#endif /* LES && MPI */
-#ifdef MPI /* SOFT CORE */
- use softcore, only : ifsc, scmask, scalpha, scbeta, dvdl_norest, &
- sceeorder, logdvdl, dynlmb, tishake
- use mbar, only : ifmbar, bar_intervall, bar_l_min, bar_l_max, bar_l_incr
-! REMD
- use remd, only : rem, rremd
-#endif
- use crg_reloc, only: ifcr, cropt, crcut, crskin, crprintcharges
- use linear_response, only: ilrt, lrt_interval, lrtmask
-! SGLD
- use sgld, only : isgld
-
- implicit none
- _REAL_ x(*)
-# include "../include/memory.h"
- integer ix(lasti),ipairs(*)
- character(len=4) ih(*)
- integer nbond
- integer atom1,atom2
- integer ntmp
- logical belly,konst
- character(len=1) atsymb,atsymb2
- character(len=2) atype
- integer atomicnumber, hybridization
- integer ngrp,inerr,nr,iaci,ir,i,mxresat,j
- integer noshakegp( natom ), natnos
- integer iwrap_maskgp( natom ) , ier
- logical errFlag
- integer crggp( natom )
- _REAL_ dummy,rvdw,dcharge,emtmd
- logical newstyle
-
-#ifdef MPI
- ! =========================== AMBER/MPI ===========================
-#ifdef MPI_DOUBLE_PRECISION
-# undef MPI_DOUBLE_PRECISION
-#endif
- include 'mpif.h'
-# include "parallel.h"
- integer ist(MPI_STATUS_SIZE), partner, ierr, nbonh_c, num_noshake_c
- integer nquant_c, noshake_overlap_c
-#ifdef CRAY_PVP
-# define MPI_DOUBLE_PRECISION MPI_REAL8
-#endif
- ! ========================= END AMBER/MPI =========================
-#endif
-# include "../include/md.h"
-# include "box.h"
-# include "mmtsb.h"
-# include "nmr.h"
-# include "extra_pts.h"
-# include "ew_cntrl.h"
-# include "ew_pme_recip.h"
-# include "ew_erfc_spline.h"
-# include "ew_mpole.h"
-# include "ew_legal.h"
-# include "def_time.h"
-# include "tgtmd.h"
-# include "multitmd.h"
-#ifdef LES
-# include "les.h"
-#endif
-
- ! -------------------------------------------------------------------
- ! --- set up resat array, containing string identifying
- ! residue for each atom
- ! -------------------------------------------------------------------
-
- mxresat = min( natom, matom )
- ir = 0
- do i=1,mxresat
- if (i >= ix(ir+i02)) ir=ir+1
- write(resat(i),'(a4,1x,a4,i4)') ih(m04+i-1), &
- ih(ir+m02-1),ir
- ! ---null terminator:
- resat(i)(14:14) = char(0)
- end do
- close(unit=8)
-
- ! -------------------------------------------------------------------
- ! ----- SET THE DEFAULT VALUES FOR SOME VARIABLES -----
- ! -------------------------------------------------------------------
-
- nrp = natom
-
- if (ifbox == 1) write(6, '(/5x,''BOX TYPE: RECTILINEAR'')')
- if (ifbox == 2) write(6, '(/5x,''BOX TYPE: TRUNCATED OCTAHEDRON'')')
- if (ifbox == 3) write(6, '(/5x,''BOX TYPE: GENERAL'')')
-
- ! For 0< ipimd <= 3, no removal of COM motion
- if (ipimd>0.and.ipimd<=3) then
- nscm = 0
- ndfmin = 0
- endif
-
- if (ntr.eq.1) &
- nscm = 0
-
- nsolut = nrp
- if ( nscm > 0 .and. ntb == 0 ) then
- ndfmin = 6 ! both translation and rotation com motion removed
- if (nsolut == 1) ndfmin = 3
- if (nsolut == 2) ndfmin = 5
- else if ( nscm > 0 ) then
- ndfmin = 3 ! just translation com will be removed
- else
- ndfmin = 0
- end if
- if (ibelly > 0) then ! No COM Motion Removal, ever.
- nscm = 0
- ndfmin = 0
-
- !Do not allow ntt=3 with ibelly=1 - this does not make sense and will cause
- !issues.
- if (ntt==3) then
- call sander_bomb("mdread2","ibelly=1 with ntt=3 is not a valid option.", &
- "Either use a different thermostat or avoid using ibelly.")
- end if
- end if
- if(nscm <= 0) nscm = 0
- if(gamma_ln > 0.0d0)ndfmin=0 ! No COM motion removal for LD simulation
- if(ntt == 4)ndfmin=0 ! No COM motion removal for Nose'-Hoover simulation
- init = 3
- if (irest > 0) init = 4
- if (dielc <= ZERO ) dielc = ONE
- if (tautp <= ZERO ) tautp = 0.2d0
- if (taup <= ZERO ) taup = 0.2d0
-
- ! ----- RESET THE CAP IF NEEDED -----
-
- ! ivcap == 0: Cap will be in effect if it is in the prmtop file (ifcap = 1)
-
- if(ivcap == 1) then
- ! Cap will be in effect even if not in prmtop file
- ! requires additional information in sander.in file as in the case of ivcap == 3, 4, or 5
- ifcap = 2
- else if(ivcap == 2) then
- ! Inactivate cap
- ifcap = 0
- else if(ivcap == 3) then
- ! Sphere -> not yet implemented
- ifcap = 3
- else if(ivcap == 4) then
- ! Orthorhombus
- ifcap = 4
- else if(ivcap == 5) then
- ! Shell of waters around solute
- ifcap = 5
- end if
-
- !Support for random seed using time of day in microsecs
- if( ig==-1 ) then
- !Turn on NO_NTT3_SYNC when ig=-1. This means the code no
- !longer synchronized the random numbers between streams when
- !running in parallel giving better scaling.
- no_ntt3_sync = 1
- call microsec(ig)
-#ifdef MPI
- write (6, '(a,i8,a)') "Note: ig = -1. Setting random seed to ", ig ," based on wallclock &
- &time in microseconds"
- write (6, '(a)') " and disabling the synchronization of random &
- &numbers between tasks"
- write (6, '(a)') " to improve performance."
-#else
- write (6, '(a,i8,a)') "Note: ig = -1. Setting random seed to ", ig ," based on wallclock &
- &time in microseconds."
-#endif
- end if
-
-#ifdef MPI
- !For some runs using multisander where the coordinates of the two 'replicas' need to be identical,
- !for example TI, it is critical that the random number stream is synchronized between all replicas.
- !Only use the IG value from worldrank=0. Ok to broadcast between the various sander masters since
- !they all call mdread2.
- !Also needs to be synchronized for adaptive QM/MM (qmmm_nml%vsolv > 1)
- if ( (icfe > 0) .or. (qmmm_nml%vsolv > 1) ) then
- ! no_ntt3_sync currently does not work with softcore TI simulations
- ! see sc_lngdyn in softcore.F90
- ! AWG: I think I also need to set no_ntt3_sync=0 ???
- if ( (ifsc > 0) .or. (qmmm_nml%vsolv > 1) ) no_ntt3_sync = 0
- call mpi_bcast(ig, 1, MPI_INTEGER, 0, commmaster, ierr)
- end if
-#endif
-
- ! -------------------------------------------------------------------
- ! ----- PRINT DATA CHARACTERIZING THE RUN -----
- ! -------------------------------------------------------------------
-
- nr = nrp
- write(6,9328)
- write(6,9008) title
- write(6,'(/a)') 'General flags:'
- write(6,'(5x,2(a,i8))') 'imin =',imin,', nmropt =',nmropt
-
- ! Error Checking for REMD
-#ifdef MPI
- if (rem/=0) then
- ! Make sure that the number of replicas is even so
- ! that they all have partners in the exchange step
- if (mod(numgroup,2).ne.0) then
- write (6,'(a)') "==================================="
- write (6,'(a)') "REMD requires an even # of replicas"
- write (6,'(a)') "==================================="
- call mexit (6,1)
- endif
-
- write(6,'(/a)') 'Replica exchange'
- write(6,'(5x,4(a,i8))') 'numexchg=',numexchg,', rem=',rem
-
- ! REPCRD option temporarily disabled
- if (repcrd == 0) write(6,'(a)') &
- "REMD WARNING: repcrd disabled. Only replica &
- &trajectories/output can be written."
-
- ! Check for correct number of exchanges
- if (numexchg <= 0) then
- write(6,'(a)') "REMD ERROR: numexchg must be > 0, "
- call mexit(6,1)
- endif
-
- ! RXSGLD
- if (isgld > 0 .and. rem < 0) then
- write(6, '(a)') 'Multi-D REMD and replica-exchange SGLD are not &
- &supported yet!'
- call mexit(6, 1)
- end if
-
- ! Hybrid GB
- if (numwatkeep >= 0) then
- write(6,'(5x,4(a,i8))') 'numwatkeep=',numwatkeep,', hybridgb=',hybridgb
- ! Check that user specified GB model for hybrid REMD
- if (hybridgb /= 2 .and. hybridgb /= 5 .and. hybridgb /= 1) then
- write(6,'(a)') "HYBRID REMD ERROR: hybridgb must be 1, 2, or 5."
- call mexit(6,1)
- endif
- else
- !Check that user did not specify GB model if no hybrid run.
- if (hybridgb /= 0) then
- write(6,'(a)') &
- "HYBRID REMD ERROR: numwatkeep must be >= 0 when hybridgb is set."
- call mexit(6,1)
- endif
- endif
- ! RREMD
- if (rremd>0) then
- write(6,'(5x,4(a,i8))') "rremd=",rremd
- endif
-
- ! ntp > 0 not allowed for remd
- if (ntp > 0) then
- write(6,'(a,i1)') "ERROR: ntp > 0 not allowed for rem > 0, ntp=", ntp
- call mexit(6,1)
- endif
-
- ! M-REMD (rem < 0) requires netcdf output.
- if (rem < 0 .and. ioutfm .ne. 1) then
- write(6,'(a)') "ERROR: Multi-D REMD (rem < 0) requires NetCDF &
- &trajectories (ioutfm=1)"
- call mexit(6,1)
- endif
-
-# ifdef LES
- ! DAN ROE: Temporarily disable LES REMD until it is verified with new
- ! REMD code
- if (rem==2) then
- write (6,*) "******* LES REM (rem==2) temporarily disabled. Stop. *******"
- call mexit(6,1)
- endif
-
- if (rem==2 .and. igb/=1) then
- write (6,*) ' partial REM (rem=2) only works with igb=1'
- call mexit(6,1)
- endif
-# else
- if (rem==2) then
- write(6,*) '******* For rem ==2, partial REM'
- write(6,*) 'use sander.LES with topology created by addles'
- call mexit(6,1)
- endif
-# endif
-
- endif ! rem>0
-
-#else /* _NO_ MPI */
- ! Check if user set numexchg with no MPI
- if (numexchg>0) write(6,'(a)') &
- "WARNING: numexchg > 0 - for REMD run please recompile sander for &
- ¶llel runs."
-
- ! Check if user set numwatkeep or hybridgb with no MPI - not sensible.
- if (numwatkeep>=0) write(6,'(a)') &
- "WARNING: numwatkeep >= 0 - for hybrid REMD run please recompile &
- &sander for parallel runs."
-
- if (hybridgb>0) write(6,'(a)') &
- "WARNING: hybridgb > 0 - for hybrid REMD run please recompile &
- &sander for parallel runs."
-#endif /* MPI */
- ! End error checking for REMD
-
- write(6,'(/a)') 'Nature and format of input:'
- write(6,'(5x,4(a,i8))') 'ntx =',ntx,', irest =',irest, &
- ', ntrx =',ntrx
-
- write(6,'(/a)') 'Nature and format of output:'
- write(6,'(5x,4(a,i8))') 'ntxo =',ntxo,', ntpr =',ntpr, &
- ', ntrx =',ntrx,', ntwr =',ntwr
- write(6,'(5x,5(a,i8))') 'iwrap =',iwrap,', ntwx =',ntwx, &
- ', ntwv =',ntwv,', ntwe =',ntwe
- write(6,'(5x,3(a,i8),a,i7)') 'ioutfm =',ioutfm, &
- ', ntwprt =',ntwprt, &
- ', idecomp =',idecomp,', rbornstat=',rbornstat
- if (ntwf > 0) &
- write(6,'(5x, a,i8)') 'ntwf =',ntwf
- write(6,'(/a)') 'Potential function:'
- write(6,'(5x,5(a,i8))') 'ntf =',ntf,', ntb =',ntb, &
- ', igb =',igb,', nsnb =',nsnb
- write(6,'(5x,3(a,i8))') 'ipol =',ipol,', gbsa =',gbsa, &
- ', iesp =',iesp
- write(6,'(5x,3(a,f10.5))') 'dielc =',dielc, &
- ', cut =',cut,', intdiel =',intdiel
-
- ! charge relocation
- if ( ifcr /= 0 ) then
- write(6,'(/a)') 'Charge relocation:'
- write(6,'(5x,2(a,i8))') 'cropt =', cropt, &
- ', crprintcharges=', crprintcharges
- write(6,'(5x,2(a,f10.5))') 'crcut =', crcut, ', crskin =', crskin
- end if
-
- if (( igb /= 0 .and. igb /= 10 .and. ipb == 0 .and. igb /= 8) &
- .or.hybridgb>0.or.icnstph>1) then
- write(6,'(5x,3(a,f10.5))') 'saltcon =',saltcon, &
- ', offset =',offset,', gbalpha= ',gbalpha
- write(6,'(5x,3(a,f10.5))') 'gbbeta =',gbbeta, &
- ', gbgamma =',gbgamma,', surften =',surften
- write(6,'(5x,3(a,f10.5))') 'rdt =',rdt, ', rgbmax =',rgbmax, &
- ' extdiel =',extdiel
- write(6,'(5x,3(a,i8))') 'alpb = ',alpb
- end if
-
- !Hai Nguyen: print output for igb=8
- if ( igb == 8 ) then
- write(6,'(5x,3(a,f10.5))') 'saltcon =',saltcon, &
- ', offset =',offset,', surften =',surften
- write(6,'(5x,3(a,f10.5))') 'rdt =',rdt, ', rgbmax =',rgbmax, &
- ' extdiel =',extdiel
- write(6,'(5x,3(a,i8))') 'alpb = ',alpb
- write(6,'(5x,3(a,f10.5))') 'gbalphaH =',gbalphaH, &
- ', gbbetaH =',gbbetaH,', gbgammaH = ',gbgammaH
- write(6,'(5x,3(a,f10.5))') 'gbalphaC =',gbalphaC, &
- ', gbbetaC =',gbbetaC,', gbgammaC = ',gbgammaC
- write(6,'(5x,3(a,f10.5))') 'gbalphaN =',gbalphaN, &
- ', gbbetaN =',gbbetaN,', gbgammaN = ',gbgammaN
- write(6,'(5x,3(a,f10.5))') 'gbalphaOS =',gbalphaOS, &
- ', gbbetaOS =',gbbetaOS,', gbgammaOS = ',gbgammaOS
- write(6,'(5x,3(a,f10.5))') 'gbalphaP =',gbalphaP, &
- ', gbbetaP =',gbbetaP,', gbgammaP = ',gbgammaP
- end if
-
-
- if( alpb /= 0 ) then
- write(6,'(5x,3(a,f10.5))') 'Arad =', Arad
- end if
-
- write(6,'(/a)') 'Frozen or restrained atoms:'
- write(6,'(5x,4(a,i8))') 'ibelly =',ibelly,', ntr =',ntr
- if( ntr == 1 ) write(6,'(5x,a,f10.5)') 'restraint_wt =', restraint_wt
-
- if( imin /= 0 ) then
- if( ipimd > 0 ) then
- write(6,'(/a)') 'pimd cannot be used in energy minimization'
- stop
- end if
-
- write(6,'(/a)') 'Energy minimization:'
- ! print inputable variables applicable to all minimization methods.
- write(6,'(5x,4(a,i8))') 'maxcyc =',maxcyc,', ncyc =',ncyc, &
- ', ntmin =',ntmin
- write(6,'(5x,2(a,f10.5))') 'dx0 =',dx0, ', drms =',drms
-
- ! Input flag ntmin determines the method of minimization
- select case ( ntmin )
- case ( 0, 1, 2 )
- ! no specific output
- case ( LMOD_NTMIN_XMIN, LMOD_NTMIN_LMOD )
- call write_lmod_namelist( )
- case default
- ! invalid ntmin
- write(6,'(/2x,a,i3,a)') 'Error: Invalid NTMIN (',ntmin,').'
- stop
- end select
- else
- write(6,'(/a)') 'Molecular dynamics:'
- write(6,'(5x,4(a,i10))') 'nstlim =',nstlim,', nscm =',nscm, &
- ', nrespa =',nrespa
- write(6,'(5x,3(a,f10.5))') 't =',t, &
- ', dt =',dt,', vlimit =',vlimit
-
- if ( ntt == 0 .and. tempi > 0.0d0 .and. irest == 0 ) then
- write(6,'(/a)') 'Initial temperature generation:'
- write(6,'(5x,a,i8)') 'ig =',ig
- write(6,'(5x,a,f10.5)') 'tempi =',tempi
- else if( ntt == 1 ) then
- write(6,'(/a)') 'Berendsen (weak-coupling) temperature regulation:'
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, &
- ', tempi =',tempi,', tautp =', tautp
-#ifdef LES
- write(6,'(5x,3(a,f10.5))') 'temp0LES =',temp0les
-#endif
- else if( ntt == 2 ) then
- write(6,'(/a)') 'Anderson (strong collision) temperature regulation:'
- write(6,'(5x,4(a,i8))') 'ig =',ig, ', vrand =',vrand
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, ', tempi =',tempi
- else if( ntt == 3 ) then
- write(6,'(/a)') 'Langevin dynamics temperature regulation:'
- write(6,'(5x,4(a,i8))') 'ig =',ig
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, &
- ', tempi =',tempi,', gamma_ln=', gamma_ln
- else if( ntt == 4 ) then
- write(6,'(/a)') 'Nose-Hoover chains'
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain
- else if( ntt == 5 ) then ! APJ
- write(6,'(/a)') 'Nose-Hoover chains Langevin' ! APJ
- write(6,'(5x,4(a,i8))') 'ig =',ig ! APJ
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln ! APJ
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain ! APJ
- else if( ntt == 6 ) then ! APJ
- write(6,'(/a)') 'Adaptive Langevin temperature regulation:' ! APJ
- write(6,'(5x,4(a,i8))') 'ig =',ig ! APJ
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, & ! APJ
- ', tempi =',tempi,', gamma_ln=', gamma_ln ! APJ
- else if( ntt == 7 ) then ! APJ
- write(6,'(/a)') 'Adaptive Nose-Hoover chains' ! APJ
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln ! APJ
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain ! APJ
- else if( ntt == 8 ) then ! APJ
- write(6,'(/a)') 'Adaptive Nose-Hoover chains Langevin' ! APJ
- write(6,'(5x,4(a,i8))') 'ig =',ig ! APJ
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln ! APJ
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain ! APJ
- end if
-
- if( ntp /= 0 ) then
- write(6,'(/a)') 'Pressure regulation:'
- write(6,'(5x,4(a,i8))') 'ntp =',ntp
- write(6,'(5x,3(a,f10.5))') 'pres0 =',pres0, &
- ', comp =',comp,', taup =',taup
- if (barostat == 2) then
- write(6, '(5x,a)') 'Monte-Carlo Barostat:'
- write(6, '(5x,a,i8)') 'mcbarint =', mcbarint
- end if
- end if
-
- if (csurften /= 0) then
- write(6,'(/a)') 'Constant surface tension:'
- write(6,'(5x,a,i8)') 'csurften =', csurften
- write(6,'(5x,a,f10.5,a,i8)') 'gamma_ten =', gamma_ten, ' ninterface =', ninterface
- end if
-
- end if
-
- if( ntc /= 1 ) then
- write(6,'(/a)') 'SHAKE:'
- write(6,'(5x,4(a,i8))') 'ntc =',ntc,', jfastw =',jfastw
- write(6,'(5x,3(a,f10.5))') 'tol =',tol
- end if
-
- if( ifcap == 1 .or. ifcap == 2 .or. ifcap == 3 ) then
- write(6,'(/a)') 'Water cap:'
- write(6,'(5x,2(a,i8))') 'ivcap =',ivcap,', natcap =',natcap
- write(6,'(5x,2(a,f10.5))') 'fcap =',fcap, ', cutcap =',cutcap
- write(6,'(5x,3(a,f10.5))') 'xcap =',xcap, ', ycap =',ycap, &
- ', zcap =',zcap
- else if( ifcap == 4 ) then
- write(6,'(/a)') 'Orthorhombus:'
- write(6,'(5x,1(a,i8))') 'ivcap =',ivcap
- write(6,'(5x,1(a,f10.5))') 'forth =',forth
- write(6,'(5x,3(a,f10.5))') 'xlorth =',xlorth,', ylorth =',ylorth, &
- ', zlorth =',zlorth
- write(6,'(5x,3(a,f10.5))') 'xorth =',xorth, ', yorth =',yorth, &
- ', zorth =',zorth
- else if( ifcap == 5 ) then
- write(6,'(/a)') 'Water shell:'
- write(6,'(5x,(a,i8,a,f10.5))') 'ivcap =',ivcap,', cutcap =',cutcap
- endif
-
- if( nmropt > 0 ) then
- write(6,'(/a)') 'NMR refinement options:'
- write(6,'(5x,4(a,i8))')'iscale =',iscale,', noeskp =',noeskp, &
- ', ipnlty =',ipnlty,', mxsub =',mxsub
- write(6,'(5x,3(a,f10.5))') 'scalm =',scalm, &
- ', pencut =',pencut,', tausw =',tausw
- end if
-
- if( numextra > 0 ) then
- write(6,'(/a)') 'Extra-points options:'
- write(6,'(5x,4(a,i8))') 'frameon =',frameon, &
- ', chngmask=',chngmask
- end if
-
- if( ipol > 0 ) then
- write(6,'(/a)') 'Polarizable options:'
- write(6,'(5x,4(a,i8))') 'indmeth =',indmeth, &
- ', maxiter =',maxiter,', irstdip =',irstdip, &
- ', scaldip =',scaldip
- write(6,'(5x,3(a,f10.5))') &
- 'diptau =',diptau,', dipmass =',dipmass
- if ( ipol > 1 ) then
- write(6,'(5x,3(a,f10.5))') &
- 'Default Thole coefficient = ',dipdamp
- end if
- end if
-
-#ifdef MPI /* SOFT CORE */
- if( icfe /= 0 .or. ifsc/=0) then
- write(6,'(/a)') 'Free energy options:'
- write(6,'(5x,a,i8,a,i8,a,i8)') 'icfe =', icfe , ', ifsc =', ifsc, ', klambda =', klambda
- write(6,'(5x,a,f8.4,a,f8.4,a,f8.4)') 'clambda =', clambda, ', scalpha =', scalpha, ', scbeta =', scbeta
- write(6,'(5x,a,i8,a,i8)') 'sceeorder =', sceeorder, ' dvdl_norest =', dvdl_norest
- write(6,'(5x,a,f8.4,a,i8)') 'dynlmb =', dynlmb, ' logdvdl =', logdvdl
- end if
- if ( ifmbar /= 0 ) then
- write (6,'(/a)') 'FEP MBAR options:'
- write(6,'(5x,a,i8,a,i8)') 'ifmbar =', ifmbar, ', bar_intervall = ', bar_intervall
- write(6,'(5x,a,f6.4,a,f6.4,a,f6.4)') 'bar_l_min =', bar_l_min, ', bar_l_max =', bar_l_max, ', bar_l_incr =', bar_l_incr
- end if
-#endif
-
- if (ilrt /= 0) then
- write (6,*)
- write (6,'(a,i4,a,i4)') ' Linear Response Theory: ilrt =', ilrt, ' lrt_interval =', lrt_interval
- write (6,*)
- end if
-
- ! Options for TI w.r.t. mass.
- select case (itimass)
- case (0) ! Default: no TI wrt. mass.
- case (1,2) ! 1 = use virial est., 2 = use thermodynamic est.
- write(6,'(/a)') 'Isotope effects (thermodynamic integration w.r.t. mass):'
- write(6,'(5x,4(a,i8))') 'itimass =',itimass
- write(6,'(5x,3(a,f10.5))') 'clambda =',clambda
- if (icfe /= 0) then
- write(6,'(/2x,a,i2,a,i2,a)') 'Error: Cannot do TI w.r.t. both potential (icfe =', &
- icfe, ') and mass (itimass =', itimass, ').'
- stop
- endif
- if (ipimd == 0) then
- write(6,'(/2x,a)') 'Error (IPIMD=0): TI w.r.t. mass requires a PIMD run.'
- stop
- endif
- case default ! Invalid itimass
- write(6,'(/2x,a,i2,a)') 'Error: Invalid ITIMASS (', itimass, ' ).'
- stop
- end select
-
-!KFW
-! call mpi_bcast ( ievb, 1, MPI_INTEGER, 0, commworld, ierr )
-! call mpi_barrier ( commworld, ierr )
-
-! if( ievb == 1 ) then
-!KFW write(6,'(/a)') 'EVB options:'
-!KFW write(6,'(5x,3(a,f10.5))') 'V11 =',v11,', V22 =', v22, &
-!KFW ', V12 =', v12
-!kfw write(6,'(5x,3(a,f10.5))') 'kevb =',kevb,', evbt =', evbt
-! end if
-
- if( itgtmd == 1 ) then
- write(6,'(/a)') 'Targeted molecular dynamics:'
- write(6,'(5x,3(a,f10.5))') 'tgtrmsd =',tgtrmsd, &
- ', tgtmdfrc=',tgtmdfrc
- end if
-
- if( icnstph /= 0) then
- write(6, '(/a)') 'Constant pH options:'
- if ( icnstph .ne. 1 ) &
- write(6, '(5x,a,i8)') 'icnstph =', icnstph
- write(6, '(5x,a,i8)') 'ntcnstph =', ntcnstph
- write(6, '(5x,a,f10.5)') 'solvph =', solvph
- if ( icnstph .ne. 1 ) &
- write(6,'(5x,2(a,i8))') 'ntrelax =', ntrelax, ' mccycles =', mccycles
- end if
- if( icnstph /= 2) then
- ntrelax = 0 ! needed for proper behavior of timing
- end if
-
- if( ntb > 0 ) then
- write(6,'(/a)') 'Ewald parameters:'
- write(6,'(5x,4(a,i8))') 'verbose =',verbose, &
- ', ew_type =',ew_type,', nbflag =',nbflag, &
- ', use_pme =',use_pme
- write(6,'(5x,4(a,i8))') 'vdwmeth =',vdwmeth, &
- ', eedmeth =',eedmeth,', netfrc =',netfrc
- write(6, 9002) a, b, c
- write(6, 9003) alpha, beta, gamma
- write(6, 9004) nfft1, nfft2, nfft3
- write(6, 9006) cutoffnb, dsum_tol
- write(6, 9007) ew_coeff
- write(6, 9005) order
- 9002 format (5x,'Box X =',f9.3,3x,'Box Y =',f9.3,3x,'Box Z =',f9.3)
- 9003 format (5x,'Alpha =',f9.3,3x,'Beta =',f9.3,3x,'Gamma =',f9.3)
- 9004 format (5x,'NFFT1 =',i5 ,7x,'NFFT2 =',i5 ,7x,'NFFT3 =',i5)
- 9005 format (5x,'Interpolation order =',i5)
- 9006 format (5x,'Cutoff=',f9.3,3x,'Tol =',e9.3)
- 9007 format (5x,'Ewald Coefficient =',f9.5)
- end if
-
- if( mmtsb_switch /= mmtsb_off ) then
- call mmtsb_print_banner()
- call mmtsb_init( temp0, clambda )
- end if
-
-!---- QMMM Options ----
-
- if( qmmm_nml%ifqnt ) then
- write(6, '(/a)') 'QMMM options:'
- write(6, '(5x," ifqnt = True nquant = ",i8)') &
- qmmm_struct%nquant
- write(6, '(5x," qmgb = ",i8," qmcharge = ",i8," adjust_q = ",i8)') &
- qmmm_nml%qmgb, qmmm_nml%qmcharge, qmmm_nml%adjust_q
- write(6, '(5x," spin = ",i8," qmcut = ",f8.4, " qmshake = ",i8)') qmmm_nml%spin, &
- qmmm_nml%qmcut, qmmm_nml%qmshake
- write(6, '(5x," qmmm_int = ",i8)') qmmm_nml%qmmm_int
- write(6, '(5x,"lnk_atomic_no = ",i8," lnk_dis = ",f8.4," lnk_method = ",i8)') &
- qmmm_nml%lnk_atomic_no,qmmm_nml%lnk_dis, qmmm_nml%lnk_method
- if ( qmmm_nml%qmtheory%PM3 ) then
- write(6, '(5x," qm_theory = PM3")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%AM1 ) then
- write(6, '(5x," qm_theory = AM1")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%AM1D ) then
- write(6, '(5x," qm_theory = AM1/d")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%MNDO ) then
- write(6, '(5x," qm_theory = MNDO")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%MNDOD ) then
- write(6, '(5x," qm_theory = MNDO/d")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PDDGPM3 ) then
- write(6, '(5x," qm_theory = PDDGPM3")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PDDGMNDO ) then
- write(6, '(5x," qm_theory =PDDGMNDO")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM3CARB1 ) then
- write(6, '(5x," qm_theory =PM3CARB1")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%DFTB ) then
- write(6, '(5x," qm_theory = DFTB")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%RM1 ) then
- write(6, '(5x," qm_theory = RM1")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PDDGPM3_08 ) then
- write(6, '(5x," qm_theory = PDDGPM3_08")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM6 ) then
- write(6, '(5x," qm_theory = PM6")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM3ZNB ) then
- write(6, '(5x," qm_theory = PM3/ZnB")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM3MAIS ) then
- write(6, '(5x," qm_theory = PM3-MAIS")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%EXTERN ) then
- write(6, '(5x," qm_theory = EXTERN")',ADVANCE='NO')
- else
- write(6, '(5x," qm_theory = UNKNOWN!")',ADVANCE='NO')
- end if
- write (6, '(" verbosity = ",i8)') qmmm_nml%verbosity
- if (qmmm_nml%qmqm_analyt) then
- write(6, '(5x," qmqmdx = Analytical")')
- else
- write(6, '(5x," qmqmdx = Numerical")')
- end if
- !AWG: if EXTERN in use, skip printing of options that do not apply
- EXTERN: if ( .not. qmmm_nml%qmtheory%EXTERN ) then
- if (qmmm_nml%tight_p_conv) then
- write(6, '(5x," tight_p_conv = True (converge density to SCFCRT)")')
- else
- write(6, '(5x," tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT])")')
- end if
- write(6, '(5x," scfconv = ",e9.3," itrmax = ",i8)') qmmm_nml%scfconv, qmmm_nml%itrmax
- if (qmmm_nml%printcharges) then
- write(6, '(5x," printcharges = True ")',ADVANCE='NO')
- else
- write(6, '(5x," printcharges = False")',ADVANCE='NO')
- end if
- select case (qmmm_nml%printdipole)
- case (1)
- write(6, '(5x," printdipole = QM ")',ADVANCE='NO')
- case (2)
- write(6, '(5x," printdipole = QM+MM")',ADVANCE='NO')
- case default
- write(6, '(5x," printdipole = False")',ADVANCE='NO')
- end select
- if (qmmm_nml%peptide_corr) then
- write(6, '(5x," peptide_corr = True")')
- else
- write(6, '(5x," peptide_corr = False")')
- end if
- if (qmmm_nml%qmmmrij_incore) then
- write(6, '(4x,"qmmmrij_incore = True ")')
- else
- write(6, '(4x,"qmmmrij_incore = False")')
- end if
- if (qmmm_nml%qmqm_erep_incore) then
- write(6, '(2x,"qmqm_erep_incore = True ")')
- else
- write(6, '(2x,"qmqm_erep_incore = False")')
- end if
- if (qmmm_nml%allow_pseudo_diag) then
- write(6, '(7x,"pseudo_diag = True ")',ADVANCE='NO')
- write(6, '("pseudo_diag_criteria = ",f8.4)') qmmm_nml%pseudo_diag_criteria
- else
- write(6, '(7x,"pseudo_diag = False")')
- end if
- write(6, '(6x,"diag_routine = ",i8)') qmmm_nml%diag_routine
- end if EXTERN
- !If ntb=0 or use_pme =0 then we can't do qm_ewald so overide what the user may
- !have put in the namelist and set the value to false.
- if (qmmm_nml%qm_ewald>0) then
- if (qmmm_nml%qm_pme) then
- write(6, '(10x,"qm_ewald = ",i8, " qm_pme = True ")') qmmm_nml%qm_ewald
- else
- write(6, '(10x,"qm_ewald = ",i8, " qm_pme = False ")') qmmm_nml%qm_ewald
- end if
- write(6, '(10x," kmaxqx = ",i4," kmaxqy = ",i4," kmaxqz = ",i4," ksqmaxq = ",i4)') &
- qmmm_nml%kmaxqx, qmmm_nml%kmaxqy, qmmm_nml%kmaxqz, qmmm_nml%ksqmaxq
- else
- write(6, '(10x,"qm_ewald = ",i8, " qm_pme = False ")') qmmm_nml%qm_ewald
- end if
- !Print the fock matrix prediction params if it is in use.
- if (qmmm_nml%fock_predict>0) then
- write(6, '(6x,"fock_predict = ",i4)') qmmm_nml%fock_predict
- write(6, '(6x," fockp_d1 = ",f8.4," fockp_d2 = ",f8.4)') qmmm_nml%fockp_d1, qmmm_nml%fockp_d2
- write(6, '(6x," fockp_d2 = ",f8.4," fockp_d4 = ",f8.4)') qmmm_nml%fockp_d3, qmmm_nml%fockp_d4
- end if
-
- if (qmmm_nml%qmmm_switch) then
- write(6, '(7x,"qmmm_switch = True",3x,"r_switch_lo =",f8.4,3x,"r_switch_hi =",f8.4)') &
- & qmmm_nml%r_switch_lo, qmmm_nml%r_switch_hi
- !else
- ! write(6, '(7x,"qmmm_switch = False")')
- end if
-
- if (qmmm_nml%printdipole==2) then
- write(6, '("|",2x,"INFO: To compute MM dipole WAT residues will be stripped")')
- end if
- end if
-
- if (qmmm_nml%vsolv > 0) then
- call print(qmmm_vsolv)
- end if
-
-!---- SEBOMD options ----
-
- if (sebomd_obj%do_sebomd) then
- call sebomd_write_info()
- call sebomd_write_options()
- endif
-
-#ifdef _XRAY
-!---- XRAY Options ----
- call xray_write_options()
-#endif
-
-! ----EMAP Options-----
- if(temap)call emap_options(5)
-! ---------------------
-
-#ifdef EMIL
-! ----EMIL Options-----
- if(emil_do_calc.gt.0)call init_emil_dat(5, 6)
-! ---------------------
-#endif
-
-
-#ifdef MPI
-! --- MPI TIMING OPTIONS ---
- write(6, '(/a)') '| MPI Timing options:'
- write(6, '("|",5x," profile_mpi = ",i8)') profile_mpi
-! Sanity check for profile_mpi
- call int_legal_range('profile_mpi',profile_mpi,0,1)
-! --------------------------
-#endif
-
- cut = cut*cut
- cut_inner = cut_inner*cut_inner
-
- !------------------------------------------------------------------------
- ! If user has requested generalized born electrostatics, set up variables
- !------------------------------------------------------------------------
-
- if( igb == 0 .and. gbsa > 0 ) then
- write(0,*) 'GB/SA calculation is performed only when igb>0'
- call mexit( 6,1 )
- end if
- if( gbsa == 2 .and. &
- ((imin == 0 .and. nstlim > 1) .or. &
- (imin == 1 .and. maxcyc > 1)) ) then
- write(0,*) 'GBSA=2 only works for single point energy calc'
- call mexit( 6,1 )
- end if
-#ifdef APBS
- if( igb /= 0 .and. igb /= 10 .and. ipb == 0 .and. .not. mdin_apbs) then
-#else
- if (( igb /= 0 .and. igb /= 10 .and. ipb == 0 ).or.hybridgb>0.or.icnstph>1) then
-#endif /* APBS */
-#ifdef LES
- write(6,*) 'igb=1,5,7 are working with LES, no SA term included'
-#endif
- ! igb7 uses special S_x screening params.
- ! overwrite the tinker values read from the prmtop
- if (igb == 7) then
- do i=1,natom
- if(ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
-
- if (atomicnumber .eq. 6) then
- x(l96+i-1) = 4.84353823306d-1
- else if (atomicnumber .eq. 1) then
- x(l96+i-1) = 1.09085413633d0
- else if (atomicnumber .eq. 7) then
- x(l96+i-1) = 7.00147318409d-1
- else if (atomicnumber .eq. 8) then
- x(l96+i-1) = 1.06557401132d0
- else if (atomicnumber .eq. 16) then
- x(l96+i-1) = 6.02256336067d-1
- else if (atomicnumber .eq. 15) then
- x(l96+i-1) = 5d-1
- else
- x(l96+i-1) = 5d-1
- end if
- end do
- end if
-
- ! Hai Nguyen: changing S_x screening params for igb = 8
- ! overwrite the tinker values read from the prmtop
-
- if (igb == 8) then
- do i=1,natom
- if (ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
-
- if (atomicnumber .eq. 6) then
- x(l96+i-1) = Sc
- else if (atomicnumber .eq. 1) then
- x(l96+i-1) = Sh
- else if (atomicnumber .eq. 7) then
- x(l96+i-1) = Sn
- else if (atomicnumber .eq. 8) then
- x(l96+i-1) = So
- else if (atomicnumber .eq. 16) then
- x(l96+i-1) = Ss
- else if (atomicnumber .eq. 15) then
- x(l96+i-1) = Sp ! Hai Nguyen: We still don't have an optimized Sp parameter
- else
- !for atom type Cl,Br,...
- !These parameters are also not optimized.
- x(l96+i-1) = 5d-1
- end if
- end do
- end if
-
-
- ! Hai Nguyen: set up for igb == 2, 5, 7, 8
- ! Put gb parameters in arrays
- if ( igb == 2 .or. igb == 5 .or. igb == 7 .or. &
- hybridgb == 2 .or. hybridgb == 5) then
- do i=1,natom
- x(l2402+i-1) = gbalpha
- x(l2403+i-1) = gbbeta
- x(l2404+i-1) = gbgamma
- end do
- end if
-
- !Hai Nguyen: IGB = 8
- if ( igb == 8 ) then
- do i=1,natom
- if (ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
-
- if (atomicnumber .eq. 1) then
- x(l2402+i-1) = gbalphaH
- x(l2403+i-1) = gbbetaH
- x(l2404+i-1) = gbgammaH
- else if (atomicnumber .eq. 6) then
- x(l2402+i-1) = gbalphaC
- x(l2403+i-1) = gbbetaC
- x(l2404+i-1) = gbgammaC
- else if (atomicnumber .eq. 7) then
- x(l2402+i-1) = gbalphaN
- x(l2403+i-1) = gbbetaN
- x(l2404+i-1) = gbgammaN
- else if (atomicnumber .eq. 8) then
- x(l2402+i-1) = gbalphaOS
- x(l2403+i-1) = gbbetaOS
- x(l2404+i-1) = gbgammaOS
- else if (atomicnumber .eq. 16) then
- x(l2402+i-1) = gbalphaOS
- x(l2403+i-1) = gbbetaOS
- x(l2404+i-1) = gbgammaOS
- else if (atomicnumber .eq. 15) then
- x(l2402+i-1) = gbalphaP
- x(l2403+i-1) = gbbetaP
- x(l2404+i-1) = gbgammaP
- else
- !use GBOBC set for other atom types
- x(l2402+i-1) = 1.0d0
- x(l2403+i-1) = 0.8d0
- x(l2404+i-1) = 4.85d0
- end if
- end do
- end if ! end Hai Nguyen section
-
- ! put fs(i)*(rborn(i) - offset) into the "fs" array
-
- fsmax = 0.d0
- do i=1,natom
- x(l96-1+i) = x(l96-1+i)*( x(l97-1+i) - offset )
- fsmax = max( fsmax, x(l96-1+i) )
- if (rbornstat == 1) then
- x(l186-1+i) = 0.d0
- x(l187-1+i) = 999.d0
- x(l188-1+i) = 0.d0
- x(l189-1+i) = 0.d0
- end if
- end do
-
- ! ---------------------------------------------------------------------
- ! ---get Debye-Huckel kappa (A**-1) from salt concentration (M), assuming:
- ! T = 298.15, epsext=78.5,
-
- kappa = sqrt( 0.10806d0 * saltcon )
-
- ! ---scale kappa by 0.73 to account(?) for lack of ion exclusions:
-
- kappa = 0.73d0* kappa
-
- !Set kappa for qmmm if needed
- qm_gb%kappa = kappa
- ! ---------------------------------------------------------------------
-
- if ( gbsa == 1 ) then
-
- ! --- assign parameters for calculating SASA according to the
- ! LCPO method ---
-
- do i=1,natom
- ix(i80+i-1)=0
- end do
-
- ! --- get the number of bonded neighbors for each atom:
-
- do i=1,nbona
- atom1=ix(iiba+i-1)/3+1
- atom2=ix(ijba+i-1)/3+1
- ix(i80+atom1-1)=ix(i80+atom1-1)+1
- ix(i80+atom2-1)=ix(i80+atom2-1)+1
- end do
-
- do i=1,natom
- ix(i80-i)=ix(i80+i-1)
- end do
-
- do i=1,nbonh
- atom1=ix(iibh+i-1)/3+1
- atom2=ix(ijbh+i-1)/3+1
- ix(i80-atom1)=ix(i80-atom1)+1
- ix(i80-atom2)=ix(i80-atom2)+1
- end do
-
-
- ! --- construct parameters for SA calculation; note that the
- ! radii stored in L165 are augmented by 1.4 Ang.
-
- do i=1,natom
- write(atype,'(a2)') ih(m06+i-1)
- call upper(atype)
- if (ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
- hybridization = ix(i80-i)
- nbond=ix(i80+i-1)
- if (atomicnumber .eq. 6) then
- if (hybridization .eq. 4) then
- if (nbond == 1) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.77887d0
- x(l175-1+i) = -0.28063d0
- x(l180-1+i) = -0.0012968d0
- x(l185-1+i) = 0.00039328d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.56482d0
- x(l175-1+i) = -0.19608d0
- x(l180-1+i) = -0.0010219d0
- x(l185-1+i) = 0.0002658d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.23348d0
- x(l175-1+i) = -0.072627d0
- x(l180-1+i) = -0.00020079d0
- x(l185-1+i) = 0.00007967d0
- else if (nbond == 4) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.00000d0
- x(l175-1+i) = 0.00000d0
- x(l180-1+i) = 0.00000d0
- x(l185-1+i) = 0.00000d0
- else
- write(6,*) 'Unusual nbond for CT:', i, nbond, &
- ' Using default carbon LCPO parameters'
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.77887d0
- x(l175-1+i) = -0.28063d0
- x(l180-1+i) = -0.0012968d0
- x(l185-1+i) = 0.00039328d0
- end if
- else
- if (nbond == 2) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.51245d0
- x(l175-1+i) = -0.15966d0
- x(l180-1+i) = -0.00019781d0
- x(l185-1+i) = 0.00016392d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.070344d0
- x(l175-1+i) = -0.019015d0
- x(l180-1+i) = -0.000022009d0
- x(l185-1+i) = 0.000016875d0
- else
- write(6,*) 'Unusual nbond for C :', i, nbond, &
- ' Using default carbon LCPO parameters'
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.77887d0
- x(l175-1+i) = -0.28063d0
- x(l180-1+i) = -0.0012968d0
- x(l185-1+i) = 0.00039328d0
- end if
- end if
- else if (atomicnumber .eq. 8) then
- if (atype == 'O ') then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.68563d0
- x(l175-1+i) = -0.1868d0
- x(l180-1+i) = -0.00135573d0
- x(l185-1+i) = 0.00023743d0
- else if (atype == 'O2') then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.88857d0
- x(l175-1+i) = -0.33421d0
- x(l180-1+i) = -0.0018683d0
- x(l185-1+i) = 0.00049372d0
- else
- if (nbond == 1) then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.77914d0
- x(l175-1+i) = -0.25262d0
- x(l180-1+i) = -0.0016056d0
- x(l185-1+i) = 0.00035071d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.49392d0
- x(l175-1+i) = -0.16038d0
- x(l180-1+i) = -0.00015512d0
- x(l185-1+i) = 0.00016453d0
- else
- write(6,*) 'Unusual nbond for O:', i, nbond, &
- ' Using default oxygen LCPO parameters'
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.77914d0
- x(l175-1+i) = -0.25262d0
- x(l180-1+i) = -0.0016056d0
- x(l185-1+i) = 0.00035071d0
- end if
- end if
- else if(atomicnumber .eq. 7) then
- if (atype == 'N3') then
- if (nbond == 1) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.078602d0
- x(l175-1+i) = -0.29198d0
- x(l180-1+i) = -0.0006537d0
- x(l185-1+i) = 0.00036247d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.22599d0
- x(l175-1+i) = -0.036648d0
- x(l180-1+i) = -0.0012297d0
- x(l185-1+i) = 0.000080038d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.051481d0
- x(l175-1+i) = -0.012603d0
- x(l180-1+i) = -0.00032006d0
- x(l185-1+i) = 0.000024774d0
- else
- write(6,*) 'Unusual nbond for N3:', i, nbond, &
- ' Using default nitrogen LCPO parameters'
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.078602d0
- x(l175-1+i) = -0.29198d0
- x(l180-1+i) = -0.0006537d0
- x(l185-1+i) = 0.00036247d0
- end if
- else
- if (nbond == 1) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.73511d0
- x(l175-1+i) = -0.22116d0
- x(l180-1+i) = -0.00089148d0
- x(l185-1+i) = 0.0002523d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.41102d0
- x(l175-1+i) = -0.12254d0
- x(l180-1+i) = -0.000075448d0
- x(l185-1+i) = 0.00011804d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.062577d0
- x(l175-1+i) = -0.017874d0
- x(l180-1+i) = -0.00008312d0
- x(l185-1+i) = 0.000019849d0
- else
- write(6,*) 'Unusual nbond for N:', i, nbond, &
- ' Using default nitrogen LCPO parameters'
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.078602d0
- x(l175-1+i) = -0.29198d0
- x(l180-1+i) = -0.0006537d0
- x(l185-1+i) = 0.00036247d0
- end if
- end if
- else if(atomicnumber .eq. 16) then
- if (atype == 'SH') then
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.7722d0
- x(l175-1+i) = -0.26393d0
- x(l180-1+i) = 0.0010629d0
- x(l185-1+i) = 0.0002179d0
- else
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.54581d0
- x(l175-1+i) = -0.19477d0
- x(l180-1+i) = -0.0012873d0
- x(l185-1+i) = 0.00029247d0
- end if
- else if (atomicnumber .eq. 15) then
- if (nbond == 3) then
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.3865d0
- x(l175-1+i) = -0.18249d0
- x(l180-1+i) = -0.0036598d0
- x(l185-1+i) = 0.0004264d0
- else if (nbond == 4) then
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.03873d0
- x(l175-1+i) = -0.0089339d0
- x(l180-1+i) = 0.0000083582d0
- x(l185-1+i) = 0.0000030381d0
- else
- write(6,*) 'Unusual nbond for P:', i, nbond, &
- ' Using default phosphorus LCPO parameters'
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.3865d0
- x(l175-1+i) = -0.18249d0
- x(l180-1+i) = -0.0036598d0
- x(l185-1+i) = 0.0004264d0
- end if
- else if (atype(1:1) == 'Z') then
- x(l165-1+i) = 0.00000d0 + 1.4d0
- x(l170-1+i) = 0.00000d0
- x(l175-1+i) = 0.00000d0
- x(l180-1+i) = 0.00000d0
- x(l185-1+i) = 0.00000d0
- else if (atomicnumber .eq. 1) then
- x(l165-1+i) = 0.00000d0 + 1.4d0
- x(l170-1+i) = 0.00000d0
- x(l175-1+i) = 0.00000d0
- x(l180-1+i) = 0.00000d0
- x(l185-1+i) = 0.00000d0
- else if (atype == 'MG') then
- ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.45A: Aqvist 1992
- x(l165-1+i) = 1.18d0 + 1.4d0
- ! The following values were taken from O.sp3 with two bonded
- ! neighbors -> O has the smallest van der Waals radius
- ! compared to all other elements which had been parametrized
- x(l170-1+i) = 0.49392d0
- x(l175-1+i) = -0.16038d0
- x(l180-1+i) = -0.00015512d0
- x(l185-1+i) = 0.00016453d0
- else if (atype == 'F') then
- x(l165-1+i) = 1.47d0 + 1.4d0
- x(l170-1+i) = 0.68563d0
- x(l175-1+i) = -0.1868d0
- x(l180-1+i) = -0.00135573d0
- x(l185-1+i) = 0.00023743d0
- else
- ! write( 0,* ) 'bad atom type: ',atype
- ! call mexit( 6,1 )
- x(l165-1+i) = 1.70 + 1.4;
- x(l170-1+i) = 0.51245;
- x(l175-1+i) = -0.15966;
- x(l180-1+i) = -0.00019781;
- x(l185-1+i) = 0.00016392;
- write(6,'(a,a)') 'Using carbon SA parms for atom type', atype
- end if
- end do ! i=1,natom
- !
- else if ( gbsa == 2 ) then
-
- ! --- assign parameters for calculating SASA according to the
- ! ICOSA method; the radii are augmented by 1.4 A ---
-
- do i=1,natom
- write(atype,'(a2)') ih(m06+i-1)
- if(ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
- if (atomicnumber .eq. 7) then
- x(L165-1+i) = 1.55d0 + 1.4d0
- else if (atomicnumber .eq. 6) then
- x(L165-1+i) = 1.70d0 + 1.4d0
- else if (atomicnumber .eq. 1) then
- x(L165-1+i) = 1.20d0 + 1.4d0
- else if (atomicnumber .eq. 8) then
- x(L165-1+i) = 1.50d0 + 1.4d0
- else if (atomicnumber .eq. 15) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 16) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 17) then
- ! Cl radius
- x(L165-1+i) = 1.70d0 + 1.4d0
- else if (atomicnumber .eq. 9) then
- ! F radius
- x(L165-1+i) = 1.50d0 + 1.4d0
- else if (atomicnumber .eq. 35) then
- ! Br radius
- ! Bondi, J. Phys. Chem. 1964, 68, 441.
- x(L165-1+i) = 1.85d0 + 1.4d0
- else if (atomicnumber .eq. 20) then
- ! Ca radius
- ! Calculated from Aqvist, J. Phys. Chem. 1990, 94, 8021.
- x(L165-1+i) = 1.33d0 + 1.4d0
- else if (atomicnumber .eq. 11) then
- ! Na radius
- ! Calculated from Aqvist, J. Phys. Chem. 1990, 94, 8021.
- x(L165-1+i) = 1.87d0 + 1.4d0
- else if (atomicnumber .eq. 30) then
- ! Zn radius
- ! Hoops, Anderson, Merz, JACS 1991, 113, 8262.
- x(L165-1+i) = 1.10d0 + 1.4d0
- else if (atomicnumber .eq. 12) then
- ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.45A: Aqvist 1992
- x(L165-1+i) = 1.18d0 + 1.4d0
- else
- write( 0,* ) 'bad atom type: ',atype
- call mexit( 6,1 )
- end if
-
- ! dummy LCPO values:
- x(L170-1+i) = 0.0d0
- x(L175-1+i) = 0.0d0
- x(L180-1+i) = 0.0d0
- x(L185-1+i) = 0.0d0
- ! write(6,*) i,' ',atype,x(L165-1+i)
- end do ! i=1,natom
-
- end if ! ( gbsa == 1 )
-
- end if ! ( igb /= 0 .and. igb /= 10 .and. ipb == 0 )
-
- !-----------------------------------
- ! If a LRT calculation is requested,
- ! setup the icosa-SASA parameters
- ! this code is copied from above
- !-----------------------------------
-
- if ( ilrt /= 0 ) then
- ! --- assign parameters for calculating SASA according to the
- ! ICOSA method; the radii are augmented by 1.4 A ---
- do i=1,natom
- write(atype,'(a2)') ih(m06+i-1)
- if(ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
- if (atomicnumber .eq. 7) then
- x(L165-1+i) = 1.55d0 + 1.4d0
- else if (atomicnumber .eq. 6) then
- x(L165-1+i) = 1.70d0 + 1.4d0
- else if (atomicnumber .eq. 1 .or. &
- ! added for lone pairs
- atype == 'EP') then
- x(L165-1+i) = 1.20d0 + 1.4d0
- else if (atomicnumber .eq. 8) then
- x(L165-1+i) = 1.50d0 + 1.4d0
- else if (atomicnumber .eq. 15) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 16) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 12) then
- ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.45A: Aqvist 1992
- x(L165-1+i) = 1.18d0 + 1.4d0
- else
- write( 0,* ) 'bad atom type: ',atype,' cannot perform SASA calculation'
- call mexit( 6,1 )
- end if ! atype(1:1) == 'N'
- x(L170-1+i) = 0.0d0
- x(L175-1+i) = 0.0d0
- x(L180-1+i) = 0.0d0
- x(L185-1+i) = 0.0d0
- !write(6,*) i,' ',atype,x(L165-1+i)
- end do ! i=1,natom
-
- end if ! ( ilrt /= 0 )
-
- !------------------------------------------------------------------------
- ! If user has requested Poisson-Boltzmann electrostatics, set up variables
- !------------------------------------------------------------------------
-
- if ( igb == 10 .or. ipb /= 0 ) then
- call pb_init(ifcap,natom,nres,ntypes,nbonh,nbona,ix(i02),ix(i04),ix(i06),ix(i08),ix(i10),&
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),ix(ibellygp),ih(m02),ih(m04),ih(m06),x(l15),x(l97))
- end if ! ( igb == 10 .or. ipb /= 0 )
-
- if (icnstph /= 0) then
- ! Initialize all constant pH data to 0 and read it in
- call cnstph_zero()
- call cnstphread(x(l15))
-
- ! Fill proposed charges array from current charges
- do i=1,natom
- x(l190-1+i) = x(l15-1+i)
- end do
-
- ! If we're doing explicit CpH, fill gbv* arrays
- if ( icnstph .gt. 1 .and. cph_igb == 2 .or. cph_igb == 5) then
- do i=1,natom
- x(l2402+i-1) = gbalpha
- x(l2403+i-1) = gbbeta
- x(l2404+i-1) = gbgamma
- end do
- end if
- end if
-
-! +---------------------------------------------------------------+
-! | Read EVB input file |
-! +---------------------------------------------------------------+
-
- if( ievb /= 0 ) then
-#ifdef MPI
- call evb_input
- call evb_init
-# if defined(LES)
-!KFW call evb_pimd_init
-# endif
-#else
- write(6,'(/2x,a)') 'Setting ievb>0 requires compilation with MPI'
- call mexit(6,1)
-#endif
- endif
-
- if( iyammp /= 0 ) write( 6, '(a)' ) ' Using yammp non-bonded potential'
-
- ! -------------------------------------------------------------------
- !
- ! -- add check to see if the space in nmr.h is likely to be
- ! too small for this run:
- ! [Note: this check does *not* indicate if MXTAU and MXP are
- ! too small. There is no easy way to ensure this, since
- ! the experimental intensities are read in a namelist
- ! command: if too many intensities are input, the read
- ! statment may cause a coredump before returning control
- ! to the main program. Be careful. sigh....]
-
- if (natom > matom .and. nmropt > 1) then
- write(6,*) 'WARNING: MATOM in nmr.h is smaller than the ', &
- natom,' atoms in this molecule.'
- write(6,*) 'Printout of NMR violations may be compromised.'
- end if
-
- ! -------------------------------------------------------------------
- ! --- checks on bogus data ---
- ! -------------------------------------------------------------------
-
- inerr = 0
-
- if( icfe < 0 .or. icfe > 1 ) then
- write(6,*) 'icfe must be 0 or 1 (icfe=2 is no longer supported)'
- inerr = 1
- end if
- if( icfe /= 0 .and. numgroup /= 2 ) then
- write(6,*) 'numgroup must be 2 if icfe is set'
- inerr = 1
- end if
- if (ievb>0) then
-#ifdef MPI
-!KFW if( numgroup /= 2 ) then
-!KFW write(6,*) 'numgroup must be 2 if ievb is set'
-!KFW inerr = 1
-!KFW end if
-#else
- write(6,'(/2x,a)') 'Setting ievb>0 requires compilation with MPI'
- inerr = 1
-#endif
- end if
-#ifdef PUPIL_SUPPORT
- ! BPR: PUPIL does not work with GB (or, I suppose, PB) for the
- ! time being. It is known to either crash or produce bogus
- ! results.
- if (igb > 0 .or. ipb /= 0) then
- write(6,'(a)') 'Cannot use implicit solvation (GB or PB) with PUPIL'
- inerr = 1
- end if
-#endif /*PUPIL_SUPPORT*/
- if( (igb > 0 .or. ipb /= 0) .and. numextra > 0) then
- write(6,'(a)') 'Cannot use igb>0 with extra-point force fields'
- inerr = 1
- end if
-
-!AMD validation
- if(iamd.gt.0)then
- if (EthreshD .eq. 0.d0 .and. alphaD .eq. 0.d0 .and. EthreshP .eq. 0.d0 .and. alphaP .eq. 0.d0) then
- write(6,'(a,i3)')'| AMD error all main parameters are 0.0 for Accelerated MD (AMD) or Windowed Accelerated MD (wAMD) '
- inerr = 1
- endif
- if(w_amd.gt.0)then
- if (EthreshD_w .eq. 0.d0 .and. alphaD_w .eq. 0.d0 .and. EthreshP_w .eq. 0.d0 .and. alphaP_w .eq. 0.d0) then
- write(6,'(a,i3)')'| AMD error all extra parameters are 0.0 for Windowed Accelerated MD (wAMD) LOWERING BARRIERS'
- inerr = 1
- endif
- endif
- endif
- if (iamd .gt. 0 .and. iamoeba ==1) then
- write(6,*)'amoeba is incompatible with AMD for now'
- inerr=1
- end if
-
- if (ips < 0 .or. ips > 6) then
- write(6,'(/2x,a,i3,a)') 'IPS (',ips,') must be between 0 and 6'
- inerr = 1
- end if
- if (ips /= 0 .and. ipol > 0 ) then
- write(6,'(/2x,a)') 'IPS and IPOL are inconsistent options'
- inerr = 1
- endif
- if (ips /= 0 .and. lj1264 /= 0) then
- write(6, '(/2x,a)') 'IPS and the LJ 12-6-4 potential are incompatible'
- inerr = 1
- endif
- if ( (igb > 0 .or. ipb /= 0) .and. ips > 0 ) then
- write(6,'(/2x,a,i3,a,i3,a)') 'IGB (',igb,') and ips (',ips, &
- ') cannot both be turned on'
- inerr = 1
- end if
- if (igb /= 0 .and. igb /= 1 .and. igb /= 2 .and. igb /= 5 &
- .and. igb /= 6 .and. igb /= 7 .and. igb /= 8 .and. igb /= 10) then
- write(6,'(/2x,a,i3,a)') 'IGB (',igb,') must be 0,1,2,5,6,7,8 or 10.'
- inerr = 1
- end if
- if (alpb /= 0 .and. alpb /= 1 ) then
- write(6,'(/2x,a,i3,a)') 'ALPB (',alpb,') must be 0 or 1.'
- inerr = 1
- end if
- if (alpb /= 0 .and. igb /= 1 .and. igb /= 2 .and. igb /= 5 .and. igb /=7 ) then
- write(6,'(/2x,a,i3,a)') 'IGB (',igb,') must be 1,2,5, or 7 if ALPB > 0.'
- inerr = 1
- end if
-
- if (jar < 0 .or. jar > 1) then
- write(6,'(/2x,a,i3,a)') 'JAR (',jar,') must be 0 or 1'
- inerr = 1
- end if
-
-#ifdef LES
- if( igb /= 0 .and. igb /= 1 .and. igb /= 5 .and. igb /=7 ) then
- write(6,'(/,a)') 'Error: LES is only compatible with IGB > 0,1,5,7'
- inerr = 1
- end if
- if( alpb /= 0) then
- write(6,'(/,a)') 'Error: LES is not compatible with ALPB'
- inerr = 1
- end if
- if( gbsa > 0 ) then
- write(6,'(/,a)') 'Error: LES is not compatible with GBSA > 0'
- inerr = 1
- end if
- if( qmmm_nml%ifqnt ) then
- write(6,'(/,a)') 'Error: LES is not compatible with QM/MM'
- inerr = 1
- end if
- if( ipol > 0 ) then
- write(6,'(/,a)') 'Error: LES is not compatible with IPOL > 0'
- inerr = 1
- end if
- if (temp0les >= 0.d0 .and. iscale > 0 ) then
- write (6,'(/,a)') 'Error: iscale cannot be used with temp0les'
- inerr = 1
- end if
-#endif
- if (irest /= 0 .and. irest /= 1) then
- write(6,'(/2x,a,i3,a)') 'IREST (',irest,') must be 0 or 1.'
- inerr = 1
- end if
- if (ibelly /= 0 .and. ibelly /= 1) then
- write(6,'(/2x,a,i3,a)') 'IBELLY (',ibelly,') must be 0 or 1.'
- inerr = 1
- end if
- if (imin < 0) then
- write(6,'(/2x,a,i3,a)') 'IMIN (',imin,') must be >= 0.'
- inerr = 1
- end if
- if (imin == 5) then
- if (ifbox /= 0 .and. ntb == 2) then
- write(6,'(/2x,a)') 'WARNING: IMIN=5 with changing periodic boundaries (NTB=2) can result in'
- write(6,'(/2x,a)') ' odd energies being calculated. Use with caution.'
- endif
-#ifdef MPI
- if (sandersize > 1 .and. ntb == 2) then
- write(6,'(/2x,a)') 'ERROR: IMIN=5 and NTB=2 cannot be run with multiple processors.'
- inerr = 1
- endif
-#endif
- end if
-
-
- if (iscale > mxvar) then
- write(6,9501) iscale,mxvar
- 9501 format('ERROR: ISCALE (',i5,') exceeds MXVAR (',i5, &
- '). See nmr.h')
- inerr = 1
- end if
- if (ntx < 1 .or. ntx > 7) then
- write(6,'(/2x,a,i3,a)') 'NTX (',ntx,') must be in 1..7'
- inerr = 1
- end if
-
- if (ntb /= 0 .and. ntb /= 1 .and. ntb /= 2) then
- write(6,'(/2x,a,i3,a)') 'NTB (',ntb,') must be 0, 1 or 2.'
- inerr = 1
- end if
- if (ntb == 0 .and. iwrap > 0) then
- write(6,'(/2x,a)') 'Error: IWRAP > 0 cannot be used without a periodic box.'
- inerr = 1
- end if
-
- if (ntt < 0 .or. ntt > 8) then ! APJ
- write(6,'(/2x,a,i3,a)') 'NTT (',ntt,') must be between 0 and 8.' ! APJ
- inerr = 1
- end if
- if (ntt == 1 .and. tautp < dt) then
- write(6, '(/2x,a,f6.2,a)') 'TAUTP (',tautp,') < DT (step size)'
- inerr = 1
- end if
- if( ntt < 3 .or. ntt > 8 ) then ! APJ
- if( gamma_ln > 0.d0 ) then
- write(6,'(a)') 'ntt must be 3 to 8 if gamma_ln > 0' ! APJ
- inerr = 1
- end if
- end if
-
- if ( ntt==3 .or. ntt==6 ) nchain = 0 !APJ: Langevin, Adaptive-Langevin must have chain set to zero. ! APJ
-
- if (ntt == 3 .or. ntt == 4) then
- if ( ntb == 2) then
- !Require gamma_ln > 0.0d0 for ntt=3 and ntb=2 - strange things happen
- !if you run NPT with NTT=3 and gamma_ln = 0.
- if ( gamma_ln <= 0.0d0 ) then
- write(6,'(a)') 'gamma_ln must be > 0 for ntt=3 .or. 4 with ntb=2.'
- inerr = 1
- end if
- end if
- end if
-
- if (ntp /= 0 .and. ntp /= 1 .and. ntp /= 2 .and. ntp /= 3) then
- write(6,'(/2x,a,i3,a)') 'NTP (',ntp,') must be 0, 1, 2, or 3.'
- inerr = 1
- end if
- if (ntp == 3 .and. csurften < 1) then
- write(6,'(/2x,a)') 'csurften must be greater than 0 for ntp=3.'
- inerr = 1
- end if
- if (ntp > 0 .and. taup < dt .and. barostat == 1) then
- write(6, '(/2x,a,f6.2,a)') 'TAUP (',taup,') < DT (step size)'
- inerr = 1
- end if
- if (npscal < 0 .or. npscal > 1) then
- write(6,'(/2x,a,i3,a)') 'NPSCAL (',npscal,') must be 0 or 1.'
- inerr = 1
- end if
- if (ntp > 0) then
- if (barostat /= 1 .and. barostat /= 2) then
- write(6, '(/2x,a,i3,a)') 'BAROSTAT (', barostat, ') must be 1 or 2'
- inerr = 1
- end if
- if (barostat == 2) then
- if (mcbarint <= 0) then
- write(6, '(/2x,a,i3,a)') 'MCBARINT (',mcbarint,') must be positive'
- inerr = 1
- end if
- if (mcbarint >= nstlim) then
- write(6, '(a)') 'WARNING: mcbarint is greater than the number of &
- &steps. This is effectively constant volume.'
- end if
- end if
- end if
-
- if (ntc < 1 .or. ntc > 4) then
- write(6,'(/2x,a,i3,a)') 'NTC (',ntc,') must be 1,2,3 or 4.'
- inerr = 1
- end if
- if (jfastw < 0 .or. jfastw > 4) then
- write(6,'(/2x,a,i3,a)') 'JFASTW (',jfastw,') must be 0->4.'
- inerr = 1
- end if
-
- if (ntf < 1 .or. ntf > 8) then
- write(6,'(/2x,a,i3,a)') 'NTF (',ntf,') must be in 1..8.'
- inerr = 1
- end if
-
- if (ioutfm /= 0 .and. ioutfm /= 1) then
- write(6,'(/2x,a,i3,a)') 'IOUTFM (',ioutfm,') must be 0 or 1.'
- inerr = 1
- end if
-
- if (ntpr < 0) then
- write(6,'(/2x,a,i3,a)') 'NTPR (',ntpr,') must be >= 0.'
- inerr = 1
- end if
- if (ntwx < 0) then
- write(6,'(/2x,a,i3,a)') 'NTWX (',ntwx,') must be >= 0.'
- inerr = 1
- end if
- if (ntwv < -1) then
- write(6,'(/2x,a,i3,a)') 'NTWV (',ntwv,') must be >= -1.'
- inerr = 1
- end if
- if (ntwf < -1) then
- write(6, '(/2x,a,i3,a)') 'NTWF (',ntwf,') must be >= -1.'
- inerr = 1
- end if
- if (ntwv == -1 .and. ioutfm /= 1) then
- write (6, '(/2x,a)') 'IOUTFM must be 1 for NTWV == -1.'
- inerr = 1
- end if
- if (ntwf == -1 .and. ioutfm /= 1) then
- write(6, '(/2x,a)') 'IOUTFM must be 1 for NTWF == -1.'
- inerr = 1
- end if
- if (ntwv == -1 .and. ntwx == 0) then
- write (6, '(/2x,a)') 'NTWX must be > 0 for NTWV == -1.'
- inerr = 1
- end if
- if (ntwe < 0) then
- write(6,'(/2x,a,i3,a)') 'NTWE (',ntwe,') must be >= 0.'
- inerr = 1
- end if
- if (ntave < 0) then
- write(6,'(/2x,a,i3,a)') 'NTAVE (',ntave,') must be >= 0.'
- inerr = 1
- end if
- if (ntr /= 0 .and. ntr /= 1) then
- write(6,'(/2x,a,i3,a)') 'NTR (',ntr,') must be 0 or 1.'
- inerr = 1
- end if
- if (ntrx /= 0 .and. ntrx /= 1) then
- write(6,'(/2x,a,i3,a)') 'NTRX (',ntrx,') must be 0 or 1.'
- inerr = 1
- end if
- if (nmropt < 0 .or. nmropt > 2) then
- write(6,'(/2x,a,i3,a)') 'NMROPT (',nmropt,') must be in 0..2.'
- inerr = 1
- end if
-
- if (idecomp < 0 .or. idecomp > 4) then
- write(6,'(/2x,a)') 'IDECOMP must be 0..4'
- inerr = 1
- end if
-
- ! check settings related to ivcap
-
- if(ivcap == 3 .or. ivcap == 4) then
- write(6,'(/2x,a)') 'IVCAP == 3 and IVCAP == 4 currently not implemented'
- inerr = 1
- endif
- if (ivcap < 0 .and. ivcap > 5) then
- write(6,'(/2x,a)') 'IVCAP must be 0 ... 5'
- inerr = 1
- end if
- if ((ivcap == 1 .or. ivcap == 5) .and. igb /= 10 .and. ipb == 0) then
- write(6,'(/2x,a)') 'IVCAP == 1,5 only works with Poisson Boltzmann (igb=10 or ipb/=0)'
- inerr = 1
- end if
- if((ivcap == 1 .or. ivcap == 3 .or. ivcap == 5 ) .and. cutcap <= 0.0d0) then
- write(6,'(/2x,a)') 'For IVCAP == 1,3, or 5, cutcap must be > 0.0'
- inerr = 1
- endif
- if (ivcap == 4 .and. &
- (xlorth < ZERO .or. ylorth < ZERO .or. zlorth < ZERO .or. &
-! give magic numbers a name srb aug 2007 !
- xorth > 47114710.0d0 .or. &
-! give magic numbers a name !
- yorth > 47114710.0d0 .or. &
-! give magic numbers a name !
- zorth > 47114710.0d0)) then
- write(6,'(/2x,a)') &
- 'For IVCAP == 4, xlorth, ylorth, zlorth, xorth, yorth, zorth must be set'
- inerr = 1
- end if
- if ((ivcap == 3 .or. ivcap == 4) .and. ibelly == 0) then
- write(6,'(/2x,a,a)') &
- 'For IVCAP == 3 or 4, ibelly must be 1 and all atoms', &
- ' not in the spherical or orthorhombic region must be set NOT moving'
- inerr = 1
- end if
- if (ivcap == 5 .and. (imin /= 1 .or. maxcyc > 1)) then
- write(6,'(/2x,a,a)') &
- 'IVCAP == 5 only works for single-point energy calculation'
- inerr = 1
- end if
-
- ! check if ifbox variable from prmtop file matches actual angles:
-
- if ( igb == 0 .and. ipb == 0 .and. ntb /= 0 ) then
- if ( ifbox == 1 ) then
- if ( abs(alpha - 90.0d0) > 1.d-5 .or. &
- abs(beta - 90.0d0) > 1.d-5 .or. &
- abs(gamma - 90.0d0) > 1.d-5 ) then
- ifbox =3
- write(6,'(a)') ' Setting ifbox to 3 for non-orthogonal unit cell'
- end if
- end if
-
- if ( ifbox == 2 ) then
- if ( abs(alpha - 109.4712190d0) > 1.d-5 .or. &
- abs(beta - 109.4712190d0) > 1.d-5 .or. &
- abs(gamma - 109.4712190d0) > 1.d-5 ) then
- write(6,'(/2x,a)') &
- 'Error: ifbox=2 in prmtop but angles are not correct'
- inerr = 1
- end if
- end if
- end if
-
- ! checks for targeted MD
- if (itgtmd /= 0 .and. itgtmd > 2) then
- write(6,'(/2x,a,i3,a)') 'ITGTMD (',itgtmd,') must be 0, 1 or 2.'
- inerr = 1
- end if
- if (itgtmd == 1 .and. ntr == 1) then
- if (len_trim(tgtfitmask) > 0 .or. len_trim(tgtrmsmask) <= 0) then
- write(6,'(/2x,a)') 'ITGTMD: tgtrmsmask (and not tgtfitmask) ' // &
- 'should be specified if NTR=1'
- inerr = 1
- end if
- end if
- ! skip this test until fallback to rgroup() is supported
- !if (itgtmd == 1 .and. ntr == 0) then
- ! if (len_trim(tgtfitmask) == 0 .and. len_trim(tgtrmsmask) == 0) then
- ! write(6,'(/2x,a)') &
- ! 'ITGTMD: both tgtfitmask and tgtrmsmask should be specified if NTR=0'
- ! inerr = 1
- ! end if
- !end if
-
- ! -- consistency checking
-
- if (imin > 0.and.nrespa > 1) then
- write(6,'(/2x,a)') 'For minimization, set nrespa,nrespai=1'
- inerr = 1
- end if
- if (ntp > 0 .and. nrespa > 1) then
- write(6,'(/2x,a)') 'nrespa must be 1 if ntp>0'
- inerr = 1
- end if
- if (ntx < 4.and.init /= 3) then
- write(6,'(/2x,a)') 'NTX / IREST inconsistency'
- inerr = 1
- end if
- if (ntb == 2 .and. ntp == 0) then
- write(6,'(/2x,a)') 'NTB set but no NTP option (must be 1 or 2)'
- inerr = 1
- end if
- if (ntp /= 0 .and. ntb /= 2) then
- write(6,'(/,a,a)')' NTP > 0 but not constant pressure P.B.C.', &
- ' (NTB = 2) must be used'
- inerr = 1
- end if
- if (ntb /= 0 .and. ifbox == 0 .and. ntp /= 0) then
- write(6,'(/,a)') ' (NTB /= 0 and NTP /= 0) but IFBOX == 0'
- write(6,'(/,a)') ' This combination is not supported'
- inerr = 1
- end if
- if (ntb /= 0 .and. &
- ( box(1) < 1.d0 .or. &
- box(2) < 1.d0 .or. &
- box(3) < 1.d0 ) ) then
- write(6,'(/,a,3f10.3)') ' BOX is too small: ',box(1),box(2),box(3)
- inerr = 1
- else if (ntb /= 0 .and. &
- (sqrt(cut) >= box(1)*0.5d0 .or. &
- sqrt(cut) >= box(2)*0.5d0 .or. &
- sqrt(cut) >= box(3)*0.5d0) ) then
- write(6,'(/,a)') ' CUT must be < half smallest box dimension'
- inerr = 1
- end if
- if (ntb /= 0 .and. (igb > 0 .or. ipb /= 0) ) then
- write(6,'(/,a)') ' igb>0 is only compatible with ntb=0'
- inerr = 1
- end if
-#ifdef APBS
- if ( ntb == 0 .and. sqrt(cut) < 8.05 .and. igb /= 10 .and. ipb == 0 .and. &
- .not. mdin_apbs) then
-#else
- if ( ntb == 0 .and. sqrt(cut) < 8.05 .and. igb /= 10 .and. ipb == 0 ) then
-#endif /* APBS */
- write(6,'(/,a,f8.2)') ' unreasonably small cut for non-periodic run: ', &
- sqrt(cut)
- inerr = 1
- end if
- if ( rgbmax < 5.d0*fsmax ) then
- write(6,'(/,a,f8.2)') ' rgbmax must be at least ', 5.d0*fsmax
- inerr = 1
- end if
- if (icfe /= 0 .and. indmeth == 3 ) then
- write(6,'(/,a)') ' indmeth=3 cannot be used with icfe>0'
- inerr = 1
- end if
- if (icfe /= 0 .and. ibelly /= 0 ) then
- write(6,'(/,a)') ' ibelly cannot be used with icfe'
- inerr = 1
- end if
-#ifdef MPI /* SOFT CORE */
- if (icfe /= 0 .and. dvdl_norest /= 0 ) then
- write(6,'(/,a)') 'dvdl_norest must == 0!'
- write(6,'(/,a)') 'The dvdl_norest option is deprecated.'
- write(6,'(/,a)') 'Restraint energies are seperated, &
- &and do not contribute to dvdl.'
- inerr = 1
- end if
-#endif
- ! Modification done by Ilyas Yildirim
- if (icfe == 1 .and. (klambda < 1 .or. klambda > 6)) then
- write(6,'(/,a)') ' klambda must be between 1 and 6'
- inerr = 1
- end if
- ! End of modification done by Ilyas Yildirim
-
- if (clambda < 0.d0 .or. clambda > 1.d0 ) then
- write(6,'(/,a)') ' clambda must be between 0 and 1'
- inerr = 1
- end if
-
- if (icfe /= 0 .and. (idecomp == 3 .or. idecomp == 4)) then
- write(6,'(/,a)') ' Pairwise decomposition for thermodynamic integration not implemented'
- inerr = 1
- end if
- if (icfe /= 0 .and. idecomp /= 0 .and. ipol > 0) then
- write(6,'(/,a)') ' IPOL is incompatible with IDECOMP and ICFE'
- inerr = 1
- end if
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) then
- if (ifsc == 2) then
- write (6,'(/,a)') 'The ifsc=2 option is no longer supported. &
- &Internal energies of the soft core region.'
- write (6,'(a)') 'are now handled implicitly and setting ifsc=2 &
- &is no longer needed'
- inerr = 1
- end if
- if (icfe /= 1 .and. ifsc==1) then
- write (6,'(/,a)') ' Softcore potential requires a standard TI run, set icfe to 1'
- inerr = 1
- end if
- if ( igb > 0 .or. ipb /= 0 ) then
- write (6,'(/,a)') ' Softcore potential is incompatible with GB (for now)'
- inerr = 1
- end if
- if ( ntf > 1 ) then
- write (6,'(/,a)') ' Softcore potentials require ntf=1 because SHAKE &
- &constraints on some bonds might be removed'
- inerr = 1
- end if
- if (clambda > 0.995 .or. clambda < 0.005) then
- write (6,'(/,a)') ' Softcore potentials cannot be used with clambda < 0.005 or > 0.995'
- inerr = 1
- end if
- if (klambda /= 1) then
- write (6,'(/,a)') ' Softcore potential requires linear mixing, set klambda to 1'
- inerr = 1
- end if
- if (imin == 1 .and. ntmin /= 2) then
- write (6,'(/,a)') ' Minimizations with ifsc=1 require the steepest descent algorithm.'
- write (6,'(/,a)') ' Set ntmin to 2 and restart'
- inerr = 1
- end if
- end if
- if (ifmbar /= 0) then
- if (icfe /= 1) then
- write (6,'(/,a)') ' MBAR requires a standard TI run, set icfe to 1'
- inerr = 1
- end if
- if (ifsc /=0 .and. (bar_l_max > 0.995 .or. bar_l_min < 0.005) ) then
- write (6,'(/,a)') ' Softcore potentials cannot be used with &
- &bar_l_min < 0.005 or bar_l_max > 0.995'
- inerr = 1
- end if
- if (klambda /= 1) then
- write (6,'(/,a)') ' MBAR requires linear mixing, set klambda to 1'
- inerr = 1
- end if
- end if
-#endif
-
- if (ilrt /= 0 .and. lrtmask == '') then
- write (6,'(a)') 'Linear Response Theory activated, but lrtmask is not set'
- inerr = 1
- end if
-
- if (idecomp > 0 .and. (ntr > 0 .or. ibelly > 0)) then
- write(6,'(/,a)') 'IDECOMP is not compatible with NTR or IBELLY'
- inerr = 1
- end if
- if (icnstph /= 0) then
-
- if ( icnstph < 0 ) then
- write(6, '(/,a)') 'icnstph must be greater than 0'
- inerr = 1
- end if
- if ( igb == 0 .and. ipb == 0 .and. icnstph == 1 ) then
- write(6, '(/,a)') 'Constant pH using icnstph = 1 requires &
- &GB implicit solvent'
- inerr = 1
- end if
- if ( ntb .eq. 0 .and. icnstph .gt. 1 ) then
- write(6, '(/,a)') 'Constant pH using icnstph = 2 requires &
- &periodic boundary conditions'
- inerr = 1
- end if
- if (icfe /= 0) then
- write(6, '(/,a)') &
- 'Constant pH and thermodynamic integration are incompatable'
- inerr = 1
- end if
-
- if (ntcnstph <= 0) then
- write(6, '(/,a)') 'ntcnstph must be a positive integer.'
- inerr = 1
- end if
-
- if (icnstph > 1 .and. mccycles <= 0) then
- write(6, '(/,a)') 'mccycles must be a positive integer.'
- inerr = 1
- end if
-
- end if ! icnstph
-
-#ifdef noVIRIAL
- if( ntp > 0 .and. barostat == 1 ) then
- write(6,'(/,a)') 'Error: Berendsen barostat is incompatible with noVIRIAL'
- inerr = 1
- end if
-#endif
-
- !-----------------------------------------------------
- ! ----sanity checks for Ewald
- !-----------------------------------------------------
-
- if( igb == 0 .and. ipb == 0 ) then
- call float_legal_range('skinnb: (nonbond list skin) ', &
- skinnb,skinlo,skinhi)
-
- ! --- Will check on sanity of settings after coords are read in
- ! and the extent of the system is determined.
-
- if(periodic == 1)then
- call float_legal_range('skinnb+cutoffnb: (nonbond list cut) ', &
- skinnb+cutoffnb,zero,sphere)
- end if
- if (ntb==0 .and. use_pme/=0) then
- write(6,'(/,a)') &
- 'Using PME with a non-periodic simulation does not make sense. Set either ntb>0 of use_pme=0.'
- inerr = 1
- end if
- call float_legal_range('a: (unit cell size) ',a,boxlo,boxhi)
- call float_legal_range('b: (unit cell size) ',b,boxlo,boxhi)
- call float_legal_range('c: (unit cell size) ',c,boxlo,boxhi)
- call float_legal_range('alpha: (unit cell angle) ', &
- alpha,anglo,anghi)
- call float_legal_range('beta: (unit cell angle) ', &
- beta,anglo,anghi)
- call float_legal_range('gamma: (unit cell angle) ', &
- gamma,anglo,anghi)
- call int_legal_range('order: (interpolation order) ', &
- order,orderlo,orderhi)
- call opt_legal_range('verbose: ',verbose,0,4)
- call opt_legal_range('netfrc: ',netfrc,0,1)
- call opt_legal_range('nbflag: ',nbflag,0,1)
- call opt_legal_range('nbtell: ',nbtell,0,2)
- call opt_legal_range('ew_type: ',ew_type,0,1)
- call opt_legal_range('vdwmeth: ',vdwmeth,0,2)
- call opt_legal_range('eedmeth: ',eedmeth,1,6)
- call opt_legal_range('ee_type: ',ee_type,1,2)
- call opt_legal_range('maxiter: ',maxiter,1,50)
- call opt_legal_range('indmeth: ',indmeth,0,3)
- call opt_legal_range('fix_quad: ',fix_quad,0,1)
- call float_legal_range('eedtbdns: (erfc table density) ', &
- eedtbdns,denslo,denshi)
- end if ! ( igb == 0 .and. ipb == 0 )
-
- if( ntb==2 .and. ipimd==1) then
- write(6,*) 'primitive PIMD is incompatible with NTP ensemble'
- inerr=1
- endif
-
- if( ntb==2 .and. ipimd==3 ) then
- write(6,*) 'CMD is incompatible with NTP ensemble'
- inerr=1
- endif
-
- if( ipimd==3 .and. adiab_param>=1.0 ) then
- write(6,*) 'For CMD adiab_param must be <=1'
- inerr=1
- endif
-
- if( ntb==2 .and. ipimd==4 ) then
- write(6,*) 'RPMD is incompatible with NTP ensemble'
- inerr=1
- endif
-
- if( ntt/=0 .and. ipimd==4 ) then
- write(6,*) 'RPMD is incompatible with NVT ensemble'
- inerr=1
- endif
-
- if( ntt/=4 .and. ipimd==2 ) then
- write(6,*) 'NMPIMD requires Nose-Hoover chains (ntt=4)'
- inerr=1
- endif
-
- if( ntt/=4 .and. ipimd==3 ) then
- write(6,*) 'CMD requires Nose-Hoover chains (ntt=4)'
- inerr=1
- endif
-
-#if !defined(MPI)
- if( ineb > 0 ) then
- write(6,*) 'NEB requires MPI'
- inerr=1
- endif
-#endif
-
-#ifdef LES
- if( ineb > 0 ) then
- write(6,*) 'NEB no longer works with LES: use multiple groups and a groupfile instead'
- inerr=1
- endif
-#endif
-
- if( ineb > 0 .and. ipimd > 0 ) then
- write(6,*) 'ineb>0 and ipimd>0 are incompatible options'
- inerr=1
- endif
-
- if( iamoeba == 1 )then
-#ifdef LES
- write(6,*)'amoeba is incompatible with LES'
- inerr=1
-#endif
-
- if( ntc > 1 ) then
- write(6,*) 'SHAKE (ntc>1) and amoeba are incompatible options'
- inerr=1
- end if
- if( ntp > 1 .and. beeman_integrator > 0 ) then
- write(6,*) 'ntp>1 is not consistent with the beeman integrator'
- inerr=1
- end if
- if ( igb /= 0 ) then
- write (6,'(/,a)') 'amoeba (iamoeba=1) is incompatible with GB (igb>0)'
- inerr=1
- end if
- if ( ipb /= 0 ) then
- write (6,'(/,a)') 'amoeba (iamoeba=1) is incompatible with PB (ipb>0)'
- inerr=1
- end if
-#ifdef MPI
- if (numtasks > 1) then
- write(6, '(/,a)') 'amoeba (iamoeba=1) cannot be run in parallel in &
- &sander'
- inerr=1
- end if
-#endif
-
- end if
-
- ! ---WARNINGS:
-
- if ( ibelly == 1 .and. igb == 0 .and. ipb == 0 .and. ntb /= 0 ) then
- write(6,'(/,a,/,a,/,a)') &
- 'Warning: Although EWALD will work with belly', &
- '(for equilibration), it is not strictly correct!'
- end if
-
- if (inerr == 1) then
- write(6, '(/,a)') ' *** input error(s)'
- call mexit(6,1)
- end if
-
- ! Load the restrained atoms (ntr=1) or the belly atoms (ibelly=1)
- ! or atoms for targeted md (itgtmd=1). Selections are read from
- ! &cntrl variables or, if these are not defined, it falls back to
- ! the old group input format.
-
- if(mtmd /= 'mtmd') then
- itgtmd = 2
- ntr = 0
- emtmd = 0.0d0
- end if
- konst = ntr > 0
- dotgtmd = itgtmd > 0
- belly = .false.
- natc = 0
- ngrp = 0
- natbel = 0
- nattgtfit = 0 ! number of atoms for tgtmd fitting (=overlap)
- nattgtrms = 0 ! number of atoms for tgtmd rmsd calculation
- nrc = 0
- if(konst.or.dotgtmd) then
-
- ! inserted here to fix the bug that coords are not available
- ! yet when distance based selection (<,>) is requested
-#ifdef LES
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0les,.FALSE.,solvph)
-#else
- call AMOEBA_check_newstyle_inpcrd(inpcrd,newstyle)
- if ( newstyle )then
- call AM_RUNMD_get_coords(natom,t,irest,ntb,x(lcrd),x(lvel))
- else
- if( irest == 1 .and. beeman_integrator > 0 ) then
- write(6,*) 'Cannot do a beeman_integrator restart with old-style coordinates'
- call mexit(6,1)
- end if
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.FALSE.,solvph)
- endif
-#endif
-
- if(itgtmd == 2) then
- call mtmdcall(emtmd,x(lmtmd01),ix(imtmd02),x(lcrd),x(lforce),ih(m04),ih(m02),ix(i02),&
- ih(m06),x(lmass),natom,nres,'READ')
- else
- ! DRR - Open and close calls are now in rdrest
- !if (ntrx <= 0) then
- ! call amopen(10,refc,'O','U','R')
- !else
- ! call amopen(10,refc,'O','F','R')
- !end if
- ! these messages should be written after "5. REFERENCE..." ?
- if (konst) write(6,9408)
- if (dotgtmd) write(6,9409)
-
- call rdrest(natom,ntrx,refc,x(lcrdr))
- !close(10)
-
-
-
-
- ! VH - tgtmd change: preferably call atommask() instead of rgroup()
- if (konst) then
- if( len_trim(restraintmask) <= 0 ) then
- call rgroup(natom,natc,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp),jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- else
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), restraintmask, ix(icnstrgp) )
-
- ! for now, emulate the "GATHER ALL THE CONSTRAINED ATOMS TOGETHER"
- ! section of rgroup(); later, the various masks should be done
- ! differently, i.e. without the "gather", as in the following:
- ! x(l60:l60+natom-1) = restraint_wt
- ! natc = sum(ix(icnstrgp:icnstrgp+natom-1))
-
- natc = 0
- do i=1,natom
- if( ix(icnstrgp-1+i) <= 0 ) cycle
- natc = natc + 1
- ix(icnstrgp-1+natc) = i
- x(l60-1+natc) = restraint_wt
- end do
- write(6,'(a,a,a,i5,a)') ' Mask ', &
- restraintmask(1:len_trim(restraintmask)), ' matches ',natc,' atoms'
- end if
- end if
- nrc = natc
-
- if (itgtmd == 1) then
- if (len_trim(tgtfitmask) <= 0 .and. len_trim(tgtrmsmask) <= 0) then
- ! the following if-endif can be deleted when we stop
- ! supporting rgroup()
- if (konst) then
- ! cannot do both ntr and tgtmd together using old group format
- write(6,'(/2x,a)') 'NTR must be 0 for targeted MD (TGTMD=1)'
- call mexit(6,1)
- else ! the following only for backward compatibility
- call rgroup(natom,natc,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp), &
- jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- ! tgtmd atoms are now stored in nattgt, igroup -> icnstrgp
- nattgtfit = natc
- nattgtrms = natc
- do i=1,nattgtfit
- ix(itgtfitgp-1+i) = ix(icnstrgp-1+i)
- ix(itgtrmsgp-1+i) = ix(icnstrgp-1+i)
- end do
- end if
- else
- if (ntr == 0) then ! read tgtfitmask only if ntr=1
- ! read in atom group for tgtmd fitting (=overlap region)
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtfitmask, ix(itgtfitgp) )
- ! see comments above (for ntr) for the following reduction cycle
- nattgtfit = 0
- do i=1,natom
- if( ix(itgtfitgp-1+i) <= 0 ) cycle
- nattgtfit = nattgtfit + 1
- ix(itgtfitgp-1+nattgtfit) = i
- end do
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtfitmask(1:len_trim(tgtfitmask)-1), &
- '" matches ',nattgtfit,' atoms'
- end if
- ! read in atom group for tgtmd rmsd calculation
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtrmsmask, ix(itgtrmsgp) )
- nattgtrms = 0
- do i=1,natom
- if( ix(itgtrmsgp-1+i) <= 0 ) cycle
- nattgtrms = nattgtrms + 1
- ix(itgtrmsgp-1+nattgtrms) = i
- end do
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtrmsmask(1:len_trim(tgtrmsmask)-1), &
- '" matches ',nattgtrms,' atoms'
- end if
- end if
-
- end if ! (itgtmd == 2)
-
- end if ! (konst.or.dotgtmd)
-
- if (ineb>0) then
- ! carlos: read in fitmask and rmsmask info for NEB, just as done for tgtmd
- ! init last_neb_atom, which is used to determine the limits for the
- ! communication of neighbor coordinates (to reduce size for explicit
- ! water)
- last_neb_atom = 0
-
- if (ntr /= 0) then
- write(6,'(/2x,a)') 'cannot use NEB with ntr restraints'
-! CARLOS: WHY NOT? SHOULD BE OK.
-! potential for user error is restrained region overlaps with NEB region. would
-! blow up.
- call mexit(6,1)
- else
- ! read in atom group for fitting (=overlap region)
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtfitmask, ix(itgtfitgp) )
- ! see comments above (for ntr) for the following reduction cycle
- nattgtfit = 0
- do i=1,natom
- if( ix(itgtfitgp-1+i) <= 0 ) cycle
- nattgtfit = nattgtfit + 1
- ix(itgtfitgp-1+nattgtfit) = i
- if (i.gt.last_neb_atom) last_neb_atom = i
- end do
- write(6,'(a)') "The following selection will be used for NEB structure fitting"
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtfitmask(1:len_trim(tgtfitmask)-1), &
- '" matches ',nattgtfit,' atoms'
- end if
- ! read in atom group for tgtmd rmsd calculation
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtrmsmask, ix(itgtrmsgp) )
- nattgtrms = 0
- do i=1,natom
- if( ix(itgtrmsgp-1+i) <= 0 ) cycle
- nattgtrms = nattgtrms + 1
- ix(itgtrmsgp-1+nattgtrms) = i
- if (i.gt.last_neb_atom) last_neb_atom = i
- end do
- write(6,'(a)') "The following selection will be used for NEB force application"
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtrmsmask(1:len_trim(tgtrmsmask)-1), &
- '" matches ',nattgtrms,' atoms'
- write(6,'(/2x,a,i6)') "Last atom in NEB fitmask or rmsmask is ",last_neb_atom
-
- if (nattgtrms<=0 .or. nattgtfit <= 0) then
- write(6,'(/2x,a)') 'NEB requires use of tgtfitmask and tgtrmsmask'
- call mexit(6,1)
- endif
- endif
-
- ! dotgtmd may be false here even if doing tgtmd
- ! this is so belly info is read properly? following existing KONST code
-
- dotgtmd=.false.
- konst = .false.
- belly = ibelly > 0
- ngrp = 0
- if(belly) then
- ! inserted here to fix the bug that coords are not available
- ! yet when distance based selection (<,>) is requested
-#ifdef LES
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0les,.FALSE.,solvph)
-#else
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.FALSE.,solvph)
-#endif
- write(6,9418)
- if( len_trim(bellymask) <= 0 ) then
- call rgroup(natom,natbel,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(ibellygp), &
- jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- else
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), bellymask, ix(ibellygp) )
- natbel = sum(ix(ibellygp:ibellygp+natom-1))
- write(6,'(a,a,a,i5,a)') ' Mask ', &
- bellymask(1:len_trim(bellymask)), ' matches ',natbel,' atoms'
- end if
- end if
- call setvar(ix,belly)
-
- ! see if the user has input a noshakemask string, and process it:
- natnos = 0
- if( len_trim(noshakemask) > 0 ) then
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), noshakemask, noshakegp )
- natnos = sum(noshakegp(1:natom))
- write(6,*)
- write(6,'(a,a,a,i5,a)') 'Noshake mask ', &
- noshakemask(1:len_trim(noshakemask)), ' matches ',natnos,' atoms'
- call setnoshake(ix,noshakegp,ntc,num_noshake)
- if( ntf > 1 ) then
- write(6,'(a)') ' Setting ntf to 1'
- ntf = 1
- end if
- end if
-
- ! GMS ------------------------------------
- ! Check for 'iwrap_mask', and process it.
- ! ----------------------------------------
- n_iwrap_mask_atoms = 0
- if( len_trim(iwrap_mask) > 0 .and. iwrap == 2) then
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), iwrap_mask, iwrap_maskgp )
- ! iwrap_maskgp is a natom long integer array, with elements:
- ! 0 --> atom is not in iwrap_mask
- ! 1 --> atom is in iwrap_mask
- n_iwrap_mask_atoms = sum(iwrap_maskgp(1:natom))
- write(6,*)
- write(6,'(a,a,a,i5,a)') 'Wrap mask ', &
- iwrap_mask(1:len_trim(iwrap_mask)), ' matches ',n_iwrap_mask_atoms,' atoms:'
- ! Set an array to store the atom numbers of the atoms
- ! in the iwrap_mask
- allocate(iwrap_mask_atoms(n_iwrap_mask_atoms), stat=ier)
- REQUIRE(ier == 0)
-
- j = 0
- do i=1,natom
- if( iwrap_maskgp(i)>0 ) then
- j = j+1
- iwrap_mask_atoms(j) = i
- end if
- end do
-
- write(6,'(10i5)') (iwrap_mask_atoms(i),i=1,n_iwrap_mask_atoms)
- end if
-
-#ifdef MPI /* SOFT CORE */
- ! lower charges if a crgmask is set
- if ( len_trim(crgmask) > 0 ) then
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), crgmask, crggp )
- write(6,'(a,a,a,i5,a)') 'Zero-Charge Mask ',crgmask(1:len_trim(crgmask)), ' matches ',sum(crggp(1:natom)),' atoms'
- call remove_charges(crggp, natom, x(l15))
- end if
-#endif
-
- konst = .false.
- belly = .false.
- if(idecomp > 0) then
- write(6,9428)
- call rgroup(natom,ntmp,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(ibellygp), &
- jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- end if
-
- if( ibelly > 0 .and. (igb > 0 .or. ipb /= 0) ) then
-
- ! ---here, the only allowable belly has just the first
- ! NATBEL atoms in the moving part. Check to see that this
- ! requirement is satisfied:
-
- do i=natbel+1,natom
- if( ix(ibellygp+i-1) /= 0 ) then
- write(6,*) 'When igb>0, the moving part must be at the'
- write(6,*) ' start of the molecule. This does not seem'
- write(6,*) ' to be the case here.'
- write(6,*) 'natbel,i,igroup(i) = ' &
- ,natbel,i,ix(ibellygp+i-1)
- call mexit(6,1)
- end if
- end do
- end if
-
-
- ! ----- CALCULATE THE SQUARE OF THE BOND PARAMETERS FOR SHAKE
- ! THE PARAMETERS ARE PUT SEQUENTIALLY IN THE ARRAY CONP -----
-
- do i=1,nbonh + nbona + nbper
- j = ix(iicbh+i-1)
- x(l50+i-1) = req(j)**2
- end do
-
-#ifdef MPI
- if( icfe /= 0 ) then
-
- ! use the masses of the prmtop file for the first group for both groups:
- ! [only the master nodes communicate here, since non-master nodes
- ! have not yet allocated space]
- ! This leads to problems for dual topology runs, and is therefore skipped
- ! if ifsc is set to one, the masses from both prmtop files are used
- if (ifsc == 0) then
- call mpi_bcast(x(lmass),natom,MPI_DOUBLE_PRECISION,0,commmaster,ierr)
- call mpi_bcast(x(lwinv),natom,MPI_DOUBLE_PRECISION,0,commmaster,ierr)
- call mpi_bcast(x(l75),natom,MPI_DOUBLE_PRECISION,0,commmaster,ierr)
- end if
- tmass = sum(x(lmass:lmass+natom-1))
- tmassinv = 1.d0/tmass
-
- ! next, do a minimal sanity check that the SHAKE parameters are
- ! consistent on the two processors:
-
- ! For Softcore this might be allowed
- ! Put a better check here later
- if( ntc == 2 .and. ifsc == 0) then
- partner = ieor(masterrank,1)
- call mpi_sendrecv( nbonh, 1, MPI_INTEGER, partner, 5, &
- nbonh_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( num_noshake, 1, MPI_INTEGER, partner, 5, &
- num_noshake_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr )
- if (qmmm_nml%ifqnt .and. qmmm_nml%qmshake == 0) then
- ! qtw - if qmshake=0, we need to check the QM atoms
- call mpi_sendrecv( &
- qmmm_struct%nquant, 1, MPI_INTEGER, partner, 5, &
- nquant_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr)
- call mpi_sendrecv( &
- qmmm_struct%noshake_overlap, 1, MPI_INTEGER,partner, 5, &
- noshake_overlap_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr)
- if ( (qmmm_struct%nquant-qmmm_struct%noshake_overlap) /= &
- (nquant_c-noshake_overlap_c) ) then
- call sander_bomb('mdread2', &
- 'QMMM: NOSHAKE lists are not match in two groups!', &
- 'try noshakemask in cntrl to match the noshake list')
- end if
- else if( nbonh - num_noshake /= nbonh_c - num_noshake_c ) then
- write(6,*) 'SHAKE lists are not compatible in the two groups!'
- call mexit(6,1)
- end if
- else if( ntc == 3 ) then
- write(6,*) 'ntc = 3 is not compatible with icfe>0'
- call mexit(6,1)
- end if
-
- end if
-#endif
-
- if ( iamoeba /= 1 )then
- if( igb == 0 .and. ipb == 0 ) &
- call init_extra_pts( &
- ix(iibh),ix(ijbh),ix(iicbh), &
- ix(iiba),ix(ijba),ix(iicba), &
- ix(i24),ix(i26),ix(i28),ix(i30), &
- ix(i32),ix(i34),ix(i36),ix(i38), &
- ix(i40),ix(i42),ix(i44),ix(i46),ix(i48), &
- ix(i50),ix(i52),ix(i54),ix(i56),ix(i58), &
- ih(m06),ix,x,ix(i08),ix(i10), &
- nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req)
- endif
-
- ! DEBUG input; force checking
- call load_debug(5)
-
- return
- ! -------------------------------------------------------------------------
- ! Standard format statements:
-
- 9328 format(/80('-')/,' 2. CONTROL DATA FOR THE RUN',/80('-')/)
- 9408 format(/4x,'LOADING THE CONSTRAINED ATOMS AS GROUPS',/)
- 9409 format(/4x,'LOADING THE TARGETED MD ATOMS AS GROUPS',/)
- 9418 format(/4x,'LOADING THE BELLY ATOMS AS GROUPS',/)
- 9428 format(/4x,'LOADING THE DECOMP ATOMS AS GROUPS',/)
- 9008 format(a80)
-end subroutine mdread2
-
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Emit defined preprocessor names, ie, flags.
-subroutine printflags()
-
- implicit none
- integer max_line_length
- parameter ( max_line_length = 80 )
-
- character(len=max_line_length) line ! output string of active flags
- integer n ! len(line)
-
- line = '| Flags:'
- n = 8
-
-#ifdef ISTAR2
- call printflags2(' ISTAR2',7,n,line,.false.)
-#endif
-#ifdef MPI
- call printflags2(' MPI',4,n,line,.false.)
-# ifdef USE_MPI_IN_PLACE
- call printflags2(' USE_MPI_IN_PLACE',17,n,line,.false.)
-# endif
-#endif
-#ifdef LES
- call printflags2(' LES',4,n,line,.false.)
-#endif
-#ifdef NMODE
- call printflags2(' NMODE',6,n,line,.false.)
-#endif
-#ifdef HAS_10_12
- call printflags2(' HAS_10_12',10,n,line,.false.)
-#endif
-#ifdef DNA_SHIFT
- call printflags2(' DNA_SHIFT',10,n,line,.false.)
-#endif
-#ifdef MMTSB
- call printflags2(' MMTSB',6,n,line,.false.)
-#endif
-
-#ifdef noVIRIAL
- call printflags2(' noVIRIAL',9,n,line,.false.)
-#endif
-
- call printflags2(' ',1,n,line,.true.)
- return
-end subroutine printflags
-
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Primitive pre-Fortran90 implementation of printflags.
-subroutine printflags2(flag,flag_len,line_len,line,last)
-
- implicit none
- integer max_line_length
- parameter ( max_line_length = 80 )
-
- character(*) flag ! flag name with blank prefix, intent(in)
- integer flag_len ! len(flag), intent(in)
- integer line_len ! len(line), intent(inout)
- character(len=max_line_length) line ! intent(inout)
- logical last ! is this the last flag ?, intent(in)
-
- if (line_len + flag_len > max_line_length) then
- write( 6,'(a)') line
- ! begin another line
- line = '| Flags:'
- line_len=8
- end if
- line=line(1:line_len) // flag(1:flag_len)
- line_len=line_len+flag_len
- if(last)write( 6,'(a)') line
- return
-end subroutine printflags2
-
-!-------------------------------------------------
-! --- FLOAT_LEGAL_RANGE ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Check the range of a float; abort on illegal values.
-subroutine float_legal_range(string,param,lo,hi)
- implicit none
- _REAL_ param,lo,hi
- character(len=*)string
-
- if ( param < lo .or. param > hi )then
- write(6,59)
- write(6,60)string,param
- write(6,61)
- write(6,62)lo,hi
- write(6,63)
- call mexit(6,1)
- end if
- 59 format(/,1x,'Ewald PARAMETER RANGE CHECKING: ')
- 60 format(1x,'parameter ',a,' has value ',e12.5)
- 61 format(1x,'This is outside the legal range')
- 62 format(1x,'Lower limit: ',e12.5,' Upper limit: ',e12.5)
- 63 format(1x,'Check ew_legal.h')
- return
-end subroutine float_legal_range
-
-!-------------------------------------------------
-! --- INT_LEGAL_RANGE ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Check the range of an integer; abort on illegal values.
-subroutine int_legal_range(string,param,lo,hi)
- implicit none
- integer param,lo,hi
- character(len=*)string
-
- if ( param < lo .or. param > hi )then
- write(6,59)
- write(6,60)string,param
- write(6,61)
- write(6,62)lo,hi
- write(6,63)
- call mexit(6,1)
- end if
- 59 format(/,1x,'PARAMETER RANGE CHECKING: ')
- 60 format(1x,'parameter ',a,' has value ',i8)
- 61 format(1x,'This is outside the legal range')
- 62 format(1x,'Lower limit: ',i8,' Upper limit: ',i8)
- 63 format(1x,'The limits may be adjustable; search in the .h files ')
- return
-end subroutine int_legal_range
-
-!-------------------------------------------------
-! --- OPT_LEGAL_RANGE ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Check the range of an integer option; abort on illegal values.
-subroutine opt_legal_range(string,param,lo,hi)
- implicit none
- integer param,lo,hi
- character(len=*)string
-
- if ( param < lo .or. param > hi )then
- write(6,59)
- write(6,60)string,param
- write(6,61)
- write(6,62)lo,hi
- write(6,63)
- call mexit(6,1)
- end if
- 59 format(/,1x,'Ewald OPTION CHECKING: ')
- 60 format(1x,'option ',a,' has value ',i5)
- 61 format(1x,'This is outside the legal range')
- 62 format(1x,'Lower limit: ',i5,' Upper limit: ',i5)
- 63 format(1x,'Check the manual')
- return
-end subroutine opt_legal_range
-#endif /*ifndef PBSA*/
-
-!-------------------------------------------------
-! --- SANDER_BOMB ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Print an error message and quit
-subroutine sander_bomb(routine,string1,string2)
- implicit none
- character(len=*) routine,string1,string2
-
- write(6, '(1x,2a)') &
- 'SANDER BOMB in subroutine ', routine
- write(6, '(1x,a)') string1
- write(6, '(1x,a)') string2
- call mexit(6,1)
-end subroutine sander_bomb
-!-------------------------------------------------
-
-!-------------------------------------------------
-! --- remove_charges ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Zero charges on some atoms
-subroutine remove_charges(crggp,natom,charge)
- use constants, only: INV_AMBER_ELECTROSTATIC
- implicit none
- integer natom, crggp(*),i
- _REAL_ charge(*), charge_removed
-
- charge_removed = 0.d0
- do i=1,natom
- if (crggp(i)==1) then
- charge_removed = charge_removed + charge(i) * INV_AMBER_ELECTROSTATIC
- write (6,'(a,f12.4,a,i5)') 'Removing charge of ', charge(i) * INV_AMBER_ELECTROSTATIC,' from atom ',i
- charge(i)=0
- end if
- end do
- write(6, '(a,f12.4,a)') 'Total charge of ',charge_removed,' removed'
- RETURN
-end subroutine remove_charges
-!-------------------------------------------------
diff --git a/patches/amber14.diff/AmberTools/src/sander/mdread.F90.preplumed b/patches/amber14.diff/AmberTools/src/sander/mdread.F90.preplumed
deleted file mode 100644
index d920d10eef47eadf587040da530f1689d3bc930d..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/mdread.F90.preplumed
+++ /dev/null
@@ -1,3847 +0,0 @@
-#include "copyright.h"
-#include "../include/dprec.fh"
-#include "ncsu-config.h"
-#include "../include/assert.fh"
-#ifndef PBSA
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Open input files and read cntrl namelist.
-subroutine mdread1()
-
- use file_io_dat
- use lmod_driver, only : read_lmod_namelist
- use qmmm_module, only : qmmm_nml,qmmm_struct, qm_gb
- use constants, only : RETIRED_INPUT_OPTION, zero, one, two, three, seven, &
- eight, NO_INPUT_VALUE_FLOAT, NO_INPUT_VALUE
- use constantph, only : mccycles
- use amoeba_mdin, only: AMOEBA_read_mdin, iamoeba
- use nose_hoover_module, only: nchain ! APJ
- use lscivr_vars, only: ilscivr, icorf_lsc
- use pimd_vars, only: ipimd,itimass
- use neb_vars, only: ineb
- use cmd_vars, only: restart_cmd, eq_cmd, adiab_param
- use stack, only: lastist,lastrst
- use nmr, only: echoin
- use crg_reloc, only: ifcr, cropt, crcut, crskin, crin, crprintcharges
- use sgld, only : isgld, isgsta,isgend,fixcom, &
- tsgavg,sgft,sgff,sgfd,tempsg,treflf,tsgavp
- use amd_mod, only: iamd,iamdlag,EthreshD,alphaD,EthreshP,alphaP, &
- w_amd,EthreshD_w,alphaD_w,EthreshP_w,alphaP_w
- use scaledMD_mod, only: scaledMD,scaledMD_lambda
- use nbips, only: ips,teips,tvips,teaips,tvaips,raips,mipsx,mipsy,mipsz, &
- mipso,gridips,dvbips
- use emap,only: temap,gammamap
-#ifdef DSSP
- use dssp, only: idssp
-#endif /* DSSP */
-
- use emil_mod, only : emil_do_calc
- use mdin_emil_dat_mod, only : error_hdr
-
-#if !defined(DISABLE_NCSU) && defined(MPI)
- use ncsu_sander_hooks, only : ncsu_on_mdread1 => on_mdread1
-#endif /* ! DISABLE_NCSU && MPI */
-#ifdef _XRAY
- use xray_interface_module, only: xray_active, xray_read_mdin
-#endif /* _XRAY */
-#ifdef MPI /* SOFT CORE */
- use softcore, only : scalpha,scbeta,ifsc,scmask,logdvdl,dvdl_norest,dynlmb, &
- sceeorder, tishake, emil_sc
- use mbar, only : ifmbar, bar_intervall, bar_l_min, bar_l_max, bar_l_incr
- use remd, only : rem
-#endif /* MPI */
- ! Parameter for LIE module
- use linear_response, only: ilrt, lrt_interval, lrtmask
-#ifdef RISMSANDER
- use sander_rism_interface, only: rismprm,xvvfile, guvfile, huvfile, cuvfile,&
- uuvfile, asympfile, quvFile, chgDistFile
-#endif /*RISMSANDER*/
-#ifdef APBS
- use apbs
-#endif /* APBS */
- use sebomd_module, only: read_sebomd_namelist, sebomd_namelist_default
- implicit none
-# include "box.h"
-# include "def_time.h"
-# include "ew_cntrl.h"
-# include "ew_pme_recip.h"
-# include "../include/md.h"
-# include "../include/memory.h"
-# include "mmtsb.h"
-# include "nmr.h"
-# include "tgtmd.h"
-# include "multitmd.h"
-# include "ew_erfc_spline.h"
-#ifdef LES
-# include "les.h"
-#else
- _REAL_ temp0les
-#endif
-
- character(len=4) watdef(4),watnam,owtnm,hwtnm1,hwtnm2
-
- _REAL_ dele
- integer ierr
- integer ifind
- integer imcdo
- integer itotst
- integer jn
- integer inerr
- logical mdin_cntrl, mdin_lmod, mdin_qmmm ! true if namelists are in mdin
- logical mdin_sebomd
- integer :: ifqnt ! local here --> put into qmmm_nml%ifqnt after read here
- integer mxgrp
- integer iemap
- character(len=8) date
- character(len=10) time
- character(len=512) :: char_tmp_512
- _REAL_ dtemp ! retired
- _REAL_ dxm ! retired
- _REAL_ heat ! retired
- _REAL_ timlim ! retired
-
-#ifdef RISMSANDER
- integer irism
-#endif /*RISMSANDER*/
-
- namelist /cntrl/ irest,ibelly, &
- ntx,ntxo,ntcx,ig,tempi, &
- ntb,ntt,nchain,temp0,tautp, &
- ntp,pres0,comp,taup,barostat,mcbarint, &
- nscm,nstlim,t,dt, &
- ntc,ntcc,nconp,tol,ntf,ntn,nsnb, &
- cut,dielc, &
- ntpr,ntwx,ntwv,ntwe,ntwf,ntave,ntpp,ioutfm, &
- ntr,nrc,ntrx,taur,nmropt, &
- ivcap,cutcap,xcap,ycap,zcap,fcap, &
- xlorth,ylorth,zlorth,xorth,yorth,zorth,forth, &
- imin,drms,dele,dx0, &
- pencut,ipnlty,iscale,scalm,noeskp, &
- maxcyc,ncyc,ntmin,vlimit, &
- mxsub,ipol,jfastw,watnam,owtnm,hwtnm1,hwtnm2, iesp, &
- skmin, skmax, vv,vfac, tmode, ips, &
- mipsx,mipsy,mipsz,mipso,gridips,raips,dvbips, &
- iamd,iamdlag,EthreshD,alphaD,EthreshP,alphaP, &
- w_amd,EthreshD_w,alphaD_w,EthreshP_w,alphaP_w, &
- scaledMD,scaledMD_lambda, &
- iemap,gammamap, &
- isgld,isgsta,isgend,fixcom,tsgavg,sgft,sgff,sgfd,tempsg,treflf,tsgavp,&
- jar, iamoeba, &
- numexchg, repcrd, numwatkeep, hybridgb, &
- ntwprt,tausw, &
- ntwr,iyammp,imcdo, &
- igb,alpb,Arad,rgbmax,saltcon,offset,gbsa,vrand, &
- surften,iwrap,nrespa,nrespai,gamma_ln,extdiel,intdiel, &
- cut_inner,icfe,clambda,klambda, rbornstat,lastrst,lastist, &
- itgtmd,tgtrmsd,tgtmdfrc,tgtfitmask,tgtrmsmask, dec_verbose, &
- idecomp,temp0les,restraintmask,restraint_wt,bellymask, &
- noshakemask,crgmask, iwrap_mask,mmtsb_switch,mmtsb_iterations, &
- rdt,icnstph,solvph,ntcnstph,ntrelax, mccycles, &
- ifqnt,ievb, ipimd, itimass, ineb,profile_mpi, ilscivr, icorf_lsc, &
- ipb, inp, &
- gbneckscale, &
- gbalphaH,gbbetaH,gbgammaH, &
- gbalphaC,gbbetaC,gbgammaC, &
- gbalphaN,gbbetaN,gbgammaN, &
- gbalphaOS,gbbetaOS,gbgammaOS, &
- gbalphaP,gbbetaP,gbgammaP, &
- Sh,Sc,Sn,So,Ss,Sp, &
- lj1264, &
- ifcr, cropt, crcut, crskin, crin, crprintcharges, &
- csurften, ninterface, gamma_ten, &
-#ifdef MPI /* SOFT CORE */
- scalpha, scbeta, ifsc, scmask, logdvdl, dvdl_norest, dynlmb, &
- sceeorder, &
- ifmbar, bar_intervall, bar_l_min, bar_l_max, bar_l_incr, tishake, &
- emil_sc, &
-#endif
- ilrt, lrt_interval, lrtmask, &
-#ifdef DSSP
- idssp, &
-#endif
-#ifdef RISMSANDER
- irism,&
-#endif /*RISMSANDER*/
- emil_do_calc, &
- restart_cmd, eq_cmd, adiab_param, &
- vdwmodel, & ! mjhsieh - the model used for van der Waals
- dtemp, heat, timlim !all retired
-
- ! Define default water residue name and the names of water oxygen & hydrogens
-
- data watdef/'WAT ','O ','H1 ','H2 '/
-
- ! ----- READ THE CONTROL DATA AND OPEN DIFFERENT FILES -----
-
- if (mdout /= "stdout" ) &
- call amopen(6,mdout,owrite,'F','W')
- call amopen(5,mdin,'O','F','R')
- write(6,9308)
- call date_and_time( DATE=date, TIME=time )
- write(6,'(12(a))') '| Run on ', date(5:6), '/', date(7:8), '/', &
- date(1:4), ' at ', time(1:2), ':', time(3:4), ':', time(5:6)
-
- ! Write the path of the current executable and working directory
- call get_command_argument(0, char_tmp_512)
- write(6,'(/,a,a)') '| Executable path: ', trim(char_tmp_512)
- call getcwd(char_tmp_512)
- write(6,'(a,a)') '| Working directory: ', trim(char_tmp_512)
-! Write the hostname if we can get it from environment variable
-! Note: get_environment_variable is part of the F2003 standard but seems
-! to be supported by GNU, Intel, IBM and Portland (2010+) compilers
- call get_environment_variable("HOSTNAME", char_tmp_512, inerr)
- if (inerr .eq. 0) then
- write(6,'(a,a,/)') '| Hostname: Unknown'
- else
- write(6,'(a,a,/)') '| Hostname: ', trim(char_tmp_512)
- end if
-
- if (owrite /= 'N') write(6, '(2x,a)') '[-O]verwriting output'
-
- ! Echo the file assignments to the user:
-
- write(6,9700) 'MDIN' ,mdin(1:70) , 'MDOUT' ,mdout(1:70) , &
- 'INPCRD' ,inpcrd(1:70), 'PARM' ,parm(1:70) , &
- 'RESTRT',restrt(1:70) , 'REFC' ,refc(1:70) , &
- 'MDVEL' ,mdvel(1:70) , 'MDFRC' ,mdfrc(1:70) , &
- 'MDEN' ,mden(1:70) , &
- 'MDCRD' ,mdcrd(1:70) , 'MDINFO' ,mdinfo(1:70), &
- 'MTMD' ,mtmd(1:70) , 'INPDIP', inpdip(1:70), &
- 'RSTDIP', rstdip(1:70), 'INPTRAJ', inptraj(1:70)
-# ifdef MPI
- write(6,9702) 'REMLOG', trim(remlog), &
- 'REMTYPE', trim(remtype), &
- 'REMSTRIP', trim(remstripcoord), &
- 'SAVEENE', trim(saveenefile), &
- 'CLUSTERINF', trim(clusterinfofile), &
- 'RESERVOIR', trim(reservoirname), &
- 'REMDDIM', trim(remd_dimension_file)
-# endif
-#ifdef RISMSANDER
- if(len_trim(xvvfile) > 0)&
- write(6,9701) 'Xvv',trim(xvvfile)
- if(len_trim(guvfile) > 0)&
- write(6,9701) 'Guv',trim(Guvfile)
- if(len_trim(huvfile) > 0)&
- write(6,9701) 'Huv',trim(Huvfile)
- if(len_trim(cuvfile) > 0)&
- write(6,9701) 'Cuv',trim(Cuvfile)
- if(len_trim(uuvfile) > 0)&
- write(6,9701) 'Uuv',trim(Uuvfile)
- if(len_trim(asympfile) > 0)&
- write(6,9701) 'Asymptotics',trim(asympfile)
- if(len_trim(quvfile) > 0)&
- write(6,9701) 'Quv',trim(Quvfile)
- if(len_trim(chgDistfile) > 0)&
- write(6,9701) 'ChgDist',trim(chgDistfile)
-#endif /*RISMSANDER*/
-
- ! Echo the input file to the user:
- call echoin(5,6)
- ! ----- READ DATA CHARACTERIZING THE MD-RUN -----
- read(5,'(a80)') title
- ! ----read input in namelist format, first setting up defaults
-
- dtemp = RETIRED_INPUT_OPTION
- dxm = RETIRED_INPUT_OPTION
- heat = RETIRED_INPUT_OPTION
- timlim = RETIRED_INPUT_OPTION
- irest = 0
- ibelly = 0
- ipol = RETIRED_INPUT_OPTION
- iesp = 0
- ntx = 1
- ntxo = NO_INPUT_VALUE
- ig = 71277
- tempi = ZERO
- ntb = NO_INPUT_VALUE
- ntt = 0
- nchain = 1
- temp0 = 300.0d0
-#ifdef LES
- ! alternate temp for LES copies, if negative then use single bath
- ! single bath not the same as 2 baths with same target T
- temp0les = -ONE
- rdt = ZERO
-#endif
- ipimd =0
- itimass = 0 ! Default = no TI w.r.t. mass.
- ineb =0
-
- tautp = ONE
- ntp = 0
- barostat = 1
- mcbarint = 100
- pres0 = ONE
- comp = 44.6d0
- taup = ONE
- npscal = 1
- nscm = 1000
- nstlim = 1
- t = ZERO
- dt = 0.001d0
- ntc = 1
- tol = 0.00001
- ntf = 1
- nsnb = 25
- cut = NO_INPUT_VALUE_FLOAT
- dielc = ONE
- ntpr = 50
- ntwr = 500
- ntwx = 0
- ntwv = 0
- ntwf = 0
- ntwe = 0
- ipb = 0
- inp = 2
-
-#ifdef RISMSANDER
- irism = 0
-#endif /*RISMSANDER*/
-
- ntave = 0
- ioutfm = 0
- ntr = 0
- ntrx = 1
- ivcap = 0
- natcap = 0
- fcap = 1.5d0
- cutcap = 0.0d0
- xcap = 0.0d0
- ycap = 0.0d0
- zcap = 0.0d0
- forth = 1.5d0
- xlorth = -1.0d0
- ylorth = -1.0d0
- zlorth = -1.0d0
- xorth = 47114711.0d0
- yorth = 47114711.0d0
- zorth = 47114711.0d0
- numexchg = 0
- repcrd = 1
- lj1264 = 0
-
- profile_mpi = 0 !whether to write profile_mpi timing file - default = 0 (NO).
-
- ! number of waters to keep for hybrid model,
- ! numwatkeep: the number of closest
- ! waters to keep. close is defined as close to non-water.
- ! for simulations with ions, ions should be stripped too
- ! or at least ignored in the "closest" calculation. this
- ! is not currently done.
-
- ! if it stays at -1 then we keep all waters
- ! 0 would mean to strip them all
-
- numwatkeep=-1
-
- ! hybridgb: gb model to use with hybrid REMD.
- hybridgb=0
-
- ! carlos targeted MD, like ntr
-
- itgtmd=0
- tgtrmsd=0.
- tgtmdfrc=0.
- tgtfitmask=''
- tgtrmsmask=''
-
- pencut = 0.1d0
- taumet = 0.0001d0
- omega = 500.0d0
- ipnlty = 1
- scalm = 100.0d0
- iscale = 0
- noeskp = 1
- nmropt = 0
- jar = 0
- tausw = 0.1d0
- imin = 0
- isftrp = 0
- rwell = ONE
- maxcyc = 1
- ncyc = 10
- ntmin = 1
- dx0 = 0.01d0
- drms = 1.0d-4
- vlimit = 20.0d0
- mxsub = 1
- jfastw = 0
- watnam = ' '
- owtnm = ' '
- hwtnm1 = ' '
- hwtnm2 = ' '
- ntwprt = 0
- igb = 0
- alpb = 0
- Arad = 15.0d0
- rgbmax = 25.d0
- saltcon = ZERO
-
- ! default offset depends on igb value, and users need to
- ! be able to modify it, so we need to set a dummy value. if it's still the
- ! dummy after we read the namelist, we set the default based on igb. if not,
- ! we leave it at what the user set.
- ! best solution would be to create a GB namelist.
- offset = -999999.d0
- gbneckscale = -999999.d0
-
- iyammp = 0
- imcdo = -1
- gbsa = 0
- vrand=1000
- surften = 0.005d0
- iwrap = 0
- nrespa = 1
- nrespai = 1
- irespa = 1
- gamma_ln = ZERO
- extdiel = 78.5d0
- intdiel = ONE
- gbgamma = ZERO
- gbbeta = ZERO
- gbalpha = ONE
-
- !Hai Nguyen: set default parameters for igb = 8
- ! NOTE THAT NONE OF THESE ARE USED UNLESS IGB=8, SO USERS SHOULD NOT EVEN SET
- ! THEM
- gbalphaH = 0.788440d0
- gbbetaH = 0.798699d0
- gbgammaH = 0.437334d0
- gbalphaC = 0.733756d0
- gbbetaC = 0.506378d0
- gbgammaC = 0.205844d0
- gbalphaN = 0.503364d0
- gbbetaN = 0.316828d0
- gbgammaN = 0.192915d0
- gbalphaOS = 0.867814d0
- gbbetaOS = 0.876635d0
- gbgammaOS = 0.387882d0
- gbalphaP = 1.0d0 !P parameters are not optimized yet
- gbbetaP = 0.8d0 !P parameters are not optimized yet
- gbgammaP = 4.85d0 !P parameters are not optimized yet
- !scaling parameters below will only be used for igb=8.
- ! the actual code does not use these variables, it uses X(l96)
- ! if igb=8, we will use these to set the X(l96) array.
- Sh = 1.425952d0
- Sc = 1.058554d0
- Sn = 0.733599d0
- So = 1.061039d0
- Ss = -0.703469d0
- Sp = 0.5d0 !P parameters are not optimized yet
- !End Hai Nguyen
-
- iconstreff = 0
- cut_inner = EIGHT
- icfe = 0
- clambda = ZERO
- klambda = 1
- ievb = 0
- rbornstat = 0
- idecomp = 0
- ! added a flag to control output of BDC/SDC synonymous with MMPBSA.py's
- ! version of the same variable.
- dec_verbose = 3
- lastrst = 1
- lastist = 1
- restraintmask=''
- restraint_wt = ZERO
- bellymask=''
- noshakemask=''
- iwrap_mask='' ! GMS: mask to wrap around if iwrap == 2
- crgmask=''
- mmtsb_switch = mmtsb_off ! MMTSB Replica Exchange Off by Default
- mmtsb_iterations = 100 ! MMTSB Replica Exchange Frequency in Iterations
-
- icnstph = 0
- solvph = SEVEN
- ntcnstph = 10
- ntrelax = 500 ! how long to let waters relax
- mccycles = 1 ! How many cycles of Monte Carlo steps to run
- skmin = 50 !used by neb calculation
- skmax = 100 !used by neb calculation
- vv = 0 !velocity verlet -- off if vv/=1
- vfac = 0 !velocity verlet scaling factor, 0 by default
- tmode = 1 !default tangent mode for NEB calculation
-
- ifqnt = NO_INPUT_VALUE
-
- ifcr = 0 ! no charge relocation
- cropt = 0 ! 1-4 EEL is calculated with the original charges
- crcut = 3.0
- crskin = 2.0
- crin = ''
- crprintcharges = 0
-
- ips = 0 ! no isotropic periodic sum
- raips=-1.0d0 ! automatically determined
- mipsx=-1 ! number of grids in x direction, <0 for automatically determined
- mipsy=-1 ! number of grids in y direction, <0 for automatically determined
- mipsz=-1 ! number of grids in z direction, <0 for automatically determined
- mipso=4 ! default 4th order b-spline
- gridips=2 ! grid size. used to determine grid number if not defined
- dvbips=1.0d-8 ! Volume change tolerance. aips will be done when change more than dvbips
-
- iamd = 0 ! No accelerated MD used
- iamdlag = 0 !frequency of boosting in steps
- EthreshD = 0.d0
- alphaD = 0.d0
- EthreshP = 0.d0
- alphaP = 0.d0
- w_amd = 0 ! windowed amd
- EthreshD_w = 0.d0
- alphaD_w = 0.d0
- EthreshP_w = 0.d0
- alphaP_w = 0.d0
-
- scaledMD = 0 ! No scaled MD used
- scaledMD_lambda = 0.d0
-
- iemap=0 ! no emap constraint
- gammamap=1 ! default friction constant for map motion, 1/ps
- isgld = 0 ! no self-guiding
- isgsta=1 ! Begining index of SGLD range
- isgend=0 ! Ending index of SGLD range
- fixcom=-1 ! fix center of mass in SGLD simulation
- tsgavg=0.2d0 ! Local averaging time of SGLD simulation
- sgft=-1.0d3 ! Guiding factor of SGLD simulation
- sgff=-1.0d3 ! Guiding factor of SGLD simulation
- sgfd=-1.0d3 ! Guiding factor of SGLD simulation
- tempsg=0.0d0 ! Guiding temperature of SGLD simulation
- treflf=0.0d0 ! Reference low frequency temperature of SGLD simulation
- tsgavp=2.0d0 ! Convergency time of SGLD simulation
-
- ! Check to see if "cntrl" namelist has been defined.
- mdin_cntrl=.false.
- mdin_qmmm = .false.
- mdin_ewald=.false.
- mdin_pb=.false.
-#ifdef APBS
- mdin_apbs = .false.
-#endif /* APBS */
- mdin_lmod=.false.
- mdin_amoeba=.false.
- mdin_sebomd=.false.
- iamoeba = 0
-#ifdef MPI /* SOFT CORE */
- scalpha=0.5
- scbeta=12.0
- sceeorder=2
- ifsc=0
- logdvdl=0
- dvdl_norest=0
- dynlmb=0.0
- ifmbar=0
- bar_intervall=100
- bar_l_min=0.1
- bar_l_max=0.9
- bar_l_incr=0.1
- tishake = 0
- emil_sc = 0
-#endif
- ilrt = 0
- lrt_interval = 50
- lrtmask=''
-#ifdef DSSP
- idssp = 0
-#endif
- emil_do_calc = 0
-
-! Constant Surface Tension
- csurften = 0 !constant surface tension off (valid options are 0,1,2,3)
- gamma_ten = 0.0d0 !0.0 dyne/cm - default used in charmm. Ignored for csurften=0
- ninterface = 2 !Number of interfaces in the surface tension (Must be greater than 2)
-
- call nmlsrc('cntrl',5,ifind)
- if (ifind /= 0) mdin_cntrl=.true.
-
- call nmlsrc('ewald',5,ifind)
- if (ifind /= 0) mdin_ewald=.true.
-
- call nmlsrc('pb',5,ifind)
- if (ifind /= 0) mdin_pb=.true.
-
- call nmlsrc('qmmm', 5, ifind)
- if (ifind /= 0) mdin_qmmm = .true.
-
-#ifdef APBS
- call nmlsrc('apbs',5,ifind)
- if (ifind /= 0) mdin_apbs=.true.
-#endif /* APBS */
-
- call nmlsrc('lmod',5,ifind)
- if (ifind /= 0) mdin_lmod=.true.
-
- call nmlsrc('amoeba',5,ifind)
- if (ifind /= 0) mdin_amoeba=.true.
-
- call nmlsrc('sebomd',5,ifind)
- if (ifind /= 0) mdin_sebomd=.true.
-
-#ifdef _XRAY
- call nmlsrc('xray',5,ifind)
- xray_active = (ifind /= 0)
-#endif
-
- rewind 5
- if ( mdin_cntrl ) then
- read(5,nml=cntrl,err=999)
- else
- write(6, '(1x,a,/)') 'Could not find cntrl namelist'
- call mexit(6,1)
- end if
-
- if ( igb == 10 .and. ipb == 0 ) ipb = 2
- if ( igb == 0 .and. ipb /= 0 ) igb = 10
-
- if (ifqnt == NO_INPUT_VALUE) then
- ifqnt = 0 ! default value
- if (mdin_qmmm) then
- write(6, '(1x,a,/)') &
- '| WARNING qmmm namelist found, but ifqnt was not set! QMMM NOT &
- &active.'
- end if
- end if
-
- ! Now that we've read the input file, set up the defaults for variables
- ! whose values depend on other input values (ntb, cut)
- if (ntb == NO_INPUT_VALUE) then
- if (ntp > 0) then
- ntb = 2
- else if (igb > 0) then
- ntb = 0
- else
- ntb = 1
- end if
- end if
-
- if (ntxo == NO_INPUT_VALUE) then
-#ifdef MPI
- if (rem < 0) then
- ntxo = 2
- else
- ntxo = 1
- end if
-#else
- ntxo = 1
-#endif
- end if
-
- if (cut == NO_INPUT_VALUE_FLOAT) then
- if (igb == 0) then
- cut = EIGHT
- else
- cut = 9999.d0
- end if
- end if
-
-#ifdef RISMSANDER
- !force igb=6 to get vacuum electrostatics. This must be done ASAP to ensure SANDER's
- !electrostatics are initialized properly
- rismprm%irism=irism
- if(irism/=0) then
- write(6,'(a)') "|3D-RISM Forcing igb=6"
- igb=6
- end if
-#endif /*RISMSANDER*/
-
-
- if (ifqnt>0) then
- qmmm_nml%ifqnt = .true.
- if (saltcon /= 0.0d0) then
- qm_gb%saltcon_on = .true.
- else
- qm_gb%saltcon_on = .false.
- end if
- if (alpb == 1) then
- qm_gb%alpb_on = .true.
- else
- qm_gb%alpb_on = .false.
- end if
- if (igb == 10 .or. ipb /= 0) then
- write(6, '(1x,a,/)') 'QMMM is not compatible with Poisson Boltzmann (igb=10 or ipb/=0).'
- call mexit(6,1)
- end if
- else
- qmmm_nml%ifqnt = .false.
- end if
-
- if ( mdin_lmod ) then
- rewind 5
- call read_lmod_namelist()
- end if
-
- !--------------------------------------------------------------------
- ! --- vars have been read ---
- !--------------------------------------------------------------------
-
- write(6,9309)
-
- ! emit warnings for retired cntrl namelist variables
-
- if ( dtemp /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: dtemp has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- end if
- if ( dxm /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: dxm has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- ! ' The step length will be unlimited.'
- end if
- if ( heat /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: heat has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- end if
-
- if ( timlim /= RETIRED_INPUT_OPTION ) then
- write(6,'(/,a,/,a,/,a)') 'Warning: timlim has been retired.', &
- ' Check the Retired Namelist Variables Appendix in the manual.'
- end if
-
-! Constant surface tension valid options
- if (csurften > 0) then
- if (csurften < 0 .or. csurften > 3) then
- write(6,'(/2x,a)') &
- 'Invalid csurften value. csurften must be between 0 and 3'
- call mexit(6,1)
- end if
- if (ntb /= 2) then
- write(6,'(/2x,a)') &
- 'ntb invalid. ntb must be 2 for constant surface tension.'
- call mexit(6,1)
- end if
- if (ntp < 2) then
- write(6,'(/2x,a)') &
- 'ntp invalid. ntp must be 2 or 3 for constant surface tension.'
- call mexit(6,1)
- end if
- if (ninterface < 2) then
- write(6,'(/2x,a)') &
- 'ninterface must be greater than 2 for constant surface tension.'
- call mexit(6,1)
- end if
-
- if (iamoeba > 0 ) then
- write(6,'(/2x,a)') &
- 'Constant Surface Tension is not compatible with Amoeba Runs.'
- call mexit(6,1)
- end if
-
- if (ipimd > 0 ) then
- write(6,'(/2x,a)') &
- 'Constant Surface Tension is not compatible with PIMD Runs.'
- call mexit(6,1)
- end if
-
- end if
-
-! MC Barostat valid options. Some of these may work, but disable them until they
-! are fully tested.
-
- if (ntp > 0 .and. barostat == 2) then
- inerr = 0
- if (ievb /= 0) then
- write(6, '(/2x,a)') 'AMOEBA is not compatible with the MC Barostat'
- inerr = 1
- end if
- if (ipimd /= 0) then
- write(6, '(/2x,a)') 'PIMD is not compatible with the MC Barostat'
- inerr = 1
- end if
- if (icfe /= 0) then
- write(6, '(/2x,a)') 'TI is not compatible with the MC Barostat'
- inerr = 1
- end if
-#ifdef LES
- write(6, '(/2x,a)') 'LES is not compatible with the MC Barostat'
- inerr = 1
-#endif
- ! Any others? Hopefully most or all of the above can be made compatible.
- if (inerr == 1) &
- call mexit(6, 1)
- end if
-
- call printflags()
-
- !--------------------------------------------------------------------
- ! If user has requested ewald electrostatics, read some more input
- !--------------------------------------------------------------------
-
- if( igb == 0 .and. ipb == 0 ) call load_ewald_info(parm,inpcrd,ntp)
-
- !--------------------------------------------------------------------
- ! parameters for IPS and for SGLD:
- ! ips=1 3D IPS for electrostatic and Lennard-Jones potentials
- ! ips=2 3D IPS for electrostatic potential only
- ! ips=3 3D IPS for Lennard-Jones potential only
- ! ips=4 3D IPS/DFFT for electrostatic and Lennard-Jones potentials
- ! ips=5 3D IPS/DFFT for electrostatic potential only
- ! ips=6 3D IPS/DFFT for Lennard-Jones potential only
- !--------------------------------------------------------------------
-
- teips=.false.
- tvips=.false.
- teaips=.false.
- tvaips=.false.
- if((ips-4)*(ips-6) == 0 )tvaips =.true.
- if ( (ips-4)*(ips-5) == 0 )teaips =.true.
- if( tvaips.OR.( (ips -1)*(ips-3) == 0 ))tvips =.true.
- if( teaips.OR.((ips -1)*(ips-2) == 0 ))teips =.true.
- if( teips ) then
- use_pme = 0
- eedmeth = 6
- end if
- if( tvips ) then
- vdwmeth = 2
- if(use_pme/=0.and.tvaips)then
- mipsx=nfft1 ! number of grids in x direction, <0 for automatically determined
- mipsy=nfft2 ! number of grids in y direction, <0 for automatically determined
- mipsz=nfft3 ! number of grids in z direction, <0 for automatically determined
- mipso=order ! default 6th order b-spline
- endif
- end if
- temap=iemap>0
- ishake = 0
- if (ntc > 1) ishake = 1
-
- !--------------------------------------------------------------------
- ! Set up some parameters for AMD simulations:
- ! AMD initialization
- ! iamd=0 no boost is used, 1 boost on the total energy,
- ! 2 boost on the dohedrals, 3 boost on dihedrals and total energy
- !--------------------------------------------------------------------
- if(iamd.gt.0)then
- if(iamd.eq.1)then !only total potential energy will be boosted
- EthreshD=0.d0
- alphaD=0.d0
- else if(iamd.eq.2)then !only dihedral energy will be boosted
- EthreshP=0.d0
- alphaP=0.d0
- endif
- if(w_amd.gt.0)then
- if(iamd.eq.1)then !only total potential energy will be boosted
- EthreshD_w=0.d0
- alphaD_w=0.d0
- else if(iamd.eq.2)then !only dihedral energy will be boosted
- EthreshP_w=0.d0
- alphaP_w=0.d0
- endif
- write(6,'(a,i3)')'| Using Windowed Accelerated MD (wAMD) &
- &LOWERING BARRIERS to enhance sampling w_amd =', w_amd
- write(6,'(a,2f22.12)')'| AMD boost to total energy: EthreshP,alphaP',&
- EthreshP, alphaP
- write(6,'(a,2f22.12)')'| AMD boost to dihedrals: EthreshD,alphaD',&
- EthreshD,alphaD
- write(6,'(a,2f22.12)')'| AMD extra parameters boost to total energy: &
- &EthreshP_w,alphaP_w', EthreshP_w, alphaP_w
- write(6,'(a,2f22.12)')'| AMD extra parameters boost to dihedrals: &
- &EthreshD_w,alphaD_w', EthreshD_w, alphaD_w
- else
- write(6,'(a,i3)')'| Using Accelerated MD (AMD) RASING VALLEYS to &
- &enhance sampling iamd =',iamd
- write(6,'(a,2f22.12)')'| AMD boost to total energy: EthreshP,alphaP', &
- EthreshP, alphaP
- write(6,'(a,2f22.12)')'| AMD boost to dihedrals: EthreshD,alphaD', &
- EthreshD, alphaD
- endif
- endif
-
-
- !--------------------------------------------------------------------
- ! Set up some parameters for scaledMD simulations:
- ! scaledMD initialization
- ! scaledMD=0 no scaling is used, 1 scale the potential energy
- !--------------------------------------------------------------------
- if(scaledMD.gt.0)then
- write(6,'(a,i3)')'| Using Scaled MD to enhance sampling scaledMD =',&
- scaledMD
- write(6,'(a,f22.12)')'| scaledMD scaling factor lambda: ',scaledMD_lambda
- endif
-
-
-
-
- !--------------------------------------------------------------------
- ! Set up some parameters for GB simulations:
- !--------------------------------------------------------------------
- !Hai Nguyen: update offset = 0.09d0 for igb /= 8
- !I add this step because I want to use different offset value as default value
- !for igb = 8
-
- if ( igb == 8 ) then
- if (offset == -999999.d0) then
- offset = 0.195141d0 !set to default for igb=8
- end if
- if (gbneckscale == -999999.d0) then
- gbneckscale = 0.826836d0
- end if
- else
- ! not igb=8, use old defaults
- if (offset == -999999.d0) then
- offset = 0.09d0
- end if
- if (gbneckscale == -999999.d0) then
- gbneckscale = 0.361825d0
- end if
- endif
-
- if( igb == 2 .or. hybridgb == 2 ) then
- ! --- use our best guesses for Onufriev/Case GB (GB^OBC I)
-
- gbgamma = 2.90912499999d0 ! (the "99999" to force roundoff on print)
- gbbeta = ZERO
- gbalpha = 0.8d0
- end if
-
- if( igb == 5 .or. hybridgb == 5 ) then
-
- ! --- use our second best guesses for Onufriev/Case GB (GB^OBC II)
-
- gbgamma = 4.850d0
- gbbeta = 0.8d0
- gbalpha = ONE
- end if
-
- if( igb == 7 ) then
-
- ! --- use parameters for Mongan et al. CFA GBNECK
-
- gbgamma = 2.50798245d0
- gbbeta = 1.90792938d0
- gbalpha = 1.09511284d0
- end if
-
- !--------------------------------------------------------------------
- ! If user has requested PB electrostatics, read some more input
- !--------------------------------------------------------------------
-
- if ( igb == 10 .or. ipb /= 0 ) then
-#ifdef MPI
- write(6,'(a)') "PBSA currently doesn't work with MPI inside SANDER."
- call mexit(6,1)
-#endif /*MPI*/
- call pb_read
- end if
-
-#ifdef APBS
- if ( mdin_apbs ) then
- call apbs_read
- end if
-#endif /* APBS */
-
-#ifdef _XRAY
- call xray_read_mdin(mdin_lun=5)
-#endif
-
- call sebomd_namelist_default
- if (mdin_sebomd) then
- rewind 5
- call read_sebomd_namelist
- endif
-
- if( iamoeba == 1 ) then
- if( mdin_amoeba ) then
- call AMOEBA_read_mdin(5)
- else
- write(6,*) ' iamoeba is set but the &amoeba namelist was not found'
- call mexit(6,1)
- end if
- end if
-
- ! -------------------------------------------------------------------
- ! If the user has requested NMR restraints, do a cursory read of the
- ! restraints file(s) now to determine the amount of memory necessary
- ! for these restraints:
- ! -------------------------------------------------------------------
-
- if (jar == 1 ) nmropt = 1
- intreq = 0
- irlreq = 0
- if (nmropt > 0) then
- mxgrp = 0
- itotst = 1
-
- ! Set ITOTST to 0 if IMIN equals 1 (i.e. if minimization, not dynamics)
- ! This will cause any "time-averaged" requests to be over-ridden.
-
- if (imin == 1) then
- itotst = 0
- end if
- ! CALL AMOPEN(31,NMR,'O','F','R')
- call restlx(5,itotst,mxgrp,dt,6,ierr)
- ! CLOSE(31)
- end if
-
- ! -------------------------------------------------------------------
- ! If EMIL was requested, make sure it was compiled in, and validate.
- ! -------------------------------------------------------------------
- if( emil_do_calc .gt. 0 ) then
-#ifdef EMIL
- if( ntc .ne. 1 ) then
- write (6, '(a,a)') error_hdr, 'emil_do_calc == 1,'
- write (6, '(a)') ' and ntc != 1.'
- write (6, '(a)') ' Current thinking is that SHAKE and '
- write (6, '(a)') ' EMIL do not mix well, consider setting ntc = 1, ntf = 1,'
- write (6, '(a)') ' and dt = 0.001.'
- call mexit(6,1)
- end if
-#else
- write (6, '(a,a)') error_hdr, 'emil_do_calc = 1,'
- write (6, '(a)') ' but AMBER was compiled with EMIL switched out.'
- write (6, '(a)') ' Run $AMBERHOME/configure --help for more info.'
- call mexit(6,1)
-#endif
- end if
-
-
- ! Set the definition of the water molecule. The default definition is in
- ! WATDEF(4).
-
- read(watdef(1),'(A4)') iwtnm
- read(watdef(2),'(A4)') iowtnm
- read(watdef(3),'(A4)') ihwtnm(1)
- read(watdef(4),'(A4)') ihwtnm(2)
- if (watnam /= ' ') read(watnam,'(A4)') iwtnm
- if (owtnm /= ' ') read(owtnm, '(A4)') iowtnm
- if (hwtnm1 /= ' ') read(hwtnm1,'(A4)') ihwtnm(1)
- if (hwtnm2 /= ' ') read(hwtnm2,'(A4)') ihwtnm(2)
-
-#if !defined(DISABLE_NCSU) && defined(MPI)
- call ncsu_on_mdread1()
-#endif
-
- return
- 999 continue ! bad cntrl read
- write(6,*) 'error in reading namelist cntrl'
- call mexit(6,1)
-
- ! --- input file polar opts read err trapping:
-
- 9308 format(/10x,55('-'),/10x, &
- 'Amber 14 SANDER 2014', &
- /10x,55('-')/)
- 9309 format(/80('-')/' 1. RESOURCE USE: ',/80('-')/)
- 9700 format(/,'File Assignments:',/,15('|',a6,': ',a,/))
- 9701 format('|',a6,': ',a)
- 9702 format(7('|',a10,': ',a,/))
-end subroutine mdread1
-#endif /*ifndef PBSA*/
-
-#ifndef PBSA
-!======================================================================
-! MDREAD2
-!======================================================================
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Initialize to defaults and print the inputable variables.
-subroutine mdread2(x,ix,ih,ipairs)
-
- use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms
- use lmod_driver, only : LMOD_NTMIN_LMOD, LMOD_NTMIN_XMIN, write_lmod_namelist
- use decomp, only : jgroup, indx, irespw
- use findmask
- use qmmm_module, only : qmmm_nml,qmmm_struct, qm2_struct, qm2_rij_eqns, qm_gb, qmmm_vsolv
- use qmmm_vsolv_module, only : print
- use constants, only : ZERO, ONE, TWO
- use parms, only: req
- use nbips, only: ips
- use amd_mod, only: iamd,iamdlag,EthreshD,alphaD,EthreshP,alphaP, &
- w_amd,EthreshD_w,alphaD_w,EthreshP_w,alphaP_w
- use scaledMD_mod, only: scaledMD
- use nblist, only: a,b,c,alpha,beta,gamma,nbflag,skinnb,sphere,nbtell,cutoffnb
- use amoeba_mdin, only : iamoeba,beeman_integrator
- use amoeba_runmd, only : AM_RUNMD_get_coords
- use nose_hoover_module, only: nchain ! APJ
- use pimd_vars, only: ipimd, itimass
- use neb_vars, only: last_neb_atom, ineb
- use cmd_vars, only: restart_cmd, eq_cmd, adiab_param
- use constantph, only: cnstphread, cnstph_zero, cph_igb, mccycles
- use file_io_dat
- use sander_lib, only: upper
-
- use emap,only: temap,emap_options
-
- use qmmm_module, only: get_atomic_number
-
- use sebomd_module, only: sebomd_obj, sebomd_write_info, sebomd_write_options
-
-#ifdef APBS
- use apbs
-#endif /* APBS */
-#ifdef EMIL
- use emil_mod, only : emil_do_calc
- use mdin_emil_dat_mod, only : error_hdr, init_emil_dat
-#endif /* EMIL */
-#ifdef _XRAY
- use xray_interface_module, only: xray_write_options
-#endif /* _XRAY */
-#if defined(LES) && defined(MPI)
- use evb_pimd, only: evb_pimd_init
-#endif /* LES && MPI */
-#ifdef MPI /* SOFT CORE */
- use softcore, only : ifsc, scmask, scalpha, scbeta, dvdl_norest, &
- sceeorder, logdvdl, dynlmb, tishake
- use mbar, only : ifmbar, bar_intervall, bar_l_min, bar_l_max, bar_l_incr
-! REMD
- use remd, only : rem, rremd
-#endif
- use crg_reloc, only: ifcr, cropt, crcut, crskin, crprintcharges
- use linear_response, only: ilrt, lrt_interval, lrtmask
-! SGLD
- use sgld, only : isgld
-
- implicit none
- _REAL_ x(*)
-# include "../include/memory.h"
- integer ix(lasti),ipairs(*)
- character(len=4) ih(*)
- integer nbond
- integer atom1,atom2
- integer ntmp
- logical belly,konst
- character(len=1) atsymb,atsymb2
- character(len=2) atype
- integer atomicnumber, hybridization
- integer ngrp,inerr,nr,iaci,ir,i,mxresat,j
- integer noshakegp( natom ), natnos
- integer iwrap_maskgp( natom ) , ier
- logical errFlag
- integer crggp( natom )
- _REAL_ dummy,rvdw,dcharge,emtmd
- logical newstyle
-
-#ifdef MPI
- ! =========================== AMBER/MPI ===========================
-#ifdef MPI_DOUBLE_PRECISION
-# undef MPI_DOUBLE_PRECISION
-#endif
- include 'mpif.h'
-# include "parallel.h"
- integer ist(MPI_STATUS_SIZE), partner, ierr, nbonh_c, num_noshake_c
- integer nquant_c, noshake_overlap_c
-#ifdef CRAY_PVP
-# define MPI_DOUBLE_PRECISION MPI_REAL8
-#endif
- ! ========================= END AMBER/MPI =========================
-#endif
-# include "../include/md.h"
-# include "box.h"
-# include "mmtsb.h"
-# include "nmr.h"
-# include "extra_pts.h"
-# include "ew_cntrl.h"
-# include "ew_pme_recip.h"
-# include "ew_erfc_spline.h"
-# include "ew_mpole.h"
-# include "ew_legal.h"
-# include "def_time.h"
-# include "tgtmd.h"
-# include "multitmd.h"
-#ifdef LES
-# include "les.h"
-#endif
-
- ! -------------------------------------------------------------------
- ! --- set up resat array, containing string identifying
- ! residue for each atom
- ! -------------------------------------------------------------------
-
- mxresat = min( natom, matom )
- ir = 0
- do i=1,mxresat
- if (i >= ix(ir+i02)) ir=ir+1
- write(resat(i),'(a4,1x,a4,i4)') ih(m04+i-1), &
- ih(ir+m02-1),ir
- ! ---null terminator:
- resat(i)(14:14) = char(0)
- end do
- close(unit=8)
-
- ! -------------------------------------------------------------------
- ! ----- SET THE DEFAULT VALUES FOR SOME VARIABLES -----
- ! -------------------------------------------------------------------
-
- nrp = natom
-
- if (ifbox == 1) write(6, '(/5x,''BOX TYPE: RECTILINEAR'')')
- if (ifbox == 2) write(6, '(/5x,''BOX TYPE: TRUNCATED OCTAHEDRON'')')
- if (ifbox == 3) write(6, '(/5x,''BOX TYPE: GENERAL'')')
-
- ! For 0< ipimd <= 3, no removal of COM motion
- if (ipimd>0.and.ipimd<=3) then
- nscm = 0
- ndfmin = 0
- endif
-
- if (ntr.eq.1) &
- nscm = 0
-
- nsolut = nrp
- if ( nscm > 0 .and. ntb == 0 ) then
- ndfmin = 6 ! both translation and rotation com motion removed
- if (nsolut == 1) ndfmin = 3
- if (nsolut == 2) ndfmin = 5
- else if ( nscm > 0 ) then
- ndfmin = 3 ! just translation com will be removed
- else
- ndfmin = 0
- end if
- if (ibelly > 0) then ! No COM Motion Removal, ever.
- nscm = 0
- ndfmin = 0
-
- !Do not allow ntt=3 with ibelly=1 - this does not make sense and will cause
- !issues.
- if (ntt==3) then
- call sander_bomb("mdread2","ibelly=1 with ntt=3 is not a valid option.", &
- "Either use a different thermostat or avoid using ibelly.")
- end if
- end if
- if(nscm <= 0) nscm = 0
- if(gamma_ln > 0.0d0)ndfmin=0 ! No COM motion removal for LD simulation
- if(ntt == 4)ndfmin=0 ! No COM motion removal for Nose'-Hoover simulation
- init = 3
- if (irest > 0) init = 4
- if (dielc <= ZERO ) dielc = ONE
- if (tautp <= ZERO ) tautp = 0.2d0
- if (taup <= ZERO ) taup = 0.2d0
-
- ! ----- RESET THE CAP IF NEEDED -----
-
- ! ivcap == 0: Cap will be in effect if it is in the prmtop file (ifcap = 1)
-
- if(ivcap == 1) then
- ! Cap will be in effect even if not in prmtop file
- ! requires additional information in sander.in file as in the case of ivcap == 3, 4, or 5
- ifcap = 2
- else if(ivcap == 2) then
- ! Inactivate cap
- ifcap = 0
- else if(ivcap == 3) then
- ! Sphere -> not yet implemented
- ifcap = 3
- else if(ivcap == 4) then
- ! Orthorhombus
- ifcap = 4
- else if(ivcap == 5) then
- ! Shell of waters around solute
- ifcap = 5
- end if
-
- !Support for random seed using time of day in microsecs
- if( ig==-1 ) then
- !Turn on NO_NTT3_SYNC when ig=-1. This means the code no
- !longer synchronized the random numbers between streams when
- !running in parallel giving better scaling.
- no_ntt3_sync = 1
- call microsec(ig)
-#ifdef MPI
- write (6, '(a,i8,a)') "Note: ig = -1. Setting random seed to ", ig ," based on wallclock &
- &time in microseconds"
- write (6, '(a)') " and disabling the synchronization of random &
- &numbers between tasks"
- write (6, '(a)') " to improve performance."
-#else
- write (6, '(a,i8,a)') "Note: ig = -1. Setting random seed to ", ig ," based on wallclock &
- &time in microseconds."
-#endif
- end if
-
-#ifdef MPI
- !For some runs using multisander where the coordinates of the two 'replicas' need to be identical,
- !for example TI, it is critical that the random number stream is synchronized between all replicas.
- !Only use the IG value from worldrank=0. Ok to broadcast between the various sander masters since
- !they all call mdread2.
- !Also needs to be synchronized for adaptive QM/MM (qmmm_nml%vsolv > 1)
- if ( (icfe > 0) .or. (qmmm_nml%vsolv > 1) ) then
- ! no_ntt3_sync currently does not work with softcore TI simulations
- ! see sc_lngdyn in softcore.F90
- ! AWG: I think I also need to set no_ntt3_sync=0 ???
- if ( (ifsc > 0) .or. (qmmm_nml%vsolv > 1) ) no_ntt3_sync = 0
- call mpi_bcast(ig, 1, MPI_INTEGER, 0, commmaster, ierr)
- end if
-#endif
-
- ! -------------------------------------------------------------------
- ! ----- PRINT DATA CHARACTERIZING THE RUN -----
- ! -------------------------------------------------------------------
-
- nr = nrp
- write(6,9328)
- write(6,9008) title
- write(6,'(/a)') 'General flags:'
- write(6,'(5x,2(a,i8))') 'imin =',imin,', nmropt =',nmropt
-
- ! Error Checking for REMD
-#ifdef MPI
- if (rem/=0) then
- ! Make sure that the number of replicas is even so
- ! that they all have partners in the exchange step
- if (mod(numgroup,2).ne.0) then
- write (6,'(a)') "==================================="
- write (6,'(a)') "REMD requires an even # of replicas"
- write (6,'(a)') "==================================="
- call mexit (6,1)
- endif
-
- write(6,'(/a)') 'Replica exchange'
- write(6,'(5x,4(a,i8))') 'numexchg=',numexchg,', rem=',rem
-
- ! REPCRD option temporarily disabled
- if (repcrd == 0) write(6,'(a)') &
- "REMD WARNING: repcrd disabled. Only replica &
- &trajectories/output can be written."
-
- ! Check for correct number of exchanges
- if (numexchg <= 0) then
- write(6,'(a)') "REMD ERROR: numexchg must be > 0, "
- call mexit(6,1)
- endif
-
- ! RXSGLD
- if (isgld > 0 .and. rem < 0) then
- write(6, '(a)') 'Multi-D REMD and replica-exchange SGLD are not &
- &supported yet!'
- call mexit(6, 1)
- end if
-
- ! Hybrid GB
- if (numwatkeep >= 0) then
- write(6,'(5x,4(a,i8))') 'numwatkeep=',numwatkeep,', hybridgb=',hybridgb
- ! Check that user specified GB model for hybrid REMD
- if (hybridgb /= 2 .and. hybridgb /= 5 .and. hybridgb /= 1) then
- write(6,'(a)') "HYBRID REMD ERROR: hybridgb must be 1, 2, or 5."
- call mexit(6,1)
- endif
- else
- !Check that user did not specify GB model if no hybrid run.
- if (hybridgb /= 0) then
- write(6,'(a)') &
- "HYBRID REMD ERROR: numwatkeep must be >= 0 when hybridgb is set."
- call mexit(6,1)
- endif
- endif
- ! RREMD
- if (rremd>0) then
- write(6,'(5x,4(a,i8))') "rremd=",rremd
- endif
-
- ! ntp > 0 not allowed for remd
- if (ntp > 0) then
- write(6,'(a,i1)') "ERROR: ntp > 0 not allowed for rem > 0, ntp=", ntp
- call mexit(6,1)
- endif
-
- ! M-REMD (rem < 0) requires netcdf output.
- if (rem < 0 .and. ioutfm .ne. 1) then
- write(6,'(a)') "ERROR: Multi-D REMD (rem < 0) requires NetCDF &
- &trajectories (ioutfm=1)"
- call mexit(6,1)
- endif
-
-# ifdef LES
- ! DAN ROE: Temporarily disable LES REMD until it is verified with new
- ! REMD code
- if (rem==2) then
- write (6,*) "******* LES REM (rem==2) temporarily disabled. Stop. *******"
- call mexit(6,1)
- endif
-
- if (rem==2 .and. igb/=1) then
- write (6,*) ' partial REM (rem=2) only works with igb=1'
- call mexit(6,1)
- endif
-# else
- if (rem==2) then
- write(6,*) '******* For rem ==2, partial REM'
- write(6,*) 'use sander.LES with topology created by addles'
- call mexit(6,1)
- endif
-# endif
-
- endif ! rem>0
-
-#else /* _NO_ MPI */
- ! Check if user set numexchg with no MPI
- if (numexchg>0) write(6,'(a)') &
- "WARNING: numexchg > 0 - for REMD run please recompile sander for &
- ¶llel runs."
-
- ! Check if user set numwatkeep or hybridgb with no MPI - not sensible.
- if (numwatkeep>=0) write(6,'(a)') &
- "WARNING: numwatkeep >= 0 - for hybrid REMD run please recompile &
- &sander for parallel runs."
-
- if (hybridgb>0) write(6,'(a)') &
- "WARNING: hybridgb > 0 - for hybrid REMD run please recompile &
- &sander for parallel runs."
-#endif /* MPI */
- ! End error checking for REMD
-
- write(6,'(/a)') 'Nature and format of input:'
- write(6,'(5x,4(a,i8))') 'ntx =',ntx,', irest =',irest, &
- ', ntrx =',ntrx
-
- write(6,'(/a)') 'Nature and format of output:'
- write(6,'(5x,4(a,i8))') 'ntxo =',ntxo,', ntpr =',ntpr, &
- ', ntrx =',ntrx,', ntwr =',ntwr
- write(6,'(5x,5(a,i8))') 'iwrap =',iwrap,', ntwx =',ntwx, &
- ', ntwv =',ntwv,', ntwe =',ntwe
- write(6,'(5x,3(a,i8),a,i7)') 'ioutfm =',ioutfm, &
- ', ntwprt =',ntwprt, &
- ', idecomp =',idecomp,', rbornstat=',rbornstat
- if (ntwf > 0) &
- write(6,'(5x, a,i8)') 'ntwf =',ntwf
- write(6,'(/a)') 'Potential function:'
- write(6,'(5x,5(a,i8))') 'ntf =',ntf,', ntb =',ntb, &
- ', igb =',igb,', nsnb =',nsnb
- write(6,'(5x,3(a,i8))') 'ipol =',ipol,', gbsa =',gbsa, &
- ', iesp =',iesp
- write(6,'(5x,3(a,f10.5))') 'dielc =',dielc, &
- ', cut =',cut,', intdiel =',intdiel
-
- ! charge relocation
- if ( ifcr /= 0 ) then
- write(6,'(/a)') 'Charge relocation:'
- write(6,'(5x,2(a,i8))') 'cropt =', cropt, &
- ', crprintcharges=', crprintcharges
- write(6,'(5x,2(a,f10.5))') 'crcut =', crcut, ', crskin =', crskin
- end if
-
- if (( igb /= 0 .and. igb /= 10 .and. ipb == 0 .and. igb /= 8) &
- .or.hybridgb>0.or.icnstph>1) then
- write(6,'(5x,3(a,f10.5))') 'saltcon =',saltcon, &
- ', offset =',offset,', gbalpha= ',gbalpha
- write(6,'(5x,3(a,f10.5))') 'gbbeta =',gbbeta, &
- ', gbgamma =',gbgamma,', surften =',surften
- write(6,'(5x,3(a,f10.5))') 'rdt =',rdt, ', rgbmax =',rgbmax, &
- ' extdiel =',extdiel
- write(6,'(5x,3(a,i8))') 'alpb = ',alpb
- end if
-
- !Hai Nguyen: print output for igb=8
- if ( igb == 8 ) then
- write(6,'(5x,3(a,f10.5))') 'saltcon =',saltcon, &
- ', offset =',offset,', surften =',surften
- write(6,'(5x,3(a,f10.5))') 'rdt =',rdt, ', rgbmax =',rgbmax, &
- ' extdiel =',extdiel
- write(6,'(5x,3(a,i8))') 'alpb = ',alpb
- write(6,'(5x,3(a,f10.5))') 'gbalphaH =',gbalphaH, &
- ', gbbetaH =',gbbetaH,', gbgammaH = ',gbgammaH
- write(6,'(5x,3(a,f10.5))') 'gbalphaC =',gbalphaC, &
- ', gbbetaC =',gbbetaC,', gbgammaC = ',gbgammaC
- write(6,'(5x,3(a,f10.5))') 'gbalphaN =',gbalphaN, &
- ', gbbetaN =',gbbetaN,', gbgammaN = ',gbgammaN
- write(6,'(5x,3(a,f10.5))') 'gbalphaOS =',gbalphaOS, &
- ', gbbetaOS =',gbbetaOS,', gbgammaOS = ',gbgammaOS
- write(6,'(5x,3(a,f10.5))') 'gbalphaP =',gbalphaP, &
- ', gbbetaP =',gbbetaP,', gbgammaP = ',gbgammaP
- end if
-
-
- if( alpb /= 0 ) then
- write(6,'(5x,3(a,f10.5))') 'Arad =', Arad
- end if
-
- write(6,'(/a)') 'Frozen or restrained atoms:'
- write(6,'(5x,4(a,i8))') 'ibelly =',ibelly,', ntr =',ntr
- if( ntr == 1 ) write(6,'(5x,a,f10.5)') 'restraint_wt =', restraint_wt
-
- if( imin /= 0 ) then
- if( ipimd > 0 ) then
- write(6,'(/a)') 'pimd cannot be used in energy minimization'
- stop
- end if
-
- write(6,'(/a)') 'Energy minimization:'
- ! print inputable variables applicable to all minimization methods.
- write(6,'(5x,4(a,i8))') 'maxcyc =',maxcyc,', ncyc =',ncyc, &
- ', ntmin =',ntmin
- write(6,'(5x,2(a,f10.5))') 'dx0 =',dx0, ', drms =',drms
-
- ! Input flag ntmin determines the method of minimization
- select case ( ntmin )
- case ( 0, 1, 2 )
- ! no specific output
- case ( LMOD_NTMIN_XMIN, LMOD_NTMIN_LMOD )
- call write_lmod_namelist( )
- case default
- ! invalid ntmin
- write(6,'(/2x,a,i3,a)') 'Error: Invalid NTMIN (',ntmin,').'
- stop
- end select
- else
- write(6,'(/a)') 'Molecular dynamics:'
- write(6,'(5x,4(a,i10))') 'nstlim =',nstlim,', nscm =',nscm, &
- ', nrespa =',nrespa
- write(6,'(5x,3(a,f10.5))') 't =',t, &
- ', dt =',dt,', vlimit =',vlimit
-
- if ( ntt == 0 .and. tempi > 0.0d0 .and. irest == 0 ) then
- write(6,'(/a)') 'Initial temperature generation:'
- write(6,'(5x,a,i8)') 'ig =',ig
- write(6,'(5x,a,f10.5)') 'tempi =',tempi
- else if( ntt == 1 ) then
- write(6,'(/a)') 'Berendsen (weak-coupling) temperature regulation:'
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, &
- ', tempi =',tempi,', tautp =', tautp
-#ifdef LES
- write(6,'(5x,3(a,f10.5))') 'temp0LES =',temp0les
-#endif
- else if( ntt == 2 ) then
- write(6,'(/a)') 'Anderson (strong collision) temperature regulation:'
- write(6,'(5x,4(a,i8))') 'ig =',ig, ', vrand =',vrand
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, ', tempi =',tempi
- else if( ntt == 3 ) then
- write(6,'(/a)') 'Langevin dynamics temperature regulation:'
- write(6,'(5x,4(a,i8))') 'ig =',ig
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, &
- ', tempi =',tempi,', gamma_ln=', gamma_ln
- else if( ntt == 4 ) then
- write(6,'(/a)') 'Nose-Hoover chains'
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain
- else if( ntt == 5 ) then ! APJ
- write(6,'(/a)') 'Nose-Hoover chains Langevin' ! APJ
- write(6,'(5x,4(a,i8))') 'ig =',ig ! APJ
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln ! APJ
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain ! APJ
- else if( ntt == 6 ) then ! APJ
- write(6,'(/a)') 'Adaptive Langevin temperature regulation:' ! APJ
- write(6,'(5x,4(a,i8))') 'ig =',ig ! APJ
- write(6,'(5x,3(a,f10.5))') 'temp0 =',temp0, & ! APJ
- ', tempi =',tempi,', gamma_ln=', gamma_ln ! APJ
- else if( ntt == 7 ) then ! APJ
- write(6,'(/a)') 'Adaptive Nose-Hoover chains' ! APJ
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln ! APJ
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain ! APJ
- else if( ntt == 8 ) then ! APJ
- write(6,'(/a)') 'Adaptive Nose-Hoover chains Langevin' ! APJ
- write(6,'(5x,4(a,i8))') 'ig =',ig ! APJ
- write(6,'(5x,(a,f10.5))') 'gamma_ln=', gamma_ln ! APJ
- write(6,'(5x,(a,i8))') 'number of oscillators=', nchain ! APJ
- end if
-
- if( ntp /= 0 ) then
- write(6,'(/a)') 'Pressure regulation:'
- write(6,'(5x,4(a,i8))') 'ntp =',ntp
- write(6,'(5x,3(a,f10.5))') 'pres0 =',pres0, &
- ', comp =',comp,', taup =',taup
- if (barostat == 2) then
- write(6, '(5x,a)') 'Monte-Carlo Barostat:'
- write(6, '(5x,a,i8)') 'mcbarint =', mcbarint
- end if
- end if
-
- if (csurften /= 0) then
- write(6,'(/a)') 'Constant surface tension:'
- write(6,'(5x,a,i8)') 'csurften =', csurften
- write(6,'(5x,a,f10.5,a,i8)') 'gamma_ten =', gamma_ten, ' ninterface =', ninterface
- end if
-
- end if
-
- if( ntc /= 1 ) then
- write(6,'(/a)') 'SHAKE:'
- write(6,'(5x,4(a,i8))') 'ntc =',ntc,', jfastw =',jfastw
- write(6,'(5x,3(a,f10.5))') 'tol =',tol
- end if
-
- if( ifcap == 1 .or. ifcap == 2 .or. ifcap == 3 ) then
- write(6,'(/a)') 'Water cap:'
- write(6,'(5x,2(a,i8))') 'ivcap =',ivcap,', natcap =',natcap
- write(6,'(5x,2(a,f10.5))') 'fcap =',fcap, ', cutcap =',cutcap
- write(6,'(5x,3(a,f10.5))') 'xcap =',xcap, ', ycap =',ycap, &
- ', zcap =',zcap
- else if( ifcap == 4 ) then
- write(6,'(/a)') 'Orthorhombus:'
- write(6,'(5x,1(a,i8))') 'ivcap =',ivcap
- write(6,'(5x,1(a,f10.5))') 'forth =',forth
- write(6,'(5x,3(a,f10.5))') 'xlorth =',xlorth,', ylorth =',ylorth, &
- ', zlorth =',zlorth
- write(6,'(5x,3(a,f10.5))') 'xorth =',xorth, ', yorth =',yorth, &
- ', zorth =',zorth
- else if( ifcap == 5 ) then
- write(6,'(/a)') 'Water shell:'
- write(6,'(5x,(a,i8,a,f10.5))') 'ivcap =',ivcap,', cutcap =',cutcap
- endif
-
- if( nmropt > 0 ) then
- write(6,'(/a)') 'NMR refinement options:'
- write(6,'(5x,4(a,i8))')'iscale =',iscale,', noeskp =',noeskp, &
- ', ipnlty =',ipnlty,', mxsub =',mxsub
- write(6,'(5x,3(a,f10.5))') 'scalm =',scalm, &
- ', pencut =',pencut,', tausw =',tausw
- end if
-
- if( numextra > 0 ) then
- write(6,'(/a)') 'Extra-points options:'
- write(6,'(5x,4(a,i8))') 'frameon =',frameon, &
- ', chngmask=',chngmask
- end if
-
- if( ipol > 0 ) then
- write(6,'(/a)') 'Polarizable options:'
- write(6,'(5x,4(a,i8))') 'indmeth =',indmeth, &
- ', maxiter =',maxiter,', irstdip =',irstdip, &
- ', scaldip =',scaldip
- write(6,'(5x,3(a,f10.5))') &
- 'diptau =',diptau,', dipmass =',dipmass
- if ( ipol > 1 ) then
- write(6,'(5x,3(a,f10.5))') &
- 'Default Thole coefficient = ',dipdamp
- end if
- end if
-
-#ifdef MPI /* SOFT CORE */
- if( icfe /= 0 .or. ifsc/=0) then
- write(6,'(/a)') 'Free energy options:'
- write(6,'(5x,a,i8,a,i8,a,i8)') 'icfe =', icfe , ', ifsc =', ifsc, ', klambda =', klambda
- write(6,'(5x,a,f8.4,a,f8.4,a,f8.4)') 'clambda =', clambda, ', scalpha =', scalpha, ', scbeta =', scbeta
- write(6,'(5x,a,i8,a,i8)') 'sceeorder =', sceeorder, ' dvdl_norest =', dvdl_norest
- write(6,'(5x,a,f8.4,a,i8)') 'dynlmb =', dynlmb, ' logdvdl =', logdvdl
- end if
- if ( ifmbar /= 0 ) then
- write (6,'(/a)') 'FEP MBAR options:'
- write(6,'(5x,a,i8,a,i8)') 'ifmbar =', ifmbar, ', bar_intervall = ', bar_intervall
- write(6,'(5x,a,f6.4,a,f6.4,a,f6.4)') 'bar_l_min =', bar_l_min, ', bar_l_max =', bar_l_max, ', bar_l_incr =', bar_l_incr
- end if
-#endif
-
- if (ilrt /= 0) then
- write (6,*)
- write (6,'(a,i4,a,i4)') ' Linear Response Theory: ilrt =', ilrt, ' lrt_interval =', lrt_interval
- write (6,*)
- end if
-
- ! Options for TI w.r.t. mass.
- select case (itimass)
- case (0) ! Default: no TI wrt. mass.
- case (1,2) ! 1 = use virial est., 2 = use thermodynamic est.
- write(6,'(/a)') 'Isotope effects (thermodynamic integration w.r.t. mass):'
- write(6,'(5x,4(a,i8))') 'itimass =',itimass
- write(6,'(5x,3(a,f10.5))') 'clambda =',clambda
- if (icfe /= 0) then
- write(6,'(/2x,a,i2,a,i2,a)') 'Error: Cannot do TI w.r.t. both potential (icfe =', &
- icfe, ') and mass (itimass =', itimass, ').'
- stop
- endif
- if (ipimd == 0) then
- write(6,'(/2x,a)') 'Error (IPIMD=0): TI w.r.t. mass requires a PIMD run.'
- stop
- endif
- case default ! Invalid itimass
- write(6,'(/2x,a,i2,a)') 'Error: Invalid ITIMASS (', itimass, ' ).'
- stop
- end select
-
-!KFW
-! call mpi_bcast ( ievb, 1, MPI_INTEGER, 0, commworld, ierr )
-! call mpi_barrier ( commworld, ierr )
-
-! if( ievb == 1 ) then
-!KFW write(6,'(/a)') 'EVB options:'
-!KFW write(6,'(5x,3(a,f10.5))') 'V11 =',v11,', V22 =', v22, &
-!KFW ', V12 =', v12
-!kfw write(6,'(5x,3(a,f10.5))') 'kevb =',kevb,', evbt =', evbt
-! end if
-
- if( itgtmd == 1 ) then
- write(6,'(/a)') 'Targeted molecular dynamics:'
- write(6,'(5x,3(a,f10.5))') 'tgtrmsd =',tgtrmsd, &
- ', tgtmdfrc=',tgtmdfrc
- end if
-
- if( icnstph /= 0) then
- write(6, '(/a)') 'Constant pH options:'
- if ( icnstph .ne. 1 ) &
- write(6, '(5x,a,i8)') 'icnstph =', icnstph
- write(6, '(5x,a,i8)') 'ntcnstph =', ntcnstph
- write(6, '(5x,a,f10.5)') 'solvph =', solvph
- if ( icnstph .ne. 1 ) &
- write(6,'(5x,2(a,i8))') 'ntrelax =', ntrelax, ' mccycles =', mccycles
- end if
- if( icnstph /= 2) then
- ntrelax = 0 ! needed for proper behavior of timing
- end if
-
- if( ntb > 0 ) then
- write(6,'(/a)') 'Ewald parameters:'
- write(6,'(5x,4(a,i8))') 'verbose =',verbose, &
- ', ew_type =',ew_type,', nbflag =',nbflag, &
- ', use_pme =',use_pme
- write(6,'(5x,4(a,i8))') 'vdwmeth =',vdwmeth, &
- ', eedmeth =',eedmeth,', netfrc =',netfrc
- write(6, 9002) a, b, c
- write(6, 9003) alpha, beta, gamma
- write(6, 9004) nfft1, nfft2, nfft3
- write(6, 9006) cutoffnb, dsum_tol
- write(6, 9007) ew_coeff
- write(6, 9005) order
- 9002 format (5x,'Box X =',f9.3,3x,'Box Y =',f9.3,3x,'Box Z =',f9.3)
- 9003 format (5x,'Alpha =',f9.3,3x,'Beta =',f9.3,3x,'Gamma =',f9.3)
- 9004 format (5x,'NFFT1 =',i5 ,7x,'NFFT2 =',i5 ,7x,'NFFT3 =',i5)
- 9005 format (5x,'Interpolation order =',i5)
- 9006 format (5x,'Cutoff=',f9.3,3x,'Tol =',e9.3)
- 9007 format (5x,'Ewald Coefficient =',f9.5)
- end if
-
- if( mmtsb_switch /= mmtsb_off ) then
- call mmtsb_print_banner()
- call mmtsb_init( temp0, clambda )
- end if
-
-!---- QMMM Options ----
-
- if( qmmm_nml%ifqnt ) then
- write(6, '(/a)') 'QMMM options:'
- write(6, '(5x," ifqnt = True nquant = ",i8)') &
- qmmm_struct%nquant
- write(6, '(5x," qmgb = ",i8," qmcharge = ",i8," adjust_q = ",i8)') &
- qmmm_nml%qmgb, qmmm_nml%qmcharge, qmmm_nml%adjust_q
- write(6, '(5x," spin = ",i8," qmcut = ",f8.4, " qmshake = ",i8)') qmmm_nml%spin, &
- qmmm_nml%qmcut, qmmm_nml%qmshake
- write(6, '(5x," qmmm_int = ",i8)') qmmm_nml%qmmm_int
- write(6, '(5x,"lnk_atomic_no = ",i8," lnk_dis = ",f8.4," lnk_method = ",i8)') &
- qmmm_nml%lnk_atomic_no,qmmm_nml%lnk_dis, qmmm_nml%lnk_method
- if ( qmmm_nml%qmtheory%PM3 ) then
- write(6, '(5x," qm_theory = PM3")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%AM1 ) then
- write(6, '(5x," qm_theory = AM1")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%AM1D ) then
- write(6, '(5x," qm_theory = AM1/d")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%MNDO ) then
- write(6, '(5x," qm_theory = MNDO")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%MNDOD ) then
- write(6, '(5x," qm_theory = MNDO/d")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PDDGPM3 ) then
- write(6, '(5x," qm_theory = PDDGPM3")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PDDGMNDO ) then
- write(6, '(5x," qm_theory =PDDGMNDO")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM3CARB1 ) then
- write(6, '(5x," qm_theory =PM3CARB1")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%DFTB ) then
- write(6, '(5x," qm_theory = DFTB")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%RM1 ) then
- write(6, '(5x," qm_theory = RM1")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PDDGPM3_08 ) then
- write(6, '(5x," qm_theory = PDDGPM3_08")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM6 ) then
- write(6, '(5x," qm_theory = PM6")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM3ZNB ) then
- write(6, '(5x," qm_theory = PM3/ZnB")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%PM3MAIS ) then
- write(6, '(5x," qm_theory = PM3-MAIS")',ADVANCE='NO')
- else if ( qmmm_nml%qmtheory%EXTERN ) then
- write(6, '(5x," qm_theory = EXTERN")',ADVANCE='NO')
- else
- write(6, '(5x," qm_theory = UNKNOWN!")',ADVANCE='NO')
- end if
- write (6, '(" verbosity = ",i8)') qmmm_nml%verbosity
- if (qmmm_nml%qmqm_analyt) then
- write(6, '(5x," qmqmdx = Analytical")')
- else
- write(6, '(5x," qmqmdx = Numerical")')
- end if
- !AWG: if EXTERN in use, skip printing of options that do not apply
- EXTERN: if ( .not. qmmm_nml%qmtheory%EXTERN ) then
- if (qmmm_nml%tight_p_conv) then
- write(6, '(5x," tight_p_conv = True (converge density to SCFCRT)")')
- else
- write(6, '(5x," tight_p_conv = False (converge density to 0.05xSqrt[SCFCRT])")')
- end if
- write(6, '(5x," scfconv = ",e9.3," itrmax = ",i8)') qmmm_nml%scfconv, qmmm_nml%itrmax
- if (qmmm_nml%printcharges) then
- write(6, '(5x," printcharges = True ")',ADVANCE='NO')
- else
- write(6, '(5x," printcharges = False")',ADVANCE='NO')
- end if
- select case (qmmm_nml%printdipole)
- case (1)
- write(6, '(5x," printdipole = QM ")',ADVANCE='NO')
- case (2)
- write(6, '(5x," printdipole = QM+MM")',ADVANCE='NO')
- case default
- write(6, '(5x," printdipole = False")',ADVANCE='NO')
- end select
- if (qmmm_nml%peptide_corr) then
- write(6, '(5x," peptide_corr = True")')
- else
- write(6, '(5x," peptide_corr = False")')
- end if
- if (qmmm_nml%qmmmrij_incore) then
- write(6, '(4x,"qmmmrij_incore = True ")')
- else
- write(6, '(4x,"qmmmrij_incore = False")')
- end if
- if (qmmm_nml%qmqm_erep_incore) then
- write(6, '(2x,"qmqm_erep_incore = True ")')
- else
- write(6, '(2x,"qmqm_erep_incore = False")')
- end if
- if (qmmm_nml%allow_pseudo_diag) then
- write(6, '(7x,"pseudo_diag = True ")',ADVANCE='NO')
- write(6, '("pseudo_diag_criteria = ",f8.4)') qmmm_nml%pseudo_diag_criteria
- else
- write(6, '(7x,"pseudo_diag = False")')
- end if
- write(6, '(6x,"diag_routine = ",i8)') qmmm_nml%diag_routine
- end if EXTERN
- !If ntb=0 or use_pme =0 then we can't do qm_ewald so overide what the user may
- !have put in the namelist and set the value to false.
- if (qmmm_nml%qm_ewald>0) then
- if (qmmm_nml%qm_pme) then
- write(6, '(10x,"qm_ewald = ",i8, " qm_pme = True ")') qmmm_nml%qm_ewald
- else
- write(6, '(10x,"qm_ewald = ",i8, " qm_pme = False ")') qmmm_nml%qm_ewald
- end if
- write(6, '(10x," kmaxqx = ",i4," kmaxqy = ",i4," kmaxqz = ",i4," ksqmaxq = ",i4)') &
- qmmm_nml%kmaxqx, qmmm_nml%kmaxqy, qmmm_nml%kmaxqz, qmmm_nml%ksqmaxq
- else
- write(6, '(10x,"qm_ewald = ",i8, " qm_pme = False ")') qmmm_nml%qm_ewald
- end if
- !Print the fock matrix prediction params if it is in use.
- if (qmmm_nml%fock_predict>0) then
- write(6, '(6x,"fock_predict = ",i4)') qmmm_nml%fock_predict
- write(6, '(6x," fockp_d1 = ",f8.4," fockp_d2 = ",f8.4)') qmmm_nml%fockp_d1, qmmm_nml%fockp_d2
- write(6, '(6x," fockp_d2 = ",f8.4," fockp_d4 = ",f8.4)') qmmm_nml%fockp_d3, qmmm_nml%fockp_d4
- end if
-
- if (qmmm_nml%qmmm_switch) then
- write(6, '(7x,"qmmm_switch = True",3x,"r_switch_lo =",f8.4,3x,"r_switch_hi =",f8.4)') &
- & qmmm_nml%r_switch_lo, qmmm_nml%r_switch_hi
- !else
- ! write(6, '(7x,"qmmm_switch = False")')
- end if
-
- if (qmmm_nml%printdipole==2) then
- write(6, '("|",2x,"INFO: To compute MM dipole WAT residues will be stripped")')
- end if
- end if
-
- if (qmmm_nml%vsolv > 0) then
- call print(qmmm_vsolv)
- end if
-
-!---- SEBOMD options ----
-
- if (sebomd_obj%do_sebomd) then
- call sebomd_write_info()
- call sebomd_write_options()
- endif
-
-#ifdef _XRAY
-!---- XRAY Options ----
- call xray_write_options()
-#endif
-
-! ----EMAP Options-----
- if(temap)call emap_options(5)
-! ---------------------
-
-#ifdef EMIL
-! ----EMIL Options-----
- if(emil_do_calc.gt.0)call init_emil_dat(5, 6)
-! ---------------------
-#endif
-
-
-#ifdef MPI
-! --- MPI TIMING OPTIONS ---
- write(6, '(/a)') '| MPI Timing options:'
- write(6, '("|",5x," profile_mpi = ",i8)') profile_mpi
-! Sanity check for profile_mpi
- call int_legal_range('profile_mpi',profile_mpi,0,1)
-! --------------------------
-#endif
-
- cut = cut*cut
- cut_inner = cut_inner*cut_inner
-
- !------------------------------------------------------------------------
- ! If user has requested generalized born electrostatics, set up variables
- !------------------------------------------------------------------------
-
- if( igb == 0 .and. gbsa > 0 ) then
- write(0,*) 'GB/SA calculation is performed only when igb>0'
- call mexit( 6,1 )
- end if
- if( gbsa == 2 .and. &
- ((imin == 0 .and. nstlim > 1) .or. &
- (imin == 1 .and. maxcyc > 1)) ) then
- write(0,*) 'GBSA=2 only works for single point energy calc'
- call mexit( 6,1 )
- end if
-#ifdef APBS
- if( igb /= 0 .and. igb /= 10 .and. ipb == 0 .and. .not. mdin_apbs) then
-#else
- if (( igb /= 0 .and. igb /= 10 .and. ipb == 0 ).or.hybridgb>0.or.icnstph>1) then
-#endif /* APBS */
-#ifdef LES
- write(6,*) 'igb=1,5,7 are working with LES, no SA term included'
-#endif
- ! igb7 uses special S_x screening params.
- ! overwrite the tinker values read from the prmtop
- if (igb == 7) then
- do i=1,natom
- if(ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
-
- if (atomicnumber .eq. 6) then
- x(l96+i-1) = 4.84353823306d-1
- else if (atomicnumber .eq. 1) then
- x(l96+i-1) = 1.09085413633d0
- else if (atomicnumber .eq. 7) then
- x(l96+i-1) = 7.00147318409d-1
- else if (atomicnumber .eq. 8) then
- x(l96+i-1) = 1.06557401132d0
- else if (atomicnumber .eq. 16) then
- x(l96+i-1) = 6.02256336067d-1
- else if (atomicnumber .eq. 15) then
- x(l96+i-1) = 5d-1
- else
- x(l96+i-1) = 5d-1
- end if
- end do
- end if
-
- ! Hai Nguyen: changing S_x screening params for igb = 8
- ! overwrite the tinker values read from the prmtop
-
- if (igb == 8) then
- do i=1,natom
- if (ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
-
- if (atomicnumber .eq. 6) then
- x(l96+i-1) = Sc
- else if (atomicnumber .eq. 1) then
- x(l96+i-1) = Sh
- else if (atomicnumber .eq. 7) then
- x(l96+i-1) = Sn
- else if (atomicnumber .eq. 8) then
- x(l96+i-1) = So
- else if (atomicnumber .eq. 16) then
- x(l96+i-1) = Ss
- else if (atomicnumber .eq. 15) then
- x(l96+i-1) = Sp ! Hai Nguyen: We still don't have an optimized Sp parameter
- else
- !for atom type Cl,Br,...
- !These parameters are also not optimized.
- x(l96+i-1) = 5d-1
- end if
- end do
- end if
-
-
- ! Hai Nguyen: set up for igb == 2, 5, 7, 8
- ! Put gb parameters in arrays
- if ( igb == 2 .or. igb == 5 .or. igb == 7 .or. &
- hybridgb == 2 .or. hybridgb == 5) then
- do i=1,natom
- x(l2402+i-1) = gbalpha
- x(l2403+i-1) = gbbeta
- x(l2404+i-1) = gbgamma
- end do
- end if
-
- !Hai Nguyen: IGB = 8
- if ( igb == 8 ) then
- do i=1,natom
- if (ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
-
- if (atomicnumber .eq. 1) then
- x(l2402+i-1) = gbalphaH
- x(l2403+i-1) = gbbetaH
- x(l2404+i-1) = gbgammaH
- else if (atomicnumber .eq. 6) then
- x(l2402+i-1) = gbalphaC
- x(l2403+i-1) = gbbetaC
- x(l2404+i-1) = gbgammaC
- else if (atomicnumber .eq. 7) then
- x(l2402+i-1) = gbalphaN
- x(l2403+i-1) = gbbetaN
- x(l2404+i-1) = gbgammaN
- else if (atomicnumber .eq. 8) then
- x(l2402+i-1) = gbalphaOS
- x(l2403+i-1) = gbbetaOS
- x(l2404+i-1) = gbgammaOS
- else if (atomicnumber .eq. 16) then
- x(l2402+i-1) = gbalphaOS
- x(l2403+i-1) = gbbetaOS
- x(l2404+i-1) = gbgammaOS
- else if (atomicnumber .eq. 15) then
- x(l2402+i-1) = gbalphaP
- x(l2403+i-1) = gbbetaP
- x(l2404+i-1) = gbgammaP
- else
- !use GBOBC set for other atom types
- x(l2402+i-1) = 1.0d0
- x(l2403+i-1) = 0.8d0
- x(l2404+i-1) = 4.85d0
- end if
- end do
- end if ! end Hai Nguyen section
-
- ! put fs(i)*(rborn(i) - offset) into the "fs" array
-
- fsmax = 0.d0
- do i=1,natom
- x(l96-1+i) = x(l96-1+i)*( x(l97-1+i) - offset )
- fsmax = max( fsmax, x(l96-1+i) )
- if (rbornstat == 1) then
- x(l186-1+i) = 0.d0
- x(l187-1+i) = 999.d0
- x(l188-1+i) = 0.d0
- x(l189-1+i) = 0.d0
- end if
- end do
-
- ! ---------------------------------------------------------------------
- ! ---get Debye-Huckel kappa (A**-1) from salt concentration (M), assuming:
- ! T = 298.15, epsext=78.5,
-
- kappa = sqrt( 0.10806d0 * saltcon )
-
- ! ---scale kappa by 0.73 to account(?) for lack of ion exclusions:
-
- kappa = 0.73d0* kappa
-
- !Set kappa for qmmm if needed
- qm_gb%kappa = kappa
- ! ---------------------------------------------------------------------
-
- if ( gbsa == 1 ) then
-
- ! --- assign parameters for calculating SASA according to the
- ! LCPO method ---
-
- do i=1,natom
- ix(i80+i-1)=0
- end do
-
- ! --- get the number of bonded neighbors for each atom:
-
- do i=1,nbona
- atom1=ix(iiba+i-1)/3+1
- atom2=ix(ijba+i-1)/3+1
- ix(i80+atom1-1)=ix(i80+atom1-1)+1
- ix(i80+atom2-1)=ix(i80+atom2-1)+1
- end do
-
- do i=1,natom
- ix(i80-i)=ix(i80+i-1)
- end do
-
- do i=1,nbonh
- atom1=ix(iibh+i-1)/3+1
- atom2=ix(ijbh+i-1)/3+1
- ix(i80-atom1)=ix(i80-atom1)+1
- ix(i80-atom2)=ix(i80-atom2)+1
- end do
-
-
- ! --- construct parameters for SA calculation; note that the
- ! radii stored in L165 are augmented by 1.4 Ang.
-
- do i=1,natom
- write(atype,'(a2)') ih(m06+i-1)
- call upper(atype)
- if (ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
- hybridization = ix(i80-i)
- nbond=ix(i80+i-1)
- if (atomicnumber .eq. 6) then
- if (hybridization .eq. 4) then
- if (nbond == 1) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.77887d0
- x(l175-1+i) = -0.28063d0
- x(l180-1+i) = -0.0012968d0
- x(l185-1+i) = 0.00039328d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.56482d0
- x(l175-1+i) = -0.19608d0
- x(l180-1+i) = -0.0010219d0
- x(l185-1+i) = 0.0002658d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.23348d0
- x(l175-1+i) = -0.072627d0
- x(l180-1+i) = -0.00020079d0
- x(l185-1+i) = 0.00007967d0
- else if (nbond == 4) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.00000d0
- x(l175-1+i) = 0.00000d0
- x(l180-1+i) = 0.00000d0
- x(l185-1+i) = 0.00000d0
- else
- write(6,*) 'Unusual nbond for CT:', i, nbond, &
- ' Using default carbon LCPO parameters'
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.77887d0
- x(l175-1+i) = -0.28063d0
- x(l180-1+i) = -0.0012968d0
- x(l185-1+i) = 0.00039328d0
- end if
- else
- if (nbond == 2) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.51245d0
- x(l175-1+i) = -0.15966d0
- x(l180-1+i) = -0.00019781d0
- x(l185-1+i) = 0.00016392d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.070344d0
- x(l175-1+i) = -0.019015d0
- x(l180-1+i) = -0.000022009d0
- x(l185-1+i) = 0.000016875d0
- else
- write(6,*) 'Unusual nbond for C :', i, nbond, &
- ' Using default carbon LCPO parameters'
- x(l165-1+i) = 1.70d0 + 1.4d0
- x(l170-1+i) = 0.77887d0
- x(l175-1+i) = -0.28063d0
- x(l180-1+i) = -0.0012968d0
- x(l185-1+i) = 0.00039328d0
- end if
- end if
- else if (atomicnumber .eq. 8) then
- if (atype == 'O ') then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.68563d0
- x(l175-1+i) = -0.1868d0
- x(l180-1+i) = -0.00135573d0
- x(l185-1+i) = 0.00023743d0
- else if (atype == 'O2') then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.88857d0
- x(l175-1+i) = -0.33421d0
- x(l180-1+i) = -0.0018683d0
- x(l185-1+i) = 0.00049372d0
- else
- if (nbond == 1) then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.77914d0
- x(l175-1+i) = -0.25262d0
- x(l180-1+i) = -0.0016056d0
- x(l185-1+i) = 0.00035071d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.49392d0
- x(l175-1+i) = -0.16038d0
- x(l180-1+i) = -0.00015512d0
- x(l185-1+i) = 0.00016453d0
- else
- write(6,*) 'Unusual nbond for O:', i, nbond, &
- ' Using default oxygen LCPO parameters'
- x(l165-1+i) = 1.60d0 + 1.4d0
- x(l170-1+i) = 0.77914d0
- x(l175-1+i) = -0.25262d0
- x(l180-1+i) = -0.0016056d0
- x(l185-1+i) = 0.00035071d0
- end if
- end if
- else if(atomicnumber .eq. 7) then
- if (atype == 'N3') then
- if (nbond == 1) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.078602d0
- x(l175-1+i) = -0.29198d0
- x(l180-1+i) = -0.0006537d0
- x(l185-1+i) = 0.00036247d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.22599d0
- x(l175-1+i) = -0.036648d0
- x(l180-1+i) = -0.0012297d0
- x(l185-1+i) = 0.000080038d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.051481d0
- x(l175-1+i) = -0.012603d0
- x(l180-1+i) = -0.00032006d0
- x(l185-1+i) = 0.000024774d0
- else
- write(6,*) 'Unusual nbond for N3:', i, nbond, &
- ' Using default nitrogen LCPO parameters'
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.078602d0
- x(l175-1+i) = -0.29198d0
- x(l180-1+i) = -0.0006537d0
- x(l185-1+i) = 0.00036247d0
- end if
- else
- if (nbond == 1) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.73511d0
- x(l175-1+i) = -0.22116d0
- x(l180-1+i) = -0.00089148d0
- x(l185-1+i) = 0.0002523d0
- else if (nbond == 2) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.41102d0
- x(l175-1+i) = -0.12254d0
- x(l180-1+i) = -0.000075448d0
- x(l185-1+i) = 0.00011804d0
- else if (nbond == 3) then
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.062577d0
- x(l175-1+i) = -0.017874d0
- x(l180-1+i) = -0.00008312d0
- x(l185-1+i) = 0.000019849d0
- else
- write(6,*) 'Unusual nbond for N:', i, nbond, &
- ' Using default nitrogen LCPO parameters'
- x(l165-1+i) = 1.65d0 + 1.4d0
- x(l170-1+i) = 0.078602d0
- x(l175-1+i) = -0.29198d0
- x(l180-1+i) = -0.0006537d0
- x(l185-1+i) = 0.00036247d0
- end if
- end if
- else if(atomicnumber .eq. 16) then
- if (atype == 'SH') then
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.7722d0
- x(l175-1+i) = -0.26393d0
- x(l180-1+i) = 0.0010629d0
- x(l185-1+i) = 0.0002179d0
- else
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.54581d0
- x(l175-1+i) = -0.19477d0
- x(l180-1+i) = -0.0012873d0
- x(l185-1+i) = 0.00029247d0
- end if
- else if (atomicnumber .eq. 15) then
- if (nbond == 3) then
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.3865d0
- x(l175-1+i) = -0.18249d0
- x(l180-1+i) = -0.0036598d0
- x(l185-1+i) = 0.0004264d0
- else if (nbond == 4) then
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.03873d0
- x(l175-1+i) = -0.0089339d0
- x(l180-1+i) = 0.0000083582d0
- x(l185-1+i) = 0.0000030381d0
- else
- write(6,*) 'Unusual nbond for P:', i, nbond, &
- ' Using default phosphorus LCPO parameters'
- x(l165-1+i) = 1.90d0 + 1.4d0
- x(l170-1+i) = 0.3865d0
- x(l175-1+i) = -0.18249d0
- x(l180-1+i) = -0.0036598d0
- x(l185-1+i) = 0.0004264d0
- end if
- else if (atype(1:1) == 'Z') then
- x(l165-1+i) = 0.00000d0 + 1.4d0
- x(l170-1+i) = 0.00000d0
- x(l175-1+i) = 0.00000d0
- x(l180-1+i) = 0.00000d0
- x(l185-1+i) = 0.00000d0
- else if (atomicnumber .eq. 1) then
- x(l165-1+i) = 0.00000d0 + 1.4d0
- x(l170-1+i) = 0.00000d0
- x(l175-1+i) = 0.00000d0
- x(l180-1+i) = 0.00000d0
- x(l185-1+i) = 0.00000d0
- else if (atype == 'MG') then
- ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.45A: Aqvist 1992
- x(l165-1+i) = 1.18d0 + 1.4d0
- ! The following values were taken from O.sp3 with two bonded
- ! neighbors -> O has the smallest van der Waals radius
- ! compared to all other elements which had been parametrized
- x(l170-1+i) = 0.49392d0
- x(l175-1+i) = -0.16038d0
- x(l180-1+i) = -0.00015512d0
- x(l185-1+i) = 0.00016453d0
- else if (atype == 'F') then
- x(l165-1+i) = 1.47d0 + 1.4d0
- x(l170-1+i) = 0.68563d0
- x(l175-1+i) = -0.1868d0
- x(l180-1+i) = -0.00135573d0
- x(l185-1+i) = 0.00023743d0
- else
- ! write( 0,* ) 'bad atom type: ',atype
- ! call mexit( 6,1 )
- x(l165-1+i) = 1.70 + 1.4;
- x(l170-1+i) = 0.51245;
- x(l175-1+i) = -0.15966;
- x(l180-1+i) = -0.00019781;
- x(l185-1+i) = 0.00016392;
- write(6,'(a,a)') 'Using carbon SA parms for atom type', atype
- end if
- end do ! i=1,natom
- !
- else if ( gbsa == 2 ) then
-
- ! --- assign parameters for calculating SASA according to the
- ! ICOSA method; the radii are augmented by 1.4 A ---
-
- do i=1,natom
- write(atype,'(a2)') ih(m06+i-1)
- if(ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
- if (atomicnumber .eq. 7) then
- x(L165-1+i) = 1.55d0 + 1.4d0
- else if (atomicnumber .eq. 6) then
- x(L165-1+i) = 1.70d0 + 1.4d0
- else if (atomicnumber .eq. 1) then
- x(L165-1+i) = 1.20d0 + 1.4d0
- else if (atomicnumber .eq. 8) then
- x(L165-1+i) = 1.50d0 + 1.4d0
- else if (atomicnumber .eq. 15) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 16) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 17) then
- ! Cl radius
- x(L165-1+i) = 1.70d0 + 1.4d0
- else if (atomicnumber .eq. 9) then
- ! F radius
- x(L165-1+i) = 1.50d0 + 1.4d0
- else if (atomicnumber .eq. 35) then
- ! Br radius
- ! Bondi, J. Phys. Chem. 1964, 68, 441.
- x(L165-1+i) = 1.85d0 + 1.4d0
- else if (atomicnumber .eq. 20) then
- ! Ca radius
- ! Calculated from Aqvist, J. Phys. Chem. 1990, 94, 8021.
- x(L165-1+i) = 1.33d0 + 1.4d0
- else if (atomicnumber .eq. 11) then
- ! Na radius
- ! Calculated from Aqvist, J. Phys. Chem. 1990, 94, 8021.
- x(L165-1+i) = 1.87d0 + 1.4d0
- else if (atomicnumber .eq. 30) then
- ! Zn radius
- ! Hoops, Anderson, Merz, JACS 1991, 113, 8262.
- x(L165-1+i) = 1.10d0 + 1.4d0
- else if (atomicnumber .eq. 12) then
- ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.45A: Aqvist 1992
- x(L165-1+i) = 1.18d0 + 1.4d0
- else
- write( 0,* ) 'bad atom type: ',atype
- call mexit( 6,1 )
- end if
-
- ! dummy LCPO values:
- x(L170-1+i) = 0.0d0
- x(L175-1+i) = 0.0d0
- x(L180-1+i) = 0.0d0
- x(L185-1+i) = 0.0d0
- ! write(6,*) i,' ',atype,x(L165-1+i)
- end do ! i=1,natom
-
- end if ! ( gbsa == 1 )
-
- end if ! ( igb /= 0 .and. igb /= 10 .and. ipb == 0 )
-
- !-----------------------------------
- ! If a LRT calculation is requested,
- ! setup the icosa-SASA parameters
- ! this code is copied from above
- !-----------------------------------
-
- if ( ilrt /= 0 ) then
- ! --- assign parameters for calculating SASA according to the
- ! ICOSA method; the radii are augmented by 1.4 A ---
- do i=1,natom
- write(atype,'(a2)') ih(m06+i-1)
- if(ix(i100) .eq. 1) then
- atomicnumber = ix(i100+i)
- else
- call get_atomic_number(ih(m04+i-1), x(lmass+i-1), &
- atomicnumber, errFlag)
-#ifdef LES
- if(errFlag) then
- call get_atomic_number(ih(m04+i-1), &
- x(lmass+i-1)*lesfac((lestyp(i)-1)*nlesty+lestyp(i)), &
- atomicnumber, errFlag)
- end if
-#endif
- end if
- if (atomicnumber .eq. 7) then
- x(L165-1+i) = 1.55d0 + 1.4d0
- else if (atomicnumber .eq. 6) then
- x(L165-1+i) = 1.70d0 + 1.4d0
- else if (atomicnumber .eq. 1 .or. &
- ! added for lone pairs
- atype == 'EP') then
- x(L165-1+i) = 1.20d0 + 1.4d0
- else if (atomicnumber .eq. 8) then
- x(L165-1+i) = 1.50d0 + 1.4d0
- else if (atomicnumber .eq. 15) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 16) then
- x(L165-1+i) = 1.80d0 + 1.4d0
- else if (atomicnumber .eq. 12) then
- ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
- ! Mg radius = 1.45A: Aqvist 1992
- x(L165-1+i) = 1.18d0 + 1.4d0
- else
- write( 0,* ) 'bad atom type: ',atype,' cannot perform SASA calculation'
- call mexit( 6,1 )
- end if ! atype(1:1) == 'N'
- x(L170-1+i) = 0.0d0
- x(L175-1+i) = 0.0d0
- x(L180-1+i) = 0.0d0
- x(L185-1+i) = 0.0d0
- !write(6,*) i,' ',atype,x(L165-1+i)
- end do ! i=1,natom
-
- end if ! ( ilrt /= 0 )
-
- !------------------------------------------------------------------------
- ! If user has requested Poisson-Boltzmann electrostatics, set up variables
- !------------------------------------------------------------------------
-
- if ( igb == 10 .or. ipb /= 0 ) then
- call pb_init(ifcap,natom,nres,ntypes,nbonh,nbona,ix(i02),ix(i04),ix(i06),ix(i08),ix(i10),&
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),ix(ibellygp),ih(m02),ih(m04),ih(m06),x(l15),x(l97))
- end if ! ( igb == 10 .or. ipb /= 0 )
-
- if (icnstph /= 0) then
- ! Initialize all constant pH data to 0 and read it in
- call cnstph_zero()
- call cnstphread(x(l15))
-
- ! Fill proposed charges array from current charges
- do i=1,natom
- x(l190-1+i) = x(l15-1+i)
- end do
-
- ! If we're doing explicit CpH, fill gbv* arrays
- if ( icnstph .gt. 1 .and. cph_igb == 2 .or. cph_igb == 5) then
- do i=1,natom
- x(l2402+i-1) = gbalpha
- x(l2403+i-1) = gbbeta
- x(l2404+i-1) = gbgamma
- end do
- end if
- end if
-
-! +---------------------------------------------------------------+
-! | Read EVB input file |
-! +---------------------------------------------------------------+
-
- if( ievb /= 0 ) then
-#ifdef MPI
- call evb_input
- call evb_init
-# if defined(LES)
-!KFW call evb_pimd_init
-# endif
-#else
- write(6,'(/2x,a)') 'Setting ievb>0 requires compilation with MPI'
- call mexit(6,1)
-#endif
- endif
-
- if( iyammp /= 0 ) write( 6, '(a)' ) ' Using yammp non-bonded potential'
-
- ! -------------------------------------------------------------------
- !
- ! -- add check to see if the space in nmr.h is likely to be
- ! too small for this run:
- ! [Note: this check does *not* indicate if MXTAU and MXP are
- ! too small. There is no easy way to ensure this, since
- ! the experimental intensities are read in a namelist
- ! command: if too many intensities are input, the read
- ! statment may cause a coredump before returning control
- ! to the main program. Be careful. sigh....]
-
- if (natom > matom .and. nmropt > 1) then
- write(6,*) 'WARNING: MATOM in nmr.h is smaller than the ', &
- natom,' atoms in this molecule.'
- write(6,*) 'Printout of NMR violations may be compromised.'
- end if
-
- ! -------------------------------------------------------------------
- ! --- checks on bogus data ---
- ! -------------------------------------------------------------------
-
- inerr = 0
-
- if( icfe < 0 .or. icfe > 1 ) then
- write(6,*) 'icfe must be 0 or 1 (icfe=2 is no longer supported)'
- inerr = 1
- end if
- if( icfe /= 0 .and. numgroup /= 2 ) then
- write(6,*) 'numgroup must be 2 if icfe is set'
- inerr = 1
- end if
- if (ievb>0) then
-#ifdef MPI
-!KFW if( numgroup /= 2 ) then
-!KFW write(6,*) 'numgroup must be 2 if ievb is set'
-!KFW inerr = 1
-!KFW end if
-#else
- write(6,'(/2x,a)') 'Setting ievb>0 requires compilation with MPI'
- inerr = 1
-#endif
- end if
-#ifdef PUPIL_SUPPORT
- ! BPR: PUPIL does not work with GB (or, I suppose, PB) for the
- ! time being. It is known to either crash or produce bogus
- ! results.
- if (igb > 0 .or. ipb /= 0) then
- write(6,'(a)') 'Cannot use implicit solvation (GB or PB) with PUPIL'
- inerr = 1
- end if
-#endif /*PUPIL_SUPPORT*/
- if( (igb > 0 .or. ipb /= 0) .and. numextra > 0) then
- write(6,'(a)') 'Cannot use igb>0 with extra-point force fields'
- inerr = 1
- end if
-
-!AMD validation
- if(iamd.gt.0)then
- if (EthreshD .eq. 0.d0 .and. alphaD .eq. 0.d0 .and. EthreshP .eq. 0.d0 .and. alphaP .eq. 0.d0) then
- write(6,'(a,i3)')'| AMD error all main parameters are 0.0 for Accelerated MD (AMD) or Windowed Accelerated MD (wAMD) '
- inerr = 1
- endif
- if(w_amd.gt.0)then
- if (EthreshD_w .eq. 0.d0 .and. alphaD_w .eq. 0.d0 .and. EthreshP_w .eq. 0.d0 .and. alphaP_w .eq. 0.d0) then
- write(6,'(a,i3)')'| AMD error all extra parameters are 0.0 for Windowed Accelerated MD (wAMD) LOWERING BARRIERS'
- inerr = 1
- endif
- endif
- endif
- if (iamd .gt. 0 .and. iamoeba ==1) then
- write(6,*)'amoeba is incompatible with AMD for now'
- inerr=1
- end if
-
- if (ips < 0 .or. ips > 6) then
- write(6,'(/2x,a,i3,a)') 'IPS (',ips,') must be between 0 and 6'
- inerr = 1
- end if
- if (ips /= 0 .and. ipol > 0 ) then
- write(6,'(/2x,a)') 'IPS and IPOL are inconsistent options'
- inerr = 1
- endif
- if (ips /= 0 .and. lj1264 /= 0) then
- write(6, '(/2x,a)') 'IPS and the LJ 12-6-4 potential are incompatible'
- inerr = 1
- endif
- if ( (igb > 0 .or. ipb /= 0) .and. ips > 0 ) then
- write(6,'(/2x,a,i3,a,i3,a)') 'IGB (',igb,') and ips (',ips, &
- ') cannot both be turned on'
- inerr = 1
- end if
- if (igb /= 0 .and. igb /= 1 .and. igb /= 2 .and. igb /= 5 &
- .and. igb /= 6 .and. igb /= 7 .and. igb /= 8 .and. igb /= 10) then
- write(6,'(/2x,a,i3,a)') 'IGB (',igb,') must be 0,1,2,5,6,7,8 or 10.'
- inerr = 1
- end if
- if (alpb /= 0 .and. alpb /= 1 ) then
- write(6,'(/2x,a,i3,a)') 'ALPB (',alpb,') must be 0 or 1.'
- inerr = 1
- end if
- if (alpb /= 0 .and. igb /= 1 .and. igb /= 2 .and. igb /= 5 .and. igb /=7 ) then
- write(6,'(/2x,a,i3,a)') 'IGB (',igb,') must be 1,2,5, or 7 if ALPB > 0.'
- inerr = 1
- end if
-
- if (jar < 0 .or. jar > 1) then
- write(6,'(/2x,a,i3,a)') 'JAR (',jar,') must be 0 or 1'
- inerr = 1
- end if
-
-#ifdef LES
- if( igb /= 0 .and. igb /= 1 .and. igb /= 5 .and. igb /=7 ) then
- write(6,'(/,a)') 'Error: LES is only compatible with IGB > 0,1,5,7'
- inerr = 1
- end if
- if( alpb /= 0) then
- write(6,'(/,a)') 'Error: LES is not compatible with ALPB'
- inerr = 1
- end if
- if( gbsa > 0 ) then
- write(6,'(/,a)') 'Error: LES is not compatible with GBSA > 0'
- inerr = 1
- end if
- if( qmmm_nml%ifqnt ) then
- write(6,'(/,a)') 'Error: LES is not compatible with QM/MM'
- inerr = 1
- end if
- if( ipol > 0 ) then
- write(6,'(/,a)') 'Error: LES is not compatible with IPOL > 0'
- inerr = 1
- end if
- if (temp0les >= 0.d0 .and. iscale > 0 ) then
- write (6,'(/,a)') 'Error: iscale cannot be used with temp0les'
- inerr = 1
- end if
-#endif
- if (irest /= 0 .and. irest /= 1) then
- write(6,'(/2x,a,i3,a)') 'IREST (',irest,') must be 0 or 1.'
- inerr = 1
- end if
- if (ibelly /= 0 .and. ibelly /= 1) then
- write(6,'(/2x,a,i3,a)') 'IBELLY (',ibelly,') must be 0 or 1.'
- inerr = 1
- end if
- if (imin < 0) then
- write(6,'(/2x,a,i3,a)') 'IMIN (',imin,') must be >= 0.'
- inerr = 1
- end if
- if (imin == 5) then
- if (ifbox /= 0 .and. ntb == 2) then
- write(6,'(/2x,a)') 'WARNING: IMIN=5 with changing periodic boundaries (NTB=2) can result in'
- write(6,'(/2x,a)') ' odd energies being calculated. Use with caution.'
- endif
-#ifdef MPI
- if (sandersize > 1 .and. ntb == 2) then
- write(6,'(/2x,a)') 'ERROR: IMIN=5 and NTB=2 cannot be run with multiple processors.'
- inerr = 1
- endif
-#endif
- end if
-
-
- if (iscale > mxvar) then
- write(6,9501) iscale,mxvar
- 9501 format('ERROR: ISCALE (',i5,') exceeds MXVAR (',i5, &
- '). See nmr.h')
- inerr = 1
- end if
- if (ntx < 1 .or. ntx > 7) then
- write(6,'(/2x,a,i3,a)') 'NTX (',ntx,') must be in 1..7'
- inerr = 1
- end if
-
- if (ntb /= 0 .and. ntb /= 1 .and. ntb /= 2) then
- write(6,'(/2x,a,i3,a)') 'NTB (',ntb,') must be 0, 1 or 2.'
- inerr = 1
- end if
- if (ntb == 0 .and. iwrap > 0) then
- write(6,'(/2x,a)') 'Error: IWRAP > 0 cannot be used without a periodic box.'
- inerr = 1
- end if
-
- if (ntt < 0 .or. ntt > 8) then ! APJ
- write(6,'(/2x,a,i3,a)') 'NTT (',ntt,') must be between 0 and 8.' ! APJ
- inerr = 1
- end if
- if (ntt == 1 .and. tautp < dt) then
- write(6, '(/2x,a,f6.2,a)') 'TAUTP (',tautp,') < DT (step size)'
- inerr = 1
- end if
- if( ntt < 3 .or. ntt > 8 ) then ! APJ
- if( gamma_ln > 0.d0 ) then
- write(6,'(a)') 'ntt must be 3 to 8 if gamma_ln > 0' ! APJ
- inerr = 1
- end if
- end if
-
- if ( ntt==3 .or. ntt==6 ) nchain = 0 !APJ: Langevin, Adaptive-Langevin must have chain set to zero. ! APJ
-
- if (ntt == 3 .or. ntt == 4) then
- if ( ntb == 2) then
- !Require gamma_ln > 0.0d0 for ntt=3 and ntb=2 - strange things happen
- !if you run NPT with NTT=3 and gamma_ln = 0.
- if ( gamma_ln <= 0.0d0 ) then
- write(6,'(a)') 'gamma_ln must be > 0 for ntt=3 .or. 4 with ntb=2.'
- inerr = 1
- end if
- end if
- end if
-
- if (ntp /= 0 .and. ntp /= 1 .and. ntp /= 2 .and. ntp /= 3) then
- write(6,'(/2x,a,i3,a)') 'NTP (',ntp,') must be 0, 1, 2, or 3.'
- inerr = 1
- end if
- if (ntp == 3 .and. csurften < 1) then
- write(6,'(/2x,a)') 'csurften must be greater than 0 for ntp=3.'
- inerr = 1
- end if
- if (ntp > 0 .and. taup < dt .and. barostat == 1) then
- write(6, '(/2x,a,f6.2,a)') 'TAUP (',taup,') < DT (step size)'
- inerr = 1
- end if
- if (npscal < 0 .or. npscal > 1) then
- write(6,'(/2x,a,i3,a)') 'NPSCAL (',npscal,') must be 0 or 1.'
- inerr = 1
- end if
- if (ntp > 0) then
- if (barostat /= 1 .and. barostat /= 2) then
- write(6, '(/2x,a,i3,a)') 'BAROSTAT (', barostat, ') must be 1 or 2'
- inerr = 1
- end if
- if (barostat == 2) then
- if (mcbarint <= 0) then
- write(6, '(/2x,a,i3,a)') 'MCBARINT (',mcbarint,') must be positive'
- inerr = 1
- end if
- if (mcbarint >= nstlim) then
- write(6, '(a)') 'WARNING: mcbarint is greater than the number of &
- &steps. This is effectively constant volume.'
- end if
- end if
- end if
-
- if (ntc < 1 .or. ntc > 4) then
- write(6,'(/2x,a,i3,a)') 'NTC (',ntc,') must be 1,2,3 or 4.'
- inerr = 1
- end if
- if (jfastw < 0 .or. jfastw > 4) then
- write(6,'(/2x,a,i3,a)') 'JFASTW (',jfastw,') must be 0->4.'
- inerr = 1
- end if
-
- if (ntf < 1 .or. ntf > 8) then
- write(6,'(/2x,a,i3,a)') 'NTF (',ntf,') must be in 1..8.'
- inerr = 1
- end if
-
- if (ioutfm /= 0 .and. ioutfm /= 1) then
- write(6,'(/2x,a,i3,a)') 'IOUTFM (',ioutfm,') must be 0 or 1.'
- inerr = 1
- end if
-
- if (ntpr < 0) then
- write(6,'(/2x,a,i3,a)') 'NTPR (',ntpr,') must be >= 0.'
- inerr = 1
- end if
- if (ntwx < 0) then
- write(6,'(/2x,a,i3,a)') 'NTWX (',ntwx,') must be >= 0.'
- inerr = 1
- end if
- if (ntwv < -1) then
- write(6,'(/2x,a,i3,a)') 'NTWV (',ntwv,') must be >= -1.'
- inerr = 1
- end if
- if (ntwf < -1) then
- write(6, '(/2x,a,i3,a)') 'NTWF (',ntwf,') must be >= -1.'
- inerr = 1
- end if
- if (ntwv == -1 .and. ioutfm /= 1) then
- write (6, '(/2x,a)') 'IOUTFM must be 1 for NTWV == -1.'
- inerr = 1
- end if
- if (ntwf == -1 .and. ioutfm /= 1) then
- write(6, '(/2x,a)') 'IOUTFM must be 1 for NTWF == -1.'
- inerr = 1
- end if
- if (ntwv == -1 .and. ntwx == 0) then
- write (6, '(/2x,a)') 'NTWX must be > 0 for NTWV == -1.'
- inerr = 1
- end if
- if (ntwe < 0) then
- write(6,'(/2x,a,i3,a)') 'NTWE (',ntwe,') must be >= 0.'
- inerr = 1
- end if
- if (ntave < 0) then
- write(6,'(/2x,a,i3,a)') 'NTAVE (',ntave,') must be >= 0.'
- inerr = 1
- end if
- if (ntr /= 0 .and. ntr /= 1) then
- write(6,'(/2x,a,i3,a)') 'NTR (',ntr,') must be 0 or 1.'
- inerr = 1
- end if
- if (ntrx /= 0 .and. ntrx /= 1) then
- write(6,'(/2x,a,i3,a)') 'NTRX (',ntrx,') must be 0 or 1.'
- inerr = 1
- end if
- if (nmropt < 0 .or. nmropt > 2) then
- write(6,'(/2x,a,i3,a)') 'NMROPT (',nmropt,') must be in 0..2.'
- inerr = 1
- end if
-
- if (idecomp < 0 .or. idecomp > 4) then
- write(6,'(/2x,a)') 'IDECOMP must be 0..4'
- inerr = 1
- end if
-
- ! check settings related to ivcap
-
- if(ivcap == 3 .or. ivcap == 4) then
- write(6,'(/2x,a)') 'IVCAP == 3 and IVCAP == 4 currently not implemented'
- inerr = 1
- endif
- if (ivcap < 0 .and. ivcap > 5) then
- write(6,'(/2x,a)') 'IVCAP must be 0 ... 5'
- inerr = 1
- end if
- if ((ivcap == 1 .or. ivcap == 5) .and. igb /= 10 .and. ipb == 0) then
- write(6,'(/2x,a)') 'IVCAP == 1,5 only works with Poisson Boltzmann (igb=10 or ipb/=0)'
- inerr = 1
- end if
- if((ivcap == 1 .or. ivcap == 3 .or. ivcap == 5 ) .and. cutcap <= 0.0d0) then
- write(6,'(/2x,a)') 'For IVCAP == 1,3, or 5, cutcap must be > 0.0'
- inerr = 1
- endif
- if (ivcap == 4 .and. &
- (xlorth < ZERO .or. ylorth < ZERO .or. zlorth < ZERO .or. &
-! give magic numbers a name srb aug 2007 !
- xorth > 47114710.0d0 .or. &
-! give magic numbers a name !
- yorth > 47114710.0d0 .or. &
-! give magic numbers a name !
- zorth > 47114710.0d0)) then
- write(6,'(/2x,a)') &
- 'For IVCAP == 4, xlorth, ylorth, zlorth, xorth, yorth, zorth must be set'
- inerr = 1
- end if
- if ((ivcap == 3 .or. ivcap == 4) .and. ibelly == 0) then
- write(6,'(/2x,a,a)') &
- 'For IVCAP == 3 or 4, ibelly must be 1 and all atoms', &
- ' not in the spherical or orthorhombic region must be set NOT moving'
- inerr = 1
- end if
- if (ivcap == 5 .and. (imin /= 1 .or. maxcyc > 1)) then
- write(6,'(/2x,a,a)') &
- 'IVCAP == 5 only works for single-point energy calculation'
- inerr = 1
- end if
-
- ! check if ifbox variable from prmtop file matches actual angles:
-
- if ( igb == 0 .and. ipb == 0 .and. ntb /= 0 ) then
- if ( ifbox == 1 ) then
- if ( abs(alpha - 90.0d0) > 1.d-5 .or. &
- abs(beta - 90.0d0) > 1.d-5 .or. &
- abs(gamma - 90.0d0) > 1.d-5 ) then
- ifbox =3
- write(6,'(a)') ' Setting ifbox to 3 for non-orthogonal unit cell'
- end if
- end if
-
- if ( ifbox == 2 ) then
- if ( abs(alpha - 109.4712190d0) > 1.d-5 .or. &
- abs(beta - 109.4712190d0) > 1.d-5 .or. &
- abs(gamma - 109.4712190d0) > 1.d-5 ) then
- write(6,'(/2x,a)') &
- 'Error: ifbox=2 in prmtop but angles are not correct'
- inerr = 1
- end if
- end if
- end if
-
- ! checks for targeted MD
- if (itgtmd /= 0 .and. itgtmd > 2) then
- write(6,'(/2x,a,i3,a)') 'ITGTMD (',itgtmd,') must be 0, 1 or 2.'
- inerr = 1
- end if
- if (itgtmd == 1 .and. ntr == 1) then
- if (len_trim(tgtfitmask) > 0 .or. len_trim(tgtrmsmask) <= 0) then
- write(6,'(/2x,a)') 'ITGTMD: tgtrmsmask (and not tgtfitmask) ' // &
- 'should be specified if NTR=1'
- inerr = 1
- end if
- end if
- ! skip this test until fallback to rgroup() is supported
- !if (itgtmd == 1 .and. ntr == 0) then
- ! if (len_trim(tgtfitmask) == 0 .and. len_trim(tgtrmsmask) == 0) then
- ! write(6,'(/2x,a)') &
- ! 'ITGTMD: both tgtfitmask and tgtrmsmask should be specified if NTR=0'
- ! inerr = 1
- ! end if
- !end if
-
- ! -- consistency checking
-
- if (imin > 0.and.nrespa > 1) then
- write(6,'(/2x,a)') 'For minimization, set nrespa,nrespai=1'
- inerr = 1
- end if
- if (ntp > 0 .and. nrespa > 1) then
- write(6,'(/2x,a)') 'nrespa must be 1 if ntp>0'
- inerr = 1
- end if
- if (ntx < 4.and.init /= 3) then
- write(6,'(/2x,a)') 'NTX / IREST inconsistency'
- inerr = 1
- end if
- if (ntb == 2 .and. ntp == 0) then
- write(6,'(/2x,a)') 'NTB set but no NTP option (must be 1 or 2)'
- inerr = 1
- end if
- if (ntp /= 0 .and. ntb /= 2) then
- write(6,'(/,a,a)')' NTP > 0 but not constant pressure P.B.C.', &
- ' (NTB = 2) must be used'
- inerr = 1
- end if
- if (ntb /= 0 .and. ifbox == 0 .and. ntp /= 0) then
- write(6,'(/,a)') ' (NTB /= 0 and NTP /= 0) but IFBOX == 0'
- write(6,'(/,a)') ' This combination is not supported'
- inerr = 1
- end if
- if (ntb /= 0 .and. &
- ( box(1) < 1.d0 .or. &
- box(2) < 1.d0 .or. &
- box(3) < 1.d0 ) ) then
- write(6,'(/,a,3f10.3)') ' BOX is too small: ',box(1),box(2),box(3)
- inerr = 1
- else if (ntb /= 0 .and. &
- (sqrt(cut) >= box(1)*0.5d0 .or. &
- sqrt(cut) >= box(2)*0.5d0 .or. &
- sqrt(cut) >= box(3)*0.5d0) ) then
- write(6,'(/,a)') ' CUT must be < half smallest box dimension'
- inerr = 1
- end if
- if (ntb /= 0 .and. (igb > 0 .or. ipb /= 0) ) then
- write(6,'(/,a)') ' igb>0 is only compatible with ntb=0'
- inerr = 1
- end if
-#ifdef APBS
- if ( ntb == 0 .and. sqrt(cut) < 8.05 .and. igb /= 10 .and. ipb == 0 .and. &
- .not. mdin_apbs) then
-#else
- if ( ntb == 0 .and. sqrt(cut) < 8.05 .and. igb /= 10 .and. ipb == 0 ) then
-#endif /* APBS */
- write(6,'(/,a,f8.2)') ' unreasonably small cut for non-periodic run: ', &
- sqrt(cut)
- inerr = 1
- end if
- if ( rgbmax < 5.d0*fsmax ) then
- write(6,'(/,a,f8.2)') ' rgbmax must be at least ', 5.d0*fsmax
- inerr = 1
- end if
- if (icfe /= 0 .and. indmeth == 3 ) then
- write(6,'(/,a)') ' indmeth=3 cannot be used with icfe>0'
- inerr = 1
- end if
- if (icfe /= 0 .and. ibelly /= 0 ) then
- write(6,'(/,a)') ' ibelly cannot be used with icfe'
- inerr = 1
- end if
-#ifdef MPI /* SOFT CORE */
- if (icfe /= 0 .and. dvdl_norest /= 0 ) then
- write(6,'(/,a)') 'dvdl_norest must == 0!'
- write(6,'(/,a)') 'The dvdl_norest option is deprecated.'
- write(6,'(/,a)') 'Restraint energies are seperated, &
- &and do not contribute to dvdl.'
- inerr = 1
- end if
-#endif
- ! Modification done by Ilyas Yildirim
- if (icfe == 1 .and. (klambda < 1 .or. klambda > 6)) then
- write(6,'(/,a)') ' klambda must be between 1 and 6'
- inerr = 1
- end if
- ! End of modification done by Ilyas Yildirim
-
- if (clambda < 0.d0 .or. clambda > 1.d0 ) then
- write(6,'(/,a)') ' clambda must be between 0 and 1'
- inerr = 1
- end if
-
- if (icfe /= 0 .and. (idecomp == 3 .or. idecomp == 4)) then
- write(6,'(/,a)') ' Pairwise decomposition for thermodynamic integration not implemented'
- inerr = 1
- end if
- if (icfe /= 0 .and. idecomp /= 0 .and. ipol > 0) then
- write(6,'(/,a)') ' IPOL is incompatible with IDECOMP and ICFE'
- inerr = 1
- end if
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) then
- if (ifsc == 2) then
- write (6,'(/,a)') 'The ifsc=2 option is no longer supported. &
- &Internal energies of the soft core region.'
- write (6,'(a)') 'are now handled implicitly and setting ifsc=2 &
- &is no longer needed'
- inerr = 1
- end if
- if (icfe /= 1 .and. ifsc==1) then
- write (6,'(/,a)') ' Softcore potential requires a standard TI run, set icfe to 1'
- inerr = 1
- end if
- if ( igb > 0 .or. ipb /= 0 ) then
- write (6,'(/,a)') ' Softcore potential is incompatible with GB (for now)'
- inerr = 1
- end if
- if ( ntf > 1 ) then
- write (6,'(/,a)') ' Softcore potentials require ntf=1 because SHAKE &
- &constraints on some bonds might be removed'
- inerr = 1
- end if
- if (clambda > 0.995 .or. clambda < 0.005) then
- write (6,'(/,a)') ' Softcore potentials cannot be used with clambda < 0.005 or > 0.995'
- inerr = 1
- end if
- if (klambda /= 1) then
- write (6,'(/,a)') ' Softcore potential requires linear mixing, set klambda to 1'
- inerr = 1
- end if
- if (imin == 1 .and. ntmin /= 2) then
- write (6,'(/,a)') ' Minimizations with ifsc=1 require the steepest descent algorithm.'
- write (6,'(/,a)') ' Set ntmin to 2 and restart'
- inerr = 1
- end if
- end if
- if (ifmbar /= 0) then
- if (icfe /= 1) then
- write (6,'(/,a)') ' MBAR requires a standard TI run, set icfe to 1'
- inerr = 1
- end if
- if (ifsc /=0 .and. (bar_l_max > 0.995 .or. bar_l_min < 0.005) ) then
- write (6,'(/,a)') ' Softcore potentials cannot be used with &
- &bar_l_min < 0.005 or bar_l_max > 0.995'
- inerr = 1
- end if
- if (klambda /= 1) then
- write (6,'(/,a)') ' MBAR requires linear mixing, set klambda to 1'
- inerr = 1
- end if
- end if
-#endif
-
- if (ilrt /= 0 .and. lrtmask == '') then
- write (6,'(a)') 'Linear Response Theory activated, but lrtmask is not set'
- inerr = 1
- end if
-
- if (idecomp > 0 .and. (ntr > 0 .or. ibelly > 0)) then
- write(6,'(/,a)') 'IDECOMP is not compatible with NTR or IBELLY'
- inerr = 1
- end if
- if (icnstph /= 0) then
-
- if ( icnstph < 0 ) then
- write(6, '(/,a)') 'icnstph must be greater than 0'
- inerr = 1
- end if
- if ( igb == 0 .and. ipb == 0 .and. icnstph == 1 ) then
- write(6, '(/,a)') 'Constant pH using icnstph = 1 requires &
- &GB implicit solvent'
- inerr = 1
- end if
- if ( ntb .eq. 0 .and. icnstph .gt. 1 ) then
- write(6, '(/,a)') 'Constant pH using icnstph = 2 requires &
- &periodic boundary conditions'
- inerr = 1
- end if
- if (icfe /= 0) then
- write(6, '(/,a)') &
- 'Constant pH and thermodynamic integration are incompatable'
- inerr = 1
- end if
-
- if (ntcnstph <= 0) then
- write(6, '(/,a)') 'ntcnstph must be a positive integer.'
- inerr = 1
- end if
-
- if (icnstph > 1 .and. mccycles <= 0) then
- write(6, '(/,a)') 'mccycles must be a positive integer.'
- inerr = 1
- end if
-
- end if ! icnstph
-
-#ifdef noVIRIAL
- if( ntp > 0 .and. barostat == 1 ) then
- write(6,'(/,a)') 'Error: Berendsen barostat is incompatible with noVIRIAL'
- inerr = 1
- end if
-#endif
-
- !-----------------------------------------------------
- ! ----sanity checks for Ewald
- !-----------------------------------------------------
-
- if( igb == 0 .and. ipb == 0 ) then
- call float_legal_range('skinnb: (nonbond list skin) ', &
- skinnb,skinlo,skinhi)
-
- ! --- Will check on sanity of settings after coords are read in
- ! and the extent of the system is determined.
-
- if(periodic == 1)then
- call float_legal_range('skinnb+cutoffnb: (nonbond list cut) ', &
- skinnb+cutoffnb,zero,sphere)
- end if
- if (ntb==0 .and. use_pme/=0) then
- write(6,'(/,a)') &
- 'Using PME with a non-periodic simulation does not make sense. Set either ntb>0 of use_pme=0.'
- inerr = 1
- end if
- call float_legal_range('a: (unit cell size) ',a,boxlo,boxhi)
- call float_legal_range('b: (unit cell size) ',b,boxlo,boxhi)
- call float_legal_range('c: (unit cell size) ',c,boxlo,boxhi)
- call float_legal_range('alpha: (unit cell angle) ', &
- alpha,anglo,anghi)
- call float_legal_range('beta: (unit cell angle) ', &
- beta,anglo,anghi)
- call float_legal_range('gamma: (unit cell angle) ', &
- gamma,anglo,anghi)
- call int_legal_range('order: (interpolation order) ', &
- order,orderlo,orderhi)
- call opt_legal_range('verbose: ',verbose,0,4)
- call opt_legal_range('netfrc: ',netfrc,0,1)
- call opt_legal_range('nbflag: ',nbflag,0,1)
- call opt_legal_range('nbtell: ',nbtell,0,2)
- call opt_legal_range('ew_type: ',ew_type,0,1)
- call opt_legal_range('vdwmeth: ',vdwmeth,0,2)
- call opt_legal_range('eedmeth: ',eedmeth,1,6)
- call opt_legal_range('ee_type: ',ee_type,1,2)
- call opt_legal_range('maxiter: ',maxiter,1,50)
- call opt_legal_range('indmeth: ',indmeth,0,3)
- call opt_legal_range('fix_quad: ',fix_quad,0,1)
- call float_legal_range('eedtbdns: (erfc table density) ', &
- eedtbdns,denslo,denshi)
- end if ! ( igb == 0 .and. ipb == 0 )
-
- if( ntb==2 .and. ipimd==1) then
- write(6,*) 'primitive PIMD is incompatible with NTP ensemble'
- inerr=1
- endif
-
- if( ntb==2 .and. ipimd==3 ) then
- write(6,*) 'CMD is incompatible with NTP ensemble'
- inerr=1
- endif
-
- if( ipimd==3 .and. adiab_param>=1.0 ) then
- write(6,*) 'For CMD adiab_param must be <=1'
- inerr=1
- endif
-
- if( ntb==2 .and. ipimd==4 ) then
- write(6,*) 'RPMD is incompatible with NTP ensemble'
- inerr=1
- endif
-
- if( ntt/=0 .and. ipimd==4 ) then
- write(6,*) 'RPMD is incompatible with NVT ensemble'
- inerr=1
- endif
-
- if( ntt/=4 .and. ipimd==2 ) then
- write(6,*) 'NMPIMD requires Nose-Hoover chains (ntt=4)'
- inerr=1
- endif
-
- if( ntt/=4 .and. ipimd==3 ) then
- write(6,*) 'CMD requires Nose-Hoover chains (ntt=4)'
- inerr=1
- endif
-
-#if !defined(MPI)
- if( ineb > 0 ) then
- write(6,*) 'NEB requires MPI'
- inerr=1
- endif
-#endif
-
-#ifdef LES
- if( ineb > 0 ) then
- write(6,*) 'NEB no longer works with LES: use multiple groups and a groupfile instead'
- inerr=1
- endif
-#endif
-
- if( ineb > 0 .and. ipimd > 0 ) then
- write(6,*) 'ineb>0 and ipimd>0 are incompatible options'
- inerr=1
- endif
-
- if( iamoeba == 1 )then
-#ifdef LES
- write(6,*)'amoeba is incompatible with LES'
- inerr=1
-#endif
-
- if( ntc > 1 ) then
- write(6,*) 'SHAKE (ntc>1) and amoeba are incompatible options'
- inerr=1
- end if
- if( ntp > 1 .and. beeman_integrator > 0 ) then
- write(6,*) 'ntp>1 is not consistent with the beeman integrator'
- inerr=1
- end if
- if ( igb /= 0 ) then
- write (6,'(/,a)') 'amoeba (iamoeba=1) is incompatible with GB (igb>0)'
- inerr=1
- end if
- if ( ipb /= 0 ) then
- write (6,'(/,a)') 'amoeba (iamoeba=1) is incompatible with PB (ipb>0)'
- inerr=1
- end if
-#ifdef MPI
- if (numtasks > 1) then
- write(6, '(/,a)') 'amoeba (iamoeba=1) cannot be run in parallel in &
- &sander'
- inerr=1
- end if
-#endif
-
- end if
-
- ! ---WARNINGS:
-
- if ( ibelly == 1 .and. igb == 0 .and. ipb == 0 .and. ntb /= 0 ) then
- write(6,'(/,a,/,a,/,a)') &
- 'Warning: Although EWALD will work with belly', &
- '(for equilibration), it is not strictly correct!'
- end if
-
- if (inerr == 1) then
- write(6, '(/,a)') ' *** input error(s)'
- call mexit(6,1)
- end if
-
- ! Load the restrained atoms (ntr=1) or the belly atoms (ibelly=1)
- ! or atoms for targeted md (itgtmd=1). Selections are read from
- ! &cntrl variables or, if these are not defined, it falls back to
- ! the old group input format.
-
- if(mtmd /= 'mtmd') then
- itgtmd = 2
- ntr = 0
- emtmd = 0.0d0
- end if
- konst = ntr > 0
- dotgtmd = itgtmd > 0
- belly = .false.
- natc = 0
- ngrp = 0
- natbel = 0
- nattgtfit = 0 ! number of atoms for tgtmd fitting (=overlap)
- nattgtrms = 0 ! number of atoms for tgtmd rmsd calculation
- nrc = 0
- if(konst.or.dotgtmd) then
-
- ! inserted here to fix the bug that coords are not available
- ! yet when distance based selection (<,>) is requested
-#ifdef LES
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0les,.FALSE.,solvph)
-#else
- call AMOEBA_check_newstyle_inpcrd(inpcrd,newstyle)
- if ( newstyle )then
- call AM_RUNMD_get_coords(natom,t,irest,ntb,x(lcrd),x(lvel))
- else
- if( irest == 1 .and. beeman_integrator > 0 ) then
- write(6,*) 'Cannot do a beeman_integrator restart with old-style coordinates'
- call mexit(6,1)
- end if
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.FALSE.,solvph)
- endif
-#endif
-
- if(itgtmd == 2) then
- call mtmdcall(emtmd,x(lmtmd01),ix(imtmd02),x(lcrd),x(lforce),ih(m04),ih(m02),ix(i02),&
- ih(m06),x(lmass),natom,nres,'READ')
- else
- ! DRR - Open and close calls are now in rdrest
- !if (ntrx <= 0) then
- ! call amopen(10,refc,'O','U','R')
- !else
- ! call amopen(10,refc,'O','F','R')
- !end if
- ! these messages should be written after "5. REFERENCE..." ?
- if (konst) write(6,9408)
- if (dotgtmd) write(6,9409)
-
- call rdrest(natom,ntrx,refc,x(lcrdr))
- !close(10)
-
-
-
-
- ! VH - tgtmd change: preferably call atommask() instead of rgroup()
- if (konst) then
- if( len_trim(restraintmask) <= 0 ) then
- call rgroup(natom,natc,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp),jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- else
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), restraintmask, ix(icnstrgp) )
-
- ! for now, emulate the "GATHER ALL THE CONSTRAINED ATOMS TOGETHER"
- ! section of rgroup(); later, the various masks should be done
- ! differently, i.e. without the "gather", as in the following:
- ! x(l60:l60+natom-1) = restraint_wt
- ! natc = sum(ix(icnstrgp:icnstrgp+natom-1))
-
- natc = 0
- do i=1,natom
- if( ix(icnstrgp-1+i) <= 0 ) cycle
- natc = natc + 1
- ix(icnstrgp-1+natc) = i
- x(l60-1+natc) = restraint_wt
- end do
- write(6,'(a,a,a,i5,a)') ' Mask ', &
- restraintmask(1:len_trim(restraintmask)), ' matches ',natc,' atoms'
- end if
- end if
- nrc = natc
-
- if (itgtmd == 1) then
- if (len_trim(tgtfitmask) <= 0 .and. len_trim(tgtrmsmask) <= 0) then
- ! the following if-endif can be deleted when we stop
- ! supporting rgroup()
- if (konst) then
- ! cannot do both ntr and tgtmd together using old group format
- write(6,'(/2x,a)') 'NTR must be 0 for targeted MD (TGTMD=1)'
- call mexit(6,1)
- else ! the following only for backward compatibility
- call rgroup(natom,natc,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp), &
- jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- ! tgtmd atoms are now stored in nattgt, igroup -> icnstrgp
- nattgtfit = natc
- nattgtrms = natc
- do i=1,nattgtfit
- ix(itgtfitgp-1+i) = ix(icnstrgp-1+i)
- ix(itgtrmsgp-1+i) = ix(icnstrgp-1+i)
- end do
- end if
- else
- if (ntr == 0) then ! read tgtfitmask only if ntr=1
- ! read in atom group for tgtmd fitting (=overlap region)
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtfitmask, ix(itgtfitgp) )
- ! see comments above (for ntr) for the following reduction cycle
- nattgtfit = 0
- do i=1,natom
- if( ix(itgtfitgp-1+i) <= 0 ) cycle
- nattgtfit = nattgtfit + 1
- ix(itgtfitgp-1+nattgtfit) = i
- end do
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtfitmask(1:len_trim(tgtfitmask)-1), &
- '" matches ',nattgtfit,' atoms'
- end if
- ! read in atom group for tgtmd rmsd calculation
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtrmsmask, ix(itgtrmsgp) )
- nattgtrms = 0
- do i=1,natom
- if( ix(itgtrmsgp-1+i) <= 0 ) cycle
- nattgtrms = nattgtrms + 1
- ix(itgtrmsgp-1+nattgtrms) = i
- end do
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtrmsmask(1:len_trim(tgtrmsmask)-1), &
- '" matches ',nattgtrms,' atoms'
- end if
- end if
-
- end if ! (itgtmd == 2)
-
- end if ! (konst.or.dotgtmd)
-
- if (ineb>0) then
- ! carlos: read in fitmask and rmsmask info for NEB, just as done for tgtmd
- ! init last_neb_atom, which is used to determine the limits for the
- ! communication of neighbor coordinates (to reduce size for explicit
- ! water)
- last_neb_atom = 0
-
- if (ntr /= 0) then
- write(6,'(/2x,a)') 'cannot use NEB with ntr restraints'
-! CARLOS: WHY NOT? SHOULD BE OK.
-! potential for user error is restrained region overlaps with NEB region. would
-! blow up.
- call mexit(6,1)
- else
- ! read in atom group for fitting (=overlap region)
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtfitmask, ix(itgtfitgp) )
- ! see comments above (for ntr) for the following reduction cycle
- nattgtfit = 0
- do i=1,natom
- if( ix(itgtfitgp-1+i) <= 0 ) cycle
- nattgtfit = nattgtfit + 1
- ix(itgtfitgp-1+nattgtfit) = i
- if (i.gt.last_neb_atom) last_neb_atom = i
- end do
- write(6,'(a)') "The following selection will be used for NEB structure fitting"
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtfitmask(1:len_trim(tgtfitmask)-1), &
- '" matches ',nattgtfit,' atoms'
- end if
- ! read in atom group for tgtmd rmsd calculation
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), tgtrmsmask, ix(itgtrmsgp) )
- nattgtrms = 0
- do i=1,natom
- if( ix(itgtrmsgp-1+i) <= 0 ) cycle
- nattgtrms = nattgtrms + 1
- ix(itgtrmsgp-1+nattgtrms) = i
- if (i.gt.last_neb_atom) last_neb_atom = i
- end do
- write(6,'(a)') "The following selection will be used for NEB force application"
- write(6,'(a,a,a,i5,a)') &
- ' Mask "', tgtrmsmask(1:len_trim(tgtrmsmask)-1), &
- '" matches ',nattgtrms,' atoms'
- write(6,'(/2x,a,i6)') "Last atom in NEB fitmask or rmsmask is ",last_neb_atom
-
- if (nattgtrms<=0 .or. nattgtfit <= 0) then
- write(6,'(/2x,a)') 'NEB requires use of tgtfitmask and tgtrmsmask'
- call mexit(6,1)
- endif
- endif
-
- ! dotgtmd may be false here even if doing tgtmd
- ! this is so belly info is read properly? following existing KONST code
-
- dotgtmd=.false.
- konst = .false.
- belly = ibelly > 0
- ngrp = 0
- if(belly) then
- ! inserted here to fix the bug that coords are not available
- ! yet when distance based selection (<,>) is requested
-#ifdef LES
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0les,.FALSE.,solvph)
-#else
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.FALSE.,solvph)
-#endif
- write(6,9418)
- if( len_trim(bellymask) <= 0 ) then
- call rgroup(natom,natbel,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(ibellygp), &
- jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- else
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), bellymask, ix(ibellygp) )
- natbel = sum(ix(ibellygp:ibellygp+natom-1))
- write(6,'(a,a,a,i5,a)') ' Mask ', &
- bellymask(1:len_trim(bellymask)), ' matches ',natbel,' atoms'
- end if
- end if
- call setvar(ix,belly)
-
- ! see if the user has input a noshakemask string, and process it:
- natnos = 0
- if( len_trim(noshakemask) > 0 ) then
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), noshakemask, noshakegp )
- natnos = sum(noshakegp(1:natom))
- write(6,*)
- write(6,'(a,a,a,i5,a)') 'Noshake mask ', &
- noshakemask(1:len_trim(noshakemask)), ' matches ',natnos,' atoms'
- call setnoshake(ix,noshakegp,ntc,num_noshake)
- if( ntf > 1 ) then
- write(6,'(a)') ' Setting ntf to 1'
- ntf = 1
- end if
- end if
-
- ! GMS ------------------------------------
- ! Check for 'iwrap_mask', and process it.
- ! ----------------------------------------
- n_iwrap_mask_atoms = 0
- if( len_trim(iwrap_mask) > 0 .and. iwrap == 2) then
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), iwrap_mask, iwrap_maskgp )
- ! iwrap_maskgp is a natom long integer array, with elements:
- ! 0 --> atom is not in iwrap_mask
- ! 1 --> atom is in iwrap_mask
- n_iwrap_mask_atoms = sum(iwrap_maskgp(1:natom))
- write(6,*)
- write(6,'(a,a,a,i5,a)') 'Wrap mask ', &
- iwrap_mask(1:len_trim(iwrap_mask)), ' matches ',n_iwrap_mask_atoms,' atoms:'
- ! Set an array to store the atom numbers of the atoms
- ! in the iwrap_mask
- allocate(iwrap_mask_atoms(n_iwrap_mask_atoms), stat=ier)
- REQUIRE(ier == 0)
-
- j = 0
- do i=1,natom
- if( iwrap_maskgp(i)>0 ) then
- j = j+1
- iwrap_mask_atoms(j) = i
- end if
- end do
-
- write(6,'(10i5)') (iwrap_mask_atoms(i),i=1,n_iwrap_mask_atoms)
- end if
-
-#ifdef MPI /* SOFT CORE */
- ! lower charges if a crgmask is set
- if ( len_trim(crgmask) > 0 ) then
- call atommask( natom, nres, 0, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), crgmask, crggp )
- write(6,'(a,a,a,i5,a)') 'Zero-Charge Mask ',crgmask(1:len_trim(crgmask)), ' matches ',sum(crggp(1:natom)),' atoms'
- call remove_charges(crggp, natom, x(l15))
- end if
-#endif
-
- konst = .false.
- belly = .false.
- if(idecomp > 0) then
- write(6,9428)
- call rgroup(natom,ntmp,nres,ngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(ibellygp), &
- jgroup,indx,irespw,npdec, &
- x(l60),x(lcrdr),konst,dotgtmd,belly,idecomp,5,.true.)
- end if
-
- if( ibelly > 0 .and. (igb > 0 .or. ipb /= 0) ) then
-
- ! ---here, the only allowable belly has just the first
- ! NATBEL atoms in the moving part. Check to see that this
- ! requirement is satisfied:
-
- do i=natbel+1,natom
- if( ix(ibellygp+i-1) /= 0 ) then
- write(6,*) 'When igb>0, the moving part must be at the'
- write(6,*) ' start of the molecule. This does not seem'
- write(6,*) ' to be the case here.'
- write(6,*) 'natbel,i,igroup(i) = ' &
- ,natbel,i,ix(ibellygp+i-1)
- call mexit(6,1)
- end if
- end do
- end if
-
-
- ! ----- CALCULATE THE SQUARE OF THE BOND PARAMETERS FOR SHAKE
- ! THE PARAMETERS ARE PUT SEQUENTIALLY IN THE ARRAY CONP -----
-
- do i=1,nbonh + nbona + nbper
- j = ix(iicbh+i-1)
- x(l50+i-1) = req(j)**2
- end do
-
-#ifdef MPI
- if( icfe /= 0 ) then
-
- ! use the masses of the prmtop file for the first group for both groups:
- ! [only the master nodes communicate here, since non-master nodes
- ! have not yet allocated space]
- ! This leads to problems for dual topology runs, and is therefore skipped
- ! if ifsc is set to one, the masses from both prmtop files are used
- if (ifsc == 0) then
- call mpi_bcast(x(lmass),natom,MPI_DOUBLE_PRECISION,0,commmaster,ierr)
- call mpi_bcast(x(lwinv),natom,MPI_DOUBLE_PRECISION,0,commmaster,ierr)
- call mpi_bcast(x(l75),natom,MPI_DOUBLE_PRECISION,0,commmaster,ierr)
- end if
- tmass = sum(x(lmass:lmass+natom-1))
- tmassinv = 1.d0/tmass
-
- ! next, do a minimal sanity check that the SHAKE parameters are
- ! consistent on the two processors:
-
- ! For Softcore this might be allowed
- ! Put a better check here later
- if( ntc == 2 .and. ifsc == 0) then
- partner = ieor(masterrank,1)
- call mpi_sendrecv( nbonh, 1, MPI_INTEGER, partner, 5, &
- nbonh_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( num_noshake, 1, MPI_INTEGER, partner, 5, &
- num_noshake_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr )
- if (qmmm_nml%ifqnt .and. qmmm_nml%qmshake == 0) then
- ! qtw - if qmshake=0, we need to check the QM atoms
- call mpi_sendrecv( &
- qmmm_struct%nquant, 1, MPI_INTEGER, partner, 5, &
- nquant_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr)
- call mpi_sendrecv( &
- qmmm_struct%noshake_overlap, 1, MPI_INTEGER,partner, 5, &
- noshake_overlap_c, 1, MPI_INTEGER, partner, 5, &
- commmaster, ist, ierr)
- if ( (qmmm_struct%nquant-qmmm_struct%noshake_overlap) /= &
- (nquant_c-noshake_overlap_c) ) then
- call sander_bomb('mdread2', &
- 'QMMM: NOSHAKE lists are not match in two groups!', &
- 'try noshakemask in cntrl to match the noshake list')
- end if
- else if( nbonh - num_noshake /= nbonh_c - num_noshake_c ) then
- write(6,*) 'SHAKE lists are not compatible in the two groups!'
- call mexit(6,1)
- end if
- else if( ntc == 3 ) then
- write(6,*) 'ntc = 3 is not compatible with icfe>0'
- call mexit(6,1)
- end if
-
- end if
-#endif
-
- if ( iamoeba /= 1 )then
- if( igb == 0 .and. ipb == 0 ) &
- call init_extra_pts( &
- ix(iibh),ix(ijbh),ix(iicbh), &
- ix(iiba),ix(ijba),ix(iicba), &
- ix(i24),ix(i26),ix(i28),ix(i30), &
- ix(i32),ix(i34),ix(i36),ix(i38), &
- ix(i40),ix(i42),ix(i44),ix(i46),ix(i48), &
- ix(i50),ix(i52),ix(i54),ix(i56),ix(i58), &
- ih(m06),ix,x,ix(i08),ix(i10), &
- nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req)
- endif
-
- ! DEBUG input; force checking
- call load_debug(5)
-
- return
- ! -------------------------------------------------------------------------
- ! Standard format statements:
-
- 9328 format(/80('-')/,' 2. CONTROL DATA FOR THE RUN',/80('-')/)
- 9408 format(/4x,'LOADING THE CONSTRAINED ATOMS AS GROUPS',/)
- 9409 format(/4x,'LOADING THE TARGETED MD ATOMS AS GROUPS',/)
- 9418 format(/4x,'LOADING THE BELLY ATOMS AS GROUPS',/)
- 9428 format(/4x,'LOADING THE DECOMP ATOMS AS GROUPS',/)
- 9008 format(a80)
-end subroutine mdread2
-
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Emit defined preprocessor names, ie, flags.
-subroutine printflags()
-
- implicit none
- integer max_line_length
- parameter ( max_line_length = 80 )
-
- character(len=max_line_length) line ! output string of active flags
- integer n ! len(line)
-
- line = '| Flags:'
- n = 8
-
-#ifdef ISTAR2
- call printflags2(' ISTAR2',7,n,line,.false.)
-#endif
-#ifdef MPI
- call printflags2(' MPI',4,n,line,.false.)
-# ifdef USE_MPI_IN_PLACE
- call printflags2(' USE_MPI_IN_PLACE',17,n,line,.false.)
-# endif
-#endif
-#ifdef LES
- call printflags2(' LES',4,n,line,.false.)
-#endif
-#ifdef NMODE
- call printflags2(' NMODE',6,n,line,.false.)
-#endif
-#ifdef HAS_10_12
- call printflags2(' HAS_10_12',10,n,line,.false.)
-#endif
-#ifdef DNA_SHIFT
- call printflags2(' DNA_SHIFT',10,n,line,.false.)
-#endif
-#ifdef MMTSB
- call printflags2(' MMTSB',6,n,line,.false.)
-#endif
-
-#ifdef noVIRIAL
- call printflags2(' noVIRIAL',9,n,line,.false.)
-#endif
-
- call printflags2(' ',1,n,line,.true.)
- return
-end subroutine printflags
-
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Primitive pre-Fortran90 implementation of printflags.
-subroutine printflags2(flag,flag_len,line_len,line,last)
-
- implicit none
- integer max_line_length
- parameter ( max_line_length = 80 )
-
- character(*) flag ! flag name with blank prefix, intent(in)
- integer flag_len ! len(flag), intent(in)
- integer line_len ! len(line), intent(inout)
- character(len=max_line_length) line ! intent(inout)
- logical last ! is this the last flag ?, intent(in)
-
- if (line_len + flag_len > max_line_length) then
- write( 6,'(a)') line
- ! begin another line
- line = '| Flags:'
- line_len=8
- end if
- line=line(1:line_len) // flag(1:flag_len)
- line_len=line_len+flag_len
- if(last)write( 6,'(a)') line
- return
-end subroutine printflags2
-
-!-------------------------------------------------
-! --- FLOAT_LEGAL_RANGE ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Check the range of a float; abort on illegal values.
-subroutine float_legal_range(string,param,lo,hi)
- implicit none
- _REAL_ param,lo,hi
- character(len=*)string
-
- if ( param < lo .or. param > hi )then
- write(6,59)
- write(6,60)string,param
- write(6,61)
- write(6,62)lo,hi
- write(6,63)
- call mexit(6,1)
- end if
- 59 format(/,1x,'Ewald PARAMETER RANGE CHECKING: ')
- 60 format(1x,'parameter ',a,' has value ',e12.5)
- 61 format(1x,'This is outside the legal range')
- 62 format(1x,'Lower limit: ',e12.5,' Upper limit: ',e12.5)
- 63 format(1x,'Check ew_legal.h')
- return
-end subroutine float_legal_range
-
-!-------------------------------------------------
-! --- INT_LEGAL_RANGE ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Check the range of an integer; abort on illegal values.
-subroutine int_legal_range(string,param,lo,hi)
- implicit none
- integer param,lo,hi
- character(len=*)string
-
- if ( param < lo .or. param > hi )then
- write(6,59)
- write(6,60)string,param
- write(6,61)
- write(6,62)lo,hi
- write(6,63)
- call mexit(6,1)
- end if
- 59 format(/,1x,'PARAMETER RANGE CHECKING: ')
- 60 format(1x,'parameter ',a,' has value ',i8)
- 61 format(1x,'This is outside the legal range')
- 62 format(1x,'Lower limit: ',i8,' Upper limit: ',i8)
- 63 format(1x,'The limits may be adjustable; search in the .h files ')
- return
-end subroutine int_legal_range
-
-!-------------------------------------------------
-! --- OPT_LEGAL_RANGE ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Check the range of an integer option; abort on illegal values.
-subroutine opt_legal_range(string,param,lo,hi)
- implicit none
- integer param,lo,hi
- character(len=*)string
-
- if ( param < lo .or. param > hi )then
- write(6,59)
- write(6,60)string,param
- write(6,61)
- write(6,62)lo,hi
- write(6,63)
- call mexit(6,1)
- end if
- 59 format(/,1x,'Ewald OPTION CHECKING: ')
- 60 format(1x,'option ',a,' has value ',i5)
- 61 format(1x,'This is outside the legal range')
- 62 format(1x,'Lower limit: ',i5,' Upper limit: ',i5)
- 63 format(1x,'Check the manual')
- return
-end subroutine opt_legal_range
-#endif /*ifndef PBSA*/
-
-!-------------------------------------------------
-! --- SANDER_BOMB ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Print an error message and quit
-subroutine sander_bomb(routine,string1,string2)
- implicit none
- character(len=*) routine,string1,string2
-
- write(6, '(1x,2a)') &
- 'SANDER BOMB in subroutine ', routine
- write(6, '(1x,a)') string1
- write(6, '(1x,a)') string2
- call mexit(6,1)
-end subroutine sander_bomb
-!-------------------------------------------------
-
-!-------------------------------------------------
-! --- remove_charges ---
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Zero charges on some atoms
-subroutine remove_charges(crggp,natom,charge)
- use constants, only: INV_AMBER_ELECTROSTATIC
- implicit none
- integer natom, crggp(*),i
- _REAL_ charge(*), charge_removed
-
- charge_removed = 0.d0
- do i=1,natom
- if (crggp(i)==1) then
- charge_removed = charge_removed + charge(i) * INV_AMBER_ELECTROSTATIC
- write (6,'(a,f12.4,a,i5)') 'Removing charge of ', charge(i) * INV_AMBER_ELECTROSTATIC,' from atom ',i
- charge(i)=0
- end if
- end do
- write(6, '(a,f12.4,a)') 'Total charge of ',charge_removed,' removed'
- RETURN
-end subroutine remove_charges
-!-------------------------------------------------
diff --git a/patches/amber14.diff/AmberTools/src/sander/runmd.F90 b/patches/amber14.diff/AmberTools/src/sander/runmd.F90
deleted file mode 100644
index 636fb881eac4c946d6778b65636f5abdf19457bc..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/runmd.F90
+++ /dev/null
@@ -1,5450 +0,0 @@
-! <compile=optimized>
-#include "copyright.h"
-#include "../include/dprec.fh"
-#include "../include/assert.fh"
-#include "ncsu-config.h"
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ driver routine for molecular dynamics
-subroutine runmd(xx,ix,ih,ipairs,x,winv,amass,f, &
- v,vold,xr,xc,conp,skip,nsp,tma,erstop, qsetup)
-
- ! Runmd operates in kcal/mol units for energy, amu for masses,
- ! and angstroms for distances. To convert the input time parameters
- ! from picoseconds to internal units, multiply by 20.455
- ! (which is 10.0*sqrt(4.184)).
-
- use state
-
-#if !defined(DISABLE_NCSU) && defined(NCSU_ENABLE_BBMD)
- use ncsu_sander_hooks, only : ncsu_on_mdstep => on_mdstep
-#endif
-
- use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms
- use cmd_vars, only: activate, file_pos_cmd, file_vel_cmd, file_nrg_cmd, &
- nstep_cmd, t_cmd, eq_cmd, restart_cmd, &
- etot_cmd, eke_cmd, temp_cmd
-
- use pimd_vars, only: ipimd, nbead, natomCL, &
- bnd_vir, Eimp_virial, equal_part, Epot_deriv, &
- tau_vol, Epot_spring, NMPIMD, CMD, cartpos, cartvel, &
- itimass, real_mass
-
- use neb_vars, only: ineb, neb_nbead
-
- use lscivr_vars, only: ilscivr, ndof_lsc, natom_lsc, mass_lsc, v2_lsc, &
- ilsc, x_lsc, f_lsc, dx_lsc
-
- use nose_hoover_module, only : thermo_lnv, x_lnv, x_lnv_old, v_lnv, &
- f_lnv_p, f_lnv_v, c2_lnv, mass_lnv, &
- Thermostat_init
-
-#ifdef RISMSANDER
- use sander_rism_interface, only: rismprm,rism_3d, RISM_NONE, RISM_FULL, RISM_INTERP, &
- rism_calc_type, rism_solvdist_thermo_calc, mylcm
-#endif
-
- use full_pimd_vars, only: totener,totenert,totenert2,mybeadid
-
- use qmmm_module, only : qmmm_nml,qmmm_struct, qmmm_mpi, qm2_struct, &
- qmmm_vsolv
- use file_io_dat
- use constants, only : third, ten_to_minus3, plumed, plumedfile
- use trace
- use stack
- use decomp, only : nat, nrs, decpr, jgroup, indx, irespw, &
-#ifdef MPI
- ! -- ti decomp
- collect_dec, &
-#endif
- checkdec, printdec
- use fastwt
- use bintraj, only: end_binary_frame
- use nblist,only: fill_tranvec,volume,oldrecip,ucell
-
- use nose_hoover_module, only: Thermostat_switch, &
- Thermostat_integrate_1, Thermostat_integrate_2, & ! APJ
- Thermostat_hamiltonian, & ! APJ
- Adaptive_Thermostat_integrate, & ! APJ
- Adaptive_Thermostat_hamiltonian, & ! APJ
- file_nhc, nchain, thermo, nthermo, Econserved ! APJ
-
-#ifdef MPI
- use evb_parm, only: evb_dyn, nbias
- use evb_data, only: evb_frc, evb_vel0, evb_bias, evb_nrg, evb_nrg_ave &
- , evb_nrg_rms, evb_nrg_tmp, evb_nrg_old, evb_nrg_tmp2 &
- , evb_nrg_old2
- use wigner, only: rflux
- use remd, only : rem, mdloop, remd_ekmh, repnum, stagid, my_remd_data, &
- hybrid_remd_ene, next_rem_method
-# ifdef LES
- use evb_pimd, only: evb_pimd_dealloc
- use miller, only: i_qi
-# endif
- use softcore, only: ifsc, sc_dvdl, sc_tot_dvdl, sc_tot_dvdl_partner, &
- sc_dvdl_ee, sc_tot_dvdl_ee, sc_tot_dvdl_partner_ee, &
- extra_atoms, mix_temp_scaling, sc_pscale, &
- adj_dvdl_stat, sc_mix_velocities, &
- sc_nomix_frc, sc_sync_x, sc_print_energies, &
- calc_softcore_ekin, &
- sc_ener, sc_ener_ave, sc_ener_rms, sc_lngdyn, &
- sc_ener_tmp, sc_ener_tmp2, sc_ener_old, sc_ener_old2, &
- sc_mix_position, sc_print_dvdl_values, &
- sc_degrees_o_freedom, dynlmb, sc_change_clambda, ti_ene_cnt, &
- sc_compare
- use mbar, only : ifmbar, bar_intervall, calc_mbar_energies, &
- bar_collect_cont, do_mbar
-#endif
-
- use amoeba_mdin, only: iamoeba
- use amoeba_runmd, only: AM_RUNMD_scale_cell
- use constantph, only: cnstphinit, cnstphwrite, cnstphupdatepairs, &
- cnstphbeginstep, cnstphendstep, chrgdat, &
- cnstph_explicitmd, cnstphwriterestart, cphfirst_sol
- use emap, only:temap,emap_move
- use barostats, only : mcbar_trial, mcbar_summary
-#ifdef EMIL
- use emil_mod, only : emil_do_calc, emil_calc_AMBER, &
- emil_save_pme, emil_save_gb, &
- emil_init, emil_step
-#endif
- use memory_module, only: coordinate, velocity, mass
-
-! Self-Guided molecular/Langevin Dynamics (SGLD)
- use sgld, only : isgld, isgsta,isgend,trxsgld, &
- sgenergy,sgldw,sgmdw,sgfshake, sg_fix_degree_count
-
- !AWG adaptive QM/MM
- use qmmm_adaptive_module, only: adaptive_qmmm
-
- use crg_reloc, only: ifcr, crprintcharges, cr_print_charge
-
- use abfqmmm_module, only: abfqmmm_param, abfqmmm_combine_forces ! lam81
-!AMD
- use amd_mod
-
-!scaledMD
- use scaledMD_mod
-
-!SEBOMD
- use sebomd_module, only : sebomd_obj, sebomd_gradient_write, sebomd_hessian_compute
-
-! Variable Descriptions
-!
-! Passed variables
-! xx : global real array. See locmem.f for structure/pointers
-! ix : global integer array. See locmem.f for structure/pointers
-! ih : global hollerith array. See locmem.f for structure/pointers
-! ipairs : ?? Global pairlist ?? --add description (JMS 11/2010)
-! x : global position array *
-! winv : array with inverse masses *
-! amass : mass array *
-! f : force array, used to hold old coordinates temporarily, too
-! v : velocity array
-! vold : old velocity array, from the previous step
-! xr : coordinates with respect to COM of molecule
-! conp : bond parameters for SHAKE
-! skip : logical skip array for SHAKE (and QM/MM too, I think)
-! nsp : submolecule index array (?)
-! tma : submolecular weight array (?)
-! erstop : should we stop in error (?)
-! qsetup : Not quite sure what this does, if anything anymore.
-!
-! Local variables
-! factt : degree-of-freedom correction factor for temperature scaling
-! nr : local copy of nrp, number of atoms
-! nr3 : 3 * nr, used for runtime efficiency
-!
-! Common memory variables
-! nrp : number of atoms, adjusted for LES copies
-
- implicit none
- character(kind=1,len=5) :: routine="runmd"
- integer ipairs(*), ix(*)
- _REAL_ xx(*)
- character(len=4) ih(*)
- _REAL_ combination, rem_val
-
-#ifdef MPI
-# include "parallel.h"
- include 'mpif.h'
-# ifdef LES
- _REAL_ :: fbead(3,natomCL), xbead(3,natomCL)
- integer :: mm, n
-# endif
- _REAL_ mpitmp(8) !Use for temporary packing of mpi messages.
- integer ist(MPI_STATUS_SIZE), partner, ierr
-#else
- ! mdloop and REM is always 0 in serial
- integer, parameter :: mdloop = 0, rem = 0
-#endif
-
-! The following variables are needed since nstep and nstlim
-! behave differently in a REMD run.
-! In certain places where output is required, total_nstep and total_nstlim
-! take the place of nstep and nstlim. This allows replica runs to output
-! less often than every exchange.
-! They are the absolute step # of the REMD or MD simulation.
- integer total_nstep, total_nstlim
-
-#include "../include/md.h"
-#include "box.h"
-#include "nmr.h"
-#include "tgtmd.h"
-#include "multitmd.h"
-#include "../include/memory.h"
-#include "extra.h"
-#include "ew_frc.h"
-#include "ew_cntrl.h"
-#include "ew_mpole.h"
-#include "def_time.h"
-#include "extra_pts.h"
-#if defined(LES)
-# include "les.h"
-#endif
-#include "../pbsa/pb_md.h"
-#include "../lib/random.h"
-
-! additional variables for PIMD output
- _REAL_ :: xcmd(3*natomCL),vcmd(3*natomCL)
- integer :: ncmd
- ! for const press PIMD
- _REAL_ tmpvir(3,3),atomvir
-
- _REAL_ sgsta_rndfp, sgend_rndfp, ignore_solvent
- _REAL_ sysx,sysy,sysz,sysrange(3,2)
- logical mv_flag
-
-#ifdef MMTSB
-# include "mmtsb.h"
- logical is_done_mmtsb ! MMTSB replica exchange calculation completed
- _REAL_ lambda_mmtsb ! MMTSB replica exchange new lambda
- _REAL_ pert_pe_mmtsb ! MMTSB lambda replica exchange perturbed PE
- _REAL_ temp_mmtsb ! MMTSB replica exchange new temperature
- _REAL_ unpert_pe_mmtsb ! MMTSB lambda replica exchange unperturbed PE
-#endif
-
- _REAL_ , dimension(1) :: shkh
- integer, dimension(1) :: ifstwr2
- integer :: nshkh
-
- integer idx, iatom, iatomCL,m
- _REAL_ Ekin2_tot,tmp ! APJ
- integer :: idim, ithermo
- _REAL_ :: E_nhc, exp1, exp2, v_sum
-
- logical ivscm
- logical qspatial
- character(len=6)fnam
-
- logical resetvelo
- integer nshak
- _REAL_ ekgs,eold3,eold4,etot_save,ekpbs
-
- logical do_list_update
- logical skip(*),belly,lout,loutfm,erstop,vlim,onstep
- _REAL_ x(*),winv(*),amass(*),f(*),v(*),vold(*), &
- xr(*),xc(*),conp(*)
- type(state_rec) :: ener ! energy values per time step
- type(state_rec) :: enert ! energy values tallied over the time steps
- type(state_rec) :: enert2 ! energy values squared tallied over the time steps
- type(state_rec) :: enert_old, enert2_old
- type(state_rec) :: enert_tmp, enert2_tmp
- type(state_rec) :: ecopy, edvdl
- type(state_rec) :: edvdl_r
- _REAL_ rmu(3),fac(3),onefac(3),clfac, etot_start
- _REAL_ tma(*)
-
- _REAL_ tspan,atempdrop,fln,scaltp,scaltpo
- _REAL_ vel,vel2,vcmx,vcmy,vcmz,vmax,vx,vy,vz
- _REAL_ winf,aamass,rterm,ekmh,ekph,ekpht,wfac,rsd,ekav
- _REAL_ fit,fiti,fit2,vscalt
- logical is_langevin ! Is this a Langevin dynamics simulation
- _REAL_ gammai,c_implic,c_explic,c_ave,sdfac,ekins0
- _REAL_ dtx,dtxinv,dt5,factt,ekin0,ekinp0,dtcp,dttp
- _REAL_ rndf,rndfs,rndfp,boltz2,pconv,tempsu
- _REAL_ xcm(3),acm(3),ocm(3),vcm(3),ekcm,ekrot
- _REAL_ emtmd
-
-! Variables and parameters for constant surface tension:
- _REAL_, parameter :: ten_conv = 100.0d0 !ten_conv - converts
- !dyne/cm to bar angstroms
- _REAL_ :: pres0x
- _REAL_ :: pres0y
- _REAL_ :: pres0z
- _REAL_ :: gamma_ten_int
- _REAL_ :: press_tan_ave
-
- integer nsp(*)
- integer idumar(4)
- integer l_temp
- integer i,j,im,i3,nitp,nits, iskip_start,iskip_end ! APJ
- integer nstep,nrep,nrek,nren,iend,istart3,iend3
- integer nrx,nr,nr3,ntcmt,izero,istart
- logical ixdump,ivdump,itdump,ifdump
- logical qsetup
- _REAL_, allocatable, dimension(:) :: for ! lam81
-#ifdef RISMSANDER
- logical irismdump
- _REAL_ cm(3),angvel(3),r(3),rxv(3),proj(3),moi,erot
-#endif
-
- integer nvalid, nvalidi
- _REAL_ eke,eket
- _REAL_ extent
-
- _REAL_ xcen,ycen,zcen,extents(3,2)
- _REAL_, allocatable, dimension(:) :: frcti
- integer ier
-
- _REAL_ small
- data small/1.0d-7/
- data nren/51/
-
- !--- VARIABLES FOR DIPOLE PRINTING ---
- integer prndipngrp
- integer prndipfind
- character(len=4) prndiptest
-
- _REAL_,parameter :: pressure_constant = 6.85695d+4
- ! variables used in constant pressure PIMD
- _REAL_ :: Nkt,centvir,pressure, aa, arg2, poly, e2, e4, e6, e8
- ! variable used in CMD
- real(8) :: tmp_eke_cmd !Use for temporary packing of mpi messages.
-
- _REAL_ :: box_center(3)
-
-! for adaptive qm/mm runs
-
- _REAL_ :: adqmmm_first_energy, etotcorr, tadc
- integer :: nstepadc
- logical :: flag_first_energy = .true.
-
- _REAL_ :: xold(3*natom)
- _REAL_ :: corrected_energy
- _REAL_ :: kinetic_E_save(2)
- integer :: aqmmm_flag
-
-! variables for plumed
- _REAL_ :: plumed_box(3,3),plumed_virial(3,3), plumed_kbt
- integer :: plumed_version,plumed_stopflag,plumed_ms
- _REAL_ :: plumed_energyUnits,plumed_timeUnits,plumed_lengthUnits,plumed_chargeUnits
-
- !==========================================================================
-
- call trace_enter( 'runmd' )
-
- ! ----- INITIALIZE SOME VARIABLES -----
-
-#ifdef MPI
- if( master ) then
- ! If remd, runmd will be called many times, so we dont want to open every
- ! time. For normal md, mdloop will just be 0.
- if (mdloop.eq.0) call amopen(7,mdinfo,'U','F',facc)
- endif
-
- if (rem < 3) then
- rem_val = temp0
- else if (rem == 4) then
- rem_val = solvph
- else
- rem_val = 0.d0
- end if
-#else
- if( master ) call amopen(7,mdinfo,'U','F','W')
-#endif
- vlim = vlimit > small
- ntcmt = 0
- izero = 0
- belly = ibelly > 0
- lout = .true.
- loutfm = ioutfm <= 0
- nr = nrp
- nr3 = 3*nr
- ekmh = 0.d0
-
- aqmmm_flag = 0
-
-#ifdef LES
- ekmhles = 0.d0
-#endif
- do_list_update=.false.
-#ifdef MPI
- if ( mpi_orig ) then
- istart = 1
- iend = natom
- else
- istart = iparpt(mytaskid) + 1
- iend = iparpt(mytaskid+1)
- end if
-#else
- istart = 1
- iend = nr
-#endif
- istart3 = 3*istart -2
- iend3 = 3*iend
-
-#ifdef MPI
- if( icfe /= 0 ) then
- allocate( frcti( nr3+3*extra_atoms ), stat = ier )
- REQUIRE( ier == 0 )
- end if
-#endif
-
- ! If NTWPRT.NE.0, only print the atoms up to this value
- nrx = nr3
- if (ntwprt > 0) nrx = ntwprt*3
-
- if (.not. allocated(for)) allocate(for(nr3)) ! lam81
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- if(abfqmmm_param%system == 1) then ! lam81
- if(abfqmmm_param%qmstep == 1) abfqmmm_param%v(1:nr3+iscale) = v(1:nr3+iscale) ! lam81
- v(1:nr3+iscale) = 0.d0 ! lam81
- t = t+dt ! lam81
- if(abfqmmm_param%maxqmstep == 0) t = 0 ! lam81
- else ! lam81
- v(1:nr3+iscale) = abfqmmm_param%v(1:nr3+iscale) ! lam81
- endif ! lam81
- endif ! lam81
-
- ! Cleanup the velocity if belly run
- if(belly) call bellyf(nr,ix(ibellygp),v)
-
- !=======================================================================
- ! Determine system degrees of freedom (for T scaling, reporting)
-
- ! Call DEGCNT to get the actual number of degrees of freedom for the
- ! solute and solvent. This call returns the correct numbers for belly
- ! simulations and simulations with separate solute/solvent scaling -- dap
- ! "IDUMAR" is dummy array. Used since this routine was also used w/ GIBBS.
-
-#ifdef LES
- ! return LES and non-LES degrees,
- ! since separate solvent coupling no longer used
- ! large changes to degcnt were made
- ! cnum is now passed (LES copy number of each atom)
- call degcnt(ibelly,nr,ix(ibellygp),nsolut,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0, &
- idumar,rndfp,rndfles,cnum,temp0les)
-
- ! RNDFP = # degrees of freedom for solute
- ! RNDFS = # degrees of freedom for solvent
- ! RNDF = total number of degrees of freedom.
- ! RNDFLES = # degrees of freedom for LES groups
-
- ! temp0les was init to negative number to signify not to use a LES bath
- ! just do standard code (meaning use solute/solvent baths)
- ! any positive (or zero) means to use LES bath with that target
-
- ! degcnt returns rndfs or rndfles in the rndfles variable
- ! depending on whether a LES bath was specified
- ! do this instead of duplicating call with rndfs or rndfles
-
- if (temp0les < 0.d0) then
- rndfs=rndfles
- rndfles=0.d0
- else
- rndfs=0.d0
- end if
-
- if (master) then
- write (6,'(a,f8.0)') &
- "# degrees of freedom in non-LES region: ",rndfp
- write (6,'(a,f8.0)') &
- "# degrees of freedom in LES region: ",rndfles
- end if
-
- ! modify RNDFP to reflect NDFMIN (set in mdread)
-
- rndfp = rndfp - ndfmin
-
- if (temp0les < 0.d0) then
- rndf = rndfp+rndfs
- else
- rndf = rndfp+rndfles
- end if
-
-#else
-
- call degcnt(ibelly,nr,ix(ibellygp),nsolut,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0, &
- idumar,rndfp,rndfs)
-
- ! RNDFP = # degrees of freedom for solute
- ! RNDFS = # degrees of freedom for solvent
- ! RNDF = total number of degrees of freedom.
-
-#ifdef MPI
- if (mdloop .eq. 0 .and. master) then
-#else
- if (master) then
-#endif
- if (abfqmmm_param%abfqmmm /= 1 .or. (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1)) then ! lam81
- write (6,'(a,f8.0)') &
- "| # of SOLUTE degrees of freedom (RNDFP): ",rndfp
- write (6,'(a,f8.0)') &
- "| # of SOLVENT degrees of freedom (RNDFS): ",rndfs
- end if ! lam81
- end if
- ! qtw - substract the number of overlapping noshake QM atoms in noshakemask
- rndfp = rndfp - qmmm_struct%noshake_overlap
- ! modify RNDFP to reflect NDFMIN (set in mdread) and num_noshake
- rndfp = rndfp - ndfmin + num_noshake
- rndf = rndfp + rndfs
-#ifdef MPI
- if (mdloop .eq. 0 .and. master) then
-#else
- if (master) then
-#endif
- if (abfqmmm_param%abfqmmm /= 1 .or. (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1)) then ! lam81
- if (qmmm_nml%ifqnt) then
- write (6,'(a,i6)') &
- "| QMSHAKE_NOSHAKEMASK_OVERLAP = ", qmmm_struct%noshake_overlap
- endif
- write (6,'(a,f8.0,a,i6,a,f8.0)') &
- "| NDFMIN = ",rndfp, " NUM_NOSHAKE = ",num_noshake, " CORRECTED RNDFP = ", rndfp
- write (6,'(a,f8.0)') &
- "| TOTAL # of degrees of freedom (RNDF) = ", rndf
- end if ! lam81
- end if
-
-#endif
-
- call fix_degree_count(rndf) ! correct for extra points
-! Warning - NOTE that rndfp, rndfs are uncorrected in an extra points context!
-
-#ifndef LES
- if (isgld > 0) then
- ! number of degrees of freedom in the SGLD part
- if (isgsta == 1) then
- sgsta_rndfp = 0
- else
- call degcnt(ibelly,nr,ix(ibellygp),isgsta-1,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0,idumar,sgsta_rndfp,ignore_solvent)
- end if
- if (isgend == nr) then
- sgend_rndfp = rndf
- else
- call degcnt(ibelly,nr,ix(ibellygp),isgend,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0,idumar,sgend_rndfp,ignore_solvent)
- end if
-! Warning - NOTE that the solute ndf outputs above from degcnt are uncorrected
-! for qmmm_struct%noshake_overlap, num_noshake, and extra points;
-! also ndfmin is not always being handled.
- call sg_fix_degree_count(sgsta_rndfp, sgend_rndfp, ndfmin, rndf)
- end if
-#endif
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /=0 ) call sc_degrees_o_freedom(ndfmin)
-#endif
-
- ! End of degrees of freedom setup
- !=======================================================================
-
- boltz2 = 8.31441d-3 * 0.5d0
- pconv = 1.6604345d+04 ! factor to convert the pressure kcal/mole to bar
-
- ! ---convert to kcal/mol units
-
- boltz2 = boltz2/4.184d0 ! k-sub-B/2
- dtx = dt*20.455d+00
- dtxinv = 1.0d0 / dtx
- dt5 = dtx * 0.5d0
- pconv = pconv*4.184d0
-
- ! FAC() are #deg freedom * kboltz / 2
- ! multiply by T to get expected kinetic energy
- ! FAC(1) is for total system
-
- fac(1) = boltz2*rndf
- fac(2) = boltz2*rndfp
-
- if(rndfp < 0.1d0) fac(2) = 1.d-6
-
-#ifdef LES
- ! replaced solvent variables with LES ones
- ! since separate solvent coupling no longer used
- ! ASSUME SAME COUPLING CONSTANT FOR BOTH BATHS, just different target T
-
- ! will also have to accumulate LES and non-LES kinetic energies separately
-
- if (temp0les < 0.d0) then
- fac(3) = boltz2*rndfs
- if(rndfs < 0.1d0) fac(3) = 1.d-6
- else
- fac(3) = boltz2*rndfles
- if(rndfles < 0.1d0) fac(3) = 1.d-6
- end if
-#else
- fac(3) = boltz2*rndfs
- if(rndfs < 0.1d0) fac(3) = 1.d-6
-#endif
- if ( ipimd==CMD ) then
- if ( eq_cmd ) then
- fac(1) = boltz2 * dble( 3*natomCL )
- else
- fac(1) = boltz2 * dble( 3*(natomCL-1) )
- endif
- endif
- onefac(1) = 1.0d0/fac(1)
- onefac(2) = 1.0d0/fac(2)
- onefac(3) = 1.0d0/fac(3)
- factt = rndf/(rndf+ndfmin)
-
- ! these are "desired" kinetic energies based on
- ! # degrees freedom and target temperature
- ! they will be used for calculating the velocity scaling factor
-
- ekinp0 = fac(2)*temp0
-#ifdef LES
-
- ! modified for LES temperature
-
- ekins0=0.d0
- ekinles0=0.d0
- if (temp0les < 0.d0) then
- ekins0 = fac(3) * temp0
- ekin0 = fac(1) * temp0
- if (master) &
- write (6,*) "Single temperature bath for LES and non-LES"
- else
- ekinles0 = fac(3)*temp0les
- ekin0 = ekinp0 + ekinles0
- if (master) then
- write (6,*) "LES particles coupled to separate bath"
- write (6,'(a,f8.2)')" LES target temperature: ",temp0les
- write (6,'(a,f8.2)')" LES target kinetic energy: ",ekinles0
- write (6,'(a,f8.2)')"non-LES target temperature: ",temp0
- write (6,'(a,f8.2)')"non-LES target kinetic energy: ",ekinp0
- end if
- end if
-#else
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-#endif
-
-#ifdef LES
- if(abfqmmm_param%abfqmmm /= 1) then ! lam81
- if ( ntt==4 ) call nose_hoover_init_LES(amass,v,f) ! APJ
- else ! lam81
- if ( ntt==4 .and. abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1 ) & ! lam81
- call nose_hoover_init_LES(amass,abfqmmm_param%v,abfqmmm_param%f) ! lam81
- endif ! lam81
-#else
- if(abfqmmm_param%abfqmmm /= 1) then ! lam81
- if ( ntt>=4 .and. ntt<=8 ) call nose_hoover_init(amass,v,f) ! APJ
- else ! lam81
- if ( ntt>=4 .and. ntt<=8 .and. abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1 ) & ! lam81
- call nose_hoover_init(amass,abfqmmm_param%v,abfqmmm_param%f) ! lam81
- endif
-#endif
-
- ! Langevin dynamics setup:
-
- is_langevin = gamma_ln > 0.0d0
- gammai = gamma_ln/20.455d0
- c_implic = 1.d0/(1.d0+gammai*dt5)
- c_explic = 1.d0 - gammai*dt5
- c_ave = 1.d0+gammai*dt5
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
-#ifdef LES
- if( temp0les < 0.d0 ) then
- sdfacles = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
- else
- sdfacles = sqrt( 4.d0*gammai*boltz2*temp0les/dtx )
- endif
-#endif
- if (is_langevin .and. ifbox==0) then
- call get_position(nr,x,sysx,sysy,sysz,sysrange,0)
-#ifdef MPI /* SOFT CORE */
- if (ifsc == 1) call sc_mix_position(sysx,sysy,sysz,clambda)
-#endif
- end if
-
- ! Constant pH setup
- !
- if (icnstph /= 0 .and. mdloop .eq. 0) &
- call cnstphinit(x, ig)
-
- if (ntt == 1) dttp = dt/tautp
- if (ntp > 0) dtcp = comp * 1.0d-06 * dt / taup
-
- ! Constant surface tension setup:
-
- if (csurften > 0) then
-
- ! Set pres0 in direction of surface tension.
- ! The reference pressure is held constant in on direction dependent
- ! on what the surface tension direction is set to.
- if (csurften .eq. 1) then ! pres0 in the x direction
- pres0x = pres0
-
- else if (csurften .eq. 2) then ! pres0 in the y direction
- pres0y = pres0
-
- !else if (csurften .eq. 3) then ! pres0 in the z direction
- else
- pres0z = pres0
-
- end if
-
- ! Multiply surface tension by the number of interfaces
- gamma_ten_int = dble(ninterface) * gamma_ten
-
- end if
-
- nrek = 4
- nrep = 15
-
- nvalid = 0
- nvalidi = 0
- nstep = 0
- total_nstep = 0
-#ifdef MPI
- ! For REMD, total_nstep is the number of steps * the number of exchanges
- ! we've already attempted
- if (rem /= 0) &
- total_nstep = (mdloop - 1) * nstlim
-#endif
- fit = 0.d0
- fiti = 0.d0
- fit2 = 0.d0
-
- ! Zero all elements of these sequence types
- ener = null_state_rec
- enert = null_state_rec
- enert2 = null_state_rec
- enert_old = null_state_rec
- enert2_old = null_state_rec
- edvdl = null_state_rec
- edvdl_r = null_state_rec
- ! for PIMD/NMPIMD/CMD/RPMD:
- totenert = null_state_rec
- totenert2 = null_state_rec
-
- ener%kin%pres_scale_solt = 1.d0
- ener%kin%pres_scale_solv = 1.d0
- ener%box(1:3) = box(1:3)
-
-
- ener%cmt(1:4) = 0.d0
- nitp = 0
- nits = 0
-
-! init PLUMED
- if(plumed.eq.1) then
- call plumed_f_gcreate()
-#ifdef DPREC
- call plumed_f_gcmd("setRealPrecision"//char(0),8)
-#else
- call plumed_f_gcmd("setRealPrecision"//char(0),4)
-#endif
- call plumed_f_gcmd("getApiVersion"//char(0),plumed_version)
- if(plumed_version>1)then
- plumed_kbt=2.0*temp0*boltz2
- call plumed_f_gcmd("setKbT"//char(0),plumed_kbt)
- endif
- plumed_energyUnits=4.184
- plumed_lengthUnits=0.1
- plumed_timeUnits=1.0
- plumed_chargeUnits=1.0/18.2223
- call plumed_f_gcmd("setMDEnergyUnits"//char(0),plumed_energyUnits)
- call plumed_f_gcmd("setMDLengthUnits"//char(0),plumed_lengthUnits)
- call plumed_f_gcmd("setMDTimeUnits"//char(0),plumed_timeUnits)
- if(plumed_version>3)then
- call plumed_f_gcmd("setMDChargeUnits"//char(0),plumed_chargeUnits)
- endif
- call plumed_f_gcmd("setPlumedDat"//char(0),trim(adjustl(plumedfile))//char(0))
- call plumed_f_gcmd("setNatoms"//char(0),nr)
- call plumed_f_gcmd("setMDEngine"//char(0),"amber")
- call plumed_f_gcmd("setTimestep"//char(0),dt)
-# ifdef MPI
- call plumed_f_gcmd("setMPIFComm"//char(0),commsander)
- if(numgroup>1)then
- call plumed_f_gcmd("GREX setMPIFIntracomm"//char(0),commsander)
- if(master) then
- call plumed_f_gcmd("GREX setMPIFIntercomm"//char(0),commmaster)
- endif
- call plumed_f_gcmd("GREX init"//char(0),0)
- endif
-# endif
- call plumed_f_gcmd("init"//char(0),0);
-
-
-! if(ifbox/=0 .and. ifbox/=1 .and. ifbox/=2) then
-! write (6,*) "!!!!! PLUMED ERROR: Only orthorhombic and truncted octahedron cells are supported in this release."
-! write (6,*) "!!!!! ABORTING RUN"
-! stop
-! endif
-! call init_metadyn(nr,dt,amass,xx(l15),ifbox,0,trim(adjustl(plumedfile))//char(0))
- continue
- endif
- ! end init PLUMED
-
-
-
- !=======================================================================
- ! ----- MAKE A FIRST DYNAMICS STEP -----
- !=======================================================================
- ! init = 3: general startup if not continuing a previous run
-
- if( ipimd.eq.NMPIMD .or. ipimd.eq.CMD) then
- call trans_pos_cart_to_nmode( x )
- end if
-
- if( init == 3 .or. nstlim == 0 .or. (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1) ) then ! lam81
- if (ntp > 0 .and. iamoeba==0 .and. ipimd==0) then
- xr(1:nr3) = x(1:nr3)
-
- ! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
- ! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
- ! MASS -----
- call ekcmr(nspm,nsp,tma,ener%cmt,xr,v,amass,1,nr)
- end if
-
- ! ----- CALCULATE THE FORCE -----
-
- ! --- set irespa to get full energies calculated on step "0":
- irespa = 0
- iprint = 1
-
- if(ipimd==NMPIMD .or. ipimd==CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- call force(xx,ix,ih,ipairs,cartpos,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-#if defined(MPI) && defined(LES)
- if ( ievb == 1 .and. i_qi > 0) then
- call evb_umb ( f, cartpos, real_mass, natom, istart3, iend3 )
-! 03132009 if( i_qi == 2 ) call qi_corrf_les ( cartpos, amass )
- if( i_qi == 2 ) call qi_corrf_les ( cartpos, real_mass )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- call trans_frc_cart_to_nmode(f)
- i3 = 3*(istart-1)
-
-#if defined(MPI) && defined(LES)
- if ( ievb /= 0 .and. i_qi == 0 ) then
- call evb_umb ( f, x, real_mass, natom, istart3, iend3 )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- else if ( ilscivr == 1 )then
- ! prepare the Hessian Matrix of the potential for the LSC-IVR
- ! at this point, x is the position a bead at equilibrium
- ! initialize the LSC-IVR variables
- natom_lsc = natom
- ndof_lsc = natom * 3
-
- call lsc_init
- do ilsc = 1, natom_lsc
- mass_lsc(3*ilsc-2) = amass(ilsc)
- mass_lsc(3*ilsc-1) = amass(ilsc)
- mass_lsc(3*ilsc ) = amass(ilsc)
- end do
- v2_lsc = 0.0d0
- do ilsc = 1, ndof_lsc
- ! ith vector of the Hesian matrix
- x_lsc = 0.0d0
- x_lsc(1:ndof_lsc) = x(1:ndof_lsc)
- x_lsc(ilsc) = x(ilsc) + dx_lsc
- call force(xx,ix,ih,ipairs,x_lsc,f_lsc,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
-#ifdef MPI
- call xdist( f_lsc, xx(lfrctmp), natom )
-#endif
- v2_lsc(1:ndof_lsc,ilsc) = f_lsc(1:ndof_lsc)
- enddo
-
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
-#ifdef MPI
- call xdist(f, xx(lfrctmp), natom)
-#endif
- ! 2nd derivative of the potential:
- do ilsc = 1, ndof_lsc
- v2_lsc(1:ndof_lsc,ilsc) = &
- ( f(1:ndof_lsc) - v2_lsc(1:ndof_lsc,ilsc) )/dx_lsc
- end do
-
- ! get the iniital position of the momentum:
- call lsc_xp(x,v)
-
- else
-
- ! -- ti decomp
- if(idecomp > 0) then
- decpr = .false.
- if(mod(nstep+1,ntpr) == 0) decpr = .true.
- end if
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-#ifdef MPI
- if ( ievb /= 0 ) then
-#ifdef LES
- call evb_umb_primitive ( f, x, real_mass, natom, istart, iend )
-#else
- call evb_umb_primitive ( f, x, amass, natom, istart, iend )
-#endif
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- endif
-
- if (sebomd_obj%do_sebomd) then
- ! computes hessian matrix if necessary
- if (sebomd_obj%ntwh /= 0) then
- ! don't output atomic charges
- sebomd_obj%iflagch_old = sebomd_obj%iflagch
- sebomd_obj%iflagch = 0
- call sebomd_gradient_write(f,3*natom)
- call sebomd_hessian_compute(xx,ix,ih,ipairs,x,f,ener, &
- qsetup, do_list_update, nstep)
- sebomd_obj%iflagch = sebomd_obj%iflagch_old
- endif
- endif
-
-
- if (icnstph /= 0 .and. master .and. &
- ((rem /= 0 .and. mdloop > 0) .or. rem == 0)) call cnstphwrite(rem)
-
- for(1:nr3) = f(1:nr3) ! lam81
-#ifdef MPI
- call xdist(for,xx(lfrctmp),natom) ! lam81
-#endif
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-
- if(abfqmmm_param%system == 1) abfqmmm_param%f1(1:nr3) = for(1:nr3) ! lam81
-
- if(abfqmmm_param%system == 2) then ! lam81
- abfqmmm_param%f2(1:nr3) = for(1:nr3) ! lam81
- call abfqmmm_combine_forces() ! lam81
- for(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- f(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- end if ! lam81
-
- end if ! lam81
-
- ! This FORCE call does not count as a "step". CALL NMRDCP to decrement
- ! local NMR step counter and MTMDUNSTEP to decrease the local MTMD step
- ! counter
- call nmrdcp
- call mtmdunstep
-
- !PLUMED force added
- plumed_stopflag=0
- if(plumed.eq.1) then
- call plumed_f_gcmd("setStep"//char(0),nstep)
- call plumed_f_gcmd("setPositions"//char(0),x)
- call plumed_f_gcmd("setMasses"//char(0),amass)
- call plumed_f_gcmd("setCharges"//char(0),xx(l15))
- call plumed_f_gcmd("setEnergy"//char(0),ener%pot)
- call plumed_f_gcmd("setForces"//char(0),f)
- call plumed_f_gcmd("setStopFlag"//char(0),plumed_stopflag)
- plumed_box=0.0
- if(ifbox==0) then
- continue
- else if(ifbox==1) then
- plumed_box(1,1)=box(1)
- plumed_box(2,2)=box(2)
- plumed_box(3,3)=box(3)
- else if(ifbox==2) then
-! truncated octahedron, corresponding to a bcc lattice
-! in AMBER convention, box(1) is the length of the lattice vector
-! a is defined so as the bcc lattice is (a/2,a/2,a/2) (-a/2,-a/2,a/2) (a/2,-a/2,-a/2)
- plumed_box(1,1)=sqrt(1.0/3.0)*box(1)
- plumed_box(2,1)=sqrt(1.0/3.0)*box(1)
- plumed_box(3,1)=sqrt(1.0/3.0)*box(1)
- plumed_box(1,2)=-sqrt(1.0/3.0)*box(1)
- plumed_box(2,2)=-sqrt(1.0/3.0)*box(1)
- plumed_box(3,2)=sqrt(1.0/3.0)*box(1)
- plumed_box(1,3)=sqrt(1.0/3.0)*box(1)
- plumed_box(2,3)=-sqrt(1.0/3.0)*box(1)
- plumed_box(3,3)=-sqrt(1.0/3.0)*box(1)
- else
- write (6,*) "!!!!! PLUMED ERROR: Only orthorhombic and truncted octahedron cells are supported in this release."
- write (6,*) "!!!!! ABORTING RUN"
- stop
- endif
- plumed_virial=0.0
- plumed_virial(1,1)=2.0*ener%vir(1)
- plumed_virial(2,2)=2.0*ener%vir(2)
- plumed_virial(3,3)=2.0*ener%vir(3)
- call plumed_f_gcmd("setVirial"//char(0),plumed_virial)
- call plumed_f_gcmd("setBox"//char(0),plumed_box)
- call plumed_f_gcmd("calc"//char(0),0);
-#ifdef MPI
-! this is required since PLUMED only updates virial on master processor
-#ifdef DPREC
- call mpi_bcast(plumed_virial,9,MPI_DOUBLE_PRECISION,0,commsander,ierr)
-#else
- call mpi_bcast(plumed_virial,9,MPI_REAL,0,commsander,ierr)
-#endif
-#endif
- ener%vir(1)=0.5*plumed_virial(1,1)
- ener%vir(2)=0.5*plumed_virial(2,2)
- ener%vir(3)=0.5*plumed_virial(3,3)
- end if
-
- !PLUMED end
-
-
-#ifdef MPI /* SOFT CORE */
- ! If softcore potentials are used, collect their dvdl contributions:
- if ( ifsc /= 0 ) then
- call mpi_reduce(sc_dvdl, sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl=0.0d0 ! zero for next step
- call mpi_reduce(sc_dvdl_ee, sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl_ee=0.0d0 ! zero for next step
- call mpi_reduce(sc_ener, sc_ener_tmp, ti_ene_cnt, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_ener(1:ti_ene_cnt) = sc_ener_tmp(1:ti_ene_cnt)
- end if
- if ( ifsc == 2 ) then
- ! If this is a perturb to nothing run, scale forces and calculate dvdl
- call sc_nomix_frc(f,nr3,ener)
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-
- if( icfe /= 0 )then
- ! ---free energies using thermodynamic integration (icfe /= 0)
-
- if( master ) then
- ! --- first, send the forces and energy to your partner:
- partner = ieor(masterrank,1)
- call mpi_sendrecv( f, nr3, MPI_DOUBLE_PRECISION, partner, 5, &
- frcti, nr3+3*extra_atoms, MPI_DOUBLE_PRECISION, &
- partner, 5, commmaster, ist, ierr )
- call mpi_sendrecv( ener, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- ecopy, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr)
- ! exchange sc-dvdl contributions between masters
- call mpi_sendrecv( sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, partner, &
- 5, sc_tot_dvdl_partner, 1, &
- MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, partner, &
- 5, sc_tot_dvdl_partner_ee, 1, &
- MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- if( masterrank==0 ) then
- call mix_frcti(frcti,ecopy,f,ener,nr3,clambda,klambda)
- else
- call mix_frcti(f,ener,frcti,ecopy,nr3,clambda,klambda)
- end if
- end if
-
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
-
- end if
-
-#endif /* MPI SOFT CORE */
-
- irespa = 1
-
- ! Reset quantities depending on TEMP0 and TAUTP (which may have been
- ! changed by MODWT during FORCE call).
- ! Recalculate target kinetic energies.
-
- ekinp0 = fac(2) * temp0
-
-#ifdef LES
-
- ! modified for LES temperature, not solvent
-
- ekins0 = 0.d0
- ekinles0 = 0.d0
- if (temp0les < 0.d0) then
- ekins0 = fac(3) * temp0
- ekin0 = fac(1) * temp0
- else
- ekinles0 = fac(3) * temp0les
- ekin0 = ekinp0 + ekinles0
- end if
-#else
- ekins0 = fac(3) * temp0
- ekin0 = fac(1) * temp0
-#endif
-
- if (ntt == 1) dttp = dt / tautp
-
- if (ntp > 0) then
- ener%volume = volume
- ener%density = tmass / (0.602204d0*volume)
-
- if( iamoeba == 0 ) then
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = 0.d0
- do m = 1,3
- ener%cmt(m) = ener%cmt(m) * 0.5d0
- ener%cmt(4) = ener%cmt(4) + ener%cmt(m)
- ener%vir(4) = ener%vir(4) + ener%vir(m)
- ener%pres(m) = (pconv+pconv) * (ener%cmt(m)-ener%vir(m)) / volume
- ener%pres(4) = ener%pres(4) + ener%pres(m)
- end do
- ener%pres(4) = ener%pres(4) / 3.d0
- end if
- end if
-
- ntnb = 0
- i3 = 0
- tempsu = 0.0d0
-
-#ifdef LES
- ! added LES tempsu (actual LES sum of m*v**2 )
- tempsules = 0.0d0
-#endif
- eke_cmd = 0.d0
- do j = 1,nrp
- winf = winv(j) * dt5
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- rterm = v(i3)*v(i3) * aamass
-#ifdef LES
- if (temp0les < 0.d0) then
- tempsu = tempsu + rterm
- if (ipimd.eq.CMD.and.(cnum(j).eq.0.or.cnum(j).eq.1)) then
- eke_cmd = eke_cmd + aamass*v(i3)*v(i3)
- endif
- else
- if (cnum(j) == 0) then
- tempsu = tempsu + rterm
- else
- tempsules = tempsules + rterm
- end if
- end if
-#else
- if(ipimd.eq.CMD.and.mybeadid==1) then
- eke_cmd = eke_cmd + aamass*v(i3)*v(i3)
- end if
- tempsu = tempsu + rterm
-#endif
- if(ipimd.ne.NMPIMD.and.ipimd.ne.CMD) v(i3) = v(i3) - f(i3) * winf
- if (vlim) v(i3) = sign(min(abs(v(i3)),vlimit),v(i3))
- end do
- end do
-
-#ifdef MPI /* SOFT CORE */
- if ( ifsc /= 0 ) then
- call calc_softcore_ekin(amass,v,v,istart,iend)
- sc_ener(13) = sc_ener(6) + sc_ener(12)
- end if
-#endif
-
- do im=1,iscale
- v(nr3+im) = v(nr3+im) - f(nr3+im) * dt5 / scalm
- tempsu = tempsu + scalm * v(nr3+im)*v(nr3+im)
- end do
- ener%kin%solt = tempsu * 0.5d0
-
-#ifdef LES
-
- ! added for LES temperature using old solvent variable for ener(4)
-
- if (temp0les < 0.d0) then
- ener%kin%solv = 0.d0
- ener%kin%tot = ener%kin%solt
- ! for CMD:
- if( ipimd > 0 ) then
- ener%kin%solv = equal_part + Epot_deriv ! "virial" estimate of KE
- ener%tot = ener%kin%solv + ener%pot%tot
- else
- ener%tot = ener%kin%tot + ener%pot%tot
- endif
- if (ipimd.eq.CMD) then
- ener%kin%tot = eke_cmd*0.5d0
- ener%kin%solv = ener%kin%tot
- endif
- else
- ener%kin%solv = tempsules * 0.5d0
- ener%kin%tot = ener%kin%solt + ener%kin%solv
- end if
-#else
- ! for better output for parallel PIMD/NMPIM/CMD/RPMD
- if (ipimd>0) then
- ener%tot = 0.d0
- ener%kin%tot = 0.d0
- ener%kin%solt = 0.d0
- ener%kin%solv = 0.d0
- ener%volume = 0.d0
- endif
- ener%kin%tot = ener%kin%solt
- ener%tot = ener%kin%tot+ener%pot%tot
-
-#endif
-
- if(ntt == 1) then
-#ifdef LES
- if (temp0les >= 0.d0) then
- ekmh = max(ener%kin%solt,fac(2)*10.d0)
- ekmhles = max(ener%kin%solv,fac(3)*10.d0)
- else
- ekmh = max(ener%kin%solt,fac(1)*10.d0)
- end if
-#else
- ekmh = max(ener%kin%solt,fac(1)*10.d0)
-#endif
- end if
-
- end if ! ( init == 3 )
-
- !-------------------------------------------------------------------------
- ! init = 4: continuation of a previous trajectory
- ! this code also done for init=3
- !
- ! Note: if the last printed energy from the previous trajectory was
- ! at time "t", then the restrt file has velocities at time
- ! t + 0.5dt, and coordinates at time t + dt
- !-------------------------------------------------------------------------
-
- ! -------------------------------------------------------------------
- ekmh = 0.0d0
-#ifdef LES
- ekmhles = 0.0d0
-#endif
-
- i3 = 0
- do j = 1,nrp
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- rterm = v(i3)*v(i3) * aamass
-# ifdef LES
- ! use copy number, not solute/solvent
- if (temp0les < 0.d0) then
- ! 1 bath
- ekmh = ekmh + rterm
- else
- if (cnum(j) == 0) then
- ekmh = ekmh + rterm
- else
- ekmhles = ekmhles + rterm
- end if
- end if
-# else
- ekmh = ekmh + rterm
-# endif
- end do
- end do
-
-#ifdef MPI /* SOFT CORE */
- if ( ifsc /= 0 ) then
- call calc_softcore_ekin(amass,v,v,istart,iend)
- sc_ener(13) = sc_ener(6) + sc_ener(12)
- end if
-#endif
-
- do im=1,iscale
- ekmh = ekmh + scalm*v(nr3+im)*v(nr3+im)
- end do
- ekmh = ekmh * 0.5d0
-#ifdef LES
- ekmhles = ekmhles * 0.5d0
-#endif
-
- do i=1,nr3+iscale
- vold(i) = v(i)
- end do
-
-#ifdef EMIL
- !--Setup the emil calculation if required
- if ( emil_do_calc .gt. 0 ) then
- call emil_init( natom, nstep, 1.0/(temp0 * 2 * boltz2 ), &
- mass, xx(lcrd), f, v, ener%box)
- end if
-#endif
-
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
- nstep=abfqmmm_param%qmstep ! lam81
- if(abfqmmm_param%maxqmstep == 0) nstep = 0 ! lam81
- end if ! lam81
-
- if (init /= 4 .or. nstlim == 0 .or. (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1)) then ! lam81
-
- !-------------------------------------------------------------------
- ! PRINT THE INITIAL ENERGIES AND TEMPERATURES
- !-------------------------------------------------------------------
-#ifdef RISMSANDER
- if ( rismprm%irism == 1 .and. rismprm%write_thermo==1 &
- .and. nstep <= 0 .and. facc /= 'A') then
- if( rism_calc_type(0) == RISM_FULL)&
- call rism_solvdist_thermo_calc(.false.,0)
- end if
-#endif /*RISMSANDER*/
-
- if ( (nstep <= 0 .and. master .and. facc /= 'A') .or. & ! lam81
- (master .and. abfqmmm_param%abfqmmm == 1 .and. mod(abfqmmm_param%qmstep,ntpr) == 0) ) then ! lam81
-
- if (isgld > 0) call sgenergy(ener)
- rewind(7)
-#ifdef LES
- if (.not.ipimd.gt.0) &
- ener%tot = ener%kin%tot+ener%pot%tot
-#endif /* LES */
- if(abfqmmm_param%abfqmmm /= 1 .or. abfqmmm_param%system == 1 .or. nstep == 0) & ! lam81
- call prntmd(nstep,nitp,nits,t,ener,onefac,7,.false.)
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener)
- if (ifsc /= 0) call sc_print_energies(7, sc_ener)
-#endif
- if ( ifcr > 0 .and. crprintcharges > 0 ) then
- call cr_print_charge( xx(l15), nstep )
- end if
-
- !--- BEGIN DIPOLE PRINTING CODE ---
- ! See code further on for comments-explanations
- call nmlsrc('dipoles',5,prndipfind)
- if(prndipfind /= 0 ) then
- write(6,*) '------------------------------- DIPOLE &
- &INFO ----------------------------------'
- write(6,9018) nstep,t
- read (5,'(a)') prndiptest
- call rgroup(natom,natc,nres,prndipngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp), &
- jgroup,indx,irespw,npdec, &
- xx(l60),xx(lcrdr),0,0,0,idecomp,5,.false.)
- rewind(5)
- if(prndipngrp > 0) then
- call printdip(prndipngrp,ix(icnstrgp),xx(lcrd), &
- xx(l15),xx(linddip),xx(Lmass), natom)
- end if
- write(6,*) '----------------------------- END DIPOLE &
- &INFO --------------------------------'
- end if
- !--- END DIPOLE PRINTING CODE ---
-
- if (nmropt > 0) then
- call nmrptx(6)
- end if
- call amflsh(7)
- end if
-
- if (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1) then ! lam81
- deallocate(for, stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- return ! lam81
- end if ! lam81
- if (nstlim == 0) then ! lam81
- if(abfqmmm_param%abfqmmm == 1) v(1:nr3) = abfqmmm_param%v(1:nr3) ! lam81
-#ifdef MPI
- call xdist(x, xx(lfrctmp), natom) ! lam81
- call xdist(v, xx(lfrctmp), natom) ! lam81
-
- if(master) then ! lam81
-#endif
- if(ntwr>0) call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, & ! lam81
- x,v,xx(lcrdr),box,t,temp0) ! lam81
- if(ntwx>0) call corpac(x,1,nrx,MDCRD_UNIT,loutfm) ! lam81
- if(ntwv>0) call corpac(v,1,nrx,MDVEL_UNIT,loutfm) ! lam81
- if(ntwf>0) call corpac(for,1,nrx,MDFRC_UNIT,loutfm) ! lam81
- if(ntwe>0) call mdeng(15,nstep,t,ener,onefac,ntp,csurften) ! lam81
-#ifdef MPI
- end if ! lam81
-#endif
- return ! lam81
- end if ! lam81
- init = 4
- end if
-
-
- if(ntp > 0 .and. ipimd > 0 ) then
- REQUIRE(ipimd.eq.NMPIMD)
-#ifdef LES
- call part_setup_cnst_press_pimd(Nkt,tau_vol)
-#else
- call full_setup_cnst_press_pimd(Nkt,tau_vol)
-#endif
- e2 = 1.0/ (2.0*3.0)
- e4 = e2 / (4.0*5.0)
- e6 = e4 / (6.0*7.0)
- e8 = e6 / (8.0*9.0)
- x_lnv = log( box(1)*box(2)*box(3) ) / 3
- end if
-
- ! For CMD.
- if ( ipimd==CMD ) then
-
- if ( .not.eq_cmd ) then
-
- ! De-activate thermostat for path-centroid.
-#ifdef LES
- do iatom = 1, natom
- do idim = 1, 3
- if ( cnum(iatom)==0 .or. cnum(iatom)==1 ) then
- activate = .false.
- else
- activate = .true.
- end if
- call Thermostat_switch(thermo(idim,iatom),activate)
- enddo
- enddo
- if ( .not.restart_cmd ) then
- ! Scale path-centroid velocity and set total momentum equal to zero.
- call part_scale_vel_centroid(v,amass,istart,iend)
- nstep_cmd = 0
- t_cmd = 0.d0
- else
- t_cmd = t
- nstep_cmd = int( t / dt )
- end if
-#else
- if ( mybeadid.eq.1 ) then
- activate = .false.
- else
- activate = .true.
- end if
- do iatom = 1, natom
- do idim = 1, 3
- call Thermostat_switch(thermo(idim,iatom),activate)
- enddo
- enddo
- if ( .not.restart_cmd ) then
- ! Scale path-centroid velocity and set total momentum equal to zero.
- call full_scale_vel_centroid(v,amass,istart,iend)
- nstep_cmd = 0
- t_cmd = 0.d0
- else
- nstep_cmd = nstep
- t_cmd = t
- end if
-#endif /* LES */
-
- else
-
- nstep_cmd = nstep
- t_cmd = t
-
- end if
-
- end if ! ipimd.eq.CMD and adiab_param<1.d0
-
-#ifdef MPI
- ! If this is a replica run and we are on exchange > 1, restore the
- ! old ekmh value since it was reset after we left runmd last time.
- ! DAN ROE: Only for ntt==1??
- if (rem /= 0 .and. mdloop >= 1) then
- ekmh = remd_ekmh
- endif
-#endif
-
-
- !=======================================================================
- ! ----- MAIN LOOP FOR PERFORMING THE DYNAMICS STEP -----
- ! (at this point, the coordinates are a half-step "ahead"
- ! of the velocities; the variable EKMH holds the kinetic
- ! energy at these "-1/2" velocities, which are stored in
- ! the array VOLD.)
- !=======================================================================
-
- 260 continue
- onstep = mod(irespa,nrespa) == 0
-
- ! Constant pH setup
- if (icnstph /= 0 .and. &
- ((rem /= 0 .and. mdloop > 0) .or. rem == 0)) then
-
- if (ntnb == 1) then ! rebuild pairlist
- call cnstphupdatepairs(x)
- end if
-
- if (mod(irespa+nstlim*mdloop,ntcnstph) == 0) then
- if (icnstph .eq. 1) then
- call cnstphbeginstep(xx(l190))
- else
- call cnstph_explicitmd( xx,ix,ih,ipairs,x,winv,amass,f,v,vold, &
- xr,xc,conp,skip,nsp,tma,erstop,qsetup, &
- do_list_update,rem)
- end if
- end if
-
- end if
-
-! x+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++x
-! | EVB reactive flux |
-! +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::+
-! | Driver for coordinating backward and forward propagation as |
-! | well as for enforcing stopping criteria |
-! +---------------------------------------------------------------+
-
-#if defined(MPI)
- if( ievb /= 0 .and. trim( adjustl( evb_dyn) ) == "react_flux" ) then
- REQUIRE( ipimd.eq.0 .or. ipimd.eq.NMPIMD )
- call react_flux ( x, v, f, winv, tempi * factt, dt5, dtx &
- , nr, nstep, nstlim )
- endif
-#endif
-
- !---------------------------------------------------------------
- ! ---Step 1a: do some setup for pressure calculations:
- !---------------------------------------------------------------
-
- if (ntp > 0 .and. iamoeba == 0 .and. ipimd==0) then
- ener%cmt(1:3) = 0.d0
- xr(1:nr3) = x(1:nr3)
-
- ! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
- ! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
- ! MASS -----
-
- call timer_start(TIME_EKCMR)
- call ekcmr(nspm,nsp,tma,ener%cmt,xr,v,amass,istart,iend)
-#ifdef MPI
- call trace_mpi('mpi_allreduce', &
- 3,'MPI_DOUBLE_PRECISION',mpi_sum)
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,ener%cmt,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
-# else
- call mpi_allreduce(ener%cmt,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- ener%cmt(1:3) = mpitmp(1:3)
-# endif
-#endif
- call timer_stop(TIME_EKCMR)
- end if
-
- ! If we're using the MC barostat, go ahead and do the trial move now
- if (ntp > 0 .and. barostat == 2 .and. mod(total_nstep+1, mcbarint) == 0) &
- call mcbar_trial(xx, ix, ih, ipairs, x, xc, f, ener%vir, xx(l96), &
- xx(l97), xx(l98), xx(l99), qsetup, do_list_update, &
- nstep, nsp, amass)
-
- !--------------------------------------------------------------
- ! ---Step 1b: Get the forces for the current coordinates:
- !--------------------------------------------------------------
-
- npbstep = nstep
- iprint = 0
- if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
-
- if (sebomd_obj%do_sebomd) then
- ! write down atomic charges and density matrix if needed
- sebomd_obj%iflagch = 0
- if (sebomd_obj%ntwc /= 0) then
- if (mod(nstep+1,sebomd_obj%ntwc) == 0) sebomd_obj%iflagch = 1
- endif
-! sebomd_obj%pdmx = 0
-! if (sebomd_obj%pdump /= 0) then
-! if (mod(nstep+1,ntwr) == 0) sebomd_obj%pdmx = 1
-! if (nstep+1 == nstlim) sebomd_obj%pdmx = 1
-! endif
- endif
-
-#ifdef MPI
- ! set do_mbar for the force contributions
- if (ifmbar /= 0) then
- do_mbar = .false.
- if ( mod(nstep+1,bar_intervall) == 0) then
- do_mbar = .true.
- end if
- end if
-#endif
-
- if ( ipimd==NMPIMD .or. ipimd==CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- call force(xx,ix,ih,ipairs,cartpos,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
-#if defined(MPI) && defined(LES)
- if ( ievb == 1 .and. i_qi > 0) then
- call evb_umb ( f, cartpos, real_mass, natom, istart3, iend3 )
-! 03132009 if( i_qi == 2 ) call qi_corrf_les ( cartpos, amass )
- if( i_qi == 2 ) call qi_corrf_les ( cartpos, real_mass )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- call trans_frc_cart_to_nmode(f)
-
-#if defined(MPI) && defined(LES)
- if ( ievb /= 0 .and. i_qi == 0 ) then
- call evb_umb ( f, x, real_mass, natom, istart3, iend3 )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-
-#endif
-
- else
- ! -- ti decomp
- if(idecomp > 0) then
- decpr = .false.
- if(mod(nstep+1,ntpr) == 0) decpr = .true.
- end if
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-#if defined(MPI)
- if ( ievb /= 0 ) then
-#ifdef LES
- call evb_umb_primitive ( f, x, real_mass, natom, istart, iend )
-#else
- call evb_umb_primitive ( f, x, amass, natom, istart, iend )
-#endif
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- endif
-
- if (sebomd_obj%do_sebomd) then
- ! computes hessian matrix if necessary
- if (sebomd_obj%ntwh /= 0 .and. mod(nstep+1,sebomd_obj%ntwh) == 0) then
- ! don't output atomic charges
- sebomd_obj%iflagch_old = sebomd_obj%iflagch
- sebomd_obj%iflagch = 0
- call sebomd_gradient_write(f,3*natom)
- call sebomd_hessian_compute(xx,ix,ih,ipairs,x,f,ener, &
- qsetup, do_list_update, nstep)
- sebomd_obj%iflagch = sebomd_obj%iflagch_old
- endif
- endif
-
- for(1:nr3) = f(1:nr3) ! lam81
-#ifdef MPI
- call xdist(for,xx(lfrctmp),natom) ! lam81
-#endif
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- abfqmmm_param%f2(1:nr3) = for(1:nr3) ! lam81
- call abfqmmm_combine_forces() ! lam81
-#ifdef MPI
- call mpi_bcast(abfqmmm_param%f, 3*natom, mpi_double_precision, 0, commsander, ierr) ! lam81
-#endif
- for(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- f(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- end if ! lam81
-
- ! Constant pH transition evaluation for GB CpHMD (not explicit CpHMD)
- if ((icnstph == 1) .and. (mod(irespa+mdloop*nstlim,ntcnstph) == 0)) then
- call cnstphendstep(xx(l190), xx(l15), ener%pot%dvdl, temp0, solvph)
- if (master) call cnstphwrite(rem)
- end if
-
- !PLUMED force added
- if(plumed.eq.1) then
- plumed_stopflag=0
- call plumed_f_gcmd("setStep"//char(0),nstep)
- call plumed_f_gcmd("setPositions"//char(0),x)
- call plumed_f_gcmd("setMasses"//char(0),amass)
- call plumed_f_gcmd("setCharges"//char(0),xx(l15))
- call plumed_f_gcmd("setEnergy"//char(0),ener%pot)
- call plumed_f_gcmd("setForces"//char(0),f)
- call plumed_f_gcmd("setStopFlag"//char(0),plumed_stopflag)
- plumed_box=0.0
- if(ifbox==0) then
- continue
- else if(ifbox==1) then
- plumed_box(1,1)=box(1)
- plumed_box(2,2)=box(2)
- plumed_box(3,3)=box(3)
- else if(ifbox==2) then
-! truncated octahedron, corresponding to a bcc lattice
-! in AMBER convention, box(1) is the length of the lattice vector
-! a is defined so as the bcc lattice is (a/2,a/2,a/2) (-a/2,-a/2,a/2) (a/2,-a/2,-a/2)
- plumed_box(1,1)=sqrt(1.0/3.0)*box(1)
- plumed_box(2,1)=sqrt(1.0/3.0)*box(1)
- plumed_box(3,1)=sqrt(1.0/3.0)*box(1)
- plumed_box(1,2)=-sqrt(1.0/3.0)*box(1)
- plumed_box(2,2)=-sqrt(1.0/3.0)*box(1)
- plumed_box(3,2)=sqrt(1.0/3.0)*box(1)
- plumed_box(1,3)=sqrt(1.0/3.0)*box(1)
- plumed_box(2,3)=-sqrt(1.0/3.0)*box(1)
- plumed_box(3,3)=-sqrt(1.0/3.0)*box(1)
- else
- write (6,*) "!!!!! PLUMED ERROR: Only orthorhombic and truncted octahedron cells are supported in this release."
- write (6,*) "!!!!! ABORTING RUN"
- stop
- endif
- plumed_virial=0.0
-! It's not completely clear where the factor 2.0 comes from
-! Anyway, I was able to match a change in press of 1000 bar with
-! a corresponding SLOPE=66.02 added to VOLUME CV in PLUMED
-! GB
- plumed_virial(1,1)=2.0*ener%vir(1)
- plumed_virial(2,2)=2.0*ener%vir(2)
- plumed_virial(3,3)=2.0*ener%vir(3)
- call plumed_f_gcmd("setVirial"//char(0),plumed_virial)
- call plumed_f_gcmd("setBox"//char(0),plumed_box)
- call plumed_f_gcmd("calc"//char(0),0);
-#ifdef MPI
-! this is required since PLUMED only updates virial on master processor
-#ifdef DPREC
- call mpi_bcast(plumed_virial,9,MPI_DOUBLE_PRECISION,0,commsander,ierr)
-#else
- call mpi_bcast(plumed_virial,9,MPI_REAL,0,commsander,ierr)
-#endif
-#endif
- ener%vir(1)=0.5*plumed_virial(1,1)
- ener%vir(2)=0.5*plumed_virial(2,2)
- ener%vir(3)=0.5*plumed_virial(3,3)
- end if
-
- !PLUMED end
-
-
-#ifdef MPI
- ! If softcore potentials are used, collect their dvdl contributions:
- if ( ifsc /= 0 ) then
- call mpi_reduce(sc_dvdl, sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl=0.0d0 ! zero for next step
- call mpi_reduce(sc_dvdl_ee, sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl_ee=0.0d0 ! zero for next step
- call mpi_reduce(sc_ener, sc_ener_tmp, ti_ene_cnt, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_ener(1:ti_ene_cnt) = sc_ener_tmp(1:ti_ene_cnt)
- end if
- if ( ifsc == 2 ) then
- ! If this is a perturb to nothing run, scale forces and calculate dvdl
- call sc_nomix_frc(f,nr3,ener)
-
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-
- if (ifmbar /=0 .and. do_mbar) then
- call bar_collect_cont()
- end if
-
- if ( icfe /= 0 )then
-
- ! --- free energies using thermodynamic integration (icfe /= 0)
-
- ! --- first, send the forces, energy, and virial to your partner:
-
- if( master ) then
- partner = ieor(masterrank,1)
- call mpi_sendrecv( f, nr3, MPI_DOUBLE_PRECISION, partner, 5, &
- frcti, nr3+3*extra_atoms, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( ener, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- ecopy, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr)
-
- ! exchange sc-dvdl contributions between masters:
- call mpi_sendrecv( sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- sc_tot_dvdl_partner, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- sc_tot_dvdl_partner_ee, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
-
- ! ---- collect statistics for free energy calculations:
-
- if( onstep ) then
- if( masterrank==0 ) then
- if( klambda == 1 ) then
- edvdl = edvdl - ener + ecopy
- edvdl_r = edvdl_r - ener + ecopy
- else
- clfac = klambda*(1.d0 - clambda)**(klambda-1)
- edvdl = edvdl - (ener - ecopy)*clfac
- edvdl_r = edvdl_r - (ener - ecopy)*clfac
- end if
- else
- if( klambda == 1 ) then
- edvdl = edvdl + ener - ecopy
- edvdl_r = edvdl_r + ener - ecopy
- else
- clfac = klambda*(1.d0 - clambda)**(klambda-1)
- edvdl = edvdl + (ener - ecopy)*clfac
- edvdl_r = edvdl_r + (ener - ecopy)*clfac
- end if
- end if
- ! This includes the sc-dvdl contribution into the vdw-part
- ! and potential energy parts of the dvdl-statistics
- if (ifsc == 1) then
- call adj_dvdl_stat(edvdl, edvdl_r)
- end if
- end if
-
- ! Do energy collection for MBAR FEP runs
- if (ifmbar /= 0 .and. do_mbar) then
- call calc_mbar_energies(ener%pot%tot, ecopy%pot%tot)
- end if
-
- if( masterrank==0 ) then
- call mix_frcti(frcti,ecopy,f,ener,nr3,clambda,klambda)
- else
- call mix_frcti(f,ener,frcti,ecopy,nr3,clambda,klambda)
- endif
- endif
-
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
-
- end if ! ( icfe /= 0 )
-
-#endif /* MPI */
-
-#ifdef EMIL
- ! Call the EMIL absolute free energy calculation.
- if ( emil_do_calc .gt. 0 ) then
-
- call emil_step(natom, nstep, 1.0 / (temp0 * 2 * boltz2),&
- mass, xx(lcrd), f, v, ener%pot, ener%pot, ener%box)
- end if
-#endif
-
-
-
- ! Reset quantities depending on TEMP0 and TAUTP (which may have been
- ! changed by MODWT during FORCE call).
- ekinp0 = fac(2)*temp0
-
-#ifdef LES
- ! TEMP0LES may have changed too
-
- ekinles0=0.d0
- ekins0=0.d0
- if (temp0les >= 0.d0) then
- ekinles0 = fac(3)*temp0les
- ekin0 = ekinp0 + ekinles0
- else
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
- end if
-#else
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-#endif
-
- if (ntt == 1) dttp = dt/tautp
-
- ! Pressure coupling:
- if (ntp > 0.and.ipimd>0) then
- REQUIRE(ipimd.eq.NMPIMD)
- centvir=0.0
-
-#ifdef LES
- do iatom=istart,iend
- if(cnum(iatom).eq.0.or.cnum(iatom).eq.1) then
- centvir=centvir-x(3*iatom-2)*f(3*iatom-2)
- centvir=centvir-x(3*iatom-1)*f(3*iatom-1)
- centvir=centvir-x(3*iatom )*f(3*iatom)
- end if
- end do
-#else
- if(mybeadid.eq.1) then
- do iatom=istart,iend
- centvir=centvir-x(3*iatom-2)*f(3*iatom-2)
- centvir=centvir-x(3*iatom-1)*f(3*iatom-1)
- centvir=centvir-x(3*iatom )*f(3*iatom)
- end do
- end if
-#endif /* LES */
-
- if(iamoeba.eq.1) then
- atomvir=sum(ener%vir(1:3))
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,centvir,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- call mpi_allreduce(MPI_IN_PLACE,atomvir,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# else
- call mpi_allreduce(centvir,mpitmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- centvir=mpitmp(1)
- tmp=0.0
- call mpi_allreduce(atomvir,tmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- atomvir=tmp
-# endif
-#endif
- else
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,centvir,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- call mpi_allreduce(MPI_IN_PLACE,bnd_vir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- call mpi_allreduce(MPI_IN_PLACE,e14vir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# ifndef LES
- if (master) &
- call mpi_allreduce(MPI_IN_PLACE,atvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commmaster,ierr)
-# endif
-# else
- call mpi_allreduce(centvir,tmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- centvir=tmp
- tmpvir=0.0
- call mpi_allreduce(bnd_vir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- bnd_vir=tmpvir
-
-# ifndef LES
- if (master) then
- tmpvir=0.0
- call mpi_allreduce(e14vir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commmaster,ierr)
- e14vir=tmpvir
-
- tmpvir=0.0
- call mpi_allreduce(atvir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commmaster,ierr)
- atvir=tmpvir
- endif
-# else
- tmpvir=0.0
- call mpi_allreduce(e14vir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- e14vir=tmpvir
-# endif
-# endif
- call mpi_bcast(atvir,9,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(e14vir,9,MPI_DOUBLE_PRECISION,0,commsander,ierr)
-#endif
- atomvir=0.0
- atomvir=atomvir+atvir(1,1)+bnd_vir(1,1)+e14vir(1,1)
- atomvir=atomvir+atvir(2,2)+bnd_vir(2,2)+e14vir(2,2)
- atomvir=atomvir+atvir(3,3)+bnd_vir(3,3)+e14vir(3,3)
- end if
- pressure = (Nkt*3.0-centvir-(atomvir-Eimp_virial))/(3.0*volume)
- f_lnv_p = (pressure-pres0/pconv)*volume*3.0
- end if
-
-
- if (ntp > 0) then
- ener%volume = volume
- ener%density = tmass / (0.602204d0*volume)
- if( iamoeba == 0 .and. ipimd==0 ) then
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = 0.d0
- do m = 1,3
- ener%cmt(m) = ener%cmt(m)*0.5d0
- ener%cmt(4) = ener%cmt(4)+ener%cmt(m)
- ener%vir(4) = ener%vir(4)+ener%vir(m)
- ener%pres(m) = (pconv+pconv)*(ener%cmt(m)-ener%vir(m))/volume
- ener%pres(4) = ener%pres(4)+ener%pres(m)
- end do
- ener%pres(4) = ener%pres(4)/3.d0
-
- ! Constant surface tension output:
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! Surface tension in the x direction
- ener%surface_ten = &
- box(1) * (ener%pres(1) - 0.5d0 * &
- (ener%pres(2) + ener%pres(3))) / (ninterface * ten_conv)
-
- else if (csurften .eq. 2) then ! Surface tension in the y direction
- ener%surface_ten = &
- box(2) * (ener%pres(2) - 0.5d0 * &
- (ener%pres(1) + ener%pres(3))) / (ninterface * ten_conv)
-
- else ! if (csurften .eq. 3) ! Surface tension in the z direction
- ener%surface_ten = &
- box(3) * (ener%pres(3) - 0.5d0 * &
- (ener%pres(1) + ener%pres(2))) / (ninterface * ten_conv)
-
- end if
-
- end if
-
- end if
- end if
-
-#ifdef MPI
-! ------====== REMD ======------
-! If rem /= 0 and mdloop == 0, this is the first sander call and we don't want to
-! actually do any MD or change the initial coordinates.
-! Exit here since we only wanted to get the potential energy for the first
-! subrem exchange probability calc.
- if (rem /= 0 .and. mdloop == 0) then
-# ifdef VERBOSE_REMD
- if (master) write (6,'(a,i3)') &
- 'REMD: Exiting runmd after getting initial energies for replica',repnum
-# endif
- goto 480 ! Go to the end of the runmd loop.
- endif ! (rem /= 0 and mdloop == 0)
-
- !REB Do adaptive QMMM
- if ( qmmm_nml%vsolv > 1 ) then
- ! mix forces for adaptive QM/MM and
- ! calculate adaptive energy if requested
- ! note: nstep is zero during first call; this is the energy/force calculation
- ! with the starting geometry / velocities
- call adaptive_qmmm(nstep,natom,x,xold,f,ener%pot%tot, ntpr, ntwx, &
- xx, ix, ih, ipairs, qsetup, do_list_update, &
- corrected_energy, aqmmm_flag)
-
-! ALTERNATIVE APPROACH:
-! if (ad_qmmm%calc_wbk) then
-! call ad_qmmm_check_matching_partitions()
-! if (ad_qmmm%mismatch) then
-! call force()
-! end if
-! call ad_qmmm_energy()
-! end if
-
-! test
- i3 = 3*(istart-1)
- do j=istart,iend
- do idim = 1, 3
- xold(i3+idim)=x(i3+idim)
- enddo
- i3 = i3 + 3
- enddo
-! test
- endif
-
-#endif
-
- !----------------------------------------------------------------
- ! ---Step 1c: do randomization of velocities, if needed:
- !----------------------------------------------------------------
- ! ---Assign new random velocities every Vrand steps, if ntt=2
-
- resetvelo=.false.
- if (vrand /= 0 .and. ntt == 2) then
- if (mod((nstep+1),vrand) == 0) resetvelo=.true.
- end if
-
-#ifdef MMTSB
- if ( mmtsb_switch == mmtsb_temp_rex .and. mmtsb_is_exchanged ) &
- resetvelo = .true.
-#endif
-
- if (resetvelo) then
- ! DAN ROE: Why are only the masters doing this? Even if the velocities
- ! are broadcast to the child processes, the wont the different # of random
- ! calls put the randomg num generators out of sync, or do we not care?
-
- if (master) then
- write (6,'(a,i8)') 'Setting new random velocities at step ', &
- nstep + 1
- call setvel(nr,v,winv,temp0*factt,init,iscale,scalm)
-
-#ifdef MPI /* SOFT CORE */
- ! Make sure all common atoms have the same v (that of V0) in TI runs:
- if (icfe /=0 .and. ifsc /=0) call sc_sync_x(v,nr3)
-#endif
-
-#ifdef LES
-
- ! newvel call is fixed for the dual target temperatures
-
- if (temp0les >= 0.d0.and.temp0 /= temp0les) then
- vscalt = sqrt (temp0les/temp0)
- do j=1,natom
- if(cnum(j) > 0) then
- i3 = 3*(j-1)
- v(i3+1) = v(i3+1) * vscalt
- v(i3+2) = v(i3+2) * vscalt
- v(i3+3) = v(i3+3) * vscalt
- endif
- end do
- end if
-#endif
- if (ibelly > 0) call bellyf(nr,ix(ibellygp),v)
- end if
-# ifdef MPI
- call trace_mpi('mpi_bcast',3*natom,'MPI_DOUBLE_PRECISION',0)
- call mpi_bcast(v, 3*natom, MPI_DOUBLE_PRECISION, 0, commsander, ierr)
-# endif
-
- ! At this point in the code, the velocities lag the positions
- ! by half a timestep. If we intend for the velocities to be drawn
- ! from a Maxwell distribution at the timepoint where the positions and
- ! velocities are synchronized, we have to correct these newly
- ! redrawn velocities by backing them up half a step using the
- ! current force.
- ! Note that this fix only works for Newtonian dynamics.
- if( gammai==0.d0.and.(ipimd.ne.NMPIMD.or.ipimd.ne.CMD)) then
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dt5
- v(i3+1) = v(i3+1) - f(i3+1)*wfac
- v(i3+2) = v(i3+2) - f(i3+2)*wfac
- v(i3+3) = v(i3+3) - f(i3+3)*wfac
- i3 = i3+3
- end do
- end if
-
- end if ! (resetvelo)
-
- call timer_start(TIME_VERLET)
-
- !-----------------------------------------------------
- ! ---Step 2: Do the velocity update:
- !-----------------------------------------------------
-
- !step 2a: apply quenched MD if needed. This is useful in NEB>0
- if (vv==1) call quench(f,v)
-
- ! Car-Parrinello on dipoles: note that the (small?) kinetic energy
- ! of the dipoles is included in the epol energy
-! M_WJ
-! if ( induced == 1 .and. indmeth == 3 ) call cp_dips(natom,xx(lpol),xx,dt)
- if ( induced > 0 .and. indmeth == 3 ) call cp_dips(natom,xx(lpol),xx,dt)
-
-
-
-! i3 = 3*(istart-1) !! Add Brownian noise for testing. ! APJ
-! do j=istart,iend ! APJ
-! do idim=1,3 ! APJ
-! call gauss( 0.d0, sqrt(0.1d0*boltz2*temp0)/dtx,fln ) ! APJ
-! f(i3+idim) = f(i3+idim) + fln ! APJ
-! enddo ! APJ
-! i3 = i3+3 ! APJ
-! end do ! APJ
-
-
- ! Nose'-Hoover thermostat (1st step).
- if ( ntt == 4 ) then
-
- Ekin2_tot = 0.d0
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = dtx/amass(j)
- do idim = 1, 3
-#ifdef LES
- if( ntp>0.and.ipimd.eq.NMPIMD .and. &
- (cnum(j).eq.0.or.cnum(j).eq.1) ) then
-#else
- if(ntp>0.and.ipimd.eq.NMPIMD.and.mybeadid.eq.1) then
-#endif
- exp1 = exp(-dt5*thermo(idim,j)%v(1)-dt5*v_lnv*c2_lnv)
- Ekin2_tot = Ekin2_tot + amass(j)*v(i3+idim)*v(i3+idim)
- else
- exp1 = exp( -dt5 * thermo(idim,j)%v(1) )
- end if
- exp2 = exp1*exp1
- vold(i3+idim)=v(i3+idim)
- v(i3+idim) = v(i3+idim) * exp2 + f(i3+idim) * wfac * exp1
- end do
- i3 = i3+3
- end do
-
- if(ntp>0.and.ipimd.eq.NMPIMD) then
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,Ekin2_tot,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# else
- call mpi_allreduce(Ekin2_tot,mpitmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- Ekin2_tot=mpitmp(1)
-# endif
-#endif
- f_lnv_v = Ekin2_tot*(c2_lnv-1)
- tmp = exp(-dt5*thermo_lnv%v(1))
- v_lnv = tmp*(tmp*v_lnv+dtx*(f_lnv_v+f_lnv_p)/mass_lnv)
- end if
-
- call Thermostat_integrate_1(nchain,thermo,nthermo,dtx,ntp)
-
- else if ( ntt>4 .and. ntt<=8 ) then ! APJ
-
- Ekin2_tot = 0.d0
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = dtx/amass(j)
- do idim = 1, 3
-#ifdef LES
- if( ntp>0.and.ipimd.eq.NMPIMD .and. &
- (cnum(j).eq.0.or.cnum(j).eq.1) ) then
-#else
- if(ntp>0.and.ipimd.eq.NMPIMD.and.mybeadid.eq.1) then
-#endif
- Ekin2_tot = Ekin2_tot + amass(j)*v(i3+idim)*v(i3+idim)
- !exp1 = exp(-dt5*thermo(idim,j)%v(1)-dt5*v_lnv*c2_lnv) ! APJ
- exp1 = exp(-dt5*v_lnv*c2_lnv) ! APJ
- else
- !exp1 = exp( -dt5 * thermo(idim,j)%v(1) ) ! APJ
- exp1 = 1.d0 ! APJ
- end if
- exp2 = exp1*exp1
- vold(i3+idim)=v(i3+idim)
- !v(i3+idim) = v(i3+idim) * exp2 + f(i3+idim) * wfac * exp1 ! APJ
- v(i3+idim)=v(i3+idim)*exp2 ! APJ
- f(i3+idim)=f(i3+idim)*exp1 ! APJ
- end do
- i3 = i3+3
- end do
-
- if(ntp>0.and.ipimd.eq.NMPIMD) then
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,Ekin2_tot,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# else
- call mpi_allreduce(Ekin2_tot,mpitmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- Ekin2_tot=mpitmp(1)
-# endif
-#endif
- f_lnv_v = Ekin2_tot*(c2_lnv-1)
- !tmp = exp(-dt5*thermo_lnv%v(1)) ! APJ
- !v_lnv = tmp*(tmp*v_lnv+dtx*(f_lnv_v+f_lnv_p)/mass_lnv) ! APJ
- end if
-
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
- call xdist(f, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- abfqmmm_param%f(1:nr3+iscale)=f(1:nr3+iscale) ! lam81
- end if ! lam81
- call Adaptive_Thermostat_integrate(nchain,thermo,nthermo,dtx,ntp,1) ! APJ
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
- v(1:nr3+iscale)=abfqmmm_param%v(1:nr3+iscale) ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- end if ! lam81
-
-
- else if( gammai == 0.d0 ) then
-
- ! ---Newtonian dynamics:
-
- ! Applying guiding force effect:
- if (isgld > 0) then
- call sgmdw(natom,istart,iend,ntp,dtx,ener,amass,winv,x,f,v)
- end if
-
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dtx
- v(i3+1) = v(i3+1) + f(i3+1)*wfac
- v(i3+2) = v(i3+2) + f(i3+2)*wfac
- v(i3+3) = v(i3+3) + f(i3+3)*wfac
- i3 = i3+3
- end do
-
- else if (isgld > 0) then
- ! Using SGLD algorithm:
- call sgldw(natom,istart,iend,ntp,dtx,temp0,ener,amass,winv,x,f,v)
- else ! gamma_ln .ne. 0, which also implies ntt=3 (see mdread.f)
-
- ! ---simple model for Langevin dynamics, basically taken from
- ! Loncharich, Brooks and Pastor, Biopolymers 32:523-535 (1992),
- ! Eq. 11. (Note that the first term on the rhs of Eq. 11b
- ! should not be there.)
-
- ! Update Langevin parameters, since temp0 might have changed:
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
-# ifdef LES
- sdfacles = sqrt( 4.d0*gammai*boltz2*temp0les/dtx )
-# endif
-
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc == 1) then
- call sc_lngdyn(winv,amass,v,f,sdfac,c_explic,c_implic, &
- istart, iend, nr, dtx)
- else
-#endif
-
-
- if (no_ntt3_sync == 1) then ! APJ
- !We don't worry about synchronizing the random number stream ! APJ
- !across processors. ! APJ
- iskip_start = 0 ! APJ
- iskip_end = 0 ! APJ
- else ! APJ
- ! In order to generate the same sequence of pseudorandom numbers that ! APJ
- ! you would using a single processor you have to go through the atoms ! APJ
- ! in order: skip those that have are being used on other processors ! APJ
- iskip_start = 3*(istart-1) ! APJ
- iskip_end = 3*(nr-iend) ! APJ
-#ifndef LES
- ! Always sync random number stream for PIMD ! APJ
- ! (AWG: not sure if this is required) ! APJ
- if (ipimd>0) then ! APJ
- iskip_start = iskip_start + 3*nr*(mybeadid-1) ! APJ
- iskip_end = iskip_end + 3*nr*(nbead-mybeadid) ! APJ
- end if ! APJ
-#endif
- endif ! APJ
-
- do j=1,iskip_start ! APJ
- ! Skip some random numbers ! APJ
- call gauss( 0.d0, 1.d0, fln ) ! APJ
- end do ! APJ
-
- ! Do Langevin step ! APJ
- i3 = 3*(istart-1) ! APJ
- do j=istart,iend ! APJ
-
- wfac = winv(j) * dtx ! APJ
- aamass = amass(j) ! APJ
-# ifdef LES
- if (temp0les >= 0 .and. temp0 /= temp0les .and. cnum(j) /= 0 ) then ! APJ
- rsd =sdfacles*sqrt(aamass) ! APJ
- else ! APJ
- rsd = sdfac*sqrt(aamass) ! APJ
- endif ! APJ
-# else
- rsd = sdfac*sqrt(aamass) ! APJ
-# endif
- call gauss( 0.d0, rsd, fln ) ! APJ
- v(i3+1) = (v(i3+1)*c_explic + (f(i3+1)+fln)*wfac) * c_implic ! APJ
- call gauss( 0.d0, rsd, fln ) ! APJ
- v(i3+2) = (v(i3+2)*c_explic + (f(i3+2)+fln)*wfac) * c_implic ! APJ
- call gauss( 0.d0, rsd, fln ) ! APJ
- v(i3+3) = (v(i3+3)*c_explic + (f(i3+3)+fln)*wfac) * c_implic ! APJ
-
- i3 = i3 + 3 ! APJ
- end do ! APJ
-
- do j=1,iskip_end ! APJ
- ! Skip some random numbers ! APJ
- call gauss( 0.d0, 1.d0, fln ) ! APJ
- end do ! APJ
-
-
-#ifdef MPI /* SOFT CORE */
- end if ! for (ifsc==1) call sc_lngdyn
-#endif
- end if ! ( gammai == 0.d0 )
-
- ! Update EMAP rigid domains
- if(temap) call emap_move()
-
- ! --- consider vlimit
-
- if (vlim.and.ipimd==0) then
- vmax = 0.0d0
- do i=istart3,iend3
- vmax = max(vmax,abs(v(i)))
- v(i) = sign(min(abs(v(i)),vlimit),v(i))
- end do
-
- ! Only violations on the master node are actually reported
- ! to avoid both MPI communication and non-master writes.
- if (vmax > vlimit) then
- if (master) then
- write(6,'(a,i6,a,f10.4)') 'vlimit exceeded for step ',nstep, &
- '; vmax = ',vmax
- end if
- end if
- end if
-
- do im=1,iscale
- v(nr3+im) = (v(nr3+im) + f(nr3+im)*dtx/scalm)
- end do
-
- ! We do the force dump here if requested, since the 'old' positions are about
- ! to be dumped into the force array...
-
- if (master) then
- ifdump = .false. ! Write forces this step?
- if (ntwf>0) ifdump = mod(total_nstep+1,ntwf) == 0 ! forces
- if (ntwf == -1 .and. mod(total_nstep+1,ntwx) == 0) &
- ifdump = .true. !Combined crdfrc file
- if (abfqmmm_param%abfqmmm == 1) ifdump = .false. ! lam81
-#ifdef MPI
- ! For adaptive QM/MM, only the master does a dump.
- if ( qmmm_nml%vsolv > 1 ) then
- if ( nodeid /= 0 ) then
- ifdump = .false.
- end if
- end if
-
- if (ifdump) then
- call xdist(f, xx(lfrctmp), natom)
- end if
-#endif
- ! Force archive:
- if (ifdump) then
-
-#ifdef MPI
- ! Write out current replica#, exchange#, step#, and mytargettemp
- ! If mdloop==0 this is a normal md run (since REMD never calls corpac
- ! when mdloop==0) and we don't want the REMD header.
- if (mdloop>0.and.loutfm) then
- if (trxsgld) then
- write (MDFRC_UNIT,'(a,4(1x,i8))') "RXSGLD ", repnum, mdloop, &
- total_nstep+1, stagid
- else
- write (MDFRC_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum, mdloop, &
- total_nstep+1, my_remd_data%mytargettemp
- end if
- end if
-#endif
-
- ! ipimd forces will probably not be right if some type of
- ! transformation is necessary. This is from the vel dump code -- keep
- ! it here as a holder in case somebody wants to fix it.
-! if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
-! call corpac(cartvel,1,nrx,MDVEL_UNIT,loutfm)
-! else
- call corpac(f,1,nrx,MDFRC_UNIT,loutfm)
-! endif
- end if
-
- else ! slaves need to participate in force distribution
- ifdump = .false. ! Write forces this step?
- if (ntwf>0) ifdump = mod(total_nstep+1,ntwf) == 0 ! forces
- if (ntwf == -1 .and. mod(total_nstep+1,ntwx) == 0) &
- ifdump = .true. !Combined crdfrc file
- if (abfqmmm_param%abfqmmm == 1) ifdump = .false. ! lam81
-#ifdef MPI
- if (ifdump) call xdist(f, xx(lfrctmp), natom)
-#endif
- end if ! master
- !-------------------------------------------------------------------
- ! Step 3: update the positions, putting the "old" positions into F:
- !-------------------------------------------------------------------
-
-# ifdef LES
- if(ntp>0.and.ipimd.eq.NMPIMD) then
- aa = exp(dt5*v_lnv)
- arg2 = v_lnv*dt5*v_lnv*dt5
- poly = 1.0d0+arg2*(e2+arg2*(e4+arg2*(e6+arg2*e8)))
- endif
-
- i3 = 3*(istart-1)
- do j=istart,iend
- if(ntp>0.and.ipimd.eq.NMPIMD.and.(cnum(j).eq.0.or.cnum(j).eq.1)) then
- do idim = 1, 3
- f(i3+idim)=x(i3+idim)
- x(i3+idim)=aa*(x(i3+idim)*aa+v(i3+idim)*poly*dtx)
- enddo
- else
- do idim = 1, 3
- f(i3+idim) = x(i3+idim)
- x(i3+idim) = x(i3+idim)+v(i3+idim)*dtx
- enddo
- endif
- i3 = i3 + 3
- enddo
-
-# else
-
- if(ntp>0.and.ipimd.eq.NMPIMD.and.mybeadid==1) then
- aa = exp(dt5*v_lnv)
- arg2 = v_lnv*dt5*v_lnv*dt5
- poly = 1.0d0+arg2*(e2+arg2*(e4+arg2*(e6+arg2*e8)))
- do i3=istart3,iend3
- f(i3)=x(i3)
- x(i3)=aa*(x(i3)*aa+v(i3)*poly*dtx)
- end do
- else
- do i3 = istart3, iend3
- f(i3) = x(i3)
- x(i3) = x(i3) + v(i3)*dtx
- end do
- end if
-
-# endif /* LES */
-
- !Nose'-Hoover thermostat (2nd step).
- if ( ntt==4 ) then
- call Thermostat_integrate_2(nchain,thermo,nthermo,dtx,ntp)
- E_nhc = Thermostat_hamiltonian(nchain,thermo,nthermo)
- else if ( ntt>=4 .and. ntt<=8 ) then ! APJ
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- end if ! lam81
- call Adaptive_Thermostat_integrate(nchain,thermo,nthermo,dtx,ntp,2) ! APJ
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
- v(1:nr3+iscale)=abfqmmm_param%v(1:nr3+iscale) ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- end if ! lam81
- E_nhc = Adaptive_Thermostat_hamiltonian(nchain,thermo,nthermo)
- end if
-
- do i = 1,iscale
- f(nr3+i) = x(nr3+i)
- x(nr3+i) = x(nr3+i)+v(nr3+i)*dtx
- end do
-
- call timer_stop(TIME_VERLET)
-
- if (ntc /= 1) then
-
- !-------------------------------------------------------------------
- ! Step 4a: if shake is being used, update the new positions to fix
- ! the bond lengths.
- !-------------------------------------------------------------------
-
- call timer_start(TIME_SHAKE)
- if (isgld > 0) call sgfshake(istart,iend,dtx,amass,x,.false.)
- qspatial=.false.
- call shake(nrp,nbonh,nbona,0,ix(iibh),ix(ijbh),ix(ibellygp), &
- winv,conp,skip,f,x,nitp,belly,ix(iifstwt),ix(noshake), &
- shkh,qspatial)
- call quick3(f,x,ix(iifstwr),natom,nres,ix(i02))
- if(nitp == 0) then
- erstop = .true.
- goto 480
- end if
- ! Including constraint forces in self-guiding force calculation
- if (isgld > 0) call sgfshake(istart,iend,dtx,amass,x,.true.)
-
- ! Need to synchronize coordinates for linearly scaled atoms after shake
-#ifdef MPI
- if( icfe /= 0 ) then
- call timer_barrier( commsander )
- call timer_stop_start(TIME_SHAKE,TIME_DISTCRD)
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call xdist(x, xx(lfrctmp), natom)
- end if
- ! In dual-topology this is done within softcore.f
- if (ifsc /= 1) then
- if( master ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commmaster,ierr)
- else
- if( master ) call sc_sync_x(x,nr3)
- end if
- if( numtasks>1 ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commsander,ierr)
- call timer_stop_start(TIME_DISTCRD,TIME_SHAKE)
- end if
-#endif /* MPI */
- !-----------------------------------------------------------------
- ! Step 4b: Now fix the velocities and calculate KE
- !-----------------------------------------------------------------
-
- ! ---re-estimate the velocities from differences in positions:
-
- if( .not.(ipimd==NMPIMD.and.ipimd==CMD.and.mybeadid.ne.1) ) then
- v(istart3:iend3) = (x(istart3:iend3)-f(istart3:iend3)) * dtxinv
- end if
-
- call timer_stop(TIME_SHAKE)
- end if
- call timer_start(TIME_VERLET)
-
- if(ineb>0.and.(mybeadid==1.or.mybeadid==neb_nbead) ) then
- x(1:3*natom)=f(1:3*natom)
- ! CARLOS: NEB- remove velocities but ONLY for the end beads so V doesn't
- ! accumulate if high forces
- v(1:3*natom)=0.d0
-
- end if
-
- if( ntt == 1 .or. onstep ) then
-
- !-----------------------------------------------------------------
- ! Step 4c: get the KE, either for averaging or for Berendsen:
- !-----------------------------------------------------------------
-
- eke = 0.d0
- ekph = 0.d0
- ekpbs = 0.d0
-#ifdef LES
- ekeles = 0.d0
- ekphles = 0.d0
-#endif
- eke_cmd = 0.d0
-
- if (gammai == 0.0d0) then
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
-#ifdef LES
- if (temp0les < 0.d0) then
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
- ekph = ekph + aamass*v(i3)**2
- if(ipimd.eq.CMD.and.(cnum(j).eq.0.or.cnum(j).eq.1)) then
- eke_cmd = eke_cmd + aamass*0.25d0*(v(i3)+vold(i3))**2
- endif
- else
- if (cnum(j) == 0) then
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
- ekph = ekph + aamass*v(i3)**2
- else
- ekeles = ekeles + aamass*0.25d0*(v(i3)+vold(i3))**2
- ekphles = ekphles + aamass*v(i3)**2
- end if
- end if
-
-#else
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
-
- if(mybeadid==1) then
- eke_cmd = eke_cmd + aamass*0.25d0*(v(i3)+vold(i3))**2
- end if
- ! try pseudo KE from Eq. 4.7b of Pastor, Brooks & Szabo,
- ! Mol. Phys. 65, 1409-1419 (1988):
-
- ekpbs = ekpbs + aamass*v(i3)*vold(i3)
- ekph = ekph + aamass*v(i3)**2
-
-#endif
- end do
- end do
-
- else
-
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
-#ifdef LES
- if (temp0les < 0.d0) then
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- else
- if (cnum(j) == 0) then
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- else
- ekeles = ekeles + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- end if
- end if
-#else
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
-
-#endif
- end do
-
- end do
-
- end if ! (if gammai == 0.0d0)
-
-#ifdef MPI
-
- ! --- sum up the partial kinetic energies:
-
- if ( ipimd.eq.CMD ) then
- call mpi_reduce(eke_cmd,tmp_eke_cmd,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,0,commsander,ierr)
- eke_cmd = tmp_eke_cmd
- endif
-
-# ifdef LES
- !if ( ipimd.eq.CMD ) then
- ! call mpi_reduce(eke_cmd,tmp_eke_cmd,1,MPI_DOUBLE_PRECISION, &
- ! mpi_sum,0,commsander,ierr)
- ! eke_cmd = tmp_eke_cmd
- !endif
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- if ( temp0les < 0 ) then
- mpitmp(1) = eke
- mpitmp(2) = ekph
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,2, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
-# else
- call mpi_allreduce(mpitmp,mpitmp(3),2, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(3)
- ekph = mpitmp(4)
-# endif
- else
- mpitmp(1) = eke
- mpitmp(2) = ekph
- mpitmp(3) = ekeles
- mpitmp(4) = ekphles
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,4, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
- ekeles = mpitmp(3)
- ekphles = mpitmp(4)
-# else
- call mpi_allreduce(mpitmp,mpitmp(5),4, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(5)
- ekph = mpitmp(6)
- ekeles = mpitmp(7)
- ekphles = mpitmp(8)
-# endif
- endif
- end if
-# else
-
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call trace_mpi('mpi_allreduce', &
- 1,'MPI_DOUBLE_PRECISION',mpi_sum)
- mpitmp(1) = eke
- mpitmp(2) = ekph
- mpitmp(3) = ekpbs
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
- ekpbs = mpitmp(3)
-
-# else
-
- call mpi_allreduce(mpitmp,mpitmp(4),3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(4)
- ekph = mpitmp(5)
- ekpbs = mpitmp(6)
-
-# endif
- end if
-# endif
-
- ! Calculate Ekin of the softcore part of the system
- if (ifsc /= 0 ) then
- call calc_softcore_ekin(amass,v,vold,istart,iend)
- sc_ener(13) = sc_ener(6) + sc_ener(12)
- end if
-#endif
-
- ! --- all processors handle the "extra" variables:
-
- do im=1,iscale
- eke = eke + scalm*0.25d0*(v(nr3+im)+vold(nr3+im))**2
- ekpbs = ekpbs + scalm*v(nr3+im)*vold(nr3+im)
- ekph = ekph + scalm*v(nr3+im)**2
- end do
-
- eke = eke * 0.5d0
- ekph = ekph * 0.5d0
- ekpbs = ekpbs * 0.5d0
-#ifdef LES
- ekeles = ekeles * 0.5d0
- ekphles = ekphles * 0.5d0
-#endif
-
- if( ntt == 1 ) then
-#ifdef LES
-
- if (temp0les < 0.d0) then
- scaltp = sqrt(1.d0 + 2.d0*dttp*(ekin0-eke)/(ekmh+ekph))
- else
- scaltp = sqrt(1.d0+2.d0*dttp*(ekinp0-eke)/(ekmh+ekph))
- scaltles = sqrt(1.d0+2.d0*dttp*(ekinles0-ekeles)/(ekmhles+ekphles))
- end if
-#else
-
- ! --- following is from T.E. Cheatham, III and B.R. Brooks,
- ! Theor. Chem. Acc. 99:279, 1998.
-
- scaltp = sqrt(1.d0 + 2.d0*dttp*(ekin0-eke)/(ekmh+ekph))
-
- ! --- following is the "old" (amber7 and before) method:
-
- ! scaltpo = sqrt(1.d0 + dttp*(ekin0/ekph - 1.d0))
- ! write(6,*) 'scaltp: ',2.d0*dttp*(ekin0-eke)/(ekmh+ekph), &
- ! dttp*(ekin0/ekmh - 1.d0)
-
- ! following line reverts to the "old" behavior:
- ! scaltp = scaltpo
-
-#endif
-
-#ifdef MPI /* SOFT CORE */
- if (icfe /= 0) then
- if (ifsc == 1) then
- if (master) then
- ! Linearly combine the scaling factors from both processes
- ! the combined factor is broadcast to all nodes
- ! the subroutine also correctly scales the softcore atom v's
- call mix_temp_scaling(scaltp,clambda,v)
- end if
- call mpi_bcast(scaltp,1,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-#endif
-
- do j = istart,iend
- i3=(j-1)*3+1
-#ifdef LES
- if (temp0les > 0.d0 .and. cnum(j) /= 0 ) then
- v(i3 ) = v(i3 )*scaltles
- v(i3+1) = v(i3+1)*scaltles
- v(i3+2) = v(i3+2)*scaltles
- else
- v(i3 ) = v(i3 ) *scaltp
- v(i3+1) = v(i3+1) *scaltp
- v(i3+2) = v(i3+2) *scaltp
- end if
-#else
- v(i3 ) = v(i3 ) *scaltp
- v(i3+1) = v(i3+1) *scaltp
- v(i3+2) = v(i3+2) *scaltp
-#endif
- end do
- do im=1,iscale
- v(nr3+im) = v(nr3+im)*scaltp
- end do
- end if ! (ntt == 1 )
-
- end if ! ( ntt == 1 .or. onstep; end of step 4c )
-
- !-----------------------------------------------------------------
- ! Step 5: several tasks related to dumping of trajectory information
- !-----------------------------------------------------------------
-
- itdump = .false. ! Write coordinates this step?
- ivdump = .false. ! Write velocities this step?
- ifdump = .false. ! Write forces this step? lam81
- ixdump = .false. ! Write restart this step?
- ifdump = .false. ! Write forces this step?
- ivscm = .false. ! Do com removal this step?
-#ifdef RISMSANDER
- irismdump = .false. ! Write RISM files this step?
-#endif
-
- ! --- Determine if trajectory, velocity, or restart
- ! writing is imminent, or if the center of mass
- ! motion will be removed.
- ! These require xdist of velocities or dipoles in parallel runs:
- !
- ! Modified so that when running REMD, writing can occur less often
- ! than exchanges (e.g. ntwx > nstlim)
- ! DAN ROE: Added two new variables, total_nstep and total_nstlim.
- ! For non-REMD runs, total_nstep=nstep+1 and total_nstlim=nstlim
- ! just like before.
- ! For REMD runs, total_nstep=(mdloop-1)*nstlim+nstep+1, where
- ! mdloop is the current exchange - this is the current
- ! replica exchange MD step. total_nstlim=numexchg*nstlim, which is
- ! the maximum number of REMD steps.
- total_nstep=nstep+1
- total_nstlim=nstlim
- if(abfqmmm_param%abfqmmm == 1) total_nstep=abfqmmm_param%qmstep ! lam81
-
-#ifdef MPI
- if (rem /= 0) then
- total_nstep = (mdloop - 1) * nstlim + nstep + 1
- total_nstlim = nstlim * numexchg
- endif
-#endif
- if (ntwx>0) itdump = mod(total_nstep,ntwx) == 0 ! Trajectory coords
- if (ntwv>0) ivdump = mod(total_nstep,ntwv) == 0 ! Velocity
- if (ntwf>0) ifdump = mod(total_nstep,ntwf) == 0 ! Force
- if( ntwr /= 0 ) then
- if ( mod(total_nstep, ntwr ) == 0 ) ixdump = .true. ! Restart
- endif
- if( total_nstep >= total_nstlim ) ixdump = .true. ! Final restart
- if ( nscm > 0 ) then
- if( mod(total_nstep,nscm) == 0 ) ivscm =.true. ! C.o.M. removal
- end if
- if (ntwv == -1 .and. itdump) ivdump = .true. !Combined crdvel file
-
-#ifdef MPI
- ! adaptive QM/MM via multisander
- ! all groups have identical coords and velocities
- ! only master of first group needs to dump results
- ! We have to leave the dump values for all threads in the group, though
- ! since for dumping the coords, these are broadcast within the group
- ! (see call to xdist() below)
- if ( qmmm_nml%vsolv > 1 ) then
- if ( nodeid /= 0 ) then
- ixdump = .false.
- itdump = .false.
- ivdump = .false.
- end if
- end if
-#endif
-
-#ifdef RISMSANDER
- if(rismprm%irism ==1)then
- if(rismprm%ntwrism > 0 )then
- irismdump = mod(nstep+1,rismprm%ntwrism) == 0
- if( nstep+1 >= nstlim ) then !! do we want to do this?
- irismdump = .true.
- end if
- end if
- end if
-#endif
-
-
-#ifdef MPI
-
- !-----------------------------------------------------------------
- ! --- now distribute the coordinates, and if necessary, dipoles and vel:
- !-----------------------------------------------------------------
-
- call timer_barrier( commsander )
- call timer_stop_start(TIME_VERLET,TIME_DISTCRD)
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call xdist(x, xx(lfrctmp), natom)
- end if
- ! dac/knut change: force the coordinates to be the same on both masters.
- ! For certain compilers, addition may not be strictly commutative, so
- ! the forces on group 0 may be different by roundoff from the forces on
- ! group 1. This can lead to divergent trajectories. The interval at
- ! which they are resynchronized is hard-wired here to 20, which seems to
- ! work fine in our tests.
- ! jwk change: coordinates are synchronized when shake is enabled above
- if( icfe /= 0 .and. mod(nstep+1,20) == 0 .and. ntc == 1 ) then
-
- ! In dual-topology this is done within softcore.f
- if (ifsc /= 1) then
- if( master ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commmaster,ierr)
- else
- if( master ) then
- call sc_compare(x,nr3,'CRD') ! first, check if coordinates have desynced
- if (numtasks==1 ) call sc_compare(v,nr3,'VEL') ! do the same for velocities
- call sc_sync_x(x,nr3) ! then resync them
- end if
- end if
- if( numtasks>1 ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commsander,ierr)
- end if
- call timer_stop(TIME_DISTCRD)
-
-#endif /* MPI */
-
- ! ----fix lone pair positions:
- if( numextra > 0 )call local_to_global(x,xx,ix)
-
-#ifdef MPI
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call timer_start(TIME_DISTCRD)
-
- ! ---Here we provide every processor a full copy of the velocities
- ! for removal of center of mass motion, or for archiving.
- ! (Note: this is actually over-kill: for example, only the master
- ! node really needs the velocities for archiving. But the extra
- ! overhead of doing it this way is probably small in most cases.)
-
- if( ivdump .or. ivscm .or. ixdump ) then
- call xdist(v, xx(lfrctmp), natom)
- endif
-
-! M-WJ
-! if( ixdump .and. (induced == 1 .and. indmeth == 3 ) )then
- if( ixdump .and. (induced > 0 .and. indmeth == 3 ) )then
-!
- call xdist(xx(ldipvel), xx(lfrctmp), natom)
- call xdist(xx(linddip), xx(lfrctmp), natom)
- end if
- call timer_stop(TIME_DISTCRD)
- end if
- call timer_start(TIME_VERLET)
-
- ! ========================= END AMBER/MPI =========================
-#endif /* MPI */
-
- !-------------------------------------------------------------------
- ! Step 6: zero COM velocity if requested; used for preventing
- ! ewald "block of ice flying thru space" phenomenon, or accumulation
- ! of rotational momentum in vacuum simulations
- !-------------------------------------------------------------------
-
- if (ivscm) then
- if (mod(nstep,nsnb) == 0) ntnb = 1
- if( ifbox == 0 ) then
- if (is_langevin) then
- ! Get current center of the system
- call get_position(nr,x,vcmx,vcmy,vcmz,sysrange,0)
-
-#ifdef MMPI /* SOFT CORE */
- if (ifsc == 1) call sc_mix_position(vcmx,vcmy,vcmz,clambda)
-#endif
- ! Center the system to the original center
- call re_position(nr,ntr,x,xc, &
- vcmx,vcmy,vcmz,sysx,sysy,sysz,sysrange,mv_flag,0)
- else
- ! ---Non-periodic simulation: remove both translation and rotation.
- ! Back the coords up 1/2 step, so that the correspond to the
- ! velocities; temporarily store in the F() array:
- f(1:nr3) = x(1:nr3) - v(1:nr3)*dt5
- ! --- now compute the com motion, remove it, and recompute (just
- ! to check that it is really gone.....)
- call cenmas(nr,f,v,amass,ekcm,xcm,vcm,acm,ekrot,ocm,4)
- call stopcm(nr,f,v,xcm,vcm,ocm, .true.)
- call cenmas(nr,f,v,amass,ekcm,xcm,vcm,acm,ekrot,ocm,4)
- end if
- else
- if (.not. is_langevin) then
- ! ---Periodic simulation: just remove the translational velocity:
- vcmx = 0.d0
- vcmy = 0.d0
- vcmz = 0.d0
- j = 1
- do i = 1, 3*natom,3
- aamass = amass(j)
- vcmx = vcmx + aamass * v(i)
- vcmy = vcmy + aamass * v(i+1)
- vcmz = vcmz + aamass * v(i+2)
- j = j + 1
- end do
- vcmx = vcmx * tmassinv
- vcmy = vcmy * tmassinv
- vcmz = vcmz * tmassinv
- vel2 = vcmx*vcmx + vcmy*vcmy + vcmz*vcmz
- atempdrop = 0.5d0 * tmass * vel2 * onefac(1) !onefac(1) = 1.0d0/fac(1)
- vel = sqrt(vel2)
- if ( master ) write (6,'(a,f15.6,f9.2,a)') &
- 'check COM velocity, temp: ',vel,atempdrop, '(Removed)'
- do i = 1, 3*natom, 3
- v(i) = v(i) - vcmx
- v(i+1) = v(i+1) - vcmy
- v(i+2) = v(i+2) - vcmz
- end do
-
-#ifdef MPI /* SOFT CORE */
- if (icfe==1) then
- if (ifsc==1) then
- if (master) then
- call sc_mix_velocities(v,nr3,clambda)
- end if
- call mpi_bcast(v,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-#endif
- end if ! (.not. is_langevin)
- end if ! ( ifbox == 0 )
- end if ! (ivscm)
-
- ! Also zero out the non-moving velocities if a belly is active:
- if (belly) call bellyf(nr,ix(ibellygp),v)
-
- !-----------------------------------------------------------------
- ! --- put current velocities into VOLD
- !-----------------------------------------------------------------
-
- vold(istart3:iend3) = v(istart3:iend3)
- do im=1,iscale
- vold(nr3+im) = v(nr3+im)
- end do
-
- !-------------------------------------------------------------------
- ! Step 7: scale coordinates if NPT with Berendsen barostat:
- !-------------------------------------------------------------------
- if( ntp > 0 .and. ipimd > 0 .and. barostat == 1 ) then
- x_lnv_old = x_lnv
- x_lnv = x_lnv_old + v_lnv * dtx
- rmu(1:3) = exp( ( x_lnv - x_lnv_old ) )
- box(1:3) = box(1:3) * rmu(1:3)
- volume = box(1) * box(2) * box(3)
- ener%box(1:3) = box(1:3)
- ! only for NMPIMD in sander.LES
- ! (in sander.MPI volume, pressure and density printed in pimdout)
-#ifdef LES
- ener%volume = volume
-#else
- ener%volume = 0.
- totener%volume = volume
-#endif
- call redo_ucell(rmu)
- call fill_tranvec()
- call ew_pscale(natom,x,amass,nspm,nsp,2)
- end if
-
- if( iamoeba == 0 .and. barostat == 1 ) then
-
- ! ntp = 1, isotropic pressure coupling
-
- if (ntp == 1) then
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(4)))**third
- rmu(2) = rmu(1)
- rmu(3) = rmu(1)
-
-
- ! ntp = 2, anisotropic pressure scaling
-
- else if (ntp == 2) then
-
- if (csurften > 0) then
-
- ! Constant surface tension adjusts the tangential pressures
- ! See Zhang, Feller, Brooks, Pastor. J. Chem. Phys. 1995
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
-
- end if
-
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- else
-
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(1)))**third
- rmu(2) = (1.d0-dtcp*(pres0-ener%pres(2)))**third
- rmu(3) = (1.d0-dtcp*(pres0-ener%pres(3)))**third
-
- end if
-
- ! ntp = 3, semiisotropic pressure coupling
- ! (currently only for csurften>0, constant surface tension)
-
- !else if (ntp > 2) then
- else
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
- press_tan_ave = (ener%pres(2) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(2))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- end if
- end if
- ! Add semiisotropic pressure scaling in any direction with no constant
- ! surface tension here
- end if
-
- if (ntp > 0) then
- box(1:3) = box(1:3)*rmu(1:3)
- ener%box(1:3) = box(1:3)
-
- ! WARNING!! This is not correct for non-orthogonal boxes if
- ! NTP > 1 (i.e. non-isotropic scaling). Currently general cell
- ! updates which allow cell angles to change are not implemented.
- ! The viral tensor computed for ewald is the general Nose Klein,
- ! however the cell response needs a more general treatment.
-
- call redo_ucell(rmu)
- ! keep tranvec up to date, rather than recomputing each MD step.
- call fill_tranvec() ! tranvec is dependent on only ucell
-
-#ifdef MPI /* SOFT CORE */
- ! if softcore potentials and the dual topology approach are used
- ! C.O.M. scaling has to be changed to account for different masses
- ! of the same molecule in V0 and V1. This is quite inefficient and is
- ! therefore done in a separate routine in softcore.f
- ! only both masters actually do the computation for ifsc==1
- ! the scaled coordinates are then broadcast to the nodes
- if (icfe /= 0 .and. ifsc == 1) then
- if (master) then
- call sc_pscale(natom,x,amass,nspm,nsp,oldrecip,ucell)
- end if
- call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- else
-#endif
- call ew_pscale(natom,x,amass,nspm,nsp,npscal)
-#ifdef MPI /* SOFT CORE */
- end if
-#endif
- if (ntr > 0 .and. nrc > 0) &
- call ew_pscale(natom,xc,amass,nspm,nsp,npscal)
- endif
- if (ipimd==NMPIMD.and.ntp>0) then
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = pressure*pconv
- endif
- else if (barostat == 1) then
- if (ntp>0) then
- if (ipimd==0) then ! for classical AMOEBA
- ener%cmt(4) = eke ! for printing in prntmd()
- ener%vir(4) = ener%vir(1) + ener%vir(2) + ener%vir(3)
- ener%pres(4) = (pressure_constant/volume)*(2.d0*eke - ener%vir(4)) / 3.d0
- elseif (ipimd==NMPIMD) then ! for NMPIMD AMOEBA
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = pressure*pconv
- endif
- call AM_RUNMD_scale_cell(natom,ener%pres(4),dt,pres0,taup,x)
- call fill_tranvec()
- end if
- end if
-
-#ifdef LES
- ener%kin%solt = eke
- ener%kin%solv = ekeles
- ener%kin%tot = ener%kin%solt + ener%kin%solv
- if (ntt == 1 .and. onstep) then
- if ( temp0les < 0 ) then
- ekmh = max(ekph,fac(1)*10.d0)
- else
- ekmh = max(ekph,fac(2)*10.d0)
- ekmhles = max(ekphles,fac(3)*10.d0)
- endif
- end if
-
- if( ipimd > 0 ) then
- ener%kin%solv = equal_part + Epot_deriv ! "virial" estimate of KE
- ener%tot = ener%kin%solv + ener%pot%tot
- endif
-#else
- if( ipimd > 0 ) then
- ! use a "virial" estimator for the KE, rather than one derived from the
- ! bead velocities:
- totener%kin%solv = equal_part + Epot_deriv
- else
- ener%kin%solv = ekpbs + ener%pot%tot
- ! Pastor, Brooks, Szabo conserved quantity
- ! for harmonic oscillator: Eq. 4.7b of Mol.
- ! Phys. 65:1409-1419, 1988
- endif
- ener%kin%solt = eke
- ener%kin%tot = ener%kin%solt
- if (ntt == 1 .and. onstep) then
- ekmh = max(ekph,fac(1)*10.d0)
- end if
-#endif
-
- ! ---if velocities were reset, the KE is not accurate; fudge it
- ! here to keep the same total energy as on the previous step.
- ! Note that this only affects printout and averages for Etot
- ! and KE -- it has no effect on the trajectory, or on any averages
- ! of potential energy terms.
-
- if( resetvelo ) ener%kin%tot = etot_save - ener%pot%tot
-
- ! --- total energy is sum of KE + PE:
-
- if( ipimd > 0 ) then
- totener%tot = totener%kin%solv + totener%pot%tot
- etot_save = totener%kin%tot + totener%pot%tot
- if (ipimd==CMD) then
- etot_cmd = eke_cmd*0.5 + ener%pot%tot
-
- totener%tot= etot_cmd
-
- ener%tot = etot_cmd
- ener%kin%tot = eke_cmd*0.5
- ener%kin%solv = ener%kin%tot
- endif
- else
- ener%tot = ener%kin%tot + ener%pot%tot
- etot_save = ener%tot
- end if
-
- !-------------------------------------------------------------------
- ! Step 8: update the step counter and the integration time:
- !-------------------------------------------------------------------
-
- if(abfqmmm_param%abfqmmm /= 1) then ! lam81
- nstep = nstep+1
- t = t+dt
- end if ! lam81
-
- !For CMD
- if ( ipimd==CMD ) then
- nstep_cmd = nstep_cmd + 1
- t_cmd = t_cmd + dt
- end if
-
- ! ---full energies are only calculated every nrespa steps
- ! nvalid is the number of steps where all energies are calculated
-
- if (onstep .or. aqmmm_flag > 0) then
- nvalid = nvalid + 1
- ! Update all elements of these sequence types
- enert = enert + ener
- enert2 = enert2 + (ener*ener)
-#ifdef MPI
- if( ievb /= 0 ) then
- evb_nrg_ave(:) = evb_nrg_ave(:) + evb_nrg(:)
- evb_nrg_rms(:) = evb_nrg_rms(:) + evb_nrg(:)**2
- endif
- if ( ifsc /= 0 ) then
- sc_ener_ave(1:ti_ene_cnt) = sc_ener_ave(1:ti_ene_cnt) + sc_ener(1:ti_ene_cnt)
- sc_ener_rms(1:ti_ene_cnt) = sc_ener_rms(1:ti_ene_cnt) + sc_ener(1:ti_ene_cnt)**2
- end if
-#endif
- if( nvalid == 1 ) etot_start = ener%tot
-
-#ifndef LES
- if ( ipimd>0 .or. ineb>0 ) then
-# ifdef MPI
- if (master) call mpi_reduce(ener%kin%tot,totener%kin%tot,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,0,commmaster,ierr)
-
-# endif
- endif
-
- ! Passing of dvdl=dV/dl for TI w.r.t. mass
- ! Note that ener(39) (in runmd and mix_frcti) =
- ! = ener(17) = ene(21) (in force). All denote dvdl.
- ! Note, ener() is now historical, MJW Feb 2010
- if (ipimd>0 .and. itimass>0) totener%pot%dvdl = ener%pot%dvdl
-
- if(ipimd.eq.NMPIMD.and.ntp>0) then
- totener%pres(4) = pressure * pconv
- totener%density = tmass / (0.602204d0*volume)
- endif
- if(ipimd.eq.CMD) then
- totener%kin%tot = eke_cmd*0.5d0
- totener%kin%solv = totener%kin%tot
- totener%tot = totener%kin%tot + totener%pot%tot
- endif
- totenert = totenert + totener
- totenert2 = totenert2 + (totener*totener)
-
-#endif /* LES */
-
- kinetic_E_save(2) = kinetic_E_save(1)
- kinetic_E_save(1) = ener%kin%tot
-
- end if
-
- ! added for rbornstat
-!!FIX: TL - do we need to put in rismnrespa here?
- if (mod(irespa,nrespai) == 0 .or. irespa < 2) nvalidi = nvalidi + 1
-
- ntnb = 0
- if (mod(nstep,nsnb) == 0) ntnb = 1
-
- ! Since nstep has been incremented, total_nstep is now equal to
- ! (mdloop-1)*nstlim+nstep for REMD and nstep for MD.
- lout = mod(total_nstep,ntpr) == 0 .and. onstep
-
- irespa = irespa + 1
-
- ! reset pb-related flags
-#ifdef MPI
- if(mytaskid == 0)then
-#endif
- if ( igb == 10 .or. ipb /= 0 ) then
- if ( mod(nstep,npbgrid) == 0 .and. nstep /= nstlim ) pbgrid = .true.
- if ( mod(nstep,ntpr) == 0 .or. nstep == nstlim ) pbprint = .true.
- if ( mod(nstep,nsnbr) == 0 .and. nstep /= nstlim ) ntnbr = 1
- if ( mod(nstep,nsnba) == 0 .and. nstep /= nstlim ) ntnba = 1
- end if
-#ifdef MPI
- endif
-#endif
-
- !-------------------------------------------------------------------
- ! Step 9: output from this step if required:
- !-------------------------------------------------------------------
-
-#ifdef RISMSANDER
- !some 3D-RISM files require all processes to participate in output
- !due to the distributed memory
- ! RISM archive:
- if(rismprm%irism==1)then
-!!$ if(irismdump)&
-!!$ call rism_writeSolvDistF(rism_3d,nstep)
- ! combined thermodynamics and distribution output
- ! Execute if we need to do either
- if(irismdump .or. (rism_calc_type(nstep) == RISM_FULL &
- .and. rismprm%write_thermo==1 .and. lout))&
- call rism_solvdist_thermo_calc(irismdump,nstep)
- endif
-#endif
-
- ! ...only the master needs to do the output
- if (ixdump) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- call trans_vel_nmode_to_cart(v,cartvel)
- endif
- endif
-
- if (itdump) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- endif
-!AMD Flush amdlog file
- if(iamd.gt.0)then
-# ifdef MPI
- if (worldrank.eq.0) &
-# endif
- call write_amd_weights(ntwx,total_nstep)
- end if
-!scaledMD Flush scaledMDlog file
- if(scaledMD.gt.0)then
-# ifdef MPI
- if (worldrank.eq.0) &
-# endif
- call write_scaledMD_log(ntwx,total_nstep)
- end if
-
- endif
-
- if (ivdump) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call trans_vel_nmode_to_cart(v,cartvel)
- endif
- endif
-
-
- if (master) then
-
- ! -- restrt:
-
- if (ixdump) then
-
- ! NOTE - This assumes that if numextra > 0, then velocities are
- ! found in the array v...
- if (numextra > 0) call zero_extra_pnts_vec(v,ix)
-
- if( iwrap == 0 ) then
- nr = nrp
-#ifdef LES
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- cartpos,cartvel,xx(lcrdr),box,t,temp0)
- else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- x,v,xx(lcrdr),box,t,temp0les)
- endif
-#else
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- cartpos,cartvel,xx(lcrdr),box,t,rem_val)
- else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- x,v,xx(lcrdr),box,t,rem_val)
- endif
-#endif
- else if (iwrap == 1) then
-
- ! --- use temp. array to hold coords. so that the master's values
- ! are always identical to those on all other nodes:
-
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1)=cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- end if
-
- call wrap_molecules(nspm,nsp,r_stack(l_temp))
- if(ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
- nr = nrp
-#ifdef LES
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,temp0les)
-#else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,rem_val)
-#endif
- call free_stack(l_temp,routine)
- else if (iwrap == 2) then
- ! GMS ------------------------------------------
- ! We are wrapping around a pre-determined mask
- ! Need to center it on the mask COM first, then
- ! wrap it normally as it happens on the iwrap=1
- ! case.
- ! GMS ------------------------------------------
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1)=cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- end if
- nr = nrp
-
- ! Now, wrap the coordinates around the iwrap_mask:
- call iwrap2(n_iwrap_mask_atoms,iwrap_mask_atoms,r_stack(l_temp), &
- box_center)
-#ifdef LES
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,temp0les)
-#else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,rem_val)
-#endif
- call free_stack(l_temp,routine)
- end if ! ( iwrap == 0 )
-
-! M-WJ
-! if( igb == 0 .and. induced == 1 .and. indmeth == 3) &
- if( igb == 0 .and. ipb == 0 .and. induced > 0 .and. indmeth == 3) &
-!
- call wrt_dips(xx(linddip),xx(ldipvel),nr,t,title)
-
- if (icnstph /= 0 .and. ((rem /= 0 .and. mdloop > 0) .or. rem == 0)) then
- call cnstphwriterestart(chrgdat)
- end if
-
- end if ! (ixdump)
-
- ! -- Coordinate archive:
- ! For formatted writes and replica exchange, write out a header line.
-
- if (itdump) then
-#ifdef MPI
- ! Write out current replica#, exchange#, step#, and mytargettemp
- ! If mdloop==0 this is a normal md run (since REMD never calls corpac
- ! when mdloop==0) and we don't want the REMD header.
- ! total_nstep is set in step 5.
- if (mdloop > 0 .and. loutfm) then
- if (trxsgld) then
- write (MDCRD_UNIT,'(a,4(1x,i8))') "RXSGLD ", repnum, mdloop, &
- total_nstep, stagid
- else
- write (MDCRD_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum, mdloop, &
- total_nstep, my_remd_data%mytargettemp
- end if
- end if
-#endif
-
- if( iwrap == 0 ) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call corpac(cartpos,1,nrx,MDCRD_UNIT,loutfm)
- else
- call corpac(x,1,nrx,MDCRD_UNIT,loutfm)
- endif
- if(ntb > 0) call corpac(box,1,3,MDCRD_UNIT,loutfm)
- else if (iwrap == 1) then
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1) = cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- endif
-
- call wrap_molecules(nspm,nsp,r_stack(l_temp))
- if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
-
- call corpac(r_stack(l_temp),1,nrx,MDCRD_UNIT,loutfm)
- call corpac(box,1,3,MDCRD_UNIT,loutfm)
- call free_stack(l_temp,routine)
- else if (iwrap == 2) then
- ! GMS ------------------------------------------
- ! We are wrapping around a pre-determined mask
- ! Need to center it on the mask COM first, then
- ! wrap it normally as it happens on the iwrap=1
- ! case.
- ! GMS ------------------------------------------
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1) = cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- endif
-
- call iwrap2(n_iwrap_mask_atoms,iwrap_mask_atoms, r_stack(l_temp), &
- box_center)
-
- call corpac(r_stack(l_temp),1,nrx,MDCRD_UNIT,loutfm)
- call corpac(box,1,3,MDCRD_UNIT,loutfm)
- call free_stack(l_temp,routine)
-
-
- end if ! if (iwrap == 0) ...
-
-
- !GMS: If using variable QM solvent, try to write a new pdb file
- ! with the QM coordinates for this step. This is done here
- ! to keep the PDB file in sync with the mdcrd file, which
- ! makes it easier to check later.
- if (qmmm_nml%vsolv > 0 .and. qmmm_nml%verbosity == 0) &
- call qm_print_coords(nstep,.false.)
- end if ! (itdump)
-
- ! Velocity archive:
-
- if (ivdump) then
-
- ! NOTE - This assumes that if numextra > 0, then velocities are
- ! found in the array v...
- if (numextra > 0) call zero_extra_pnts_vec(v,ix)
-
-#ifdef MPI
- ! Write out current replica#, exchange#, step#, and mytargettemp
- ! If mdloop==0 this is a normal md run (since REMD never calls corpac
- ! when mdloop==0) and we don't want the REMD header.
- if (mdloop>0.and.loutfm) then
- if (trxsgld) then
- write (MDVEL_UNIT,'(a,4(1x,i8))') "RXSGLD ", repnum, mdloop, &
- total_nstep, stagid
- else
- write (MDVEL_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum, mdloop, &
- total_nstep, my_remd_data%mytargettemp
- end if
- end if
-#endif
-
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call corpac(cartvel,1,nrx,MDVEL_UNIT,loutfm)
- else
- call corpac(v,1,nrx,MDVEL_UNIT,loutfm)
- endif
- end if
- ! Force archive lam81
- if (ifdump .and. (abfqmmm_param%abfqmmm == 1)) call corpac(for,1,nrx,MDFRC_UNIT,loutfm) ! lam81
-
- ! Energy archive:
- ! (total_nstep set in Step 5.)
- if (ntwe > 0) then
- if (mod(total_nstep,ntwe) == 0.and.onstep) &
- call mdeng(15,nstep,t,ener,onefac,ntp,csurften)
- end if
-
- if (ioutfm > 0) then
- if (itdump) call end_binary_frame(MDCRD_UNIT)
- if (ivdump .and. ntwv>0 ) call end_binary_frame(MDVEL_UNIT)
- if (ifdump .and. ntwf>0 ) call end_binary_frame(MDFRC_UNIT)
- end if
-
-#ifdef MPI
- if( ievb /= 0 ) call out_evb ( nstep )
-#endif
-
- ! General printed output:
-
- if (lout) then
- if (facc /= 'A') rewind(7)
-
- ! Conserved quantity for Nose'-Hoover based thermostats. ! APJ
- if (ipimd.eq.0 .and. ntt > 4 .and. ntt <= 8 ) then ! APJ
- Econserved = ener%kin%tot + ener%pot%tot + E_nhc ! APJ
- if( ntp>0 ) Econserved = Econserved + pres0 / pconv * volume ! APJ
-# ifdef MPI
- if ( worldrank.eq.0 ) & ! APJ
-# endif
- write(file_nhc,'(I10,F14.4)') nstep, Econserved ! APJ
- endif ! APJ
-#ifdef LES
- if (ipimd>0.and.ntt==4) then
- Econserved = ener%kin%tot + ener%pot%tot + E_nhc
- Econserved = Econserved + Epot_spring
- if( ntp>0 ) Econserved = Econserved + pres0 / pconv * volume
- write(file_nhc,'(I10,F14.4)') nstep, Econserved
- endif
- if ( ipimd.eq.CMD ) then
- ener%kin%tot = eke_cmd*0.5d0
- ener%kin%solv = ener%kin%tot
- ener%tot = ener%kin%tot + ener%pot%tot
-
- end if
-#else
- if ( ipimd>0 ) then
- ener%tot = 0.d0
- ener%kin%tot = 0.d0
- ! Conserved quantity for Nose'-Hoover thermostat.
- if ( ntt==4 ) then
- Econserved = totener%kin%tot + totener%pot%tot + E_nhc
- Econserved = Econserved + Epot_spring
- if ( ntp>0 ) Econserved=Econserved+pres0/pconv*volume
-# ifdef MPI
- if ( worldrank.eq.0 ) &
-# endif
- write(file_nhc,'(I10,F14.4)') nstep, Econserved
- endif
-# ifdef MPI
- if(worldrank.eq.0) &
-# endif
- call pimd_report(nstep,t,pimd_unit,totener,onefac)
- end if
-#endif /* LES */
- call prntmd(total_nstep,nitp,nits,t,ener,onefac,7,.false.)
-
-# ifdef MPI
- ! print corrected energy for adaptive qm/mm runs
- ! note: nstep has already been increased here
- ! (it was not increased when adaptive_qmmm() was called above)
- if ( qmmm_nml%vsolv > 1 ) then
-
- if ( masterrank == 0 ) then
-
- if (aqmmm_flag > 0 .and. nstep > aqmmm_flag) then
-
- etotcorr = corrected_energy + kinetic_E_save(aqmmm_flag)
- nstepadc = nstep - aqmmm_flag + 1
- tadc = t - dt * (dble( aqmmm_flag - 1) )
-
- write(6,'(a)')' Adaptive QM/MM energies:'
- write(6,'(x,a,i5,x,a,f11.4,x,2(a,f15.4,x))') &
- 'adQMMM STEP=', nstepadc, &
- 'TIME(PS)=', tadc, &
- 'ETC=', etotcorr, &
- 'EPC=', corrected_energy
-
- ! print total energy for adaptive qm/mm into a separate file
- ! when qmmm_vsolv%verbosity > 0
- ! set reference energy to zero only for energy dumping purposes
- if (flag_first_energy) then
- flag_first_energy = .false.
- adqmmm_first_energy = etotcorr
- etotcorr = 0.0d0
- else
- etotcorr = etotcorr - adqmmm_first_energy
- end if
-
- if (qmmm_vsolv%verbosity > 0) then
- open(80,file='adqmmm_tot_energy.dat',position='append')
- write(80,'(i9,5x,f11.4,5x,f15.4)') nstepadc, tadc, etotcorr
- close(80)
- end if
-
- end if
- end if
- end if
-# endif
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener)
- if (ifsc /= 0) call sc_print_energies(7, sc_ener)
-#endif
- if ( ifcr > 0 .and. crprintcharges > 0 ) then
- call cr_print_charge( xx(l15), total_nstep )
- end if
-
- ! Output for CMD.
-#ifdef LES
- if (ipimd.eq.CMD) then
-
- ncmd = 0
- do iatom = 1, natom
- if ( cnum(iatom)==0 .or. cnum(iatom)==1 ) then
- xcmd(ncmd+1) = x(3*iatom-2)
- xcmd(ncmd+2) = x(3*iatom-1)
- xcmd(ncmd+3) = x(3*iatom)
- vcmd(ncmd+1) = v(3*iatom-2)
- vcmd(ncmd+2) = v(3*iatom-1)
- vcmd(ncmd+3) = v(3*iatom)
- ncmd = ncmd+3
- endif
- enddo
- write(file_pos_cmd,'(10f8.3)') xcmd(1:ncmd)
- write(file_vel_cmd,'(10f8.3)') vcmd(1:ncmd)
- write(file_pos_cmd,'(10f8.3)') box(1:3)
-
- eke_cmd = eke_cmd * 0.5d0
- etot_cmd = eke_cmd + ener%pot%tot
-
- if (eq_cmd) then
- temp_cmd = eke_cmd/boltz2/dble(3*natomCL)
- else
- temp_cmd = eke_cmd/boltz2/dble(3*(natomCL-1))
- endif
-
- endif
-#else
- if (ipimd.eq.CMD.and.mybeadid.eq.1) then
- write(file_pos_cmd,'(10f8.3)') x(1:3*natom)
- write(file_vel_cmd,'(10f8.3)') v(1:3*natom)
- write(file_pos_cmd,'(10f8.3)') box(1:3)
-
- eke_cmd = eke_cmd * 0.5d0
- etot_cmd = eke_cmd + totener%pot%tot
-
- if (eq_cmd) then
- temp_cmd = eke_cmd/boltz2/dble(3*natom)
- else
- temp_cmd = eke_cmd/boltz2/dble(3*(natom-1))
- endif
- end if
-#endif /* LES */
-
- !--- Print QMMM Muliken Charges if needed ---
- if (qmmm_nml%ifqnt) then
- if (qmmm_nml%printcharges .and. qmmm_mpi%commqmmm_master) then
- call qm2_print_charges(nstep,qmmm_nml%dftb_chg,qmmm_struct%nquant_nlink, &
- qm2_struct%scf_mchg,qmmm_struct%iqm_atomic_numbers)
- end if
- end if
- if (qmmm_nml%printdipole /= 0) then
- call qmmm_dipole(x,xx(Lmass),ix(i02),ih(m02),nres)
- end if
-
- !--- BEGIN DIPOLE PRINTING CODE ---
-
- ! RCW 2nd Dec 2003 - also output dipole information if
- ! the dipoles namelist has been specified and corresponding
- ! groups defined.
-
- ! Check input unit 5 for namelist dipoles
- ! We expect to find &dipoles followed by a group
- ! specification of the dipoles to output.
- call nmlsrc('dipoles',5,prndipfind)
-
- if(prndipfind /= 0 ) then
- !We calculate the dipoles
- write(6,*) '------------------------------- DIPOLE INFO ----------------------------------'
- write(6,9018) nstep,t
- 9018 format(/1x, 'NSTEP =',i7,1x,'TIME(PS) =',f10.3)
-
- !Get the groups for the dipoles - Ideally we only really want
- !to call this the once but for the time being I will call it
- !every time
-
- read (5,'(a)') prndiptest
-
- call rgroup(natom,natc,nres,prndipngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp), &
- jgroup,indx,irespw,npdec, &
- xx(l60),xx(lcrdr),0,0,0,idecomp,5,.false.)
-
- ! Need to rewind input file after rgroup so it is available
- ! when we next loop through
-
- rewind(5)
-
- if(prndipngrp > 0) then
- !prndipngrp - holds number of groups specified + 1
- !ix(icnstrgp) - holds map of group membership for each atom
- !x(lcrd) - X,Y,Z coords of atoms - (3,*)
- !x(l15) - Partial Charges
- !x(linddip) - induced dipoles X,Y,Z for each atom (3,*)
- !x(Lmass) - Mass of each atom
- call printdip(prndipngrp,ix(icnstrgp),xx(lcrd), &
- xx(l15),xx(linddip),xx(Lmass), natom)
- end if
- write(6,*) '----------------------------- END DIPOLE INFO --------------------------------'
- end if
- !--- END DIPOLE PRINTING CODE ---
-
- if (nmropt > 0) then
- call nmrptx(6)
- end if
- if (itgtmd == 2) then
- emtmd = 0.0d0
- call mtmdcall(emtmd,xx(lmtmd01),ix(imtmd02),x,f,ih(m04),ih(m02),ix(i02),&
- ih(m06),xx(lmass),natom,nres,'PRNT')
- end if
- call amflsh(7)
- end if
-
- ! Output running averages:
- ! DAN ROE: total_nstep==Total nstep REMD/MD, set in step 5
- if ( ntave > 0 )then
- if ( mod(total_nstep,ntave) == 0 .and. onstep )then
- write(6,542)
-#ifdef RISMSANDER
- if(rismprm%irism==1)then
- tspan = ntave/mylcm(nrespa,rismprm%rismnrespa)
- else
- tspan = ntave/nrespa
- end if
-#else
- tspan = ntave/nrespa
-#endif
-
- ! Update all elements of these sequence types
- enert_tmp = enert - enert_old
- enert2_tmp = enert2 - enert2_old
- enert_old = enert
- enert2_old = enert2
- enert_tmp = enert_tmp/tspan
- enert2_tmp = enert2_tmp/tspan - &
- enert_tmp*enert_tmp
- call zero_neg_values_state(enert2_tmp)
- enert2_tmp = sqrt(enert2_tmp)
-
-#ifdef MPI
- if( ievb /= 0 ) then
- evb_nrg_tmp (:) = evb_nrg_ave(:) - evb_nrg_old (:)
- evb_nrg_tmp2(:) = evb_nrg_rms(:) - evb_nrg_old2(:)
- evb_nrg_old (:) = evb_nrg_ave(:)
- evb_nrg_old2(:) = evb_nrg_rms(:)
- evb_nrg_tmp (:) = evb_nrg_tmp (:) / tspan
- evb_nrg_tmp2(:) = evb_nrg_tmp2(:) / tspan - evb_nrg_tmp(:)**2
- evb_nrg_tmp2(:) = max( evb_nrg_tmp2(:), 0.0d0 )
- evb_nrg_tmp2(:) = sqrt( evb_nrg_tmp2(:) )
- endif
- if ( ifsc /= 0 ) then
- do m = 1,ti_ene_cnt
- sc_ener_tmp(m) = sc_ener_ave(m)-sc_ener_old(m)
- sc_ener_tmp2(m) = sc_ener_rms(m)-sc_ener_old2(m)
- sc_ener_old(m) = sc_ener_ave(m)
- sc_ener_old2(m) = sc_ener_rms(m)
- sc_ener_tmp(m) = sc_ener_tmp(m)/tspan
- sc_ener_tmp2(m) = sc_ener_tmp2(m)/tspan - sc_ener_tmp(m)**2
- if (sc_ener_tmp2(m) < 0.0d0) sc_ener_tmp2(m) = 0.0d0
- sc_ener_tmp2(m) = sqrt(sc_ener_tmp2(m))
- end do
- end if
- if( ievb /= 0 ) evb_frc%evb_ave = .true.
-#endif
-#ifdef RISMSANDER
- if(rismprm%irism==1)then
- write(6,540) ntave/mylcm(nrespa,rismprm%rismnrespa)!nrespa
- else
- write(6,540) ntave/nrespa
- end if
-#else
- write(6,540) ntave/nrespa
-#endif
- call prntmd(total_nstep,izero,izero,t,enert_tmp,onefac,0,.false.)
-#ifdef MPI
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_tmp)
- if( ievb /= 0 ) evb_frc%evb_rms = .true.
-#endif
- write(6,550)
- call prntmd(total_nstep,izero,izero,t,enert2_tmp,onefac,0,.true.)
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_tmp2)
-#endif
- if( icfe > 0 ) then
-#ifdef RISMSANDER
- if(rismprm%irism==1)then
- write(6,541) ntave/mylcm(nrespa,rismprm%rismnrespa)!nrespa
- else
- write(6,541) ntave/nrespa
- end if
-#else
- write(6,541) ntave/nrespa
-#endif
- edvdl_r = edvdl_r/tspan
- edvdl_r%pot%dvdl = enert_tmp%pot%dvdl ! fix for DV/DL output
- edvdl_r%virvsene = 0.d0 ! virvsene should not but included here
- call prntmd(total_nstep,izero,izero,t,edvdl_r,onefac,0,.false.)
- edvdl_r = null_state_rec
-
- end if
- write(6,542)
- end if
- end if ! ( ntave > 0 )
-
- ! --- end masters output ---
-
- end if ! (master)
-
-#ifdef MPI /* SOFT CORE */
- if (ntave > 0 .and. icfe > 0 .and. dynlmb > 0) then
- if ( mod(nstep,ntave) == 0 .and. onstep ) then
- ! For runs with dynamically changing lambda, raise lambda here
- ! and flush all buffers for the next averages
- clambda = clambda + dynlmb
- call sc_change_clambda(clambda)
- if (master) then
- sc_ener(1:ti_ene_cnt) = 0.0d0
- sc_ener_ave(1:ti_ene_cnt) = 0.0d0
- sc_ener_rms(1:ti_ene_cnt) = 0.0d0
- sc_ener_old(1:ti_ene_cnt) = 0.0d0
- sc_ener_old2(1:ti_ene_cnt) = 0.0d0
- enert = null_state_rec
- enert2 = null_state_rec
- enert_old = null_state_rec
- enert2_old = null_state_rec
- write (6,*)
- write (6,'(a,f12.4,a,f12.4)') &
- 'Dynamically changing lambda: Increased clambda by ', &
- dynlmb, ' to ', clambda
- write (6,*)
- end if
- end if
- end if
-#endif
-
- !=======================================================================
-
- ! ---major cycle back to new step unless we have reached our limit:
-
-#ifdef MMTSB
- if ( mmtsb_switch /= mmtsb_off ) then
- if ( mod( nstep, mmtsb_iterations ) == 0 ) then
- write(6,'(a,i8)') &
- 'MMTSB Replica Exchange iterations completed at NSTEP = ', &
- nstep
- ! apparently 23 is the magic number for potential energy.
- ! ener%pot%tot is the new 23 ;) MJW
- write(6,'(a,f12.4)') &
- 'MMTSB Replica Exchange potential energy = ', ener%pot%tot
- ! write coordinates; preferred format is pdb, but can't do that
- ! so write a restart file; server will post process with ambpdb.
-# ifdef LES
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, x,v, &
- xx(lcrdr),box,t,temp0les)
-# else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, x,v, &
- xx(lcrdr),box,t,rem_val)
-# endif
- ! Chop up trajectory files for later continuous temp splicing.
- call close_dump_files
- ! contact server
- if ( mmtsb_switch == mmtsb_temp_rex ) then
- call mmtsb_newtemp( ener%pot%tot, temp_mmtsb, is_done_mmtsb )
- else if ( mmtsb_switch == mmtsb_lambda_rex ) then
- ! currently temp_mmtsb is ignored, but multidimensional soon
- call mmtsb_newlambda( unpert_pe_mmtsb, pert_pe_mmtsb, &
- lambda_mmtsb, temp_mmtsb, is_done_mmtsb )
- end if
- call open_dump_files
- if ( is_done_mmtsb ) then
- goto 480
- end if
-
- ! in the future we may want amber based tracking of exchanges
- ! perhaps we can use the Simmerling group's code ?
- if ( mmtsb_switch == mmtsb_temp_rex ) then
- if ( abs( temp_mmtsb - temp0 ) <= TEN_TO_MINUS3 ) then
- ! no exchange, continue at the same reference temp.
- mmtsb_is_exchanged = .false.
- write(6,'(a,i8,a,f12.4)') &
- 'MMTSB Replica Exchange temperature unchanged'
- else
- ! exchange temp via changing the reference temp.
- ! the velocities will be randomly reset at the new temp via
- ! the resetvelo variable.
- mmtsb_is_exchanged = .true.
- write(6,'(a,f8.2,a,f8.2)') &
- 'MMTSB Replica Exchange temperature change from ', &
- temp0, ' to ', temp_mmtsb
- temp0 = temp_mmtsb
- end if
- else if ( mmtsb_switch == mmtsb_lambda_rex ) then
- if ( abs( lambda_mmtsb - clambda ) <= TEN_TO_MINUS3 ) then
- ! no exchange, continue at the same lambda
- mmtsb_is_exchanged = .false.
- write(6,'(a,i8,a,f12.4)') &
- 'MMTSB Replica Exchange lambda unchanged'
- else
- ! exchange lambda
- ! the velocities will be randomly reset via
- ! the resetvelo variable.
- mmtsb_is_exchanged = .true.
- write(6,'(a,f8.2,a,f8.2)') &
- 'MMTSB Replica Exchange lambda change from ', &
- clambda, ' to ', lambda_mmtsb
- clambda = lambda_mmtsb
- end if
- end if ! ( mmtsb_switch == mmtsb_temp_rex )
- else
- ! not a replica exchange update iteration.
- mmtsb_is_exchanged = .false.
- end if ! ( mod( nstep, mmtsb_iterations ) == 0 )
- end if ! ( mmtsb_switch /= mmtsb_off )
-#endif
-
-
- call trace_integer( 'end of step', nstep )
- call trace_output_mpi_tally( )
- call timer_stop(TIME_VERLET)
-#if !defined(DISABLE_NCSU) && defined(NCSU_ENABLE_BBMD)
- call ncsu_on_mdstep(ener%pot%tot, v, ekmh)
-#endif /* !defined(DISABLE_NCSU) && defined(NCSU_ENABLE_BBMD) */
-
-#if defined(RISMSANDER) && defined(RISM_DEBUG)
- if(rismprm%irism == 1) then
-!!$ write(6,*) "END OF STEP",natom
-! call calc_cm(x,cm,amass,natom)
- angvel=0
- do m=1,natom
- r = x((m-1)*3+1:(m-1)*3+3)-cm
-!!$ write(6,*) m,v((m-1)*3+1:(m-1)*3+3)
- call cross(r,v((m-1)*3+1:(m-1)*3+3),rxv)
- angvel = angvel + rxv/sum(r**2)
- end do
- moi=0
- erot=0
- do m=1,natom
- r = x((m-1)*3+1:(m-1)*3+3)-cm
- call cross(r,v((m-1)*3+1:(m-1)*3+3),rxv)
- proj = sum(r*angvel)/sum(angvel**2)*angvel
-!!$ write(6,*) "angvel ",angvel
-!!$ write(6,*) "r ",r,sum((r)**2)
-!!$ write(6,*) "proj",proj
-!!$ write(6,*) "r-proj",r-proj,sum((r-proj)**2)
- moi=moi+amass(m)*sum((r-proj)**2)
- erot = erot + .5*amass(m)*sum((r-proj)**2)*sum((rxv/sum(r**2))**2)
- end do
-!!$ write(6,*) moi
-!!$ do m=1,3
-!!$ write(6,*) m,sum(v(m:3*natom:3))
-!!$ write(6,*) m,sum(amass(1:natom)*v(m:3*natom:3))
-!!$ write(6,*) m,angvel(m),sum(angvel**2)
-!!$ end do
-!!$ write(6,*) "EROT", 0.5*moi*sum(angvel**2), erot
-!!$ write(6,*) "EROT", erot
-!!$ call mexit(6,1)
- end if
-#endif /*RISMSANDER && RISM_DEBUG*/
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale) = v(1:nr3+iscale) ! lam81
- deallocate(for, stat=ier) ! lam81
- return ! lam81
- end if ! lam81
-
- if (plumed.eq.1 .and. plumed_stopflag/=0) goto 480
-
- if (nstep < nstlim) goto 260
- 480 continue
-
-#ifdef MPI
-! ------====== REMD Post-Dynamics ======------
- if(next_rem_method == 1) then
- remd_ekmh=ekmh
-
- ! ---=== HYBRID REMD ===---
- if (numwatkeep>=0) then
- ! This is a hybrid REMD run. Get energy of stripped system for next
- ! exchange.
- call hybrid_remd_ene(xx,ix,ih,ipairs,qsetup, &
- numwatkeep,hybridgb,igb,ntr,nspm,t,temp0, &
- ntb,cut, &
- ener,ener%vir,do_list_update,nstep, &
- nitp,nits,onefac,loutfm )
- else ! numwatkeep>=0
- ! The positions are currently one step ahead of the energy ener%pot%tot,
- ! since force was called prior to the position propagation. Thus, call
- ! force one more time to update ener%pot%tot to reflect the current
- ! coordinates.
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
- endif ! numwatkeep>=0
-
- ! Set myeptot, mytemp, and mytargettemp
-! if (mdloop>0) mytemp = ener%kin%tot * onefac(1)
- my_remd_data%mytemp = ener%kin%tot * onefac(1)
- my_remd_data%myeptot = ener%pot%tot
-
-
- my_remd_data%mytargettemp = temp0
-# ifdef VERBOSE_REMD
- if (master) write(6,'(a,f15.4,2(a,f6.2))') &
- "REMD: myEptot= ",my_remd_data%myeptot," myTargetTemp= ", &
- my_remd_data%mytargettemp," mytemp= ",my_remd_data%mytemp
-# endif
-# ifdef LES
- else if(next_rem_method == 2 ) then
- my_remd_data%mytemp = ener%kin%solv * onefac(3)
- my_remd_data%myeptot = ener%eptot
- my_remd_data%mytargettemp = temp0les
-# endif
- else if (next_rem_method == 3) then
- remd_ekmh = ekmh
- if (mdloop > 0) my_remd_data%mytemp = ener%kin%tot * onefac(1)
- my_remd_data%mytargettemp = temp0
-! Call force here to bring all energies up-to-date
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir,xx(l96),xx(l97),xx(l98), &
- xx(l99),qsetup,do_list_update)
-
- my_remd_data%myeptot = ener%pot%tot
-
-! Call nmrdcp to decrement the NMR counter, since this should not count as
-! a real step (JMS 2/12). This is OK, since the counter got incremented at
-! the _very_ end of nmrcal, so we haven't already printed an unwanted value
- if (nmropt /= 0) call nmrdcp
-! Call xdist such that master has all the velocities(DSD 09/12)
- call xdist(v, xx(lfrctmp), natom)
-
- else if (next_rem_method == 4) then
- remd_ekmh = ekmh
-
- endif ! rem == 1
-! ------====== END REMD Post-Dynamics ======------
-#endif /* MPI */
-
- !=======================================================================
- ! ----- PRINT AVERAGES -----
- !=======================================================================
-
-# ifdef MPI
- ! -- ti decomp
- if (icfe /= 0 .and. idecomp /= 0) then
- if( idecomp == 1 .or. idecomp == 2 ) then
- call collect_dec(nrs)
- !else if( idecomp == 3 .or. idecomp == 4 ) then
- ! call collect_dec(npdec*npdec)
- end if
- end if
-
- ! Turn off avg. for REMD. and explicit solvent CpHMD, since it's not
- ! accumulated correctly in that case for each compiler
- if (master.and.rem == 0) then
-# else
- if (master) then
-# endif /*MPI*/
- tspan = nvalid
- if (nvalid > 0) then
-
- ! Update all elements of these sequence types
- enert = enert/tspan
- enert2 = enert2/tspan - enert*enert
- call zero_neg_values_state(enert2)
- enert2 = sqrt(enert2)
- edvdl = edvdl/tspan
-
- ! for PIMD/NMPIMD/CMD/RPMD averages
- if (ipimd>0) then
- totenert = totenert/tspan
- totenert2 = totenert2/tspan - (totenert*totenert)
- call zero_neg_values_state(totenert2)
- totenert2 = sqrt(totenert2)
- endif
-
-#ifdef MPI
- if( ievb /= 0 ) then
- evb_nrg_ave(:) = evb_nrg_ave(:) / tspan
- evb_nrg_rms(:) = evb_nrg_rms(:) / tspan - evb_nrg_ave(:)**2
- evb_nrg_rms(:) = max( evb_nrg_rms(:), 0.0d0 )
- evb_nrg_rms(:) = sqrt( evb_nrg_rms(:) )
- endif
- if ( ifsc /= 0 ) then
- do m = 1,ti_ene_cnt
- sc_ener_ave(m) = sc_ener_ave(m)/tspan
- sc_ener_rms(m) = sc_ener_rms(m)/tspan - sc_ener_ave(m)**2
- if(sc_ener_rms(m) < 0.0d0) sc_ener_rms(m) = 0.0d0
- sc_ener_rms(m) = sqrt(sc_ener_rms(m))
- end do
- end if
- if( ievb /= 0 ) evb_frc%evb_ave = .true.
-#endif
- write(6,540) nvalid
- call prntmd(total_nstep,izero,izero,t,enert,onefac,0,.false.)
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_ave)
- if( ievb /= 0 ) evb_frc%evb_rms = .true.
- if ( ipimd > 0 .and. worldrank==0 ) then
- write(pimd_unit,540) nvalid
- call pimd_report(nstep,t,pimd_unit,totenert,onefac)
- write(pimd_unit,550)
- call pimd_report(nstep,t,pimd_unit,totenert2,onefac)
- endif
-#endif
- if (nmropt > 0) call nmrptx(6)
- write(6,550)
- call prntmd(total_nstep,izero,izero,t,enert2,onefac,0,.true.)
-
-#ifdef MPI
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_rms)
- if (ifsc /= 0) call sc_print_dvdl_values()
-
- if( icfe > 0 ) then
- write(6,541) nvalid
- edvdl%pot%dvdl = enert%pot%dvdl ! fix for DV/DL output
- edvdl%virvsene = 0.d0 ! virvsene should not but included here
- call prntmd(total_nstep,izero,izero,t,edvdl,onefac,0,.false.)
- ! -- ti decomp
- if(worldrank == 0 .and. idecomp /= 0) then
- call checkdec(idecomp)
- if(idecomp == 1 .or. idecomp == 2) call printdec(ix)
- end if
- end if
-#endif
-
- if (nmropt >= 1) then
- write(6,500)
- if (iredir(7) /= 0) call pcshift(-1,x,f)
- call ndvptx(x,f,ih(m04),ih(m02),ix(i02),nres,xx(l95), &
- natom, xx(lwinv),ntb,xx(lnmr01),ix(inmr02),6)
- end if
-
- ! Print Born radii statistics
-
- if ((rbornstat == 1).and.(igb /= 0 .or. ipb /= 0)) then
-
- ! Born radii stats collected every nrespai step not nrespa step
- tspan = nvalidi
-
- write(6,580) nstep
- write(6,590)
- do m = 1,natom
- xx(l188-1+m) = xx(l188-1+m)/tspan
- xx(l189-1+m) = xx(l189-1+m)/tspan - &
- xx(l188-1+m)*xx(l188-1+m)
- xx(l189-1+m) = sqrt(xx(l189-1+m))
- write(6,600) m, xx(l186-1+m), xx(l187-1+m), &
- xx(l188-1+m), xx(l189-1+m)
- end do
- end if
-
- enert%kin%tot = enert%kin%tot*onefac(1)
- enert2%kin%tot = enert2%kin%tot*onefac(1)
- enert%kin%solt = enert%kin%solt*onefac(2)
- enert2%kin%solt = enert2%kin%solt*onefac(2)
- enert%kin%solv = enert%kin%solv*onefac(3)
- enert2%kin%solv = enert2%kin%solv*onefac(3)
-
- temp = enert%kin%tot
- end if ! (nvalid > 0)
-
- if (ntp > 0 .and. barostat == 2) call mcbar_summary
-
- end if ! (master)
-
-#ifdef MPI
- if( ievb /= 0 ) then
- call evb_dealloc
-#if defined(LES)
- if( master ) call evb_pimd_dealloc
-#endif
- endif
-#endif
-
- if( icfe /= 0 ) then
- deallocate( frcti, stat = ier )
- REQUIRE( ier == 0 )
- end if
-
- if (plumed.eq.1) then
- call plumed_f_gfinalize()
- end if
-
- 500 format(/,' NMR restraints on final step:'/)
- 540 format(/5x,' A V E R A G E S O V E R ',i7,' S T E P S',/)
- 541 format(/5x,' DV/DL, AVERAGES OVER ',i7,' STEPS',/)
- 542 format('|',79('='))
- 550 format(/5x,' R M S F L U C T U A T I O N S',/)
- 580 format('STATISTICS OF EFFECTIVE BORN RADII OVER ',i7,' STEPS')
- 590 format('ATOMNUM MAX RAD MIN RAD AVE RAD FLUCT')
- 600 format(i4,2x,4f12.4)
- call trace_exit( 'runmd' )
- return
-end subroutine runmd
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Stripped-down runmd routine for running relaxation dynamics on a given mask
-subroutine relaxmd(xx,ix,ih,ipairs,x,winv,amass,f, &
- v,vold,xr,xc,conp,skip,nsp,tma,erstop, qsetup, &
- relax_nstlim, mobile_atoms, increment_nmropt)
-
- ! Runmd operates in kcal/mol units for energy, amu for masses,
- ! and angstroms for distances. To convert the input time parameters
- ! from picoseconds to internal units, multiply by 20.455
- ! (which is 10.0*sqrt(4.184)).
-
- use bintraj, only: end_binary_frame
- use barostats, only : mcbar_trial
- use constants, only : third, ten_to_minus3
- use crg_reloc, only: ifcr, crprintcharges, cr_print_charge
- use fastwt
- use file_io_dat
- use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms
- use nblist,only: fill_tranvec,volume,oldrecip,ucell
- use qmmm_module, only : qmmm_nml,qmmm_struct, qmmm_mpi, qm2_struct, &
- qmmm_vsolv
- use stack
- use state
- use trace
-
-! Variable Descriptions
-!
-! Passed variables
-! xx : global real array. See locmem.f for structure/pointers
-! ix : global integer array. See locmem.f for structure/pointers
-! ih : global hollerith array. See locmem.f for structure/pointers
-! ipairs : ?? Global pairlist ?? --add description (JMS 11/2010)
-! x : global position array *
-! winv : array with inverse masses *
-! amass : mass array *
-! f : force array, used to hold old coordinates temporarily, too
-! v : velocity array
-! vold : old velocity array, from the previous step
-! xr : coordinates with respect to COM of molecule
-! conp : bond parameters for SHAKE
-! skip : logical skip array for SHAKE (and QM/MM too, I think)
-! nsp : submolecule index array (?)
-! tma : submolecular weight array (?)
-! erstop : should we stop in error (?)
-! qsetup : Not quite sure what this does, if anything anymore.
-! mobile_atoms: bellymask-style array with 1s for moving atoms and 0s for
-! frozen atoms
-! relax_nstlim: Number of relaxation dynamics steps to run
-! increment_nmropt: Do we allow the nmropt counter to increment?
-!
-! Local variables
-! factt : degree-of-freedom correction factor for temperature scaling
-! nr : local copy of nrp, number of atoms
-! nr3 : 3 * nr, used for runtime efficiency
-!
-! Common memory variables
-! nrp : number of atoms, adjusted for LES copies
-
- implicit none
- character(kind=1,len=7) :: routine="relaxmd"
- integer ipairs(*), ix(*), relax_nstlim
- integer, intent(in) :: mobile_atoms(*)
- logical, intent(in) :: increment_nmropt
- _REAL_ xx(*)
- character(len=4) ih(*)
- _REAL_ combination
-
-#ifdef MPI
-# include "parallel.h"
- include 'mpif.h'
- _REAL_ mpitmp(8) !Use for temporary packing of mpi messages.
- integer ist(MPI_STATUS_SIZE), partner, ierr
-#else
- ! mdloop and REM is always 0 in serial
- integer, parameter :: mdloop = 0, rem = 0
-#endif
-
-#include "../include/md.h"
-#include "box.h"
-#include "nmr.h"
-#include "../include/memory.h"
-#include "extra.h"
-#include "ew_frc.h"
-#include "ew_cntrl.h"
-#include "ew_mpole.h"
-#include "def_time.h"
-#include "extra_pts.h"
-#include "../lib/random.h"
-
- _REAL_ sysx,sysy,sysz,sysrange(3,2)
- logical mv_flag
-
- _REAL_ , dimension(1) :: shkh
- integer, dimension(1) :: ifstwr2
- integer :: nshkh
-
- integer idx, iatom, iatomCL,m
- _REAL_ Ekin2_tot,tmp,f_lnv
- integer :: idim, ithermo
- _REAL_ :: E_nhc, exp1, exp2, v_sum
-
- logical ivscm
- logical qspatial
- character(len=6)fnam
-
- logical resetvelo
- integer nshak
- _REAL_ ekgs,eold3,eold4,etot_save,ekpbs
-
- logical do_list_update
- logical skip(*),lout,loutfm,erstop,vlim,onstep
- _REAL_ x(*),winv(*),amass(*),f(*),v(*),vold(*), &
- xr(*),xc(*),conp(*)
- type(state_rec) :: ener
- type(state_rec) :: ecopy, edvdl
- type(state_rec) :: edvdl_r
- _REAL_ rmu(3),fac(3),onefac(3),clfac, etot_start
- _REAL_ tma(*)
-
- _REAL_ tspan,atempdrop,fln,scaltp,scaltpo
- _REAL_ vel,vel2,vcmx,vcmy,vcmz,vmax,vx,vy,vz
- _REAL_ winf,aamass,rterm,ekmh,ekph,ekpht,wfac,rsd,ekav
- _REAL_ fit,fiti,fit2,vscalt
- logical is_langevin ! Is this a Langevin dynamics simulation
- _REAL_ gammai,c_implic,c_explic,c_ave,sdfac,ekins0
- _REAL_ dtx,dtxinv,dt5,factt,ekin0,ekinp0,dtcp,dttp
- _REAL_ rndf,rndfs,rndfp,boltz2,pconv,tempsu
- _REAL_ xcm(3),acm(3),ocm(3),vcm(3),ekcm,ekrot
- _REAL_ emtmd
-
-! Variables and parameters for constant surface tension:
- _REAL_, parameter :: ten_conv = 100.0d0 !ten_conv - converts
- !dyne/cm to bar angstroms
- _REAL_ :: pres0x
- _REAL_ :: pres0y
- _REAL_ :: pres0z
- _REAL_ :: gamma_ten_int
- _REAL_ :: press_tan_ave
-
- integer nsp(*)
- integer idumar(4)
- integer l_temp
- integer i,j,im,i3,nitp,nits
- integer nstep,nrep,nrek,nren,iend,istart3,iend3
- integer nrx,nr,nr3,ntcmt,izero,istart
- logical qsetup
-
- integer nvalid, nvalidi
- _REAL_ eke,eket
- _REAL_ extent
-
- _REAL_ xcen,ycen,zcen,extents(3,2)
- _REAL_, allocatable, dimension(:) :: frcti
- integer ier
-
- _REAL_ small
- data small/1.0d-7/
- data nren/51/
-
- !--- VARIABLES FOR DIPOLE PRINTING ---
- integer prndipngrp
- integer prndipfind
- character(len=4) prndiptest
-
- _REAL_,parameter :: pressure_constant = 6.85695d+4
- ! variables used in constant pressure PIMD
- _REAL_ :: Nkt,centvir,pressure, aa, arg2, poly, e2, e4, e6, e8
- ! variable used in CMD
- real(8) :: tmp_eke_cmd !Use for temporary packing of mpi messages.
-
- _REAL_ :: box_center(3)
-
- !==========================================================================
-
- call trace_enter( 'relaxmd' )
-
- ! ----- INITIALIZE SOME VARIABLES -----
-
- vlim = vlimit > small
- ntcmt = 0
- izero = 0
- lout = .true.
- loutfm = ioutfm <= 0
- nr = natom
- nr3 = 3*nr
- ekmh = 0.d0
- onstep = .true.
-
- do_list_update=.false.
-#ifdef MPI
- istart = iparpt(mytaskid) + 1
- iend = iparpt(mytaskid+1)
-#else
- istart = 1
- iend = nr
-#endif
- istart3 = 3*istart -2
- iend3 = 3*iend
-
- ! If NTWPRT.NE.0, only print the atoms up to this value
- nrx = nr3
- if (ntwprt > 0) nrx = ntwprt*3
-
- !=======================================================================
- ! Determine system degrees of freedom (for T scaling, reporting)
-
- ! Call DEGCNT to get the actual number of degrees of freedom for the
- ! solute and solvent. The 'belly' atoms are just the mobile ones
-
- call degcnt(1,nr,mobile_atoms,nsolut,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0, &
- idumar,rndfp,rndfs)
-
- ! RNDFP = # degrees of freedom for solute
- ! RNDFS = # degrees of freedom for solvent
- ! RNDF = total number of degrees of freedom.
-
- ! qtw - substract the number of overlapping noshake QM atoms in noshakemask
- rndfp = rndfp - qmmm_struct%noshake_overlap
- ! modify RNDFP to reflect NDFMIN (set in mdread) and num_noshake
- rndfp = rndfp - ndfmin + num_noshake
- rndf = rndfp+rndfs
-
- call fix_degree_count(rndf) ! correct for extra points
-
- ! End of degrees of freedom stuff
- !=======================================================================
-
- boltz2 = 8.31441d-3 * 0.5d0
- pconv = 1.6604345d+04 ! factor to convert the pressure kcal/mole to bar
-
- ! ---convert to kcal/mol units
-
- boltz2 = boltz2/4.184d0 ! k-sub-B/2
- dtx = dt*20.455d+00
- dtxinv = 1.0d0 / dtx
- dt5 = dtx * 0.5d0
- pconv = pconv*4.184d0
-
- ! FAC() are #deg freedom * kboltz / 2
- ! multiply by T to get expected kinetic energy
- ! FAC(1) is for total system
-
- fac(1) = boltz2*rndf
- fac(2) = boltz2*rndfp
-
- if(rndfp < 0.1d0) fac(2) = 1.d-6
-
- fac(3) = boltz2*rndfs
- if(rndfs < 0.1d0) fac(3) = 1.d-6
- onefac(1) = 1.0d0/fac(1)
- onefac(2) = 1.0d0/fac(2)
- onefac(3) = 1.0d0/fac(3)
- factt = rndf/(rndf+ndfmin)
-
- ! these are "desired" kinetic energies based on
- ! # degrees freedom and target temperature
- ! they will be used for calculating the velocity scaling factor
-
- ekinp0 = fac(2)*temp0
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-
- ! Langevin dynamics setup:
-
- is_langevin = gamma_ln > 0.0d0
- gammai = gamma_ln/20.455d0
- c_implic = 1.d0/(1.d0+gammai*dt5)
- c_explic = 1.d0 - gammai*dt5
- c_ave = 1.d0+gammai*dt5
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
- if (is_langevin .and. ifbox==0) then
- call get_position(nr,x,sysx,sysy,sysz,sysrange,0)
- end if
- if (ntt == 1) dttp = dt/tautp
- if (ntp > 0) dtcp = comp * 1.0d-06 * dt / taup
-
- ! Constant surface tension setup:
-
- if (csurften > 0) then
-
- ! Set pres0 in direction of surface tension.
- ! The reference pressure is held constant in on direction dependent
- ! on what the surface tension direction is set to.
- if (csurften .eq. 1) then ! pres0 in the x direction
- pres0x = pres0
-
- else if (csurften .eq. 2) then ! pres0 in the y direction
- pres0y = pres0
-
- !else if (csurften .eq. 3) then ! pres0 in the z direction
- else
- pres0z = pres0
-
- end if
-
- ! Multiply surface tension by the number of interfaces
- gamma_ten_int = dble(ninterface) * gamma_ten
-
- end if
-
- nrek = 4
- nrep = 15
-
- nvalid = 0
- nvalidi = 0
- nstep = 0
- fit = 0.d0
- fiti = 0.d0
- fit2 = 0.d0
-
- ener = null_state_rec ! Zeros all elements
- ener%kin%pres_scale_solt = 1.d0
- ener%kin%pres_scale_solv = 1.d0
- ener%box(1:3) = box(1:3)
- ener%cmt(1:4) = 0.d0
- nitp = 0
- nits = 0
-
- ekmh = 0.0d0
-
- i3 = 0
- do j = 1,nrp
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- rterm = v(i3)*v(i3) * aamass
- ekmh = ekmh + rterm
- end do
- end do
-
- do im=1,iscale
- ekmh = ekmh + scalm*v(nr3+im)*v(nr3+im)
- end do
- ekmh = ekmh * 0.5d0
- do i=1,nr3+iscale
- vold(i) = v(i)
- end do
-
- !=======================================================================
- ! ----- MAIN LOOP FOR PERFORMING THE DYNAMICS STEP -----
- ! (at this point, the coordinates are a half-step "ahead"
- ! of the velocities; the variable EKMH holds the kinetic
- ! energy at these "-1/2" velocities, which are stored in
- ! the array VOLD.)
- !=======================================================================
-
- 260 continue
-
- !---------------------------------------------------------------
- ! ---Step 1a: do some setup for pressure calculations:
- !---------------------------------------------------------------
-
- if (ntp > 0) then
- ener%cmt(1:3) = 0.d0
- xr(1:nr3) = x(1:nr3)
-
- ! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
- ! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
- ! MASS -----
-
- call timer_start(TIME_EKCMR)
- call ekcmr(nspm,nsp,tma,ener%cmt,xr,v,amass,istart,iend)
-#ifdef MPI
- call trace_mpi('mpi_allreduce', &
- 3,'MPI_DOUBLE_PRECISION',mpi_sum)
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,ener%cmt,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
-# else
- call mpi_allreduce(ener%cmt,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- ener%cmt(1:3) = mpitmp(1:3)
-# endif
-#endif
- call timer_stop(TIME_EKCMR)
- end if
-
- ! If we're using the MC barostat, go ahead and do the trial move now
- if (ntp > 0 .and. barostat == 2 .and. mod(nstep+1, mcbarint) == 0) &
- call mcbar_trial(xx, ix, ih, ipairs, x, xc, f, ener%vir, xx(l96), &
- xx(l97), xx(l98), xx(l99), qsetup, do_list_update, nstep, nsp, &
- amass)
-
- !--------------------------------------------------------------
- ! ---Step 1b: Get the forces for the current coordinates:
- !--------------------------------------------------------------
-
- iprint = 0
- if( nstep == 0 .or. nstep+1 == relax_nstlim ) iprint = 1
-
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
- ! If we don't want to increment the NMROPT counter, decrement it here.
- if (.not. increment_nmropt) &
- call nmrdcp
-
- ! Reset quantities depending on TEMP0 and TAUTP (which may have been
- ! changed by MODWT during FORCE call).
- ekinp0 = fac(2)*temp0
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-
- if (ntt == 1) dttp = dt/tautp
-
- if (ntp > 0) then
- ener%volume = volume
- ener%density = tmass / (0.602204d0*volume)
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = 0.d0
- do m = 1,3
- ener%cmt(m) = ener%cmt(m)*0.5d0
- ener%cmt(4) = ener%cmt(4)+ener%cmt(m)
- ener%vir(4) = ener%vir(4)+ener%vir(m)
- ener%pres(m) = (pconv+pconv)*(ener%cmt(m)-ener%vir(m))/volume
- ener%pres(4) = ener%pres(4)+ener%pres(m)
- end do
- ener%pres(4) = ener%pres(4)/3.d0
-
- ! Constant surface tension output:
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! Surface tension in the x direction
- ener%surface_ten = &
- box(1) * (ener%pres(1) - 0.5d0 * &
- (ener%pres(2) + ener%pres(3))) / (ninterface * ten_conv)
-
- else if (csurften .eq. 2) then ! Surface tension in the y direction
- ener%surface_ten = &
- box(2) * (ener%pres(2) - 0.5d0 * &
- (ener%pres(1) + ener%pres(3))) / (ninterface * ten_conv)
-
- else ! if (csurften .eq. 3) then ! Surface tension in the z direction
- ener%surface_ten = &
- box(3) * (ener%pres(3) - 0.5d0 * &
- (ener%pres(1) + ener%pres(2))) / (ninterface * ten_conv )
-
- end if
-
- end if
-
- end if
-
- !----------------------------------------------------------------
- ! ---Step 1c: do randomization of velocities, if needed:
- !----------------------------------------------------------------
- ! ---Assign new random velocities every Vrand steps, if ntt=2
-
- resetvelo=.false.
- if (vrand /= 0 .and. ntt == 2) then
- if (mod((nstep+1),vrand) == 0) resetvelo=.true.
- end if
-
- if (resetvelo) then
- ! DAN ROE: Why are only the masters doing this? Even if the velocities
- ! are broadcast to the child processes, the wont the different # of random
- ! calls put the randomg num generators out of sync, or do we not care?
-
- if (master) then
-! write (6,'(a,i8)') 'Setting new random velocities at step ', &
-! nstep + 1
- call setvel(nr,v,winv,temp0*factt,init,iscale,scalm)
- end if
-
-# ifdef MPI
- call trace_mpi('mpi_bcast',3*natom,'MPI_DOUBLE_PRECISION',0)
- call mpi_bcast(v, 3*natom, MPI_DOUBLE_PRECISION, 0, commsander, ierr)
-# endif
-
- ! At this point in the code, the velocities lag the positions
- ! by half a timestep. If we intend for the velocities to be drawn
- ! from a Maxwell distribution at the timepoint where the positions and
- ! velocities are synchronized, we have to correct these newly
- ! redrawn velocities by backing them up half a step using the
- ! current force.
- ! Note that this fix only works for Newtonian dynamics.
- if( gammai==0.d0 ) then
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dt5
- v(i3+1) = v(i3+1) - f(i3+1)*wfac
- v(i3+2) = v(i3+2) - f(i3+2)*wfac
- v(i3+3) = v(i3+3) - f(i3+3)*wfac
- i3 = i3+3
- end do
- end if
-
- end if ! (resetvelo)
-
- call timer_start(TIME_VERLET)
-
- !-----------------------------------------------------
- ! ---Step 2: Do the velocity update:
- !-----------------------------------------------------
-
- !step 2a: apply quenched MD if needed. This is useful in NEB>0
- if (vv==1) call quench(f,v)
-
- if( gammai == 0.d0 ) then
-
- ! ---Newtonian dynamics:
-
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dtx
- v(i3+1) = v(i3+1) + f(i3+1)*wfac
- v(i3+2) = v(i3+2) + f(i3+2)*wfac
- v(i3+3) = v(i3+3) + f(i3+3)*wfac
- i3 = i3+3
- end do
-
- else ! gamma_ln .ne. 0, which also implies ntt=3 (see mdread.f)
-
- ! ---simple model for Langevin dynamics, basically taken from
- ! Loncharich, Brooks and Pastor, Biopolymers 32:523-535 (1992),
- ! Eq. 11. (Note that the first term on the rhs of Eq. 11b
- ! should not be there.)
-
- ! Update Langevin parameters, since temp0 might have changed:
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
-
- i3 = 3*(istart-1)
-
- if (no_ntt3_sync == 1) then
- !We don't worry about synchronizing the random number stream
- !across processors.
- do j=istart,iend
-
- wfac = winv(j) * dtx
- aamass = amass(j)
- rsd = sdfac*sqrt(aamass)
- call gauss( 0.d0, rsd, fln )
- v(i3+1) = (v(i3+1)*c_explic + (f(i3+1)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+2) = (v(i3+2)*c_explic + (f(i3+2)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+3) = (v(i3+3)*c_explic + (f(i3+3)+fln)*wfac) * c_implic
- i3 = i3+3
- end do
-
- else
-
- do j=1,nr
- if( j<istart .or. j>iend ) then
- ! In order to generate the same sequence of pseudorandom numbers that
- ! you would using a single processor you have to go through the atoms
- ! in order. The unused results are thrown away
- call gauss( 0.d0, 1.d0, fln )
- call gauss( 0.d0, 1.d0, fln )
- call gauss( 0.d0, 1.d0, fln )
- cycle
- end if
-
- wfac = winv(j) * dtx
- aamass = amass(j)
- rsd = sdfac*sqrt(aamass)
- call gauss( 0.d0, rsd, fln )
- v(i3+1) = (v(i3+1)*c_explic + (f(i3+1)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+2) = (v(i3+2)*c_explic + (f(i3+2)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+3) = (v(i3+3)*c_explic + (f(i3+3)+fln)*wfac) * c_implic
- i3 = i3+3
- end do
- end if ! no_ntt3_sync
-
- end if ! ( gammai == 0.d0 )
-
- if (vlim) then
- vmax = 0.0d0
- do i=istart3,iend3
- vmax = max(vmax,abs(v(i)))
- v(i) = sign(min(abs(v(i)),vlimit),v(i))
- end do
-
- ! Only violations on the master node are actually reported
- ! to avoid both MPI communication and non-master writes.
- if (vmax > vlimit) then
- if (master) then
- write(6,'(a,i6,a,f10.4)') 'vlimit exceeded for step ',nstep, &
- '; vmax = ',vmax
- end if
- end if
- end if
-
- do im=1,iscale
- v(nr3+im) = (v(nr3+im) + f(nr3+im)*dtx/scalm)
- end do
-
- !-------------------------------------------------------------------
- ! Step 3: update the positions, putting the "old" positions into F:
- !-------------------------------------------------------------------
-
- i = istart - 1
- do i3 = istart3, iend3, 3
- f(i3 ) = x(i3 )
- f(i3+1) = x(i3+1)
- f(i3+2) = x(i3+2)
- if (mobile_atoms(i) == 1) then
- x(i3 ) = x(i3 ) + v(i3 )*dtx
- x(i3+1) = x(i3+1) + v(i3+1)*dtx
- x(i3+2) = x(i3+2) + v(i3+2)*dtx
- end if
- i = i + 1
- end do
-
- do i = 1,iscale
- f(nr3+i) = x(nr3+i)
- x(nr3+i) = x(nr3+i)+v(nr3+i)*dtx
- end do
-
- call timer_stop(TIME_VERLET)
-
- if (ntc /= 1) then
-
- !-------------------------------------------------------------------
- ! Step 4a: if shake is being used, update the new positions to fix
- ! the bond lengths.
- !-------------------------------------------------------------------
-
- call timer_start(TIME_SHAKE)
- qspatial=.false.
- call shake(nrp,nbonh,nbona,0,ix(iibh),ix(ijbh),ix(ibellygp), &
- winv,conp,skip,f,x,nitp,.false.,ix(iifstwt),ix(noshake), &
- shkh,qspatial)
- call quick3(f,x,ix(iifstwr),natom,nres,ix(i02))
- if(nitp == 0) then
- erstop = .true.
- goto 480
- end if
-
- !-----------------------------------------------------------------
- ! Step 4b: Now fix the velocities and calculate KE
- !-----------------------------------------------------------------
-
- ! ---re-estimate the velocities from differences in positions:
-
- v(istart3:iend3) = (x(istart3:iend3)-f(istart3:iend3)) * dtxinv
-
- call timer_stop(TIME_SHAKE)
- end if
- call timer_start(TIME_VERLET)
-
- if( ntt == 1 .or. onstep ) then
-
- !-----------------------------------------------------------------
- ! Step 4c: get the KE, either for averaging or for Berendsen:
- !-----------------------------------------------------------------
-
- eke = 0.d0
- ekph = 0.d0
- ekpbs = 0.d0
-
- if (gammai == 0.0d0) then
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
-
- ! try pseudo KE from Eq. 4.7b of Pastor, Brooks & Szabo,
- ! Mol. Phys. 65, 1409-1419 (1988):
-
- ekpbs = ekpbs + aamass*v(i3)*vold(i3)
- ekph = ekph + aamass*v(i3)**2
-
- end do
- end do
-
- else
-
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- end do
-
- end do
-
- end if ! (if gammai == 0.0d0)
-
-#ifdef MPI
- ! --- sum up the partial kinetic energies:
-
- if ( numtasks > 1 ) then
- call trace_mpi('mpi_allreduce', &
- 1,'MPI_DOUBLE_PRECISION',mpi_sum)
- mpitmp(1) = eke
- mpitmp(2) = ekph
- mpitmp(3) = ekpbs
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
- ekpbs = mpitmp(3)
-
-# else /* USE_MPI_IN_PLACE */
-
- call mpi_allreduce(mpitmp,mpitmp(4),3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(4)
- ekph = mpitmp(5)
- ekpbs = mpitmp(6)
-
-# endif /* USE_MPI_IN_PLACE */
- end if
-#endif /* MPI */
-
- ! --- all processors handle the "extra" variables:
-
- do im=1,iscale
- eke = eke + scalm*0.25d0*(v(nr3+im)+vold(nr3+im))**2
- ekpbs = ekpbs + scalm*v(nr3+im)*vold(nr3+im)
- ekph = ekph + scalm*v(nr3+im)**2
- end do
-
- eke = eke * 0.5d0
- ekph = ekph * 0.5d0
- ekpbs = ekpbs * 0.5d0
- if( ntt == 1 ) then
-
- ! --- following is from T.E. Cheatham, III and B.R. Brooks,
- ! Theor. Chem. Acc. 99:279, 1998.
-
- scaltp = sqrt(1.d0 + 2.d0*dttp*(ekin0-eke)/(ekmh+ekph))
-
- ! --- following is the "old" (amber7 and before) method:
-
- ! scaltpo = sqrt(1.d0 + dttp*(ekin0/ekph - 1.d0))
- ! write(6,*) 'scaltp: ',2.d0*dttp*(ekin0-eke)/(ekmh+ekph), &
- ! dttp*(ekin0/ekmh - 1.d0)
-
- ! following line reverts to the "old" behavior:
- ! scaltp = scaltpo
-
- do j = istart,iend
- i3=(j-1)*3+1
- v(i3 ) = v(i3 ) *scaltp
- v(i3+1) = v(i3+1) *scaltp
- v(i3+2) = v(i3+2) *scaltp
- end do
- do im=1,iscale
- v(nr3+im) = v(nr3+im)*scaltp
- end do
- end if ! (ntt == 1 )
-
- end if ! ( ntt == 1 .or. onstep; end of step 4c )
-
- !-----------------------------------------------------------------
- ! Step 5: several tasks related to dumping of trajectory information
- !-----------------------------------------------------------------
-
- ! --- Determine if trajectory, velocity, or restart
- ! writing is imminent, or if the center of mass
- ! motion will be removed.
- ! These require xdist of velocities or dipoles in parallel runs:
- !
- ! Modified so that when running REMD, writing can occur less often
- ! than exchanges (e.g. ntwx > nstlim)
- ! DAN ROE: Added two new variables, total_nstep and total_nstlim.
- ! For non-REMD runs, total_nstep=nstep+1 and total_nstlim=nstlim
- ! just like before.
- ! For REMD runs, total_nstep=(mdloop-1)*nstlim+nstep+1, where
- ! mdloop is the current exchange - this is the current
- ! replica exchange MD step. total_nstlim=numexchg*nstlim, which is
- ! the maximum number of REMD steps.
-
-#ifdef MPI
-
- !-----------------------------------------------------------------
- ! --- now distribute the coordinates, and if necessary, dipoles and vel:
- !-----------------------------------------------------------------
-
- call timer_barrier( commsander )
- call timer_stop_start(TIME_VERLET,TIME_DISTCRD)
- if ( numtasks > 1 ) then
- call xdist(x, xx(lfrctmp), natom)
- end if
- call timer_stop(TIME_DISTCRD)
-
-#endif /* MPI */
-
- ! ----fix lone pair positions:
- if( numextra > 0 )call local_to_global(x,xx,ix)
-
-#ifdef MPI
- call timer_start(TIME_VERLET)
- ! ========================= END AMBER/MPI =========================
-#endif /* MPI */
-
- !-------------------------------------------------------------------
- ! Step 6: zero COM velocity if requested; used for preventing
- ! ewald "block of ice flying thru space" phenomenon, or accumulation
- ! of rotational momentum in vacuum simulations
- !-------------------------------------------------------------------
-
- !-----------------------------------------------------------------
- ! --- put current velocities into VOLD
- !-----------------------------------------------------------------
-
- vold(istart3:iend3) = v(istart3:iend3)
- do im=1,iscale
- vold(nr3+im) = v(nr3+im)
- end do
-
- !-------------------------------------------------------------------
- ! Step 7: scale coordinates if constant pressure run:
- !-------------------------------------------------------------------
-
- ! ntp = 1, isotropic pressure coupling
-
- if (ntp == 1) then
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(4)))**third
- rmu(2) = rmu(1)
- rmu(3) = rmu(1)
-
-
- ! ntp = 2, anisotropic pressure scaling
-
- else if (ntp == 2) then
-
- if (csurften > 0) then
-
- ! Constant surface tension adjusts the tangential pressures
- ! See Zhang, Feller, Brooks, Pastor. J. Chem. Phys. 1995
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
-
- end if
-
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- else
-
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(1)))**third
- rmu(2) = (1.d0-dtcp*(pres0-ener%pres(2)))**third
- rmu(3) = (1.d0-dtcp*(pres0-ener%pres(3)))**third
-
- end if
-
- ! ntp = 3, semiisotropic pressure coupling
- ! (currently only for csurften>0, constant surface tension)
-
- !else if (ntp > 2) then
- else
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
- press_tan_ave = (ener%pres(2) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(2))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- end if ! csurften == 1
- end if ! csurften > 0
- ! Add semiisotropic pressure scaling in any direction with no constant
- ! surface tension here
- end if
-
- if (ntp > 0) then
- box(1:3) = box(1:3)*rmu(1:3)
- ener%box(1:3) = box(1:3)
-
- ! WARNING!! This is not correct for non-orthogonal boxes if
- ! NTP > 1 (i.e. non-isotropic scaling). Currently general cell
- ! updates which allow cell angles to change are not implemented.
- ! The viral tensor computed for ewald is the general Nose Klein,
- ! however the cell response needs a more general treatment.
-
- call redo_ucell(rmu)
- ! keep tranvec up to date, rather than recomputing each MD step.
- call fill_tranvec() ! tranvec is dependent on only ucell
-
- call ew_pscale(natom,x,amass,nspm,nsp,npscal)
- if (ntr > 0 .and. nrc > 0) &
- call ew_pscale(natom,xc,amass,nspm,nsp,npscal)
- endif
-
- ener%kin%solv = ekpbs + ener%pot%tot
- ! Pastor, Brooks, Szabo conserved quantity
- ! for harmonic oscillator: Eq. 4.7b of Mol.
- ! Phys. 65:1409-1419, 1988
- ener%kin%solt = eke
- ener%kin%tot = ener%kin%solt
- if (ntt == 1 .and. onstep) then
- ekmh = max(ekph,fac(1)*10.d0)
- end if
-
- ! ---if velocities were reset, the KE is not accurate; fudge it
- ! here to keep the same total energy as on the previous step.
- ! Note that this only affects printout and averages for Etot
- ! and KE -- it has no effect on the trajectory, or on any averages
- ! of potential energy terms.
-
- if( resetvelo ) ener%kin%tot = etot_save - ener%pot%tot
-
- ! --- total energy is sum of KE + PE:
-
- ener%tot = ener%kin%tot + ener%pot%tot
- etot_save = ener%tot
-
- !-------------------------------------------------------------------
- ! Step 8: update the step counter and the integration time:
- !-------------------------------------------------------------------
-
- nstep = nstep+1
-
- ! ---full energies are only calculated every nrespa steps
- ! nvalid is the number of steps where all energies are calculated
-
- ntnb = 0
- if (mod(nstep,nsnb) == 0) ntnb = 1
-
-#if 0
-! DEBUG code -- this will print out every frame of the relaxation dynamics to
-! the trajectory if uncommented
-
- if (master) then
-
- ! -- Coordinate archive:
- if (.true.) then
- if( iwrap == 0 ) then
- call corpac(x,1,nrx,MDCRD_UNIT,loutfm)
- if(ntb > 0) call corpac(box,1,3,MDCRD_UNIT,loutfm)
- else if (iwrap == 1) then
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
-
- call wrap_molecules(nspm,nsp,r_stack(l_temp))
- if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
-
- call corpac(r_stack(l_temp),1,nrx,MDCRD_UNIT,loutfm)
- call corpac(box,1,3,MDCRD_UNIT,loutfm)
- call free_stack(l_temp,routine)
- end if ! if (iwrap == 0) ...
-
-
- !GMS: If using variable QM solvent, try to write a new pdb file
- ! with the QM coordinates for this step. This is done here
- ! to keep the PDB file in sync with the mdcrd file, which
- ! makes it easier to check later.
- if (qmmm_nml%vsolv > 0 .and. qmmm_nml%verbosity == 0) &
- call qm_print_coords(nstep,.false.)
- end if ! (itdump)
-
- if (ioutfm > 0) then
- if (.true.) call end_binary_frame(MDCRD_UNIT)
- end if
-
- end if ! (master)
-#endif /* 0 */
-
- !=======================================================================
-
- ! ---major cycle back to new step unless we have reached our limit:
-
- call trace_integer( 'end of step', nstep )
- call trace_output_mpi_tally( )
- call timer_stop(TIME_VERLET)
-
- if (nstep < relax_nstlim) goto 260
- 480 continue
-
-end subroutine relaxmd
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Enter description for quench here.
-subroutine quench(f,v)
- implicit none
-
-#include "../include/md.h"
-!need access to vv - temp verlet scaling
-#include "../include/memory.h"
-!need access to natom
-
- _REAL_ f(*),v(*),dotproduct,force
- !f is the forces and v is the velocity
-
- integer index
- dotproduct = 0.d0
- force = 0.d0
-
- do index=1,3*natom
- force = force + f(index)**2
- dotproduct = dotproduct + v(index)*f(index)
- enddo
-
- if (force/=0.0d0) then
- force = 1.0d0/sqrt(force)
- dotproduct = dotproduct*force
- end if
-
- if (dotproduct>0.0d0) then
- v(1:3*natom) = dotproduct*f(1:3*natom)*force
- else
- !v(1:3*natom) = 0.0d0
- v(1:3*natom) = vfac*dotproduct*f(1:3*natom)*force
- end if
-
-end subroutine quench
diff --git a/patches/amber14.diff/AmberTools/src/sander/runmd.F90.preplumed b/patches/amber14.diff/AmberTools/src/sander/runmd.F90.preplumed
deleted file mode 100644
index 476dd425da998baf64b080141bef04e76821f585..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/runmd.F90.preplumed
+++ /dev/null
@@ -1,5268 +0,0 @@
-! <compile=optimized>
-#include "copyright.h"
-#include "../include/dprec.fh"
-#include "../include/assert.fh"
-#include "ncsu-config.h"
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ driver routine for molecular dynamics
-subroutine runmd(xx,ix,ih,ipairs,x,winv,amass,f, &
- v,vold,xr,xc,conp,skip,nsp,tma,erstop, qsetup)
-
- ! Runmd operates in kcal/mol units for energy, amu for masses,
- ! and angstroms for distances. To convert the input time parameters
- ! from picoseconds to internal units, multiply by 20.455
- ! (which is 10.0*sqrt(4.184)).
-
- use state
-
-#if !defined(DISABLE_NCSU) && defined(NCSU_ENABLE_BBMD)
- use ncsu_sander_hooks, only : ncsu_on_mdstep => on_mdstep
-#endif
-
- use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms
- use cmd_vars, only: activate, file_pos_cmd, file_vel_cmd, file_nrg_cmd, &
- nstep_cmd, t_cmd, eq_cmd, restart_cmd, &
- etot_cmd, eke_cmd, temp_cmd
-
- use pimd_vars, only: ipimd, nbead, natomCL, &
- bnd_vir, Eimp_virial, equal_part, Epot_deriv, &
- tau_vol, Epot_spring, NMPIMD, CMD, cartpos, cartvel, &
- itimass, real_mass
-
- use neb_vars, only: ineb, neb_nbead
-
- use lscivr_vars, only: ilscivr, ndof_lsc, natom_lsc, mass_lsc, v2_lsc, &
- ilsc, x_lsc, f_lsc, dx_lsc
-
- use nose_hoover_module, only : thermo_lnv, x_lnv, x_lnv_old, v_lnv, &
- f_lnv_p, f_lnv_v, c2_lnv, mass_lnv, &
- Thermostat_init
-
-#ifdef RISMSANDER
- use sander_rism_interface, only: rismprm,rism_3d, RISM_NONE, RISM_FULL, RISM_INTERP, &
- rism_calc_type, rism_solvdist_thermo_calc, mylcm
-#endif
-
- use full_pimd_vars, only: totener,totenert,totenert2,mybeadid
-
- use qmmm_module, only : qmmm_nml,qmmm_struct, qmmm_mpi, qm2_struct, &
- qmmm_vsolv
- use file_io_dat
- use constants, only : third, ten_to_minus3
- use trace
- use stack
- use decomp, only : nat, nrs, decpr, jgroup, indx, irespw, &
-#ifdef MPI
- ! -- ti decomp
- collect_dec, &
-#endif
- checkdec, printdec
- use fastwt
- use bintraj, only: end_binary_frame
- use nblist,only: fill_tranvec,volume,oldrecip,ucell
-
- use nose_hoover_module, only: Thermostat_switch, &
- Thermostat_integrate_1, Thermostat_integrate_2, & ! APJ
- Thermostat_hamiltonian, & ! APJ
- Adaptive_Thermostat_integrate, & ! APJ
- Adaptive_Thermostat_hamiltonian, & ! APJ
- file_nhc, nchain, thermo, nthermo, Econserved ! APJ
-
-#ifdef MPI
- use evb_parm, only: evb_dyn, nbias
- use evb_data, only: evb_frc, evb_vel0, evb_bias, evb_nrg, evb_nrg_ave &
- , evb_nrg_rms, evb_nrg_tmp, evb_nrg_old, evb_nrg_tmp2 &
- , evb_nrg_old2
- use wigner, only: rflux
- use remd, only : rem, mdloop, remd_ekmh, repnum, stagid, my_remd_data, &
- hybrid_remd_ene, next_rem_method
-# ifdef LES
- use evb_pimd, only: evb_pimd_dealloc
- use miller, only: i_qi
-# endif
- use softcore, only: ifsc, sc_dvdl, sc_tot_dvdl, sc_tot_dvdl_partner, &
- sc_dvdl_ee, sc_tot_dvdl_ee, sc_tot_dvdl_partner_ee, &
- extra_atoms, mix_temp_scaling, sc_pscale, &
- adj_dvdl_stat, sc_mix_velocities, &
- sc_nomix_frc, sc_sync_x, sc_print_energies, &
- calc_softcore_ekin, &
- sc_ener, sc_ener_ave, sc_ener_rms, sc_lngdyn, &
- sc_ener_tmp, sc_ener_tmp2, sc_ener_old, sc_ener_old2, &
- sc_mix_position, sc_print_dvdl_values, &
- sc_degrees_o_freedom, dynlmb, sc_change_clambda, ti_ene_cnt, &
- sc_compare
- use mbar, only : ifmbar, bar_intervall, calc_mbar_energies, &
- bar_collect_cont, do_mbar
-#endif
-
- use amoeba_mdin, only: iamoeba
- use amoeba_runmd, only: AM_RUNMD_scale_cell
- use constantph, only: cnstphinit, cnstphwrite, cnstphupdatepairs, &
- cnstphbeginstep, cnstphendstep, chrgdat, &
- cnstph_explicitmd, cnstphwriterestart, cphfirst_sol
- use emap, only:temap,emap_move
- use barostats, only : mcbar_trial, mcbar_summary
-#ifdef EMIL
- use emil_mod, only : emil_do_calc, emil_calc_AMBER, &
- emil_save_pme, emil_save_gb, &
- emil_init, emil_step
-#endif
- use memory_module, only: coordinate, velocity, mass
-
-! Self-Guided molecular/Langevin Dynamics (SGLD)
- use sgld, only : isgld, isgsta,isgend,trxsgld, &
- sgenergy,sgldw,sgmdw,sgfshake, sg_fix_degree_count
-
- !AWG adaptive QM/MM
- use qmmm_adaptive_module, only: adaptive_qmmm
-
- use crg_reloc, only: ifcr, crprintcharges, cr_print_charge
-
- use abfqmmm_module, only: abfqmmm_param, abfqmmm_combine_forces ! lam81
-!AMD
- use amd_mod
-
-!scaledMD
- use scaledMD_mod
-
-!SEBOMD
- use sebomd_module, only : sebomd_obj, sebomd_gradient_write, sebomd_hessian_compute
-
-! Variable Descriptions
-!
-! Passed variables
-! xx : global real array. See locmem.f for structure/pointers
-! ix : global integer array. See locmem.f for structure/pointers
-! ih : global hollerith array. See locmem.f for structure/pointers
-! ipairs : ?? Global pairlist ?? --add description (JMS 11/2010)
-! x : global position array *
-! winv : array with inverse masses *
-! amass : mass array *
-! f : force array, used to hold old coordinates temporarily, too
-! v : velocity array
-! vold : old velocity array, from the previous step
-! xr : coordinates with respect to COM of molecule
-! conp : bond parameters for SHAKE
-! skip : logical skip array for SHAKE (and QM/MM too, I think)
-! nsp : submolecule index array (?)
-! tma : submolecular weight array (?)
-! erstop : should we stop in error (?)
-! qsetup : Not quite sure what this does, if anything anymore.
-!
-! Local variables
-! factt : degree-of-freedom correction factor for temperature scaling
-! nr : local copy of nrp, number of atoms
-! nr3 : 3 * nr, used for runtime efficiency
-!
-! Common memory variables
-! nrp : number of atoms, adjusted for LES copies
-
- implicit none
- character(kind=1,len=5) :: routine="runmd"
- integer ipairs(*), ix(*)
- _REAL_ xx(*)
- character(len=4) ih(*)
- _REAL_ combination, rem_val
-
-#ifdef MPI
-# include "parallel.h"
- include 'mpif.h'
-# ifdef LES
- _REAL_ :: fbead(3,natomCL), xbead(3,natomCL)
- integer :: mm, n
-# endif
- _REAL_ mpitmp(8) !Use for temporary packing of mpi messages.
- integer ist(MPI_STATUS_SIZE), partner, ierr
-#else
- ! mdloop and REM is always 0 in serial
- integer, parameter :: mdloop = 0, rem = 0
-#endif
-
-! The following variables are needed since nstep and nstlim
-! behave differently in a REMD run.
-! In certain places where output is required, total_nstep and total_nstlim
-! take the place of nstep and nstlim. This allows replica runs to output
-! less often than every exchange.
-! They are the absolute step # of the REMD or MD simulation.
- integer total_nstep, total_nstlim
-
-#include "../include/md.h"
-#include "box.h"
-#include "nmr.h"
-#include "tgtmd.h"
-#include "multitmd.h"
-#include "../include/memory.h"
-#include "extra.h"
-#include "ew_frc.h"
-#include "ew_cntrl.h"
-#include "ew_mpole.h"
-#include "def_time.h"
-#include "extra_pts.h"
-#if defined(LES)
-# include "les.h"
-#endif
-#include "../pbsa/pb_md.h"
-#include "../lib/random.h"
-
-! additional variables for PIMD output
- _REAL_ :: xcmd(3*natomCL),vcmd(3*natomCL)
- integer :: ncmd
- ! for const press PIMD
- _REAL_ tmpvir(3,3),atomvir
-
- _REAL_ sgsta_rndfp, sgend_rndfp, ignore_solvent
- _REAL_ sysx,sysy,sysz,sysrange(3,2)
- logical mv_flag
-
-#ifdef MMTSB
-# include "mmtsb.h"
- logical is_done_mmtsb ! MMTSB replica exchange calculation completed
- _REAL_ lambda_mmtsb ! MMTSB replica exchange new lambda
- _REAL_ pert_pe_mmtsb ! MMTSB lambda replica exchange perturbed PE
- _REAL_ temp_mmtsb ! MMTSB replica exchange new temperature
- _REAL_ unpert_pe_mmtsb ! MMTSB lambda replica exchange unperturbed PE
-#endif
-
- _REAL_ , dimension(1) :: shkh
- integer, dimension(1) :: ifstwr2
- integer :: nshkh
-
- integer idx, iatom, iatomCL,m
- _REAL_ Ekin2_tot,tmp ! APJ
- integer :: idim, ithermo
- _REAL_ :: E_nhc, exp1, exp2, v_sum
-
- logical ivscm
- logical qspatial
- character(len=6)fnam
-
- logical resetvelo
- integer nshak
- _REAL_ ekgs,eold3,eold4,etot_save,ekpbs
-
- logical do_list_update
- logical skip(*),belly,lout,loutfm,erstop,vlim,onstep
- _REAL_ x(*),winv(*),amass(*),f(*),v(*),vold(*), &
- xr(*),xc(*),conp(*)
- type(state_rec) :: ener ! energy values per time step
- type(state_rec) :: enert ! energy values tallied over the time steps
- type(state_rec) :: enert2 ! energy values squared tallied over the time steps
- type(state_rec) :: enert_old, enert2_old
- type(state_rec) :: enert_tmp, enert2_tmp
- type(state_rec) :: ecopy, edvdl
- type(state_rec) :: edvdl_r
- _REAL_ rmu(3),fac(3),onefac(3),clfac, etot_start
- _REAL_ tma(*)
-
- _REAL_ tspan,atempdrop,fln,scaltp,scaltpo
- _REAL_ vel,vel2,vcmx,vcmy,vcmz,vmax,vx,vy,vz
- _REAL_ winf,aamass,rterm,ekmh,ekph,ekpht,wfac,rsd,ekav
- _REAL_ fit,fiti,fit2,vscalt
- logical is_langevin ! Is this a Langevin dynamics simulation
- _REAL_ gammai,c_implic,c_explic,c_ave,sdfac,ekins0
- _REAL_ dtx,dtxinv,dt5,factt,ekin0,ekinp0,dtcp,dttp
- _REAL_ rndf,rndfs,rndfp,boltz2,pconv,tempsu
- _REAL_ xcm(3),acm(3),ocm(3),vcm(3),ekcm,ekrot
- _REAL_ emtmd
-
-! Variables and parameters for constant surface tension:
- _REAL_, parameter :: ten_conv = 100.0d0 !ten_conv - converts
- !dyne/cm to bar angstroms
- _REAL_ :: pres0x
- _REAL_ :: pres0y
- _REAL_ :: pres0z
- _REAL_ :: gamma_ten_int
- _REAL_ :: press_tan_ave
-
- integer nsp(*)
- integer idumar(4)
- integer l_temp
- integer i,j,im,i3,nitp,nits, iskip_start,iskip_end ! APJ
- integer nstep,nrep,nrek,nren,iend,istart3,iend3
- integer nrx,nr,nr3,ntcmt,izero,istart
- logical ixdump,ivdump,itdump,ifdump
- logical qsetup
- _REAL_, allocatable, dimension(:) :: for ! lam81
-#ifdef RISMSANDER
- logical irismdump
- _REAL_ cm(3),angvel(3),r(3),rxv(3),proj(3),moi,erot
-#endif
-
- integer nvalid, nvalidi
- _REAL_ eke,eket
- _REAL_ extent
-
- _REAL_ xcen,ycen,zcen,extents(3,2)
- _REAL_, allocatable, dimension(:) :: frcti
- integer ier
-
- _REAL_ small
- data small/1.0d-7/
- data nren/51/
-
- !--- VARIABLES FOR DIPOLE PRINTING ---
- integer prndipngrp
- integer prndipfind
- character(len=4) prndiptest
-
- _REAL_,parameter :: pressure_constant = 6.85695d+4
- ! variables used in constant pressure PIMD
- _REAL_ :: Nkt,centvir,pressure, aa, arg2, poly, e2, e4, e6, e8
- ! variable used in CMD
- real(8) :: tmp_eke_cmd !Use for temporary packing of mpi messages.
-
- _REAL_ :: box_center(3)
-
-! for adaptive qm/mm runs
-
- _REAL_ :: adqmmm_first_energy, etotcorr, tadc
- integer :: nstepadc
- logical :: flag_first_energy = .true.
-
- _REAL_ :: xold(3*natom)
- _REAL_ :: corrected_energy
- _REAL_ :: kinetic_E_save(2)
- integer :: aqmmm_flag
-
- !==========================================================================
-
- call trace_enter( 'runmd' )
-
- ! ----- INITIALIZE SOME VARIABLES -----
-
-#ifdef MPI
- if( master ) then
- ! If remd, runmd will be called many times, so we dont want to open every
- ! time. For normal md, mdloop will just be 0.
- if (mdloop.eq.0) call amopen(7,mdinfo,'U','F',facc)
- endif
-
- if (rem < 3) then
- rem_val = temp0
- else if (rem == 4) then
- rem_val = solvph
- else
- rem_val = 0.d0
- end if
-#else
- if( master ) call amopen(7,mdinfo,'U','F','W')
-#endif
- vlim = vlimit > small
- ntcmt = 0
- izero = 0
- belly = ibelly > 0
- lout = .true.
- loutfm = ioutfm <= 0
- nr = nrp
- nr3 = 3*nr
- ekmh = 0.d0
-
- aqmmm_flag = 0
-
-#ifdef LES
- ekmhles = 0.d0
-#endif
- do_list_update=.false.
-#ifdef MPI
- if ( mpi_orig ) then
- istart = 1
- iend = natom
- else
- istart = iparpt(mytaskid) + 1
- iend = iparpt(mytaskid+1)
- end if
-#else
- istart = 1
- iend = nr
-#endif
- istart3 = 3*istart -2
- iend3 = 3*iend
-
-#ifdef MPI
- if( icfe /= 0 ) then
- allocate( frcti( nr3+3*extra_atoms ), stat = ier )
- REQUIRE( ier == 0 )
- end if
-#endif
-
- ! If NTWPRT.NE.0, only print the atoms up to this value
- nrx = nr3
- if (ntwprt > 0) nrx = ntwprt*3
-
- if (.not. allocated(for)) allocate(for(nr3)) ! lam81
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- if(abfqmmm_param%system == 1) then ! lam81
- if(abfqmmm_param%qmstep == 1) abfqmmm_param%v(1:nr3+iscale) = v(1:nr3+iscale) ! lam81
- v(1:nr3+iscale) = 0.d0 ! lam81
- t = t+dt ! lam81
- if(abfqmmm_param%maxqmstep == 0) t = 0 ! lam81
- else ! lam81
- v(1:nr3+iscale) = abfqmmm_param%v(1:nr3+iscale) ! lam81
- endif ! lam81
- endif ! lam81
-
- ! Cleanup the velocity if belly run
- if(belly) call bellyf(nr,ix(ibellygp),v)
-
- !=======================================================================
- ! Determine system degrees of freedom (for T scaling, reporting)
-
- ! Call DEGCNT to get the actual number of degrees of freedom for the
- ! solute and solvent. This call returns the correct numbers for belly
- ! simulations and simulations with separate solute/solvent scaling -- dap
- ! "IDUMAR" is dummy array. Used since this routine was also used w/ GIBBS.
-
-#ifdef LES
- ! return LES and non-LES degrees,
- ! since separate solvent coupling no longer used
- ! large changes to degcnt were made
- ! cnum is now passed (LES copy number of each atom)
- call degcnt(ibelly,nr,ix(ibellygp),nsolut,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0, &
- idumar,rndfp,rndfles,cnum,temp0les)
-
- ! RNDFP = # degrees of freedom for solute
- ! RNDFS = # degrees of freedom for solvent
- ! RNDF = total number of degrees of freedom.
- ! RNDFLES = # degrees of freedom for LES groups
-
- ! temp0les was init to negative number to signify not to use a LES bath
- ! just do standard code (meaning use solute/solvent baths)
- ! any positive (or zero) means to use LES bath with that target
-
- ! degcnt returns rndfs or rndfles in the rndfles variable
- ! depending on whether a LES bath was specified
- ! do this instead of duplicating call with rndfs or rndfles
-
- if (temp0les < 0.d0) then
- rndfs=rndfles
- rndfles=0.d0
- else
- rndfs=0.d0
- end if
-
- if (master) then
- write (6,'(a,f8.0)') &
- "# degrees of freedom in non-LES region: ",rndfp
- write (6,'(a,f8.0)') &
- "# degrees of freedom in LES region: ",rndfles
- end if
-
- ! modify RNDFP to reflect NDFMIN (set in mdread)
-
- rndfp = rndfp - ndfmin
-
- if (temp0les < 0.d0) then
- rndf = rndfp+rndfs
- else
- rndf = rndfp+rndfles
- end if
-
-#else
-
- call degcnt(ibelly,nr,ix(ibellygp),nsolut,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0, &
- idumar,rndfp,rndfs)
-
- ! RNDFP = # degrees of freedom for solute
- ! RNDFS = # degrees of freedom for solvent
- ! RNDF = total number of degrees of freedom.
-
-#ifdef MPI
- if (mdloop .eq. 0 .and. master) then
-#else
- if (master) then
-#endif
- if (abfqmmm_param%abfqmmm /= 1 .or. (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1)) then ! lam81
- write (6,'(a,f8.0)') &
- "| # of SOLUTE degrees of freedom (RNDFP): ",rndfp
- write (6,'(a,f8.0)') &
- "| # of SOLVENT degrees of freedom (RNDFS): ",rndfs
- end if ! lam81
- end if
- ! qtw - substract the number of overlapping noshake QM atoms in noshakemask
- rndfp = rndfp - qmmm_struct%noshake_overlap
- ! modify RNDFP to reflect NDFMIN (set in mdread) and num_noshake
- rndfp = rndfp - ndfmin + num_noshake
- rndf = rndfp + rndfs
-#ifdef MPI
- if (mdloop .eq. 0 .and. master) then
-#else
- if (master) then
-#endif
- if (abfqmmm_param%abfqmmm /= 1 .or. (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1)) then ! lam81
- if (qmmm_nml%ifqnt) then
- write (6,'(a,i6)') &
- "| QMSHAKE_NOSHAKEMASK_OVERLAP = ", qmmm_struct%noshake_overlap
- endif
- write (6,'(a,f8.0,a,i6,a,f8.0)') &
- "| NDFMIN = ",rndfp, " NUM_NOSHAKE = ",num_noshake, " CORRECTED RNDFP = ", rndfp
- write (6,'(a,f8.0)') &
- "| TOTAL # of degrees of freedom (RNDF) = ", rndf
- end if ! lam81
- end if
-
-#endif
-
- call fix_degree_count(rndf) ! correct for extra points
-! Warning - NOTE that rndfp, rndfs are uncorrected in an extra points context!
-
-#ifndef LES
- if (isgld > 0) then
- ! number of degrees of freedom in the SGLD part
- if (isgsta == 1) then
- sgsta_rndfp = 0
- else
- call degcnt(ibelly,nr,ix(ibellygp),isgsta-1,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0,idumar,sgsta_rndfp,ignore_solvent)
- end if
- if (isgend == nr) then
- sgend_rndfp = rndf
- else
- call degcnt(ibelly,nr,ix(ibellygp),isgend,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0,idumar,sgend_rndfp,ignore_solvent)
- end if
-! Warning - NOTE that the solute ndf outputs above from degcnt are uncorrected
-! for qmmm_struct%noshake_overlap, num_noshake, and extra points;
-! also ndfmin is not always being handled.
- call sg_fix_degree_count(sgsta_rndfp, sgend_rndfp, ndfmin, rndf)
- end if
-#endif
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /=0 ) call sc_degrees_o_freedom(ndfmin)
-#endif
-
- ! End of degrees of freedom setup
- !=======================================================================
-
- boltz2 = 8.31441d-3 * 0.5d0
- pconv = 1.6604345d+04 ! factor to convert the pressure kcal/mole to bar
-
- ! ---convert to kcal/mol units
-
- boltz2 = boltz2/4.184d0 ! k-sub-B/2
- dtx = dt*20.455d+00
- dtxinv = 1.0d0 / dtx
- dt5 = dtx * 0.5d0
- pconv = pconv*4.184d0
-
- ! FAC() are #deg freedom * kboltz / 2
- ! multiply by T to get expected kinetic energy
- ! FAC(1) is for total system
-
- fac(1) = boltz2*rndf
- fac(2) = boltz2*rndfp
-
- if(rndfp < 0.1d0) fac(2) = 1.d-6
-
-#ifdef LES
- ! replaced solvent variables with LES ones
- ! since separate solvent coupling no longer used
- ! ASSUME SAME COUPLING CONSTANT FOR BOTH BATHS, just different target T
-
- ! will also have to accumulate LES and non-LES kinetic energies separately
-
- if (temp0les < 0.d0) then
- fac(3) = boltz2*rndfs
- if(rndfs < 0.1d0) fac(3) = 1.d-6
- else
- fac(3) = boltz2*rndfles
- if(rndfles < 0.1d0) fac(3) = 1.d-6
- end if
-#else
- fac(3) = boltz2*rndfs
- if(rndfs < 0.1d0) fac(3) = 1.d-6
-#endif
- if ( ipimd==CMD ) then
- if ( eq_cmd ) then
- fac(1) = boltz2 * dble( 3*natomCL )
- else
- fac(1) = boltz2 * dble( 3*(natomCL-1) )
- endif
- endif
- onefac(1) = 1.0d0/fac(1)
- onefac(2) = 1.0d0/fac(2)
- onefac(3) = 1.0d0/fac(3)
- factt = rndf/(rndf+ndfmin)
-
- ! these are "desired" kinetic energies based on
- ! # degrees freedom and target temperature
- ! they will be used for calculating the velocity scaling factor
-
- ekinp0 = fac(2)*temp0
-#ifdef LES
-
- ! modified for LES temperature
-
- ekins0=0.d0
- ekinles0=0.d0
- if (temp0les < 0.d0) then
- ekins0 = fac(3) * temp0
- ekin0 = fac(1) * temp0
- if (master) &
- write (6,*) "Single temperature bath for LES and non-LES"
- else
- ekinles0 = fac(3)*temp0les
- ekin0 = ekinp0 + ekinles0
- if (master) then
- write (6,*) "LES particles coupled to separate bath"
- write (6,'(a,f8.2)')" LES target temperature: ",temp0les
- write (6,'(a,f8.2)')" LES target kinetic energy: ",ekinles0
- write (6,'(a,f8.2)')"non-LES target temperature: ",temp0
- write (6,'(a,f8.2)')"non-LES target kinetic energy: ",ekinp0
- end if
- end if
-#else
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-#endif
-
-#ifdef LES
- if(abfqmmm_param%abfqmmm /= 1) then ! lam81
- if ( ntt==4 ) call nose_hoover_init_LES(amass,v,f) ! APJ
- else ! lam81
- if ( ntt==4 .and. abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1 ) & ! lam81
- call nose_hoover_init_LES(amass,abfqmmm_param%v,abfqmmm_param%f) ! lam81
- endif ! lam81
-#else
- if(abfqmmm_param%abfqmmm /= 1) then ! lam81
- if ( ntt>=4 .and. ntt<=8 ) call nose_hoover_init(amass,v,f) ! APJ
- else ! lam81
- if ( ntt>=4 .and. ntt<=8 .and. abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1 ) & ! lam81
- call nose_hoover_init(amass,abfqmmm_param%v,abfqmmm_param%f) ! lam81
- endif
-#endif
-
- ! Langevin dynamics setup:
-
- is_langevin = gamma_ln > 0.0d0
- gammai = gamma_ln/20.455d0
- c_implic = 1.d0/(1.d0+gammai*dt5)
- c_explic = 1.d0 - gammai*dt5
- c_ave = 1.d0+gammai*dt5
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
-#ifdef LES
- if( temp0les < 0.d0 ) then
- sdfacles = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
- else
- sdfacles = sqrt( 4.d0*gammai*boltz2*temp0les/dtx )
- endif
-#endif
- if (is_langevin .and. ifbox==0) then
- call get_position(nr,x,sysx,sysy,sysz,sysrange,0)
-#ifdef MPI /* SOFT CORE */
- if (ifsc == 1) call sc_mix_position(sysx,sysy,sysz,clambda)
-#endif
- end if
-
- ! Constant pH setup
- !
- if (icnstph /= 0 .and. mdloop .eq. 0) &
- call cnstphinit(x, ig)
-
- if (ntt == 1) dttp = dt/tautp
- if (ntp > 0) dtcp = comp * 1.0d-06 * dt / taup
-
- ! Constant surface tension setup:
-
- if (csurften > 0) then
-
- ! Set pres0 in direction of surface tension.
- ! The reference pressure is held constant in on direction dependent
- ! on what the surface tension direction is set to.
- if (csurften .eq. 1) then ! pres0 in the x direction
- pres0x = pres0
-
- else if (csurften .eq. 2) then ! pres0 in the y direction
- pres0y = pres0
-
- !else if (csurften .eq. 3) then ! pres0 in the z direction
- else
- pres0z = pres0
-
- end if
-
- ! Multiply surface tension by the number of interfaces
- gamma_ten_int = dble(ninterface) * gamma_ten
-
- end if
-
- nrek = 4
- nrep = 15
-
- nvalid = 0
- nvalidi = 0
- nstep = 0
- total_nstep = 0
-#ifdef MPI
- ! For REMD, total_nstep is the number of steps * the number of exchanges
- ! we've already attempted
- if (rem /= 0) &
- total_nstep = (mdloop - 1) * nstlim
-#endif
- fit = 0.d0
- fiti = 0.d0
- fit2 = 0.d0
-
- ! Zero all elements of these sequence types
- ener = null_state_rec
- enert = null_state_rec
- enert2 = null_state_rec
- enert_old = null_state_rec
- enert2_old = null_state_rec
- edvdl = null_state_rec
- edvdl_r = null_state_rec
- ! for PIMD/NMPIMD/CMD/RPMD:
- totenert = null_state_rec
- totenert2 = null_state_rec
-
- ener%kin%pres_scale_solt = 1.d0
- ener%kin%pres_scale_solv = 1.d0
- ener%box(1:3) = box(1:3)
-
-
- ener%cmt(1:4) = 0.d0
- nitp = 0
- nits = 0
-
-
- !=======================================================================
- ! ----- MAKE A FIRST DYNAMICS STEP -----
- !=======================================================================
- ! init = 3: general startup if not continuing a previous run
-
- if( ipimd.eq.NMPIMD .or. ipimd.eq.CMD) then
- call trans_pos_cart_to_nmode( x )
- end if
-
- if( init == 3 .or. nstlim == 0 .or. (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1) ) then ! lam81
- if (ntp > 0 .and. iamoeba==0 .and. ipimd==0) then
- xr(1:nr3) = x(1:nr3)
-
- ! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
- ! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
- ! MASS -----
- call ekcmr(nspm,nsp,tma,ener%cmt,xr,v,amass,1,nr)
- end if
-
- ! ----- CALCULATE THE FORCE -----
-
- ! --- set irespa to get full energies calculated on step "0":
- irespa = 0
- iprint = 1
-
- if(ipimd==NMPIMD .or. ipimd==CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- call force(xx,ix,ih,ipairs,cartpos,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-#if defined(MPI) && defined(LES)
- if ( ievb == 1 .and. i_qi > 0) then
- call evb_umb ( f, cartpos, real_mass, natom, istart3, iend3 )
-! 03132009 if( i_qi == 2 ) call qi_corrf_les ( cartpos, amass )
- if( i_qi == 2 ) call qi_corrf_les ( cartpos, real_mass )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- call trans_frc_cart_to_nmode(f)
- i3 = 3*(istart-1)
-
-#if defined(MPI) && defined(LES)
- if ( ievb /= 0 .and. i_qi == 0 ) then
- call evb_umb ( f, x, real_mass, natom, istart3, iend3 )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- else if ( ilscivr == 1 )then
- ! prepare the Hessian Matrix of the potential for the LSC-IVR
- ! at this point, x is the position a bead at equilibrium
- ! initialize the LSC-IVR variables
- natom_lsc = natom
- ndof_lsc = natom * 3
-
- call lsc_init
- do ilsc = 1, natom_lsc
- mass_lsc(3*ilsc-2) = amass(ilsc)
- mass_lsc(3*ilsc-1) = amass(ilsc)
- mass_lsc(3*ilsc ) = amass(ilsc)
- end do
- v2_lsc = 0.0d0
- do ilsc = 1, ndof_lsc
- ! ith vector of the Hesian matrix
- x_lsc = 0.0d0
- x_lsc(1:ndof_lsc) = x(1:ndof_lsc)
- x_lsc(ilsc) = x(ilsc) + dx_lsc
- call force(xx,ix,ih,ipairs,x_lsc,f_lsc,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
-#ifdef MPI
- call xdist( f_lsc, xx(lfrctmp), natom )
-#endif
- v2_lsc(1:ndof_lsc,ilsc) = f_lsc(1:ndof_lsc)
- enddo
-
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
-#ifdef MPI
- call xdist(f, xx(lfrctmp), natom)
-#endif
- ! 2nd derivative of the potential:
- do ilsc = 1, ndof_lsc
- v2_lsc(1:ndof_lsc,ilsc) = &
- ( f(1:ndof_lsc) - v2_lsc(1:ndof_lsc,ilsc) )/dx_lsc
- end do
-
- ! get the iniital position of the momentum:
- call lsc_xp(x,v)
-
- else
-
- ! -- ti decomp
- if(idecomp > 0) then
- decpr = .false.
- if(mod(nstep+1,ntpr) == 0) decpr = .true.
- end if
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-#ifdef MPI
- if ( ievb /= 0 ) then
-#ifdef LES
- call evb_umb_primitive ( f, x, real_mass, natom, istart, iend )
-#else
- call evb_umb_primitive ( f, x, amass, natom, istart, iend )
-#endif
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- endif
-
- if (sebomd_obj%do_sebomd) then
- ! computes hessian matrix if necessary
- if (sebomd_obj%ntwh /= 0) then
- ! don't output atomic charges
- sebomd_obj%iflagch_old = sebomd_obj%iflagch
- sebomd_obj%iflagch = 0
- call sebomd_gradient_write(f,3*natom)
- call sebomd_hessian_compute(xx,ix,ih,ipairs,x,f,ener, &
- qsetup, do_list_update, nstep)
- sebomd_obj%iflagch = sebomd_obj%iflagch_old
- endif
- endif
-
-
- if (icnstph /= 0 .and. master .and. &
- ((rem /= 0 .and. mdloop > 0) .or. rem == 0)) call cnstphwrite(rem)
-
- for(1:nr3) = f(1:nr3) ! lam81
-#ifdef MPI
- call xdist(for,xx(lfrctmp),natom) ! lam81
-#endif
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-
- if(abfqmmm_param%system == 1) abfqmmm_param%f1(1:nr3) = for(1:nr3) ! lam81
-
- if(abfqmmm_param%system == 2) then ! lam81
- abfqmmm_param%f2(1:nr3) = for(1:nr3) ! lam81
- call abfqmmm_combine_forces() ! lam81
- for(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- f(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- end if ! lam81
-
- end if ! lam81
-
- ! This FORCE call does not count as a "step". CALL NMRDCP to decrement
- ! local NMR step counter and MTMDUNSTEP to decrease the local MTMD step
- ! counter
- call nmrdcp
- call mtmdunstep
-
-#ifdef MPI /* SOFT CORE */
- ! If softcore potentials are used, collect their dvdl contributions:
- if ( ifsc /= 0 ) then
- call mpi_reduce(sc_dvdl, sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl=0.0d0 ! zero for next step
- call mpi_reduce(sc_dvdl_ee, sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl_ee=0.0d0 ! zero for next step
- call mpi_reduce(sc_ener, sc_ener_tmp, ti_ene_cnt, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_ener(1:ti_ene_cnt) = sc_ener_tmp(1:ti_ene_cnt)
- end if
- if ( ifsc == 2 ) then
- ! If this is a perturb to nothing run, scale forces and calculate dvdl
- call sc_nomix_frc(f,nr3,ener)
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-
- if( icfe /= 0 )then
- ! ---free energies using thermodynamic integration (icfe /= 0)
-
- if( master ) then
- ! --- first, send the forces and energy to your partner:
- partner = ieor(masterrank,1)
- call mpi_sendrecv( f, nr3, MPI_DOUBLE_PRECISION, partner, 5, &
- frcti, nr3+3*extra_atoms, MPI_DOUBLE_PRECISION, &
- partner, 5, commmaster, ist, ierr )
- call mpi_sendrecv( ener, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- ecopy, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr)
- ! exchange sc-dvdl contributions between masters
- call mpi_sendrecv( sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, partner, &
- 5, sc_tot_dvdl_partner, 1, &
- MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, partner, &
- 5, sc_tot_dvdl_partner_ee, 1, &
- MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- if( masterrank==0 ) then
- call mix_frcti(frcti,ecopy,f,ener,nr3,clambda,klambda)
- else
- call mix_frcti(f,ener,frcti,ecopy,nr3,clambda,klambda)
- end if
- end if
-
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
-
- end if
-
-#endif /* MPI SOFT CORE */
-
- irespa = 1
-
- ! Reset quantities depending on TEMP0 and TAUTP (which may have been
- ! changed by MODWT during FORCE call).
- ! Recalculate target kinetic energies.
-
- ekinp0 = fac(2) * temp0
-
-#ifdef LES
-
- ! modified for LES temperature, not solvent
-
- ekins0 = 0.d0
- ekinles0 = 0.d0
- if (temp0les < 0.d0) then
- ekins0 = fac(3) * temp0
- ekin0 = fac(1) * temp0
- else
- ekinles0 = fac(3) * temp0les
- ekin0 = ekinp0 + ekinles0
- end if
-#else
- ekins0 = fac(3) * temp0
- ekin0 = fac(1) * temp0
-#endif
-
- if (ntt == 1) dttp = dt / tautp
-
- if (ntp > 0) then
- ener%volume = volume
- ener%density = tmass / (0.602204d0*volume)
-
- if( iamoeba == 0 ) then
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = 0.d0
- do m = 1,3
- ener%cmt(m) = ener%cmt(m) * 0.5d0
- ener%cmt(4) = ener%cmt(4) + ener%cmt(m)
- ener%vir(4) = ener%vir(4) + ener%vir(m)
- ener%pres(m) = (pconv+pconv) * (ener%cmt(m)-ener%vir(m)) / volume
- ener%pres(4) = ener%pres(4) + ener%pres(m)
- end do
- ener%pres(4) = ener%pres(4) / 3.d0
- end if
- end if
-
- ntnb = 0
- i3 = 0
- tempsu = 0.0d0
-
-#ifdef LES
- ! added LES tempsu (actual LES sum of m*v**2 )
- tempsules = 0.0d0
-#endif
- eke_cmd = 0.d0
- do j = 1,nrp
- winf = winv(j) * dt5
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- rterm = v(i3)*v(i3) * aamass
-#ifdef LES
- if (temp0les < 0.d0) then
- tempsu = tempsu + rterm
- if (ipimd.eq.CMD.and.(cnum(j).eq.0.or.cnum(j).eq.1)) then
- eke_cmd = eke_cmd + aamass*v(i3)*v(i3)
- endif
- else
- if (cnum(j) == 0) then
- tempsu = tempsu + rterm
- else
- tempsules = tempsules + rterm
- end if
- end if
-#else
- if(ipimd.eq.CMD.and.mybeadid==1) then
- eke_cmd = eke_cmd + aamass*v(i3)*v(i3)
- end if
- tempsu = tempsu + rterm
-#endif
- if(ipimd.ne.NMPIMD.and.ipimd.ne.CMD) v(i3) = v(i3) - f(i3) * winf
- if (vlim) v(i3) = sign(min(abs(v(i3)),vlimit),v(i3))
- end do
- end do
-
-#ifdef MPI /* SOFT CORE */
- if ( ifsc /= 0 ) then
- call calc_softcore_ekin(amass,v,v,istart,iend)
- sc_ener(13) = sc_ener(6) + sc_ener(12)
- end if
-#endif
-
- do im=1,iscale
- v(nr3+im) = v(nr3+im) - f(nr3+im) * dt5 / scalm
- tempsu = tempsu + scalm * v(nr3+im)*v(nr3+im)
- end do
- ener%kin%solt = tempsu * 0.5d0
-
-#ifdef LES
-
- ! added for LES temperature using old solvent variable for ener(4)
-
- if (temp0les < 0.d0) then
- ener%kin%solv = 0.d0
- ener%kin%tot = ener%kin%solt
- ! for CMD:
- if( ipimd > 0 ) then
- ener%kin%solv = equal_part + Epot_deriv ! "virial" estimate of KE
- ener%tot = ener%kin%solv + ener%pot%tot
- else
- ener%tot = ener%kin%tot + ener%pot%tot
- endif
- if (ipimd.eq.CMD) then
- ener%kin%tot = eke_cmd*0.5d0
- ener%kin%solv = ener%kin%tot
- endif
- else
- ener%kin%solv = tempsules * 0.5d0
- ener%kin%tot = ener%kin%solt + ener%kin%solv
- end if
-#else
- ! for better output for parallel PIMD/NMPIM/CMD/RPMD
- if (ipimd>0) then
- ener%tot = 0.d0
- ener%kin%tot = 0.d0
- ener%kin%solt = 0.d0
- ener%kin%solv = 0.d0
- ener%volume = 0.d0
- endif
- ener%kin%tot = ener%kin%solt
- ener%tot = ener%kin%tot+ener%pot%tot
-
-#endif
-
- if(ntt == 1) then
-#ifdef LES
- if (temp0les >= 0.d0) then
- ekmh = max(ener%kin%solt,fac(2)*10.d0)
- ekmhles = max(ener%kin%solv,fac(3)*10.d0)
- else
- ekmh = max(ener%kin%solt,fac(1)*10.d0)
- end if
-#else
- ekmh = max(ener%kin%solt,fac(1)*10.d0)
-#endif
- end if
-
- end if ! ( init == 3 )
-
- !-------------------------------------------------------------------------
- ! init = 4: continuation of a previous trajectory
- ! this code also done for init=3
- !
- ! Note: if the last printed energy from the previous trajectory was
- ! at time "t", then the restrt file has velocities at time
- ! t + 0.5dt, and coordinates at time t + dt
- !-------------------------------------------------------------------------
-
- ! -------------------------------------------------------------------
- ekmh = 0.0d0
-#ifdef LES
- ekmhles = 0.0d0
-#endif
-
- i3 = 0
- do j = 1,nrp
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- rterm = v(i3)*v(i3) * aamass
-# ifdef LES
- ! use copy number, not solute/solvent
- if (temp0les < 0.d0) then
- ! 1 bath
- ekmh = ekmh + rterm
- else
- if (cnum(j) == 0) then
- ekmh = ekmh + rterm
- else
- ekmhles = ekmhles + rterm
- end if
- end if
-# else
- ekmh = ekmh + rterm
-# endif
- end do
- end do
-
-#ifdef MPI /* SOFT CORE */
- if ( ifsc /= 0 ) then
- call calc_softcore_ekin(amass,v,v,istart,iend)
- sc_ener(13) = sc_ener(6) + sc_ener(12)
- end if
-#endif
-
- do im=1,iscale
- ekmh = ekmh + scalm*v(nr3+im)*v(nr3+im)
- end do
- ekmh = ekmh * 0.5d0
-#ifdef LES
- ekmhles = ekmhles * 0.5d0
-#endif
-
- do i=1,nr3+iscale
- vold(i) = v(i)
- end do
-
-#ifdef EMIL
- !--Setup the emil calculation if required
- if ( emil_do_calc .gt. 0 ) then
- call emil_init( natom, nstep, 1.0/(temp0 * 2 * boltz2 ), &
- mass, xx(lcrd), f, v, ener%box)
- end if
-#endif
-
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
- nstep=abfqmmm_param%qmstep ! lam81
- if(abfqmmm_param%maxqmstep == 0) nstep = 0 ! lam81
- end if ! lam81
-
- if (init /= 4 .or. nstlim == 0 .or. (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1)) then ! lam81
-
- !-------------------------------------------------------------------
- ! PRINT THE INITIAL ENERGIES AND TEMPERATURES
- !-------------------------------------------------------------------
-#ifdef RISMSANDER
- if ( rismprm%irism == 1 .and. rismprm%write_thermo==1 &
- .and. nstep <= 0 .and. facc /= 'A') then
- if( rism_calc_type(0) == RISM_FULL)&
- call rism_solvdist_thermo_calc(.false.,0)
- end if
-#endif /*RISMSANDER*/
-
- if ( (nstep <= 0 .and. master .and. facc /= 'A') .or. & ! lam81
- (master .and. abfqmmm_param%abfqmmm == 1 .and. mod(abfqmmm_param%qmstep,ntpr) == 0) ) then ! lam81
-
- if (isgld > 0) call sgenergy(ener)
- rewind(7)
-#ifdef LES
- if (.not.ipimd.gt.0) &
- ener%tot = ener%kin%tot+ener%pot%tot
-#endif /* LES */
- if(abfqmmm_param%abfqmmm /= 1 .or. abfqmmm_param%system == 1 .or. nstep == 0) & ! lam81
- call prntmd(nstep,nitp,nits,t,ener,onefac,7,.false.)
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener)
- if (ifsc /= 0) call sc_print_energies(7, sc_ener)
-#endif
- if ( ifcr > 0 .and. crprintcharges > 0 ) then
- call cr_print_charge( xx(l15), nstep )
- end if
-
- !--- BEGIN DIPOLE PRINTING CODE ---
- ! See code further on for comments-explanations
- call nmlsrc('dipoles',5,prndipfind)
- if(prndipfind /= 0 ) then
- write(6,*) '------------------------------- DIPOLE &
- &INFO ----------------------------------'
- write(6,9018) nstep,t
- read (5,'(a)') prndiptest
- call rgroup(natom,natc,nres,prndipngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp), &
- jgroup,indx,irespw,npdec, &
- xx(l60),xx(lcrdr),0,0,0,idecomp,5,.false.)
- rewind(5)
- if(prndipngrp > 0) then
- call printdip(prndipngrp,ix(icnstrgp),xx(lcrd), &
- xx(l15),xx(linddip),xx(Lmass), natom)
- end if
- write(6,*) '----------------------------- END DIPOLE &
- &INFO --------------------------------'
- end if
- !--- END DIPOLE PRINTING CODE ---
-
- if (nmropt > 0) then
- call nmrptx(6)
- end if
- call amflsh(7)
- end if
-
- if (abfqmmm_param%abfqmmm == 1 .and. abfqmmm_param%system == 1) then ! lam81
- deallocate(for, stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- return ! lam81
- end if ! lam81
- if (nstlim == 0) then ! lam81
- if(abfqmmm_param%abfqmmm == 1) v(1:nr3) = abfqmmm_param%v(1:nr3) ! lam81
-#ifdef MPI
- call xdist(x, xx(lfrctmp), natom) ! lam81
- call xdist(v, xx(lfrctmp), natom) ! lam81
-
- if(master) then ! lam81
-#endif
- if(ntwr>0) call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, & ! lam81
- x,v,xx(lcrdr),box,t,temp0) ! lam81
- if(ntwx>0) call corpac(x,1,nrx,MDCRD_UNIT,loutfm) ! lam81
- if(ntwv>0) call corpac(v,1,nrx,MDVEL_UNIT,loutfm) ! lam81
- if(ntwf>0) call corpac(for,1,nrx,MDFRC_UNIT,loutfm) ! lam81
- if(ntwe>0) call mdeng(15,nstep,t,ener,onefac,ntp,csurften) ! lam81
-#ifdef MPI
- end if ! lam81
-#endif
- return ! lam81
- end if ! lam81
- init = 4
- end if
-
-
- if(ntp > 0 .and. ipimd > 0 ) then
- REQUIRE(ipimd.eq.NMPIMD)
-#ifdef LES
- call part_setup_cnst_press_pimd(Nkt,tau_vol)
-#else
- call full_setup_cnst_press_pimd(Nkt,tau_vol)
-#endif
- e2 = 1.0/ (2.0*3.0)
- e4 = e2 / (4.0*5.0)
- e6 = e4 / (6.0*7.0)
- e8 = e6 / (8.0*9.0)
- x_lnv = log( box(1)*box(2)*box(3) ) / 3
- end if
-
- ! For CMD.
- if ( ipimd==CMD ) then
-
- if ( .not.eq_cmd ) then
-
- ! De-activate thermostat for path-centroid.
-#ifdef LES
- do iatom = 1, natom
- do idim = 1, 3
- if ( cnum(iatom)==0 .or. cnum(iatom)==1 ) then
- activate = .false.
- else
- activate = .true.
- end if
- call Thermostat_switch(thermo(idim,iatom),activate)
- enddo
- enddo
- if ( .not.restart_cmd ) then
- ! Scale path-centroid velocity and set total momentum equal to zero.
- call part_scale_vel_centroid(v,amass,istart,iend)
- nstep_cmd = 0
- t_cmd = 0.d0
- else
- t_cmd = t
- nstep_cmd = int( t / dt )
- end if
-#else
- if ( mybeadid.eq.1 ) then
- activate = .false.
- else
- activate = .true.
- end if
- do iatom = 1, natom
- do idim = 1, 3
- call Thermostat_switch(thermo(idim,iatom),activate)
- enddo
- enddo
- if ( .not.restart_cmd ) then
- ! Scale path-centroid velocity and set total momentum equal to zero.
- call full_scale_vel_centroid(v,amass,istart,iend)
- nstep_cmd = 0
- t_cmd = 0.d0
- else
- nstep_cmd = nstep
- t_cmd = t
- end if
-#endif /* LES */
-
- else
-
- nstep_cmd = nstep
- t_cmd = t
-
- end if
-
- end if ! ipimd.eq.CMD and adiab_param<1.d0
-
-#ifdef MPI
- ! If this is a replica run and we are on exchange > 1, restore the
- ! old ekmh value since it was reset after we left runmd last time.
- ! DAN ROE: Only for ntt==1??
- if (rem /= 0 .and. mdloop >= 1) then
- ekmh = remd_ekmh
- endif
-#endif
-
-
- !=======================================================================
- ! ----- MAIN LOOP FOR PERFORMING THE DYNAMICS STEP -----
- ! (at this point, the coordinates are a half-step "ahead"
- ! of the velocities; the variable EKMH holds the kinetic
- ! energy at these "-1/2" velocities, which are stored in
- ! the array VOLD.)
- !=======================================================================
-
- 260 continue
- onstep = mod(irespa,nrespa) == 0
-
- ! Constant pH setup
- if (icnstph /= 0 .and. &
- ((rem /= 0 .and. mdloop > 0) .or. rem == 0)) then
-
- if (ntnb == 1) then ! rebuild pairlist
- call cnstphupdatepairs(x)
- end if
-
- if (mod(irespa+nstlim*mdloop,ntcnstph) == 0) then
- if (icnstph .eq. 1) then
- call cnstphbeginstep(xx(l190))
- else
- call cnstph_explicitmd( xx,ix,ih,ipairs,x,winv,amass,f,v,vold, &
- xr,xc,conp,skip,nsp,tma,erstop,qsetup, &
- do_list_update,rem)
- end if
- end if
-
- end if
-
-! x+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++x
-! | EVB reactive flux |
-! +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::+
-! | Driver for coordinating backward and forward propagation as |
-! | well as for enforcing stopping criteria |
-! +---------------------------------------------------------------+
-
-#if defined(MPI)
- if( ievb /= 0 .and. trim( adjustl( evb_dyn) ) == "react_flux" ) then
- REQUIRE( ipimd.eq.0 .or. ipimd.eq.NMPIMD )
- call react_flux ( x, v, f, winv, tempi * factt, dt5, dtx &
- , nr, nstep, nstlim )
- endif
-#endif
-
- !---------------------------------------------------------------
- ! ---Step 1a: do some setup for pressure calculations:
- !---------------------------------------------------------------
-
- if (ntp > 0 .and. iamoeba == 0 .and. ipimd==0) then
- ener%cmt(1:3) = 0.d0
- xr(1:nr3) = x(1:nr3)
-
- ! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
- ! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
- ! MASS -----
-
- call timer_start(TIME_EKCMR)
- call ekcmr(nspm,nsp,tma,ener%cmt,xr,v,amass,istart,iend)
-#ifdef MPI
- call trace_mpi('mpi_allreduce', &
- 3,'MPI_DOUBLE_PRECISION',mpi_sum)
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,ener%cmt,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
-# else
- call mpi_allreduce(ener%cmt,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- ener%cmt(1:3) = mpitmp(1:3)
-# endif
-#endif
- call timer_stop(TIME_EKCMR)
- end if
-
- ! If we're using the MC barostat, go ahead and do the trial move now
- if (ntp > 0 .and. barostat == 2 .and. mod(total_nstep+1, mcbarint) == 0) &
- call mcbar_trial(xx, ix, ih, ipairs, x, xc, f, ener%vir, xx(l96), &
- xx(l97), xx(l98), xx(l99), qsetup, do_list_update, &
- nstep, nsp, amass)
-
- !--------------------------------------------------------------
- ! ---Step 1b: Get the forces for the current coordinates:
- !--------------------------------------------------------------
-
- npbstep = nstep
- iprint = 0
- if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
-
- if (sebomd_obj%do_sebomd) then
- ! write down atomic charges and density matrix if needed
- sebomd_obj%iflagch = 0
- if (sebomd_obj%ntwc /= 0) then
- if (mod(nstep+1,sebomd_obj%ntwc) == 0) sebomd_obj%iflagch = 1
- endif
-! sebomd_obj%pdmx = 0
-! if (sebomd_obj%pdump /= 0) then
-! if (mod(nstep+1,ntwr) == 0) sebomd_obj%pdmx = 1
-! if (nstep+1 == nstlim) sebomd_obj%pdmx = 1
-! endif
- endif
-
-#ifdef MPI
- ! set do_mbar for the force contributions
- if (ifmbar /= 0) then
- do_mbar = .false.
- if ( mod(nstep+1,bar_intervall) == 0) then
- do_mbar = .true.
- end if
- end if
-#endif
-
- if ( ipimd==NMPIMD .or. ipimd==CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- call force(xx,ix,ih,ipairs,cartpos,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
-#if defined(MPI) && defined(LES)
- if ( ievb == 1 .and. i_qi > 0) then
- call evb_umb ( f, cartpos, real_mass, natom, istart3, iend3 )
-! 03132009 if( i_qi == 2 ) call qi_corrf_les ( cartpos, amass )
- if( i_qi == 2 ) call qi_corrf_les ( cartpos, real_mass )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- call trans_frc_cart_to_nmode(f)
-
-#if defined(MPI) && defined(LES)
- if ( ievb /= 0 .and. i_qi == 0 ) then
- call evb_umb ( f, x, real_mass, natom, istart3, iend3 )
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-
-#endif
-
- else
- ! -- ti decomp
- if(idecomp > 0) then
- decpr = .false.
- if(mod(nstep+1,ntpr) == 0) decpr = .true.
- end if
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-#if defined(MPI)
- if ( ievb /= 0 ) then
-#ifdef LES
- call evb_umb_primitive ( f, x, real_mass, natom, istart, iend )
-#else
- call evb_umb_primitive ( f, x, amass, natom, istart, iend )
-#endif
- evb_nrg(1) = evb_frc%evb_nrg
- evb_nrg(2) = evb_vel0%evb_nrg
- if( nbias > 0 ) evb_nrg(3) = sum( evb_bias%nrg_bias(:) )
- endif
-#endif
-
- endif
-
- if (sebomd_obj%do_sebomd) then
- ! computes hessian matrix if necessary
- if (sebomd_obj%ntwh /= 0 .and. mod(nstep+1,sebomd_obj%ntwh) == 0) then
- ! don't output atomic charges
- sebomd_obj%iflagch_old = sebomd_obj%iflagch
- sebomd_obj%iflagch = 0
- call sebomd_gradient_write(f,3*natom)
- call sebomd_hessian_compute(xx,ix,ih,ipairs,x,f,ener, &
- qsetup, do_list_update, nstep)
- sebomd_obj%iflagch = sebomd_obj%iflagch_old
- endif
- endif
-
- for(1:nr3) = f(1:nr3) ! lam81
-#ifdef MPI
- call xdist(for,xx(lfrctmp),natom) ! lam81
-#endif
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- abfqmmm_param%f2(1:nr3) = for(1:nr3) ! lam81
- call abfqmmm_combine_forces() ! lam81
-#ifdef MPI
- call mpi_bcast(abfqmmm_param%f, 3*natom, mpi_double_precision, 0, commsander, ierr) ! lam81
-#endif
- for(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- f(1:nr3) = abfqmmm_param%f(1:nr3) ! lam81
- end if ! lam81
-
- ! Constant pH transition evaluation for GB CpHMD (not explicit CpHMD)
- if ((icnstph == 1) .and. (mod(irespa+mdloop*nstlim,ntcnstph) == 0)) then
- call cnstphendstep(xx(l190), xx(l15), ener%pot%dvdl, temp0, solvph)
- if (master) call cnstphwrite(rem)
- end if
-
-#ifdef MPI
- ! If softcore potentials are used, collect their dvdl contributions:
- if ( ifsc /= 0 ) then
- call mpi_reduce(sc_dvdl, sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl=0.0d0 ! zero for next step
- call mpi_reduce(sc_dvdl_ee, sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_dvdl_ee=0.0d0 ! zero for next step
- call mpi_reduce(sc_ener, sc_ener_tmp, ti_ene_cnt, MPI_DOUBLE_PRECISION, &
- MPI_SUM, 0, commsander, ierr)
- sc_ener(1:ti_ene_cnt) = sc_ener_tmp(1:ti_ene_cnt)
- end if
- if ( ifsc == 2 ) then
- ! If this is a perturb to nothing run, scale forces and calculate dvdl
- call sc_nomix_frc(f,nr3,ener)
-
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-
- if (ifmbar /=0 .and. do_mbar) then
- call bar_collect_cont()
- end if
-
- if ( icfe /= 0 )then
-
- ! --- free energies using thermodynamic integration (icfe /= 0)
-
- ! --- first, send the forces, energy, and virial to your partner:
-
- if( master ) then
- partner = ieor(masterrank,1)
- call mpi_sendrecv( f, nr3, MPI_DOUBLE_PRECISION, partner, 5, &
- frcti, nr3+3*extra_atoms, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( ener, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- ecopy, state_rec_len, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr)
-
- ! exchange sc-dvdl contributions between masters:
- call mpi_sendrecv( sc_tot_dvdl, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- sc_tot_dvdl_partner, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
- call mpi_sendrecv( sc_tot_dvdl_ee, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- sc_tot_dvdl_partner_ee, 1, MPI_DOUBLE_PRECISION, partner, 5, &
- commmaster, ist, ierr )
-
- ! ---- collect statistics for free energy calculations:
-
- if( onstep ) then
- if( masterrank==0 ) then
- if( klambda == 1 ) then
- edvdl = edvdl - ener + ecopy
- edvdl_r = edvdl_r - ener + ecopy
- else
- clfac = klambda*(1.d0 - clambda)**(klambda-1)
- edvdl = edvdl - (ener - ecopy)*clfac
- edvdl_r = edvdl_r - (ener - ecopy)*clfac
- end if
- else
- if( klambda == 1 ) then
- edvdl = edvdl + ener - ecopy
- edvdl_r = edvdl_r + ener - ecopy
- else
- clfac = klambda*(1.d0 - clambda)**(klambda-1)
- edvdl = edvdl + (ener - ecopy)*clfac
- edvdl_r = edvdl_r + (ener - ecopy)*clfac
- end if
- end if
- ! This includes the sc-dvdl contribution into the vdw-part
- ! and potential energy parts of the dvdl-statistics
- if (ifsc == 1) then
- call adj_dvdl_stat(edvdl, edvdl_r)
- end if
- end if
-
- ! Do energy collection for MBAR FEP runs
- if (ifmbar /= 0 .and. do_mbar) then
- call calc_mbar_energies(ener%pot%tot, ecopy%pot%tot)
- end if
-
- if( masterrank==0 ) then
- call mix_frcti(frcti,ecopy,f,ener,nr3,clambda,klambda)
- else
- call mix_frcti(f,ener,frcti,ecopy,nr3,clambda,klambda)
- endif
- endif
-
- if( numtasks>1 ) then
- call mpi_bcast(f,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(ener,state_rec_len,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
-
- end if ! ( icfe /= 0 )
-
-#endif /* MPI */
-
-#ifdef EMIL
- ! Call the EMIL absolute free energy calculation.
- if ( emil_do_calc .gt. 0 ) then
-
- call emil_step(natom, nstep, 1.0 / (temp0 * 2 * boltz2),&
- mass, xx(lcrd), f, v, ener%pot, ener%pot, ener%box)
- end if
-#endif
-
-
-
- ! Reset quantities depending on TEMP0 and TAUTP (which may have been
- ! changed by MODWT during FORCE call).
- ekinp0 = fac(2)*temp0
-
-#ifdef LES
- ! TEMP0LES may have changed too
-
- ekinles0=0.d0
- ekins0=0.d0
- if (temp0les >= 0.d0) then
- ekinles0 = fac(3)*temp0les
- ekin0 = ekinp0 + ekinles0
- else
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
- end if
-#else
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-#endif
-
- if (ntt == 1) dttp = dt/tautp
-
- ! Pressure coupling:
- if (ntp > 0.and.ipimd>0) then
- REQUIRE(ipimd.eq.NMPIMD)
- centvir=0.0
-
-#ifdef LES
- do iatom=istart,iend
- if(cnum(iatom).eq.0.or.cnum(iatom).eq.1) then
- centvir=centvir-x(3*iatom-2)*f(3*iatom-2)
- centvir=centvir-x(3*iatom-1)*f(3*iatom-1)
- centvir=centvir-x(3*iatom )*f(3*iatom)
- end if
- end do
-#else
- if(mybeadid.eq.1) then
- do iatom=istart,iend
- centvir=centvir-x(3*iatom-2)*f(3*iatom-2)
- centvir=centvir-x(3*iatom-1)*f(3*iatom-1)
- centvir=centvir-x(3*iatom )*f(3*iatom)
- end do
- end if
-#endif /* LES */
-
- if(iamoeba.eq.1) then
- atomvir=sum(ener%vir(1:3))
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,centvir,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- call mpi_allreduce(MPI_IN_PLACE,atomvir,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# else
- call mpi_allreduce(centvir,mpitmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- centvir=mpitmp(1)
- tmp=0.0
- call mpi_allreduce(atomvir,tmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- atomvir=tmp
-# endif
-#endif
- else
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,centvir,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- call mpi_allreduce(MPI_IN_PLACE,bnd_vir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- call mpi_allreduce(MPI_IN_PLACE,e14vir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# ifndef LES
- if (master) &
- call mpi_allreduce(MPI_IN_PLACE,atvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commmaster,ierr)
-# endif
-# else
- call mpi_allreduce(centvir,tmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- centvir=tmp
- tmpvir=0.0
- call mpi_allreduce(bnd_vir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- bnd_vir=tmpvir
-
-# ifndef LES
- if (master) then
- tmpvir=0.0
- call mpi_allreduce(e14vir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commmaster,ierr)
- e14vir=tmpvir
-
- tmpvir=0.0
- call mpi_allreduce(atvir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commmaster,ierr)
- atvir=tmpvir
- endif
-# else
- tmpvir=0.0
- call mpi_allreduce(e14vir,tmpvir,9,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- e14vir=tmpvir
-# endif
-# endif
- call mpi_bcast(atvir,9,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- call mpi_bcast(e14vir,9,MPI_DOUBLE_PRECISION,0,commsander,ierr)
-#endif
- atomvir=0.0
- atomvir=atomvir+atvir(1,1)+bnd_vir(1,1)+e14vir(1,1)
- atomvir=atomvir+atvir(2,2)+bnd_vir(2,2)+e14vir(2,2)
- atomvir=atomvir+atvir(3,3)+bnd_vir(3,3)+e14vir(3,3)
- end if
- pressure = (Nkt*3.0-centvir-(atomvir-Eimp_virial))/(3.0*volume)
- f_lnv_p = (pressure-pres0/pconv)*volume*3.0
- end if
-
-
- if (ntp > 0) then
- ener%volume = volume
- ener%density = tmass / (0.602204d0*volume)
- if( iamoeba == 0 .and. ipimd==0 ) then
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = 0.d0
- do m = 1,3
- ener%cmt(m) = ener%cmt(m)*0.5d0
- ener%cmt(4) = ener%cmt(4)+ener%cmt(m)
- ener%vir(4) = ener%vir(4)+ener%vir(m)
- ener%pres(m) = (pconv+pconv)*(ener%cmt(m)-ener%vir(m))/volume
- ener%pres(4) = ener%pres(4)+ener%pres(m)
- end do
- ener%pres(4) = ener%pres(4)/3.d0
-
- ! Constant surface tension output:
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! Surface tension in the x direction
- ener%surface_ten = &
- box(1) * (ener%pres(1) - 0.5d0 * &
- (ener%pres(2) + ener%pres(3))) / (ninterface * ten_conv)
-
- else if (csurften .eq. 2) then ! Surface tension in the y direction
- ener%surface_ten = &
- box(2) * (ener%pres(2) - 0.5d0 * &
- (ener%pres(1) + ener%pres(3))) / (ninterface * ten_conv)
-
- else ! if (csurften .eq. 3) ! Surface tension in the z direction
- ener%surface_ten = &
- box(3) * (ener%pres(3) - 0.5d0 * &
- (ener%pres(1) + ener%pres(2))) / (ninterface * ten_conv)
-
- end if
-
- end if
-
- end if
- end if
-
-#ifdef MPI
-! ------====== REMD ======------
-! If rem /= 0 and mdloop == 0, this is the first sander call and we don't want to
-! actually do any MD or change the initial coordinates.
-! Exit here since we only wanted to get the potential energy for the first
-! subrem exchange probability calc.
- if (rem /= 0 .and. mdloop == 0) then
-# ifdef VERBOSE_REMD
- if (master) write (6,'(a,i3)') &
- 'REMD: Exiting runmd after getting initial energies for replica',repnum
-# endif
- goto 480 ! Go to the end of the runmd loop.
- endif ! (rem /= 0 and mdloop == 0)
-
- !REB Do adaptive QMMM
- if ( qmmm_nml%vsolv > 1 ) then
- ! mix forces for adaptive QM/MM and
- ! calculate adaptive energy if requested
- ! note: nstep is zero during first call; this is the energy/force calculation
- ! with the starting geometry / velocities
- call adaptive_qmmm(nstep,natom,x,xold,f,ener%pot%tot, ntpr, ntwx, &
- xx, ix, ih, ipairs, qsetup, do_list_update, &
- corrected_energy, aqmmm_flag)
-
-! ALTERNATIVE APPROACH:
-! if (ad_qmmm%calc_wbk) then
-! call ad_qmmm_check_matching_partitions()
-! if (ad_qmmm%mismatch) then
-! call force()
-! end if
-! call ad_qmmm_energy()
-! end if
-
-! test
- i3 = 3*(istart-1)
- do j=istart,iend
- do idim = 1, 3
- xold(i3+idim)=x(i3+idim)
- enddo
- i3 = i3 + 3
- enddo
-! test
- endif
-
-#endif
-
- !----------------------------------------------------------------
- ! ---Step 1c: do randomization of velocities, if needed:
- !----------------------------------------------------------------
- ! ---Assign new random velocities every Vrand steps, if ntt=2
-
- resetvelo=.false.
- if (vrand /= 0 .and. ntt == 2) then
- if (mod((nstep+1),vrand) == 0) resetvelo=.true.
- end if
-
-#ifdef MMTSB
- if ( mmtsb_switch == mmtsb_temp_rex .and. mmtsb_is_exchanged ) &
- resetvelo = .true.
-#endif
-
- if (resetvelo) then
- ! DAN ROE: Why are only the masters doing this? Even if the velocities
- ! are broadcast to the child processes, the wont the different # of random
- ! calls put the randomg num generators out of sync, or do we not care?
-
- if (master) then
- write (6,'(a,i8)') 'Setting new random velocities at step ', &
- nstep + 1
- call setvel(nr,v,winv,temp0*factt,init,iscale,scalm)
-
-#ifdef MPI /* SOFT CORE */
- ! Make sure all common atoms have the same v (that of V0) in TI runs:
- if (icfe /=0 .and. ifsc /=0) call sc_sync_x(v,nr3)
-#endif
-
-#ifdef LES
-
- ! newvel call is fixed for the dual target temperatures
-
- if (temp0les >= 0.d0.and.temp0 /= temp0les) then
- vscalt = sqrt (temp0les/temp0)
- do j=1,natom
- if(cnum(j) > 0) then
- i3 = 3*(j-1)
- v(i3+1) = v(i3+1) * vscalt
- v(i3+2) = v(i3+2) * vscalt
- v(i3+3) = v(i3+3) * vscalt
- endif
- end do
- end if
-#endif
- if (ibelly > 0) call bellyf(nr,ix(ibellygp),v)
- end if
-# ifdef MPI
- call trace_mpi('mpi_bcast',3*natom,'MPI_DOUBLE_PRECISION',0)
- call mpi_bcast(v, 3*natom, MPI_DOUBLE_PRECISION, 0, commsander, ierr)
-# endif
-
- ! At this point in the code, the velocities lag the positions
- ! by half a timestep. If we intend for the velocities to be drawn
- ! from a Maxwell distribution at the timepoint where the positions and
- ! velocities are synchronized, we have to correct these newly
- ! redrawn velocities by backing them up half a step using the
- ! current force.
- ! Note that this fix only works for Newtonian dynamics.
- if( gammai==0.d0.and.(ipimd.ne.NMPIMD.or.ipimd.ne.CMD)) then
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dt5
- v(i3+1) = v(i3+1) - f(i3+1)*wfac
- v(i3+2) = v(i3+2) - f(i3+2)*wfac
- v(i3+3) = v(i3+3) - f(i3+3)*wfac
- i3 = i3+3
- end do
- end if
-
- end if ! (resetvelo)
-
- call timer_start(TIME_VERLET)
-
- !-----------------------------------------------------
- ! ---Step 2: Do the velocity update:
- !-----------------------------------------------------
-
- !step 2a: apply quenched MD if needed. This is useful in NEB>0
- if (vv==1) call quench(f,v)
-
- ! Car-Parrinello on dipoles: note that the (small?) kinetic energy
- ! of the dipoles is included in the epol energy
-! M_WJ
-! if ( induced == 1 .and. indmeth == 3 ) call cp_dips(natom,xx(lpol),xx,dt)
- if ( induced > 0 .and. indmeth == 3 ) call cp_dips(natom,xx(lpol),xx,dt)
-
-
-
-! i3 = 3*(istart-1) !! Add Brownian noise for testing. ! APJ
-! do j=istart,iend ! APJ
-! do idim=1,3 ! APJ
-! call gauss( 0.d0, sqrt(0.1d0*boltz2*temp0)/dtx,fln ) ! APJ
-! f(i3+idim) = f(i3+idim) + fln ! APJ
-! enddo ! APJ
-! i3 = i3+3 ! APJ
-! end do ! APJ
-
-
- ! Nose'-Hoover thermostat (1st step).
- if ( ntt == 4 ) then
-
- Ekin2_tot = 0.d0
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = dtx/amass(j)
- do idim = 1, 3
-#ifdef LES
- if( ntp>0.and.ipimd.eq.NMPIMD .and. &
- (cnum(j).eq.0.or.cnum(j).eq.1) ) then
-#else
- if(ntp>0.and.ipimd.eq.NMPIMD.and.mybeadid.eq.1) then
-#endif
- exp1 = exp(-dt5*thermo(idim,j)%v(1)-dt5*v_lnv*c2_lnv)
- Ekin2_tot = Ekin2_tot + amass(j)*v(i3+idim)*v(i3+idim)
- else
- exp1 = exp( -dt5 * thermo(idim,j)%v(1) )
- end if
- exp2 = exp1*exp1
- vold(i3+idim)=v(i3+idim)
- v(i3+idim) = v(i3+idim) * exp2 + f(i3+idim) * wfac * exp1
- end do
- i3 = i3+3
- end do
-
- if(ntp>0.and.ipimd.eq.NMPIMD) then
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,Ekin2_tot,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# else
- call mpi_allreduce(Ekin2_tot,mpitmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- Ekin2_tot=mpitmp(1)
-# endif
-#endif
- f_lnv_v = Ekin2_tot*(c2_lnv-1)
- tmp = exp(-dt5*thermo_lnv%v(1))
- v_lnv = tmp*(tmp*v_lnv+dtx*(f_lnv_v+f_lnv_p)/mass_lnv)
- end if
-
- call Thermostat_integrate_1(nchain,thermo,nthermo,dtx,ntp)
-
- else if ( ntt>4 .and. ntt<=8 ) then ! APJ
-
- Ekin2_tot = 0.d0
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = dtx/amass(j)
- do idim = 1, 3
-#ifdef LES
- if( ntp>0.and.ipimd.eq.NMPIMD .and. &
- (cnum(j).eq.0.or.cnum(j).eq.1) ) then
-#else
- if(ntp>0.and.ipimd.eq.NMPIMD.and.mybeadid.eq.1) then
-#endif
- Ekin2_tot = Ekin2_tot + amass(j)*v(i3+idim)*v(i3+idim)
- !exp1 = exp(-dt5*thermo(idim,j)%v(1)-dt5*v_lnv*c2_lnv) ! APJ
- exp1 = exp(-dt5*v_lnv*c2_lnv) ! APJ
- else
- !exp1 = exp( -dt5 * thermo(idim,j)%v(1) ) ! APJ
- exp1 = 1.d0 ! APJ
- end if
- exp2 = exp1*exp1
- vold(i3+idim)=v(i3+idim)
- !v(i3+idim) = v(i3+idim) * exp2 + f(i3+idim) * wfac * exp1 ! APJ
- v(i3+idim)=v(i3+idim)*exp2 ! APJ
- f(i3+idim)=f(i3+idim)*exp1 ! APJ
- end do
- i3 = i3+3
- end do
-
- if(ntp>0.and.ipimd.eq.NMPIMD) then
-#ifdef MPI
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,Ekin2_tot,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
-# else
- call mpi_allreduce(Ekin2_tot,mpitmp,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,commworld,ierr)
- Ekin2_tot=mpitmp(1)
-# endif
-#endif
- f_lnv_v = Ekin2_tot*(c2_lnv-1)
- !tmp = exp(-dt5*thermo_lnv%v(1)) ! APJ
- !v_lnv = tmp*(tmp*v_lnv+dtx*(f_lnv_v+f_lnv_p)/mass_lnv) ! APJ
- end if
-
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
- call xdist(f, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- abfqmmm_param%f(1:nr3+iscale)=f(1:nr3+iscale) ! lam81
- end if ! lam81
- call Adaptive_Thermostat_integrate(nchain,thermo,nthermo,dtx,ntp,1) ! APJ
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
- v(1:nr3+iscale)=abfqmmm_param%v(1:nr3+iscale) ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- end if ! lam81
-
-
- else if( gammai == 0.d0 ) then
-
- ! ---Newtonian dynamics:
-
- ! Applying guiding force effect:
- if (isgld > 0) then
- call sgmdw(natom,istart,iend,ntp,dtx,ener,amass,winv,x,f,v)
- end if
-
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dtx
- v(i3+1) = v(i3+1) + f(i3+1)*wfac
- v(i3+2) = v(i3+2) + f(i3+2)*wfac
- v(i3+3) = v(i3+3) + f(i3+3)*wfac
- i3 = i3+3
- end do
-
- else if (isgld > 0) then
- ! Using SGLD algorithm:
- call sgldw(natom,istart,iend,ntp,dtx,temp0,ener,amass,winv,x,f,v)
- else ! gamma_ln .ne. 0, which also implies ntt=3 (see mdread.f)
-
- ! ---simple model for Langevin dynamics, basically taken from
- ! Loncharich, Brooks and Pastor, Biopolymers 32:523-535 (1992),
- ! Eq. 11. (Note that the first term on the rhs of Eq. 11b
- ! should not be there.)
-
- ! Update Langevin parameters, since temp0 might have changed:
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
-# ifdef LES
- sdfacles = sqrt( 4.d0*gammai*boltz2*temp0les/dtx )
-# endif
-
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc == 1) then
- call sc_lngdyn(winv,amass,v,f,sdfac,c_explic,c_implic, &
- istart, iend, nr, dtx)
- else
-#endif
-
-
- if (no_ntt3_sync == 1) then ! APJ
- !We don't worry about synchronizing the random number stream ! APJ
- !across processors. ! APJ
- iskip_start = 0 ! APJ
- iskip_end = 0 ! APJ
- else ! APJ
- ! In order to generate the same sequence of pseudorandom numbers that ! APJ
- ! you would using a single processor you have to go through the atoms ! APJ
- ! in order: skip those that have are being used on other processors ! APJ
- iskip_start = 3*(istart-1) ! APJ
- iskip_end = 3*(nr-iend) ! APJ
-#ifndef LES
- ! Always sync random number stream for PIMD ! APJ
- ! (AWG: not sure if this is required) ! APJ
- if (ipimd>0) then ! APJ
- iskip_start = iskip_start + 3*nr*(mybeadid-1) ! APJ
- iskip_end = iskip_end + 3*nr*(nbead-mybeadid) ! APJ
- end if ! APJ
-#endif
- endif ! APJ
-
- do j=1,iskip_start ! APJ
- ! Skip some random numbers ! APJ
- call gauss( 0.d0, 1.d0, fln ) ! APJ
- end do ! APJ
-
- ! Do Langevin step ! APJ
- i3 = 3*(istart-1) ! APJ
- do j=istart,iend ! APJ
-
- wfac = winv(j) * dtx ! APJ
- aamass = amass(j) ! APJ
-# ifdef LES
- if (temp0les >= 0 .and. temp0 /= temp0les .and. cnum(j) /= 0 ) then ! APJ
- rsd =sdfacles*sqrt(aamass) ! APJ
- else ! APJ
- rsd = sdfac*sqrt(aamass) ! APJ
- endif ! APJ
-# else
- rsd = sdfac*sqrt(aamass) ! APJ
-# endif
- call gauss( 0.d0, rsd, fln ) ! APJ
- v(i3+1) = (v(i3+1)*c_explic + (f(i3+1)+fln)*wfac) * c_implic ! APJ
- call gauss( 0.d0, rsd, fln ) ! APJ
- v(i3+2) = (v(i3+2)*c_explic + (f(i3+2)+fln)*wfac) * c_implic ! APJ
- call gauss( 0.d0, rsd, fln ) ! APJ
- v(i3+3) = (v(i3+3)*c_explic + (f(i3+3)+fln)*wfac) * c_implic ! APJ
-
- i3 = i3 + 3 ! APJ
- end do ! APJ
-
- do j=1,iskip_end ! APJ
- ! Skip some random numbers ! APJ
- call gauss( 0.d0, 1.d0, fln ) ! APJ
- end do ! APJ
-
-
-#ifdef MPI /* SOFT CORE */
- end if ! for (ifsc==1) call sc_lngdyn
-#endif
- end if ! ( gammai == 0.d0 )
-
- ! Update EMAP rigid domains
- if(temap) call emap_move()
-
- ! --- consider vlimit
-
- if (vlim.and.ipimd==0) then
- vmax = 0.0d0
- do i=istart3,iend3
- vmax = max(vmax,abs(v(i)))
- v(i) = sign(min(abs(v(i)),vlimit),v(i))
- end do
-
- ! Only violations on the master node are actually reported
- ! to avoid both MPI communication and non-master writes.
- if (vmax > vlimit) then
- if (master) then
- write(6,'(a,i6,a,f10.4)') 'vlimit exceeded for step ',nstep, &
- '; vmax = ',vmax
- end if
- end if
- end if
-
- do im=1,iscale
- v(nr3+im) = (v(nr3+im) + f(nr3+im)*dtx/scalm)
- end do
-
- ! We do the force dump here if requested, since the 'old' positions are about
- ! to be dumped into the force array...
-
- if (master) then
- ifdump = .false. ! Write forces this step?
- if (ntwf>0) ifdump = mod(total_nstep+1,ntwf) == 0 ! forces
- if (ntwf == -1 .and. mod(total_nstep+1,ntwx) == 0) &
- ifdump = .true. !Combined crdfrc file
- if (abfqmmm_param%abfqmmm == 1) ifdump = .false. ! lam81
-#ifdef MPI
- ! For adaptive QM/MM, only the master does a dump.
- if ( qmmm_nml%vsolv > 1 ) then
- if ( nodeid /= 0 ) then
- ifdump = .false.
- end if
- end if
-
- if (ifdump) then
- call xdist(f, xx(lfrctmp), natom)
- end if
-#endif
- ! Force archive:
- if (ifdump) then
-
-#ifdef MPI
- ! Write out current replica#, exchange#, step#, and mytargettemp
- ! If mdloop==0 this is a normal md run (since REMD never calls corpac
- ! when mdloop==0) and we don't want the REMD header.
- if (mdloop>0.and.loutfm) then
- if (trxsgld) then
- write (MDFRC_UNIT,'(a,4(1x,i8))') "RXSGLD ", repnum, mdloop, &
- total_nstep+1, stagid
- else
- write (MDFRC_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum, mdloop, &
- total_nstep+1, my_remd_data%mytargettemp
- end if
- end if
-#endif
-
- ! ipimd forces will probably not be right if some type of
- ! transformation is necessary. This is from the vel dump code -- keep
- ! it here as a holder in case somebody wants to fix it.
-! if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
-! call corpac(cartvel,1,nrx,MDVEL_UNIT,loutfm)
-! else
- call corpac(f,1,nrx,MDFRC_UNIT,loutfm)
-! endif
- end if
-
- else ! slaves need to participate in force distribution
- ifdump = .false. ! Write forces this step?
- if (ntwf>0) ifdump = mod(total_nstep+1,ntwf) == 0 ! forces
- if (ntwf == -1 .and. mod(total_nstep+1,ntwx) == 0) &
- ifdump = .true. !Combined crdfrc file
- if (abfqmmm_param%abfqmmm == 1) ifdump = .false. ! lam81
-#ifdef MPI
- if (ifdump) call xdist(f, xx(lfrctmp), natom)
-#endif
- end if ! master
- !-------------------------------------------------------------------
- ! Step 3: update the positions, putting the "old" positions into F:
- !-------------------------------------------------------------------
-
-# ifdef LES
- if(ntp>0.and.ipimd.eq.NMPIMD) then
- aa = exp(dt5*v_lnv)
- arg2 = v_lnv*dt5*v_lnv*dt5
- poly = 1.0d0+arg2*(e2+arg2*(e4+arg2*(e6+arg2*e8)))
- endif
-
- i3 = 3*(istart-1)
- do j=istart,iend
- if(ntp>0.and.ipimd.eq.NMPIMD.and.(cnum(j).eq.0.or.cnum(j).eq.1)) then
- do idim = 1, 3
- f(i3+idim)=x(i3+idim)
- x(i3+idim)=aa*(x(i3+idim)*aa+v(i3+idim)*poly*dtx)
- enddo
- else
- do idim = 1, 3
- f(i3+idim) = x(i3+idim)
- x(i3+idim) = x(i3+idim)+v(i3+idim)*dtx
- enddo
- endif
- i3 = i3 + 3
- enddo
-
-# else
-
- if(ntp>0.and.ipimd.eq.NMPIMD.and.mybeadid==1) then
- aa = exp(dt5*v_lnv)
- arg2 = v_lnv*dt5*v_lnv*dt5
- poly = 1.0d0+arg2*(e2+arg2*(e4+arg2*(e6+arg2*e8)))
- do i3=istart3,iend3
- f(i3)=x(i3)
- x(i3)=aa*(x(i3)*aa+v(i3)*poly*dtx)
- end do
- else
- do i3 = istart3, iend3
- f(i3) = x(i3)
- x(i3) = x(i3) + v(i3)*dtx
- end do
- end if
-
-# endif /* LES */
-
- !Nose'-Hoover thermostat (2nd step).
- if ( ntt==4 ) then
- call Thermostat_integrate_2(nchain,thermo,nthermo,dtx,ntp)
- E_nhc = Thermostat_hamiltonian(nchain,thermo,nthermo)
- else if ( ntt>=4 .and. ntt<=8 ) then ! APJ
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- end if ! lam81
- call Adaptive_Thermostat_integrate(nchain,thermo,nthermo,dtx,ntp,2) ! APJ
- if (abfqmmm_param%abfqmmm == 1) then ! lam81
- v(1:nr3+iscale)=abfqmmm_param%v(1:nr3+iscale) ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale)=v(1:nr3+iscale) ! lam81
- end if ! lam81
- E_nhc = Adaptive_Thermostat_hamiltonian(nchain,thermo,nthermo)
- end if
-
- do i = 1,iscale
- f(nr3+i) = x(nr3+i)
- x(nr3+i) = x(nr3+i)+v(nr3+i)*dtx
- end do
-
- call timer_stop(TIME_VERLET)
-
- if (ntc /= 1) then
-
- !-------------------------------------------------------------------
- ! Step 4a: if shake is being used, update the new positions to fix
- ! the bond lengths.
- !-------------------------------------------------------------------
-
- call timer_start(TIME_SHAKE)
- if (isgld > 0) call sgfshake(istart,iend,dtx,amass,x,.false.)
- qspatial=.false.
- call shake(nrp,nbonh,nbona,0,ix(iibh),ix(ijbh),ix(ibellygp), &
- winv,conp,skip,f,x,nitp,belly,ix(iifstwt),ix(noshake), &
- shkh,qspatial)
- call quick3(f,x,ix(iifstwr),natom,nres,ix(i02))
- if(nitp == 0) then
- erstop = .true.
- goto 480
- end if
- ! Including constraint forces in self-guiding force calculation
- if (isgld > 0) call sgfshake(istart,iend,dtx,amass,x,.true.)
-
- ! Need to synchronize coordinates for linearly scaled atoms after shake
-#ifdef MPI
- if( icfe /= 0 ) then
- call timer_barrier( commsander )
- call timer_stop_start(TIME_SHAKE,TIME_DISTCRD)
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call xdist(x, xx(lfrctmp), natom)
- end if
- ! In dual-topology this is done within softcore.f
- if (ifsc /= 1) then
- if( master ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commmaster,ierr)
- else
- if( master ) call sc_sync_x(x,nr3)
- end if
- if( numtasks>1 ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commsander,ierr)
- call timer_stop_start(TIME_DISTCRD,TIME_SHAKE)
- end if
-#endif /* MPI */
- !-----------------------------------------------------------------
- ! Step 4b: Now fix the velocities and calculate KE
- !-----------------------------------------------------------------
-
- ! ---re-estimate the velocities from differences in positions:
-
- if( .not.(ipimd==NMPIMD.and.ipimd==CMD.and.mybeadid.ne.1) ) then
- v(istart3:iend3) = (x(istart3:iend3)-f(istart3:iend3)) * dtxinv
- end if
-
- call timer_stop(TIME_SHAKE)
- end if
- call timer_start(TIME_VERLET)
-
- if(ineb>0.and.(mybeadid==1.or.mybeadid==neb_nbead) ) then
- x(1:3*natom)=f(1:3*natom)
- ! CARLOS: NEB- remove velocities but ONLY for the end beads so V doesn't
- ! accumulate if high forces
- v(1:3*natom)=0.d0
-
- end if
-
- if( ntt == 1 .or. onstep ) then
-
- !-----------------------------------------------------------------
- ! Step 4c: get the KE, either for averaging or for Berendsen:
- !-----------------------------------------------------------------
-
- eke = 0.d0
- ekph = 0.d0
- ekpbs = 0.d0
-#ifdef LES
- ekeles = 0.d0
- ekphles = 0.d0
-#endif
- eke_cmd = 0.d0
-
- if (gammai == 0.0d0) then
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
-#ifdef LES
- if (temp0les < 0.d0) then
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
- ekph = ekph + aamass*v(i3)**2
- if(ipimd.eq.CMD.and.(cnum(j).eq.0.or.cnum(j).eq.1)) then
- eke_cmd = eke_cmd + aamass*0.25d0*(v(i3)+vold(i3))**2
- endif
- else
- if (cnum(j) == 0) then
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
- ekph = ekph + aamass*v(i3)**2
- else
- ekeles = ekeles + aamass*0.25d0*(v(i3)+vold(i3))**2
- ekphles = ekphles + aamass*v(i3)**2
- end if
- end if
-
-#else
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
-
- if(mybeadid==1) then
- eke_cmd = eke_cmd + aamass*0.25d0*(v(i3)+vold(i3))**2
- end if
- ! try pseudo KE from Eq. 4.7b of Pastor, Brooks & Szabo,
- ! Mol. Phys. 65, 1409-1419 (1988):
-
- ekpbs = ekpbs + aamass*v(i3)*vold(i3)
- ekph = ekph + aamass*v(i3)**2
-
-#endif
- end do
- end do
-
- else
-
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
-#ifdef LES
- if (temp0les < 0.d0) then
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- else
- if (cnum(j) == 0) then
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- else
- ekeles = ekeles + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- end if
- end if
-#else
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
-
-#endif
- end do
-
- end do
-
- end if ! (if gammai == 0.0d0)
-
-#ifdef MPI
-
- ! --- sum up the partial kinetic energies:
-
- if ( ipimd.eq.CMD ) then
- call mpi_reduce(eke_cmd,tmp_eke_cmd,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,0,commsander,ierr)
- eke_cmd = tmp_eke_cmd
- endif
-
-# ifdef LES
- !if ( ipimd.eq.CMD ) then
- ! call mpi_reduce(eke_cmd,tmp_eke_cmd,1,MPI_DOUBLE_PRECISION, &
- ! mpi_sum,0,commsander,ierr)
- ! eke_cmd = tmp_eke_cmd
- !endif
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- if ( temp0les < 0 ) then
- mpitmp(1) = eke
- mpitmp(2) = ekph
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,2, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
-# else
- call mpi_allreduce(mpitmp,mpitmp(3),2, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(3)
- ekph = mpitmp(4)
-# endif
- else
- mpitmp(1) = eke
- mpitmp(2) = ekph
- mpitmp(3) = ekeles
- mpitmp(4) = ekphles
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,4, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
- ekeles = mpitmp(3)
- ekphles = mpitmp(4)
-# else
- call mpi_allreduce(mpitmp,mpitmp(5),4, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(5)
- ekph = mpitmp(6)
- ekeles = mpitmp(7)
- ekphles = mpitmp(8)
-# endif
- endif
- end if
-# else
-
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call trace_mpi('mpi_allreduce', &
- 1,'MPI_DOUBLE_PRECISION',mpi_sum)
- mpitmp(1) = eke
- mpitmp(2) = ekph
- mpitmp(3) = ekpbs
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
- ekpbs = mpitmp(3)
-
-# else
-
- call mpi_allreduce(mpitmp,mpitmp(4),3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(4)
- ekph = mpitmp(5)
- ekpbs = mpitmp(6)
-
-# endif
- end if
-# endif
-
- ! Calculate Ekin of the softcore part of the system
- if (ifsc /= 0 ) then
- call calc_softcore_ekin(amass,v,vold,istart,iend)
- sc_ener(13) = sc_ener(6) + sc_ener(12)
- end if
-#endif
-
- ! --- all processors handle the "extra" variables:
-
- do im=1,iscale
- eke = eke + scalm*0.25d0*(v(nr3+im)+vold(nr3+im))**2
- ekpbs = ekpbs + scalm*v(nr3+im)*vold(nr3+im)
- ekph = ekph + scalm*v(nr3+im)**2
- end do
-
- eke = eke * 0.5d0
- ekph = ekph * 0.5d0
- ekpbs = ekpbs * 0.5d0
-#ifdef LES
- ekeles = ekeles * 0.5d0
- ekphles = ekphles * 0.5d0
-#endif
-
- if( ntt == 1 ) then
-#ifdef LES
-
- if (temp0les < 0.d0) then
- scaltp = sqrt(1.d0 + 2.d0*dttp*(ekin0-eke)/(ekmh+ekph))
- else
- scaltp = sqrt(1.d0+2.d0*dttp*(ekinp0-eke)/(ekmh+ekph))
- scaltles = sqrt(1.d0+2.d0*dttp*(ekinles0-ekeles)/(ekmhles+ekphles))
- end if
-#else
-
- ! --- following is from T.E. Cheatham, III and B.R. Brooks,
- ! Theor. Chem. Acc. 99:279, 1998.
-
- scaltp = sqrt(1.d0 + 2.d0*dttp*(ekin0-eke)/(ekmh+ekph))
-
- ! --- following is the "old" (amber7 and before) method:
-
- ! scaltpo = sqrt(1.d0 + dttp*(ekin0/ekph - 1.d0))
- ! write(6,*) 'scaltp: ',2.d0*dttp*(ekin0-eke)/(ekmh+ekph), &
- ! dttp*(ekin0/ekmh - 1.d0)
-
- ! following line reverts to the "old" behavior:
- ! scaltp = scaltpo
-
-#endif
-
-#ifdef MPI /* SOFT CORE */
- if (icfe /= 0) then
- if (ifsc == 1) then
- if (master) then
- ! Linearly combine the scaling factors from both processes
- ! the combined factor is broadcast to all nodes
- ! the subroutine also correctly scales the softcore atom v's
- call mix_temp_scaling(scaltp,clambda,v)
- end if
- call mpi_bcast(scaltp,1,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-#endif
-
- do j = istart,iend
- i3=(j-1)*3+1
-#ifdef LES
- if (temp0les > 0.d0 .and. cnum(j) /= 0 ) then
- v(i3 ) = v(i3 )*scaltles
- v(i3+1) = v(i3+1)*scaltles
- v(i3+2) = v(i3+2)*scaltles
- else
- v(i3 ) = v(i3 ) *scaltp
- v(i3+1) = v(i3+1) *scaltp
- v(i3+2) = v(i3+2) *scaltp
- end if
-#else
- v(i3 ) = v(i3 ) *scaltp
- v(i3+1) = v(i3+1) *scaltp
- v(i3+2) = v(i3+2) *scaltp
-#endif
- end do
- do im=1,iscale
- v(nr3+im) = v(nr3+im)*scaltp
- end do
- end if ! (ntt == 1 )
-
- end if ! ( ntt == 1 .or. onstep; end of step 4c )
-
- !-----------------------------------------------------------------
- ! Step 5: several tasks related to dumping of trajectory information
- !-----------------------------------------------------------------
-
- itdump = .false. ! Write coordinates this step?
- ivdump = .false. ! Write velocities this step?
- ifdump = .false. ! Write forces this step? lam81
- ixdump = .false. ! Write restart this step?
- ifdump = .false. ! Write forces this step?
- ivscm = .false. ! Do com removal this step?
-#ifdef RISMSANDER
- irismdump = .false. ! Write RISM files this step?
-#endif
-
- ! --- Determine if trajectory, velocity, or restart
- ! writing is imminent, or if the center of mass
- ! motion will be removed.
- ! These require xdist of velocities or dipoles in parallel runs:
- !
- ! Modified so that when running REMD, writing can occur less often
- ! than exchanges (e.g. ntwx > nstlim)
- ! DAN ROE: Added two new variables, total_nstep and total_nstlim.
- ! For non-REMD runs, total_nstep=nstep+1 and total_nstlim=nstlim
- ! just like before.
- ! For REMD runs, total_nstep=(mdloop-1)*nstlim+nstep+1, where
- ! mdloop is the current exchange - this is the current
- ! replica exchange MD step. total_nstlim=numexchg*nstlim, which is
- ! the maximum number of REMD steps.
- total_nstep=nstep+1
- total_nstlim=nstlim
- if(abfqmmm_param%abfqmmm == 1) total_nstep=abfqmmm_param%qmstep ! lam81
-
-#ifdef MPI
- if (rem /= 0) then
- total_nstep = (mdloop - 1) * nstlim + nstep + 1
- total_nstlim = nstlim * numexchg
- endif
-#endif
- if (ntwx>0) itdump = mod(total_nstep,ntwx) == 0 ! Trajectory coords
- if (ntwv>0) ivdump = mod(total_nstep,ntwv) == 0 ! Velocity
- if (ntwf>0) ifdump = mod(total_nstep,ntwf) == 0 ! Force
- if( ntwr /= 0 ) then
- if ( mod(total_nstep, ntwr ) == 0 ) ixdump = .true. ! Restart
- endif
- if( total_nstep >= total_nstlim ) ixdump = .true. ! Final restart
- if ( nscm > 0 ) then
- if( mod(total_nstep,nscm) == 0 ) ivscm =.true. ! C.o.M. removal
- end if
- if (ntwv == -1 .and. itdump) ivdump = .true. !Combined crdvel file
-
-#ifdef MPI
- ! adaptive QM/MM via multisander
- ! all groups have identical coords and velocities
- ! only master of first group needs to dump results
- ! We have to leave the dump values for all threads in the group, though
- ! since for dumping the coords, these are broadcast within the group
- ! (see call to xdist() below)
- if ( qmmm_nml%vsolv > 1 ) then
- if ( nodeid /= 0 ) then
- ixdump = .false.
- itdump = .false.
- ivdump = .false.
- end if
- end if
-#endif
-
-#ifdef RISMSANDER
- if(rismprm%irism ==1)then
- if(rismprm%ntwrism > 0 )then
- irismdump = mod(nstep+1,rismprm%ntwrism) == 0
- if( nstep+1 >= nstlim ) then !! do we want to do this?
- irismdump = .true.
- end if
- end if
- end if
-#endif
-
-
-#ifdef MPI
-
- !-----------------------------------------------------------------
- ! --- now distribute the coordinates, and if necessary, dipoles and vel:
- !-----------------------------------------------------------------
-
- call timer_barrier( commsander )
- call timer_stop_start(TIME_VERLET,TIME_DISTCRD)
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call xdist(x, xx(lfrctmp), natom)
- end if
- ! dac/knut change: force the coordinates to be the same on both masters.
- ! For certain compilers, addition may not be strictly commutative, so
- ! the forces on group 0 may be different by roundoff from the forces on
- ! group 1. This can lead to divergent trajectories. The interval at
- ! which they are resynchronized is hard-wired here to 20, which seems to
- ! work fine in our tests.
- ! jwk change: coordinates are synchronized when shake is enabled above
- if( icfe /= 0 .and. mod(nstep+1,20) == 0 .and. ntc == 1 ) then
-
- ! In dual-topology this is done within softcore.f
- if (ifsc /= 1) then
- if( master ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commmaster,ierr)
- else
- if( master ) then
- call sc_compare(x,nr3,'CRD') ! first, check if coordinates have desynced
- if (numtasks==1 ) call sc_compare(v,nr3,'VEL') ! do the same for velocities
- call sc_sync_x(x,nr3) ! then resync them
- end if
- end if
- if( numtasks>1 ) call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION, &
- 0,commsander,ierr)
- end if
- call timer_stop(TIME_DISTCRD)
-
-#endif /* MPI */
-
- ! ----fix lone pair positions:
- if( numextra > 0 )call local_to_global(x,xx,ix)
-
-#ifdef MPI
- if ( .not. mpi_orig .and. numtasks > 1 ) then
- call timer_start(TIME_DISTCRD)
-
- ! ---Here we provide every processor a full copy of the velocities
- ! for removal of center of mass motion, or for archiving.
- ! (Note: this is actually over-kill: for example, only the master
- ! node really needs the velocities for archiving. But the extra
- ! overhead of doing it this way is probably small in most cases.)
-
- if( ivdump .or. ivscm .or. ixdump ) then
- call xdist(v, xx(lfrctmp), natom)
- endif
-
-! M-WJ
-! if( ixdump .and. (induced == 1 .and. indmeth == 3 ) )then
- if( ixdump .and. (induced > 0 .and. indmeth == 3 ) )then
-!
- call xdist(xx(ldipvel), xx(lfrctmp), natom)
- call xdist(xx(linddip), xx(lfrctmp), natom)
- end if
- call timer_stop(TIME_DISTCRD)
- end if
- call timer_start(TIME_VERLET)
-
- ! ========================= END AMBER/MPI =========================
-#endif /* MPI */
-
- !-------------------------------------------------------------------
- ! Step 6: zero COM velocity if requested; used for preventing
- ! ewald "block of ice flying thru space" phenomenon, or accumulation
- ! of rotational momentum in vacuum simulations
- !-------------------------------------------------------------------
-
- if (ivscm) then
- if (mod(nstep,nsnb) == 0) ntnb = 1
- if( ifbox == 0 ) then
- if (is_langevin) then
- ! Get current center of the system
- call get_position(nr,x,vcmx,vcmy,vcmz,sysrange,0)
-
-#ifdef MMPI /* SOFT CORE */
- if (ifsc == 1) call sc_mix_position(vcmx,vcmy,vcmz,clambda)
-#endif
- ! Center the system to the original center
- call re_position(nr,ntr,x,xc, &
- vcmx,vcmy,vcmz,sysx,sysy,sysz,sysrange,mv_flag,0)
- else
- ! ---Non-periodic simulation: remove both translation and rotation.
- ! Back the coords up 1/2 step, so that the correspond to the
- ! velocities; temporarily store in the F() array:
- f(1:nr3) = x(1:nr3) - v(1:nr3)*dt5
- ! --- now compute the com motion, remove it, and recompute (just
- ! to check that it is really gone.....)
- call cenmas(nr,f,v,amass,ekcm,xcm,vcm,acm,ekrot,ocm,4)
- call stopcm(nr,f,v,xcm,vcm,ocm, .true.)
- call cenmas(nr,f,v,amass,ekcm,xcm,vcm,acm,ekrot,ocm,4)
- end if
- else
- if (.not. is_langevin) then
- ! ---Periodic simulation: just remove the translational velocity:
- vcmx = 0.d0
- vcmy = 0.d0
- vcmz = 0.d0
- j = 1
- do i = 1, 3*natom,3
- aamass = amass(j)
- vcmx = vcmx + aamass * v(i)
- vcmy = vcmy + aamass * v(i+1)
- vcmz = vcmz + aamass * v(i+2)
- j = j + 1
- end do
- vcmx = vcmx * tmassinv
- vcmy = vcmy * tmassinv
- vcmz = vcmz * tmassinv
- vel2 = vcmx*vcmx + vcmy*vcmy + vcmz*vcmz
- atempdrop = 0.5d0 * tmass * vel2 * onefac(1) !onefac(1) = 1.0d0/fac(1)
- vel = sqrt(vel2)
- if ( master ) write (6,'(a,f15.6,f9.2,a)') &
- 'check COM velocity, temp: ',vel,atempdrop, '(Removed)'
- do i = 1, 3*natom, 3
- v(i) = v(i) - vcmx
- v(i+1) = v(i+1) - vcmy
- v(i+2) = v(i+2) - vcmz
- end do
-
-#ifdef MPI /* SOFT CORE */
- if (icfe==1) then
- if (ifsc==1) then
- if (master) then
- call sc_mix_velocities(v,nr3,clambda)
- end if
- call mpi_bcast(v,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
-#endif
- end if ! (.not. is_langevin)
- end if ! ( ifbox == 0 )
- end if ! (ivscm)
-
- ! Also zero out the non-moving velocities if a belly is active:
- if (belly) call bellyf(nr,ix(ibellygp),v)
-
- !-----------------------------------------------------------------
- ! --- put current velocities into VOLD
- !-----------------------------------------------------------------
-
- vold(istart3:iend3) = v(istart3:iend3)
- do im=1,iscale
- vold(nr3+im) = v(nr3+im)
- end do
-
- !-------------------------------------------------------------------
- ! Step 7: scale coordinates if NPT with Berendsen barostat:
- !-------------------------------------------------------------------
- if( ntp > 0 .and. ipimd > 0 .and. barostat == 1 ) then
- x_lnv_old = x_lnv
- x_lnv = x_lnv_old + v_lnv * dtx
- rmu(1:3) = exp( ( x_lnv - x_lnv_old ) )
- box(1:3) = box(1:3) * rmu(1:3)
- volume = box(1) * box(2) * box(3)
- ener%box(1:3) = box(1:3)
- ! only for NMPIMD in sander.LES
- ! (in sander.MPI volume, pressure and density printed in pimdout)
-#ifdef LES
- ener%volume = volume
-#else
- ener%volume = 0.
- totener%volume = volume
-#endif
- call redo_ucell(rmu)
- call fill_tranvec()
- call ew_pscale(natom,x,amass,nspm,nsp,2)
- end if
-
- if( iamoeba == 0 .and. barostat == 1 ) then
-
- ! ntp = 1, isotropic pressure coupling
-
- if (ntp == 1) then
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(4)))**third
- rmu(2) = rmu(1)
- rmu(3) = rmu(1)
-
-
- ! ntp = 2, anisotropic pressure scaling
-
- else if (ntp == 2) then
-
- if (csurften > 0) then
-
- ! Constant surface tension adjusts the tangential pressures
- ! See Zhang, Feller, Brooks, Pastor. J. Chem. Phys. 1995
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
-
- end if
-
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- else
-
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(1)))**third
- rmu(2) = (1.d0-dtcp*(pres0-ener%pres(2)))**third
- rmu(3) = (1.d0-dtcp*(pres0-ener%pres(3)))**third
-
- end if
-
- ! ntp = 3, semiisotropic pressure coupling
- ! (currently only for csurften>0, constant surface tension)
-
- !else if (ntp > 2) then
- else
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
- press_tan_ave = (ener%pres(2) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(2))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- end if
- end if
- ! Add semiisotropic pressure scaling in any direction with no constant
- ! surface tension here
- end if
-
- if (ntp > 0) then
- box(1:3) = box(1:3)*rmu(1:3)
- ener%box(1:3) = box(1:3)
-
- ! WARNING!! This is not correct for non-orthogonal boxes if
- ! NTP > 1 (i.e. non-isotropic scaling). Currently general cell
- ! updates which allow cell angles to change are not implemented.
- ! The viral tensor computed for ewald is the general Nose Klein,
- ! however the cell response needs a more general treatment.
-
- call redo_ucell(rmu)
- ! keep tranvec up to date, rather than recomputing each MD step.
- call fill_tranvec() ! tranvec is dependent on only ucell
-
-#ifdef MPI /* SOFT CORE */
- ! if softcore potentials and the dual topology approach are used
- ! C.O.M. scaling has to be changed to account for different masses
- ! of the same molecule in V0 and V1. This is quite inefficient and is
- ! therefore done in a separate routine in softcore.f
- ! only both masters actually do the computation for ifsc==1
- ! the scaled coordinates are then broadcast to the nodes
- if (icfe /= 0 .and. ifsc == 1) then
- if (master) then
- call sc_pscale(natom,x,amass,nspm,nsp,oldrecip,ucell)
- end if
- call mpi_bcast(x,nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- else
-#endif
- call ew_pscale(natom,x,amass,nspm,nsp,npscal)
-#ifdef MPI /* SOFT CORE */
- end if
-#endif
- if (ntr > 0 .and. nrc > 0) &
- call ew_pscale(natom,xc,amass,nspm,nsp,npscal)
- endif
- if (ipimd==NMPIMD.and.ntp>0) then
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = pressure*pconv
- endif
- else if (barostat == 1) then
- if (ntp>0) then
- if (ipimd==0) then ! for classical AMOEBA
- ener%cmt(4) = eke ! for printing in prntmd()
- ener%vir(4) = ener%vir(1) + ener%vir(2) + ener%vir(3)
- ener%pres(4) = (pressure_constant/volume)*(2.d0*eke - ener%vir(4)) / 3.d0
- elseif (ipimd==NMPIMD) then ! for NMPIMD AMOEBA
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = pressure*pconv
- endif
- call AM_RUNMD_scale_cell(natom,ener%pres(4),dt,pres0,taup,x)
- call fill_tranvec()
- end if
- end if
-
-#ifdef LES
- ener%kin%solt = eke
- ener%kin%solv = ekeles
- ener%kin%tot = ener%kin%solt + ener%kin%solv
- if (ntt == 1 .and. onstep) then
- if ( temp0les < 0 ) then
- ekmh = max(ekph,fac(1)*10.d0)
- else
- ekmh = max(ekph,fac(2)*10.d0)
- ekmhles = max(ekphles,fac(3)*10.d0)
- endif
- end if
-
- if( ipimd > 0 ) then
- ener%kin%solv = equal_part + Epot_deriv ! "virial" estimate of KE
- ener%tot = ener%kin%solv + ener%pot%tot
- endif
-#else
- if( ipimd > 0 ) then
- ! use a "virial" estimator for the KE, rather than one derived from the
- ! bead velocities:
- totener%kin%solv = equal_part + Epot_deriv
- else
- ener%kin%solv = ekpbs + ener%pot%tot
- ! Pastor, Brooks, Szabo conserved quantity
- ! for harmonic oscillator: Eq. 4.7b of Mol.
- ! Phys. 65:1409-1419, 1988
- endif
- ener%kin%solt = eke
- ener%kin%tot = ener%kin%solt
- if (ntt == 1 .and. onstep) then
- ekmh = max(ekph,fac(1)*10.d0)
- end if
-#endif
-
- ! ---if velocities were reset, the KE is not accurate; fudge it
- ! here to keep the same total energy as on the previous step.
- ! Note that this only affects printout and averages for Etot
- ! and KE -- it has no effect on the trajectory, or on any averages
- ! of potential energy terms.
-
- if( resetvelo ) ener%kin%tot = etot_save - ener%pot%tot
-
- ! --- total energy is sum of KE + PE:
-
- if( ipimd > 0 ) then
- totener%tot = totener%kin%solv + totener%pot%tot
- etot_save = totener%kin%tot + totener%pot%tot
- if (ipimd==CMD) then
- etot_cmd = eke_cmd*0.5 + ener%pot%tot
-
- totener%tot= etot_cmd
-
- ener%tot = etot_cmd
- ener%kin%tot = eke_cmd*0.5
- ener%kin%solv = ener%kin%tot
- endif
- else
- ener%tot = ener%kin%tot + ener%pot%tot
- etot_save = ener%tot
- end if
-
- !-------------------------------------------------------------------
- ! Step 8: update the step counter and the integration time:
- !-------------------------------------------------------------------
-
- if(abfqmmm_param%abfqmmm /= 1) then ! lam81
- nstep = nstep+1
- t = t+dt
- end if ! lam81
-
- !For CMD
- if ( ipimd==CMD ) then
- nstep_cmd = nstep_cmd + 1
- t_cmd = t_cmd + dt
- end if
-
- ! ---full energies are only calculated every nrespa steps
- ! nvalid is the number of steps where all energies are calculated
-
- if (onstep .or. aqmmm_flag > 0) then
- nvalid = nvalid + 1
- ! Update all elements of these sequence types
- enert = enert + ener
- enert2 = enert2 + (ener*ener)
-#ifdef MPI
- if( ievb /= 0 ) then
- evb_nrg_ave(:) = evb_nrg_ave(:) + evb_nrg(:)
- evb_nrg_rms(:) = evb_nrg_rms(:) + evb_nrg(:)**2
- endif
- if ( ifsc /= 0 ) then
- sc_ener_ave(1:ti_ene_cnt) = sc_ener_ave(1:ti_ene_cnt) + sc_ener(1:ti_ene_cnt)
- sc_ener_rms(1:ti_ene_cnt) = sc_ener_rms(1:ti_ene_cnt) + sc_ener(1:ti_ene_cnt)**2
- end if
-#endif
- if( nvalid == 1 ) etot_start = ener%tot
-
-#ifndef LES
- if ( ipimd>0 .or. ineb>0 ) then
-# ifdef MPI
- if (master) call mpi_reduce(ener%kin%tot,totener%kin%tot,1,MPI_DOUBLE_PRECISION, &
- mpi_sum,0,commmaster,ierr)
-
-# endif
- endif
-
- ! Passing of dvdl=dV/dl for TI w.r.t. mass
- ! Note that ener(39) (in runmd and mix_frcti) =
- ! = ener(17) = ene(21) (in force). All denote dvdl.
- ! Note, ener() is now historical, MJW Feb 2010
- if (ipimd>0 .and. itimass>0) totener%pot%dvdl = ener%pot%dvdl
-
- if(ipimd.eq.NMPIMD.and.ntp>0) then
- totener%pres(4) = pressure * pconv
- totener%density = tmass / (0.602204d0*volume)
- endif
- if(ipimd.eq.CMD) then
- totener%kin%tot = eke_cmd*0.5d0
- totener%kin%solv = totener%kin%tot
- totener%tot = totener%kin%tot + totener%pot%tot
- endif
- totenert = totenert + totener
- totenert2 = totenert2 + (totener*totener)
-
-#endif /* LES */
-
- kinetic_E_save(2) = kinetic_E_save(1)
- kinetic_E_save(1) = ener%kin%tot
-
- end if
-
- ! added for rbornstat
-!!FIX: TL - do we need to put in rismnrespa here?
- if (mod(irespa,nrespai) == 0 .or. irespa < 2) nvalidi = nvalidi + 1
-
- ntnb = 0
- if (mod(nstep,nsnb) == 0) ntnb = 1
-
- ! Since nstep has been incremented, total_nstep is now equal to
- ! (mdloop-1)*nstlim+nstep for REMD and nstep for MD.
- lout = mod(total_nstep,ntpr) == 0 .and. onstep
-
- irespa = irespa + 1
-
- ! reset pb-related flags
-#ifdef MPI
- if(mytaskid == 0)then
-#endif
- if ( igb == 10 .or. ipb /= 0 ) then
- if ( mod(nstep,npbgrid) == 0 .and. nstep /= nstlim ) pbgrid = .true.
- if ( mod(nstep,ntpr) == 0 .or. nstep == nstlim ) pbprint = .true.
- if ( mod(nstep,nsnbr) == 0 .and. nstep /= nstlim ) ntnbr = 1
- if ( mod(nstep,nsnba) == 0 .and. nstep /= nstlim ) ntnba = 1
- end if
-#ifdef MPI
- endif
-#endif
-
- !-------------------------------------------------------------------
- ! Step 9: output from this step if required:
- !-------------------------------------------------------------------
-
-#ifdef RISMSANDER
- !some 3D-RISM files require all processes to participate in output
- !due to the distributed memory
- ! RISM archive:
- if(rismprm%irism==1)then
-!!$ if(irismdump)&
-!!$ call rism_writeSolvDistF(rism_3d,nstep)
- ! combined thermodynamics and distribution output
- ! Execute if we need to do either
- if(irismdump .or. (rism_calc_type(nstep) == RISM_FULL &
- .and. rismprm%write_thermo==1 .and. lout))&
- call rism_solvdist_thermo_calc(irismdump,nstep)
- endif
-#endif
-
- ! ...only the master needs to do the output
- if (ixdump) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- call trans_vel_nmode_to_cart(v,cartvel)
- endif
- endif
-
- if (itdump) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call trans_pos_nmode_to_cart(x,cartpos)
- endif
-!AMD Flush amdlog file
- if(iamd.gt.0)then
-# ifdef MPI
- if (worldrank.eq.0) &
-# endif
- call write_amd_weights(ntwx,total_nstep)
- end if
-!scaledMD Flush scaledMDlog file
- if(scaledMD.gt.0)then
-# ifdef MPI
- if (worldrank.eq.0) &
-# endif
- call write_scaledMD_log(ntwx,total_nstep)
- end if
-
- endif
-
- if (ivdump) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call trans_vel_nmode_to_cart(v,cartvel)
- endif
- endif
-
-
- if (master) then
-
- ! -- restrt:
-
- if (ixdump) then
-
- ! NOTE - This assumes that if numextra > 0, then velocities are
- ! found in the array v...
- if (numextra > 0) call zero_extra_pnts_vec(v,ix)
-
- if( iwrap == 0 ) then
- nr = nrp
-#ifdef LES
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- cartpos,cartvel,xx(lcrdr),box,t,temp0)
- else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- x,v,xx(lcrdr),box,t,temp0les)
- endif
-#else
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- cartpos,cartvel,xx(lcrdr),box,t,rem_val)
- else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- x,v,xx(lcrdr),box,t,rem_val)
- endif
-#endif
- else if (iwrap == 1) then
-
- ! --- use temp. array to hold coords. so that the master's values
- ! are always identical to those on all other nodes:
-
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1)=cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- end if
-
- call wrap_molecules(nspm,nsp,r_stack(l_temp))
- if(ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
- nr = nrp
-#ifdef LES
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,temp0les)
-#else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,rem_val)
-#endif
- call free_stack(l_temp,routine)
- else if (iwrap == 2) then
- ! GMS ------------------------------------------
- ! We are wrapping around a pre-determined mask
- ! Need to center it on the mask COM first, then
- ! wrap it normally as it happens on the iwrap=1
- ! case.
- ! GMS ------------------------------------------
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1)=cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- end if
- nr = nrp
-
- ! Now, wrap the coordinates around the iwrap_mask:
- call iwrap2(n_iwrap_mask_atoms,iwrap_mask_atoms,r_stack(l_temp), &
- box_center)
-#ifdef LES
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,temp0les)
-#else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, &
- r_stack(l_temp),v,xx(lcrdr),box,t,rem_val)
-#endif
- call free_stack(l_temp,routine)
- end if ! ( iwrap == 0 )
-
-! M-WJ
-! if( igb == 0 .and. induced == 1 .and. indmeth == 3) &
- if( igb == 0 .and. ipb == 0 .and. induced > 0 .and. indmeth == 3) &
-!
- call wrt_dips(xx(linddip),xx(ldipvel),nr,t,title)
-
- if (icnstph /= 0 .and. ((rem /= 0 .and. mdloop > 0) .or. rem == 0)) then
- call cnstphwriterestart(chrgdat)
- end if
-
- end if ! (ixdump)
-
- ! -- Coordinate archive:
- ! For formatted writes and replica exchange, write out a header line.
-
- if (itdump) then
-#ifdef MPI
- ! Write out current replica#, exchange#, step#, and mytargettemp
- ! If mdloop==0 this is a normal md run (since REMD never calls corpac
- ! when mdloop==0) and we don't want the REMD header.
- ! total_nstep is set in step 5.
- if (mdloop > 0 .and. loutfm) then
- if (trxsgld) then
- write (MDCRD_UNIT,'(a,4(1x,i8))') "RXSGLD ", repnum, mdloop, &
- total_nstep, stagid
- else
- write (MDCRD_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum, mdloop, &
- total_nstep, my_remd_data%mytargettemp
- end if
- end if
-#endif
-
- if( iwrap == 0 ) then
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call corpac(cartpos,1,nrx,MDCRD_UNIT,loutfm)
- else
- call corpac(x,1,nrx,MDCRD_UNIT,loutfm)
- endif
- if(ntb > 0) call corpac(box,1,3,MDCRD_UNIT,loutfm)
- else if (iwrap == 1) then
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1) = cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- endif
-
- call wrap_molecules(nspm,nsp,r_stack(l_temp))
- if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
-
- call corpac(r_stack(l_temp),1,nrx,MDCRD_UNIT,loutfm)
- call corpac(box,1,3,MDCRD_UNIT,loutfm)
- call free_stack(l_temp,routine)
- else if (iwrap == 2) then
- ! GMS ------------------------------------------
- ! We are wrapping around a pre-determined mask
- ! Need to center it on the mask COM first, then
- ! wrap it normally as it happens on the iwrap=1
- ! case.
- ! GMS ------------------------------------------
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- do iatom=1,natom
- do m=1,3
- r_stack(l_temp+3*(iatom-1)+m-1) = cartpos(m,iatom)
- end do
- end do
- else
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
- endif
-
- call iwrap2(n_iwrap_mask_atoms,iwrap_mask_atoms, r_stack(l_temp), &
- box_center)
-
- call corpac(r_stack(l_temp),1,nrx,MDCRD_UNIT,loutfm)
- call corpac(box,1,3,MDCRD_UNIT,loutfm)
- call free_stack(l_temp,routine)
-
-
- end if ! if (iwrap == 0) ...
-
-
- !GMS: If using variable QM solvent, try to write a new pdb file
- ! with the QM coordinates for this step. This is done here
- ! to keep the PDB file in sync with the mdcrd file, which
- ! makes it easier to check later.
- if (qmmm_nml%vsolv > 0 .and. qmmm_nml%verbosity == 0) &
- call qm_print_coords(nstep,.false.)
- end if ! (itdump)
-
- ! Velocity archive:
-
- if (ivdump) then
-
- ! NOTE - This assumes that if numextra > 0, then velocities are
- ! found in the array v...
- if (numextra > 0) call zero_extra_pnts_vec(v,ix)
-
-#ifdef MPI
- ! Write out current replica#, exchange#, step#, and mytargettemp
- ! If mdloop==0 this is a normal md run (since REMD never calls corpac
- ! when mdloop==0) and we don't want the REMD header.
- if (mdloop>0.and.loutfm) then
- if (trxsgld) then
- write (MDVEL_UNIT,'(a,4(1x,i8))') "RXSGLD ", repnum, mdloop, &
- total_nstep, stagid
- else
- write (MDVEL_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum, mdloop, &
- total_nstep, my_remd_data%mytargettemp
- end if
- end if
-#endif
-
- if(ipimd.eq.NMPIMD.or.ipimd.eq.CMD) then
- call corpac(cartvel,1,nrx,MDVEL_UNIT,loutfm)
- else
- call corpac(v,1,nrx,MDVEL_UNIT,loutfm)
- endif
- end if
- ! Force archive lam81
- if (ifdump .and. (abfqmmm_param%abfqmmm == 1)) call corpac(for,1,nrx,MDFRC_UNIT,loutfm) ! lam81
-
- ! Energy archive:
- ! (total_nstep set in Step 5.)
- if (ntwe > 0) then
- if (mod(total_nstep,ntwe) == 0.and.onstep) &
- call mdeng(15,nstep,t,ener,onefac,ntp,csurften)
- end if
-
- if (ioutfm > 0) then
- if (itdump) call end_binary_frame(MDCRD_UNIT)
- if (ivdump .and. ntwv>0 ) call end_binary_frame(MDVEL_UNIT)
- if (ifdump .and. ntwf>0 ) call end_binary_frame(MDFRC_UNIT)
- end if
-
-#ifdef MPI
- if( ievb /= 0 ) call out_evb ( nstep )
-#endif
-
- ! General printed output:
-
- if (lout) then
- if (facc /= 'A') rewind(7)
-
- ! Conserved quantity for Nose'-Hoover based thermostats. ! APJ
- if (ipimd.eq.0 .and. ntt > 4 .and. ntt <= 8 ) then ! APJ
- Econserved = ener%kin%tot + ener%pot%tot + E_nhc ! APJ
- if( ntp>0 ) Econserved = Econserved + pres0 / pconv * volume ! APJ
-# ifdef MPI
- if ( worldrank.eq.0 ) & ! APJ
-# endif
- write(file_nhc,'(I10,F14.4)') nstep, Econserved ! APJ
- endif ! APJ
-#ifdef LES
- if (ipimd>0.and.ntt==4) then
- Econserved = ener%kin%tot + ener%pot%tot + E_nhc
- Econserved = Econserved + Epot_spring
- if( ntp>0 ) Econserved = Econserved + pres0 / pconv * volume
- write(file_nhc,'(I10,F14.4)') nstep, Econserved
- endif
- if ( ipimd.eq.CMD ) then
- ener%kin%tot = eke_cmd*0.5d0
- ener%kin%solv = ener%kin%tot
- ener%tot = ener%kin%tot + ener%pot%tot
-
- end if
-#else
- if ( ipimd>0 ) then
- ener%tot = 0.d0
- ener%kin%tot = 0.d0
- ! Conserved quantity for Nose'-Hoover thermostat.
- if ( ntt==4 ) then
- Econserved = totener%kin%tot + totener%pot%tot + E_nhc
- Econserved = Econserved + Epot_spring
- if ( ntp>0 ) Econserved=Econserved+pres0/pconv*volume
-# ifdef MPI
- if ( worldrank.eq.0 ) &
-# endif
- write(file_nhc,'(I10,F14.4)') nstep, Econserved
- endif
-# ifdef MPI
- if(worldrank.eq.0) &
-# endif
- call pimd_report(nstep,t,pimd_unit,totener,onefac)
- end if
-#endif /* LES */
- call prntmd(total_nstep,nitp,nits,t,ener,onefac,7,.false.)
-
-# ifdef MPI
- ! print corrected energy for adaptive qm/mm runs
- ! note: nstep has already been increased here
- ! (it was not increased when adaptive_qmmm() was called above)
- if ( qmmm_nml%vsolv > 1 ) then
-
- if ( masterrank == 0 ) then
-
- if (aqmmm_flag > 0 .and. nstep > aqmmm_flag) then
-
- etotcorr = corrected_energy + kinetic_E_save(aqmmm_flag)
- nstepadc = nstep - aqmmm_flag + 1
- tadc = t - dt * (dble( aqmmm_flag - 1) )
-
- write(6,'(a)')' Adaptive QM/MM energies:'
- write(6,'(x,a,i5,x,a,f11.4,x,2(a,f15.4,x))') &
- 'adQMMM STEP=', nstepadc, &
- 'TIME(PS)=', tadc, &
- 'ETC=', etotcorr, &
- 'EPC=', corrected_energy
-
- ! print total energy for adaptive qm/mm into a separate file
- ! when qmmm_vsolv%verbosity > 0
- ! set reference energy to zero only for energy dumping purposes
- if (flag_first_energy) then
- flag_first_energy = .false.
- adqmmm_first_energy = etotcorr
- etotcorr = 0.0d0
- else
- etotcorr = etotcorr - adqmmm_first_energy
- end if
-
- if (qmmm_vsolv%verbosity > 0) then
- open(80,file='adqmmm_tot_energy.dat',position='append')
- write(80,'(i9,5x,f11.4,5x,f15.4)') nstepadc, tadc, etotcorr
- close(80)
- end if
-
- end if
- end if
- end if
-# endif
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener)
- if (ifsc /= 0) call sc_print_energies(7, sc_ener)
-#endif
- if ( ifcr > 0 .and. crprintcharges > 0 ) then
- call cr_print_charge( xx(l15), total_nstep )
- end if
-
- ! Output for CMD.
-#ifdef LES
- if (ipimd.eq.CMD) then
-
- ncmd = 0
- do iatom = 1, natom
- if ( cnum(iatom)==0 .or. cnum(iatom)==1 ) then
- xcmd(ncmd+1) = x(3*iatom-2)
- xcmd(ncmd+2) = x(3*iatom-1)
- xcmd(ncmd+3) = x(3*iatom)
- vcmd(ncmd+1) = v(3*iatom-2)
- vcmd(ncmd+2) = v(3*iatom-1)
- vcmd(ncmd+3) = v(3*iatom)
- ncmd = ncmd+3
- endif
- enddo
- write(file_pos_cmd,'(10f8.3)') xcmd(1:ncmd)
- write(file_vel_cmd,'(10f8.3)') vcmd(1:ncmd)
- write(file_pos_cmd,'(10f8.3)') box(1:3)
-
- eke_cmd = eke_cmd * 0.5d0
- etot_cmd = eke_cmd + ener%pot%tot
-
- if (eq_cmd) then
- temp_cmd = eke_cmd/boltz2/dble(3*natomCL)
- else
- temp_cmd = eke_cmd/boltz2/dble(3*(natomCL-1))
- endif
-
- endif
-#else
- if (ipimd.eq.CMD.and.mybeadid.eq.1) then
- write(file_pos_cmd,'(10f8.3)') x(1:3*natom)
- write(file_vel_cmd,'(10f8.3)') v(1:3*natom)
- write(file_pos_cmd,'(10f8.3)') box(1:3)
-
- eke_cmd = eke_cmd * 0.5d0
- etot_cmd = eke_cmd + totener%pot%tot
-
- if (eq_cmd) then
- temp_cmd = eke_cmd/boltz2/dble(3*natom)
- else
- temp_cmd = eke_cmd/boltz2/dble(3*(natom-1))
- endif
- end if
-#endif /* LES */
-
- !--- Print QMMM Muliken Charges if needed ---
- if (qmmm_nml%ifqnt) then
- if (qmmm_nml%printcharges .and. qmmm_mpi%commqmmm_master) then
- call qm2_print_charges(nstep,qmmm_nml%dftb_chg,qmmm_struct%nquant_nlink, &
- qm2_struct%scf_mchg,qmmm_struct%iqm_atomic_numbers)
- end if
- end if
- if (qmmm_nml%printdipole /= 0) then
- call qmmm_dipole(x,xx(Lmass),ix(i02),ih(m02),nres)
- end if
-
- !--- BEGIN DIPOLE PRINTING CODE ---
-
- ! RCW 2nd Dec 2003 - also output dipole information if
- ! the dipoles namelist has been specified and corresponding
- ! groups defined.
-
- ! Check input unit 5 for namelist dipoles
- ! We expect to find &dipoles followed by a group
- ! specification of the dipoles to output.
- call nmlsrc('dipoles',5,prndipfind)
-
- if(prndipfind /= 0 ) then
- !We calculate the dipoles
- write(6,*) '------------------------------- DIPOLE INFO ----------------------------------'
- write(6,9018) nstep,t
- 9018 format(/1x, 'NSTEP =',i7,1x,'TIME(PS) =',f10.3)
-
- !Get the groups for the dipoles - Ideally we only really want
- !to call this the once but for the time being I will call it
- !every time
-
- read (5,'(a)') prndiptest
-
- call rgroup(natom,natc,nres,prndipngrp,ix(i02),ih(m02), &
- ih(m04),ih(m06),ih(m08),ix(icnstrgp), &
- jgroup,indx,irespw,npdec, &
- xx(l60),xx(lcrdr),0,0,0,idecomp,5,.false.)
-
- ! Need to rewind input file after rgroup so it is available
- ! when we next loop through
-
- rewind(5)
-
- if(prndipngrp > 0) then
- !prndipngrp - holds number of groups specified + 1
- !ix(icnstrgp) - holds map of group membership for each atom
- !x(lcrd) - X,Y,Z coords of atoms - (3,*)
- !x(l15) - Partial Charges
- !x(linddip) - induced dipoles X,Y,Z for each atom (3,*)
- !x(Lmass) - Mass of each atom
- call printdip(prndipngrp,ix(icnstrgp),xx(lcrd), &
- xx(l15),xx(linddip),xx(Lmass), natom)
- end if
- write(6,*) '----------------------------- END DIPOLE INFO --------------------------------'
- end if
- !--- END DIPOLE PRINTING CODE ---
-
- if (nmropt > 0) then
- call nmrptx(6)
- end if
- if (itgtmd == 2) then
- emtmd = 0.0d0
- call mtmdcall(emtmd,xx(lmtmd01),ix(imtmd02),x,f,ih(m04),ih(m02),ix(i02),&
- ih(m06),xx(lmass),natom,nres,'PRNT')
- end if
- call amflsh(7)
- end if
-
- ! Output running averages:
- ! DAN ROE: total_nstep==Total nstep REMD/MD, set in step 5
- if ( ntave > 0 )then
- if ( mod(total_nstep,ntave) == 0 .and. onstep )then
- write(6,542)
-#ifdef RISMSANDER
- if(rismprm%irism==1)then
- tspan = ntave/mylcm(nrespa,rismprm%rismnrespa)
- else
- tspan = ntave/nrespa
- end if
-#else
- tspan = ntave/nrespa
-#endif
-
- ! Update all elements of these sequence types
- enert_tmp = enert - enert_old
- enert2_tmp = enert2 - enert2_old
- enert_old = enert
- enert2_old = enert2
- enert_tmp = enert_tmp/tspan
- enert2_tmp = enert2_tmp/tspan - &
- enert_tmp*enert_tmp
- call zero_neg_values_state(enert2_tmp)
- enert2_tmp = sqrt(enert2_tmp)
-
-#ifdef MPI
- if( ievb /= 0 ) then
- evb_nrg_tmp (:) = evb_nrg_ave(:) - evb_nrg_old (:)
- evb_nrg_tmp2(:) = evb_nrg_rms(:) - evb_nrg_old2(:)
- evb_nrg_old (:) = evb_nrg_ave(:)
- evb_nrg_old2(:) = evb_nrg_rms(:)
- evb_nrg_tmp (:) = evb_nrg_tmp (:) / tspan
- evb_nrg_tmp2(:) = evb_nrg_tmp2(:) / tspan - evb_nrg_tmp(:)**2
- evb_nrg_tmp2(:) = max( evb_nrg_tmp2(:), 0.0d0 )
- evb_nrg_tmp2(:) = sqrt( evb_nrg_tmp2(:) )
- endif
- if ( ifsc /= 0 ) then
- do m = 1,ti_ene_cnt
- sc_ener_tmp(m) = sc_ener_ave(m)-sc_ener_old(m)
- sc_ener_tmp2(m) = sc_ener_rms(m)-sc_ener_old2(m)
- sc_ener_old(m) = sc_ener_ave(m)
- sc_ener_old2(m) = sc_ener_rms(m)
- sc_ener_tmp(m) = sc_ener_tmp(m)/tspan
- sc_ener_tmp2(m) = sc_ener_tmp2(m)/tspan - sc_ener_tmp(m)**2
- if (sc_ener_tmp2(m) < 0.0d0) sc_ener_tmp2(m) = 0.0d0
- sc_ener_tmp2(m) = sqrt(sc_ener_tmp2(m))
- end do
- end if
- if( ievb /= 0 ) evb_frc%evb_ave = .true.
-#endif
-#ifdef RISMSANDER
- if(rismprm%irism==1)then
- write(6,540) ntave/mylcm(nrespa,rismprm%rismnrespa)!nrespa
- else
- write(6,540) ntave/nrespa
- end if
-#else
- write(6,540) ntave/nrespa
-#endif
- call prntmd(total_nstep,izero,izero,t,enert_tmp,onefac,0,.false.)
-#ifdef MPI
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_tmp)
- if( ievb /= 0 ) evb_frc%evb_rms = .true.
-#endif
- write(6,550)
- call prntmd(total_nstep,izero,izero,t,enert2_tmp,onefac,0,.true.)
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_tmp2)
-#endif
- if( icfe > 0 ) then
-#ifdef RISMSANDER
- if(rismprm%irism==1)then
- write(6,541) ntave/mylcm(nrespa,rismprm%rismnrespa)!nrespa
- else
- write(6,541) ntave/nrespa
- end if
-#else
- write(6,541) ntave/nrespa
-#endif
- edvdl_r = edvdl_r/tspan
- edvdl_r%pot%dvdl = enert_tmp%pot%dvdl ! fix for DV/DL output
- edvdl_r%virvsene = 0.d0 ! virvsene should not but included here
- call prntmd(total_nstep,izero,izero,t,edvdl_r,onefac,0,.false.)
- edvdl_r = null_state_rec
-
- end if
- write(6,542)
- end if
- end if ! ( ntave > 0 )
-
- ! --- end masters output ---
-
- end if ! (master)
-
-#ifdef MPI /* SOFT CORE */
- if (ntave > 0 .and. icfe > 0 .and. dynlmb > 0) then
- if ( mod(nstep,ntave) == 0 .and. onstep ) then
- ! For runs with dynamically changing lambda, raise lambda here
- ! and flush all buffers for the next averages
- clambda = clambda + dynlmb
- call sc_change_clambda(clambda)
- if (master) then
- sc_ener(1:ti_ene_cnt) = 0.0d0
- sc_ener_ave(1:ti_ene_cnt) = 0.0d0
- sc_ener_rms(1:ti_ene_cnt) = 0.0d0
- sc_ener_old(1:ti_ene_cnt) = 0.0d0
- sc_ener_old2(1:ti_ene_cnt) = 0.0d0
- enert = null_state_rec
- enert2 = null_state_rec
- enert_old = null_state_rec
- enert2_old = null_state_rec
- write (6,*)
- write (6,'(a,f12.4,a,f12.4)') &
- 'Dynamically changing lambda: Increased clambda by ', &
- dynlmb, ' to ', clambda
- write (6,*)
- end if
- end if
- end if
-#endif
-
- !=======================================================================
-
- ! ---major cycle back to new step unless we have reached our limit:
-
-#ifdef MMTSB
- if ( mmtsb_switch /= mmtsb_off ) then
- if ( mod( nstep, mmtsb_iterations ) == 0 ) then
- write(6,'(a,i8)') &
- 'MMTSB Replica Exchange iterations completed at NSTEP = ', &
- nstep
- ! apparently 23 is the magic number for potential energy.
- ! ener%pot%tot is the new 23 ;) MJW
- write(6,'(a,f12.4)') &
- 'MMTSB Replica Exchange potential energy = ', ener%pot%tot
- ! write coordinates; preferred format is pdb, but can't do that
- ! so write a restart file; server will post process with ambpdb.
-# ifdef LES
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, x,v, &
- xx(lcrdr),box,t,temp0les)
-# else
- call mdwrit(nstep,nrp,nr,nres,ntxo,ntr,ntb, x,v, &
- xx(lcrdr),box,t,rem_val)
-# endif
- ! Chop up trajectory files for later continuous temp splicing.
- call close_dump_files
- ! contact server
- if ( mmtsb_switch == mmtsb_temp_rex ) then
- call mmtsb_newtemp( ener%pot%tot, temp_mmtsb, is_done_mmtsb )
- else if ( mmtsb_switch == mmtsb_lambda_rex ) then
- ! currently temp_mmtsb is ignored, but multidimensional soon
- call mmtsb_newlambda( unpert_pe_mmtsb, pert_pe_mmtsb, &
- lambda_mmtsb, temp_mmtsb, is_done_mmtsb )
- end if
- call open_dump_files
- if ( is_done_mmtsb ) then
- goto 480
- end if
-
- ! in the future we may want amber based tracking of exchanges
- ! perhaps we can use the Simmerling group's code ?
- if ( mmtsb_switch == mmtsb_temp_rex ) then
- if ( abs( temp_mmtsb - temp0 ) <= TEN_TO_MINUS3 ) then
- ! no exchange, continue at the same reference temp.
- mmtsb_is_exchanged = .false.
- write(6,'(a,i8,a,f12.4)') &
- 'MMTSB Replica Exchange temperature unchanged'
- else
- ! exchange temp via changing the reference temp.
- ! the velocities will be randomly reset at the new temp via
- ! the resetvelo variable.
- mmtsb_is_exchanged = .true.
- write(6,'(a,f8.2,a,f8.2)') &
- 'MMTSB Replica Exchange temperature change from ', &
- temp0, ' to ', temp_mmtsb
- temp0 = temp_mmtsb
- end if
- else if ( mmtsb_switch == mmtsb_lambda_rex ) then
- if ( abs( lambda_mmtsb - clambda ) <= TEN_TO_MINUS3 ) then
- ! no exchange, continue at the same lambda
- mmtsb_is_exchanged = .false.
- write(6,'(a,i8,a,f12.4)') &
- 'MMTSB Replica Exchange lambda unchanged'
- else
- ! exchange lambda
- ! the velocities will be randomly reset via
- ! the resetvelo variable.
- mmtsb_is_exchanged = .true.
- write(6,'(a,f8.2,a,f8.2)') &
- 'MMTSB Replica Exchange lambda change from ', &
- clambda, ' to ', lambda_mmtsb
- clambda = lambda_mmtsb
- end if
- end if ! ( mmtsb_switch == mmtsb_temp_rex )
- else
- ! not a replica exchange update iteration.
- mmtsb_is_exchanged = .false.
- end if ! ( mod( nstep, mmtsb_iterations ) == 0 )
- end if ! ( mmtsb_switch /= mmtsb_off )
-#endif
-
-
- call trace_integer( 'end of step', nstep )
- call trace_output_mpi_tally( )
- call timer_stop(TIME_VERLET)
-#if !defined(DISABLE_NCSU) && defined(NCSU_ENABLE_BBMD)
- call ncsu_on_mdstep(ener%pot%tot, v, ekmh)
-#endif /* !defined(DISABLE_NCSU) && defined(NCSU_ENABLE_BBMD) */
-
-#if defined(RISMSANDER) && defined(RISM_DEBUG)
- if(rismprm%irism == 1) then
-!!$ write(6,*) "END OF STEP",natom
-! call calc_cm(x,cm,amass,natom)
- angvel=0
- do m=1,natom
- r = x((m-1)*3+1:(m-1)*3+3)-cm
-!!$ write(6,*) m,v((m-1)*3+1:(m-1)*3+3)
- call cross(r,v((m-1)*3+1:(m-1)*3+3),rxv)
- angvel = angvel + rxv/sum(r**2)
- end do
- moi=0
- erot=0
- do m=1,natom
- r = x((m-1)*3+1:(m-1)*3+3)-cm
- call cross(r,v((m-1)*3+1:(m-1)*3+3),rxv)
- proj = sum(r*angvel)/sum(angvel**2)*angvel
-!!$ write(6,*) "angvel ",angvel
-!!$ write(6,*) "r ",r,sum((r)**2)
-!!$ write(6,*) "proj",proj
-!!$ write(6,*) "r-proj",r-proj,sum((r-proj)**2)
- moi=moi+amass(m)*sum((r-proj)**2)
- erot = erot + .5*amass(m)*sum((r-proj)**2)*sum((rxv/sum(r**2))**2)
- end do
-!!$ write(6,*) moi
-!!$ do m=1,3
-!!$ write(6,*) m,sum(v(m:3*natom:3))
-!!$ write(6,*) m,sum(amass(1:natom)*v(m:3*natom:3))
-!!$ write(6,*) m,angvel(m),sum(angvel**2)
-!!$ end do
-!!$ write(6,*) "EROT", 0.5*moi*sum(angvel**2), erot
-!!$ write(6,*) "EROT", erot
-!!$ call mexit(6,1)
- end if
-#endif /*RISMSANDER && RISM_DEBUG*/
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
-#ifdef MPI
- call xdist(v, xx(lfrctmp), natom) ! lam81
-#endif
- abfqmmm_param%v(1:nr3+iscale) = v(1:nr3+iscale) ! lam81
- deallocate(for, stat=ier) ! lam81
- return ! lam81
- end if ! lam81
-
- if (nstep < nstlim) goto 260
- 480 continue
-
-#ifdef MPI
-! ------====== REMD Post-Dynamics ======------
- if(next_rem_method == 1) then
- remd_ekmh=ekmh
-
- ! ---=== HYBRID REMD ===---
- if (numwatkeep>=0) then
- ! This is a hybrid REMD run. Get energy of stripped system for next
- ! exchange.
- call hybrid_remd_ene(xx,ix,ih,ipairs,qsetup, &
- numwatkeep,hybridgb,igb,ntr,nspm,t,temp0, &
- ntb,cut, &
- ener,ener%vir,do_list_update,nstep, &
- nitp,nits,onefac,loutfm )
- else ! numwatkeep>=0
- ! The positions are currently one step ahead of the energy ener%pot%tot,
- ! since force was called prior to the position propagation. Thus, call
- ! force one more time to update ener%pot%tot to reflect the current
- ! coordinates.
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
- endif ! numwatkeep>=0
-
- ! Set myeptot, mytemp, and mytargettemp
-! if (mdloop>0) mytemp = ener%kin%tot * onefac(1)
- my_remd_data%mytemp = ener%kin%tot * onefac(1)
- my_remd_data%myeptot = ener%pot%tot
-
-
- my_remd_data%mytargettemp = temp0
-# ifdef VERBOSE_REMD
- if (master) write(6,'(a,f15.4,2(a,f6.2))') &
- "REMD: myEptot= ",my_remd_data%myeptot," myTargetTemp= ", &
- my_remd_data%mytargettemp," mytemp= ",my_remd_data%mytemp
-# endif
-# ifdef LES
- else if(next_rem_method == 2 ) then
- my_remd_data%mytemp = ener%kin%solv * onefac(3)
- my_remd_data%myeptot = ener%eptot
- my_remd_data%mytargettemp = temp0les
-# endif
- else if (next_rem_method == 3) then
- remd_ekmh = ekmh
- if (mdloop > 0) my_remd_data%mytemp = ener%kin%tot * onefac(1)
- my_remd_data%mytargettemp = temp0
-! Call force here to bring all energies up-to-date
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir,xx(l96),xx(l97),xx(l98), &
- xx(l99),qsetup,do_list_update)
-
- my_remd_data%myeptot = ener%pot%tot
-
-! Call nmrdcp to decrement the NMR counter, since this should not count as
-! a real step (JMS 2/12). This is OK, since the counter got incremented at
-! the _very_ end of nmrcal, so we haven't already printed an unwanted value
- if (nmropt /= 0) call nmrdcp
-! Call xdist such that master has all the velocities(DSD 09/12)
- call xdist(v, xx(lfrctmp), natom)
-
- else if (next_rem_method == 4) then
- remd_ekmh = ekmh
-
- endif ! rem == 1
-! ------====== END REMD Post-Dynamics ======------
-#endif /* MPI */
-
- !=======================================================================
- ! ----- PRINT AVERAGES -----
- !=======================================================================
-
-# ifdef MPI
- ! -- ti decomp
- if (icfe /= 0 .and. idecomp /= 0) then
- if( idecomp == 1 .or. idecomp == 2 ) then
- call collect_dec(nrs)
- !else if( idecomp == 3 .or. idecomp == 4 ) then
- ! call collect_dec(npdec*npdec)
- end if
- end if
-
- ! Turn off avg. for REMD. and explicit solvent CpHMD, since it's not
- ! accumulated correctly in that case for each compiler
- if (master.and.rem == 0) then
-# else
- if (master) then
-# endif /*MPI*/
- tspan = nvalid
- if (nvalid > 0) then
-
- ! Update all elements of these sequence types
- enert = enert/tspan
- enert2 = enert2/tspan - enert*enert
- call zero_neg_values_state(enert2)
- enert2 = sqrt(enert2)
- edvdl = edvdl/tspan
-
- ! for PIMD/NMPIMD/CMD/RPMD averages
- if (ipimd>0) then
- totenert = totenert/tspan
- totenert2 = totenert2/tspan - (totenert*totenert)
- call zero_neg_values_state(totenert2)
- totenert2 = sqrt(totenert2)
- endif
-
-#ifdef MPI
- if( ievb /= 0 ) then
- evb_nrg_ave(:) = evb_nrg_ave(:) / tspan
- evb_nrg_rms(:) = evb_nrg_rms(:) / tspan - evb_nrg_ave(:)**2
- evb_nrg_rms(:) = max( evb_nrg_rms(:), 0.0d0 )
- evb_nrg_rms(:) = sqrt( evb_nrg_rms(:) )
- endif
- if ( ifsc /= 0 ) then
- do m = 1,ti_ene_cnt
- sc_ener_ave(m) = sc_ener_ave(m)/tspan
- sc_ener_rms(m) = sc_ener_rms(m)/tspan - sc_ener_ave(m)**2
- if(sc_ener_rms(m) < 0.0d0) sc_ener_rms(m) = 0.0d0
- sc_ener_rms(m) = sqrt(sc_ener_rms(m))
- end do
- end if
- if( ievb /= 0 ) evb_frc%evb_ave = .true.
-#endif
- write(6,540) nvalid
- call prntmd(total_nstep,izero,izero,t,enert,onefac,0,.false.)
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_ave)
- if( ievb /= 0 ) evb_frc%evb_rms = .true.
- if ( ipimd > 0 .and. worldrank==0 ) then
- write(pimd_unit,540) nvalid
- call pimd_report(nstep,t,pimd_unit,totenert,onefac)
- write(pimd_unit,550)
- call pimd_report(nstep,t,pimd_unit,totenert2,onefac)
- endif
-#endif
- if (nmropt > 0) call nmrptx(6)
- write(6,550)
- call prntmd(total_nstep,izero,izero,t,enert2,onefac,0,.true.)
-
-#ifdef MPI
- if (ifsc /= 0) call sc_print_energies(6, sc_ener_rms)
- if (ifsc /= 0) call sc_print_dvdl_values()
-
- if( icfe > 0 ) then
- write(6,541) nvalid
- edvdl%pot%dvdl = enert%pot%dvdl ! fix for DV/DL output
- edvdl%virvsene = 0.d0 ! virvsene should not but included here
- call prntmd(total_nstep,izero,izero,t,edvdl,onefac,0,.false.)
- ! -- ti decomp
- if(worldrank == 0 .and. idecomp /= 0) then
- call checkdec(idecomp)
- if(idecomp == 1 .or. idecomp == 2) call printdec(ix)
- end if
- end if
-#endif
-
- if (nmropt >= 1) then
- write(6,500)
- if (iredir(7) /= 0) call pcshift(-1,x,f)
- call ndvptx(x,f,ih(m04),ih(m02),ix(i02),nres,xx(l95), &
- natom, xx(lwinv),ntb,xx(lnmr01),ix(inmr02),6)
- end if
-
- ! Print Born radii statistics
-
- if ((rbornstat == 1).and.(igb /= 0 .or. ipb /= 0)) then
-
- ! Born radii stats collected every nrespai step not nrespa step
- tspan = nvalidi
-
- write(6,580) nstep
- write(6,590)
- do m = 1,natom
- xx(l188-1+m) = xx(l188-1+m)/tspan
- xx(l189-1+m) = xx(l189-1+m)/tspan - &
- xx(l188-1+m)*xx(l188-1+m)
- xx(l189-1+m) = sqrt(xx(l189-1+m))
- write(6,600) m, xx(l186-1+m), xx(l187-1+m), &
- xx(l188-1+m), xx(l189-1+m)
- end do
- end if
-
- enert%kin%tot = enert%kin%tot*onefac(1)
- enert2%kin%tot = enert2%kin%tot*onefac(1)
- enert%kin%solt = enert%kin%solt*onefac(2)
- enert2%kin%solt = enert2%kin%solt*onefac(2)
- enert%kin%solv = enert%kin%solv*onefac(3)
- enert2%kin%solv = enert2%kin%solv*onefac(3)
-
- temp = enert%kin%tot
- end if ! (nvalid > 0)
-
- if (ntp > 0 .and. barostat == 2) call mcbar_summary
-
- end if ! (master)
-
-#ifdef MPI
- if( ievb /= 0 ) then
- call evb_dealloc
-#if defined(LES)
- if( master ) call evb_pimd_dealloc
-#endif
- endif
-#endif
-
- if( icfe /= 0 ) then
- deallocate( frcti, stat = ier )
- REQUIRE( ier == 0 )
- end if
-
- 500 format(/,' NMR restraints on final step:'/)
- 540 format(/5x,' A V E R A G E S O V E R ',i7,' S T E P S',/)
- 541 format(/5x,' DV/DL, AVERAGES OVER ',i7,' STEPS',/)
- 542 format('|',79('='))
- 550 format(/5x,' R M S F L U C T U A T I O N S',/)
- 580 format('STATISTICS OF EFFECTIVE BORN RADII OVER ',i7,' STEPS')
- 590 format('ATOMNUM MAX RAD MIN RAD AVE RAD FLUCT')
- 600 format(i4,2x,4f12.4)
- call trace_exit( 'runmd' )
- return
-end subroutine runmd
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Stripped-down runmd routine for running relaxation dynamics on a given mask
-subroutine relaxmd(xx,ix,ih,ipairs,x,winv,amass,f, &
- v,vold,xr,xc,conp,skip,nsp,tma,erstop, qsetup, &
- relax_nstlim, mobile_atoms, increment_nmropt)
-
- ! Runmd operates in kcal/mol units for energy, amu for masses,
- ! and angstroms for distances. To convert the input time parameters
- ! from picoseconds to internal units, multiply by 20.455
- ! (which is 10.0*sqrt(4.184)).
-
- use bintraj, only: end_binary_frame
- use barostats, only : mcbar_trial
- use constants, only : third, ten_to_minus3
- use crg_reloc, only: ifcr, crprintcharges, cr_print_charge
- use fastwt
- use file_io_dat
- use molecule, only: n_iwrap_mask_atoms, iwrap_mask_atoms
- use nblist,only: fill_tranvec,volume,oldrecip,ucell
- use qmmm_module, only : qmmm_nml,qmmm_struct, qmmm_mpi, qm2_struct, &
- qmmm_vsolv
- use stack
- use state
- use trace
-
-! Variable Descriptions
-!
-! Passed variables
-! xx : global real array. See locmem.f for structure/pointers
-! ix : global integer array. See locmem.f for structure/pointers
-! ih : global hollerith array. See locmem.f for structure/pointers
-! ipairs : ?? Global pairlist ?? --add description (JMS 11/2010)
-! x : global position array *
-! winv : array with inverse masses *
-! amass : mass array *
-! f : force array, used to hold old coordinates temporarily, too
-! v : velocity array
-! vold : old velocity array, from the previous step
-! xr : coordinates with respect to COM of molecule
-! conp : bond parameters for SHAKE
-! skip : logical skip array for SHAKE (and QM/MM too, I think)
-! nsp : submolecule index array (?)
-! tma : submolecular weight array (?)
-! erstop : should we stop in error (?)
-! qsetup : Not quite sure what this does, if anything anymore.
-! mobile_atoms: bellymask-style array with 1s for moving atoms and 0s for
-! frozen atoms
-! relax_nstlim: Number of relaxation dynamics steps to run
-! increment_nmropt: Do we allow the nmropt counter to increment?
-!
-! Local variables
-! factt : degree-of-freedom correction factor for temperature scaling
-! nr : local copy of nrp, number of atoms
-! nr3 : 3 * nr, used for runtime efficiency
-!
-! Common memory variables
-! nrp : number of atoms, adjusted for LES copies
-
- implicit none
- character(kind=1,len=7) :: routine="relaxmd"
- integer ipairs(*), ix(*), relax_nstlim
- integer, intent(in) :: mobile_atoms(*)
- logical, intent(in) :: increment_nmropt
- _REAL_ xx(*)
- character(len=4) ih(*)
- _REAL_ combination
-
-#ifdef MPI
-# include "parallel.h"
- include 'mpif.h'
- _REAL_ mpitmp(8) !Use for temporary packing of mpi messages.
- integer ist(MPI_STATUS_SIZE), partner, ierr
-#else
- ! mdloop and REM is always 0 in serial
- integer, parameter :: mdloop = 0, rem = 0
-#endif
-
-#include "../include/md.h"
-#include "box.h"
-#include "nmr.h"
-#include "../include/memory.h"
-#include "extra.h"
-#include "ew_frc.h"
-#include "ew_cntrl.h"
-#include "ew_mpole.h"
-#include "def_time.h"
-#include "extra_pts.h"
-#include "../lib/random.h"
-
- _REAL_ sysx,sysy,sysz,sysrange(3,2)
- logical mv_flag
-
- _REAL_ , dimension(1) :: shkh
- integer, dimension(1) :: ifstwr2
- integer :: nshkh
-
- integer idx, iatom, iatomCL,m
- _REAL_ Ekin2_tot,tmp,f_lnv
- integer :: idim, ithermo
- _REAL_ :: E_nhc, exp1, exp2, v_sum
-
- logical ivscm
- logical qspatial
- character(len=6)fnam
-
- logical resetvelo
- integer nshak
- _REAL_ ekgs,eold3,eold4,etot_save,ekpbs
-
- logical do_list_update
- logical skip(*),lout,loutfm,erstop,vlim,onstep
- _REAL_ x(*),winv(*),amass(*),f(*),v(*),vold(*), &
- xr(*),xc(*),conp(*)
- type(state_rec) :: ener
- type(state_rec) :: ecopy, edvdl
- type(state_rec) :: edvdl_r
- _REAL_ rmu(3),fac(3),onefac(3),clfac, etot_start
- _REAL_ tma(*)
-
- _REAL_ tspan,atempdrop,fln,scaltp,scaltpo
- _REAL_ vel,vel2,vcmx,vcmy,vcmz,vmax,vx,vy,vz
- _REAL_ winf,aamass,rterm,ekmh,ekph,ekpht,wfac,rsd,ekav
- _REAL_ fit,fiti,fit2,vscalt
- logical is_langevin ! Is this a Langevin dynamics simulation
- _REAL_ gammai,c_implic,c_explic,c_ave,sdfac,ekins0
- _REAL_ dtx,dtxinv,dt5,factt,ekin0,ekinp0,dtcp,dttp
- _REAL_ rndf,rndfs,rndfp,boltz2,pconv,tempsu
- _REAL_ xcm(3),acm(3),ocm(3),vcm(3),ekcm,ekrot
- _REAL_ emtmd
-
-! Variables and parameters for constant surface tension:
- _REAL_, parameter :: ten_conv = 100.0d0 !ten_conv - converts
- !dyne/cm to bar angstroms
- _REAL_ :: pres0x
- _REAL_ :: pres0y
- _REAL_ :: pres0z
- _REAL_ :: gamma_ten_int
- _REAL_ :: press_tan_ave
-
- integer nsp(*)
- integer idumar(4)
- integer l_temp
- integer i,j,im,i3,nitp,nits
- integer nstep,nrep,nrek,nren,iend,istart3,iend3
- integer nrx,nr,nr3,ntcmt,izero,istart
- logical qsetup
-
- integer nvalid, nvalidi
- _REAL_ eke,eket
- _REAL_ extent
-
- _REAL_ xcen,ycen,zcen,extents(3,2)
- _REAL_, allocatable, dimension(:) :: frcti
- integer ier
-
- _REAL_ small
- data small/1.0d-7/
- data nren/51/
-
- !--- VARIABLES FOR DIPOLE PRINTING ---
- integer prndipngrp
- integer prndipfind
- character(len=4) prndiptest
-
- _REAL_,parameter :: pressure_constant = 6.85695d+4
- ! variables used in constant pressure PIMD
- _REAL_ :: Nkt,centvir,pressure, aa, arg2, poly, e2, e4, e6, e8
- ! variable used in CMD
- real(8) :: tmp_eke_cmd !Use for temporary packing of mpi messages.
-
- _REAL_ :: box_center(3)
-
- !==========================================================================
-
- call trace_enter( 'relaxmd' )
-
- ! ----- INITIALIZE SOME VARIABLES -----
-
- vlim = vlimit > small
- ntcmt = 0
- izero = 0
- lout = .true.
- loutfm = ioutfm <= 0
- nr = natom
- nr3 = 3*nr
- ekmh = 0.d0
- onstep = .true.
-
- do_list_update=.false.
-#ifdef MPI
- istart = iparpt(mytaskid) + 1
- iend = iparpt(mytaskid+1)
-#else
- istart = 1
- iend = nr
-#endif
- istart3 = 3*istart -2
- iend3 = 3*iend
-
- ! If NTWPRT.NE.0, only print the atoms up to this value
- nrx = nr3
- if (ntwprt > 0) nrx = ntwprt*3
-
- !=======================================================================
- ! Determine system degrees of freedom (for T scaling, reporting)
-
- ! Call DEGCNT to get the actual number of degrees of freedom for the
- ! solute and solvent. The 'belly' atoms are just the mobile ones
-
- call degcnt(1,nr,mobile_atoms,nsolut,nbonh,nbona,0, &
- ix(iibh),ix(ijbh),ix(iiba),ix(ijba),idumar, &
- idumar,ntc,idumar,0,0,0, &
- idumar,rndfp,rndfs)
-
- ! RNDFP = # degrees of freedom for solute
- ! RNDFS = # degrees of freedom for solvent
- ! RNDF = total number of degrees of freedom.
-
- ! qtw - substract the number of overlapping noshake QM atoms in noshakemask
- rndfp = rndfp - qmmm_struct%noshake_overlap
- ! modify RNDFP to reflect NDFMIN (set in mdread) and num_noshake
- rndfp = rndfp - ndfmin + num_noshake
- rndf = rndfp+rndfs
-
- call fix_degree_count(rndf) ! correct for extra points
-
- ! End of degrees of freedom stuff
- !=======================================================================
-
- boltz2 = 8.31441d-3 * 0.5d0
- pconv = 1.6604345d+04 ! factor to convert the pressure kcal/mole to bar
-
- ! ---convert to kcal/mol units
-
- boltz2 = boltz2/4.184d0 ! k-sub-B/2
- dtx = dt*20.455d+00
- dtxinv = 1.0d0 / dtx
- dt5 = dtx * 0.5d0
- pconv = pconv*4.184d0
-
- ! FAC() are #deg freedom * kboltz / 2
- ! multiply by T to get expected kinetic energy
- ! FAC(1) is for total system
-
- fac(1) = boltz2*rndf
- fac(2) = boltz2*rndfp
-
- if(rndfp < 0.1d0) fac(2) = 1.d-6
-
- fac(3) = boltz2*rndfs
- if(rndfs < 0.1d0) fac(3) = 1.d-6
- onefac(1) = 1.0d0/fac(1)
- onefac(2) = 1.0d0/fac(2)
- onefac(3) = 1.0d0/fac(3)
- factt = rndf/(rndf+ndfmin)
-
- ! these are "desired" kinetic energies based on
- ! # degrees freedom and target temperature
- ! they will be used for calculating the velocity scaling factor
-
- ekinp0 = fac(2)*temp0
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-
- ! Langevin dynamics setup:
-
- is_langevin = gamma_ln > 0.0d0
- gammai = gamma_ln/20.455d0
- c_implic = 1.d0/(1.d0+gammai*dt5)
- c_explic = 1.d0 - gammai*dt5
- c_ave = 1.d0+gammai*dt5
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
- if (is_langevin .and. ifbox==0) then
- call get_position(nr,x,sysx,sysy,sysz,sysrange,0)
- end if
- if (ntt == 1) dttp = dt/tautp
- if (ntp > 0) dtcp = comp * 1.0d-06 * dt / taup
-
- ! Constant surface tension setup:
-
- if (csurften > 0) then
-
- ! Set pres0 in direction of surface tension.
- ! The reference pressure is held constant in on direction dependent
- ! on what the surface tension direction is set to.
- if (csurften .eq. 1) then ! pres0 in the x direction
- pres0x = pres0
-
- else if (csurften .eq. 2) then ! pres0 in the y direction
- pres0y = pres0
-
- !else if (csurften .eq. 3) then ! pres0 in the z direction
- else
- pres0z = pres0
-
- end if
-
- ! Multiply surface tension by the number of interfaces
- gamma_ten_int = dble(ninterface) * gamma_ten
-
- end if
-
- nrek = 4
- nrep = 15
-
- nvalid = 0
- nvalidi = 0
- nstep = 0
- fit = 0.d0
- fiti = 0.d0
- fit2 = 0.d0
-
- ener = null_state_rec ! Zeros all elements
- ener%kin%pres_scale_solt = 1.d0
- ener%kin%pres_scale_solv = 1.d0
- ener%box(1:3) = box(1:3)
- ener%cmt(1:4) = 0.d0
- nitp = 0
- nits = 0
-
- ekmh = 0.0d0
-
- i3 = 0
- do j = 1,nrp
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- rterm = v(i3)*v(i3) * aamass
- ekmh = ekmh + rterm
- end do
- end do
-
- do im=1,iscale
- ekmh = ekmh + scalm*v(nr3+im)*v(nr3+im)
- end do
- ekmh = ekmh * 0.5d0
- do i=1,nr3+iscale
- vold(i) = v(i)
- end do
-
- !=======================================================================
- ! ----- MAIN LOOP FOR PERFORMING THE DYNAMICS STEP -----
- ! (at this point, the coordinates are a half-step "ahead"
- ! of the velocities; the variable EKMH holds the kinetic
- ! energy at these "-1/2" velocities, which are stored in
- ! the array VOLD.)
- !=======================================================================
-
- 260 continue
-
- !---------------------------------------------------------------
- ! ---Step 1a: do some setup for pressure calculations:
- !---------------------------------------------------------------
-
- if (ntp > 0) then
- ener%cmt(1:3) = 0.d0
- xr(1:nr3) = x(1:nr3)
-
- ! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
- ! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
- ! MASS -----
-
- call timer_start(TIME_EKCMR)
- call ekcmr(nspm,nsp,tma,ener%cmt,xr,v,amass,istart,iend)
-#ifdef MPI
- call trace_mpi('mpi_allreduce', &
- 3,'MPI_DOUBLE_PRECISION',mpi_sum)
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,ener%cmt,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
-# else
- call mpi_allreduce(ener%cmt,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- ener%cmt(1:3) = mpitmp(1:3)
-# endif
-#endif
- call timer_stop(TIME_EKCMR)
- end if
-
- ! If we're using the MC barostat, go ahead and do the trial move now
- if (ntp > 0 .and. barostat == 2 .and. mod(nstep+1, mcbarint) == 0) &
- call mcbar_trial(xx, ix, ih, ipairs, x, xc, f, ener%vir, xx(l96), &
- xx(l97), xx(l98), xx(l99), qsetup, do_list_update, nstep, nsp, &
- amass)
-
- !--------------------------------------------------------------
- ! ---Step 1b: Get the forces for the current coordinates:
- !--------------------------------------------------------------
-
- iprint = 0
- if( nstep == 0 .or. nstep+1 == relax_nstlim ) iprint = 1
-
- call force(xx,ix,ih,ipairs,x,f,ener,ener%vir, &
- xx(l96),xx(l97),xx(l98),xx(l99), qsetup, &
- do_list_update,nstep)
-
- ! If we don't want to increment the NMROPT counter, decrement it here.
- if (.not. increment_nmropt) &
- call nmrdcp
-
- ! Reset quantities depending on TEMP0 and TAUTP (which may have been
- ! changed by MODWT during FORCE call).
- ekinp0 = fac(2)*temp0
- ekins0 = fac(3)*temp0
- ekin0 = fac(1)*temp0
-
- if (ntt == 1) dttp = dt/tautp
-
- if (ntp > 0) then
- ener%volume = volume
- ener%density = tmass / (0.602204d0*volume)
- ener%cmt(4) = 0.d0
- ener%vir(4) = 0.d0
- ener%pres(4) = 0.d0
- do m = 1,3
- ener%cmt(m) = ener%cmt(m)*0.5d0
- ener%cmt(4) = ener%cmt(4)+ener%cmt(m)
- ener%vir(4) = ener%vir(4)+ener%vir(m)
- ener%pres(m) = (pconv+pconv)*(ener%cmt(m)-ener%vir(m))/volume
- ener%pres(4) = ener%pres(4)+ener%pres(m)
- end do
- ener%pres(4) = ener%pres(4)/3.d0
-
- ! Constant surface tension output:
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! Surface tension in the x direction
- ener%surface_ten = &
- box(1) * (ener%pres(1) - 0.5d0 * &
- (ener%pres(2) + ener%pres(3))) / (ninterface * ten_conv)
-
- else if (csurften .eq. 2) then ! Surface tension in the y direction
- ener%surface_ten = &
- box(2) * (ener%pres(2) - 0.5d0 * &
- (ener%pres(1) + ener%pres(3))) / (ninterface * ten_conv)
-
- else ! if (csurften .eq. 3) then ! Surface tension in the z direction
- ener%surface_ten = &
- box(3) * (ener%pres(3) - 0.5d0 * &
- (ener%pres(1) + ener%pres(2))) / (ninterface * ten_conv )
-
- end if
-
- end if
-
- end if
-
- !----------------------------------------------------------------
- ! ---Step 1c: do randomization of velocities, if needed:
- !----------------------------------------------------------------
- ! ---Assign new random velocities every Vrand steps, if ntt=2
-
- resetvelo=.false.
- if (vrand /= 0 .and. ntt == 2) then
- if (mod((nstep+1),vrand) == 0) resetvelo=.true.
- end if
-
- if (resetvelo) then
- ! DAN ROE: Why are only the masters doing this? Even if the velocities
- ! are broadcast to the child processes, the wont the different # of random
- ! calls put the randomg num generators out of sync, or do we not care?
-
- if (master) then
-! write (6,'(a,i8)') 'Setting new random velocities at step ', &
-! nstep + 1
- call setvel(nr,v,winv,temp0*factt,init,iscale,scalm)
- end if
-
-# ifdef MPI
- call trace_mpi('mpi_bcast',3*natom,'MPI_DOUBLE_PRECISION',0)
- call mpi_bcast(v, 3*natom, MPI_DOUBLE_PRECISION, 0, commsander, ierr)
-# endif
-
- ! At this point in the code, the velocities lag the positions
- ! by half a timestep. If we intend for the velocities to be drawn
- ! from a Maxwell distribution at the timepoint where the positions and
- ! velocities are synchronized, we have to correct these newly
- ! redrawn velocities by backing them up half a step using the
- ! current force.
- ! Note that this fix only works for Newtonian dynamics.
- if( gammai==0.d0 ) then
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dt5
- v(i3+1) = v(i3+1) - f(i3+1)*wfac
- v(i3+2) = v(i3+2) - f(i3+2)*wfac
- v(i3+3) = v(i3+3) - f(i3+3)*wfac
- i3 = i3+3
- end do
- end if
-
- end if ! (resetvelo)
-
- call timer_start(TIME_VERLET)
-
- !-----------------------------------------------------
- ! ---Step 2: Do the velocity update:
- !-----------------------------------------------------
-
- !step 2a: apply quenched MD if needed. This is useful in NEB>0
- if (vv==1) call quench(f,v)
-
- if( gammai == 0.d0 ) then
-
- ! ---Newtonian dynamics:
-
- i3 = 3*(istart-1)
- do j=istart,iend
- wfac = winv(j) * dtx
- v(i3+1) = v(i3+1) + f(i3+1)*wfac
- v(i3+2) = v(i3+2) + f(i3+2)*wfac
- v(i3+3) = v(i3+3) + f(i3+3)*wfac
- i3 = i3+3
- end do
-
- else ! gamma_ln .ne. 0, which also implies ntt=3 (see mdread.f)
-
- ! ---simple model for Langevin dynamics, basically taken from
- ! Loncharich, Brooks and Pastor, Biopolymers 32:523-535 (1992),
- ! Eq. 11. (Note that the first term on the rhs of Eq. 11b
- ! should not be there.)
-
- ! Update Langevin parameters, since temp0 might have changed:
- sdfac = sqrt( 4.d0*gammai*boltz2*temp0/dtx )
-
- i3 = 3*(istart-1)
-
- if (no_ntt3_sync == 1) then
- !We don't worry about synchronizing the random number stream
- !across processors.
- do j=istart,iend
-
- wfac = winv(j) * dtx
- aamass = amass(j)
- rsd = sdfac*sqrt(aamass)
- call gauss( 0.d0, rsd, fln )
- v(i3+1) = (v(i3+1)*c_explic + (f(i3+1)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+2) = (v(i3+2)*c_explic + (f(i3+2)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+3) = (v(i3+3)*c_explic + (f(i3+3)+fln)*wfac) * c_implic
- i3 = i3+3
- end do
-
- else
-
- do j=1,nr
- if( j<istart .or. j>iend ) then
- ! In order to generate the same sequence of pseudorandom numbers that
- ! you would using a single processor you have to go through the atoms
- ! in order. The unused results are thrown away
- call gauss( 0.d0, 1.d0, fln )
- call gauss( 0.d0, 1.d0, fln )
- call gauss( 0.d0, 1.d0, fln )
- cycle
- end if
-
- wfac = winv(j) * dtx
- aamass = amass(j)
- rsd = sdfac*sqrt(aamass)
- call gauss( 0.d0, rsd, fln )
- v(i3+1) = (v(i3+1)*c_explic + (f(i3+1)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+2) = (v(i3+2)*c_explic + (f(i3+2)+fln)*wfac) * c_implic
- call gauss( 0.d0, rsd, fln )
- v(i3+3) = (v(i3+3)*c_explic + (f(i3+3)+fln)*wfac) * c_implic
- i3 = i3+3
- end do
- end if ! no_ntt3_sync
-
- end if ! ( gammai == 0.d0 )
-
- if (vlim) then
- vmax = 0.0d0
- do i=istart3,iend3
- vmax = max(vmax,abs(v(i)))
- v(i) = sign(min(abs(v(i)),vlimit),v(i))
- end do
-
- ! Only violations on the master node are actually reported
- ! to avoid both MPI communication and non-master writes.
- if (vmax > vlimit) then
- if (master) then
- write(6,'(a,i6,a,f10.4)') 'vlimit exceeded for step ',nstep, &
- '; vmax = ',vmax
- end if
- end if
- end if
-
- do im=1,iscale
- v(nr3+im) = (v(nr3+im) + f(nr3+im)*dtx/scalm)
- end do
-
- !-------------------------------------------------------------------
- ! Step 3: update the positions, putting the "old" positions into F:
- !-------------------------------------------------------------------
-
- i = istart - 1
- do i3 = istart3, iend3, 3
- f(i3 ) = x(i3 )
- f(i3+1) = x(i3+1)
- f(i3+2) = x(i3+2)
- if (mobile_atoms(i) == 1) then
- x(i3 ) = x(i3 ) + v(i3 )*dtx
- x(i3+1) = x(i3+1) + v(i3+1)*dtx
- x(i3+2) = x(i3+2) + v(i3+2)*dtx
- end if
- i = i + 1
- end do
-
- do i = 1,iscale
- f(nr3+i) = x(nr3+i)
- x(nr3+i) = x(nr3+i)+v(nr3+i)*dtx
- end do
-
- call timer_stop(TIME_VERLET)
-
- if (ntc /= 1) then
-
- !-------------------------------------------------------------------
- ! Step 4a: if shake is being used, update the new positions to fix
- ! the bond lengths.
- !-------------------------------------------------------------------
-
- call timer_start(TIME_SHAKE)
- qspatial=.false.
- call shake(nrp,nbonh,nbona,0,ix(iibh),ix(ijbh),ix(ibellygp), &
- winv,conp,skip,f,x,nitp,.false.,ix(iifstwt),ix(noshake), &
- shkh,qspatial)
- call quick3(f,x,ix(iifstwr),natom,nres,ix(i02))
- if(nitp == 0) then
- erstop = .true.
- goto 480
- end if
-
- !-----------------------------------------------------------------
- ! Step 4b: Now fix the velocities and calculate KE
- !-----------------------------------------------------------------
-
- ! ---re-estimate the velocities from differences in positions:
-
- v(istart3:iend3) = (x(istart3:iend3)-f(istart3:iend3)) * dtxinv
-
- call timer_stop(TIME_SHAKE)
- end if
- call timer_start(TIME_VERLET)
-
- if( ntt == 1 .or. onstep ) then
-
- !-----------------------------------------------------------------
- ! Step 4c: get the KE, either for averaging or for Berendsen:
- !-----------------------------------------------------------------
-
- eke = 0.d0
- ekph = 0.d0
- ekpbs = 0.d0
-
- if (gammai == 0.0d0) then
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- eke = eke + aamass*0.25d0*(v(i3)+vold(i3))**2
-
- ! try pseudo KE from Eq. 4.7b of Pastor, Brooks & Szabo,
- ! Mol. Phys. 65, 1409-1419 (1988):
-
- ekpbs = ekpbs + aamass*v(i3)*vold(i3)
- ekph = ekph + aamass*v(i3)**2
-
- end do
- end do
-
- else
-
- i3 = 3*(istart-1)
- do j=istart,iend
- aamass = amass(j)
- do m = 1,3
- i3 = i3+1
- eke = eke + aamass*0.25d0*c_ave*(v(i3)+vold(i3))**2
- end do
-
- end do
-
- end if ! (if gammai == 0.0d0)
-
-#ifdef MPI
- ! --- sum up the partial kinetic energies:
-
- if ( numtasks > 1 ) then
- call trace_mpi('mpi_allreduce', &
- 1,'MPI_DOUBLE_PRECISION',mpi_sum)
- mpitmp(1) = eke
- mpitmp(2) = ekph
- mpitmp(3) = ekpbs
-# ifdef USE_MPI_IN_PLACE
- call mpi_allreduce(MPI_IN_PLACE,mpitmp,3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(1)
- ekph = mpitmp(2)
- ekpbs = mpitmp(3)
-
-# else /* USE_MPI_IN_PLACE */
-
- call mpi_allreduce(mpitmp,mpitmp(4),3, &
- MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
- eke = mpitmp(4)
- ekph = mpitmp(5)
- ekpbs = mpitmp(6)
-
-# endif /* USE_MPI_IN_PLACE */
- end if
-#endif /* MPI */
-
- ! --- all processors handle the "extra" variables:
-
- do im=1,iscale
- eke = eke + scalm*0.25d0*(v(nr3+im)+vold(nr3+im))**2
- ekpbs = ekpbs + scalm*v(nr3+im)*vold(nr3+im)
- ekph = ekph + scalm*v(nr3+im)**2
- end do
-
- eke = eke * 0.5d0
- ekph = ekph * 0.5d0
- ekpbs = ekpbs * 0.5d0
- if( ntt == 1 ) then
-
- ! --- following is from T.E. Cheatham, III and B.R. Brooks,
- ! Theor. Chem. Acc. 99:279, 1998.
-
- scaltp = sqrt(1.d0 + 2.d0*dttp*(ekin0-eke)/(ekmh+ekph))
-
- ! --- following is the "old" (amber7 and before) method:
-
- ! scaltpo = sqrt(1.d0 + dttp*(ekin0/ekph - 1.d0))
- ! write(6,*) 'scaltp: ',2.d0*dttp*(ekin0-eke)/(ekmh+ekph), &
- ! dttp*(ekin0/ekmh - 1.d0)
-
- ! following line reverts to the "old" behavior:
- ! scaltp = scaltpo
-
- do j = istart,iend
- i3=(j-1)*3+1
- v(i3 ) = v(i3 ) *scaltp
- v(i3+1) = v(i3+1) *scaltp
- v(i3+2) = v(i3+2) *scaltp
- end do
- do im=1,iscale
- v(nr3+im) = v(nr3+im)*scaltp
- end do
- end if ! (ntt == 1 )
-
- end if ! ( ntt == 1 .or. onstep; end of step 4c )
-
- !-----------------------------------------------------------------
- ! Step 5: several tasks related to dumping of trajectory information
- !-----------------------------------------------------------------
-
- ! --- Determine if trajectory, velocity, or restart
- ! writing is imminent, or if the center of mass
- ! motion will be removed.
- ! These require xdist of velocities or dipoles in parallel runs:
- !
- ! Modified so that when running REMD, writing can occur less often
- ! than exchanges (e.g. ntwx > nstlim)
- ! DAN ROE: Added two new variables, total_nstep and total_nstlim.
- ! For non-REMD runs, total_nstep=nstep+1 and total_nstlim=nstlim
- ! just like before.
- ! For REMD runs, total_nstep=(mdloop-1)*nstlim+nstep+1, where
- ! mdloop is the current exchange - this is the current
- ! replica exchange MD step. total_nstlim=numexchg*nstlim, which is
- ! the maximum number of REMD steps.
-
-#ifdef MPI
-
- !-----------------------------------------------------------------
- ! --- now distribute the coordinates, and if necessary, dipoles and vel:
- !-----------------------------------------------------------------
-
- call timer_barrier( commsander )
- call timer_stop_start(TIME_VERLET,TIME_DISTCRD)
- if ( numtasks > 1 ) then
- call xdist(x, xx(lfrctmp), natom)
- end if
- call timer_stop(TIME_DISTCRD)
-
-#endif /* MPI */
-
- ! ----fix lone pair positions:
- if( numextra > 0 )call local_to_global(x,xx,ix)
-
-#ifdef MPI
- call timer_start(TIME_VERLET)
- ! ========================= END AMBER/MPI =========================
-#endif /* MPI */
-
- !-------------------------------------------------------------------
- ! Step 6: zero COM velocity if requested; used for preventing
- ! ewald "block of ice flying thru space" phenomenon, or accumulation
- ! of rotational momentum in vacuum simulations
- !-------------------------------------------------------------------
-
- !-----------------------------------------------------------------
- ! --- put current velocities into VOLD
- !-----------------------------------------------------------------
-
- vold(istart3:iend3) = v(istart3:iend3)
- do im=1,iscale
- vold(nr3+im) = v(nr3+im)
- end do
-
- !-------------------------------------------------------------------
- ! Step 7: scale coordinates if constant pressure run:
- !-------------------------------------------------------------------
-
- ! ntp = 1, isotropic pressure coupling
-
- if (ntp == 1) then
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(4)))**third
- rmu(2) = rmu(1)
- rmu(3) = rmu(1)
-
-
- ! ntp = 2, anisotropic pressure scaling
-
- else if (ntp == 2) then
-
- if (csurften > 0) then
-
- ! Constant surface tension adjusts the tangential pressures
- ! See Zhang, Feller, Brooks, Pastor. J. Chem. Phys. 1995
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
-
- end if
-
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- else
-
- rmu(1) = (1.d0-dtcp*(pres0-ener%pres(1)))**third
- rmu(2) = (1.d0-dtcp*(pres0-ener%pres(2)))**third
- rmu(3) = (1.d0-dtcp*(pres0-ener%pres(3)))**third
-
- end if
-
- ! ntp = 3, semiisotropic pressure coupling
- ! (currently only for csurften>0, constant surface tension)
-
- !else if (ntp > 2) then
- else
-
- if (csurften > 0) then
-
- if (csurften == 1) then ! For surface tension in the x direction
- pres0y = pres0x - gamma_ten_int * ten_conv / box(1)
- pres0z = pres0y
- press_tan_ave = (ener%pres(2) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - ener%pres(1)))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- else if (csurften == 2) then ! For surface tension in the y direction
- pres0x = pres0y - gamma_ten_int * ten_conv / box(2)
- pres0z = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(3))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - ener%pres(2)))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - press_tan_ave))**third
-
- !else if (csurften == 3) then ! For surface tension in the z !direction
- else
- pres0x = pres0z - gamma_ten_int * ten_conv / box(3)
- pres0y = pres0x
- press_tan_ave = (ener%pres(1) + ener%pres(2))/2
- rmu(1) = (1.d0 - dtcp * (pres0x - press_tan_ave))**third
- rmu(2) = (1.d0 - dtcp * (pres0y - press_tan_ave))**third
- rmu(3) = (1.d0 - dtcp * (pres0z - ener%pres(3)))**third
-
- end if ! csurften == 1
- end if ! csurften > 0
- ! Add semiisotropic pressure scaling in any direction with no constant
- ! surface tension here
- end if
-
- if (ntp > 0) then
- box(1:3) = box(1:3)*rmu(1:3)
- ener%box(1:3) = box(1:3)
-
- ! WARNING!! This is not correct for non-orthogonal boxes if
- ! NTP > 1 (i.e. non-isotropic scaling). Currently general cell
- ! updates which allow cell angles to change are not implemented.
- ! The viral tensor computed for ewald is the general Nose Klein,
- ! however the cell response needs a more general treatment.
-
- call redo_ucell(rmu)
- ! keep tranvec up to date, rather than recomputing each MD step.
- call fill_tranvec() ! tranvec is dependent on only ucell
-
- call ew_pscale(natom,x,amass,nspm,nsp,npscal)
- if (ntr > 0 .and. nrc > 0) &
- call ew_pscale(natom,xc,amass,nspm,nsp,npscal)
- endif
-
- ener%kin%solv = ekpbs + ener%pot%tot
- ! Pastor, Brooks, Szabo conserved quantity
- ! for harmonic oscillator: Eq. 4.7b of Mol.
- ! Phys. 65:1409-1419, 1988
- ener%kin%solt = eke
- ener%kin%tot = ener%kin%solt
- if (ntt == 1 .and. onstep) then
- ekmh = max(ekph,fac(1)*10.d0)
- end if
-
- ! ---if velocities were reset, the KE is not accurate; fudge it
- ! here to keep the same total energy as on the previous step.
- ! Note that this only affects printout and averages for Etot
- ! and KE -- it has no effect on the trajectory, or on any averages
- ! of potential energy terms.
-
- if( resetvelo ) ener%kin%tot = etot_save - ener%pot%tot
-
- ! --- total energy is sum of KE + PE:
-
- ener%tot = ener%kin%tot + ener%pot%tot
- etot_save = ener%tot
-
- !-------------------------------------------------------------------
- ! Step 8: update the step counter and the integration time:
- !-------------------------------------------------------------------
-
- nstep = nstep+1
-
- ! ---full energies are only calculated every nrespa steps
- ! nvalid is the number of steps where all energies are calculated
-
- ntnb = 0
- if (mod(nstep,nsnb) == 0) ntnb = 1
-
-#if 0
-! DEBUG code -- this will print out every frame of the relaxation dynamics to
-! the trajectory if uncommented
-
- if (master) then
-
- ! -- Coordinate archive:
- if (.true.) then
- if( iwrap == 0 ) then
- call corpac(x,1,nrx,MDCRD_UNIT,loutfm)
- if(ntb > 0) call corpac(box,1,3,MDCRD_UNIT,loutfm)
- else if (iwrap == 1) then
- call get_stack(l_temp,nr3,routine)
- if(.not. rstack_ok)then
- deallocate(r_stack)
- allocate(r_stack(1:lastrst),stat=alloc_ier)
- call reassign_rstack(routine)
- endif
- REQUIRE(rstack_ok)
- do m=1,nr3
- r_stack(l_temp+m-1) = x(m)
- end do
-
- call wrap_molecules(nspm,nsp,r_stack(l_temp))
- if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
-
- call corpac(r_stack(l_temp),1,nrx,MDCRD_UNIT,loutfm)
- call corpac(box,1,3,MDCRD_UNIT,loutfm)
- call free_stack(l_temp,routine)
- end if ! if (iwrap == 0) ...
-
-
- !GMS: If using variable QM solvent, try to write a new pdb file
- ! with the QM coordinates for this step. This is done here
- ! to keep the PDB file in sync with the mdcrd file, which
- ! makes it easier to check later.
- if (qmmm_nml%vsolv > 0 .and. qmmm_nml%verbosity == 0) &
- call qm_print_coords(nstep,.false.)
- end if ! (itdump)
-
- if (ioutfm > 0) then
- if (.true.) call end_binary_frame(MDCRD_UNIT)
- end if
-
- end if ! (master)
-#endif /* 0 */
-
- !=======================================================================
-
- ! ---major cycle back to new step unless we have reached our limit:
-
- call trace_integer( 'end of step', nstep )
- call trace_output_mpi_tally( )
- call timer_stop(TIME_VERLET)
-
- if (nstep < relax_nstlim) goto 260
- 480 continue
-
-end subroutine relaxmd
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Enter description for quench here.
-subroutine quench(f,v)
- implicit none
-
-#include "../include/md.h"
-!need access to vv - temp verlet scaling
-#include "../include/memory.h"
-!need access to natom
-
- _REAL_ f(*),v(*),dotproduct,force
- !f is the forces and v is the velocity
-
- integer index
- dotproduct = 0.d0
- force = 0.d0
-
- do index=1,3*natom
- force = force + f(index)**2
- dotproduct = dotproduct + v(index)*f(index)
- enddo
-
- if (force/=0.0d0) then
- force = 1.0d0/sqrt(force)
- dotproduct = dotproduct*force
- end if
-
- if (dotproduct>0.0d0) then
- v(1:3*natom) = dotproduct*f(1:3*natom)*force
- else
- !v(1:3*natom) = 0.0d0
- v(1:3*natom) = vfac*dotproduct*f(1:3*natom)*force
- end if
-
-end subroutine quench
diff --git a/patches/amber14.diff/AmberTools/src/sander/sander.F90 b/patches/amber14.diff/AmberTools/src/sander/sander.F90
deleted file mode 100644
index bd3eb4dc4f90286a8dd8af436dfce7c2f248c9ad..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/sander.F90
+++ /dev/null
@@ -1,1925 +0,0 @@
-#include "copyright.h"
-#include "../include/dprec.fh"
-#include "../include/assert.fh"
-#include "ncsu-config.h"
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ The Molecular Dynamics/NMR Refinement/Modeling Module of the AMBER
-!-----------------------------------------------------------------------
-! --- SANDER ---
-!-----------------------------------------------------------------------
-
-subroutine sander()
-
- use state
-#ifndef DISABLE_NCSU
- use ncsu_sander_hooks, only : &
- ncsu_on_sander_init => on_sander_init, &
- ncsu_on_sander_exit => on_sander_exit
-#endif /* DISABLE_NCSU */
-
- use lmod_driver
- use constants, only : INV_AMBER_ELECTROSTATIC, plumed, plumedfile
- ! The main qmmm_struct contains all the QMMM variables and arrays
- use qmmm_module, only : qmmm_nml, qmmm_struct, deallocate_qmmm, qmmm_mpi, &
-#ifdef MPI
- qmmm_mpi_setup, &
-#endif
- qm2_struct, qmewald, qm_gb, qmmm_vsolv, qm2_params
-
- use qmmm_vsolv_module, only: qmmm_vsolv_store_parameters, new
-
- use qm2_extern_module, only: qm2_extern_finalize
- use sebomd_module, only : sebomd_obj, &
- sebomd_open_files, sebomd_close_files, &
-#ifdef MPI
- sebomd_bcast_obj, &
-#endif
- sebomd_setup
-
- use sebomd_arrays, only : init_sebomd_arrays, cleanup_sebomd_arrays
-
- use genborn
- use decomp, only : allocate_int_decomp, allocate_real_decomp, &
- deallocate_int_decomp, deallocate_real_decomp, &
-#ifdef MPI
- synchronize_dec, build_dec_mask, decmask, &
-#endif
- nat, nrs, jgroup, indx
- use fastwt
- use relax_mat
- use nmr, only: nmrrad, impnum
- use ew_recip, only: deallocate_m1m2m3,first_pme
- use parms
- use molecule, only : mol_info, n_iwrap_mask_atoms, iwrap_mask_atoms, &
- allocate_molecule, deallocate_molecule
- use nblist, only:cutoffnb,skinnb,nblist_allocate,nblist_deallocate, &
- nblist_allreal,nblist_allint, num_calls_nblist, first_list_flag
- use stack
- use amoeba_runmd, only : AM_RUNMD_get_coords,AM_RUNMD
- use amoeba_mdin, only : beeman_integrator,iamoeba,am_nbead
- use amoeba_interface, only : AMOEBA_deallocate,AMOEBA_readparm
-
-#ifdef RISMSANDER
- use sander_rism_interface, only: rismprm,rism_setparam, rism_init,rism_finalize
-#endif
-
-#ifdef PUPIL_SUPPORT
- use pupildata
-#endif /* PUPIL */
-
-#ifdef APBS
- use apbs
-#endif /* APBS */
-
-#ifdef _XRAY
- use xray_interface_module, only: xray_init, xray_read_parm, xray_fini
-#endif
-
-#ifdef MPI /* SOFT CORE */
- use softcore, only: setup_sc, cleanup_sc, ifsc, extra_atoms, sc_sync_x, &
- summarize_ti_changes, sc_check_perturbed_molecules, ti_check_neutral, tishake
- use mbar, only: setup_mbar, cleanup_mbar, ifmbar
-#endif
-
- ! for LIE calculations
- use linear_response, only: ilrt, setup_linear_response, &
- cleanup_linear_response
-
-#if defined(MPI)
- use evb_parm, only: xch_type
-# if defined(LES)
- use evb_pimd, only: evb_pimd_init, PE_slice, master_worldrank, jobs_per_node
-# endif
-! REMD
- use remd, only : rem, mdloop, repnum, remd1d_setup, remd_exchange, &
- remd_cleanup, hremd_exchange, ph_remd_exchange, &
- multid_remd_setup, multid_remd_exchange
- use bintraj, only: setup_remd_indices
-#else
-# define rem 0
-#endif /* MPI */
-
- use pimd_vars, only: ipimd
- use neb_vars, only: ineb
-
- use trajenemod, only: trajene
-
-!RCW+MJW CHARMM SUPPORT
- use charmm_mod, only : charmm_active, charmm_deallocate_arrays, &
- charmm_filter_out_qm_atoms
- use ff11_mod, only : cmap_active, deallocate_cmap_arrays
-
- use memory_module, only: x, ix, ih, memory_init
-
-! Self-Guided molecular/Langevin Dynamics (SGLD)
- use sgld, only : isgld,psgld
-
- use nbips, only: ipssys,ips
-
- use crg_reloc, only: ifcr, cr_backup_charge, cr_cleanup, cr_allocate, &
- cr_read_input, cr_check_input, cr_print_info
-
- use emap,only: temap,pemap,qemap
-
- use file_io_dat
- use constantph, only : cnstph_finalize
- use barostats, only : mcbar_setup
-
-!AMD
- use amd_mod
-!scaledMD
- use scaledMD_mod
-
- use abfqmmm_module ! lam81
-
- implicit none
-
- logical belly, erstop
- integer ier,ifind,jn,ncalls,xmin_iter
- character(len=4) itest
- logical ok
- logical newstyle
-# include "../include/memory.h"
-# include "nmr.h"
-# include "box.h"
-# include "../include/md.h"
-# include "extra.h"
-# include "tgtmd.h"
-# include "multitmd.h"
-# include "les.h"
-
-# include "parallel.h"
-#ifdef MPI
- ! =========================== AMBER/MPI ===========================
-# ifdef MPI_DOUBLE_PRECISION
-# undef MPI_DOUBLE_PRECISION
-# endif
- include 'mpif.h'
-# ifdef CRAY_PVP
-# define MPI_DOUBLE_PRECISION MPI_REAL8
-# endif
-# ifdef MPI_BUFFER_SIZE
- integer*4 mpibuf(mpi_buffer_size)
-# endif
-! REMD: loop is the current exchange. runmd is called numexchg times.
- integer loop
-
- integer nrank, istat
- _REAL_ ener(30),vir(4)
- integer ierr
- integer partner
-! ========================= END AMBER/MPI =========================
-#endif
-# include "ew_pme_recip.h"
-# include "ew_frc.h"
-# include "ew_erfc_spline.h"
-# include "ew_parallel.h"
-# include "ew_mpole.h"
-# include "ew_cntrl.h"
-# include "def_time.h"
-
- type(state_rec) :: ene
- integer native,nr3,nr
-
- ! nmrcal vars
- _REAL_ f,enmr,devdis,devang,devtor,devplpt,devpln,devgendis,ag,bg,cg
- ! Updated 9/2007 by Matthew Seetin to enable plane-point and plane-plane
- ! restraints
- _REAL_ emtmd
- integer numphi,nhb
-
- ! runmin/trajene var
- _REAL_ carrms
-
- ! dipole moment stuff
- integer ngrp
-
- character(len=8) initial_date, setup_end_date, final_date
- character(len=10) initial_time, setup_end_time, final_time
- integer nstlim_total ! for final time printout
-
- _REAL_ time0, time1
-
- integer idiff,i,j,istop,index,ierror,itemp
-
- integer, dimension(:), allocatable :: ipairs
- integer :: n_force_calls
- logical qsetup
- logical :: do_list_update=.false.
- _REAL_ :: box_center(3) ! lam81
-#ifdef MPI_DEBUGGER
- integer, volatile :: release_debug
-
- ! So only the master master thread has release_debug = 0
- release_debug = worldrank
-
- ! Lock us into an infinite loop while release_debug == 0 on any thread (only
- ! the master here). This allows you to connect a debugger to any running
- ! process without having to 'race' program execution. A debugger MUST be
- ! attached to the master thread (typically the thread with the lowest PID),
- ! and have release_debug set to NOT 0 (e.g., via "set release_debug=1").
- do
- if (release_debug .ne. 0) exit
- end do
-
- ! Prevent any other threads from progressing past this point until all
- ! threads you want to watch with a debugger are watched and all those
- ! threads are continued.
- call mpi_barrier(mpi_comm_world, ierr)
-#endif
-
- ! ---- HERE BEGIN THE EXECUTABLE STATEMENTS ----
-
- ! Initialize the cpu timer. Needed for machines where returned cpu times
- ! are relative.
- call date_and_time( initial_date, initial_time )
- call wallclock( time0 )
- call init_timers()
-
- ! Initialize the printing of ongoing time and performance summaries.
-! call print_ongoing_time_summary(0,0,0.0d0,7)
- call print_ongoing_time_summary(0,0,0.0d0,7,time0)
-
- ! BPR - original location of PUPIL interface. I moved it further down
- ! because, if it's here, it can't print stuff; write(6,...) statements
- ! assume mdread1() has already been invoked. However, moving this down
- ! may break other things.
-
- ! ==== Flag to tell list builder to print size of list on first call =======
- first_list_flag = .true.
- ! ==== Flag to tell recip space routines to allocate on first call =======
- first_pme = .true.
-
- ! ==== Initialise first_call flags for QMMM ====
- qmmm_struct%qm_mm_first_call = .true.
- qmmm_struct%fock_first_call = .true.
- qmmm_struct%fock2_2atm_first_call = .true.
- qmmm_struct%qm2_allocate_e_repul_first_call = .true.
- qmmm_struct%qm2_calc_rij_eqns_first_call = .true.
- qmmm_struct%qm2_scf_first_call = .true.
- qmmm_struct%zero_link_charges_first_call = .true.
- qmmm_struct%adj_mm_link_pair_crd_first_call = .true.
- qmmm_struct%num_qmmm_calls = 0
-
-#ifdef MPI
- ! Parallel initialization (setup is done in multisander.F90).
-
- ! Make PE 0 the master
- master = mytaskid == 0
- master_master = masterrank == 0
-
- if ( master .and. numtasks > MPI_MAX_PROCESSORS ) then
- write(0, '(a,i4,a,i4)') &
- 'Error: the number of processors must not be greater than ', &
- MPI_MAX_PROCESSORS, ', but is ', numtasks
- call mexit(6,1)
- end if
-# ifdef MPI_BUFFER_SIZE
- call mpi_buffer_attach(mpibuf, mpi_buffer_size*4, ierr)
-# endif
-#else /* not MPI follows */
- ! In the single-threaded version, the one process is master
- master = .true.
-#endif /* MPI */
-
- erstop = .false.
- qsetup = .true.
-
- ! --- generic packing scheme ---
-
- nwdvar = 1
- native = 32
-#ifdef ISTAR2
-
- ! --- Int*2 packing scheme ---
-
- nwdvar = 2
-#endif /*ISTAR2*/
- numpk = nwdvar
- nbit = native/numpk
-
- ! ----- Only the master node (only node when single-process)
- ! performs the initial setup and reading/writing -----
-
- call timer_start(TIME_TOTAL)
-
- call abfqmmm_init_param() ! lam81
-
- do while ( (abfqmmm_param%qmstep <= abfqmmm_param%maxqmstep) &
- .or. (abfqmmm_param%maxqmstep == 0 .and. abfqmmm_param%system == 2) ) ! lam81
-
- masterwork: if (master) then
-
- if (abfqmmm_param%abfqmmm == 0) then ! lam81
-
- ! ---- first, initial reads to determine memory sizes:
- call mdread1()
- call amopen(8,parm,'O','F','R')
- call rdparm1(8)
- if (mtmd /= 'mtmd' .or. itgtmd == 2) call mtmdlx(natom)
- ! --- now, we can allocate memory:
-
- call locmem()
- write(6,'(/,a,5x,a)') '|','Memory Use Allocated'
- write(6,'(a,5x,a,i14)') '|', 'Real ', lastr
- write(6,'(a,5x,a,i14)') '|', 'Hollerith ', lasth
- write(6,'(a,5x,a,i14)') '|', 'Integer ', lasti
- write(6,'(a,5x,a,i14)') '|', 'Max Pairs ', lastpr
-
- ! --- dynamic memory allocation:
-
- ! GMS:
- ! Allocate space for module molecule
- ! in the master node
- mol_info%natom = natom
- mol_info%nres = nres
- call allocate_molecule()
-
- ! Allocate all global arrays
- allocate( x(lastr), ix(lasti), ipairs(lastpr), ih(lasth), stat = ier )
- REQUIRE( ier == 0 )
- ix(1:lasti) = 0
-
- ! This sets up pointer arrays in MEMORY_MODULE to match array-offsets into
- ! the shared X, IX, and IH arrays. Eventually, LOCMEM code should be
- ! merged with MEMORY_MODULE to allocate individual allocatable arrays, but
- ! that will also require updating the MPI code to handle individual
- ! arrays.
- call memory_init()
-
- ! Allocate the parm arrays
- call allocate_parms()
-
- if ((igb /= 0 .and. igb /= 10 .and. ipb == 0) &
- .or.hybridgb>0.or.icnstph.gt.1) &
- call allocate_gb( natom, ncopy )
-
- if( idecomp > 0 ) then
-#ifdef MPI
- if (ifsc > 0) then
- call synchronize_dec(natom, nres)
- else
- nat = natom
- nrs = nres
- end if
-#else
- nat = natom
- nrs = nres
-#endif
- call allocate_int_decomp(natom, nres)
- else
- call allocate_int_decomp(1, 1)
- end if
-
- write(6,'(a,5x,a,i14)' ) '|', 'nblistReal', nblist_allreal
- write(6,'(a,5x,a,i14)' ) '|', 'nblist Int', nblist_allint
- write(6,'(a,5x,a,i14,a)') '|', ' Total ', &
- (8*(lastr+lastrst+nblist_allreal) &
- + 4*(lasth+lasti+lastpr+lastist+nblist_allint))/1024, &
- ' kbytes'
-
- ! --- finish reading the prmtop file and other user input:
- call rdparm2(x,ix,ih,ipairs,8)
-
- call AMOEBA_readparm(8,ntf,ntc,natom,x(lmass))! ntf,ntc get reset if amoeba prmtop
-#ifdef _XRAY
- call xray_read_parm(8,6)
-#endif
-
- end if ! lam81
-
- if (qmmm_nml%ifqnt .or. abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%abfqmmm == 0) then ! lam81
- call sebomd_setup
- call read_qmmm_nm_and_alloc(igb, ih, ix, x, cut, use_pme, ntb, 0) ! lam81
- if (qmmm_nml%qmtheory%SEBOMD) then
- ! don't do QM/MM
- qmmm_nml%ifqnt= .false.
- sebomd_obj%do_sebomd = .true.
- end if
- end if ! lam81
- if(qmmm_struct%abfqmmm == 1 .and. abfqmmm_param%abfqmmm == 0) then ! lam81
- call abfqmmm_setup(natom,nres,ix(i02),ih(m04),ih(m02),x(lmass), & ! lam81
- nbonh,nbona,ix(iibh),ix(ijbh),ix(iiba),ix(ijba)) ! lam81
- nr=natom ! lam81
- call AMOEBA_check_newstyle_inpcrd(inpcrd,newstyle) ! lam81
- if (newstyle) then ! lam81
- call AM_RUNMD_get_coords(natom,t,irest,ntb,x(lcrd),x(lvel)) ! lam81
- else ! lam81
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.FALSE.) ! lam81
- end if ! lam81
- abfqmmm_param%maxqmstep = nstlim ! lam81
- end if ! lam81
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%system == 1) then ! lam81
- call abfqmmm_update_qmatoms(x(lcrd)) ! lam81
- if(abfqmmm_param%ntwpdb < 0) then ! lam81
- call abfqmmm_write_pdb(x(lcrd),ix(i70)) ! lam81
- close(6) ! lam81
- call mexit(6,1) ! lam81
- end if ! lam81
- end if ! lma81
- call abfqmmm_select_system_qmatoms(natom) ! lam81
- if(qmmm_nml%ifqnt) then ! lam81
- call read_qmmm_nm_and_alloc(igb,ih,ix,x,cut,use_pme,ntb,abfqmmm_param%qmstep, & ! lam81
- abfqmmm_param%isqm,abfqmmm_param%abfcharge) ! lam81
- end if ! lam81
- endif ! lam81
- end if ! lam81
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
-
- call mdread2(x,ix,ih,ipairs)
-
- endif ! lam81
-
-#if defined(RISMSANDER)
- call rism_setparam(mdin,&
- commsander,&
- natom,ntypes,x(L15:L15+natom-1),&
- x(LMASS:LMASS+natom-1),cn1,cn2,&
- ix(i04:i04+ntypes**2-1), ix(i06:i06+natom-1))
-#endif /*RISMSANDER*/
-
- if ( ifcr /= 0 ) then
- call cr_read_input(natom)
- call cr_check_input( ips )
- !call cr_print_info(6)
- call cr_backup_charge( x(l15), natom )
- end if
-
- ! --- alloc memory for decomp module that needs info from mdread2
- if (idecomp == 1 .or. idecomp == 2) then
- call allocate_real_decomp(nrs)
-#ifdef MPI
- ! -- ti decomp
- if (ifsc > 0) then
- ! following lines don't really seem to make sense(?)
- ! partner = ieor(masterrank,1)
- ! if (nat == natom) then
- ! nrank = masterrank
- ! else
- ! nrank = partner
- ! end if
- call mpi_bcast(jgroup, nat, MPI_INTEGER, 0, commmaster, ierr)
- end if
-#endif
- else if( idecomp == 3 .or. idecomp == 4 ) then
- call allocate_real_decomp(npdec*npdec)
- end if
-
- ! ----- EVALUATE SOME CONSTANTS FROM MDREAD SETTINGS -----
-
- nr = nrp
- nr3 = 3*nr
- belly = ibelly > 0
-
- ! ========================= PUPIL INTERFACE =========================
-#ifdef PUPIL_SUPPORT
-
- ! I moved the PUPIL interface down here so that write() statements work
- ! as advertised. BPR 9/7/09
-
- ! Initialise the CORBA interface
- puperror = 0
- call fixport()
- call inicorbaintfcmd(puperror)
- if (puperror .ne. 0) then
- write(6,*) 'Error creating PUPIL CORBA interface.'
- call mexit(6,1)
- end if
- pupactive = .true.
- write(6,*) 'PUPIL CORBA interface initialized.'
-
- ! Allocation of memory and initialization
- pupStep = 0
- puperror = 0
- allocate (qcell (12 ),stat=puperror)
- allocate (pupmask (natom ),stat=puperror)
- allocate (pupqlist(natom ),stat=puperror)
- allocate (pupatm (natom ),stat=puperror)
- allocate (pupchg (natom ),stat=puperror)
- allocate (qfpup (natom*3),stat=puperror)
- allocate (qcdata (natom*9),stat=puperror)
- allocate (keyMM (natom ),stat=puperror)
- allocate (pupres (nres ),stat=puperror)
- allocate (keyres (nres ),stat=puperror)
-
- if (puperror /= 0) then
- write(6,*) 'Error allocating PUPIL interface memory.'
- call mexit(6,1)
- end if
-
- ! Initialise the "atomic numbers" and "quantum forces" vectors
- pupqatoms = 0
- iresPup = 1
- pupres(1) = 1
- do iPup=1,natom
- bs1 = (iPup-1)*3
- call get_atomic_number_pupil(ih(iPup+m06-1),x(lmass+iPup-1),pupatm(iPup))
- if (iresPup .lt. nres) then
- if (iPup .ge. ix(iresPup+i02)) then
- iresPup = iresPup + 1
- pupres(iresPup) = iPup
- end if
- end if
- write (strAux,"(A4,'.',A4)") trim(ih(iresPup+m02-1)),adjustl(ih(iPup+m04-1))
- keyres(iresPup) = trim(ih(iresPup+m02-1))
- keyMM(iPup) = trim(strAux)
-
- ! Retrieve the initial charges
- pupchg(iPup) = x(L15+iPup-1)
- !write(6,*) 'Atom num.',iPup,'Label,Mass,Atomic Num.', keyMM(iPup),x(lmass+iPup-1),pupatm(iPup), 'Charge', pupchg(iPup)
-
- do jPup=1,3
- qfpup(bs1+jPup) = 0.0d0
- end do
- end do
-
- write(6,*) 'Got all atomic numbers.'
-
- ! Initialise the PUPIL cell
- do iPup=1,12
- qcell(iPup) = 0.0d0
- end do
-
- ! Submit the KeyMM particles and their respective atomic numbers to PUPIL
- puperror = 0
- call putatomtypes(natom,puperror,pupatm,keyMM)
- if (puperror .ne. 0) then
- write(6,*) 'Error sending MM atom types to PUPIL.'
- call mexit(6,1)
- end if
-
- ! Submit the Residue Pointer vector to PUPIL
- write(6,"(a20,1x,i6,3x,a17,1x,i6)") 'Number of residues =', nres, 'Number of atoms =', natom
- !do iPup=1,nres
- ! write(6,*) 'Residue ',iPup,keyres(iPup),pupres(iPup)
- !end do
- puperror = 0
- call putresiduetypes(nres,puperror,pupres,keyres)
- if (puperror .ne. 0) then
- write(6,*) 'Error sending MM residue types to PUPIL.'
- call mexit(6,1)
- end if
-
- write(6,*) 'Sent system data to PUPIL.'
- write(*,*) 'PUPIL structure initialized.'
-#endif
- ! ========================= PUPIL INTERFACE =========================
-
- ! --- seed the random number generator ---
-
- ! DAN ROE: Note master node only here
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
-#ifdef MPI
- if (rem == 0) then
- call amrset(ig)
- else
- ! carlos: set random seed different for different replicas
- ! but keep same seed for cpus in the same replica since
- ! we want data from diff # cpus to match
- call amrset(ig + (17 * nodeid)) ! nodeid is in md.h and is repnum - 1
- end if
-#else
- call amrset(ig)
-#endif
-
- if (nbit < 32 .and. nr > 32767) then
- write(6, *) ' Too many atoms for 16 bit pairlist -'
- write(6, *) ' Recompile without ISTAR2'
- call mexit(6, 1)
- end if
-
- if (ntp > 0.and.iabs(ntb) /= 2) then
- write(6,*) 'Input of NTP/NTB inconsistent'
- call mexit(6, 1)
- end if
- end if ! lam81
-
- ! ----- READ COORDINATES AND VELOCITIES -----
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81 <<< QMSTEP=1 BLOCK >>>
-
- call timer_start(TIME_RDCRD)
-#ifdef LES
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0les,.TRUE.,solvph)
-#else
- call AMOEBA_check_newstyle_inpcrd(inpcrd,newstyle)
- if (newstyle) then
- call AM_RUNMD_get_coords(natom,t,irest,ntb,x(lcrd),x(lvel))
- else
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.TRUE.,solvph)
- end if
-#endif
- if (iamoeba > 0) then
- natom = natom*am_nbead
- nrp = nrp*am_nbead
- nr = nr*am_nbead
- nr3 = nr3*am_nbead
- ncopy = am_nbead
- end if
-
- ! M-WJ
- !if( igb == 0 .and. induced == 1 ) call get_dips(x,nr)
-! WJM if is a polarizable model, reading input dipole information
- if (igb == 0 .and. ipb == 0 .and. induced > 0) call get_dips(x,nr)
-
-#ifdef APBS
- ! APBS initialization
- if (mdin_apbs) then
- ! in: natom, coords, charge and radii (from prmtop)
- ! out: pb charges and pb radii (via apbs_vars module)
- call apbs_init(natom, x(lcrd), x(l15), x(l97))
- end if
-#endif /* APBS */
-
-#ifdef _XRAY
- call xray_init()
-#endif
-
- ! ----- SET THE INITIAL VELOCITIES -----
-
- if (ntx <= 3) then
- call setvel(nr,x(lvel),x(lwinv),tempi,init,iscale,scalm)
- ! random numbers may have been "used up" in setting the intial
- ! velocities; re-set the generator so that all nodes are back in
- ! sync
-
- ! DAN ROE: Note master node only here
-#ifdef MPI
- if (rem == 0) call amrset(ig)
-#else
- call amrset(ig)
-#endif
-
- end if
- if (belly) call bellyf(natom,ix(ibellygp),x(lvel))
- call timer_stop(TIME_RDCRD)
-
- if(abfqmmm_param%abfqmmm == 1 .and. ntb > 0) then ! lam81
- call iwrap2(abfqmmm_param%n_user_qm, abfqmmm_param%user_qm, x(lcrd), box_center) ! lam81
- end if ! lam81
-
- ! --- If we are reading NMR restraints/weight changes,
- ! read them now:
-
- if (nmropt >= 1) then
- call nmrcal(x(lcrd),f,ih(m04),ih(m02),ix(i02),x(lwinv),enmr, &
- devdis,devang,devtor,devplpt,devpln,devgendis,temp0,tautp,cut,ntb,x(lnmr01), &
- ix(inmr02),x(l95),5,6,rk,tk,pk,cn1,cn2, &
- ag,bg,cg,numbnd,numang,numphi,nimprp, &
- nhb,natom,natom,ntypes,nres,rad,wel,radhb, &
- welhb,rwell,isftrp,tgtrmsd,temp0les,-1,'READ')
- ! Updated 9/2007 by Matthew Seetin to enable plane-point and plane-plane restraints
-
- ! --- Determine how many of the torsional parameters
- ! are impropers
- call impnum(ix(i46),ix(i56),ix(i48),ix(i58),nphih,nphia, &
- 0,nptra,nimprp)
- end if
-
- ! -- Set up info related to weight changes for the non-bonds:
-
- call nmrrad(rad,wel,cn1,cn2,ntypes,0,0.0d0)
- call decnvh(asol,bsol,nphb,radhb,welhb)
-
- if (iredir(4) > 0) call noeread(x,ix,ih)
- if (iredir(8) > 0) call alignread(natom, x(lcrd))
- if (iredir(9) > 0) call csaread
-
- end if ! lam81 <<< QMSTEP=1 BLOCK >>>
-
- !---------------------------------------------------------------
- ! --- Call FASTWAT, which will tag those bonds which are part
- ! of 3-point water molecules. Constraints will be effected
- ! for these waters using a fast analytic routine -- dap.
-
- call timer_start(TIME_FASTWT)
-
- call fastwat(ih(m04),nres,ix(i02),ih(m02), &
- nbonh,nbona,ix(iibh),ix(ijbh),ibelly,ix(ibellygp), &
- iwtnm,iowtnm,ihwtnm,jfastw,ix(iifstwt), &
- ix(iifstwr),ibgwat,ienwat,ibgion,ienion,iorwat, &
- 6,natom)
- call timer_stop(TIME_FASTWT)
-
- call getwds(ih(m04), nres , ix(i02) , ih(m02) , &
- nbonh , nbona , 0 , ix(iibh) , &
- ix(ijbh) , iwtnm , iowtnm , ihwtnm , &
- jfastw , ix(iicbh) , req , x(lwinv) , &
- rbtarg , ibelly , ix(ibellygp), 6 )
-
- ! Assign link atoms between quantum mechanical and molecular mechanical
- ! atoms if quantum atoms are present.
- ! After assigning the link atoms, delete all connectivity between the
- ! QM atoms.
- if(qmmm_nml%ifqnt) then
-
- call identify_link_atoms(nbona,ix(iiba),ix(ijba))
-
- ! Variable QM solvent:
- ! Store the original bond parameters since we will need to rebuild
- ! the QM region (delete bonded terms etc) repeatedly
- if ( qmmm_nml%vsolv > 0 ) then
- call new(qmmm_vsolv, nbonh, nbona, ntheth, ntheta, nphih, nphia)
- call qmmm_vsolv_store_parameters(qmmm_vsolv, numbnd, &
- ix(iibh), ix(ijbh), ix(iicbh), &
- ix(iiba), ix(ijba), ix(iicba), &
- ix(i24), ix(i26), ix(i28), ix(i30), &
- ix(i32), ix(i34), ix(i36), ix(i38), &
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), &
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58))
- end if
-
- if( abfqmmm_param%abfqmmm == 1 ) then ! lam81
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call abfqmmm_allocate_arrays_of_parameters(numbnd, nbonh, nbona, ntheth, ntheta, nphih, nphia) ! lam81
- call abfqmmm_store_parameters(ix(iibh), ix(ijbh), ix(iicbh), & ! lam81
- ix(iiba), ix(ijba), ix(iicba), & ! lam81
- ix(i24), ix(i26), ix(i28), ix(i30), & ! lam81
- ix(i32), ix(i34), ix(i36), ix(i38), & ! lam81
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), & ! lam81
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58), & ! lam81
- x(l15), rk, req) ! lam81
- else ! lam81
- call abfqmmm_set_parameters(numbnd, nbonh, nbona, ntheth, ntheta, nphih, nphia, & ! lam81
- ix(iibh), ix(ijbh), ix(iicbh), & ! lam81
- ix(iiba), ix(ijba), ix(iicba), & ! lam81
- ix(i24), ix(i26), ix(i28), ix(i30), & ! lam81
- ix(i32), ix(i34), ix(i36), ix(i38), & ! lam81
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), & ! lam81
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58), & ! lam81
- x(l15), rk, req) ! lam81
-
- call init_extra_pts(ix(iibh),ix(ijbh),ix(iicbh), & ! lam81
- ix(iiba),ix(ijba),ix(iicba), & ! lam81
- ix(i24),ix(i26),ix(i28),ix(i30), & ! lam81
- ix(i32),ix(i34),ix(i36),ix(i38), & ! lam81
- ix(i40),ix(i42),ix(i44),ix(i46),ix(i48), & ! lam81
- ix(i50),ix(i52),ix(i54),ix(i56),ix(i58), & ! lam81
- ih(m06),ix,x,ix(i08),ix(i10), & ! lam81
- nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req) ! lam81
-
- end if ! lam81
- end if ! lam81
-
- ! Remove bonds between QM atoms from list (Hydrogen)
- if (nbonh .gt. 0) call setbon(nbonh,ix(iibh),ix(ijbh),ix(iicbh), &
- ix(ibellygp))
-
- ! Remove bonds between QM atoms from list (Heavy)
- if (nbona .gt. 0) call setbon(nbona,ix(iiba),ix(ijba),ix(iicba), &
- ix(ibellygp))
-
- ! Remove angles between QM atoms from list (Hydrogen)
- if (ntheth .gt. 0) call setang(ntheth,ix(i24),ix(i26),ix(i28),ix(i30), &
- ix(ibellygp))
-
- ! Remove angles between QM atoms from list (Heavy)
- if (ntheta .gt. 0) call setang(ntheta,ix(i32),ix(i34),ix(i36),ix(i38),&
- ix(ibellygp))
-
- ! Remove dihedrals between QM atoms from list (Hydrogen)
- if (nphih .gt. 0) call setdih(nphih,ix(i40),ix(i42),ix(i44),ix(i46), &
- ix(i48), ix(ibellygp))
-
- ! Remove dihedrals between QM atoms from list (Heavy)
- if (nphia .gt. 0) call setdih(nphia,ix(i50),ix(i52),ix(i54),ix(i56), &
- ix(i58), ix(ibellygp))
-
- ! Remove CHARMM energy terms from QM region
- call charmm_filter_out_qm_atoms()
-
- ! Now we should work out the type of each quantum atom present.
- ! This is used for our arrays of pre-computed parameters. It is
- ! essentially a re-basing of the atomic numbers and is done to save
- ! memory. Note: qm_assign_atom_types will allocate the qm_atom_type
- ! array for us. Only the master calls this routine. All other
- ! threads get this allocated and broadcast to them by the mpi setup
- ! routine.
- call qm_assign_atom_types
-
- ! Set default QMMM MPI parameters - for single cpu operation.
- ! These will get overwritten by qmmm_mpi_setup if MPI is on.
- qmmm_mpi%commqmmm_master = master
- qmmm_mpi%numthreads = 1
- qmmm_mpi%mytaskid = 0
- qmmm_mpi%natom_start = 1
- qmmm_mpi%natom_end = natom
- qmmm_mpi%nquant_nlink_start = 1
- qmmm_mpi%nquant_nlink_end = qmmm_struct%nquant_nlink
-
- ! Now we know how many link atoms we can allocate the scf_mchg array...
- allocate(qm2_struct%scf_mchg(qmmm_struct%nquant_nlink), stat = ier)
- REQUIRE(ier == 0) ! Deallocated in deallocate qmmm
-
- ! We can also allocate ewald_memory
- if (qmmm_nml%qm_ewald > 0 ) then
- call allocate_qmewald(natom)
- end if
- if (qmmm_nml%qmgb == 2 ) then ! lam81
- call allocate_qmgb(qmmm_struct%nquant_nlink)
- end if ! lam81
-
- allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat = ier )
- REQUIRE(ier == 0) ! Deallocated in deallocate qmmm
-
- else if(abfqmmm_param%abfqmmm == 1) then ! lam81
-
- call abfqmmm_set_parameters(numbnd, nbonh, nbona, ntheth, ntheta, nphih, nphia, & ! lam81
- ix(iibh), ix(ijbh), ix(iicbh), & ! lam81
- ix(iiba), ix(ijba), ix(iicba), & ! lam81
- ix(i24), ix(i26), ix(i28), ix(i30), & ! lam81
- ix(i32), ix(i34), ix(i36), ix(i38), & ! lam81
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), & ! lam81
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58), & ! lam81
- x(l15), rk, req) ! lam81
-
- call init_extra_pts(ix(iibh),ix(ijbh),ix(iicbh), & ! lam81
- ix(iiba),ix(ijba),ix(iicba), & ! lam81
- ix(i24),ix(i26),ix(i28),ix(i30), & ! lam81
- ix(i32),ix(i34),ix(i36),ix(i38), & ! lam81
- ix(i40),ix(i42),ix(i44),ix(i46),ix(i48), & ! lam81
- ix(i50),ix(i52),ix(i54),ix(i56),ix(i58), & ! lam81
- ih(m06),ix,x,ix(i08),ix(i10), & ! lam81
- nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req) ! lam81
-
- end if !if (qmmm_nml%ifqnt)
-
- ! --- Open the data dumping files and position it depending
- ! on the type of run:
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
-#ifdef MPI
- ! adaptive QM/MM (qmmm_nml%vsolv=2) via multisander
- ! all groups have identical coords and velocities
- ! only master of first group needs to dump results
- if ( (qmmm_nml%vsolv < 2) .or. (worldrank == 0) ) then
-#endif
- call open_dump_files
-#ifdef MPI
- end if
-#endif
- end if ! lam81
- if (master) call amflsh(6)
-
- ! --- end of master process setup ---
- end if masterwork ! (master)
-
-# if defined(RISMSANDER)
- call rism_init(commsander)
-# endif /* RISMSANDER */
-
-#ifdef MPI
-
- call mpi_barrier(commsander,ierr)
- ! =========================== AMBER/MPI ===========================
-
- ! NOTE: in the current AMBER/MPI implementation, two means of
- ! running in parallel within sander are supported. The value
- ! of mpi_orig determines which approach is used.
- ! This is turned on when minimization (imin .ne. 0) is requested,
- ! and is otherwise off.
-
- ! When running the mpi_orig case, a variable notdone is now
- ! set by the master and determines when to exit the force()
- ! loop. When the master has finished calling force, the
- ! master changes notdone to 0 and broadcasts the data one more
- ! time to signal end of the loop. force() is modified so that
- ! in the mpi_orig case, an initial broadcast is done to receive
- ! the value from the master to decide whether to do the work or
- ! simply exit.
-
- ! ...set up initial data and send all needed data to other nodes,
- ! now that the master has it
-
- ! First, broadcast parameters in memory.h, so that all processors
- ! will know how much memory to allocate:
-
- call mpi_bcast(natom,BC_MEMORY,mpi_integer,0,commsander,ierr)
- ! -- ti decomp
- call mpi_bcast(idecomp,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(nat,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(nrs,1,mpi_integer,0,commsander,ierr)
-
- ! ----- Set up integer stack initial size --------------
- call mpi_bcast(lastist,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(lastrst,1,mpi_integer,0,commsander,ierr)
-
- call mpi_bcast(qmmm_struct%abfqmmm,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%abfqmmm,1,mpi_integer,0,commsander,ierr) ! lam81
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- call mpi_bcast(abfqmmm_param%natom,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%qmstep,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%maxqmstep,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%system,1,mpi_integer,0,commsander,ierr) ! lam81
- end if ! lam81
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call mpi_bcast(abfqmmm_param%r_core_in,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_core_out,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_qm_in,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_qm_out,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_buffer_in,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_buffer_out,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%mom_cons_type,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%mom_cons_region,1,mpi_integer,0,commsander,ierr) ! lam81
- if (.not. master) then ! lam81
- allocate(abfqmmm_param%x(3*natom), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%id(natom), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%mass(natom), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- end if ! lam81
- allocate(abfqmmm_param%v(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f1(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f2(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- end if ! lam81
- call mpi_bcast(abfqmmm_param%x,3*natom,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%id,natom,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%mass,natom,mpi_double_precision,0,commsander,ierr) ! lam81
- end if ! lam81
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call stack_setup()
- else ! lam81
- call deallocate_stacks ! lam81
- call stack_setup() ! lam81
- end if ! lam81
-
- call mpi_bcast(plumed,1,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(plumedfile,256,MPI_CHARACTER,0,commsander,ierr)
-
- ! GMS: Broadcast parameters from module 'molecule'
- call mpi_bcast(mol_info%natom,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(mol_info%nres,1,mpi_integer,0,commsander,ierr)
- call mpi_barrier(commsander,ierr)
-
- ! ---allocate memory on the non-master nodes:
- if (.not. master) then
-
- if (abfqmmm_param%qmstep /= 1 .or. abfqmmm_param%system /= 1) then ! lam81
- deallocate(x,ix,ipairs,ih) ! lam81
- end if ! lam81
-
- allocate( x(1:lastr), stat = ier )
- REQUIRE( ier == 0 )
-
- allocate( ix(1:lasti), stat = ier )
- REQUIRE( ier == 0 )
-
- allocate( ipairs(1:lastpr), stat = ier )
- REQUIRE( ier == 0 )
-
- allocate( ih(1:lasth), stat = ier )
- REQUIRE( ier == 0 )
-
- ! GMS:
- ! Allocate space for molecule module
- ! arrays in the other nodes
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call allocate_molecule()
- else ! lam81
- call deallocate_molecule() ! lam81
- call allocate_molecule() ! lam81
- end if ! lam81
-
- ! --------------------------
-
- ! -- ti decomp
- if (idecomp > 0) then
- call allocate_int_decomp(natom, nres)
- if (idecomp == 1 .or. idecomp == 2) then
- call allocate_real_decomp(nrs)
- else if( idecomp == 3 .or. idecomp == 4 ) then
- call allocate_real_decomp(npdec*npdec)
- end if
- end if
- end if ! ( .not.master )
-
- !GMS: Broadcast arrays from module 'molecule'
- call mpi_bcast(mol_info%natom_res,mol_info%nres,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(mol_info%atom_to_resid_map,mol_info%natom,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(mol_info%atom_mass,mol_info%natom, MPI_DOUBLE_PRECISION, 0, commsander, ier)
-
- if(idecomp == 1 .or. idecomp == 2) then
- call mpi_bcast(jgroup,nat,MPI_INTEGER,0,commsander,ierr)
- end if
-
- if(icfe == 0 .and. (idecomp ==3 .or. idecomp == 4)) then
- call mpi_bcast(jgroup,natom,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(indx,nres,MPI_INTEGER,0,commsander,ierr)
- end if
-
- call startup_groups(ierr)
- call startup(x,ix,ih)
-
-! +---------------------------------------------------------------------------+
-! | Broadcast EVB/PIMD inputs/parameters to all PEs |
-! +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::+
-! | Note: The masters have all required EVB/PIMD inputs/parameters via call |
-! | to mdread2 ( evb_input, evb_init, evb_pimd_init ). For EVB/PIMD, all |
-! | PEs need the inputs/parameters ... so we perform this initialization |
-! | again for all PEs besides the masters. The alternative is to use |
-! | MPI_BCAST. |
-! +---------------------------------------------------------------------------+
-
- call mpi_bcast( ievb , 1, MPI_INTEGER, 0, commworld, ierr )
- call mpi_bcast( ipimd, 1, MPI_INTEGER, 0, commworld, ierr )
-
- ! KFW
- if (ievb /= 0) then
- call mpi_bcast(evbin, MAX_FN_LEN, MPI_CHARACTER, 0, commworld, ierr)
- if (.not. master) then
- call evb_input
- call evb_init
- end if
- end if
- ! KFW
-
-
-# if defined(LES)
- call mpi_bcast ( ncopy, 1, MPI_INTEGER, 0, commworld, ierr )
- call mpi_bcast ( cnum(1:natom), natom, MPI_INTEGER, 0, commworld, ierr )
- call mpi_bcast ( evbin, MAX_FN_LEN, MPI_CHARACTER, 0, commworld, ierr )
-# endif /* LES */
- if (ievb /= 0) then
-# if defined(LES)
- !call mpi_bcast ( mastersize, 1, MPI_INTEGER, 0, commworld, ierr )
- !call mpi_bcast ( jobs_per_node, 1, MPI_INTEGER, 0, commworld, ierr )
- !call mpi_bcast ( nsize, 1, MPI_INTEGER, 0, commworld, ierr )
- if (ipimd > 0 .and. .not. master) then
- call evb_input
- call evb_init
- !call evb_pimd_init
- end if
- call evb_pimd_init
- !call mpi_bcast ( master_worldrank, mastersize, MPI_INTEGER, 0, commworld, ierr )
- !call mpi_bcast ( PE_slice, jobs_per_node*nsize, MPI_INTEGER, 0, commworld, ierr )
-# endif /* LES */
- call evb_bcast
- call evb_alloc
- end if
-
-! +---------------------------------------------------------------------------+
-! | Obtain B vector for Schlegel's distributed Gaussian method |
-! +---------------------------------------------------------------------------+
-
- if (trim(adjustl(xch_type)) == "dist_gauss") call schlegel_dg
-
- if (ifsc /= 0) then
- ! multi-CPU minimization does not work with soft core !
- if (imin > 0 .and. numtasks > 1) then
- call sander_bomb('imin > 0 and numtasks > 1', &
- 'TI minimizations cannot be performed with > 2 CPUs','')
- end if
- call setup_sc(natom, nres, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), ntypes, clambda, nstlim)
- if (ntp > 0 .and. master) then
- ! Check which molecules are perturbed in NPT runs
- call sc_check_perturbed_molecules(nspm, ix(i70))
- end if
- ! -- ti decomp
- if (idecomp > 0) then
- if (sanderrank == 0) call build_dec_mask(natom)
- call mpi_bcast(decmask, natom, MPI_INTEGER, 0, commsander, ierr)
- end if
- ! Make sure all common atoms have the same v (that of V0) in TI runs
- if ( ifsc /= 2 ) then
- if (master) call sc_sync_x(x(lvel),nr3)
- !call mpi_barrier(commsander,ierr)
- if (numtasks > 1) then
- call mpi_bcast(nr3,1,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(x(lvel),nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
- if (tishake /= 0) call setnoshake_sc(ix,ntc,num_noshake,master)
- else
- extra_atoms=0
- end if
- if (ifmbar /= 0) then
- call setup_mbar(nstlim)
- end if
-
- if (.not. master .and. igb == 0 .and. ipb == 0) then
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call nblist_allocate(natom,ntypes,num_direct,numtasks)
- else ! lam81
- call nblist_deallocate ! lam81
- call nblist_allocate(natom,ntypes,num_direct,numtasks) ! lam81
- end if ! lam81
- end if
-
- ! --- Allocate memory for GB on the non-master nodes:
-
- if( .not.master ) then
-
- if ((igb /= 0 .and. igb /= 10 .and. ipb == 0) .or. hybridgb>0 .or. icnstph.gt.1) then ! lam81
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call allocate_gb( natom, ncopy )
- else ! lam81
- call deallocate_gb ! lam81
- call allocate_gb( natom, ncopy ) ! lam81
- end if ! lam81
- end if ! lam81
-
- end if ! ( .not.master )
-
- nr = nrp
- nr3 = 3*nr
- belly = ibelly > 0
-
- ! ---Do setup for QMMM in parallel if ifqnt is on - this is essentially
- ! everything in the QMMM namelist and a few other bits and pieces.
- ! ---Note, currently only master node knows if qmmm_nml%ifqnt is
- ! on so we need to broadcast this first and then make decisions based
- ! on this.
-
- call mpi_bcast(qmmm_nml%ifqnt, 1, mpi_logical, 0, commsander, ierror)
-
- if (qmmm_nml%ifqnt) then
- ! Broadcast all of the stuff in qmmm_nml and allocate the relevant
- ! arrays on all processors. This will also set up information for
- ! openmp on the master processor if it is in use.
- call qmmm_mpi_setup( master, natom )
- if (qmmm_nml%qm_ewald > 0 .and. .not. master) then
- call allocate_qmewald(natom)
- end if
- if (qmmm_nml%qmgb==2 .and. .not. master) then
- call allocate_qmgb(qmmm_struct%nquant_nlink)
- end if
-
- if (.not. master) then
- allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat = ier )
- REQUIRE(ier == 0) !Deallocated in deallocate qmmm
- end if
-
- end if
-
- ! --- END QMMM MPI SETUP ---
-
- ! DAN ROE: Note: all nodes are calling this. amrset(ig) has already been called
- ! by the master node (twice if initial velocities are set, ntx<=3).
- ! DAN ROE: REMD: Now need to call amrset on all child threads, masters have called
- ! it above before initial coord read
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- if(rem == 0) then
- call amrset(ig+1)
- else
- if (.not. master) call amrset(ig + 17 * nodeid)
- endif
-
- if (nmropt >= 1) &
- call nmrcal(x(lcrd),f,ih(m04),ih(m02),ix(i02),x(lwinv),enmr, &
- devdis,devang,devtor,devplpt,devpln,devgendis,temp0,tautp,cut,ntb,x(lnmr01), &
- ix(inmr02),x(l95),5,6,rk,tk,pk,cn1,cn2, &
- ag,bg,cg,numbnd,numang,numphi,nimprp, &
- nhb,natom,natom,ntypes,nres,rad,wel,radhb, &
- welhb,rwell,isftrp,tgtrmsd,temp0les,-1,'MPI ')
- end if ! lam81
- ! Updated 9/2007 by Matthew Seetin to enable plane-point and plane-plane restraints
-
- call mpi_bcast(lmtmd01,1,mpi_integer,0, commsander,ierr)
- call mpi_bcast(imtmd02,1,mpi_integer,0, commsander,ierr)
-
- if (itgtmd == 2) call mtmdcall(emtmd,x(lmtmd01),ix(imtmd02),x(lcrd),x(lforce),&
- ih(m04),ih(m02),ix(i02),ih(m06),x(lmass),natom,nres,'MPI ')
-
-
- ! ---------------- Check system is neutral and print warning message ------
- ! ---------------- adjust charges for roundoff error. ------
- if( igb == 0 .and. ipb == 0 .and. iyammp == 0 ) then
- if ( icfe == 0 ) then
- call check_neutral(x(l15),natom)
- else
- call ti_check_neutral(x(l15),natom)
- end if
- end if
-
- ! tell all nodes if this is a SEBOMD run
- call mpi_bcast(sebomd_obj%do_sebomd, 1, MPI_LOGICAL, 0, commsander, ierr)
- if (sebomd_obj%do_sebomd) then
- ! transfer SEBOMD info to the nodes
- call sebomd_bcast_obj()
- ! open necessary files
- if (master) then
- call sebomd_open_files
- end if
- ! initialize SEBOMD arrays
- call init_sebomd_arrays(natom)
- end if
-
- ! ---------------- Old parallel for minimization ----------------------
-
- if (imin /= 0) then
- mpi_orig = .true.
- notdone = 1
- else
- mpi_orig = .false.
- end if
-
- if (mpi_orig .and. .not. master) then
-
- ! ...all nodes only do the force calculations (JV)
- ! Minimisation so only only master gets past the loop below
- ! hence need to zero QM charges on non-master threads here.
-
- if (qmmm_nml%ifqnt) then
- ! Apply charge correction if required.
- if (qmmm_nml%adjust_q>0) then
- call qmmm_adjust_q(qmmm_nml%adjust_q, natom, qmmm_struct%nquant, qmmm_struct%nquant_nlink, &
- qmmm_struct%nlink, x(L15), &
- qmmm_struct%iqmatoms, qmmm_nml%qmcharge, qmmm_struct%atom_mask, &
- qmmm_struct%mm_link_mask, master,x(LCRD), qmmm_nml%vsolv)
- end if
- ! At this point we can also fill the qmmm_struct%scaled_mm_charges
- ! array - we only need to do this once as the charges are constant
- ! during a run. Having a separate array of scaled charges saves us
- ! having to do it on every qmmm routine call. Do this BEFORE zeroing
- ! the QM charges since that routine take care of these values as well.
- do i = 1, natom
- qmmm_struct%scaled_mm_charges(i) = x(L15+(i-1)) * INV_AMBER_ELECTROSTATIC &
- * qmmm_nml%chg_lambda ! charge scaling factor for FEP
- end do
- ! Zero out the charges on the quantum mechanical atoms
- call qm_zero_charges(x(L15),qmmm_struct%scaled_mm_charges,.true.)
- if (qmmm_struct%nlink > 0 ) then
- ! We need to exclude all electrostatic
- ! interactions with MM link pairs, both QM-MM and MM-MM. Do this by
- ! zeroing the MM link pair charges in the main charge array.
- ! These charges are stored in qmmm_struct%mm_link_pair_resp_charges in case
- ! they are later needed.
- call qm_zero_mm_link_pair_main_chg(qmmm_struct%nlink,qmmm_struct%link_pairs,x(L15), &
- qmmm_struct%scaled_mm_charges,.true.)
- end if
-
- end if
-
- if (igb == 7 .or. igb == 8) call igb7_init(natom, ncopy, x(l97)) !x(l97) is rborn()
- !Hai Nguyen: add igb == 8 here
-
- if ( ifcr /= 0 ) call cr_allocate( master, natom )
-
- n_force_calls = 0
- do while( notdone == 1 )
- n_force_calls = n_force_calls+1
- call force(x,ix,ih,ipairs,x(lcrd),x(lforce),ene,vir, &
- x(l96), x(l97), x(l98), x(l99), qsetup, &
- do_list_update,n_force_calls)
- end do
-
- ! Deallocate and return
- goto 999
-
- end if
-
- ! ----------------------------------------------------------------------
-
- if (master) then
- if(abfqmmm_param%abfqmmm /=1) write(6, '(a,i4,a,/)') '| Running AMBER/MPI version on ',numtasks, ' nodes' ! lam81
- !BTREE is selected by default if cpu is a power of two.
- !The number of processes is required to be a power of two for Btree
- !Print a warning about inefficiency with cpus not being a power of 2.
- if (numtasks > 1 .and. logtwo(numtasks) <= 0) then
- if(abfqmmm_param%abfqmmm /=1) write(6, '(a,i4,a,/)') '| WARNING: The number of processors is not a power of 2' ! lam81
- if(abfqmmm_param%abfqmmm /=1) write(6, '(a,i4,a,/)') '| this may be inefficient on some systems.' ! lam81
- end if
- end if
- if (master .and. numgroup > 1) write(6, '(a,i4,a,i4,a,i4,a)') &
- '| MULTISANDER: ', numgroup, ' groups. ', &
- numtasks, ' processors out of ', worldsize, ' total.'
- if (master) call amflsh(6)
-
- ! ========================= END AMBER/MPI =========================
-#else
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- allocate(abfqmmm_param%v(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f1(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f2(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- end if ! lam81
- end if ! lam81
-
- ! debug needs to copy charges at start and they can't change later
- ! ---------------- Check system is neutral and print warning message ------
- ! ---------------- adjust charges for roundoff error. ------
- if( igb == 0 .and. ipb == 0 .and. iyammp == 0 ) call check_neutral(x(l15),natom)
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call amrset(ig+1)
- end if ! lam81
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call stack_setup()
- else ! lam81
- call deallocate_stacks ! lam81
- call stack_setup() ! lam81
- end if ! lam81
-
- if (sebomd_obj%do_sebomd) then
- ! open necessary files
- call sebomd_open_files
- ! initialize SEBOMD arrays
- call init_sebomd_arrays(natom)
- endif
-
-#endif /* MPI */
-
-#ifdef OPENMP
-
- ! If -openmp was specified to configure_amber then -DOPENMP is defined and the
- ! threaded version of MKL will have been linked in. It is important here that
- ! we set the default number of openmp threads for MKL to be 1 to stop conflicts
- ! with threaded vectorization routines when running in parallel etc.
- ! Individual calls to MKL from routines that know what they are doing - e.g.
- ! QMMM calls to diagonalizers etc can increase this limit as long as they
- ! put it back afterwards.
- call omp_set_num_threads(1)
-
- ! If we are using openmp for matrix diagonalization print some information.
- if (qmmm_nml%ifqnt .and. master) call qm_print_omp_info()
-#endif
-
- ! allocate memory for crg relocation
- if (ifcr /= 0) call cr_allocate( master, natom )
-
- ! initialize LIE module if used
- if ( ilrt /= 0 ) then
- call setup_linear_response(natom,nres,ih(m04),ih(m06),ix(i02),ih(m02),x(lcrd),x(l15), &
- ntypes, ix(i04), ix(i06), cn1, cn2, master)
- end if
-
- call date_and_time( setup_end_date, setup_end_time )
-
- ! Initialize the printing of ongoing time and performance summaries.
- ! We do this quite late here to avoid including all the setup time.
- if (master) call print_ongoing_time_summary(0,0,0.0d0,7)
-
- ! ----------------------------------------------------------------------
- ! Now do the dynamics or minimization.
- ! ----------------------------------------------------------------------
-
- if (igb == 7 .or. igb == 8 ) call igb7_init(natom, ncopy, x(l97)) !x(l97) is rborn()
- !Hai Nguyen: add igb ==8 here
-
- if (qmmm_nml%ifqnt) then
- ! Apply charge correction if required.
- if (qmmm_nml%adjust_q>0) then
- call qmmm_adjust_q(qmmm_nml%adjust_q, natom, qmmm_struct%nquant, qmmm_struct%nquant_nlink, &
- qmmm_struct%nlink, x(L15), &
- qmmm_struct%iqmatoms, qmmm_nml%qmcharge, qmmm_struct%atom_mask, &
- qmmm_struct%mm_link_mask, master,x(LCRD), qmmm_nml%vsolv)
- end if
- ! At this point we can also fill the qmmm_struct%scaled_mm_charges
- ! array - we only need to do this once as the charges are constant
- ! during a run. Having a separate array of scaled charges saves us
- ! having to do it on every qmmm routine call. Do this BEFORE zeroing
- ! the QM charges since that routine take care of these values as well.
- do i = 1, natom
- qmmm_struct%scaled_mm_charges(i) = x(L15+(i-1)) * INV_AMBER_ELECTROSTATIC &
- * qmmm_nml%chg_lambda ! charge scaling factor for FEP
- end do
-
- ! Zeroing of QM charges MUST be done AFTER call to check_neutral.
- ! Zero out the charges on the quantum mechanical atoms.
- call qm_zero_charges(x(L15),qmmm_struct%scaled_mm_charges,.true.)
-
- if (qmmm_struct%nlink > 0) then
- ! We need to exclude all electrostatic
- ! interactions with MM link pairs, both QM-MM and MM-MM. Do this by
- ! zeroing the MM link pair charges in the main charge array.
- ! These charges are stored in qmmm_struct%mm_link_pair_resp_charges in case
- ! they are later needed.
- call qm_zero_mm_link_pair_main_chg(qmmm_struct%nlink,qmmm_struct%link_pairs,x(L15), &
- qmmm_struct%scaled_mm_charges,.true.)
- end if
-
- end if
-
- ! Use the debugf namelist to activate
- call debug_frc(x,ix,ih,ipairs,x(lcrd),x(lforce),cn1,cn2,qsetup)
-
- ! Prepare for SGLD simulation
- if (isgld > 0) call psgld(natom,x(lmass),x(lvel), rem)
-
- ! Prepare for EMAP constraints
- if (temap) call pemap(dt,temp0,x,ix,ih)
-
- ! Prepare for Isotropic periodic sum of nonbonded interaction
- if (ips .gt. 0) call ipssys(natom,ntypes,ntb,x(l15), &
- cut,cn1,cn2,ix(i04),ix(i06),x(lcrd))
-
- if (master .and. (.not. qmmm_nml%ifqnt) .and. (abfqmmm_param%abfqmmm /= 1)) & ! lam81
- write(6,'(/80(''-'')/,'' 4. RESULTS'',/80(''-'')/)')
-
- ! Set up the MC barostat if requested
- if (ntp > 0 .and. barostat == 2) call mcbar_setup(ig)
-
- ! Input flag imin determines the type of calculation: MD, minimization, ...
- select case (imin)
- case (0)
- ! --- Dynamics:
-
- call timer_start(TIME_RUNMD)
- ! Set up AMD
- if (iamd .gt. 0) then
- call amd_setup(ntwx)
- endif
-
- ! Set up scaledMD
- if (scaledMD .gt. 0) then
- call scaledMD_setup(ntwx)
- endif
-
- if (ipimd > 0) then
- call pimd_init(natom,x(lmass),x(lwinv),x(lvel),ipimd)
- end if
-
- if(ineb>0) call neb_init()
-
-#ifdef MPI
- ! ----===== REMD =====----
- ! If this is not a REMD run, runmd is called only once.
- ! If this is a REMD run, runmd is called 0 to numexchg times,
- ! where the 0th runmd is just for getting initial PEs (no dynamics).
- if (rem == 0) then
- ! Not a REMD run. runmd will be called once.
- loop = 0
- else if (rem > 0) then
- ! This is a REMD run. runmd will be called numexchg times.
- loop = numexchg
-
- ! Set up temptable, open remlog, etc.
- call remd1d_setup(numexchg, hybridgb, numwatkeep, &
- temp0, mxvar, natom, ig, solvph)
- else
- ! Multi-D REMD run
- loop = numexchg
- call multid_remd_setup(numexchg, hybridgb, numwatkeep, &
- temp0, mxvar, natom, ig, solvph, irest)
- ! Now set up REMD indices for traj/restart writes. Only do this on
- ! master since only master handles writes.
- if (master) call setup_remd_indices
- end if ! Replica run setup
-
- ! Loop over REMD exchanges
- do mdloop = 0, loop
-
- ! ----===== REMD EXCHANGE HANDLING =====----
- ! Note: mdloop==0 is just used to get initial energies for the
- ! first exchange.
- if (rem < 0 .and. mdloop > 0) then
- call multid_remd_exchange(x, ix, ih, ipairs, qsetup, &
- do_list_update, temp0, solvph)
- else if ((rem == 1 .or. rem == 2) .and. mdloop > 0) then
- call remd_exchange(1, rem, x(lcrd), x(lvel), x(lmass), &
- nr3, natom, nr, temp0)
- else if (rem == 3 .and. mdloop > 0) then
- call hremd_exchange(1, x, ix, ih, ipairs, qsetup, do_list_update)
- ! force was called inside hremd_exchange, so call nmrdcp
- ! to decrement the NMR counter, since this should not count
- ! as a real step. This is OK, since the counter got
- ! incremented at the _very_ end of nmrcal, so we haven't already
- ! printed an unwanted value (JMS 2/12)
- if (nmropt /= 0) call nmrdcp
- else if (rem == 4 .and. mdloop > 0) then
- call ph_remd_exchange(1, solvph)
- end if ! rem>0 and mdloop>0
-
- ! ----===== END REMD EXCHANGE HANDLING =====----
-
-#ifdef VERBOSE_REMD
- if (rem > 0 .and. mdloop .eq. 0 .and. master) &
- write (6,'(a,i4)') "REMD: Getting initial energy for replica ",repnum
-#endif /* VERBOSE_REMD */
-#endif /* MPI */
-
-#ifndef DISABLE_NCSU
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call ncsu_on_sander_init(ih, x(lmass), x(lcrd), rem)
- end if ! lam81
-#endif /* DISABLE_NCSU */
-
- if (beeman_integrator == 1) then
- call AM_RUNMD(ix,ih,ipairs, &
- x(lwinv),x(lmass),x, &
- x(lcrd),x(lvel),x(lforce),qsetup)
- else
- call runmd(x,ix,ih,ipairs, &
- x(lcrd),x(lwinv),x(lmass),x(lforce), &
- x(lvel),x(lvel2),x(l45),x(lcrdr), &
- x(l50),x(l95),ix(i70),x(l75), &
- erstop,qsetup)
- end if !beeman_integrator == 1
-
-#ifndef DISABLE_NCSU
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call ncsu_on_sander_exit()
- end if ! lam81
-#endif /* DISABLE_NCSU */
-
- ! ----===== END REMD =====----
-#ifdef MPI
- end do ! Loop over REMD exchanges (mdloop)
-
- ! Cleanup REMD files.
- if (rem /= 0) call remd_cleanup()
-
-#endif
-
- call timer_stop(TIME_RUNMD)
-
- if (master) call amflsh(6)
-
- if (erstop) then
- ! This error condition stems from subroutine shake;
- ! furthermore, it seems that erstop can never be true since shake
- ! can never return with its third last argument, niter, equal to 0.
- ! SRB, Sep 24, 2003
- if (master) then
- write(6, *) 'FATAL ERROR'
- end if
- call mexit(6,1)
- end if
-
- case (1)
-
- !--- Minimization:
-
- ! Input flag ntmin determines the method of minimization
- select case (ntmin)
- case (0, 1, 2)
- call runmin(x,ix,ih,ipairs,x(lcrd),x(lforce),x(lvel), &
- ix(iibh),ix(ijbh),x(l50),x(lwinv),ix(ibellygp), &
- x(l95),ene, carrms, qsetup)
- ! If a conventional minimisation is being done,
- ! the restart file is written inside the runmin routine.
- case (LMOD_NTMIN_XMIN)
- write(6,'(a)') ' LMOD XMIN Minimization.'
- write(6,'(a)') ''
- write(6,'(a)') ' Note: Owing to the behaviour of the XMIN algorithm,'
- write(6,'(a)') ' coordinates in the trajectory and intermediate'
- write(6,'(a)') ' restart files will not match up with energies'
- write(6,'(a)') ' in the mdout and mdinfo files. The final energy'
- write(6,'(a)') ' and final coordinates do match.'
- write(6,'(a)') ''
- xmin_iter = 0
- call run_xmin( x, ix, ih, ipairs, &
- x(lcrd), x(lforce), ene, qsetup, xmin_iter, ntpr )
- if (master) call minrit(0,nrp,ntxo,x(lcrd)) ! Write the restart file
- case (LMOD_NTMIN_LMOD)
- write(6,'(a)') ' LMOD LMOD Minimization.'
- write(6,'(a)') ''
- write(6,'(a)') ' Note: Owing to the behaviour of the XMIN algorithm,'
- write(6,'(a)') ' coordinates in the trajectory and intermediate'
- write(6,'(a)') ' restart files will not match up with energies'
- write(6,'(a)') ' in the mdout and mdinfo files. The final energy'
- write(6,'(a)') ' and final coordinates do match.'
- write(6,'(a)') ''
- call run_lmod( x, ix, ih, ipairs, &
- x(lcrd), x(lforce), ene, qsetup )
- if (master) call minrit(0,nrp,ntxo,x(lcrd)) ! Write the restart file
- case default
- ! invalid ntmin
- ! ntmin input validation occurs in mdread.f
- ASSERT( .false. )
- end select
-
-
- case (5)
- ! ---carlos modified for reading trajectories (trajene option)
-
- write (6,*) "POST-PROCESSING OF TRAJECTORY ENERGIES"
-
- ! ---read trajectories and calculate energies for each frame
-
- call trajene(x,ix,ih,ipairs,ene,ok,qsetup)
-
- if (.not. ok) then
- write (6,*) 'error in trajene()'
- call mexit(6,1)
- end if
-
- case default
- ! invalid imin
- ! imin input validation should be transferred to mdread.f
- write(6,'(/2x,a,i3,a)') 'Error: Invalid IMIN (',imin,').'
- ASSERT( .false. )
- end select
-
-#ifdef MPI /* SOFT CORE */
- if (master) then
- if (icfe /=0 .and. ifsc == 1) call summarize_ti_changes(natom,resat)
- end if
-#endif
-
- ! finish up EMAP
- if (temap) call qemap()
-
- if (abfqmmm_param%abfqmmm /= 1) then ! lam81
- exit ! lam81
- else ! lam81
-#ifdef MPI /* lam81 */
- call mpi_barrier(commsander,ierr) ! lam81
-#endif /* lam81 */
- if (abfqmmm_param%qmstep /= abfqmmm_param%maxqmstep .or. abfqmmm_param%system /= 2) then ! lam81
- if(qmmm_nml%ifqnt) call deallocate_qmmm(qmmm_nml, qmmm_struct, qmmm_vsolv, qm2_params) ! lam81
- end if ! lam81
- call deallocate_m1m2m3() ! lam81
- if (abfqmmm_param%system == 2 .and. master) then ! lam81
- call abfqmmm_write_idrst() ! lam81
- call abfqmmm_write_pdb(x(lcrd),ix(i70)) ! lam81
- end if ! lam81
- call abfqmmm_next_step() ! lam81
- end if ! lam81
-
- end do ! lam81
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- deallocate(abfqmmm_param%id, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%v, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%f, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%f1, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%f2, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- if(master) then ! lam81
- deallocate(abfqmmm_param%isqm, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- endif ! lam81
- end if ! lam81
-
- ! -- calc time spent running vs setup
- call timer_stop(TIME_TOTAL)
- call wallclock( time1 )
- call date_and_time( final_date, final_time )
- call profile_time( time1 - time0, num_calls_nblist, profile_mpi)
-
-#ifdef MPI
- ! =========================== AMBER/MPI ===========================
-
- ! Set and broadcast notdone in mpi_orig case to inform
- ! other nodes that we are finished calling force(). (tec3)
-
- if (mpi_orig) then
- notdone = 0
- call mpi_bcast(notdone,1,mpi_integer,0, commsander,ierr)
- end if
-
- ! ========================= END AMBER/MPI =========================
-#endif
-
-! ========================= PUPIL INTERFACE =========================
-#ifdef PUPIL_SUPPORT
- ! Finalize Corba Interface
- puperror = 0
- call killcorbaintfc(puperror)
- if (puperror /= 0) then
- write(6,*) 'Error ending PUPIL CORBA interface.'
- end if
- write(6,'(a)') 'PUPIL CORBA interface finalized.'
- pupactive = .false.
-#endif
-! ========================= PUPIL INTERFACE =========================
-
-#ifdef _XRAY
- !(out_lun,residue_pointer,residue_label,atom_name,coor,num_bonds,ibond,jbond)
- call xray_fini()
-#endif
-
- call amflsh(6)
- if (master) then
-#ifdef MPI
- ! adaptive QM/MM (qmmm_nml%vsolv=2) via multisander
- ! all groups have identical coords and velocities
- ! only master of first group needs to dump results
- if ( (qmmm_nml%vsolv < 2) .or. (worldrank == 0) ) then
-#endif
- call close_dump_files
-#ifdef MPI
- end if
-#endif
-
- if (icnstph /= 0) &
- call cnstph_finalize
- ! --- write out final times, taking REMD into account
-#ifdef MPI
- if (rem .ne. 0) then
- nstlim_total = nstlim * numexchg
- else
- nstlim_total = nstlim
- end if
-#else
- nstlim_total = nstlim
-#endif
- if (imin == 0) &
- call print_ongoing_time_summary(nstlim_total,nstlim_total,dt,6)
-
- write(6,'(12(a))') '| Job began at ', initial_time(1:2), &
- ':', initial_time(3:4), ':', initial_time(5:10), ' on ',&
- initial_date(5:6), '/', initial_date(7:8), '/', initial_date(1:4)
- write(6,'(12(a))') '| Setup done at ', setup_end_time(1:2), &
- ':', setup_end_time(3:4), ':', setup_end_time(5:10), ' on ', &
- setup_end_date(5:6), '/',setup_end_date(7:8),'/',setup_end_date(1:4)
- write(6,'(12(a))') '| Run done at ', final_time(1:2), &
- ':', final_time(3:4), ':', final_time(5:10), ' on ', &
- final_date(5:6), '/', final_date(7:8), '/', final_date(1:4)
- call nwallclock( ncalls )
- write(6, '(''|'',5x,''wallclock() was called'',I8,'' times'')') ncalls
- call amflsh(6)
-
- if (iesp > 0) then
- call esp(natom,x(lcrd),x(linddip))
- end if
- end if
- call amflsh(6)
-
- ! --- dynamic memory deallocation:
- 999 continue
-
- if(qmmm_nml%ifqnt .and. qmmm_nml%qmtheory%EXTERN .and. master) then
- call qm2_extern_finalize()
- endif
-
- if (qmmm_nml%ifqnt .and. .not. qmmm_struct%qm_mm_first_call) then
- ! If first_call is still true, this thread never really
- ! called the QMMM routine. E.g. more threads than PIMD replicates
- call deallocate_qmmm(qmmm_nml, qmmm_struct, qmmm_vsolv, qm2_params)
- end if
-
- if (ipimd > 0) call pimd_finalize(ipimd)
-
- if (ineb > 0) call neb_finalize()
-
- if (idecomp > 0) then
- call deallocate_real_decomp()
- call deallocate_int_decomp()
- end if
- if (master .and. idecomp == 0) call deallocate_int_decomp()
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call cleanup_sc()
- if (ifmbar /= 0) call cleanup_mbar()
-#endif
-
- ! finalize LIE module if initiated above
- if ( ilrt /= 0 ) then
- call cleanup_linear_response(master)
- end if
-
-#ifdef RISMSANDER
- call rism_finalize()
-#endif
-
- if ( ifcr /= 0 ) call cr_cleanup()
-
- if (sebomd_obj%do_sebomd) then
- if (master) then
- call sebomd_close_files
- end if
- call cleanup_sebomd_arrays
- end if
-
- if (master .and. iwrap == 2) then
- deallocate(iwrap_mask_atoms, stat=ier)
- REQUIRE(ier == 0)
- end if
- call nblist_deallocate()
- call deallocate_stacks()
- if ((igb /= 0 .and. igb /= 10 .and. ipb == 0) .or. hybridgb > 0 .or. icnstph > 1) then
- call deallocate_gb()
- end if
- if (master) then
- if(igb == 10 .or. ipb /= 0) then
- call pb_free()
- end if
- end if
- deallocate(ih, stat = ier)
- REQUIRE(ier == 0)
- deallocate(ipairs, stat = ier)
- REQUIRE(ier == 0)
- deallocate(ix, stat = ier)
- REQUIRE(ier == 0)
- deallocate(x, stat = ier)
- REQUIRE(ier == 0)
- if(ntb > 0 .and. ifbox == 1 .and. ew_type == 0 .and. mpoltype == 0) &
- call deallocate_m1m2m3()
- call AMOEBA_deallocate
- ! GMS: -- Module molecule --
- call deallocate_molecule()
- ! --------------------------
-
- if (charmm_active) call charmm_deallocate_arrays()
- if (cmap_active) call deallocate_cmap_arrays()
-
- if (master.and.mdout /= 'stdout') close(6)
-
- return
-
-end subroutine sander
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Calculate the ElectroStatic Potential
-subroutine esp(natom,x,mom_ind)
-
- ! routine to calculate the ESP due to the induced moments (only)
- ! at the same spatial points as the reference QM.
- use constants, only : zero, BOHRS_TO_A, INV_AMBER_ELECTROSTATIC
- use file_io_dat
- implicit none
- integer natom
- _REAL_ x(3,*)
- _REAL_ mom_ind(3,*)
-
-# include "ew_mpole.h"
-
- integer dat_unit, new_unit, minus_new_unit
- parameter(dat_unit=30, new_unit=31, minus_new_unit=33)
-
- integer inat, nesp, idum
- _REAL_ xin, yin, zin
- integer jn, kn
- _REAL_ esp_qm, xb_esp, yb_esp, zb_esp
- _REAL_ x_esp, y_esp, z_esp
- _REAL_ e_x, e_y, e_z, e_q, esp_new
- _REAL_ dist, dist3
- integer iptr
-
- call amopen(dat_unit,"esp.dat",'O','F','R')
- call amopen(new_unit,"esp.induced",owrite,'F','W')
- call amopen(minus_new_unit,"esp.qm-induced",owrite,'F','W')
- read (dat_unit,'(3i5)')inat,nesp,idum
- write(6,'(t2,''inat = '',i5)')inat
- write(6,'(t2,''nesp = '',i5)')nesp
-
- write(new_unit,'(2i5)')inat,nesp
- write(minus_new_unit,'(2i5)')inat,nesp
-
- if (inat /= natom) then
- write(6,'(t2,''natom mismatch with esp file'')')
- call mexit(6,1)
- end if
-
- do jn = 1,inat
- read (dat_unit,'(17x,3e16.0)')xin,yin,zin
- write(new_unit,'(17x,3e16.7)')xin,yin,zin
- write(minus_new_unit,'(17x,3e16.7)')xin,yin,zin
- end do
-
- do jn = 1,nesp
- e_x = zero
- e_y = zero
- e_z = zero
- e_q = zero
- read(dat_unit,'(1x,4e16.0)')esp_qm,xb_esp,yb_esp,zb_esp
- x_esp = xb_esp * BOHRS_TO_A
- y_esp = yb_esp * BOHRS_TO_A
- z_esp = zb_esp * BOHRS_TO_A
-
- do kn = 1,natom
- dist = (sqrt((x(1,kn)-x_esp)**2 + &
- (x(2,kn)-y_esp)**2 + &
- (x(3,kn)-z_esp)**2))
- dist3 = dist**3
- e_x = e_x - mom_ind(1,kn )*(x(1,kn)-x_esp)/dist3
- e_y = e_y - mom_ind(2,kn )*(x(2,kn)-y_esp)/dist3
- e_z = e_z - mom_ind(3,kn )*(x(3,kn)-z_esp)/dist3
- end do
-
- e_x = e_x * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- e_y = e_y * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- e_z = e_z * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- e_q = e_q * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- esp_new = e_x + e_y + e_z
-
- write(new_unit, '(1x,4e16.7)')esp_new, &
- xb_esp,yb_esp,zb_esp
- write(minus_new_unit,'(1x,4e16.7)')esp_qm-esp_new, &
- xb_esp,yb_esp,zb_esp
- end do
-
- close(dat_unit)
- close(new_unit)
- close(minus_new_unit)
-
- return
-
-end subroutine esp
-
diff --git a/patches/amber14.diff/AmberTools/src/sander/sander.F90.preplumed b/patches/amber14.diff/AmberTools/src/sander/sander.F90.preplumed
deleted file mode 100644
index c4b7bf48f29651552934994e5f9c7fa4f9755d2c..0000000000000000000000000000000000000000
--- a/patches/amber14.diff/AmberTools/src/sander/sander.F90.preplumed
+++ /dev/null
@@ -1,1922 +0,0 @@
-#include "copyright.h"
-#include "../include/dprec.fh"
-#include "../include/assert.fh"
-#include "ncsu-config.h"
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ The Molecular Dynamics/NMR Refinement/Modeling Module of the AMBER
-!-----------------------------------------------------------------------
-! --- SANDER ---
-!-----------------------------------------------------------------------
-
-subroutine sander()
-
- use state
-#ifndef DISABLE_NCSU
- use ncsu_sander_hooks, only : &
- ncsu_on_sander_init => on_sander_init, &
- ncsu_on_sander_exit => on_sander_exit
-#endif /* DISABLE_NCSU */
-
- use lmod_driver
- use constants, only : INV_AMBER_ELECTROSTATIC
- ! The main qmmm_struct contains all the QMMM variables and arrays
- use qmmm_module, only : qmmm_nml, qmmm_struct, deallocate_qmmm, qmmm_mpi, &
-#ifdef MPI
- qmmm_mpi_setup, &
-#endif
- qm2_struct, qmewald, qm_gb, qmmm_vsolv, qm2_params
-
- use qmmm_vsolv_module, only: qmmm_vsolv_store_parameters, new
-
- use qm2_extern_module, only: qm2_extern_finalize
- use sebomd_module, only : sebomd_obj, &
- sebomd_open_files, sebomd_close_files, &
-#ifdef MPI
- sebomd_bcast_obj, &
-#endif
- sebomd_setup
-
- use sebomd_arrays, only : init_sebomd_arrays, cleanup_sebomd_arrays
-
- use genborn
- use decomp, only : allocate_int_decomp, allocate_real_decomp, &
- deallocate_int_decomp, deallocate_real_decomp, &
-#ifdef MPI
- synchronize_dec, build_dec_mask, decmask, &
-#endif
- nat, nrs, jgroup, indx
- use fastwt
- use relax_mat
- use nmr, only: nmrrad, impnum
- use ew_recip, only: deallocate_m1m2m3,first_pme
- use parms
- use molecule, only : mol_info, n_iwrap_mask_atoms, iwrap_mask_atoms, &
- allocate_molecule, deallocate_molecule
- use nblist, only:cutoffnb,skinnb,nblist_allocate,nblist_deallocate, &
- nblist_allreal,nblist_allint, num_calls_nblist, first_list_flag
- use stack
- use amoeba_runmd, only : AM_RUNMD_get_coords,AM_RUNMD
- use amoeba_mdin, only : beeman_integrator,iamoeba,am_nbead
- use amoeba_interface, only : AMOEBA_deallocate,AMOEBA_readparm
-
-#ifdef RISMSANDER
- use sander_rism_interface, only: rismprm,rism_setparam, rism_init,rism_finalize
-#endif
-
-#ifdef PUPIL_SUPPORT
- use pupildata
-#endif /* PUPIL */
-
-#ifdef APBS
- use apbs
-#endif /* APBS */
-
-#ifdef _XRAY
- use xray_interface_module, only: xray_init, xray_read_parm, xray_fini
-#endif
-
-#ifdef MPI /* SOFT CORE */
- use softcore, only: setup_sc, cleanup_sc, ifsc, extra_atoms, sc_sync_x, &
- summarize_ti_changes, sc_check_perturbed_molecules, ti_check_neutral, tishake
- use mbar, only: setup_mbar, cleanup_mbar, ifmbar
-#endif
-
- ! for LIE calculations
- use linear_response, only: ilrt, setup_linear_response, &
- cleanup_linear_response
-
-#if defined(MPI)
- use evb_parm, only: xch_type
-# if defined(LES)
- use evb_pimd, only: evb_pimd_init, PE_slice, master_worldrank, jobs_per_node
-# endif
-! REMD
- use remd, only : rem, mdloop, repnum, remd1d_setup, remd_exchange, &
- remd_cleanup, hremd_exchange, ph_remd_exchange, &
- multid_remd_setup, multid_remd_exchange
- use bintraj, only: setup_remd_indices
-#else
-# define rem 0
-#endif /* MPI */
-
- use pimd_vars, only: ipimd
- use neb_vars, only: ineb
-
- use trajenemod, only: trajene
-
-!RCW+MJW CHARMM SUPPORT
- use charmm_mod, only : charmm_active, charmm_deallocate_arrays, &
- charmm_filter_out_qm_atoms
- use ff11_mod, only : cmap_active, deallocate_cmap_arrays
-
- use memory_module, only: x, ix, ih, memory_init
-
-! Self-Guided molecular/Langevin Dynamics (SGLD)
- use sgld, only : isgld,psgld
-
- use nbips, only: ipssys,ips
-
- use crg_reloc, only: ifcr, cr_backup_charge, cr_cleanup, cr_allocate, &
- cr_read_input, cr_check_input, cr_print_info
-
- use emap,only: temap,pemap,qemap
-
- use file_io_dat
- use constantph, only : cnstph_finalize
- use barostats, only : mcbar_setup
-
-!AMD
- use amd_mod
-!scaledMD
- use scaledMD_mod
-
- use abfqmmm_module ! lam81
-
- implicit none
-
- logical belly, erstop
- integer ier,ifind,jn,ncalls,xmin_iter
- character(len=4) itest
- logical ok
- logical newstyle
-# include "../include/memory.h"
-# include "nmr.h"
-# include "box.h"
-# include "../include/md.h"
-# include "extra.h"
-# include "tgtmd.h"
-# include "multitmd.h"
-# include "les.h"
-
-# include "parallel.h"
-#ifdef MPI
- ! =========================== AMBER/MPI ===========================
-# ifdef MPI_DOUBLE_PRECISION
-# undef MPI_DOUBLE_PRECISION
-# endif
- include 'mpif.h'
-# ifdef CRAY_PVP
-# define MPI_DOUBLE_PRECISION MPI_REAL8
-# endif
-# ifdef MPI_BUFFER_SIZE
- integer*4 mpibuf(mpi_buffer_size)
-# endif
-! REMD: loop is the current exchange. runmd is called numexchg times.
- integer loop
-
- integer nrank, istat
- _REAL_ ener(30),vir(4)
- integer ierr
- integer partner
-! ========================= END AMBER/MPI =========================
-#endif
-# include "ew_pme_recip.h"
-# include "ew_frc.h"
-# include "ew_erfc_spline.h"
-# include "ew_parallel.h"
-# include "ew_mpole.h"
-# include "ew_cntrl.h"
-# include "def_time.h"
-
- type(state_rec) :: ene
- integer native,nr3,nr
-
- ! nmrcal vars
- _REAL_ f,enmr,devdis,devang,devtor,devplpt,devpln,devgendis,ag,bg,cg
- ! Updated 9/2007 by Matthew Seetin to enable plane-point and plane-plane
- ! restraints
- _REAL_ emtmd
- integer numphi,nhb
-
- ! runmin/trajene var
- _REAL_ carrms
-
- ! dipole moment stuff
- integer ngrp
-
- character(len=8) initial_date, setup_end_date, final_date
- character(len=10) initial_time, setup_end_time, final_time
- integer nstlim_total ! for final time printout
-
- _REAL_ time0, time1
-
- integer idiff,i,j,istop,index,ierror,itemp
-
- integer, dimension(:), allocatable :: ipairs
- integer :: n_force_calls
- logical qsetup
- logical :: do_list_update=.false.
- _REAL_ :: box_center(3) ! lam81
-#ifdef MPI_DEBUGGER
- integer, volatile :: release_debug
-
- ! So only the master master thread has release_debug = 0
- release_debug = worldrank
-
- ! Lock us into an infinite loop while release_debug == 0 on any thread (only
- ! the master here). This allows you to connect a debugger to any running
- ! process without having to 'race' program execution. A debugger MUST be
- ! attached to the master thread (typically the thread with the lowest PID),
- ! and have release_debug set to NOT 0 (e.g., via "set release_debug=1").
- do
- if (release_debug .ne. 0) exit
- end do
-
- ! Prevent any other threads from progressing past this point until all
- ! threads you want to watch with a debugger are watched and all those
- ! threads are continued.
- call mpi_barrier(mpi_comm_world, ierr)
-#endif
-
- ! ---- HERE BEGIN THE EXECUTABLE STATEMENTS ----
-
- ! Initialize the cpu timer. Needed for machines where returned cpu times
- ! are relative.
- call date_and_time( initial_date, initial_time )
- call wallclock( time0 )
- call init_timers()
-
- ! Initialize the printing of ongoing time and performance summaries.
-! call print_ongoing_time_summary(0,0,0.0d0,7)
- call print_ongoing_time_summary(0,0,0.0d0,7,time0)
-
- ! BPR - original location of PUPIL interface. I moved it further down
- ! because, if it's here, it can't print stuff; write(6,...) statements
- ! assume mdread1() has already been invoked. However, moving this down
- ! may break other things.
-
- ! ==== Flag to tell list builder to print size of list on first call =======
- first_list_flag = .true.
- ! ==== Flag to tell recip space routines to allocate on first call =======
- first_pme = .true.
-
- ! ==== Initialise first_call flags for QMMM ====
- qmmm_struct%qm_mm_first_call = .true.
- qmmm_struct%fock_first_call = .true.
- qmmm_struct%fock2_2atm_first_call = .true.
- qmmm_struct%qm2_allocate_e_repul_first_call = .true.
- qmmm_struct%qm2_calc_rij_eqns_first_call = .true.
- qmmm_struct%qm2_scf_first_call = .true.
- qmmm_struct%zero_link_charges_first_call = .true.
- qmmm_struct%adj_mm_link_pair_crd_first_call = .true.
- qmmm_struct%num_qmmm_calls = 0
-
-#ifdef MPI
- ! Parallel initialization (setup is done in multisander.F90).
-
- ! Make PE 0 the master
- master = mytaskid == 0
- master_master = masterrank == 0
-
- if ( master .and. numtasks > MPI_MAX_PROCESSORS ) then
- write(0, '(a,i4,a,i4)') &
- 'Error: the number of processors must not be greater than ', &
- MPI_MAX_PROCESSORS, ', but is ', numtasks
- call mexit(6,1)
- end if
-# ifdef MPI_BUFFER_SIZE
- call mpi_buffer_attach(mpibuf, mpi_buffer_size*4, ierr)
-# endif
-#else /* not MPI follows */
- ! In the single-threaded version, the one process is master
- master = .true.
-#endif /* MPI */
-
- erstop = .false.
- qsetup = .true.
-
- ! --- generic packing scheme ---
-
- nwdvar = 1
- native = 32
-#ifdef ISTAR2
-
- ! --- Int*2 packing scheme ---
-
- nwdvar = 2
-#endif /*ISTAR2*/
- numpk = nwdvar
- nbit = native/numpk
-
- ! ----- Only the master node (only node when single-process)
- ! performs the initial setup and reading/writing -----
-
- call timer_start(TIME_TOTAL)
-
- call abfqmmm_init_param() ! lam81
-
- do while ( (abfqmmm_param%qmstep <= abfqmmm_param%maxqmstep) &
- .or. (abfqmmm_param%maxqmstep == 0 .and. abfqmmm_param%system == 2) ) ! lam81
-
- masterwork: if (master) then
-
- if (abfqmmm_param%abfqmmm == 0) then ! lam81
-
- ! ---- first, initial reads to determine memory sizes:
- call mdread1()
- call amopen(8,parm,'O','F','R')
- call rdparm1(8)
- if (mtmd /= 'mtmd' .or. itgtmd == 2) call mtmdlx(natom)
- ! --- now, we can allocate memory:
-
- call locmem()
- write(6,'(/,a,5x,a)') '|','Memory Use Allocated'
- write(6,'(a,5x,a,i14)') '|', 'Real ', lastr
- write(6,'(a,5x,a,i14)') '|', 'Hollerith ', lasth
- write(6,'(a,5x,a,i14)') '|', 'Integer ', lasti
- write(6,'(a,5x,a,i14)') '|', 'Max Pairs ', lastpr
-
- ! --- dynamic memory allocation:
-
- ! GMS:
- ! Allocate space for module molecule
- ! in the master node
- mol_info%natom = natom
- mol_info%nres = nres
- call allocate_molecule()
-
- ! Allocate all global arrays
- allocate( x(lastr), ix(lasti), ipairs(lastpr), ih(lasth), stat = ier )
- REQUIRE( ier == 0 )
- ix(1:lasti) = 0
-
- ! This sets up pointer arrays in MEMORY_MODULE to match array-offsets into
- ! the shared X, IX, and IH arrays. Eventually, LOCMEM code should be
- ! merged with MEMORY_MODULE to allocate individual allocatable arrays, but
- ! that will also require updating the MPI code to handle individual
- ! arrays.
- call memory_init()
-
- ! Allocate the parm arrays
- call allocate_parms()
-
- if ((igb /= 0 .and. igb /= 10 .and. ipb == 0) &
- .or.hybridgb>0.or.icnstph.gt.1) &
- call allocate_gb( natom, ncopy )
-
- if( idecomp > 0 ) then
-#ifdef MPI
- if (ifsc > 0) then
- call synchronize_dec(natom, nres)
- else
- nat = natom
- nrs = nres
- end if
-#else
- nat = natom
- nrs = nres
-#endif
- call allocate_int_decomp(natom, nres)
- else
- call allocate_int_decomp(1, 1)
- end if
-
- write(6,'(a,5x,a,i14)' ) '|', 'nblistReal', nblist_allreal
- write(6,'(a,5x,a,i14)' ) '|', 'nblist Int', nblist_allint
- write(6,'(a,5x,a,i14,a)') '|', ' Total ', &
- (8*(lastr+lastrst+nblist_allreal) &
- + 4*(lasth+lasti+lastpr+lastist+nblist_allint))/1024, &
- ' kbytes'
-
- ! --- finish reading the prmtop file and other user input:
- call rdparm2(x,ix,ih,ipairs,8)
-
- call AMOEBA_readparm(8,ntf,ntc,natom,x(lmass))! ntf,ntc get reset if amoeba prmtop
-#ifdef _XRAY
- call xray_read_parm(8,6)
-#endif
-
- end if ! lam81
-
- if (qmmm_nml%ifqnt .or. abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%abfqmmm == 0) then ! lam81
- call sebomd_setup
- call read_qmmm_nm_and_alloc(igb, ih, ix, x, cut, use_pme, ntb, 0) ! lam81
- if (qmmm_nml%qmtheory%SEBOMD) then
- ! don't do QM/MM
- qmmm_nml%ifqnt= .false.
- sebomd_obj%do_sebomd = .true.
- end if
- end if ! lam81
- if(qmmm_struct%abfqmmm == 1 .and. abfqmmm_param%abfqmmm == 0) then ! lam81
- call abfqmmm_setup(natom,nres,ix(i02),ih(m04),ih(m02),x(lmass), & ! lam81
- nbonh,nbona,ix(iibh),ix(ijbh),ix(iiba),ix(ijba)) ! lam81
- nr=natom ! lam81
- call AMOEBA_check_newstyle_inpcrd(inpcrd,newstyle) ! lam81
- if (newstyle) then ! lam81
- call AM_RUNMD_get_coords(natom,t,irest,ntb,x(lcrd),x(lvel)) ! lam81
- else ! lam81
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.FALSE.) ! lam81
- end if ! lam81
- abfqmmm_param%maxqmstep = nstlim ! lam81
- end if ! lam81
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%system == 1) then ! lam81
- call abfqmmm_update_qmatoms(x(lcrd)) ! lam81
- if(abfqmmm_param%ntwpdb < 0) then ! lam81
- call abfqmmm_write_pdb(x(lcrd),ix(i70)) ! lam81
- close(6) ! lam81
- call mexit(6,1) ! lam81
- end if ! lam81
- end if ! lma81
- call abfqmmm_select_system_qmatoms(natom) ! lam81
- if(qmmm_nml%ifqnt) then ! lam81
- call read_qmmm_nm_and_alloc(igb,ih,ix,x,cut,use_pme,ntb,abfqmmm_param%qmstep, & ! lam81
- abfqmmm_param%isqm,abfqmmm_param%abfcharge) ! lam81
- end if ! lam81
- endif ! lam81
- end if ! lam81
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
-
- call mdread2(x,ix,ih,ipairs)
-
- endif ! lam81
-
-#if defined(RISMSANDER)
- call rism_setparam(mdin,&
- commsander,&
- natom,ntypes,x(L15:L15+natom-1),&
- x(LMASS:LMASS+natom-1),cn1,cn2,&
- ix(i04:i04+ntypes**2-1), ix(i06:i06+natom-1))
-#endif /*RISMSANDER*/
-
- if ( ifcr /= 0 ) then
- call cr_read_input(natom)
- call cr_check_input( ips )
- !call cr_print_info(6)
- call cr_backup_charge( x(l15), natom )
- end if
-
- ! --- alloc memory for decomp module that needs info from mdread2
- if (idecomp == 1 .or. idecomp == 2) then
- call allocate_real_decomp(nrs)
-#ifdef MPI
- ! -- ti decomp
- if (ifsc > 0) then
- ! following lines don't really seem to make sense(?)
- ! partner = ieor(masterrank,1)
- ! if (nat == natom) then
- ! nrank = masterrank
- ! else
- ! nrank = partner
- ! end if
- call mpi_bcast(jgroup, nat, MPI_INTEGER, 0, commmaster, ierr)
- end if
-#endif
- else if( idecomp == 3 .or. idecomp == 4 ) then
- call allocate_real_decomp(npdec*npdec)
- end if
-
- ! ----- EVALUATE SOME CONSTANTS FROM MDREAD SETTINGS -----
-
- nr = nrp
- nr3 = 3*nr
- belly = ibelly > 0
-
- ! ========================= PUPIL INTERFACE =========================
-#ifdef PUPIL_SUPPORT
-
- ! I moved the PUPIL interface down here so that write() statements work
- ! as advertised. BPR 9/7/09
-
- ! Initialise the CORBA interface
- puperror = 0
- call fixport()
- call inicorbaintfcmd(puperror)
- if (puperror .ne. 0) then
- write(6,*) 'Error creating PUPIL CORBA interface.'
- call mexit(6,1)
- end if
- pupactive = .true.
- write(6,*) 'PUPIL CORBA interface initialized.'
-
- ! Allocation of memory and initialization
- pupStep = 0
- puperror = 0
- allocate (qcell (12 ),stat=puperror)
- allocate (pupmask (natom ),stat=puperror)
- allocate (pupqlist(natom ),stat=puperror)
- allocate (pupatm (natom ),stat=puperror)
- allocate (pupchg (natom ),stat=puperror)
- allocate (qfpup (natom*3),stat=puperror)
- allocate (qcdata (natom*9),stat=puperror)
- allocate (keyMM (natom ),stat=puperror)
- allocate (pupres (nres ),stat=puperror)
- allocate (keyres (nres ),stat=puperror)
-
- if (puperror /= 0) then
- write(6,*) 'Error allocating PUPIL interface memory.'
- call mexit(6,1)
- end if
-
- ! Initialise the "atomic numbers" and "quantum forces" vectors
- pupqatoms = 0
- iresPup = 1
- pupres(1) = 1
- do iPup=1,natom
- bs1 = (iPup-1)*3
- call get_atomic_number_pupil(ih(iPup+m06-1),x(lmass+iPup-1),pupatm(iPup))
- if (iresPup .lt. nres) then
- if (iPup .ge. ix(iresPup+i02)) then
- iresPup = iresPup + 1
- pupres(iresPup) = iPup
- end if
- end if
- write (strAux,"(A4,'.',A4)") trim(ih(iresPup+m02-1)),adjustl(ih(iPup+m04-1))
- keyres(iresPup) = trim(ih(iresPup+m02-1))
- keyMM(iPup) = trim(strAux)
-
- ! Retrieve the initial charges
- pupchg(iPup) = x(L15+iPup-1)
- !write(6,*) 'Atom num.',iPup,'Label,Mass,Atomic Num.', keyMM(iPup),x(lmass+iPup-1),pupatm(iPup), 'Charge', pupchg(iPup)
-
- do jPup=1,3
- qfpup(bs1+jPup) = 0.0d0
- end do
- end do
-
- write(6,*) 'Got all atomic numbers.'
-
- ! Initialise the PUPIL cell
- do iPup=1,12
- qcell(iPup) = 0.0d0
- end do
-
- ! Submit the KeyMM particles and their respective atomic numbers to PUPIL
- puperror = 0
- call putatomtypes(natom,puperror,pupatm,keyMM)
- if (puperror .ne. 0) then
- write(6,*) 'Error sending MM atom types to PUPIL.'
- call mexit(6,1)
- end if
-
- ! Submit the Residue Pointer vector to PUPIL
- write(6,"(a20,1x,i6,3x,a17,1x,i6)") 'Number of residues =', nres, 'Number of atoms =', natom
- !do iPup=1,nres
- ! write(6,*) 'Residue ',iPup,keyres(iPup),pupres(iPup)
- !end do
- puperror = 0
- call putresiduetypes(nres,puperror,pupres,keyres)
- if (puperror .ne. 0) then
- write(6,*) 'Error sending MM residue types to PUPIL.'
- call mexit(6,1)
- end if
-
- write(6,*) 'Sent system data to PUPIL.'
- write(*,*) 'PUPIL structure initialized.'
-#endif
- ! ========================= PUPIL INTERFACE =========================
-
- ! --- seed the random number generator ---
-
- ! DAN ROE: Note master node only here
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
-#ifdef MPI
- if (rem == 0) then
- call amrset(ig)
- else
- ! carlos: set random seed different for different replicas
- ! but keep same seed for cpus in the same replica since
- ! we want data from diff # cpus to match
- call amrset(ig + (17 * nodeid)) ! nodeid is in md.h and is repnum - 1
- end if
-#else
- call amrset(ig)
-#endif
-
- if (nbit < 32 .and. nr > 32767) then
- write(6, *) ' Too many atoms for 16 bit pairlist -'
- write(6, *) ' Recompile without ISTAR2'
- call mexit(6, 1)
- end if
-
- if (ntp > 0.and.iabs(ntb) /= 2) then
- write(6,*) 'Input of NTP/NTB inconsistent'
- call mexit(6, 1)
- end if
- end if ! lam81
-
- ! ----- READ COORDINATES AND VELOCITIES -----
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81 <<< QMSTEP=1 BLOCK >>>
-
- call timer_start(TIME_RDCRD)
-#ifdef LES
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0les,.TRUE.,solvph)
-#else
- call AMOEBA_check_newstyle_inpcrd(inpcrd,newstyle)
- if (newstyle) then
- call AM_RUNMD_get_coords(natom,t,irest,ntb,x(lcrd),x(lvel))
- else
- call getcor(nr,x(lcrd),x(lvel),x(lforce),ntx,box,irest,t,temp0,.TRUE.,solvph)
- end if
-#endif
- if (iamoeba > 0) then
- natom = natom*am_nbead
- nrp = nrp*am_nbead
- nr = nr*am_nbead
- nr3 = nr3*am_nbead
- ncopy = am_nbead
- end if
-
- ! M-WJ
- !if( igb == 0 .and. induced == 1 ) call get_dips(x,nr)
-! WJM if is a polarizable model, reading input dipole information
- if (igb == 0 .and. ipb == 0 .and. induced > 0) call get_dips(x,nr)
-
-#ifdef APBS
- ! APBS initialization
- if (mdin_apbs) then
- ! in: natom, coords, charge and radii (from prmtop)
- ! out: pb charges and pb radii (via apbs_vars module)
- call apbs_init(natom, x(lcrd), x(l15), x(l97))
- end if
-#endif /* APBS */
-
-#ifdef _XRAY
- call xray_init()
-#endif
-
- ! ----- SET THE INITIAL VELOCITIES -----
-
- if (ntx <= 3) then
- call setvel(nr,x(lvel),x(lwinv),tempi,init,iscale,scalm)
- ! random numbers may have been "used up" in setting the intial
- ! velocities; re-set the generator so that all nodes are back in
- ! sync
-
- ! DAN ROE: Note master node only here
-#ifdef MPI
- if (rem == 0) call amrset(ig)
-#else
- call amrset(ig)
-#endif
-
- end if
- if (belly) call bellyf(natom,ix(ibellygp),x(lvel))
- call timer_stop(TIME_RDCRD)
-
- if(abfqmmm_param%abfqmmm == 1 .and. ntb > 0) then ! lam81
- call iwrap2(abfqmmm_param%n_user_qm, abfqmmm_param%user_qm, x(lcrd), box_center) ! lam81
- end if ! lam81
-
- ! --- If we are reading NMR restraints/weight changes,
- ! read them now:
-
- if (nmropt >= 1) then
- call nmrcal(x(lcrd),f,ih(m04),ih(m02),ix(i02),x(lwinv),enmr, &
- devdis,devang,devtor,devplpt,devpln,devgendis,temp0,tautp,cut,ntb,x(lnmr01), &
- ix(inmr02),x(l95),5,6,rk,tk,pk,cn1,cn2, &
- ag,bg,cg,numbnd,numang,numphi,nimprp, &
- nhb,natom,natom,ntypes,nres,rad,wel,radhb, &
- welhb,rwell,isftrp,tgtrmsd,temp0les,-1,'READ')
- ! Updated 9/2007 by Matthew Seetin to enable plane-point and plane-plane restraints
-
- ! --- Determine how many of the torsional parameters
- ! are impropers
- call impnum(ix(i46),ix(i56),ix(i48),ix(i58),nphih,nphia, &
- 0,nptra,nimprp)
- end if
-
- ! -- Set up info related to weight changes for the non-bonds:
-
- call nmrrad(rad,wel,cn1,cn2,ntypes,0,0.0d0)
- call decnvh(asol,bsol,nphb,radhb,welhb)
-
- if (iredir(4) > 0) call noeread(x,ix,ih)
- if (iredir(8) > 0) call alignread(natom, x(lcrd))
- if (iredir(9) > 0) call csaread
-
- end if ! lam81 <<< QMSTEP=1 BLOCK >>>
-
- !---------------------------------------------------------------
- ! --- Call FASTWAT, which will tag those bonds which are part
- ! of 3-point water molecules. Constraints will be effected
- ! for these waters using a fast analytic routine -- dap.
-
- call timer_start(TIME_FASTWT)
-
- call fastwat(ih(m04),nres,ix(i02),ih(m02), &
- nbonh,nbona,ix(iibh),ix(ijbh),ibelly,ix(ibellygp), &
- iwtnm,iowtnm,ihwtnm,jfastw,ix(iifstwt), &
- ix(iifstwr),ibgwat,ienwat,ibgion,ienion,iorwat, &
- 6,natom)
- call timer_stop(TIME_FASTWT)
-
- call getwds(ih(m04), nres , ix(i02) , ih(m02) , &
- nbonh , nbona , 0 , ix(iibh) , &
- ix(ijbh) , iwtnm , iowtnm , ihwtnm , &
- jfastw , ix(iicbh) , req , x(lwinv) , &
- rbtarg , ibelly , ix(ibellygp), 6 )
-
- ! Assign link atoms between quantum mechanical and molecular mechanical
- ! atoms if quantum atoms are present.
- ! After assigning the link atoms, delete all connectivity between the
- ! QM atoms.
- if(qmmm_nml%ifqnt) then
-
- call identify_link_atoms(nbona,ix(iiba),ix(ijba))
-
- ! Variable QM solvent:
- ! Store the original bond parameters since we will need to rebuild
- ! the QM region (delete bonded terms etc) repeatedly
- if ( qmmm_nml%vsolv > 0 ) then
- call new(qmmm_vsolv, nbonh, nbona, ntheth, ntheta, nphih, nphia)
- call qmmm_vsolv_store_parameters(qmmm_vsolv, numbnd, &
- ix(iibh), ix(ijbh), ix(iicbh), &
- ix(iiba), ix(ijba), ix(iicba), &
- ix(i24), ix(i26), ix(i28), ix(i30), &
- ix(i32), ix(i34), ix(i36), ix(i38), &
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), &
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58))
- end if
-
- if( abfqmmm_param%abfqmmm == 1 ) then ! lam81
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call abfqmmm_allocate_arrays_of_parameters(numbnd, nbonh, nbona, ntheth, ntheta, nphih, nphia) ! lam81
- call abfqmmm_store_parameters(ix(iibh), ix(ijbh), ix(iicbh), & ! lam81
- ix(iiba), ix(ijba), ix(iicba), & ! lam81
- ix(i24), ix(i26), ix(i28), ix(i30), & ! lam81
- ix(i32), ix(i34), ix(i36), ix(i38), & ! lam81
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), & ! lam81
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58), & ! lam81
- x(l15), rk, req) ! lam81
- else ! lam81
- call abfqmmm_set_parameters(numbnd, nbonh, nbona, ntheth, ntheta, nphih, nphia, & ! lam81
- ix(iibh), ix(ijbh), ix(iicbh), & ! lam81
- ix(iiba), ix(ijba), ix(iicba), & ! lam81
- ix(i24), ix(i26), ix(i28), ix(i30), & ! lam81
- ix(i32), ix(i34), ix(i36), ix(i38), & ! lam81
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), & ! lam81
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58), & ! lam81
- x(l15), rk, req) ! lam81
-
- call init_extra_pts(ix(iibh),ix(ijbh),ix(iicbh), & ! lam81
- ix(iiba),ix(ijba),ix(iicba), & ! lam81
- ix(i24),ix(i26),ix(i28),ix(i30), & ! lam81
- ix(i32),ix(i34),ix(i36),ix(i38), & ! lam81
- ix(i40),ix(i42),ix(i44),ix(i46),ix(i48), & ! lam81
- ix(i50),ix(i52),ix(i54),ix(i56),ix(i58), & ! lam81
- ih(m06),ix,x,ix(i08),ix(i10), & ! lam81
- nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req) ! lam81
-
- end if ! lam81
- end if ! lam81
-
- ! Remove bonds between QM atoms from list (Hydrogen)
- if (nbonh .gt. 0) call setbon(nbonh,ix(iibh),ix(ijbh),ix(iicbh), &
- ix(ibellygp))
-
- ! Remove bonds between QM atoms from list (Heavy)
- if (nbona .gt. 0) call setbon(nbona,ix(iiba),ix(ijba),ix(iicba), &
- ix(ibellygp))
-
- ! Remove angles between QM atoms from list (Hydrogen)
- if (ntheth .gt. 0) call setang(ntheth,ix(i24),ix(i26),ix(i28),ix(i30), &
- ix(ibellygp))
-
- ! Remove angles between QM atoms from list (Heavy)
- if (ntheta .gt. 0) call setang(ntheta,ix(i32),ix(i34),ix(i36),ix(i38),&
- ix(ibellygp))
-
- ! Remove dihedrals between QM atoms from list (Hydrogen)
- if (nphih .gt. 0) call setdih(nphih,ix(i40),ix(i42),ix(i44),ix(i46), &
- ix(i48), ix(ibellygp))
-
- ! Remove dihedrals between QM atoms from list (Heavy)
- if (nphia .gt. 0) call setdih(nphia,ix(i50),ix(i52),ix(i54),ix(i56), &
- ix(i58), ix(ibellygp))
-
- ! Remove CHARMM energy terms from QM region
- call charmm_filter_out_qm_atoms()
-
- ! Now we should work out the type of each quantum atom present.
- ! This is used for our arrays of pre-computed parameters. It is
- ! essentially a re-basing of the atomic numbers and is done to save
- ! memory. Note: qm_assign_atom_types will allocate the qm_atom_type
- ! array for us. Only the master calls this routine. All other
- ! threads get this allocated and broadcast to them by the mpi setup
- ! routine.
- call qm_assign_atom_types
-
- ! Set default QMMM MPI parameters - for single cpu operation.
- ! These will get overwritten by qmmm_mpi_setup if MPI is on.
- qmmm_mpi%commqmmm_master = master
- qmmm_mpi%numthreads = 1
- qmmm_mpi%mytaskid = 0
- qmmm_mpi%natom_start = 1
- qmmm_mpi%natom_end = natom
- qmmm_mpi%nquant_nlink_start = 1
- qmmm_mpi%nquant_nlink_end = qmmm_struct%nquant_nlink
-
- ! Now we know how many link atoms we can allocate the scf_mchg array...
- allocate(qm2_struct%scf_mchg(qmmm_struct%nquant_nlink), stat = ier)
- REQUIRE(ier == 0) ! Deallocated in deallocate qmmm
-
- ! We can also allocate ewald_memory
- if (qmmm_nml%qm_ewald > 0 ) then
- call allocate_qmewald(natom)
- end if
- if (qmmm_nml%qmgb == 2 ) then ! lam81
- call allocate_qmgb(qmmm_struct%nquant_nlink)
- end if ! lam81
-
- allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat = ier )
- REQUIRE(ier == 0) ! Deallocated in deallocate qmmm
-
- else if(abfqmmm_param%abfqmmm == 1) then ! lam81
-
- call abfqmmm_set_parameters(numbnd, nbonh, nbona, ntheth, ntheta, nphih, nphia, & ! lam81
- ix(iibh), ix(ijbh), ix(iicbh), & ! lam81
- ix(iiba), ix(ijba), ix(iicba), & ! lam81
- ix(i24), ix(i26), ix(i28), ix(i30), & ! lam81
- ix(i32), ix(i34), ix(i36), ix(i38), & ! lam81
- ix(i40), ix(i42), ix(i44), ix(i46), ix(i48), & ! lam81
- ix(i50), ix(i52), ix(i54), ix(i56), ix(i58), & ! lam81
- x(l15), rk, req) ! lam81
-
- call init_extra_pts(ix(iibh),ix(ijbh),ix(iicbh), & ! lam81
- ix(iiba),ix(ijba),ix(iicba), & ! lam81
- ix(i24),ix(i26),ix(i28),ix(i30), & ! lam81
- ix(i32),ix(i34),ix(i36),ix(i38), & ! lam81
- ix(i40),ix(i42),ix(i44),ix(i46),ix(i48), & ! lam81
- ix(i50),ix(i52),ix(i54),ix(i56),ix(i58), & ! lam81
- ih(m06),ix,x,ix(i08),ix(i10), & ! lam81
- nspm,ix(i70),x(l75),tmass,tmassinv,x(lmass),x(lwinv),req) ! lam81
-
- end if !if (qmmm_nml%ifqnt)
-
- ! --- Open the data dumping files and position it depending
- ! on the type of run:
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
-#ifdef MPI
- ! adaptive QM/MM (qmmm_nml%vsolv=2) via multisander
- ! all groups have identical coords and velocities
- ! only master of first group needs to dump results
- if ( (qmmm_nml%vsolv < 2) .or. (worldrank == 0) ) then
-#endif
- call open_dump_files
-#ifdef MPI
- end if
-#endif
- end if ! lam81
- if (master) call amflsh(6)
-
- ! --- end of master process setup ---
- end if masterwork ! (master)
-
-# if defined(RISMSANDER)
- call rism_init(commsander)
-# endif /* RISMSANDER */
-
-#ifdef MPI
-
- call mpi_barrier(commsander,ierr)
- ! =========================== AMBER/MPI ===========================
-
- ! NOTE: in the current AMBER/MPI implementation, two means of
- ! running in parallel within sander are supported. The value
- ! of mpi_orig determines which approach is used.
- ! This is turned on when minimization (imin .ne. 0) is requested,
- ! and is otherwise off.
-
- ! When running the mpi_orig case, a variable notdone is now
- ! set by the master and determines when to exit the force()
- ! loop. When the master has finished calling force, the
- ! master changes notdone to 0 and broadcasts the data one more
- ! time to signal end of the loop. force() is modified so that
- ! in the mpi_orig case, an initial broadcast is done to receive
- ! the value from the master to decide whether to do the work or
- ! simply exit.
-
- ! ...set up initial data and send all needed data to other nodes,
- ! now that the master has it
-
- ! First, broadcast parameters in memory.h, so that all processors
- ! will know how much memory to allocate:
-
- call mpi_bcast(natom,BC_MEMORY,mpi_integer,0,commsander,ierr)
- ! -- ti decomp
- call mpi_bcast(idecomp,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(nat,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(nrs,1,mpi_integer,0,commsander,ierr)
-
- ! ----- Set up integer stack initial size --------------
- call mpi_bcast(lastist,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(lastrst,1,mpi_integer,0,commsander,ierr)
-
- call mpi_bcast(qmmm_struct%abfqmmm,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%abfqmmm,1,mpi_integer,0,commsander,ierr) ! lam81
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- call mpi_bcast(abfqmmm_param%natom,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%qmstep,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%maxqmstep,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%system,1,mpi_integer,0,commsander,ierr) ! lam81
- end if ! lam81
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call mpi_bcast(abfqmmm_param%r_core_in,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_core_out,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_qm_in,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_qm_out,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_buffer_in,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%r_buffer_out,1,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%mom_cons_type,1,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%mom_cons_region,1,mpi_integer,0,commsander,ierr) ! lam81
- if (.not. master) then ! lam81
- allocate(abfqmmm_param%x(3*natom), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%id(natom), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%mass(natom), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- end if ! lam81
- allocate(abfqmmm_param%v(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f1(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f2(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- end if ! lam81
- call mpi_bcast(abfqmmm_param%x,3*natom,mpi_double_precision,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%id,natom,mpi_integer,0,commsander,ierr) ! lam81
- call mpi_bcast(abfqmmm_param%mass,natom,mpi_double_precision,0,commsander,ierr) ! lam81
- end if ! lam81
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call stack_setup()
- else ! lam81
- call deallocate_stacks ! lam81
- call stack_setup() ! lam81
- end if ! lam81
-
- ! GMS: Broadcast parameters from module 'molecule'
- call mpi_bcast(mol_info%natom,1,mpi_integer,0,commsander,ierr)
- call mpi_bcast(mol_info%nres,1,mpi_integer,0,commsander,ierr)
- call mpi_barrier(commsander,ierr)
-
- ! ---allocate memory on the non-master nodes:
- if (.not. master) then
-
- if (abfqmmm_param%qmstep /= 1 .or. abfqmmm_param%system /= 1) then ! lam81
- deallocate(x,ix,ipairs,ih) ! lam81
- end if ! lam81
-
- allocate( x(1:lastr), stat = ier )
- REQUIRE( ier == 0 )
-
- allocate( ix(1:lasti), stat = ier )
- REQUIRE( ier == 0 )
-
- allocate( ipairs(1:lastpr), stat = ier )
- REQUIRE( ier == 0 )
-
- allocate( ih(1:lasth), stat = ier )
- REQUIRE( ier == 0 )
-
- ! GMS:
- ! Allocate space for molecule module
- ! arrays in the other nodes
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call allocate_molecule()
- else ! lam81
- call deallocate_molecule() ! lam81
- call allocate_molecule() ! lam81
- end if ! lam81
-
- ! --------------------------
-
- ! -- ti decomp
- if (idecomp > 0) then
- call allocate_int_decomp(natom, nres)
- if (idecomp == 1 .or. idecomp == 2) then
- call allocate_real_decomp(nrs)
- else if( idecomp == 3 .or. idecomp == 4 ) then
- call allocate_real_decomp(npdec*npdec)
- end if
- end if
- end if ! ( .not.master )
-
- !GMS: Broadcast arrays from module 'molecule'
- call mpi_bcast(mol_info%natom_res,mol_info%nres,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(mol_info%atom_to_resid_map,mol_info%natom,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(mol_info%atom_mass,mol_info%natom, MPI_DOUBLE_PRECISION, 0, commsander, ier)
-
- if(idecomp == 1 .or. idecomp == 2) then
- call mpi_bcast(jgroup,nat,MPI_INTEGER,0,commsander,ierr)
- end if
-
- if(icfe == 0 .and. (idecomp ==3 .or. idecomp == 4)) then
- call mpi_bcast(jgroup,natom,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(indx,nres,MPI_INTEGER,0,commsander,ierr)
- end if
-
- call startup_groups(ierr)
- call startup(x,ix,ih)
-
-! +---------------------------------------------------------------------------+
-! | Broadcast EVB/PIMD inputs/parameters to all PEs |
-! +:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::+
-! | Note: The masters have all required EVB/PIMD inputs/parameters via call |
-! | to mdread2 ( evb_input, evb_init, evb_pimd_init ). For EVB/PIMD, all |
-! | PEs need the inputs/parameters ... so we perform this initialization |
-! | again for all PEs besides the masters. The alternative is to use |
-! | MPI_BCAST. |
-! +---------------------------------------------------------------------------+
-
- call mpi_bcast( ievb , 1, MPI_INTEGER, 0, commworld, ierr )
- call mpi_bcast( ipimd, 1, MPI_INTEGER, 0, commworld, ierr )
-
- ! KFW
- if (ievb /= 0) then
- call mpi_bcast(evbin, MAX_FN_LEN, MPI_CHARACTER, 0, commworld, ierr)
- if (.not. master) then
- call evb_input
- call evb_init
- end if
- end if
- ! KFW
-
-
-# if defined(LES)
- call mpi_bcast ( ncopy, 1, MPI_INTEGER, 0, commworld, ierr )
- call mpi_bcast ( cnum(1:natom), natom, MPI_INTEGER, 0, commworld, ierr )
- call mpi_bcast ( evbin, MAX_FN_LEN, MPI_CHARACTER, 0, commworld, ierr )
-# endif /* LES */
- if (ievb /= 0) then
-# if defined(LES)
- !call mpi_bcast ( mastersize, 1, MPI_INTEGER, 0, commworld, ierr )
- !call mpi_bcast ( jobs_per_node, 1, MPI_INTEGER, 0, commworld, ierr )
- !call mpi_bcast ( nsize, 1, MPI_INTEGER, 0, commworld, ierr )
- if (ipimd > 0 .and. .not. master) then
- call evb_input
- call evb_init
- !call evb_pimd_init
- end if
- call evb_pimd_init
- !call mpi_bcast ( master_worldrank, mastersize, MPI_INTEGER, 0, commworld, ierr )
- !call mpi_bcast ( PE_slice, jobs_per_node*nsize, MPI_INTEGER, 0, commworld, ierr )
-# endif /* LES */
- call evb_bcast
- call evb_alloc
- end if
-
-! +---------------------------------------------------------------------------+
-! | Obtain B vector for Schlegel's distributed Gaussian method |
-! +---------------------------------------------------------------------------+
-
- if (trim(adjustl(xch_type)) == "dist_gauss") call schlegel_dg
-
- if (ifsc /= 0) then
- ! multi-CPU minimization does not work with soft core !
- if (imin > 0 .and. numtasks > 1) then
- call sander_bomb('imin > 0 and numtasks > 1', &
- 'TI minimizations cannot be performed with > 2 CPUs','')
- end if
- call setup_sc(natom, nres, ih(m04), ih(m06), &
- ix(i02), ih(m02), x(lcrd), ntypes, clambda, nstlim)
- if (ntp > 0 .and. master) then
- ! Check which molecules are perturbed in NPT runs
- call sc_check_perturbed_molecules(nspm, ix(i70))
- end if
- ! -- ti decomp
- if (idecomp > 0) then
- if (sanderrank == 0) call build_dec_mask(natom)
- call mpi_bcast(decmask, natom, MPI_INTEGER, 0, commsander, ierr)
- end if
- ! Make sure all common atoms have the same v (that of V0) in TI runs
- if ( ifsc /= 2 ) then
- if (master) call sc_sync_x(x(lvel),nr3)
- !call mpi_barrier(commsander,ierr)
- if (numtasks > 1) then
- call mpi_bcast(nr3,1,MPI_INTEGER,0,commsander,ierr)
- call mpi_bcast(x(lvel),nr3,MPI_DOUBLE_PRECISION,0,commsander,ierr)
- end if
- end if
- if (tishake /= 0) call setnoshake_sc(ix,ntc,num_noshake,master)
- else
- extra_atoms=0
- end if
- if (ifmbar /= 0) then
- call setup_mbar(nstlim)
- end if
-
- if (.not. master .and. igb == 0 .and. ipb == 0) then
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call nblist_allocate(natom,ntypes,num_direct,numtasks)
- else ! lam81
- call nblist_deallocate ! lam81
- call nblist_allocate(natom,ntypes,num_direct,numtasks) ! lam81
- end if ! lam81
- end if
-
- ! --- Allocate memory for GB on the non-master nodes:
-
- if( .not.master ) then
-
- if ((igb /= 0 .and. igb /= 10 .and. ipb == 0) .or. hybridgb>0 .or. icnstph.gt.1) then ! lam81
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call allocate_gb( natom, ncopy )
- else ! lam81
- call deallocate_gb ! lam81
- call allocate_gb( natom, ncopy ) ! lam81
- end if ! lam81
- end if ! lam81
-
- end if ! ( .not.master )
-
- nr = nrp
- nr3 = 3*nr
- belly = ibelly > 0
-
- ! ---Do setup for QMMM in parallel if ifqnt is on - this is essentially
- ! everything in the QMMM namelist and a few other bits and pieces.
- ! ---Note, currently only master node knows if qmmm_nml%ifqnt is
- ! on so we need to broadcast this first and then make decisions based
- ! on this.
-
- call mpi_bcast(qmmm_nml%ifqnt, 1, mpi_logical, 0, commsander, ierror)
-
- if (qmmm_nml%ifqnt) then
- ! Broadcast all of the stuff in qmmm_nml and allocate the relevant
- ! arrays on all processors. This will also set up information for
- ! openmp on the master processor if it is in use.
- call qmmm_mpi_setup( master, natom )
- if (qmmm_nml%qm_ewald > 0 .and. .not. master) then
- call allocate_qmewald(natom)
- end if
- if (qmmm_nml%qmgb==2 .and. .not. master) then
- call allocate_qmgb(qmmm_struct%nquant_nlink)
- end if
-
- if (.not. master) then
- allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat = ier )
- REQUIRE(ier == 0) !Deallocated in deallocate qmmm
- end if
-
- end if
-
- ! --- END QMMM MPI SETUP ---
-
- ! DAN ROE: Note: all nodes are calling this. amrset(ig) has already been called
- ! by the master node (twice if initial velocities are set, ntx<=3).
- ! DAN ROE: REMD: Now need to call amrset on all child threads, masters have called
- ! it above before initial coord read
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- if(rem == 0) then
- call amrset(ig+1)
- else
- if (.not. master) call amrset(ig + 17 * nodeid)
- endif
-
- if (nmropt >= 1) &
- call nmrcal(x(lcrd),f,ih(m04),ih(m02),ix(i02),x(lwinv),enmr, &
- devdis,devang,devtor,devplpt,devpln,devgendis,temp0,tautp,cut,ntb,x(lnmr01), &
- ix(inmr02),x(l95),5,6,rk,tk,pk,cn1,cn2, &
- ag,bg,cg,numbnd,numang,numphi,nimprp, &
- nhb,natom,natom,ntypes,nres,rad,wel,radhb, &
- welhb,rwell,isftrp,tgtrmsd,temp0les,-1,'MPI ')
- end if ! lam81
- ! Updated 9/2007 by Matthew Seetin to enable plane-point and plane-plane restraints
-
- call mpi_bcast(lmtmd01,1,mpi_integer,0, commsander,ierr)
- call mpi_bcast(imtmd02,1,mpi_integer,0, commsander,ierr)
-
- if (itgtmd == 2) call mtmdcall(emtmd,x(lmtmd01),ix(imtmd02),x(lcrd),x(lforce),&
- ih(m04),ih(m02),ix(i02),ih(m06),x(lmass),natom,nres,'MPI ')
-
-
- ! ---------------- Check system is neutral and print warning message ------
- ! ---------------- adjust charges for roundoff error. ------
- if( igb == 0 .and. ipb == 0 .and. iyammp == 0 ) then
- if ( icfe == 0 ) then
- call check_neutral(x(l15),natom)
- else
- call ti_check_neutral(x(l15),natom)
- end if
- end if
-
- ! tell all nodes if this is a SEBOMD run
- call mpi_bcast(sebomd_obj%do_sebomd, 1, MPI_LOGICAL, 0, commsander, ierr)
- if (sebomd_obj%do_sebomd) then
- ! transfer SEBOMD info to the nodes
- call sebomd_bcast_obj()
- ! open necessary files
- if (master) then
- call sebomd_open_files
- end if
- ! initialize SEBOMD arrays
- call init_sebomd_arrays(natom)
- end if
-
- ! ---------------- Old parallel for minimization ----------------------
-
- if (imin /= 0) then
- mpi_orig = .true.
- notdone = 1
- else
- mpi_orig = .false.
- end if
-
- if (mpi_orig .and. .not. master) then
-
- ! ...all nodes only do the force calculations (JV)
- ! Minimisation so only only master gets past the loop below
- ! hence need to zero QM charges on non-master threads here.
-
- if (qmmm_nml%ifqnt) then
- ! Apply charge correction if required.
- if (qmmm_nml%adjust_q>0) then
- call qmmm_adjust_q(qmmm_nml%adjust_q, natom, qmmm_struct%nquant, qmmm_struct%nquant_nlink, &
- qmmm_struct%nlink, x(L15), &
- qmmm_struct%iqmatoms, qmmm_nml%qmcharge, qmmm_struct%atom_mask, &
- qmmm_struct%mm_link_mask, master,x(LCRD), qmmm_nml%vsolv)
- end if
- ! At this point we can also fill the qmmm_struct%scaled_mm_charges
- ! array - we only need to do this once as the charges are constant
- ! during a run. Having a separate array of scaled charges saves us
- ! having to do it on every qmmm routine call. Do this BEFORE zeroing
- ! the QM charges since that routine take care of these values as well.
- do i = 1, natom
- qmmm_struct%scaled_mm_charges(i) = x(L15+(i-1)) * INV_AMBER_ELECTROSTATIC &
- * qmmm_nml%chg_lambda ! charge scaling factor for FEP
- end do
- ! Zero out the charges on the quantum mechanical atoms
- call qm_zero_charges(x(L15),qmmm_struct%scaled_mm_charges,.true.)
- if (qmmm_struct%nlink > 0 ) then
- ! We need to exclude all electrostatic
- ! interactions with MM link pairs, both QM-MM and MM-MM. Do this by
- ! zeroing the MM link pair charges in the main charge array.
- ! These charges are stored in qmmm_struct%mm_link_pair_resp_charges in case
- ! they are later needed.
- call qm_zero_mm_link_pair_main_chg(qmmm_struct%nlink,qmmm_struct%link_pairs,x(L15), &
- qmmm_struct%scaled_mm_charges,.true.)
- end if
-
- end if
-
- if (igb == 7 .or. igb == 8) call igb7_init(natom, ncopy, x(l97)) !x(l97) is rborn()
- !Hai Nguyen: add igb == 8 here
-
- if ( ifcr /= 0 ) call cr_allocate( master, natom )
-
- n_force_calls = 0
- do while( notdone == 1 )
- n_force_calls = n_force_calls+1
- call force(x,ix,ih,ipairs,x(lcrd),x(lforce),ene,vir, &
- x(l96), x(l97), x(l98), x(l99), qsetup, &
- do_list_update,n_force_calls)
- end do
-
- ! Deallocate and return
- goto 999
-
- end if
-
- ! ----------------------------------------------------------------------
-
- if (master) then
- if(abfqmmm_param%abfqmmm /=1) write(6, '(a,i4,a,/)') '| Running AMBER/MPI version on ',numtasks, ' nodes' ! lam81
- !BTREE is selected by default if cpu is a power of two.
- !The number of processes is required to be a power of two for Btree
- !Print a warning about inefficiency with cpus not being a power of 2.
- if (numtasks > 1 .and. logtwo(numtasks) <= 0) then
- if(abfqmmm_param%abfqmmm /=1) write(6, '(a,i4,a,/)') '| WARNING: The number of processors is not a power of 2' ! lam81
- if(abfqmmm_param%abfqmmm /=1) write(6, '(a,i4,a,/)') '| this may be inefficient on some systems.' ! lam81
- end if
- end if
- if (master .and. numgroup > 1) write(6, '(a,i4,a,i4,a,i4,a)') &
- '| MULTISANDER: ', numgroup, ' groups. ', &
- numtasks, ' processors out of ', worldsize, ' total.'
- if (master) call amflsh(6)
-
- ! ========================= END AMBER/MPI =========================
-#else
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- allocate(abfqmmm_param%v(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f1(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- allocate(abfqmmm_param%f2(3*natom+iscale), stat=ier) ! lam81
- REQUIRE(ier==0) ! lam81
- end if ! lam81
- end if ! lam81
-
- ! debug needs to copy charges at start and they can't change later
- ! ---------------- Check system is neutral and print warning message ------
- ! ---------------- adjust charges for roundoff error. ------
- if( igb == 0 .and. ipb == 0 .and. iyammp == 0 ) call check_neutral(x(l15),natom)
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call amrset(ig+1)
- end if ! lam81
-
- if (abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call stack_setup()
- else ! lam81
- call deallocate_stacks ! lam81
- call stack_setup() ! lam81
- end if ! lam81
-
- if (sebomd_obj%do_sebomd) then
- ! open necessary files
- call sebomd_open_files
- ! initialize SEBOMD arrays
- call init_sebomd_arrays(natom)
- endif
-
-#endif /* MPI */
-
-#ifdef OPENMP
-
- ! If -openmp was specified to configure_amber then -DOPENMP is defined and the
- ! threaded version of MKL will have been linked in. It is important here that
- ! we set the default number of openmp threads for MKL to be 1 to stop conflicts
- ! with threaded vectorization routines when running in parallel etc.
- ! Individual calls to MKL from routines that know what they are doing - e.g.
- ! QMMM calls to diagonalizers etc can increase this limit as long as they
- ! put it back afterwards.
- call omp_set_num_threads(1)
-
- ! If we are using openmp for matrix diagonalization print some information.
- if (qmmm_nml%ifqnt .and. master) call qm_print_omp_info()
-#endif
-
- ! allocate memory for crg relocation
- if (ifcr /= 0) call cr_allocate( master, natom )
-
- ! initialize LIE module if used
- if ( ilrt /= 0 ) then
- call setup_linear_response(natom,nres,ih(m04),ih(m06),ix(i02),ih(m02),x(lcrd),x(l15), &
- ntypes, ix(i04), ix(i06), cn1, cn2, master)
- end if
-
- call date_and_time( setup_end_date, setup_end_time )
-
- ! Initialize the printing of ongoing time and performance summaries.
- ! We do this quite late here to avoid including all the setup time.
- if (master) call print_ongoing_time_summary(0,0,0.0d0,7)
-
- ! ----------------------------------------------------------------------
- ! Now do the dynamics or minimization.
- ! ----------------------------------------------------------------------
-
- if (igb == 7 .or. igb == 8 ) call igb7_init(natom, ncopy, x(l97)) !x(l97) is rborn()
- !Hai Nguyen: add igb ==8 here
-
- if (qmmm_nml%ifqnt) then
- ! Apply charge correction if required.
- if (qmmm_nml%adjust_q>0) then
- call qmmm_adjust_q(qmmm_nml%adjust_q, natom, qmmm_struct%nquant, qmmm_struct%nquant_nlink, &
- qmmm_struct%nlink, x(L15), &
- qmmm_struct%iqmatoms, qmmm_nml%qmcharge, qmmm_struct%atom_mask, &
- qmmm_struct%mm_link_mask, master,x(LCRD), qmmm_nml%vsolv)
- end if
- ! At this point we can also fill the qmmm_struct%scaled_mm_charges
- ! array - we only need to do this once as the charges are constant
- ! during a run. Having a separate array of scaled charges saves us
- ! having to do it on every qmmm routine call. Do this BEFORE zeroing
- ! the QM charges since that routine take care of these values as well.
- do i = 1, natom
- qmmm_struct%scaled_mm_charges(i) = x(L15+(i-1)) * INV_AMBER_ELECTROSTATIC &
- * qmmm_nml%chg_lambda ! charge scaling factor for FEP
- end do
-
- ! Zeroing of QM charges MUST be done AFTER call to check_neutral.
- ! Zero out the charges on the quantum mechanical atoms.
- call qm_zero_charges(x(L15),qmmm_struct%scaled_mm_charges,.true.)
-
- if (qmmm_struct%nlink > 0) then
- ! We need to exclude all electrostatic
- ! interactions with MM link pairs, both QM-MM and MM-MM. Do this by
- ! zeroing the MM link pair charges in the main charge array.
- ! These charges are stored in qmmm_struct%mm_link_pair_resp_charges in case
- ! they are later needed.
- call qm_zero_mm_link_pair_main_chg(qmmm_struct%nlink,qmmm_struct%link_pairs,x(L15), &
- qmmm_struct%scaled_mm_charges,.true.)
- end if
-
- end if
-
- ! Use the debugf namelist to activate
- call debug_frc(x,ix,ih,ipairs,x(lcrd),x(lforce),cn1,cn2,qsetup)
-
- ! Prepare for SGLD simulation
- if (isgld > 0) call psgld(natom,x(lmass),x(lvel), rem)
-
- ! Prepare for EMAP constraints
- if (temap) call pemap(dt,temp0,x,ix,ih)
-
- ! Prepare for Isotropic periodic sum of nonbonded interaction
- if (ips .gt. 0) call ipssys(natom,ntypes,ntb,x(l15), &
- cut,cn1,cn2,ix(i04),ix(i06),x(lcrd))
-
- if (master .and. (.not. qmmm_nml%ifqnt) .and. (abfqmmm_param%abfqmmm /= 1)) & ! lam81
- write(6,'(/80(''-'')/,'' 4. RESULTS'',/80(''-'')/)')
-
- ! Set up the MC barostat if requested
- if (ntp > 0 .and. barostat == 2) call mcbar_setup(ig)
-
- ! Input flag imin determines the type of calculation: MD, minimization, ...
- select case (imin)
- case (0)
- ! --- Dynamics:
-
- call timer_start(TIME_RUNMD)
- ! Set up AMD
- if (iamd .gt. 0) then
- call amd_setup(ntwx)
- endif
-
- ! Set up scaledMD
- if (scaledMD .gt. 0) then
- call scaledMD_setup(ntwx)
- endif
-
- if (ipimd > 0) then
- call pimd_init(natom,x(lmass),x(lwinv),x(lvel),ipimd)
- end if
-
- if(ineb>0) call neb_init()
-
-#ifdef MPI
- ! ----===== REMD =====----
- ! If this is not a REMD run, runmd is called only once.
- ! If this is a REMD run, runmd is called 0 to numexchg times,
- ! where the 0th runmd is just for getting initial PEs (no dynamics).
- if (rem == 0) then
- ! Not a REMD run. runmd will be called once.
- loop = 0
- else if (rem > 0) then
- ! This is a REMD run. runmd will be called numexchg times.
- loop = numexchg
-
- ! Set up temptable, open remlog, etc.
- call remd1d_setup(numexchg, hybridgb, numwatkeep, &
- temp0, mxvar, natom, ig, solvph)
- else
- ! Multi-D REMD run
- loop = numexchg
- call multid_remd_setup(numexchg, hybridgb, numwatkeep, &
- temp0, mxvar, natom, ig, solvph, irest)
- ! Now set up REMD indices for traj/restart writes. Only do this on
- ! master since only master handles writes.
- if (master) call setup_remd_indices
- end if ! Replica run setup
-
- ! Loop over REMD exchanges
- do mdloop = 0, loop
-
- ! ----===== REMD EXCHANGE HANDLING =====----
- ! Note: mdloop==0 is just used to get initial energies for the
- ! first exchange.
- if (rem < 0 .and. mdloop > 0) then
- call multid_remd_exchange(x, ix, ih, ipairs, qsetup, &
- do_list_update, temp0, solvph)
- else if ((rem == 1 .or. rem == 2) .and. mdloop > 0) then
- call remd_exchange(1, rem, x(lcrd), x(lvel), x(lmass), &
- nr3, natom, nr, temp0)
- else if (rem == 3 .and. mdloop > 0) then
- call hremd_exchange(1, x, ix, ih, ipairs, qsetup, do_list_update)
- ! force was called inside hremd_exchange, so call nmrdcp
- ! to decrement the NMR counter, since this should not count
- ! as a real step. This is OK, since the counter got
- ! incremented at the _very_ end of nmrcal, so we haven't already
- ! printed an unwanted value (JMS 2/12)
- if (nmropt /= 0) call nmrdcp
- else if (rem == 4 .and. mdloop > 0) then
- call ph_remd_exchange(1, solvph)
- end if ! rem>0 and mdloop>0
-
- ! ----===== END REMD EXCHANGE HANDLING =====----
-
-#ifdef VERBOSE_REMD
- if (rem > 0 .and. mdloop .eq. 0 .and. master) &
- write (6,'(a,i4)') "REMD: Getting initial energy for replica ",repnum
-#endif /* VERBOSE_REMD */
-#endif /* MPI */
-
-#ifndef DISABLE_NCSU
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call ncsu_on_sander_init(ih, x(lmass), x(lcrd), rem)
- end if ! lam81
-#endif /* DISABLE_NCSU */
-
- if (beeman_integrator == 1) then
- call AM_RUNMD(ix,ih,ipairs, &
- x(lwinv),x(lmass),x, &
- x(lcrd),x(lvel),x(lforce),qsetup)
- else
- call runmd(x,ix,ih,ipairs, &
- x(lcrd),x(lwinv),x(lmass),x(lforce), &
- x(lvel),x(lvel2),x(l45),x(lcrdr), &
- x(l50),x(l95),ix(i70),x(l75), &
- erstop,qsetup)
- end if !beeman_integrator == 1
-
-#ifndef DISABLE_NCSU
- if(abfqmmm_param%qmstep == 1 .and. abfqmmm_param%system == 1) then ! lam81
- call ncsu_on_sander_exit()
- end if ! lam81
-#endif /* DISABLE_NCSU */
-
- ! ----===== END REMD =====----
-#ifdef MPI
- end do ! Loop over REMD exchanges (mdloop)
-
- ! Cleanup REMD files.
- if (rem /= 0) call remd_cleanup()
-
-#endif
-
- call timer_stop(TIME_RUNMD)
-
- if (master) call amflsh(6)
-
- if (erstop) then
- ! This error condition stems from subroutine shake;
- ! furthermore, it seems that erstop can never be true since shake
- ! can never return with its third last argument, niter, equal to 0.
- ! SRB, Sep 24, 2003
- if (master) then
- write(6, *) 'FATAL ERROR'
- end if
- call mexit(6,1)
- end if
-
- case (1)
-
- !--- Minimization:
-
- ! Input flag ntmin determines the method of minimization
- select case (ntmin)
- case (0, 1, 2)
- call runmin(x,ix,ih,ipairs,x(lcrd),x(lforce),x(lvel), &
- ix(iibh),ix(ijbh),x(l50),x(lwinv),ix(ibellygp), &
- x(l95),ene, carrms, qsetup)
- ! If a conventional minimisation is being done,
- ! the restart file is written inside the runmin routine.
- case (LMOD_NTMIN_XMIN)
- write(6,'(a)') ' LMOD XMIN Minimization.'
- write(6,'(a)') ''
- write(6,'(a)') ' Note: Owing to the behaviour of the XMIN algorithm,'
- write(6,'(a)') ' coordinates in the trajectory and intermediate'
- write(6,'(a)') ' restart files will not match up with energies'
- write(6,'(a)') ' in the mdout and mdinfo files. The final energy'
- write(6,'(a)') ' and final coordinates do match.'
- write(6,'(a)') ''
- xmin_iter = 0
- call run_xmin( x, ix, ih, ipairs, &
- x(lcrd), x(lforce), ene, qsetup, xmin_iter, ntpr )
- if (master) call minrit(0,nrp,ntxo,x(lcrd)) ! Write the restart file
- case (LMOD_NTMIN_LMOD)
- write(6,'(a)') ' LMOD LMOD Minimization.'
- write(6,'(a)') ''
- write(6,'(a)') ' Note: Owing to the behaviour of the XMIN algorithm,'
- write(6,'(a)') ' coordinates in the trajectory and intermediate'
- write(6,'(a)') ' restart files will not match up with energies'
- write(6,'(a)') ' in the mdout and mdinfo files. The final energy'
- write(6,'(a)') ' and final coordinates do match.'
- write(6,'(a)') ''
- call run_lmod( x, ix, ih, ipairs, &
- x(lcrd), x(lforce), ene, qsetup )
- if (master) call minrit(0,nrp,ntxo,x(lcrd)) ! Write the restart file
- case default
- ! invalid ntmin
- ! ntmin input validation occurs in mdread.f
- ASSERT( .false. )
- end select
-
-
- case (5)
- ! ---carlos modified for reading trajectories (trajene option)
-
- write (6,*) "POST-PROCESSING OF TRAJECTORY ENERGIES"
-
- ! ---read trajectories and calculate energies for each frame
-
- call trajene(x,ix,ih,ipairs,ene,ok,qsetup)
-
- if (.not. ok) then
- write (6,*) 'error in trajene()'
- call mexit(6,1)
- end if
-
- case default
- ! invalid imin
- ! imin input validation should be transferred to mdread.f
- write(6,'(/2x,a,i3,a)') 'Error: Invalid IMIN (',imin,').'
- ASSERT( .false. )
- end select
-
-#ifdef MPI /* SOFT CORE */
- if (master) then
- if (icfe /=0 .and. ifsc == 1) call summarize_ti_changes(natom,resat)
- end if
-#endif
-
- ! finish up EMAP
- if (temap) call qemap()
-
- if (abfqmmm_param%abfqmmm /= 1) then ! lam81
- exit ! lam81
- else ! lam81
-#ifdef MPI /* lam81 */
- call mpi_barrier(commsander,ierr) ! lam81
-#endif /* lam81 */
- if (abfqmmm_param%qmstep /= abfqmmm_param%maxqmstep .or. abfqmmm_param%system /= 2) then ! lam81
- if(qmmm_nml%ifqnt) call deallocate_qmmm(qmmm_nml, qmmm_struct, qmmm_vsolv, qm2_params) ! lam81
- end if ! lam81
- call deallocate_m1m2m3() ! lam81
- if (abfqmmm_param%system == 2 .and. master) then ! lam81
- call abfqmmm_write_idrst() ! lam81
- call abfqmmm_write_pdb(x(lcrd),ix(i70)) ! lam81
- end if ! lam81
- call abfqmmm_next_step() ! lam81
- end if ! lam81
-
- end do ! lam81
-
- if(abfqmmm_param%abfqmmm == 1) then ! lam81
- deallocate(abfqmmm_param%id, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%v, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%f, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%f1, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- deallocate(abfqmmm_param%f2, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- if(master) then ! lam81
- deallocate(abfqmmm_param%isqm, stat=ier) ! lam81
- REQUIRE( ier == 0 ) ! lam81
- endif ! lam81
- end if ! lam81
-
- ! -- calc time spent running vs setup
- call timer_stop(TIME_TOTAL)
- call wallclock( time1 )
- call date_and_time( final_date, final_time )
- call profile_time( time1 - time0, num_calls_nblist, profile_mpi)
-
-#ifdef MPI
- ! =========================== AMBER/MPI ===========================
-
- ! Set and broadcast notdone in mpi_orig case to inform
- ! other nodes that we are finished calling force(). (tec3)
-
- if (mpi_orig) then
- notdone = 0
- call mpi_bcast(notdone,1,mpi_integer,0, commsander,ierr)
- end if
-
- ! ========================= END AMBER/MPI =========================
-#endif
-
-! ========================= PUPIL INTERFACE =========================
-#ifdef PUPIL_SUPPORT
- ! Finalize Corba Interface
- puperror = 0
- call killcorbaintfc(puperror)
- if (puperror /= 0) then
- write(6,*) 'Error ending PUPIL CORBA interface.'
- end if
- write(6,'(a)') 'PUPIL CORBA interface finalized.'
- pupactive = .false.
-#endif
-! ========================= PUPIL INTERFACE =========================
-
-#ifdef _XRAY
- !(out_lun,residue_pointer,residue_label,atom_name,coor,num_bonds,ibond,jbond)
- call xray_fini()
-#endif
-
- call amflsh(6)
- if (master) then
-#ifdef MPI
- ! adaptive QM/MM (qmmm_nml%vsolv=2) via multisander
- ! all groups have identical coords and velocities
- ! only master of first group needs to dump results
- if ( (qmmm_nml%vsolv < 2) .or. (worldrank == 0) ) then
-#endif
- call close_dump_files
-#ifdef MPI
- end if
-#endif
-
- if (icnstph /= 0) &
- call cnstph_finalize
- ! --- write out final times, taking REMD into account
-#ifdef MPI
- if (rem .ne. 0) then
- nstlim_total = nstlim * numexchg
- else
- nstlim_total = nstlim
- end if
-#else
- nstlim_total = nstlim
-#endif
- if (imin == 0) &
- call print_ongoing_time_summary(nstlim_total,nstlim_total,dt,6)
-
- write(6,'(12(a))') '| Job began at ', initial_time(1:2), &
- ':', initial_time(3:4), ':', initial_time(5:10), ' on ',&
- initial_date(5:6), '/', initial_date(7:8), '/', initial_date(1:4)
- write(6,'(12(a))') '| Setup done at ', setup_end_time(1:2), &
- ':', setup_end_time(3:4), ':', setup_end_time(5:10), ' on ', &
- setup_end_date(5:6), '/',setup_end_date(7:8),'/',setup_end_date(1:4)
- write(6,'(12(a))') '| Run done at ', final_time(1:2), &
- ':', final_time(3:4), ':', final_time(5:10), ' on ', &
- final_date(5:6), '/', final_date(7:8), '/', final_date(1:4)
- call nwallclock( ncalls )
- write(6, '(''|'',5x,''wallclock() was called'',I8,'' times'')') ncalls
- call amflsh(6)
-
- if (iesp > 0) then
- call esp(natom,x(lcrd),x(linddip))
- end if
- end if
- call amflsh(6)
-
- ! --- dynamic memory deallocation:
- 999 continue
-
- if(qmmm_nml%ifqnt .and. qmmm_nml%qmtheory%EXTERN .and. master) then
- call qm2_extern_finalize()
- endif
-
- if (qmmm_nml%ifqnt .and. .not. qmmm_struct%qm_mm_first_call) then
- ! If first_call is still true, this thread never really
- ! called the QMMM routine. E.g. more threads than PIMD replicates
- call deallocate_qmmm(qmmm_nml, qmmm_struct, qmmm_vsolv, qm2_params)
- end if
-
- if (ipimd > 0) call pimd_finalize(ipimd)
-
- if (ineb > 0) call neb_finalize()
-
- if (idecomp > 0) then
- call deallocate_real_decomp()
- call deallocate_int_decomp()
- end if
- if (master .and. idecomp == 0) call deallocate_int_decomp()
-
-#ifdef MPI /* SOFT CORE */
- if (ifsc /= 0) call cleanup_sc()
- if (ifmbar /= 0) call cleanup_mbar()
-#endif
-
- ! finalize LIE module if initiated above
- if ( ilrt /= 0 ) then
- call cleanup_linear_response(master)
- end if
-
-#ifdef RISMSANDER
- call rism_finalize()
-#endif
-
- if ( ifcr /= 0 ) call cr_cleanup()
-
- if (sebomd_obj%do_sebomd) then
- if (master) then
- call sebomd_close_files
- end if
- call cleanup_sebomd_arrays
- end if
-
- if (master .and. iwrap == 2) then
- deallocate(iwrap_mask_atoms, stat=ier)
- REQUIRE(ier == 0)
- end if
- call nblist_deallocate()
- call deallocate_stacks()
- if ((igb /= 0 .and. igb /= 10 .and. ipb == 0) .or. hybridgb > 0 .or. icnstph > 1) then
- call deallocate_gb()
- end if
- if (master) then
- if(igb == 10 .or. ipb /= 0) then
- call pb_free()
- end if
- end if
- deallocate(ih, stat = ier)
- REQUIRE(ier == 0)
- deallocate(ipairs, stat = ier)
- REQUIRE(ier == 0)
- deallocate(ix, stat = ier)
- REQUIRE(ier == 0)
- deallocate(x, stat = ier)
- REQUIRE(ier == 0)
- if(ntb > 0 .and. ifbox == 1 .and. ew_type == 0 .and. mpoltype == 0) &
- call deallocate_m1m2m3()
- call AMOEBA_deallocate
- ! GMS: -- Module molecule --
- call deallocate_molecule()
- ! --------------------------
-
- if (charmm_active) call charmm_deallocate_arrays()
- if (cmap_active) call deallocate_cmap_arrays()
-
- if (master.and.mdout /= 'stdout') close(6)
-
- return
-
-end subroutine sander
-
-!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-!+ Calculate the ElectroStatic Potential
-subroutine esp(natom,x,mom_ind)
-
- ! routine to calculate the ESP due to the induced moments (only)
- ! at the same spatial points as the reference QM.
- use constants, only : zero, BOHRS_TO_A, INV_AMBER_ELECTROSTATIC
- use file_io_dat
- implicit none
- integer natom
- _REAL_ x(3,*)
- _REAL_ mom_ind(3,*)
-
-# include "ew_mpole.h"
-
- integer dat_unit, new_unit, minus_new_unit
- parameter(dat_unit=30, new_unit=31, minus_new_unit=33)
-
- integer inat, nesp, idum
- _REAL_ xin, yin, zin
- integer jn, kn
- _REAL_ esp_qm, xb_esp, yb_esp, zb_esp
- _REAL_ x_esp, y_esp, z_esp
- _REAL_ e_x, e_y, e_z, e_q, esp_new
- _REAL_ dist, dist3
- integer iptr
-
- call amopen(dat_unit,"esp.dat",'O','F','R')
- call amopen(new_unit,"esp.induced",owrite,'F','W')
- call amopen(minus_new_unit,"esp.qm-induced",owrite,'F','W')
- read (dat_unit,'(3i5)')inat,nesp,idum
- write(6,'(t2,''inat = '',i5)')inat
- write(6,'(t2,''nesp = '',i5)')nesp
-
- write(new_unit,'(2i5)')inat,nesp
- write(minus_new_unit,'(2i5)')inat,nesp
-
- if (inat /= natom) then
- write(6,'(t2,''natom mismatch with esp file'')')
- call mexit(6,1)
- end if
-
- do jn = 1,inat
- read (dat_unit,'(17x,3e16.0)')xin,yin,zin
- write(new_unit,'(17x,3e16.7)')xin,yin,zin
- write(minus_new_unit,'(17x,3e16.7)')xin,yin,zin
- end do
-
- do jn = 1,nesp
- e_x = zero
- e_y = zero
- e_z = zero
- e_q = zero
- read(dat_unit,'(1x,4e16.0)')esp_qm,xb_esp,yb_esp,zb_esp
- x_esp = xb_esp * BOHRS_TO_A
- y_esp = yb_esp * BOHRS_TO_A
- z_esp = zb_esp * BOHRS_TO_A
-
- do kn = 1,natom
- dist = (sqrt((x(1,kn)-x_esp)**2 + &
- (x(2,kn)-y_esp)**2 + &
- (x(3,kn)-z_esp)**2))
- dist3 = dist**3
- e_x = e_x - mom_ind(1,kn )*(x(1,kn)-x_esp)/dist3
- e_y = e_y - mom_ind(2,kn )*(x(2,kn)-y_esp)/dist3
- e_z = e_z - mom_ind(3,kn )*(x(3,kn)-z_esp)/dist3
- end do
-
- e_x = e_x * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- e_y = e_y * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- e_z = e_z * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- e_q = e_q * BOHRS_TO_A * INV_AMBER_ELECTROSTATIC
- esp_new = e_x + e_y + e_z
-
- write(new_unit, '(1x,4e16.7)')esp_new, &
- xb_esp,yb_esp,zb_esp
- write(minus_new_unit,'(1x,4e16.7)')esp_qm-esp_new, &
- xb_esp,yb_esp,zb_esp
- end do
-
- close(dat_unit)
- close(new_unit)
- close(minus_new_unit)
-
- return
-
-end subroutine esp
-
diff --git a/regtest/.gitignore b/regtest/.gitignore
index 77d7ff789046461171bba1ea62b9c12860446dbe..8e326858248a501ca63c44d6f05b640bb3a9c0f5 100644
--- a/regtest/.gitignore
+++ b/regtest/.gitignore
@@ -11,6 +11,7 @@
!/dimred
!/eds
!/drr
+!/logmfd
!/mapping
!/multicolvar
!/python
diff --git a/regtest/basic/rt-make-2/main.cpp b/regtest/basic/rt-make-2/main.cpp
index 6756773289a16114a75facadb9fb1b1bba678d70..55e837c0f5d2eb04424ce71a6d1658aaaeef2af9 100644
--- a/regtest/basic/rt-make-2/main.cpp
+++ b/regtest/basic/rt-make-2/main.cpp
@@ -38,6 +38,18 @@ void run(Communicator& comm){
comm.Sum(&a[0],a.size());
dump(comm,ofs,a);
+ reset(comm,a);
+ comm.Prod(&a[0],a.size());
+ dump(comm,ofs,a);
+
+ reset(comm,a);
+ comm.Max(&a[0],a.size());
+ dump(comm,ofs,a);
+
+ reset(comm,a);
+ comm.Min(&a[0],a.size());
+ dump(comm,ofs,a);
+
reset(comm,a);
comm.Bcast(&a[0],a.size(),0);
dump(comm,ofs,a);
diff --git a/regtest/basic/rt-make-2/output0.reference b/regtest/basic/rt-make-2/output0.reference
index daae14a3eea8e58fbe1844852502ee164aa21380..226b019270a7513e0a22c9d45090b69cf6886e8d 100644
--- a/regtest/basic/rt-make-2/output0.reference
+++ b/regtest/basic/rt-make-2/output0.reference
@@ -1,5 +1,8 @@
1
6 12 18 24 30 36 42 48 54 60 66 72
+ 6 48 162 384 750 1296 2058 3072 4374 6000 7986 10368
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 3 4 5 6 7 8 9 10 11 12
1 2 3 4 5 6 7 8 9 10 11 12
3 6 9 12 15 18 21 24 27 30 33 36
1 2 3 4 5 6 7 8 9 10 11 12
diff --git a/regtest/basic/rt-make-2/output1.reference b/regtest/basic/rt-make-2/output1.reference
index 02f889b5f80b32964dd3cc8979c34993f5a5a415..246821fb952898ef9bcca196c8fa4f7ff912cc77 100644
--- a/regtest/basic/rt-make-2/output1.reference
+++ b/regtest/basic/rt-make-2/output1.reference
@@ -1,5 +1,8 @@
1
6 12 18 24 30 36 42 48 54 60 66 72
+ 6 48 162 384 750 1296 2058 3072 4374 6000 7986 10368
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 3 4 5 6 7 8 9 10 11 12
1 2 3 4 5 6 7 8 9 10 11 12
3 6 9 12 15 18 21 24 27 30 33 36
2 4 6 8 10 12 14 16 18 20 22 24
diff --git a/regtest/basic/rt-make-2/output2.reference b/regtest/basic/rt-make-2/output2.reference
index 2baff966c4c5f4d61fe78156eef45d9057e4ec7d..7edf3e8be26505aaca067b98e4fb8191c71aeab0 100644
--- a/regtest/basic/rt-make-2/output2.reference
+++ b/regtest/basic/rt-make-2/output2.reference
@@ -1,5 +1,8 @@
1
6 12 18 24 30 36 42 48 54 60 66 72
+ 6 48 162 384 750 1296 2058 3072 4374 6000 7986 10368
+ 3 6 9 12 15 18 21 24 27 30 33 36
+ 1 2 3 4 5 6 7 8 9 10 11 12
1 2 3 4 5 6 7 8 9 10 11 12
3 6 9 12 15 18 21 24 27 30 33 36
3 6 9 12 15 18 21 24 27 30 33 36
diff --git a/regtest/basic/rt67-mpi/COLVAR.reference b/regtest/basic/rt67-mpi/COLVAR.reference
index 7d00a355feca39f9bec7a530282a1b70349104d2..2f9cce0086b9293399fcf1e494ad3111e8f91a6b 100644
--- a/regtest/basic/rt67-mpi/COLVAR.reference
+++ b/regtest/basic/rt67-mpi/COLVAR.reference
@@ -14,13 +14,13 @@
8.000000 -1.8429 1.3293 0.6692 0.5800 0.1025
9.000000 -2.2424 2.6059 0.0000 -0.1025 0.1109
10.000000 -1.1482 0.5350 1.8435 1.7326 0.1281
- 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1367
- 12.000000 -1.3186 3.0997 0.0000 -0.1367 0.1443
- 13.000000 -2.9911 2.8991 0.0000 -0.1443 0.1524
- 14.000000 -1.4112 0.0028 0.0285 -0.1239 0.1614
- 15.000000 -2.5995 2.6683 0.3230 0.1616 0.1714
- 16.000000 -1.4608 0.2622 0.9676 0.7962 0.1856
- 17.000000 -1.3791 1.1576 3.0484 2.8628 0.2090
- 18.000000 -1.6771 0.9078 1.5947 1.3857 0.2309
- 19.000000 -1.5241 1.2623 4.1823 3.9513 0.2607
- 20.000000 -1.1997 0.9529 3.1902 2.9295 0.2924
+ 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1368
+ 12.000000 -1.3186 3.0997 0.0000 -0.1368 0.1451
+ 13.000000 -2.9911 2.8991 0.0000 -0.1451 0.1534
+ 14.000000 -1.4112 0.0028 0.0285 -0.1250 0.1625
+ 15.000000 -2.5995 2.6683 0.3230 0.1606 0.1725
+ 16.000000 -1.4608 0.2622 0.9676 0.7951 0.1867
+ 17.000000 -1.3791 1.1576 3.0484 2.8617 0.2101
+ 18.000000 -1.6771 0.9078 1.5947 1.3846 0.2320
+ 19.000000 -1.5241 1.2623 4.1823 3.9503 0.2617
+ 20.000000 -1.1997 0.9529 3.1902 2.9285 0.2935
diff --git a/regtest/basic/rt67/COLVAR.reference b/regtest/basic/rt67/COLVAR.reference
index 7d00a355feca39f9bec7a530282a1b70349104d2..2f9cce0086b9293399fcf1e494ad3111e8f91a6b 100644
--- a/regtest/basic/rt67/COLVAR.reference
+++ b/regtest/basic/rt67/COLVAR.reference
@@ -14,13 +14,13 @@
8.000000 -1.8429 1.3293 0.6692 0.5800 0.1025
9.000000 -2.2424 2.6059 0.0000 -0.1025 0.1109
10.000000 -1.1482 0.5350 1.8435 1.7326 0.1281
- 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1367
- 12.000000 -1.3186 3.0997 0.0000 -0.1367 0.1443
- 13.000000 -2.9911 2.8991 0.0000 -0.1443 0.1524
- 14.000000 -1.4112 0.0028 0.0285 -0.1239 0.1614
- 15.000000 -2.5995 2.6683 0.3230 0.1616 0.1714
- 16.000000 -1.4608 0.2622 0.9676 0.7962 0.1856
- 17.000000 -1.3791 1.1576 3.0484 2.8628 0.2090
- 18.000000 -1.6771 0.9078 1.5947 1.3857 0.2309
- 19.000000 -1.5241 1.2623 4.1823 3.9513 0.2607
- 20.000000 -1.1997 0.9529 3.1902 2.9295 0.2924
+ 11.000000 -1.7580 2.0752 0.0012 -0.1269 0.1368
+ 12.000000 -1.3186 3.0997 0.0000 -0.1368 0.1451
+ 13.000000 -2.9911 2.8991 0.0000 -0.1451 0.1534
+ 14.000000 -1.4112 0.0028 0.0285 -0.1250 0.1625
+ 15.000000 -2.5995 2.6683 0.3230 0.1606 0.1725
+ 16.000000 -1.4608 0.2622 0.9676 0.7951 0.1867
+ 17.000000 -1.3791 1.1576 3.0484 2.8617 0.2101
+ 18.000000 -1.6771 0.9078 1.5947 1.3846 0.2320
+ 19.000000 -1.5241 1.2623 4.1823 3.9503 0.2617
+ 20.000000 -1.1997 0.9529 3.1902 2.9285 0.2935
diff --git a/regtest/logmfd/Makefile b/regtest/logmfd/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..42480767ae852294cf2d7269ac5a1c16064d1849
--- /dev/null
+++ b/regtest/logmfd/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/logmfd/input.xyz b/regtest/logmfd/input.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..bd0d514ea89d6c5a1a2053cf5781474e7a7f7094
--- /dev/null
+++ b/regtest/logmfd/input.xyz
@@ -0,0 +1,110 @@
+108
+5.0388 5.0388 5.0388
+Ar 0 0 0
+Ar 0.8398 0 0.8398
+Ar 0.8398 0.8398 0
+Ar 0 0.8398 0.8398
+Ar 0 0 1.6796
+Ar 0.8398 0 2.5194
+Ar 0.8398 0.8398 1.6796
+Ar 0 0.8398 2.5194
+Ar 0 0 3.3592
+Ar 0.8398 0 4.199
+Ar 0.8398 0.8398 3.3592
+Ar 0 0.8398 4.199
+Ar 0 1.6796 0
+Ar 0.8398 1.6796 0.8398
+Ar 0.8398 2.5194 0
+Ar 0 2.5194 0.8398
+Ar 0 1.6796 1.6796
+Ar 0.8398 1.6796 2.5194
+Ar 0.8398 2.5194 1.6796
+Ar 0 2.5194 2.5194
+Ar 0 1.6796 3.3592
+Ar 0.8398 1.6796 4.199
+Ar 0.8398 2.5194 3.3592
+Ar 0 2.5194 4.199
+Ar 0 3.3592 0
+Ar 0.8398 3.3592 0.8398
+Ar 0.8398 4.199 0
+Ar 0 4.199 0.8398
+Ar 0 3.3592 1.6796
+Ar 0.8398 3.3592 2.5194
+Ar 0.8398 4.199 1.6796
+Ar 0 4.199 2.5194
+Ar 0 3.3592 3.3592
+Ar 0.8398 3.3592 4.199
+Ar 0.8398 4.199 3.3592
+Ar 0 4.199 4.199
+Ar 1.6796 0 0
+Ar 2.5194 0 0.8398
+Ar 2.5194 0.8398 0
+Ar 1.6796 0.8398 0.8398
+Ar 1.6796 0 1.6796
+Ar 2.5194 0 2.5194
+Ar 2.5194 0.8398 1.6796
+Ar 1.6796 0.8398 2.5194
+Ar 1.6796 0 3.3592
+Ar 2.5194 0 4.199
+Ar 2.5194 0.8398 3.3592
+Ar 1.6796 0.8398 4.199
+Ar 1.6796 1.6796 0
+Ar 2.5194 1.6796 0.8398
+Ar 2.5194 2.5194 0
+Ar 1.6796 2.5194 0.8398
+Ar 1.6796 1.6796 1.6796
+Ar 2.5194 1.6796 2.5194
+Ar 2.5194 2.5194 1.6796
+Ar 1.6796 2.5194 2.5194
+Ar 1.6796 1.6796 3.3592
+Ar 2.5194 1.6796 4.199
+Ar 2.5194 2.5194 3.3592
+Ar 1.6796 2.5194 4.199
+Ar 1.6796 3.3592 0
+Ar 2.5194 3.3592 0.8398
+Ar 2.5194 4.199 0
+Ar 1.6796 4.199 0.8398
+Ar 1.6796 3.3592 1.6796
+Ar 2.5194 3.3592 2.5194
+Ar 2.5194 4.199 1.6796
+Ar 1.6796 4.199 2.5194
+Ar 1.6796 3.3592 3.3592
+Ar 2.5194 3.3592 4.199
+Ar 2.5194 4.199 3.3592
+Ar 1.6796 4.199 4.199
+Ar 3.3592 0 0
+Ar 4.199 0 0.8398
+Ar 4.199 0.8398 0
+Ar 3.3592 0.8398 0.8398
+Ar 3.3592 0 1.6796
+Ar 4.199 0 2.5194
+Ar 4.199 0.8398 1.6796
+Ar 3.3592 0.8398 2.5194
+Ar 3.3592 0 3.3592
+Ar 4.199 0 4.199
+Ar 4.199 0.8398 3.3592
+Ar 3.3592 0.8398 4.199
+Ar 3.3592 1.6796 0
+Ar 4.199 1.6796 0.8398
+Ar 4.199 2.5194 0
+Ar 3.3592 2.5194 0.8398
+Ar 3.3592 1.6796 1.6796
+Ar 4.199 1.6796 2.5194
+Ar 4.199 2.5194 1.6796
+Ar 3.3592 2.5194 2.5194
+Ar 3.3592 1.6796 3.3592
+Ar 4.199 1.6796 4.199
+Ar 4.199 2.5194 3.3592
+Ar 3.3592 2.5194 4.199
+Ar 3.3592 3.3592 0
+Ar 4.199 3.3592 0.8398
+Ar 4.199 4.199 0
+Ar 3.3592 4.199 0.8398
+Ar 3.3592 3.3592 1.6796
+Ar 4.199 3.3592 2.5194
+Ar 4.199 4.199 1.6796
+Ar 3.3592 4.199 2.5194
+Ar 3.3592 3.3592 3.3592
+Ar 4.199 3.3592 4.199
+Ar 4.199 4.199 3.3592
+Ar 3.3592 4.199 4.199
diff --git a/regtest/logmfd/rt-logmfd-nve/COLVAR.reference b/regtest/logmfd/rt-logmfd-nve/COLVAR.reference
new file mode 100644
index 0000000000000000000000000000000000000000..39c2211d236551a0e00e88ee1d3f52488b3bea2d
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/COLVAR.reference
@@ -0,0 +1,6 @@
+#! FIELDS time d logmfd.d_fict
+ 0.500000 1.173063 1.500000
+ 1.000000 1.207470 1.499699
+ 1.500000 1.264623 1.499227
+ 2.000000 1.364253 1.498662
+ 2.500000 1.456331 1.498167
diff --git a/regtest/logmfd/rt-logmfd-nve/Makefile b/regtest/logmfd/rt-logmfd-nve/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/logmfd/rt-logmfd-nve/config b/regtest/logmfd/rt-logmfd-nve/config
new file mode 100644
index 0000000000000000000000000000000000000000..fb67c7e879f8e91a6a8e1a18c060bb417133e050
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/config
@@ -0,0 +1,6 @@
+type=simplemd
+plumed_modules=logmfd
+arg="--plumed plumed.dat < in"
+extra_files="../input.xyz"
+
+
diff --git a/regtest/logmfd/rt-logmfd-nve/in b/regtest/logmfd/rt-logmfd-nve/in
new file mode 100644
index 0000000000000000000000000000000000000000..8dd8cd686299c8d25dae4397657dcbc57f750a33
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/in
@@ -0,0 +1,10 @@
+inputfile input.xyz
+outputfile output.xyz
+temperature 1.2
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff 3.0
+nstep 500
+nconfig 100 trajectory.xyz
+nstat 10 energies.dat
diff --git a/regtest/logmfd/rt-logmfd-nve/logmfd.out.reference b/regtest/logmfd/rt-logmfd-nve/logmfd.out.reference
new file mode 100644
index 0000000000000000000000000000000000000000..224cf98d5b2bfc31fa2a6478f539156f3d497592
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/logmfd.out.reference
@@ -0,0 +1,11 @@
+# LogMFD
+# CVs : d
+# Mass for CV particles : 1000.000000000
+# Mass for thermostat : 24943.386300000
+# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
+# 6:d_fict(t), 7:d_vfict(t), 8:d_force(t),
+ 1 9.99256918 0.04361201 0.00000000 0.00000000 1.49969891 -0.00060217 -49.37805290
+ 2 9.98176170 0.10709839 0.00000000 0.00000000 1.49922709 -0.00094364 -27.98052199
+ 3 9.97382199 0.15378142 0.00000000 0.00000000 1.49866171 -0.00113076 -15.31583986
+ 4 9.97995043 0.11774488 0.00000000 0.00000000 1.49816700 -0.00098944 11.55859414
+ 5 9.98693691 0.07668930 0.00000000 0.00000000 1.49776774 -0.00079852 15.62476247
diff --git a/regtest/logmfd/rt-logmfd-nve/plumed.dat b/regtest/logmfd/rt-logmfd-nve/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..b2f04489d98a699066648dbd1df9c2ce8a83ddde
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/plumed.dat
@@ -0,0 +1,12 @@
+# LogMFD parameters NVE
+
+d: DISTANCE ATOMS=1,2
+
+LOGMFD ...
+ LABEL=logmfd
+ ARG=d
+ KAPPA=50000 DELTA_T=0.5 INTERVAL=100 TEMP=300.0 FLOG=10.0 FICT=1.5 MFICT=1000 VFICT=0.00
+ ALPHA=4.0 THERMOSTAT=NVE FICT_MIN=0.0 FICT_MAX=10.0,
+ ... LOGMFD
+
+PRINT ARG=d,logmfd.d_fict STRIDE=100 FILE=COLVAR
diff --git a/regtest/logmfd/rt-logmfd-nve/replica.out.reference b/regtest/logmfd/rt-logmfd-nve/replica.out.reference
new file mode 100644
index 0000000000000000000000000000000000000000..7e011c95c2f400e0d700c318ff04ed47bca0c885
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nve/replica.out.reference
@@ -0,0 +1,8 @@
+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:d(q)
+ 1 0.000000e+00 1.000000e+00 1.49901244
+ 2 -8.424535e-03 1.000000e+00 1.49913930
+ 3 -1.565089e-02 1.000000e+00 1.49892078
+ 4 -9.115915e-03 1.000000e+00 1.49889289
+ 5 -1.386056e-03 1.000000e+00 1.49847949
diff --git a/regtest/logmfd/rt-logmfd-nvt/COLVAR.reference b/regtest/logmfd/rt-logmfd-nvt/COLVAR.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9d69226f11402a92bebe5c7ccdb71d7eb0b6c643
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/COLVAR.reference
@@ -0,0 +1,6 @@
+#! FIELDS time d logmfd.d_fict
+ 0.500000 1.173063 1.500000
+ 1.000000 1.207470 1.499699
+ 1.500000 1.264623 1.499227
+ 2.000000 1.364253 1.498660
+ 2.500000 1.456331 1.498163
diff --git a/regtest/logmfd/rt-logmfd-nvt/Makefile b/regtest/logmfd/rt-logmfd-nvt/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/logmfd/rt-logmfd-nvt/config b/regtest/logmfd/rt-logmfd-nvt/config
new file mode 100644
index 0000000000000000000000000000000000000000..fb67c7e879f8e91a6a8e1a18c060bb417133e050
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/config
@@ -0,0 +1,6 @@
+type=simplemd
+plumed_modules=logmfd
+arg="--plumed plumed.dat < in"
+extra_files="../input.xyz"
+
+
diff --git a/regtest/logmfd/rt-logmfd-nvt/in b/regtest/logmfd/rt-logmfd-nvt/in
new file mode 100644
index 0000000000000000000000000000000000000000..8dd8cd686299c8d25dae4397657dcbc57f750a33
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/in
@@ -0,0 +1,10 @@
+inputfile input.xyz
+outputfile output.xyz
+temperature 1.2
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff 3.0
+nstep 500
+nconfig 100 trajectory.xyz
+nstat 10 energies.dat
diff --git a/regtest/logmfd/rt-logmfd-nvt/logmfd.out.reference b/regtest/logmfd/rt-logmfd-nvt/logmfd.out.reference
new file mode 100644
index 0000000000000000000000000000000000000000..43608d959e95983a543640f651bf86e438713717
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/logmfd.out.reference
@@ -0,0 +1,11 @@
+# LogMFD
+# CVs : d
+# Mass for CV particles : 1000.000000000
+# Mass for thermostat : 1000.000000000
+# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
+# 6:d_fict(t), 7:d_vfict(t), 8:d_force(t),
+ 1 9.99257112 0.04362783 -0.00031175 -0.00124699 1.49969886 -0.00060228 -49.37805290
+ 2 9.98177141 0.10726915 -0.00124692 -0.00249371 1.49922666 -0.00094440 -27.98051515
+ 3 9.97384458 0.15435749 -0.00280541 -0.00374024 1.49866023 -0.00113287 -15.31577787
+ 4 9.97999107 0.11873308 -0.00498720 -0.00498691 1.49816344 -0.00099358 11.55896356
+ 5 9.98700853 0.07793288 -0.00779237 -0.00623376 1.49776095 -0.00080497 15.62528327
diff --git a/regtest/logmfd/rt-logmfd-nvt/plumed.dat b/regtest/logmfd/rt-logmfd-nvt/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..cb116319ac244018d73d04eeaf8296f2bc567f96
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/plumed.dat
@@ -0,0 +1,24 @@
+# LogMFD parameters NVT
+
+d: DISTANCE ATOMS=1,2
+
+LOGMFD ...
+ LABEL=logmfd
+ ARG=d
+ KAPPA=50000.0
+ DELTA_T=0.5
+ INTERVAL=100
+ TEMP=300.0
+ FLOG=10.0
+ FICT=1.5
+ MFICT=1000
+ VFICT=0.00
+ ALPHA=4.0
+ THERMOSTAT=NVT
+ FICT_MIN=0.0
+ FICT_MAX=10.0
+ VETA=0.0
+ META=1000.0
+... LOGMFD
+
+PRINT ARG=d,logmfd.d_fict STRIDE=100 FILE=COLVAR
diff --git a/regtest/logmfd/rt-logmfd-nvt/replica.out.reference b/regtest/logmfd/rt-logmfd-nvt/replica.out.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4dd31b8889746a6c81a61ea7d9d4d8b291c99e2f
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-nvt/replica.out.reference
@@ -0,0 +1,8 @@
+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:d(q)
+ 1 0.000000e+00 1.000000e+00 1.49901244
+ 2 -8.426061e-03 1.000000e+00 1.49913925
+ 3 -1.565815e-02 1.000000e+00 1.49892035
+ 4 -9.110732e-03 1.000000e+00 1.49889140
+ 5 -1.348246e-03 1.000000e+00 1.49847594
diff --git a/regtest/logmfd/rt-logmfd-vs/COLVAR.reference b/regtest/logmfd/rt-logmfd-vs/COLVAR.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e39ffed953d96ffe1d721c8670749b8969090df0
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/COLVAR.reference
@@ -0,0 +1,6 @@
+#! FIELDS time d logmfd.d_fict
+ 0.500000 1.173063 1.500000
+ 1.000000 1.206032 1.524972
+ 1.500000 1.260549 1.549943
+ 2.000000 1.350710 1.574915
+ 2.500000 1.428247 1.599887
diff --git a/regtest/logmfd/rt-logmfd-vs/Makefile b/regtest/logmfd/rt-logmfd-vs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/logmfd/rt-logmfd-vs/config b/regtest/logmfd/rt-logmfd-vs/config
new file mode 100644
index 0000000000000000000000000000000000000000..fb67c7e879f8e91a6a8e1a18c060bb417133e050
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/config
@@ -0,0 +1,6 @@
+type=simplemd
+plumed_modules=logmfd
+arg="--plumed plumed.dat < in"
+extra_files="../input.xyz"
+
+
diff --git a/regtest/logmfd/rt-logmfd-vs/energies.dat b/regtest/logmfd/rt-logmfd-vs/energies.dat
new file mode 100644
index 0000000000000000000000000000000000000000..d05f94868c2e214533133ca6fe5e8a387f64b443
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/energies.dat
@@ -0,0 +1,500 @@
+10 0.050000 14.074354 -634.565052 1645.480219 1761.212867
+20 0.100000 10.695250 -562.668342 1169.962208 1413.264578
+30 0.150000 3.636492 -561.548268 27.563475 347.606562
+40 0.200000 0.993374 -559.931505 -399.004928 4.495983
+50 0.250000 5.327557 -557.997414 305.066739 803.236811
+60 0.300000 10.381703 -565.109304 1116.726507 1696.003234
+70 0.350000 9.640969 -546.546942 1015.290083 1629.584152
+80 0.400000 4.188741 -560.744310 117.831756 800.022646
+90 0.450000 1.005476 -562.466342 -399.579255 338.894277
+100 0.500000 3.344090 -545.268649 -3.526146 809.188838
+110 0.550000 7.884009 -552.147217 725.062318 1591.422430
+120 0.600000 8.374765 -557.751181 798.960706 1763.438893
+130 0.650000 4.769539 -557.928175 214.737063 1251.105628
+140 0.700000 1.369561 -552.547273 -330.678370 754.018358
+150 0.750000 1.852360 -545.347680 -245.265297 873.442944
+160 0.800000 5.066665 -544.766162 276.033556 1446.204026
+170 0.850000 6.990580 -548.230826 584.243063 1806.012723
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+4510 22.550000 1.351216 -491.065268 -272.168275 2726.555605
+4520 22.600000 1.770298 -504.182100 -217.393802 2773.524488
+4530 22.650000 1.676200 -477.452837 -205.908385 2795.312027
+4540 22.700000 1.530972 -483.700472 -235.683052 2774.302835
+4550 22.750000 1.229573 -479.702013 -280.511181 2738.275002
+4560 22.800000 1.415555 -513.437315 -284.117421 2738.643125
+4570 22.850000 1.567553 -516.463833 -262.520275 2769.588033
+4580 22.900000 1.645241 -500.391464 -233.862496 2793.398237
+4590 22.950000 1.591805 -500.266712 -242.394367 2789.263595
+4600 23.000000 1.318056 -491.305153 -277.780029 2765.732554
+4610 23.050000 1.359479 -500.479096 -280.243461 2761.918125
+4620 23.100000 1.528601 -488.266289 -240.632933 2792.298089
+4630 23.150000 1.725311 -505.892572 -226.392231 2810.426446
+4640 23.200000 1.677021 -510.719806 -239.042427 2799.535382
+4650 23.250000 1.487149 -505.946270 -265.028201 2780.514277
+4660 23.300000 1.202246 -471.133947 -276.370055 2780.875706
+4670 23.350000 1.393854 -482.163540 -256.359113 2795.617095
+4680 23.400000 1.558420 -495.868272 -243.404239 2809.492490
+4690 23.450000 1.456526 -488.607894 -252.650760 2806.653742
+4700 23.500000 1.358352 -494.153178 -274.100181 2792.130666
+4710 23.550000 1.242431 -483.892035 -282.618143 2797.330265
+4720 23.600000 1.408901 -498.894033 -270.652064 2820.116573
+4730 23.650000 1.459738 -500.205628 -263.728127 2825.330480
+4740 23.700000 1.306582 -497.609338 -285.943005 2812.390056
+4750 23.750000 1.196443 -505.344358 -311.520614 2797.467768
+4760 23.800000 1.160766 -516.815425 -328.771321 2793.815141
+4770 23.850000 1.255772 -517.208543 -313.773490 2812.713306
+4780 23.900000 1.391945 -518.734545 -293.239487 2825.509116
+4790 23.950000 1.394961 -521.135873 -295.152136 2821.826700
+4800 24.000000 1.181185 -502.275107 -310.923119 2806.756154
+4810 24.050000 1.216579 -486.771866 -289.686139 2818.862006
+4820 24.100000 1.472187 -511.910637 -273.416421 2840.674127
+4830 24.150000 1.453892 -505.280716 -269.750252 2845.018602
+4840 24.200000 1.360292 -513.403732 -293.036486 2829.104176
+4850 24.250000 1.130015 -494.032178 -310.969678 2812.999037
+4860 24.300000 1.292429 -515.899720 -306.526249 2817.357654
+4870 24.350000 1.320635 -510.625229 -296.682282 2828.976489
+4880 24.400000 1.467297 -518.437949 -280.735763 2843.811284
+4890 24.450000 1.354582 -514.629011 -295.186798 2844.280047
+4900 24.500000 1.329741 -509.990824 -294.572860 2831.634105
+4910 24.550000 1.774217 -503.844994 -216.421850 2909.001949
+4920 24.600000 1.448440 -484.013702 -249.366491 2872.451358
+4930 24.650000 1.374013 -494.939945 -272.349831 2855.796977
+4940 24.700000 1.368716 -481.980139 -260.248159 2875.546308
+4950 24.750000 1.652378 -502.560670 -234.875459 2905.854092
+4960 24.800000 1.715543 -506.180041 -228.262128 2921.641440
+4970 24.850000 1.434096 -485.724197 -253.400674 2904.615745
+4980 24.900000 1.355164 -493.944941 -274.408306 2877.556949
+4990 24.950000 1.452223 -509.420404 -274.160232 2873.327065
+5000 25.000000 1.428150 -487.705089 -256.344815 2897.411501
diff --git a/regtest/logmfd/rt-logmfd-vs/in b/regtest/logmfd/rt-logmfd-vs/in
new file mode 100644
index 0000000000000000000000000000000000000000..8dd8cd686299c8d25dae4397657dcbc57f750a33
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/in
@@ -0,0 +1,10 @@
+inputfile input.xyz
+outputfile output.xyz
+temperature 1.2
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff 3.0
+nstep 500
+nconfig 100 trajectory.xyz
+nstat 10 energies.dat
diff --git a/regtest/logmfd/rt-logmfd-vs/logmfd.out.reference b/regtest/logmfd/rt-logmfd-vs/logmfd.out.reference
new file mode 100644
index 0000000000000000000000000000000000000000..32347a003bdd56bd25d4830e33053744c56857ad
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/logmfd.out.reference
@@ -0,0 +1,11 @@
+# LogMFD
+# CVs : d
+# Mass for CV particles : 1000.000000000
+# Mass for thermostat : 24943.386300000
+# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
+# 6:d_fict(t), 7:d_vfict(t), 8:d_force(t),
+ 1 11.31874011 300.00000000 0.00000000 0.00000000 1.52497168 0.04994335 -49.37805290
+ 2 12.11796798 300.00000000 0.00000000 0.00000000 1.54994335 0.04994335 -30.84486807
+ 3 12.64372631 300.00000000 0.00000000 0.00000000 1.57491503 0.04994335 -20.57601661
+ 4 12.62225551 300.00000000 0.00000000 0.00000000 1.59988671 0.04994335 0.86059445
+ 5 12.39455605 300.00000000 0.00000000 0.00000000 1.62485839 0.04994335 9.20815359
diff --git a/regtest/logmfd/rt-logmfd-vs/plumed.dat b/regtest/logmfd/rt-logmfd-vs/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..76d367a4ff4be3386e961e51f69fb7c8c3a7e790
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/plumed.dat
@@ -0,0 +1,22 @@
+# LogMFD parameters VS
+
+d: DISTANCE ATOMS=1,2
+
+LOGMFD ...
+ LABEL=logmfd
+ ARG=d
+ KAPPA=50000.0
+ DELTA_T=0.5
+ INTERVAL=100
+ TEMP=300.0
+ FLOG=10.0
+ FICT=1.5
+ MFICT=1000
+ VFICT=0.00
+ ALPHA=4.0
+ THERMOSTAT=VS
+ FICT_MIN=0.0
+ FICT_MAX=10.0
+... LOGMFD
+
+PRINT ARG=d,logmfd.d_fict STRIDE=100 FILE=COLVAR
diff --git a/regtest/logmfd/rt-logmfd-vs/replica.out.reference b/regtest/logmfd/rt-logmfd-vs/replica.out.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2974531ae72d84834478e302c1817beec520450b
--- /dev/null
+++ b/regtest/logmfd/rt-logmfd-vs/replica.out.reference
@@ -0,0 +1,8 @@
+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:d(q)
+ 1 1.233053e+00 1.000000e+00 1.49901244
+ 2 2.003301e+00 1.000000e+00 1.52435478
+ 3 2.517119e+00 1.000000e+00 1.54953183
+ 4 2.495628e+00 1.000000e+00 1.57493224
+ 5 2.265685e+00 1.000000e+00 1.60007087
diff --git a/regtest/multicolvar/rt25/derivatives.reference b/regtest/multicolvar/rt25/derivatives.reference
index 10e58b83c011b08740ae51bf94def9247b5c04fc..d0cb13b2f5ad38a82bde4fdfa1bc20696a776816 100644
--- a/regtest/multicolvar/rt25/derivatives.reference
+++ b/regtest/multicolvar/rt25/derivatives.reference
@@ -1,526 +1,526 @@
-#! FIELDS time parameter c1 c1num
- 0.000000 0 -0.0023 -0.0023
- 0.000000 1 0.0023 0.0023
- 0.000000 2 0.0008 0.0008
- 0.000000 3 -0.0027 -0.0027
- 0.000000 4 -0.0030 -0.0030
- 0.000000 5 -0.0010 -0.0010
- 0.000000 6 0.0126 0.0126
- 0.000000 7 0.0021 0.0021
- 0.000000 8 0.0006 0.0006
- 0.000000 9 -0.0076 -0.0076
- 0.000000 10 -0.0014 -0.0014
- 0.000000 11 -0.0004 -0.0004
- 0.000000 12 -0.1068 -0.1068
- 0.000000 13 -0.0978 -0.0978
- 0.000000 14 0.0943 0.0943
- 0.000000 15 0.0592 0.0592
- 0.000000 16 -0.0011 -0.0011
- 0.000000 17 -0.0556 -0.0556
- 0.000000 18 0.0234 0.0234
- 0.000000 19 0.1834 0.1834
- 0.000000 20 -0.0108 -0.0108
- 0.000000 21 0.0243 0.0243
- 0.000000 22 -0.0845 -0.0845
- 0.000000 23 -0.0279 -0.0279
- 0.000000 24 0.0377 0.0377
- 0.000000 25 -0.1134 -0.1134
- 0.000000 26 -0.0379 -0.0379
- 0.000000 27 0.0123 0.0123
- 0.000000 28 0.0956 0.0956
- 0.000000 29 -0.0118 -0.0118
- 0.000000 30 0.0879 0.0879
- 0.000000 31 -0.1220 -0.1220
- 0.000000 32 -0.0879 -0.0879
- 0.000000 33 -0.1379 -0.1379
- 0.000000 34 0.1399 0.1399
- 0.000000 35 0.1376 0.1376
- 0.000000 36 -0.1868 -0.1868
- 0.000000 37 0.1816 0.1816
- 0.000000 38 0.2145 0.2145
- 0.000000 39 -0.0037 -0.0037
- 0.000000 40 0.0112 0.0112
- 0.000000 41 -0.1880 -0.1880
- 0.000000 42 -0.0093 -0.0093
- 0.000000 43 0.0195 0.0195
- 0.000000 44 -0.2515 -0.2515
- 0.000000 45 0.1999 0.1999
- 0.000000 46 -0.2123 -0.2123
- 0.000000 47 0.2250 0.2250
- 0.000000 48 0.0481 0.0481
- 0.000000 49 -0.1259 -0.1259
- 0.000000 50 0.0384 0.0384
- 0.000000 51 -0.1440 -0.1440
- 0.000000 52 0.2683 0.2683
- 0.000000 53 -0.1172 -0.1172
- 0.000000 54 -0.0504 -0.0504
- 0.000000 55 0.0087 0.0087
- 0.000000 56 -0.0429 -0.0429
- 0.000000 57 0.1463 0.1463
- 0.000000 58 -0.1512 -0.1512
- 0.000000 59 0.1218 0.1218
- 0.000000 60 -0.0873 -0.0873
- 0.000000 61 -0.0686 -0.0686
- 0.000000 62 0.2131 0.2131
- 0.000000 63 0.0814 0.0814
- 0.000000 64 0.0863 0.0863
- 0.000000 65 -0.2416 -0.2416
- 0.000000 66 -0.1096 -0.1096
- 0.000000 67 0.0507 0.0507
- 0.000000 68 0.0043 0.0043
- 0.000000 69 0.1156 0.1156
- 0.000000 70 -0.0684 -0.0684
- 0.000000 71 0.0242 0.0242
- 0.000000 72 -0.9759 -0.9759
- 0.000000 73 -0.0191 -0.0191
- 0.000000 74 0.0303 0.0303
- 0.000000 75 1.3232 1.3232
- 0.000000 76 0.0240 0.0240
- 0.000000 77 -0.0463 -0.0463
- 0.000000 78 -0.6202 -0.6202
- 0.000000 79 -0.0184 -0.0184
- 0.000000 80 0.0024 0.0024
- 0.000000 81 0.2729 0.2729
- 0.000000 82 0.0135 0.0135
- 0.000000 83 0.0136 0.0136
- 0.000000 84 -0.2793 -0.2793
- 0.000000 85 -0.2587 -0.2587
- 0.000000 86 0.1898 0.1898
- 0.000000 87 0.4427 0.4427
- 0.000000 88 0.3809 0.3809
- 0.000000 89 -0.2772 -0.2772
- 0.000000 90 -0.3711 -0.3711
- 0.000000 91 -0.1266 -0.1266
- 0.000000 92 0.0760 0.0760
- 0.000000 93 0.2077 0.2077
- 0.000000 94 0.0044 0.0044
- 0.000000 95 0.0114 0.0114
- 0.000000 96 0.6933 0.6933
- 0.000000 97 -0.0140 -0.0140
- 0.000000 98 -0.4462 -0.4462
- 0.000000 99 -0.0140 -0.0140
- 0.000000 100 -0.1875 -0.1875
- 0.000000 101 0.1721 0.1721
- 0.000000 102 -0.4462 -0.4462
- 0.000000 103 0.1721 0.1721
- 0.000000 104 -0.5058 -0.5058
- 0.005000 0 -0.0357 -0.0357
- 0.005000 1 0.0361 0.0361
- 0.005000 2 0.0121 0.0121
- 0.005000 3 -0.0497 -0.0497
- 0.005000 4 -0.0589 -0.0589
- 0.005000 5 -0.0187 -0.0187
- 0.005000 6 0.2092 0.2092
- 0.005000 7 0.0610 0.0610
- 0.005000 8 0.0181 0.0181
- 0.005000 9 -0.1238 -0.1238
- 0.005000 10 -0.0383 -0.0383
- 0.005000 11 -0.0114 -0.0114
- 0.005000 12 -0.0925 -0.0925
- 0.005000 13 -0.0866 -0.0866
- 0.005000 14 0.0795 0.0795
- 0.005000 15 0.0436 0.0436
- 0.005000 16 -0.0012 -0.0012
- 0.005000 17 -0.0413 -0.0413
- 0.005000 18 0.0315 0.0315
- 0.005000 19 0.1598 0.1598
- 0.005000 20 -0.0150 -0.0150
- 0.005000 21 0.0174 0.0174
- 0.005000 22 -0.0721 -0.0721
- 0.005000 23 -0.0232 -0.0232
- 0.005000 24 0.0415 0.0415
- 0.005000 25 -0.1253 -0.1253
- 0.005000 26 -0.0411 -0.0411
- 0.005000 27 0.0128 0.0128
- 0.005000 28 0.0978 0.0978
- 0.005000 29 -0.0114 -0.0114
- 0.005000 30 0.0953 0.0953
- 0.005000 31 -0.1353 -0.1353
- 0.005000 32 -0.0930 -0.0930
- 0.005000 33 -0.1495 -0.1495
- 0.005000 34 0.1628 0.1628
- 0.005000 35 0.1455 0.1455
- 0.005000 36 -0.1637 -0.1637
- 0.005000 37 0.1539 0.1539
- 0.005000 38 0.2042 0.2042
- 0.005000 39 -0.0092 -0.0092
- 0.005000 40 0.0225 0.0225
- 0.005000 41 -0.1675 -0.1675
- 0.005000 42 -0.0029 -0.0029
- 0.005000 43 0.0232 0.0232
- 0.005000 44 -0.2600 -0.2600
- 0.005000 45 0.1758 0.1758
- 0.005000 46 -0.1997 -0.1997
- 0.005000 47 0.2233 0.2233
- 0.005000 48 0.0603 0.0603
- 0.005000 49 -0.1435 -0.1435
- 0.005000 50 0.0408 0.0408
- 0.005000 51 -0.1671 -0.1671
- 0.005000 52 0.3054 0.3054
- 0.005000 53 -0.1170 -0.1170
- 0.005000 54 -0.0508 -0.0508
- 0.005000 55 0.0091 0.0091
- 0.005000 56 -0.0390 -0.0390
- 0.005000 57 0.1576 0.1576
- 0.005000 58 -0.1711 -0.1711
- 0.005000 59 0.1151 0.1151
- 0.005000 60 -0.1012 -0.1012
- 0.005000 61 -0.0710 -0.0710
- 0.005000 62 0.2224 0.2224
- 0.005000 63 0.0955 0.0955
- 0.005000 64 0.0843 0.0843
- 0.005000 65 -0.2424 -0.2424
- 0.005000 66 -0.1189 -0.1189
- 0.005000 67 0.0594 0.0594
- 0.005000 68 -0.0067 -0.0067
- 0.005000 69 0.1245 0.1245
- 0.005000 70 -0.0727 -0.0727
- 0.005000 71 0.0267 0.0267
- 0.005000 72 -1.2302 -1.2302
- 0.005000 73 0.0179 0.0179
- 0.005000 74 0.1828 0.1828
- 0.005000 75 1.6774 1.6774
- 0.005000 76 -0.0317 -0.0317
- 0.005000 77 -0.2673 -0.2673
- 0.005000 78 -0.7339 -0.7339
- 0.005000 79 -0.0097 -0.0097
- 0.005000 80 0.0588 0.0588
- 0.005000 81 0.2867 0.2867
- 0.005000 82 0.0235 0.0235
- 0.005000 83 0.0257 0.0257
- 0.005000 84 -0.2659 -0.2659
- 0.005000 85 -0.2550 -0.2550
- 0.005000 86 0.1537 0.1537
- 0.005000 87 0.4281 0.4281
- 0.005000 88 0.3637 0.3637
- 0.005000 89 -0.2142 -0.2142
- 0.005000 90 -0.3759 -0.3759
- 0.005000 91 -0.1141 -0.1141
- 0.005000 92 0.0422 0.0422
- 0.005000 93 0.2137 0.2137
- 0.005000 94 0.0055 0.0055
- 0.005000 95 0.0182 0.0182
- 0.005000 96 0.7206 0.7206
- 0.005000 97 0.0406 0.0406
- 0.005000 98 -0.4108 -0.4108
- 0.005000 99 0.0406 0.0406
- 0.005000 100 -0.1644 -0.1644
- 0.005000 101 0.1748 0.1748
- 0.005000 102 -0.4108 -0.4108
- 0.005000 103 0.1748 0.1748
- 0.005000 104 -0.5562 -0.5562
- 0.010000 0 -0.0878 -0.0878
- 0.010000 1 0.0941 0.0941
- 0.010000 2 0.0293 0.0293
- 0.010000 3 -0.1396 -0.1396
- 0.010000 4 -0.2010 -0.2010
- 0.010000 5 -0.0619 -0.0619
- 0.010000 6 0.5550 0.5550
- 0.010000 7 0.2748 0.2748
- 0.010000 8 0.0840 0.0840
- 0.010000 9 -0.3276 -0.3276
- 0.010000 10 -0.1680 -0.1680
- 0.010000 11 -0.0513 -0.0513
- 0.010000 12 -0.0737 -0.0737
- 0.010000 13 -0.0790 -0.0790
- 0.010000 14 0.0692 0.0692
- 0.010000 15 0.0283 0.0283
- 0.010000 16 0.0040 0.0040
- 0.010000 17 -0.0286 -0.0286
- 0.010000 18 0.0321 0.0321
- 0.010000 19 0.1328 0.1328
- 0.010000 20 -0.0225 -0.0225
- 0.010000 21 0.0134 0.0134
- 0.010000 22 -0.0577 -0.0577
- 0.010000 23 -0.0182 -0.0182
- 0.010000 24 0.0392 0.0392
- 0.010000 25 -0.1362 -0.1362
- 0.010000 26 -0.0422 -0.0422
- 0.010000 27 0.0200 0.0200
- 0.010000 28 0.0971 0.0971
- 0.010000 29 -0.0148 -0.0148
- 0.010000 30 0.0947 0.0947
- 0.010000 31 -0.1522 -0.1522
- 0.010000 32 -0.0947 -0.0947
- 0.010000 33 -0.1540 -0.1540
- 0.010000 34 0.1914 0.1914
- 0.010000 35 0.1516 0.1516
- 0.010000 36 -0.1499 -0.1499
- 0.010000 37 0.1475 0.1475
- 0.010000 38 0.1960 0.1960
- 0.010000 39 -0.0286 -0.0286
- 0.010000 40 0.0465 0.0465
- 0.010000 41 -0.1645 -0.1645
- 0.010000 42 0.0153 0.0153
- 0.010000 43 0.0061 0.0061
- 0.010000 44 -0.2523 -0.2523
- 0.010000 45 0.1633 0.1633
- 0.010000 46 -0.2001 -0.2001
- 0.010000 47 0.2208 0.2208
- 0.010000 48 0.0664 0.0664
- 0.010000 49 -0.1581 -0.1581
- 0.010000 50 0.0474 0.0474
- 0.010000 51 -0.1797 -0.1797
- 0.010000 52 0.3399 0.3399
- 0.010000 53 -0.1327 -0.1327
- 0.010000 54 -0.0480 -0.0480
- 0.010000 55 0.0176 0.0176
- 0.010000 56 -0.0391 -0.0391
- 0.010000 57 0.1612 0.1612
- 0.010000 58 -0.1994 -0.1994
- 0.010000 59 0.1245 0.1245
- 0.010000 60 -0.0725 -0.0725
- 0.010000 61 -0.0708 -0.0708
- 0.010000 62 0.2184 0.2184
- 0.010000 63 0.0633 0.0633
- 0.010000 64 0.0837 0.0837
- 0.010000 65 -0.2366 -0.2366
- 0.010000 66 -0.1075 -0.1075
- 0.010000 67 0.0513 0.0513
- 0.010000 68 -0.0042 -0.0042
- 0.010000 69 0.1167 0.1167
- 0.010000 70 -0.0642 -0.0642
- 0.010000 71 0.0223 0.0223
- 0.010000 72 0.2882 0.2882
- 0.010000 73 0.0151 0.0151
- 0.010000 74 -0.0540 -0.0540
- 0.010000 75 -0.1914 -0.1914
- 0.010000 76 -0.0155 -0.0155
- 0.010000 77 0.0481 0.0481
- 0.010000 78 0.0790 0.0790
- 0.010000 79 -0.0143 -0.0143
- 0.010000 80 0.0262 0.0262
- 0.010000 81 -0.1757 -0.1757
- 0.010000 82 0.0147 0.0147
- 0.010000 83 -0.0202 -0.0202
- 0.010000 84 -0.2260 -0.2260
- 0.010000 85 -0.2493 -0.2493
- 0.010000 86 0.1549 0.1549
- 0.010000 87 0.3591 0.3591
- 0.010000 88 0.3498 0.3498
- 0.010000 89 -0.2123 -0.2123
- 0.010000 90 -0.3374 -0.3374
- 0.010000 91 -0.1078 -0.1078
- 0.010000 92 0.0378 0.0378
- 0.010000 93 0.2044 0.2044
- 0.010000 94 0.0073 0.0073
- 0.010000 95 0.0195 0.0195
- 0.010000 96 0.3275 0.3275
- 0.010000 97 0.1241 0.1241
- 0.010000 98 -0.4037 -0.4037
- 0.010000 99 0.1241 0.1241
- 0.010000 100 0.0089 0.0089
- 0.010000 101 0.1813 0.1813
- 0.010000 102 -0.4037 -0.4037
- 0.010000 103 0.1813 0.1813
- 0.010000 104 -0.3364 -0.3364
- 0.015000 0 -0.1535 -0.1535
- 0.015000 1 0.1803 0.1803
- 0.015000 2 0.0500 0.0500
- 0.015000 3 -0.2381 -0.2381
- 0.015000 4 -0.5263 -0.5263
- 0.015000 5 -0.1521 -0.1521
- 0.015000 6 0.9632 0.9632
- 0.015000 7 0.8844 0.8844
- 0.015000 8 0.2606 0.2606
- 0.015000 9 -0.5716 -0.5716
- 0.015000 10 -0.5385 -0.5385
- 0.015000 11 -0.1585 -0.1585
- 0.015000 12 -0.0624 -0.0624
- 0.015000 13 -0.0749 -0.0749
- 0.015000 14 0.0649 0.0649
- 0.015000 15 0.0176 0.0176
- 0.015000 16 0.0062 0.0062
- 0.015000 17 -0.0192 -0.0192
- 0.015000 18 0.0342 0.0342
- 0.015000 19 0.1168 0.1168
- 0.015000 20 -0.0307 -0.0307
- 0.015000 21 0.0107 0.0107
- 0.015000 22 -0.0481 -0.0481
- 0.015000 23 -0.0150 -0.0150
- 0.015000 24 0.0328 0.0328
- 0.015000 25 -0.1462 -0.1462
- 0.015000 26 -0.0414 -0.0414
- 0.015000 27 0.0294 0.0294
- 0.015000 28 0.0888 0.0888
- 0.015000 29 -0.0208 -0.0208
- 0.015000 30 0.0855 0.0855
- 0.015000 31 -0.1693 -0.1693
- 0.015000 32 -0.0921 -0.0921
- 0.015000 33 -0.1477 -0.1477
- 0.015000 34 0.2267 0.2267
- 0.015000 35 0.1543 0.1543
- 0.015000 36 -0.1412 -0.1412
- 0.015000 37 0.1563 0.1563
- 0.015000 38 0.1875 0.1875
- 0.015000 39 -0.0493 -0.0493
- 0.015000 40 0.0707 0.0707
- 0.015000 41 -0.1724 -0.1724
- 0.015000 42 0.0328 0.0328
- 0.015000 43 -0.0229 -0.0229
- 0.015000 44 -0.2415 -0.2415
- 0.015000 45 0.1577 0.1577
- 0.015000 46 -0.2041 -0.2041
- 0.015000 47 0.2264 0.2264
- 0.015000 48 0.0653 0.0653
- 0.015000 49 -0.1604 -0.1604
- 0.015000 50 0.0531 0.0531
- 0.015000 51 -0.1803 -0.1803
- 0.015000 52 0.3532 0.3532
- 0.015000 53 -0.1526 -0.1526
- 0.015000 54 -0.0428 -0.0428
- 0.015000 55 0.0255 0.0255
- 0.015000 56 -0.0402 -0.0402
- 0.015000 57 0.1578 0.1578
- 0.015000 58 -0.2183 -0.2183
- 0.015000 59 0.1398 0.1398
- 0.015000 60 -0.0302 -0.0302
- 0.015000 61 -0.0650 -0.0650
- 0.015000 62 0.1977 0.1977
- 0.015000 63 0.0179 0.0179
- 0.015000 64 0.0801 0.0801
- 0.015000 65 -0.2225 -0.2225
- 0.015000 66 -0.0904 -0.0904
- 0.015000 67 0.0344 0.0344
- 0.015000 68 0.0104 0.0104
- 0.015000 69 0.1028 0.1028
- 0.015000 70 -0.0494 -0.0494
- 0.015000 71 0.0144 0.0144
- 0.015000 72 0.2761 0.2761
- 0.015000 73 0.0238 0.0238
- 0.015000 74 -0.0571 -0.0571
- 0.015000 75 -0.1910 -0.1910
- 0.015000 76 -0.0225 -0.0225
- 0.015000 77 0.0519 0.0519
- 0.015000 78 0.0731 0.0731
- 0.015000 79 -0.0147 -0.0147
- 0.015000 80 0.0284 0.0284
- 0.015000 81 -0.1582 -0.1582
- 0.015000 82 0.0134 0.0134
- 0.015000 83 -0.0232 -0.0232
- 0.015000 84 -0.1886 -0.1886
- 0.015000 85 -0.2341 -0.2341
- 0.015000 86 0.1574 0.1574
- 0.015000 87 0.2953 0.2953
- 0.015000 88 0.3230 0.3230
- 0.015000 89 -0.2125 -0.2125
- 0.015000 90 -0.2987 -0.2987
- 0.015000 91 -0.0966 -0.0966
- 0.015000 92 0.0352 0.0352
- 0.015000 93 0.1920 0.1920
- 0.015000 94 0.0076 0.0076
- 0.015000 95 0.0199 0.0199
- 0.015000 96 0.0805 0.0805
- 0.015000 97 0.1377 0.1377
- 0.015000 98 -0.4185 -0.4185
- 0.015000 99 0.1377 0.1377
- 0.015000 100 0.2115 0.2115
- 0.015000 101 0.1624 0.1624
- 0.015000 102 -0.4185 -0.4185
- 0.015000 103 0.1624 0.1624
- 0.015000 104 -0.2920 -0.2920
- 0.020000 0 -0.2027 -0.2027
- 0.020000 1 0.2564 0.2564
- 0.020000 2 0.0632 0.0632
- 0.020000 3 -0.1626 -0.1626
- 0.020000 4 -0.9163 -0.9163
- 0.020000 5 -0.2431 -0.2431
- 0.020000 6 0.8925 0.8925
- 0.020000 7 1.6918 1.6918
- 0.020000 8 0.4605 0.4605
- 0.020000 9 -0.5272 -0.5272
- 0.020000 10 -1.0320 -1.0320
- 0.020000 11 -0.2806 -0.2806
- 0.020000 12 -0.0683 -0.0683
- 0.020000 13 -0.0827 -0.0827
- 0.020000 14 0.0756 0.0756
- 0.020000 15 0.0153 0.0153
- 0.020000 16 0.0064 0.0064
- 0.020000 17 -0.0177 -0.0177
- 0.020000 18 0.0412 0.0412
- 0.020000 19 0.1278 0.1278
- 0.020000 20 -0.0410 -0.0410
- 0.020000 21 0.0118 0.0118
- 0.020000 22 -0.0516 -0.0516
- 0.020000 23 -0.0169 -0.0169
- 0.020000 24 0.0325 0.0325
- 0.020000 25 -0.1489 -0.1489
- 0.020000 26 -0.0383 -0.0383
- 0.020000 27 0.0296 0.0296
- 0.020000 28 0.0777 0.0777
- 0.020000 29 -0.0248 -0.0248
- 0.020000 30 0.0807 0.0807
- 0.020000 31 -0.1714 -0.1714
- 0.020000 32 -0.0858 -0.0858
- 0.020000 33 -0.1429 -0.1429
- 0.020000 34 0.2426 0.2426
- 0.020000 35 0.1489 0.1489
- 0.020000 36 -0.1241 -0.1241
- 0.020000 37 0.1558 0.1558
- 0.020000 38 0.1741 0.1741
- 0.020000 39 -0.0543 -0.0543
- 0.020000 40 0.0705 0.0705
- 0.020000 41 -0.1847 -0.1847
- 0.020000 42 0.0351 0.0351
- 0.020000 43 -0.0425 -0.0425
- 0.020000 44 -0.2183 -0.2183
- 0.020000 45 0.1433 0.1433
- 0.020000 46 -0.1839 -0.1839
- 0.020000 47 0.2288 0.2288
- 0.020000 48 0.0562 0.0562
- 0.020000 49 -0.1493 -0.1493
- 0.020000 50 0.0525 0.0525
- 0.020000 51 -0.1626 -0.1626
- 0.020000 52 0.3303 0.3303
- 0.020000 53 -0.1629 -0.1629
- 0.020000 54 -0.0384 -0.0384
- 0.020000 55 0.0320 0.0320
- 0.020000 56 -0.0434 -0.0434
- 0.020000 57 0.1448 0.1448
- 0.020000 58 -0.2130 -0.2130
- 0.020000 59 0.1538 0.1538
- 0.020000 60 -0.0027 -0.0027
- 0.020000 61 -0.0548 -0.0548
- 0.020000 62 0.1651 0.1651
- 0.020000 63 -0.0126 -0.0126
- 0.020000 64 0.0708 0.0708
- 0.020000 65 -0.1933 -0.1933
- 0.020000 66 -0.0731 -0.0731
- 0.020000 67 0.0237 0.0237
- 0.020000 68 0.0207 0.0207
- 0.020000 69 0.0884 0.0884
- 0.020000 70 -0.0397 -0.0397
- 0.020000 71 0.0076 0.0076
- 0.020000 72 0.2868 0.2868
- 0.020000 73 0.0276 0.0276
- 0.020000 74 -0.0545 -0.0545
- 0.020000 75 -0.2066 -0.2066
- 0.020000 76 -0.0254 -0.0254
- 0.020000 77 0.0507 0.0507
- 0.020000 78 0.0782 0.0782
- 0.020000 79 -0.0140 -0.0140
- 0.020000 80 0.0296 0.0296
- 0.020000 81 -0.1585 -0.1585
- 0.020000 82 0.0118 0.0118
- 0.020000 83 -0.0258 -0.0258
- 0.020000 84 -0.1759 -0.1759
- 0.020000 85 -0.2245 -0.2245
- 0.020000 86 0.1480 0.1480
- 0.020000 87 0.2912 0.2912
- 0.020000 88 0.3104 0.3104
- 0.020000 89 -0.1981 -0.1981
- 0.020000 90 -0.3037 -0.3037
- 0.020000 91 -0.0940 -0.0940
- 0.020000 92 0.0306 0.0306
- 0.020000 93 0.1884 0.1884
- 0.020000 94 0.0081 0.0081
- 0.020000 95 0.0195 0.0195
- 0.020000 96 -0.0480 -0.0480
- 0.020000 97 0.0463 0.0463
- 0.020000 98 -0.4386 -0.4386
- 0.020000 99 0.0463 0.0463
- 0.020000 100 0.2798 0.2798
- 0.020000 101 0.1279 0.1279
- 0.020000 102 -0.4386 -0.4386
- 0.020000 103 0.1279 0.1279
- 0.020000 104 -0.2318 -0.2318
+#! FIELDS time parameter c1
+ 0.000000 0 -0.0023
+ 0.000000 1 0.0023
+ 0.000000 2 0.0008
+ 0.000000 3 -0.0027
+ 0.000000 4 -0.0030
+ 0.000000 5 -0.0010
+ 0.000000 6 0.0126
+ 0.000000 7 0.0021
+ 0.000000 8 0.0006
+ 0.000000 9 -0.0076
+ 0.000000 10 -0.0014
+ 0.000000 11 -0.0004
+ 0.000000 12 -0.1068
+ 0.000000 13 -0.0978
+ 0.000000 14 0.0943
+ 0.000000 15 0.0592
+ 0.000000 16 -0.0011
+ 0.000000 17 -0.0556
+ 0.000000 18 0.0234
+ 0.000000 19 0.1834
+ 0.000000 20 -0.0108
+ 0.000000 21 0.0243
+ 0.000000 22 -0.0845
+ 0.000000 23 -0.0279
+ 0.000000 24 0.0377
+ 0.000000 25 -0.1134
+ 0.000000 26 -0.0379
+ 0.000000 27 0.0123
+ 0.000000 28 0.0956
+ 0.000000 29 -0.0118
+ 0.000000 30 0.0879
+ 0.000000 31 -0.1220
+ 0.000000 32 -0.0879
+ 0.000000 33 -0.1379
+ 0.000000 34 0.1399
+ 0.000000 35 0.1376
+ 0.000000 36 -0.1868
+ 0.000000 37 0.1816
+ 0.000000 38 0.2145
+ 0.000000 39 -0.0037
+ 0.000000 40 0.0112
+ 0.000000 41 -0.1880
+ 0.000000 42 -0.0093
+ 0.000000 43 0.0195
+ 0.000000 44 -0.2515
+ 0.000000 45 0.1999
+ 0.000000 46 -0.2123
+ 0.000000 47 0.2250
+ 0.000000 48 0.0481
+ 0.000000 49 -0.1259
+ 0.000000 50 0.0384
+ 0.000000 51 -0.1440
+ 0.000000 52 0.2683
+ 0.000000 53 -0.1172
+ 0.000000 54 -0.0504
+ 0.000000 55 0.0087
+ 0.000000 56 -0.0429
+ 0.000000 57 0.1463
+ 0.000000 58 -0.1512
+ 0.000000 59 0.1218
+ 0.000000 60 -0.0873
+ 0.000000 61 -0.0686
+ 0.000000 62 0.2131
+ 0.000000 63 0.0814
+ 0.000000 64 0.0863
+ 0.000000 65 -0.2416
+ 0.000000 66 -0.1096
+ 0.000000 67 0.0507
+ 0.000000 68 0.0043
+ 0.000000 69 0.1156
+ 0.000000 70 -0.0684
+ 0.000000 71 0.0242
+ 0.000000 72 -0.9759
+ 0.000000 73 -0.0191
+ 0.000000 74 0.0303
+ 0.000000 75 1.3232
+ 0.000000 76 0.0240
+ 0.000000 77 -0.0463
+ 0.000000 78 -0.6202
+ 0.000000 79 -0.0184
+ 0.000000 80 0.0024
+ 0.000000 81 0.2729
+ 0.000000 82 0.0135
+ 0.000000 83 0.0136
+ 0.000000 84 -0.2793
+ 0.000000 85 -0.2587
+ 0.000000 86 0.1898
+ 0.000000 87 0.4427
+ 0.000000 88 0.3809
+ 0.000000 89 -0.2772
+ 0.000000 90 -0.3711
+ 0.000000 91 -0.1266
+ 0.000000 92 0.0760
+ 0.000000 93 0.2077
+ 0.000000 94 0.0044
+ 0.000000 95 0.0114
+ 0.000000 96 0.6933
+ 0.000000 97 -0.0140
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+ 0.000000 99 -0.0140
+ 0.000000 100 -0.1875
+ 0.000000 101 0.1721
+ 0.000000 102 -0.4462
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+ 0.000000 104 -0.5058
+ 0.005000 0 -0.0357
+ 0.005000 1 0.0361
+ 0.005000 2 0.0121
+ 0.005000 3 -0.0497
+ 0.005000 4 -0.0589
+ 0.005000 5 -0.0187
+ 0.005000 6 0.2092
+ 0.005000 7 0.0610
+ 0.005000 8 0.0181
+ 0.005000 9 -0.1238
+ 0.005000 10 -0.0383
+ 0.005000 11 -0.0114
+ 0.005000 12 -0.0925
+ 0.005000 13 -0.0866
+ 0.005000 14 0.0795
+ 0.005000 15 0.0436
+ 0.005000 16 -0.0012
+ 0.005000 17 -0.0413
+ 0.005000 18 0.0315
+ 0.005000 19 0.1598
+ 0.005000 20 -0.0150
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+ 0.005000 22 -0.0721
+ 0.005000 23 -0.0232
+ 0.005000 24 0.0415
+ 0.005000 25 -0.1253
+ 0.005000 26 -0.0411
+ 0.005000 27 0.0128
+ 0.005000 28 0.0978
+ 0.005000 29 -0.0114
+ 0.005000 30 0.0953
+ 0.005000 31 -0.1353
+ 0.005000 32 -0.0930
+ 0.005000 33 -0.1495
+ 0.005000 34 0.1628
+ 0.005000 35 0.1455
+ 0.005000 36 -0.1637
+ 0.005000 37 0.1539
+ 0.005000 38 0.2042
+ 0.005000 39 -0.0092
+ 0.005000 40 0.0225
+ 0.005000 41 -0.1675
+ 0.005000 42 -0.0029
+ 0.005000 43 0.0232
+ 0.005000 44 -0.2600
+ 0.005000 45 0.1758
+ 0.005000 46 -0.1997
+ 0.005000 47 0.2233
+ 0.005000 48 0.0603
+ 0.005000 49 -0.1435
+ 0.005000 50 0.0408
+ 0.005000 51 -0.1671
+ 0.005000 52 0.3054
+ 0.005000 53 -0.1170
+ 0.005000 54 -0.0508
+ 0.005000 55 0.0091
+ 0.005000 56 -0.0390
+ 0.005000 57 0.1576
+ 0.005000 58 -0.1711
+ 0.005000 59 0.1151
+ 0.005000 60 -0.1012
+ 0.005000 61 -0.0710
+ 0.005000 62 0.2224
+ 0.005000 63 0.0955
+ 0.005000 64 0.0843
+ 0.005000 65 -0.2424
+ 0.005000 66 -0.1189
+ 0.005000 67 0.0594
+ 0.005000 68 -0.0067
+ 0.005000 69 0.1245
+ 0.005000 70 -0.0727
+ 0.005000 71 0.0267
+ 0.005000 72 -1.2302
+ 0.005000 73 0.0179
+ 0.005000 74 0.1828
+ 0.005000 75 1.6774
+ 0.005000 76 -0.0317
+ 0.005000 77 -0.2673
+ 0.005000 78 -0.7339
+ 0.005000 79 -0.0097
+ 0.005000 80 0.0588
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+ 0.005000 82 0.0235
+ 0.005000 83 0.0257
+ 0.005000 84 -0.2659
+ 0.005000 85 -0.2550
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+ 0.005000 87 0.4281
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+ 0.005000 89 -0.2142
+ 0.005000 90 -0.3759
+ 0.005000 91 -0.1141
+ 0.005000 92 0.0422
+ 0.005000 93 0.2137
+ 0.005000 94 0.0055
+ 0.005000 95 0.0182
+ 0.005000 96 0.7206
+ 0.005000 97 0.0406
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+ 0.005000 100 -0.1644
+ 0.005000 101 0.1748
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+ 0.005000 103 0.1748
+ 0.005000 104 -0.5562
+ 0.010000 0 -0.0878
+ 0.010000 1 0.0941
+ 0.010000 2 0.0293
+ 0.010000 3 -0.1396
+ 0.010000 4 -0.2010
+ 0.010000 5 -0.0619
+ 0.010000 6 0.5550
+ 0.010000 7 0.2748
+ 0.010000 8 0.0840
+ 0.010000 9 -0.3276
+ 0.010000 10 -0.1680
+ 0.010000 11 -0.0513
+ 0.010000 12 -0.0737
+ 0.010000 13 -0.0790
+ 0.010000 14 0.0692
+ 0.010000 15 0.0283
+ 0.010000 16 0.0040
+ 0.010000 17 -0.0286
+ 0.010000 18 0.0321
+ 0.010000 19 0.1328
+ 0.010000 20 -0.0225
+ 0.010000 21 0.0134
+ 0.010000 22 -0.0577
+ 0.010000 23 -0.0182
+ 0.010000 24 0.0392
+ 0.010000 25 -0.1362
+ 0.010000 26 -0.0422
+ 0.010000 27 0.0200
+ 0.010000 28 0.0971
+ 0.010000 29 -0.0148
+ 0.010000 30 0.0947
+ 0.010000 31 -0.1522
+ 0.010000 32 -0.0947
+ 0.010000 33 -0.1540
+ 0.010000 34 0.1914
+ 0.010000 35 0.1516
+ 0.010000 36 -0.1499
+ 0.010000 37 0.1475
+ 0.010000 38 0.1960
+ 0.010000 39 -0.0286
+ 0.010000 40 0.0465
+ 0.010000 41 -0.1645
+ 0.010000 42 0.0153
+ 0.010000 43 0.0061
+ 0.010000 44 -0.2523
+ 0.010000 45 0.1633
+ 0.010000 46 -0.2001
+ 0.010000 47 0.2208
+ 0.010000 48 0.0664
+ 0.010000 49 -0.1581
+ 0.010000 50 0.0474
+ 0.010000 51 -0.1797
+ 0.010000 52 0.3399
+ 0.010000 53 -0.1327
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+ 0.010000 56 -0.0391
+ 0.010000 57 0.1612
+ 0.010000 58 -0.1994
+ 0.010000 59 0.1245
+ 0.010000 60 -0.0725
+ 0.010000 61 -0.0708
+ 0.010000 62 0.2184
+ 0.010000 63 0.0633
+ 0.010000 64 0.0837
+ 0.010000 65 -0.2366
+ 0.010000 66 -0.1075
+ 0.010000 67 0.0513
+ 0.010000 68 -0.0042
+ 0.010000 69 0.1167
+ 0.010000 70 -0.0642
+ 0.010000 71 0.0223
+ 0.010000 72 0.2882
+ 0.010000 73 0.0151
+ 0.010000 74 -0.0540
+ 0.010000 75 -0.1914
+ 0.010000 76 -0.0155
+ 0.010000 77 0.0481
+ 0.010000 78 0.0790
+ 0.010000 79 -0.0143
+ 0.010000 80 0.0262
+ 0.010000 81 -0.1757
+ 0.010000 82 0.0147
+ 0.010000 83 -0.0202
+ 0.010000 84 -0.2260
+ 0.010000 85 -0.2493
+ 0.010000 86 0.1549
+ 0.010000 87 0.3591
+ 0.010000 88 0.3498
+ 0.010000 89 -0.2123
+ 0.010000 90 -0.3374
+ 0.010000 91 -0.1078
+ 0.010000 92 0.0378
+ 0.010000 93 0.2044
+ 0.010000 94 0.0073
+ 0.010000 95 0.0195
+ 0.010000 96 0.3275
+ 0.010000 97 0.1241
+ 0.010000 98 -0.4037
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+ 0.010000 100 0.0089
+ 0.010000 101 0.1813
+ 0.010000 102 -0.4037
+ 0.010000 103 0.1813
+ 0.010000 104 -0.3364
+ 0.015000 0 -0.1535
+ 0.015000 1 0.1803
+ 0.015000 2 0.0500
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+ 0.015000 4 -0.5263
+ 0.015000 5 -0.1521
+ 0.015000 6 0.9632
+ 0.015000 7 0.8844
+ 0.015000 8 0.2606
+ 0.015000 9 -0.5716
+ 0.015000 10 -0.5385
+ 0.015000 11 -0.1585
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+ 0.015000 13 -0.0749
+ 0.015000 14 0.0649
+ 0.015000 15 0.0176
+ 0.015000 16 0.0062
+ 0.015000 17 -0.0192
+ 0.015000 18 0.0342
+ 0.015000 19 0.1168
+ 0.015000 20 -0.0307
+ 0.015000 21 0.0107
+ 0.015000 22 -0.0481
+ 0.015000 23 -0.0150
+ 0.015000 24 0.0328
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+ 0.015000 26 -0.0414
+ 0.015000 27 0.0294
+ 0.015000 28 0.0888
+ 0.015000 29 -0.0208
+ 0.015000 30 0.0855
+ 0.015000 31 -0.1693
+ 0.015000 32 -0.0921
+ 0.015000 33 -0.1477
+ 0.015000 34 0.2267
+ 0.015000 35 0.1543
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+ 0.015000 37 0.1563
+ 0.015000 38 0.1875
+ 0.015000 39 -0.0493
+ 0.015000 40 0.0707
+ 0.015000 41 -0.1724
+ 0.015000 42 0.0328
+ 0.015000 43 -0.0229
+ 0.015000 44 -0.2415
+ 0.015000 45 0.1577
+ 0.015000 46 -0.2041
+ 0.015000 47 0.2264
+ 0.015000 48 0.0653
+ 0.015000 49 -0.1604
+ 0.015000 50 0.0531
+ 0.015000 51 -0.1803
+ 0.015000 52 0.3532
+ 0.015000 53 -0.1526
+ 0.015000 54 -0.0428
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+ 0.015000 56 -0.0402
+ 0.015000 57 0.1578
+ 0.015000 58 -0.2183
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+ 0.015000 60 -0.0302
+ 0.015000 61 -0.0650
+ 0.015000 62 0.1977
+ 0.015000 63 0.0179
+ 0.015000 64 0.0801
+ 0.015000 65 -0.2225
+ 0.015000 66 -0.0904
+ 0.015000 67 0.0344
+ 0.015000 68 0.0104
+ 0.015000 69 0.1028
+ 0.015000 70 -0.0494
+ 0.015000 71 0.0144
+ 0.015000 72 0.2761
+ 0.015000 73 0.0238
+ 0.015000 74 -0.0571
+ 0.015000 75 -0.1910
+ 0.015000 76 -0.0225
+ 0.015000 77 0.0519
+ 0.015000 78 0.0731
+ 0.015000 79 -0.0147
+ 0.015000 80 0.0284
+ 0.015000 81 -0.1582
+ 0.015000 82 0.0134
+ 0.015000 83 -0.0232
+ 0.015000 84 -0.1886
+ 0.015000 85 -0.2341
+ 0.015000 86 0.1574
+ 0.015000 87 0.2953
+ 0.015000 88 0.3230
+ 0.015000 89 -0.2125
+ 0.015000 90 -0.2987
+ 0.015000 91 -0.0966
+ 0.015000 92 0.0352
+ 0.015000 93 0.1920
+ 0.015000 94 0.0076
+ 0.015000 95 0.0199
+ 0.015000 96 0.0805
+ 0.015000 97 0.1377
+ 0.015000 98 -0.4185
+ 0.015000 99 0.1377
+ 0.015000 100 0.2115
+ 0.015000 101 0.1624
+ 0.015000 102 -0.4185
+ 0.015000 103 0.1624
+ 0.015000 104 -0.2920
+ 0.020000 0 -0.2027
+ 0.020000 1 0.2564
+ 0.020000 2 0.0632
+ 0.020000 3 -0.1626
+ 0.020000 4 -0.9163
+ 0.020000 5 -0.2431
+ 0.020000 6 0.8925
+ 0.020000 7 1.6918
+ 0.020000 8 0.4605
+ 0.020000 9 -0.5272
+ 0.020000 10 -1.0320
+ 0.020000 11 -0.2806
+ 0.020000 12 -0.0683
+ 0.020000 13 -0.0827
+ 0.020000 14 0.0756
+ 0.020000 15 0.0153
+ 0.020000 16 0.0064
+ 0.020000 17 -0.0177
+ 0.020000 18 0.0412
+ 0.020000 19 0.1278
+ 0.020000 20 -0.0410
+ 0.020000 21 0.0118
+ 0.020000 22 -0.0516
+ 0.020000 23 -0.0169
+ 0.020000 24 0.0325
+ 0.020000 25 -0.1489
+ 0.020000 26 -0.0383
+ 0.020000 27 0.0296
+ 0.020000 28 0.0777
+ 0.020000 29 -0.0248
+ 0.020000 30 0.0807
+ 0.020000 31 -0.1714
+ 0.020000 32 -0.0858
+ 0.020000 33 -0.1429
+ 0.020000 34 0.2426
+ 0.020000 35 0.1489
+ 0.020000 36 -0.1241
+ 0.020000 37 0.1558
+ 0.020000 38 0.1741
+ 0.020000 39 -0.0543
+ 0.020000 40 0.0705
+ 0.020000 41 -0.1847
+ 0.020000 42 0.0351
+ 0.020000 43 -0.0425
+ 0.020000 44 -0.2183
+ 0.020000 45 0.1433
+ 0.020000 46 -0.1839
+ 0.020000 47 0.2288
+ 0.020000 48 0.0562
+ 0.020000 49 -0.1493
+ 0.020000 50 0.0525
+ 0.020000 51 -0.1626
+ 0.020000 52 0.3303
+ 0.020000 53 -0.1629
+ 0.020000 54 -0.0384
+ 0.020000 55 0.0320
+ 0.020000 56 -0.0434
+ 0.020000 57 0.1448
+ 0.020000 58 -0.2130
+ 0.020000 59 0.1538
+ 0.020000 60 -0.0027
+ 0.020000 61 -0.0548
+ 0.020000 62 0.1651
+ 0.020000 63 -0.0126
+ 0.020000 64 0.0708
+ 0.020000 65 -0.1933
+ 0.020000 66 -0.0731
+ 0.020000 67 0.0237
+ 0.020000 68 0.0207
+ 0.020000 69 0.0884
+ 0.020000 70 -0.0397
+ 0.020000 71 0.0076
+ 0.020000 72 0.2868
+ 0.020000 73 0.0276
+ 0.020000 74 -0.0545
+ 0.020000 75 -0.2066
+ 0.020000 76 -0.0254
+ 0.020000 77 0.0507
+ 0.020000 78 0.0782
+ 0.020000 79 -0.0140
+ 0.020000 80 0.0296
+ 0.020000 81 -0.1585
+ 0.020000 82 0.0118
+ 0.020000 83 -0.0258
+ 0.020000 84 -0.1759
+ 0.020000 85 -0.2245
+ 0.020000 86 0.1480
+ 0.020000 87 0.2912
+ 0.020000 88 0.3104
+ 0.020000 89 -0.1981
+ 0.020000 90 -0.3037
+ 0.020000 91 -0.0940
+ 0.020000 92 0.0306
+ 0.020000 93 0.1884
+ 0.020000 94 0.0081
+ 0.020000 95 0.0195
+ 0.020000 96 -0.0480
+ 0.020000 97 0.0463
+ 0.020000 98 -0.4386
+ 0.020000 99 0.0463
+ 0.020000 100 0.2798
+ 0.020000 101 0.1279
+ 0.020000 102 -0.4386
+ 0.020000 103 0.1279
+ 0.020000 104 -0.2318
diff --git a/regtest/multicolvar/rt25/plumed.dat b/regtest/multicolvar/rt25/plumed.dat
index a9fc93f014db3711a545e77e12569b9915a14888..ed370346031a361290ed3f767105e1650efd7fc3 100644
--- a/regtest/multicolvar/rt25/plumed.dat
+++ b/regtest/multicolvar/rt25/plumed.dat
@@ -10,20 +10,7 @@ ATOMS8=2,4,17,9
REFERENCE=1
LABEL=c1
...
-ALPHABETA ...
-REFERENCE=1
-NUMERICAL_DERIVATIVES
-LABEL=c1num
-ATOMS1=1,3,6,10
-ATOMS2=2,4,7,9
-ATOMS3=3,5,6,7
-ATOMS4=2,1,3,4
-ATOMS5=12,14,17,19
-ATOMS6=22,24,27,29
-ATOMS7=21,20,5,9
-ATOMS8=2,4,17,9
-...
-DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
+DUMPDERIVATIVES ARG=c1.* STRIDE=1 FILE=derivatives FMT=%8.4f
RESTRAINT ARG=c1 AT=-2 KAPPA=0 SLOPE=1
diff --git a/src/.gitignore b/src/.gitignore
index 50fcbc3710dc573993ec54146de647571d87868a..a87e8edcc06b8187c1d7cee0fce260942b667bb8 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -22,6 +22,7 @@
!/isdb
!/lapack
!/lepton
+!/logmfd
!/lib
!/main
!/maketools
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index c8baaa5d4ea0579ae695aef9ca6f52e082b657d4..baf3f3dc9f125d17f57f825b04c54d931b0d7254 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -213,6 +213,7 @@ public:
void prepareForAveraging();
void performOperations( const bool& from_update );
void finishAveraging();
+ bool threadSafe() const { return !in_apply; }
bool isPeriodic() { return false; }
unsigned getNumberOfDerivatives();
void turnOnDerivatives();
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 8fd6a61e3cbe68218f024e1d1ffb347e4558fdf1..18aed96add3f2b6980597db71672193674cbdf69 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -1964,8 +1964,8 @@ void MetaD::computeReweightingFactor()
for(unsigned i=rank; i<ntotgrid; i+=stride) {
t_index[0]=(i%rewf_grid_[0]);
unsigned kk=i;
- for(unsigned j=1; j<ncv-1; ++j) { kk=(kk-t_index[j-1])/rewf_grid_[i-1]; t_index[j]=(kk%rewf_grid_[i]); }
- if( ncv>=2 ) t_index[ncv-1]=((kk-t_index[ncv-1])/rewf_grid_[ncv-2]);
+ for(unsigned j=1; j<ncv-1; ++j) { kk=(kk-t_index[j-1])/rewf_grid_[j-1]; t_index[j]=(kk%rewf_grid_[j]); }
+ if( ncv>=2 ) t_index[ncv-1]=((kk-t_index[ncv-2])/rewf_grid_[ncv-2]);
for(unsigned j=0; j<ncv; ++j) vals[j]=dmin[j] + t_index[j]*grid_spacing[j];
diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
index 6f238e22d65f1aa3ec81813f3aa5275bce0663cb..a6b31506d3bd8535247ff6bfc6abe288b840dfb3 100644
--- a/src/colvar/ContactMap.cpp
+++ b/src/colvar/ContactMap.cpp
@@ -267,8 +267,8 @@ void ContactMap::calculate() {
Tensor virial;
std::vector<Vector> deriv(getNumberOfAtoms());
- unsigned stride=comm.Get_size();
- unsigned rank=comm.Get_rank();
+ unsigned stride;
+ unsigned rank;
if(serial) {
// when using components the parallelisation do not work
stride=1;
diff --git a/src/colvar/CoordinationBase.cpp b/src/colvar/CoordinationBase.cpp
index cade44e026f0f82a2d32c989b08f7287d69b53a4..3852d83789c8e0b792ad26dc145695882c8f6389 100644
--- a/src/colvar/CoordinationBase.cpp
+++ b/src/colvar/CoordinationBase.cpp
@@ -140,8 +140,8 @@ void CoordinationBase::calculate()
nl->update(getPositions());
}
- unsigned stride=comm.Get_size();
- unsigned rank=comm.Get_rank();
+ unsigned stride;
+ unsigned rank;
if(serial) {
stride=1;
rank=0;
diff --git a/src/core/ActionSet.cpp b/src/core/ActionSet.cpp
index e9f21e23e3e6517df9981e504276a52108a733a5..9a99be5652d15e6041bd8c21436bd24878081477 100644
--- a/src/core/ActionSet.cpp
+++ b/src/core/ActionSet.cpp
@@ -40,24 +40,4 @@ void ActionSet::clearDelete() {
clear();
}
-
-std::string ActionSet::getLabelList() const {
- std::string outlist;
- for(const auto & p : (*this)) {
- outlist+=dynamic_cast<Action*>(p.get())->getLabel()+" ";
- };
- return outlist;
-}
-
-std::vector<std::string> ActionSet::getLabelVector() const {
- std::vector<std::string> outlist;
- for(const auto & p : (*this)) {
- outlist.push_back(dynamic_cast<Action*>(p.get())->getLabel());
- };
- return outlist;
-}
-
-
-
-
}
diff --git a/src/core/ActionSet.h b/src/core/ActionSet.h
index 18d3d0973fb50c6f57864037299c4a5d1e1ac9de..42b7583b8fb831770fadba267ee9b91aec896518 100644
--- a/src/core/ActionSet.h
+++ b/src/core/ActionSet.h
@@ -62,8 +62,12 @@ public:
template <class T>
T selectWithLabel(const std::string&s)const;
/// get the labels in the list of actions in form of a string (useful to debug)
+/// Only classes that can be dynamic casted to T are reported
+ template <class T>
std::string getLabelList() const;
/// get the labels in the form of a vector of strings
+/// Only classes that can be dynamic casted to T are reported
+ template <class T>
std::vector<std::string> getLabelVector() const;
};
@@ -99,6 +103,27 @@ std::vector<Action*> ActionSet::selectNot()const {
return ret;
}
+template <class T>
+std::string ActionSet::getLabelList() const {
+ std::string outlist;
+ for(const auto & p : (*this)) {
+ if(dynamic_cast<T>(p.get())) outlist+=p->getLabel()+" ";
+ };
+ return outlist;
+}
+
+
+template <class T>
+std::vector<std::string> ActionSet::getLabelVector() const {
+ std::vector<std::string> outlist;
+ for(const auto & p : (*this)) {
+ if(dynamic_cast<T>(p.get())) outlist.push_back(p->getLabel());
+ };
+ return outlist;
+}
+
+
+
}
#endif
diff --git a/src/core/ActionWithArguments.cpp b/src/core/ActionWithArguments.cpp
index fb2bd26179232a092111dd330e1218961b45e82a..acbc60fa05a0e1752bebabe3c251ef9e163fef3c 100644
--- a/src/core/ActionWithArguments.cpp
+++ b/src/core/ActionWithArguments.cpp
@@ -146,8 +146,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
// Take all the values from an action with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action) {
- std::string str=" (hint! the actions in this ActionSet are: ";
- str+=plumed.getActionSet().getLabelList()+")";
+ std::string str=" (hint! the actions with value in this ActionSet are: ";
+ str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
error("cannot find action named " + a + str);
}
if( action->getNumberOfComponents()==0 ) error("found " + a +".* indicating use all components calculated by action with label " + a + " but this action has no components");
@@ -166,8 +166,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
// Take values with a specific name
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
if(!action) {
- std::string str=" (hint! the actions in this ActionSet are: ";
- str+=plumed.getActionSet().getLabelList()+")";
+ std::string str=" (hint! the actions with value in this ActionSet are: ";
+ str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
error("cannot find action named " + a +str);
}
if( !(action->exists(c[i])) ) {
@@ -188,8 +188,8 @@ void ActionWithArguments::interpretArgumentList(const std::vector<std::string>&
} else {
ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(c[i]);
if(!action) {
- std::string str=" (hint! the actions in this ActionSet are: ";
- str+=plumed.getActionSet().getLabelList()+")";
+ std::string str=" (hint! the actions with value in this ActionSet are: ";
+ str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
error("cannot find action named " + c[i] + str );
}
if( !(action->exists(c[i])) ) {
diff --git a/src/function/Matheval.cpp b/src/function/Custom.cpp
similarity index 88%
rename from src/function/Matheval.cpp
rename to src/function/Custom.cpp
index e608d27073eb0acd9a03c5a82242d64132971773..6d3107fb86c7863714f50e5c60c583588c6eeb0e 100644
--- a/src/function/Matheval.cpp
+++ b/src/function/Custom.cpp
@@ -29,9 +29,9 @@ using namespace std;
namespace PLMD {
namespace function {
-//+PLUMEDOC FUNCTION MATHEVAL
+//+PLUMEDOC FUNCTION CUSTOM
/*
-Calculate a combination of variables using a matheval expression.
+Calculate a combination of variables using a custom expression.
This action computes an arbitrary function of one or more
collective variables. Arguments are chosen with the ARG keyword,
@@ -40,6 +40,9 @@ string should contain no space. Within FUNC, one can refer to the
arguments as x,y,z, and t (up to four variables provided as ARG).
This names can be customized using the VAR keyword (see examples below).
+This function is implemented using the Lepton library, that allows to evaluate
+algebraic expressions and to automatically differentiate them.
+
If you want a function that depends not only on collective variables
but also on time you can use the \subpage TIME action.
@@ -50,7 +53,7 @@ using as a CV the difference between two distances.
\plumedfile
dAB: DISTANCE ATOMS=10,12
dAC: DISTANCE ATOMS=10,15
-diff: MATHEVAL ARG=dAB,dAC FUNC=y-x PERIODIC=NO
+diff: CUSTOM ARG=dAB,dAC FUNC=y-x PERIODIC=NO
# notice: the previous line could be replaced with the following
# diff: COMBINE ARG=dAB,dAC COEFFICIENTS=-1,1
METAD ARG=diff WIDTH=0.1 HEIGHT=0.5 BIASFACTOR=10 PACE=100
@@ -58,7 +61,7 @@ METAD ARG=diff WIDTH=0.1 HEIGHT=0.5 BIASFACTOR=10 PACE=100
(see also \ref DISTANCE, \ref COMBINE, and \ref METAD).
Notice that forces applied to diff will be correctly propagated
to atoms 10, 12, and 15.
-Also notice that since MATHEVAL is used without the VAR option
+Also notice that since CUSTOM is used without the VAR option
the two arguments should be referred to as x and y in the expression FUNC.
For simple functions
such as this one it is possible to use \ref COMBINE.
@@ -70,13 +73,13 @@ again as computed from the square root of the square.
\plumedfile
DISTANCE LABEL=d1 ATOMS=1,2 COMPONENTS
DISTANCE LABEL=d2 ATOMS=2,3 COMPONENTS
-MATHEVAL ...
+CUSTOM ...
LABEL=theta
ARG=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z
VAR=ax,ay,az,bx,by,bz
FUNC=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz))
PERIODIC=NO
-... MATHEVAL
+... CUSTOM
PRINT ARG=theta
\endplumedfile
(See also \ref PRINT and \ref DISTANCE).
@@ -90,7 +93,7 @@ For example, imagine that you want to implement a restraint that only acts when
distance is larger than 0.5. You can do it with
\plumedfile
d: DISTANCE ATOMS=10,15
-m: MATHEVAL ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
+m: CUSTOM ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
# check the function you are applying:
PRINT ARG=d,n FILE=checkme
RESTRAINT ARG=d AT=0.5 KAPPA=10.0
@@ -101,7 +104,7 @@ The meaning of the function `0.5*step(0.5-x)+x*step(x-0.5)` is:
- If x<0.5 (step(0.5-x)!=0) use 0.5
- If x>0.5 (step(x-0.5)!=0) use x
Notice that the same could have been obtained using an \ref UPPER_WALLS
-However, with MATHEVAL you can create way more complex definitions.
+However, with CUSTOM you can create way more complex definitions.
\warning If you apply forces on the variable (as in the previous example) you should
make sure that the variable is continuous!
@@ -121,7 +124,7 @@ create. The equivalent of the AND operator is the product: `step(1.0-x)*step(x-0
only equal to 1 when x is between 0.5 and 1.0. By combining negation and AND you can obtain an OR. That is,
`1-step(1.0-x)*step(x-0.5)` is only equal to 1 when x is outside the 0.5-1.0 interval.
-MATHEVAL can be used in combination with \ref DISTANCE to implement variants of the
+CUSTOM can be used in combination with \ref DISTANCE to implement variants of the
DISTANCE keyword that were present in PLUMED 1.3 and that allowed to compute
the distance of a point from a line defined by two other points, or the progression
along that line.
@@ -141,10 +144,10 @@ d23: DISTANCE ATOMS=p2,p3
# compute progress variable of the projection of point p3
# along the vector joining p1 and p2
# notice that progress is measured from the middle point
-onaxis: MATHEVAL ARG=d13,d23,d12 FUNC=(0.5*(y^2-x^2)/z) PERIODIC=NO
+onaxis: CUSTOM ARG=d13,d23,d12 FUNC=(0.5*(y^2-x^2)/z) PERIODIC=NO
# compute between point p3 and the vector joining p1 and p2
-fromaxis: MATHEVAL ARG=d13,d23,d12,onaxis VAR=x,y,z,o FUNC=(0.5*(y^2+x^2)-o^2-0.25*z^2) PERIODIC=NO
+fromaxis: CUSTOM ARG=d13,d23,d12,onaxis VAR=x,y,z,o FUNC=(0.5*(y^2+x^2)-o^2-0.25*z^2) PERIODIC=NO
PRINT ARG=onaxis,fromaxis
@@ -159,7 +162,7 @@ progression (S) and distance (Z) variables \cite perez2015atp.
//+ENDPLUMEDOC
-class Matheval :
+class Custom :
public Function
{
lepton::CompiledExpression expression;
@@ -169,24 +172,28 @@ class Matheval :
vector<double> values;
vector<char*> names;
public:
- explicit Matheval(const ActionOptions&);
+ explicit Custom(const ActionOptions&);
void calculate();
static void registerKeywords(Keywords& keys);
};
-PLUMED_REGISTER_ACTION(Matheval,"MATHEVAL")
+PLUMED_REGISTER_ACTION(Custom,"CUSTOM")
-//+PLUMEDOC FUNCTION CUSTOM
+//+PLUMEDOC FUNCTION MATHEVAL
/*
-An alias to the \ref MATHEVAL function.
+An alias to the \ref CUSTOM function.
+
+This alias is kept in order to maintain compatibility with previous PLUMED versions.
+However, notice that as of PLUMED 2.5 the libmatheval library is not linked anymore,
+and the \ref MATHEVAL function is implemented using the Lepton library.
\par Examples
-Just replace \ref MATHEVAL with \ref CUSTOM.
+Just replace \ref CUSTOM with \ref MATHEVAL.
\plumedfile
d: DISTANCE ATOMS=10,15
-m: CUSTOM ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
+m: MATHEVAL ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
# check the function you are applying:
PRINT ARG=d,n FILE=checkme
RESTRAINT ARG=d AT=0.5 KAPPA=10.0
@@ -196,20 +203,20 @@ RESTRAINT ARG=d AT=0.5 KAPPA=10.0
*/
//+ENDPLUMEDOC
-class Custom :
- public Matheval {
+class Matheval :
+ public Custom {
};
-PLUMED_REGISTER_ACTION(Matheval,"CUSTOM")
+PLUMED_REGISTER_ACTION(Custom,"MATHEVAL")
-void Matheval::registerKeywords(Keywords& keys) {
+void Custom::registerKeywords(Keywords& keys) {
Function::registerKeywords(keys);
keys.use("ARG"); keys.use("PERIODIC");
keys.add("compulsory","FUNC","the function you wish to evaluate");
keys.add("optional","VAR","the names to give each of the arguments in the function. If you have up to three arguments in your function you can use x, y and z to refer to them. Otherwise you must use this flag to give your variables names.");
}
-Matheval::Matheval(const ActionOptions&ao):
+Custom::Custom(const ActionOptions&ao):
Action(ao),
Function(ao),
expression_deriv(getNumberOfArguments()),
@@ -252,7 +259,7 @@ Matheval::Matheval(const ActionOptions&ao):
}
}
-void Matheval::calculate() {
+void Custom::calculate() {
for(unsigned i=0; i<getNumberOfArguments(); i++) {
try {
expression.getVariableReference(var[i])=getArgument(i);
diff --git a/src/generic/EffectiveEnergyDrift.cpp b/src/generic/EffectiveEnergyDrift.cpp
index f4185c0fc638f2603c5ef5637f6f2e176e95dc11..8debb8a8045945d46821a963a8105ea3d09c8a21 100644
--- a/src/generic/EffectiveEnergyDrift.cpp
+++ b/src/generic/EffectiveEnergyDrift.cpp
@@ -222,8 +222,6 @@ void EffectiveEnergyDrift::update() {
pNLocalAtoms = pGatindex.size();
pPositions=positions;
pForces=forces;
- pPositions=positions;
- pForces=forces;
pbox=box;
pfbox=fbox;
initialBias=plumed.getBias();
diff --git a/src/gridtools/GridToXYZ.cpp b/src/gridtools/GridToXYZ.cpp
index 2a511700128fec15af0f9403f42471c63700bc7c..e8adff0eed3f80ed72936b1def38845515fbe612 100644
--- a/src/gridtools/GridToXYZ.cpp
+++ b/src/gridtools/GridToXYZ.cpp
@@ -97,7 +97,8 @@ void GridToXYZ::printGrid( OFile& ofile ) const {
ofile.printf("Grid converted to xyz file \n");
for(unsigned i=0; i<ingrid->getNumberOfPoints(); ++i) {
ingrid->getGridPointCoordinates( i, point );
- ofile.printf("X"); double val=ingrid->getGridElement( i, 0 );
+ ofile.printf("X");
+ double val;
if( ingrid->getType()=="flat" ) val=1.0;
else val=ingrid->getGridElement( i, 0 );
for(unsigned j=0; j<3; ++j) { ofile.printf( (" " + fmt).c_str(), val*lenunit*point[j] ); }
diff --git a/src/isdb/CS2Backbone.cpp b/src/isdb/CS2Backbone.cpp
index 670c50a0cf358707efee40cdcd10c111b30f5d1a..42aabb90408c6c83b5e90a1a333e957225ec93a7 100644
--- a/src/isdb/CS2Backbone.cpp
+++ b/src/isdb/CS2Backbone.cpp
@@ -52,7 +52,7 @@ Calculates the backbone chemical shifts for a protein.
The functional form is that of CamShift \cite Kohlhoff:2009us. The chemical shift
of the selected nuclei can be saved as components. Alternatively one can calculate either
-the CAMSHIFT score (useful as a collective variable \cite Granata:2013dkor as a scoring
+the CAMSHIFT score (useful as a collective variable \cite Granata:2013dk or as a scoring
function \cite Robustelli:2010dn) or a \ref METAINFERENCE score (using DOSCORE).
For these two latter cases experimental chemical shifts must be provided.
diff --git a/src/isdb/RDC.cpp b/src/isdb/RDC.cpp
index 2d426edc3ec47567500f2c1b59a7a50d3a8ffaaf..3d3822c1fd6bb281abd64c29805f8b53dfa10d68 100644
--- a/src/isdb/RDC.cpp
+++ b/src/isdb/RDC.cpp
@@ -407,6 +407,7 @@ void RDC::do_svd()
}
gsl_matrix_free(coef_mat);
gsl_matrix_free(A);
+ gsl_matrix_free(V);
gsl_vector_free(rdc_vec);
gsl_vector_free(bc);
gsl_vector_free(Stmp);
diff --git a/src/logmfd/COPYRIGHT b/src/logmfd/COPYRIGHT
new file mode 100644
index 0000000000000000000000000000000000000000..bfc97613e4dc996aa8abc190f34ce7dce7ea380a
--- /dev/null
+++ b/src/logmfd/COPYRIGHT
@@ -0,0 +1,17 @@
+Copyright (c) 2015-2018
+National Institute of Advanced Industrial Science and Technology (AIST), Japan.
+This file contains module for LogMFD method proposed by Tetsuya Morishita(AIST).
+then written by Mizuho information and Research Institute, Inc.
+
+The LogMFD module is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+The LogMFD module is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with plumed. If not, see <http://www.gnu.org/licenses/>.
diff --git a/src/logmfd/LogMFD.cpp b/src/logmfd/LogMFD.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7a4e4cf1ea806b650bc3efd6d1f13322267e5c17
--- /dev/null
+++ b/src/logmfd/LogMFD.cpp
@@ -0,0 +1,1148 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2015-2018
+National Institute of Advanced Industrial Science and Technology (AIST), Japan.
+This file contains module for LogMFD method proposed by Tetsuya Morishita(AIST).
+then written by Mizuho information and Research Institute, Inc.
+
+The LogMFD module is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+The LogMFD module is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+
+//+PLUMEDOC LOGMFDMOD_BIAS LOGMFD
+/*
+Used to perform LogMFD, LogPD, and TAMD/d-AFED.
+
+\section LogMFD LogMFD
+
+Consider a physical system of \f$N_q\f$ particles, for which the Hamiltonian is given as
+
+\f[
+ {H_{\rm MD}}\left( {\bf{\Gamma}} \right) = \sum\limits_{j = 1}^{{N_q}} {\frac{{{\bf{p}}_j^2}}{{2{m_j}}}} + \Phi \left( {\bf{q}} \right)
+\f]
+
+where \f${\bf q}_j\f$, \f${\bf p}_j\f$ (\f$\bf{\Gamma}={\bf q},{\bf p}\f$), and \f$m_j\f$ are the position, momentum, and mass of the \f$j\f$th particle, respectively,
+and \f$\Phi\f$ is the potential energy function for \f${\bf q}\f$.
+The free energy \f$F({\bf X})\f$ as a function of a set of \f$N\f$ collective variables (CVs) is given as
+
+\f{eqnarray*}{
+ F\left( {{\bf X}} \right) &=& - {k_B}T\log \int {\exp \left[ { - \beta {H_{\rm MD}}} \right]\prod\limits_{i = 1}^N {\delta \left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)} d{\bf{\Gamma }}} \\
+ &\simeq& - {k_B}T\log \int {\exp \left[ { - \beta \left\{ {{H_{\rm MD}} + \sum\limits_i^N {\frac{{{K_i}}}{2}{{\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)}^2}} } \right\}} \right]} d{\bf{\Gamma }}
+\f}
+
+where \f$\bf{s}\f$ are the CVs, \f$k_B\f$ is Boltzmann constant, \f$\beta=k_BT\f$,
+and \f$K_i\f$ is the spring constant which is large enough to invoke
+
+\f[
+ \delta \left( x \right) = \lim_{k \to \infty } \sqrt {\beta k/2\pi} \exp \left( -\beta kx^2/2 \right)
+\f]
+
+In mean-force dynamics (MFD), \f${\bf X}\f$ are treated as fictitious dynamical variables, which are associated with the following Hamiltonian,
+
+\f[
+ {H_{\rm log}} = \sum\limits_{i = 1}^N {\frac{{P_{{X_i}}^2}}{{2{M_i}}} + \Psi \left( {{\bf X}} \right)}
+\f]
+
+where \f${P_{{X_i}}}\f$ and \f$M_i\f$ are the momentum and mass of \f$X_i\f$, respectively, and \f$\Psi\f$ is the potential function for \f${\bf X}\f$.
+We assume that \f$\Psi\f$ is a functional of \f$F({\bf X})\f$; \f$Ψ[F({\bf X})]\f$. The simplest form of \f$\Psi\f$ is \f$\Psi = F({\bf X})\f$,
+which corresponds to TAMD/d-AFED \cite AbramsJ2008, \cite Maragliano2006 (or the extended Lagrangian dynamics in the limit of the adiabatic decoupling between \f$\bf{q}\f$ and \f${\bf X}\f$).
+ In the case of LogMFD, the following form of \f$\Psi\f$ is introduced \cite MorishitaLogMFD;
+
+
+\f[
+ {\Psi _{\rm log}}\left( {{\bf X}} \right) = \gamma \log \left[ {\alpha F\left( {{\bf X}} \right) + 1} \right]
+\f]
+
+where \f$\alpha\f$ (ALPHA) and \f$\gamma\f$ (GAMMA) are positive parameters. The logarithmic form of \f$\Psi_{\rm log}\f$ ensures the dynamics of \f${\bf X}\f$ on a much smoother energy surface [i.e., \f$\Psi_{\rm log}({\bf X})\f$] than \f$F({\bf X})\f$, thus enhancing the sampling in the \f${\bf X}\f$-space. The parameters \f$\alpha\f$ and \f$\gamma\f$ determine the degree of flatness of \f$\Psi_{\rm log}\f$, but adjusting only \f$\alpha\f$ is normally sufficient to have a relatively flat surface (with keeping the relation \f$\gamma=1/\alpha\f$).
+
+The equation of motion (EOM) for \f$X_i\f$ in LogMFD (no thermostat) is
+
+\f[
+ {M_i}{\ddot X_i} = - \left( {\frac{{\alpha \gamma }}{{\alpha F + 1}}} \right)\frac{{\partial F}}{{\partial {X_i}}}
+\f]
+
+where \f$-\partial F/\partial X_i\f$ is evaluated as a canonical average under the condition that \f${\bf X}\f$ is fixed;
+
+\f{eqnarray*}{
+ - \frac{{\partial F}}{{\partial {X_i}}} &\simeq& \frac{1}{Z}\int {{K_i}\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)\exp \left[ { - \beta \left\{ {{H_{\rm MD}} + \sum\limits_i^N {\frac{{{K_i}}}{2}{{\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)}^2}} } \right\}} \right]} d{\bf{\Gamma }}\\
+ &\equiv& {\left\langle {{K_i}\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)} \right\rangle _{{\bf X}}}
+\f}
+
+where
+
+\f[
+ Z = \int {\exp \left[ { - \beta \left\{ {{H_{\rm MD}} + \sum\limits_i^N {\frac{{{K_i}}}{2}{{\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)}^2}} } \right\}} \right]} d{\bf{\Gamma }}
+\f]
+
+The mean-force (MF) is practically evaluated by performing a shot-time canonical MD run each time \f${\bf X}\f$ is updated according to the EOM for \f${\bf X}\f$.
+
+If the canonical average for the MF is effectively converged, the dynamical variables \f${\bf q}\f$ and \f${\bf X}\f$ are decoupled and they evolve adiabatically, which can be exploited for the on-the-fly evaluation of \f$F({\bf X})\f$. I.e., \f$H_{\rm log}\f$ should be a constant of motion in this case, thus \f$F({\bf X})\f$ can be evaluated each time \f${\bf X}\f$ is updated as
+
+
+\f[
+ F\left( {{{\bf X}}\left( t \right)} \right) = \frac{1}{\alpha} \left[
+ \exp \frac{1}{\gamma} \left\{ \left( H_{\rm log} - \sum_i \frac{P_{X_i}^2}{2M_i} \right) \right\} - 1 \right]
+\f]
+
+
+This means that \f$F({\bf X})\f$ can be constructed without postprocessing (on-the-fly free energy reconstruction). Note that the on-the-fly free energy reconstruction is also possible in TAMD/d-AFED if the Hamiltonian-like conserved quantity is available (e.g., the Nose-Hoover type dynamics).
+
+
+
+\section LogPD LogPD
+
+
+The accuracy in the MF is critical to the on-the-fly free energy reconstruction. To improve the evaluation of the MF, parallel-dynamics (PD) is incorporated into LogMFD, leading to logarithmic parallel-dynamics (LogPD) \cite MorishitaLogPD.
+
+
+In PD, the MF is evaluated by a nonequilibrium path-ensemble based on the Crooks-Jarzynski nonequilibrium work relation. To this end, multiple replicas of the MD system which run in parallel are introduced. The CVs [\f${\bf s}({\bf q})\f$] in each replica is restrained to the same value of \f${\bf X}(t)\f$. A canonical MD run with \f$N_m\f$ steps is performed in each replica, then the MF on \f$X_i\f$ is evaluated using the MD trajectories from all replicas.
+The MF is practically calculated as
+
+
+\f[
+ - \frac{{\partial F}}{{\partial {X_i}}} = \sum\limits_{k = 1}^{{N_r}} {{W_k}} \sum\limits_{n = 1}^{{N_m}} {\frac{1}{{{N_m}}}{K_i}\left[ {{s_i}\left( {{{\bf q}}_n^k} \right) - {X_i}} \right]}
+\f]
+
+
+
+where \f${\bf q}^k_n\f$ indicates the \f${\bf q}\f$-configuration at time step \f$n\f$ in the \f$N_m\f$-step shot-time MD run in the \f$k\f$th replica among \f$N_r\f$ replicas. \f$W_k\f$ is given as
+
+\f[
+ {W_k} = \frac{{{e^{ - \beta {w_k}\left( t \right)}}}}{{\sum\limits_{k=1}^{{N_r}} {{e^{ - \beta {w_k}\left( t \right)}}} }}
+\f]
+
+
+where
+
+
+\f[
+ {w_k}\left( t \right) = \int\limits_{{X_0}}^{X\left( t \right)} {\sum\limits_{i=1}^N {\frac{{\partial H_{\rm MD}^k}}{{\partial {X_i}}}d{X_i}} }
+\f]
+
+\f[
+ H_{\rm MD}^k\left( {{\bf{\Gamma }},{{\bf X}}} \right) = {H_{\rm MD}}\left( {{{\bf{\Gamma }}^k}} \right) + \sum\limits_{i = 1}^N {\frac{{{K_i}}}{2}{{\left( {s_i^k - {X_i}} \right)}^2}}
+\f]
+
+and \f$s^k_i\f$ is the \f$i\f$ th CV in the \f$k\f$th replica.
+
+\f$W_k\f$ comes from the Crooks-Jarzynski nonequilibrium work relation by which we can evaluate an equilibrium ensemble average from a set of nonequilibrium trajectories. Note that, to avoid possible numerical errors in the exponential function, the following form of \f$W_k\f$ is instead used in PLUMED,
+
+\f[
+ {W_k}\left( t \right) = \frac{{\exp \left[ { - \beta \left\{ {{w_k}\left( t \right) - {w_{\min }}\left( t \right)} \right\}} \right]}}{{\sum\nolimits_k {\exp \left[ { - \beta \left\{ {{w_k}\left( t \right) - {w_{\min }}\left( t \right)} \right\}} \right]} }}
+\f]
+
+where
+
+\f[
+ {w_{\min }}\left( t \right) = {\rm Min}_k\left[ {{w_k}\left( t \right)} \right]
+\f]
+
+
+With the MF evaluated using the PD approach, reconstructing free energy profiles can be performed more efficiently (requiring less elapsed computing time) in LogPD than with a single MD system in LogMFD. In the case that there exists more than one stable state separated by high energy barriers in the hidden subspace orthogonal to the CV-subspace, LogPD is particularly of use to incorporate all the contributions from such hidden states with appropriate weights (in the limit \f$N_r\to\infty\f$ ).
+
+Note that LogPD calculations should always be initiated with an equilibrium \f${\bf q}\f$-configuration in each replica, because the Crooks-Jarzynski nonequilibrium work relation is invoked. Also note that LogPD is currently available only with Gromacs, while LogMFD can be performed with Lammps, Gromacs, and NAMD.
+
+\section Thermostatted Thermostatted LogMFD/PD
+
+Thermostatting of \f${\bf X}\f$ is often recommended in LogMFD/PD to maintain the adiabatic decoupling between \f${\bf q}\f$ and \f${\bf X}\f$. In the framework of the LogMFD approach, the Nose-Hoover type thermostat and the Gaussian isokinetic (velocity scaling) thermostat can be used to control the kinetic energy of \f${\bf X}\f$.
+
+\subsection Nose-Hoover Nose-Hoover LogMFD/PD
+
+The EOM for \f$X_i\f$ coupled to a Nose-Hoover thermostat variable \f$\eta\f$ (single heat bath) is
+
+\f[
+ {M_i}{\ddot X_i} = - \left( {\frac{{\alpha \gamma }}{{\alpha F + 1}}} \right)\frac{{\partial F}}{{\partial {X_i}}} - {M_i}{\dot X_i}\dot \eta
+\f]
+
+The EOM for \f$\eta\f$ is
+
+\f[
+ Q\ddot \eta = \sum\limits_{i = 1}^N {\frac{{P_{{X_i}}^2}}{{{M_i}}} - N{k_B}T}
+\f]
+
+where \f$N\f$ is the number of the CVs. Since the following pseudo-Hamiltonian is a constant of motion in Nose-Hoover LogMFD/PD,
+
+\f[
+ H_{\rm log}^{\rm NH} = \sum\limits_{i = 1}^N {\frac{{P_{{X_i}}^2}}{{2{M_i}}} + \gamma \log \left[ {\alpha F\left( {{\bf X}} \right) + 1} \right] + \frac{1}{2}Q{{\dot \eta }^2} + N{k_B}T\eta}
+\f]
+
+\f$F({\bf X}(t))\f$ is obtained at each MFD step as
+
+\f[
+ F\left( {{{\bf X}}\left( t \right)} \right) = \frac{1}{\alpha }\left[ {\exp \left\{ {{{ \frac{1}{\gamma} \left( {H_{\rm log}^{\rm NH} - \sum_i {\frac{{P_{{X_i}}^2}}{{2{M_i}}}} - \frac{1}{2}Q{{\dot \eta }^2} - N{k_B}T\eta} \right)} }} \right\} - 1} \right]
+\f]
+
+
+
+\subsection VS Velocity scaling LogMFD/PD
+
+The velocity scaling algorithm (which is equivalent to the Gaussian isokinetic dynamics in the limit \f$\Delta t\to 0\f$) can also be employed to control the velocity of \f${\bf X}\f$, \f$\bf{V}_x\f$.
+
+The following algorithm is introduced to perform isokinetic LogMFD calculations \cite MorishitaVsLogMFD;
+
+\f{eqnarray*}{
+{V_{{X_i}}}\left( {{t_{n + 1}}} \right) &=& V_{X_i}^\prime \left( {{t_n}} \right) + \Delta t\left[ { - \left( {\frac{{\alpha \gamma }}{{\alpha F\left( {{t_n}} \right) + 1}}} \right)\frac{{\partial F\left( {{t_n}} \right)}}{{\partial {X_i}}}} \right]\\
+S\left( {{t_{n + 1}}} \right) &=& \sqrt {\frac{{N{k_B}T}}{{\sum\limits_i {{M_i}V_{{X_i}}^2\left( {{t_{n + 1}}} \right)} }}} \\
+{V_{{X_i}}}^\prime \left( {{t_{n + 1}}} \right) &=& S\left( {{t_{n + 1}}} \right){V_{{X_i}}}\left( {{t_{n + 1}}} \right)\\
+{X_i}\left( {{t_{n + 1}}} \right) &=& {X_i}\left( {{t_n}} \right) + \Delta t V_{X_i}^\prime \left( {{t_{n + 1}}} \right)\\
+{\Psi_{\rm log}}\left( {{t_{n + 1}}} \right) &=& N{k_B}T\log S\left( {{t_{n + 1}}} \right) + {\Psi_{\rm log}}\left( {{t_n}} \right)\\
+F\left( {{t_{n + 1}}} \right) &=& \frac{1}{\alpha} \left[
+ \exp \left\{ \Psi_{\rm log} \left( t_{n+1} \right) / \gamma \right\} - 1 \right]
+\f}
+
+Note that \f$V_{X_i}^\prime\left( {{t_0}} \right)\f$ is assumed to be initially given, which meets the following relation,
+
+\f[
+ \sum\limits_{i = 1}^N M_i V_{X_i}^{\prime 2} \left( t_0 \right) = N{k_B}{T}
+\f]
+
+It should be stressed that, in the same way as in the NVE and Nose-Hoover LogMFD/PD, \f$F({\bf X}(t))\f$ can be evaluated at each MFD step (on-the-fly free energy reconstruction) in Velocity Scaling LogMFD/PD.
+
+
+\par Examples
+\section Examples Examples
+
+\subsection Example-LoGMFD Example of LogMFD
+
+The following input file tells plumed to restrain collective variables
+to the fictitious dynamical variables in LogMFD/PD.
+
+plumed.dat
+\plumedfile
+UNITS TIME=fs LENGTH=1.0 ENERGY=kcal/mol Mass=1.0 CHARGE=1.0
+phi: TORSION ATOMS=5,7,9,15
+psi: TORSION ATOMS=7,9,15,17
+
+# LogMFD
+LOGMFD ...
+LABEL=logmfd
+ARG=phi,psi
+KAPPA=1000.0,1000.0
+DELTA_T=0.5
+INTERVAL=500
+TEMP=300.0
+FLOG=5.0
+MFICT=5000000.0,5000000.0
+# FICT=0.8,0.8
+VFICT=3.5e-4,3.5e-4
+ALPHA=4.0
+THERMOSTAT=NVE
+VETA=0.0
+META=20000.0
+FICT_MAX=3.1,3.1
+FICT_MIN=-3.1,-3.1
+... LOGMFD
+\endplumedfile
+
+To submit this simulation with Gromacs, use the following command line
+to execute a LogMFD run with Gromacs-MD.
+Here TOPO/topol0.tpr is an input file
+which contains atomic coordinates and Gromacs parameters.
+
+\plumedfile
+gmx_mpi mdrun -s TOPO/topol0.tpr -plumed
+\endplumedfile
+
+This command will output files named logmfd.out and replica.out.
+
+The output file logmfd.out records free energy and all fictitious dynamical variables at every MFD step.
+
+logmfd.out
+
+\plumedfile
+# LogMFD
+# CVs : phi psi
+# Mass for CV particles : 6000.000000000 6000.000000000
+# Mass for thermostat : 6000.000000000
+# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
+# 6:phi_fict(t), 7:phi_vfict(t), 8:phi_force(t),
+# 9:psi_fict(t), 10:psi_vfict(t), 11:psi_force(t),
+ 0 10.000000000 0.000000000 0.000000000 0.000000000 -2.856237341 0.000000000 0.000000000 2.791986734 0.000000000 0.000000000
+ 1 9.999998983 0.000002983 0.000000000 0.000000000 -2.856235970 0.000002741 1.348654484 2.791987168 0.000000868 0.427130489
+ 2 9.999990885 0.000026738 0.000000000 0.000000000 -2.856231815 0.000008311 2.740416731 2.791988289 0.000002243 0.676244355
+...
+\endplumedfile
+
+The output file replica.out records all collective variables at every MFD step.
+
+replica.out
+
+\plumedfile
+# Replica No. 0 of 1.
+# 1:iter_md, 2:work, 3:weight,
+# 4:phi(q),
+# 5:psi(q),
+ 0 0.000000e+00 1.000000e+00 -2.856237341 2.791986734
+ 1 0.000000e+00 1.000000e+00 -2.829264251 2.800529344
+ 2 -4.049512e-06 1.000000e+00 -2.801427636 2.805512055
+...
+\endplumedfile
+
+\subsection Example-LogPD Example of LogPD
+
+Use the following command line to execute a LogPD run using two MD replicas (note that only Gromacs is currently available for LogPD).
+Here TOPO/topol0.tpr and TOPO/topol1.tpr are input files
+which contain atomic coordinates of each replica and Gromacs parameters.
+
+\plumedfile
+mpirun -np 2 gmx_mpi mdrun -s TOPO/topol -plumed -multi 2
+\endplumedfile
+
+This command will output files named logmfd.out, replica.out.0 and replica.out.1.
+
+The output file logmfd.out records free energy and all fictitious dynamical variables at every MFD step.
+
+logmfd.out
+
+\plumedfile
+# LogPD, replica parallel of LogMFD
+# CVs : phi psi
+# number of replica : 2
+# Mass for CV particles : 6000.000000000 6000.000000000
+# Mass for thermostat : 6000.000000000
+# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,
+# 6:phi_fict(t), 7:phi_vfict(t), 8:phi_force(t),
+# 9:psi_fict(t), 10:psi_vfict(t), 11:psi_force(t),
+ 0 10.000000000 0.000000000 0.000000000 0.000000000 -0.959548298 0.000000000 0.000000000 0.789064173 0.000000000 0.000000000
+ 1 9.999999713 0.000000842 0.000000000 0.000000000 -0.959547729 0.000001138 0.559781383 0.789064682 0.000001019 0.501485083
+ 2 9.999997525 0.000007259 0.000000000 0.000000000 -0.959546257 0.000002944 0.888495415 0.789066375 0.000003384 1.163634941
+...
+\endplumedfile
+
+
+The output file replica.out.0 records all collective variables of replica No.0 at every MFD step.
+
+replica.out.0
+
+\plumedfile
+# Replica No. 0 of 2.
+# 1:iter_md, 2:work, 3:weight,
+# 4:phi(q),
+# 5:psi(q),
+ 0 0.000000e+00 5.000000e-01 -2.856237851 2.791988354
+ 1 0.000000e+00 5.000000e-01 -2.825008209 2.796384301
+ 2 9.218849e-07 4.999996e-01 -2.787512517 2.793347554
+...
+\endplumedfile
+
+The output file replica.out.1 records all collective variables of replica No.1 at every MFD step.
+
+replica.out.1
+
+\plumedfile
+# Replica No. 1 of 2.
+# 1:iter_md, 2:work, 3:weight,
+# 4:phi(q),
+# 5:psi(q),
+ 0 0.000000e+00 5.000000e-01 0.937141255 -1.213860008
+ 1 0.000000e+00 5.000000e-01 0.928302868 -1.198196552
+ 2 -3.118851e-06 5.000004e-01 0.903953885 -1.168669583
+...
+\endplumedfile
+
+*/
+//+ENDPLUMEDOC
+
+#include "bias/Bias.h"
+#include "core/ActionRegister.h"
+#include "core/Atoms.h"
+#include "core/PlumedMain.h"
+
+#include <iostream>
+
+using namespace std;
+using namespace PLMD;
+using namespace bias;
+
+namespace PLMD {
+namespace logmfd {
+/**
+ \brief class for LogMFD parameters, variables and subroutines.
+ */
+class LogMFD : public Bias {
+ bool firsttime; ///< flag that indicates first MFD step or not.
+ int interval; ///< input parameter, period of MD steps when fictitious dynamical variables are evolved.
+ double delta_t; ///< input parameter, one time step of MFD when fictitious dynamical variables are evolved.
+ string thermostat; ///< input parameter, type of thermostat for canonical dyanamics.
+ double kbt; ///< k_B*temerature
+
+ int TAMD; ///< input parameter, perform TAMD instead of LogMFD.
+ double alpha; ///< input parameter, alpha parameter for LogMFD.
+ double gamma; ///< input parameter, gamma parameter for LogMFD.
+ std::vector<double> kappa; ///< input parameter, strength of the harmonic restraining potential.
+
+ std::vector<double> fict_max; ///< input parameter, maximum of each fictitous dynamical variable.
+ std::vector<double> fict_min; ///< input parameter, minimum of each fictitous dynamical variable.
+
+ std::vector<double> fict; ///< current values of each fictitous dynamical variable.
+ std::vector<double> vfict; ///< current velocity of each fictitous dynamical variable.
+ std::vector<double> mfict; ///< mass of each fictitous dynamical variable.
+
+ double xeta; ///< current eta variable of thermostat.
+ double veta; ///< current velocity of eta variable of thermostat.
+ double meta; ///< mass of eta variable of thermostat.
+
+ double flog; ///< current free energy
+
+ double hlog; ///< value invariant
+ double phivs; ///< potential used in VS method
+ double work; ///< current works done by fictitious dynamical variables in this replica.
+ double weight; ///< current weight of this replica.
+
+ std::vector<double> ffict; ///< current force of each fictitous dynamical variable.
+ std::vector<double> fict_ave; ///< averaged values of each collective variable.
+
+ std::vector<Value*> fictValue; ///< pointers to fictitious dynamical variables
+ std::vector<Value*> vfictValue; ///< pointers to velocity of fictitious dynamical variables
+
+public:
+ static void registerKeywords(Keywords& keys);
+
+ explicit LogMFD(const ActionOptions&);
+ void calculate();
+ void update();
+ void updateNVE();
+ void updateNVT();
+ void updateVS();
+ void calcMeanForce();
+ double calcEkin();
+ double calcFlog();
+ double calcClog();
+
+private:
+ double sgn( double x ) {
+ return x>0.0 ? 1.0 : x<0.0 ? -1.0 : 0.0;
+ }
+};
+
+PLUMED_REGISTER_ACTION(LogMFD,"LOGMFD")
+
+/**
+ \brief instruction of parameters for Plumed manual.
+*/
+void LogMFD::registerKeywords(Keywords& keys) {
+ Bias::registerKeywords(keys);
+ keys.use("ARG");
+ keys.add("compulsory","INTERVAL",
+ "Period of MD steps (\\f$N_m\\f$) to update fictitious dynamical variables." );
+ keys.add("compulsory","DELTA_T",
+ "Time step for the fictitious dynamical variables (MFD step)." );
+ keys.add("compulsory","THERMOSTAT",
+ "Type of thermostat for the fictitious dynamical variables. NVE, NVT, VS are available." );
+ keys.add("optional","TEMP",
+ "Temperature of the fictitious dynamical variables in thermostatted LogMFD/PD. "
+ "If not provided or provided as 0, it will be taken from the temperature of the MD system." );
+
+ keys.add("optional","TAMD",
+ "When TAMD=1, TAMD/d-AFED calculations can be performed instead of LogMFD. Otherwise, the LogMFD protocol is switched on (default)." );
+
+ keys.add("optional","ALPHA",
+ "Alpha parameter for LogMFD. "
+ "If not provided or provided as 0, it will be taken as 1/gamma. "
+ "If gamma is also not provided, Alpha is set as 4, which is a sensible value when the unit of kcal/mol is used." );
+ keys.add("optional","GAMMA",
+ "Gamma parameter for LogMFD. "
+ "If not provided or provided as 0, it will be taken as 1/alpha. "
+ "If alpha is also not provided, Gamma is set as 0.25, which is a sensible value when the unit of kcal/mol is used." );
+ keys.add("compulsory","KAPPA",
+ "Spring constant of the harmonic restraining potential for the fictitious dynamical variables." );
+
+ keys.add("compulsory","FICT_MAX",
+ "Maximam values reachable for the fictitious dynamical variables. The variables will elastically bounce back at the boundary (mirror boundary)." );
+ keys.add("compulsory","FICT_MIN",
+ "Minimam values reachable for the fictitious dynamical variables. The variables will elastically bounce back at the boundary (mirror boundary)." );
+
+ keys.add("optional","FICT",
+ "The initial values of the fictitious dynamical variables. "
+ "If not provided, they are set equal to their corresponding CVs for the initial atomic configuration." );
+ keys.add("optional","VFICT",
+ "The initial velocities of the fictitious dynamical variables. "
+ "If not provided, they will be taken as 0." );
+ keys.add("optional","MFICT",
+ "Masses of each fictitious dynamical variable. "
+ "If not provided, they will be taken as 10000." );
+
+ keys.add("optional","XETA",
+ "The initial eta variable of the Nose-Hoover thermostat "
+ "for the fictitious dynamical variables. "
+ "If not provided, it will be taken as 0." );
+ keys.add("optional","VETA",
+ "The initial velocity of eta variable. "
+ "If not provided, it will be taken as 0." );
+ keys.add("optional","META",
+ "Mass of eta variable. "
+ "If not provided, it will be taken as N*kb*T*100*100." );
+
+ keys.add("compulsory","FLOG",
+ "The initial free energy value in the LogMFD/PD run."
+ "The origin of the free energy profile is adjusted by FLOG to "
+ "realize \\f$F({\\bf X}(t)) > 0\\f$ at any \\f${\\bf X}(t)\\f$, "
+ "resulting in enhanced barrier-crossing. "
+ "(The value of \\f$H_{\\rm log}\\f$ is automatically "
+ "set according to FLOG).");
+
+ keys.add("optional","WORK",
+ "The initial value of the work done by fictitious dynamical "
+ "variables in each replica. "
+ "If not provided, it will be taken as 0.");
+
+ componentsAreNotOptional(keys);
+ keys.addOutputComponent("_fict","default",
+ "For example, the fictitious collective variable for LogMFD is specified as "
+ "ARG=dist12 and LABEL=logmfd in LOGMFD section in Plumed input file, "
+ "the associated fictitious dynamical variable can be specified as "
+ "PRINT ARG=dist12,logmfd.dist12_fict FILE=COLVAR");
+ keys.addOutputComponent("_vfict","default",
+ "For example, the fictitious collective variable for LogMFD is specified as "
+ "ARG=dist12 and LABEL=logmfd in LOGMFD section in Plumed input file, the "
+ "velocity of the associated fictitious dynamical variable can be specified as "
+ "PRINT ARG=dist12,logmfd.dist12_vfict FILE=COLVAR");
+}
+
+
+/**
+ \brief constructor of LogMFD class
+ \details This constructor initializes all parameters and variables,
+ reads input file and set value of parameters and initial value of variables,
+ and writes messages as Plumed log.
+*/
+LogMFD::LogMFD( const ActionOptions& ao ):
+ PLUMED_BIAS_INIT(ao),
+ firsttime(true),
+ interval(10),
+ delta_t(1.0),
+ thermostat("NVE"),
+ kbt(-1.0),
+ TAMD(0),
+ alpha(0.0),
+ gamma(0.0),
+ kappa(getNumberOfArguments(),0.0),
+ fict_max(getNumberOfArguments(),0.0),
+ fict_min(getNumberOfArguments(),0.0),
+ fict (getNumberOfArguments(),0.0),
+ vfict(getNumberOfArguments(),0.0),
+ mfict(getNumberOfArguments(),10000.0),
+ xeta(0.0),
+ veta(0.0),
+ meta(0.0),
+ flog(0.0),
+ hlog(0.0),
+ phivs(0.0),
+ work(0.0),
+ weight(0.0),
+ ffict(getNumberOfArguments(),0.0),
+ fict_ave(getNumberOfArguments(),0.0),
+ fictValue(getNumberOfArguments(),NULL),
+ vfictValue(getNumberOfArguments(),NULL)
+{
+ parse("INTERVAL",interval);
+ parse("DELTA_T",delta_t);
+ parse("THERMOSTAT",thermostat);
+ parse("TEMP",kbt); // read as temperature
+
+ parse("TAMD",TAMD);
+ parse("ALPHA",alpha);
+ parse("GAMMA",gamma);
+ parseVector("KAPPA",kappa);
+
+ parseVector("FICT_MAX",fict_max);
+ parseVector("FICT_MIN",fict_min);
+
+ parseVector("FICT",fict);
+ parseVector("VFICT",vfict);
+ parseVector("MFICT",mfict);
+
+ parse("XETA",xeta);
+ parse("VETA",veta);
+ parse("META",meta);
+
+ parse("FLOG",flog);
+
+ // read initial value of work for each replica of LogPD
+ if( multi_sim_comm.Get_size()>1 ) {
+ vector<double> vwork(multi_sim_comm.Get_size(),0.0);
+ parseVector("WORK",vwork);
+ // initial work of this replica
+ work = vwork[multi_sim_comm.Get_rank()];
+ }
+ else {
+ work = 0.0;
+ }
+
+ if( kbt>=0.0 ) {
+ kbt *= plumed.getAtoms().getKBoltzmann();
+ }
+ else {
+ kbt = plumed.getAtoms().getKbT();
+ }
+
+ if( meta == 0.0 ) {
+ const double nkt = getNumberOfArguments()*kbt;
+ meta = nkt*100.0*100.0;
+ }
+
+ if(alpha == 0.0 && gamma == 0.0) {
+ alpha = 4.0;
+ gamma = 1 / alpha;
+ }
+ else if(alpha != 0.0 && gamma == 0.0) {
+ gamma = 1 / alpha;
+ }
+ else if(alpha == 0.0 && gamma != 0.0) {
+ alpha = 1 / gamma;
+ }
+
+ checkRead();
+
+ // output messaages to Plumed's log file
+ if( multi_sim_comm.Get_size()>1 ) {
+ if( TAMD ) {
+ log.printf("TAMD-PD, replica parallel of TAMD, no logarithmic flattening.\n");
+ }
+ else {
+ log.printf("LogPD, replica parallel of LogMFD.\n");
+ }
+ log.printf("number of replica : %d.\n", multi_sim_comm.Get_size() );
+ }
+ else {
+ if( TAMD ) {
+ log.printf("TAMD, no logarithmic flattening.\n");
+ }
+ else {
+ log.printf("LogMFD, logarithmic flattening.\n");
+ }
+ }
+
+ log.printf(" with harmonic force constant ");
+ for(unsigned i=0; i<kappa.size(); i++) log.printf(" %f",kappa[i]);
+ log.printf("\n");
+
+ log.printf(" with interval of cv(ideal) update ");
+ log.printf(" %d", interval);
+ log.printf("\n");
+
+ log.printf(" with time step of cv(ideal) update ");
+ log.printf(" %f", delta_t);
+ log.printf("\n");
+
+ if( !TAMD ) {
+ log.printf(" with alpha, gamma ");
+ log.printf(" %f %f", alpha, gamma);
+ log.printf("\n");
+ }
+
+ log.printf(" with Thermostat for cv(ideal) ");
+ log.printf(" %s", thermostat.c_str());
+ log.printf("\n");
+
+ log.printf(" with initial free energy ");
+ log.printf(" %f", flog);
+ log.printf("\n");
+
+ log.printf(" with mass of cv(ideal)");
+ for(unsigned i=0; i<mfict.size(); i++) log.printf(" %f", mfict[i]);
+ log.printf("\n");
+
+ log.printf(" with initial value of cv(ideal)");
+ for(unsigned i=0; i<fict.size(); i++) log.printf(" %f", fict[i]);
+ log.printf("\n");
+
+ log.printf(" with initial velocity of cv(ideal)");
+ for(unsigned i=0; i<vfict.size(); i++) log.printf(" %f", vfict[i]);
+ log.printf("\n");
+
+ log.printf(" with maximum value of cv(ideal) ");
+ for(unsigned i=0; i<fict_max.size(); i++) log.printf(" %f",fict_max[i]);
+ log.printf("\n");
+
+ log.printf(" with minimum value of cv(ideal) ");
+ for(unsigned i=0; i<fict_min.size(); i++) log.printf(" %f",fict_min[i]);
+ log.printf("\n");
+
+ log.printf(" and kbt ");
+ log.printf(" %f",kbt);
+ log.printf("\n");
+
+ // setup Value* variables
+ for(unsigned i=0; i<getNumberOfArguments(); i++) {
+ std::string comp = getPntrToArgument(i)->getName()+"_fict";
+ addComponentWithDerivatives(comp);
+
+ if(getPntrToArgument(i)->isPeriodic()) {
+ std::string a,b;
+ getPntrToArgument(i)->getDomain(a,b);
+ componentIsPeriodic(comp,a,b);
+ }
+ else {
+ componentIsNotPeriodic(comp);
+ }
+ fictValue[i] = getPntrToComponent(comp);
+
+ comp = getPntrToArgument(i)->getName()+"_vfict";
+ addComponent(comp);
+
+ componentIsNotPeriodic(comp);
+ vfictValue[i] = getPntrToComponent(comp);
+ }
+}
+
+/**
+ \brief calculate forces for fictitious variables at every MD steps.
+ \details This function calculates initial values of fictitious variables
+ and write header messages to LogMFD log files at the first MFD step,
+ calculates restraining fources comes from difference between the fictious variable
+ and collective variable at every MD steps.
+*/
+void LogMFD::calculate() {
+ if( firsttime ) {
+ firsttime = false;
+
+ // set initial values of fictitious variables if they were not specified.
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ if( fict[i] != 0.0 ) continue;
+
+ // use the collective variables as the initial of the fictitious variable.
+ fict[i] = getArgument(i);
+
+ // average values of fictitious variables by all replica.
+ if( multi_sim_comm.Get_size()>1 ) {
+ multi_sim_comm.Sum(fict[i]);
+ fict[i] /= multi_sim_comm.Get_size();
+ }
+ }
+
+ // initialize accumulation value to zero
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fict_ave[i] = 0.0;
+ }
+
+ // calculate invariant for NVE
+ if(thermostat == "NVE") {
+ // kinetic energy
+ const double ekin = calcEkin();
+ // potential energy
+ const double pot = TAMD ? flog : sgn(flog)*gamma * std::log1p( alpha*fabs(flog) );
+ // invariant
+ hlog = pot + ekin;
+ }
+ else if(thermostat == "NVT") {
+ const double nkt = getNumberOfArguments()*kbt;
+ // kinetic energy
+ const double ekin = calcEkin();
+ // bath energy
+ const double ekin_bath = 0.5*veta*veta*meta + xeta*nkt;
+ // potential energy
+ const double pot = TAMD ? flog : sgn(flog)*gamma * std::log1p( alpha*fabs(flog) );
+ // invariant
+ hlog = pot + ekin + ekin_bath;
+ }
+ else if(thermostat == "VS") {
+ // initial velocities
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ vfict[i] = sqrt(kbt/mfict[i]);
+ }
+ // initial VS potential
+ phivs = TAMD ? flog : sgn(flog)* gamma*std::log1p( alpha*fabs(flog) );
+
+ // invariant
+ hlog = 0.0;
+ }
+
+ weight = 1.0; // for replica parallel
+
+ // open LogMFD's log file
+ if( multi_sim_comm.Get_rank()==0 && comm.Get_rank()==0 ) {
+ FILE *outlog = std::fopen("logmfd.out", "w");
+
+ // output messages to LogMFD's log file
+ if( multi_sim_comm.Get_size()>1 ) {
+ fprintf(outlog, "# LogPD, replica parallel of LogMFD\n");
+ fprintf(outlog, "# number of replica : %d\n", multi_sim_comm.Get_size() );
+ }
+ else {
+ fprintf(outlog, "# LogMFD\n");
+ }
+
+ fprintf(outlog, "# CVs :");
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fprintf(outlog, " %s", getPntrToArgument(i)->getName().c_str() );
+ }
+ fprintf(outlog, "\n");
+
+ fprintf(outlog, "# Mass for CV particles :");
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fprintf(outlog, "%18.9f", mfict[i]);
+ }
+ fprintf(outlog, "\n");
+
+ fprintf(outlog, "# Mass for thermostat :");
+ fprintf(outlog, "%18.9f", meta);
+ fprintf(outlog, "\n");
+ fprintf(outlog, "# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,\n");
+
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fprintf(outlog, "# %u:%s_fict(t), %u:%s_vfict(t), %u:%s_force(t),\n",
+ 6+i*3, getPntrToArgument(i)->getName().c_str(),
+ 7+i*3, getPntrToArgument(i)->getName().c_str(),
+ 8+i*3, getPntrToArgument(i)->getName().c_str() );
+ }
+
+ fclose(outlog);
+ }
+
+ if( comm.Get_rank()==0 ) {
+ // the number of replica is added to file name to distingwish replica.
+ FILE *outlog2 = fopen("replica.out", "w");
+ fprintf(outlog2, "# Replica No. %d of %d.\n",
+ multi_sim_comm.Get_rank(), multi_sim_comm.Get_size() );
+
+ fprintf(outlog2, "# 1:iter_md, 2:work, 3:weight,\n");
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fprintf(outlog2, "# %u:%s(q)\n",
+ 4+i, getPntrToArgument(i)->getName().c_str() );
+ }
+ fclose(outlog2);
+ }
+
+ // output messages to Plumed's log file
+ // log.printf("LOGMFD thermostat parameters Xeta Veta Meta");
+ // log.printf(" %f %f %f", xeta, veta, meta);
+ // log.printf("\n");
+ // log.printf("# 1:iter_md, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,");
+ // log.printf("# 6:X1(t), 7:V1(t), 8:F1(t), 9:X2(t), 10:V2(t), 11:F2(t), ...");
+
+ } // firsttime
+
+ // calculate force for fictitious variable
+ double ene=0.0;
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ // difference between fictitious variable and collective variable.
+ const double diff = difference(i,fict[i],getArgument(i));
+ // restraining force.
+ const double f = -kappa[i]*diff;
+ setOutputForce(i,f);
+
+ // restraining energy.
+ ene += 0.5*kappa[i]*diff*diff;
+
+ // accumulate force, later it will be averaged.
+ ffict[i] += -f;
+
+ // accumulate varience of collective variable, later it will be averaged.
+ fict_ave[i] += diff;
+ }
+
+ setBias(ene);
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ // correct fict so that it is inside [min:max].
+ fict[i] = fictValue[i]->bringBackInPbc(fict[i]);
+ fictValue[i]->set(fict[i]);
+ vfictValue[i]->set(vfict[i]);
+ }
+} // calculate
+
+/**
+ \brief update fictitious variables.
+ \details This function manages evolution of fictitious variables.
+ This function calculates mean force, updates fictitious variables by one MFD step,
+ bounces back variables, updates free energy, and record logs.
+*/
+void LogMFD::update() {
+ if(getStep()%interval != 0 ) return;
+
+ // calc mean force for fictitious variables
+ calcMeanForce();
+
+ // update fictitious variables
+ if(thermostat == "NVE") {
+ updateNVE();
+ }
+ else if(thermostat == "NVT") {
+ updateNVT();
+ }
+ else if(thermostat == "VS") {
+ updateVS();
+ }
+
+ // bounce back variables if they are beyond their min and max.
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ if(fict[i] > fict_max[i]) {
+ fict[i] = fict_max[i] - (fict[i] - fict_max[i]);
+ vfict[i] *= -1.0;
+ }
+ if(fict[i] < fict_min[i]) {
+ fict[i] = fict_min[i] + (fict_min[i] - fict[i]);
+ vfict[i] *= -1.0;
+ }
+ }
+
+ // update free energy
+ flog = calcFlog();
+
+ // record log for fictitious variables
+ if( multi_sim_comm.Get_rank()==0 && comm.Get_rank()==0 ) {
+ FILE *outlog = std::fopen("logmfd.out", "a");
+
+ const double ekin = calcEkin();
+ const double temp = 2.0*ekin/getNumberOfArguments()/plumed.getAtoms().getKBoltzmann();
+
+ fprintf(outlog, "%*d", 8, (int)getStep()/interval);
+ fprintf(outlog, "%17.8f", flog);
+ fprintf(outlog, "%17.8f", temp);
+ fprintf(outlog, "%17.8f", xeta);
+ fprintf(outlog, "%17.8f", veta);
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fprintf(outlog, "%17.8f", fict[i]);
+ fprintf(outlog, "%17.8f", vfict[i]);
+ fprintf(outlog, "%17.8f", ffict[i]);
+ }
+ fprintf(outlog," \n");
+ fclose(outlog);
+ }
+
+ // record log for collective variables
+ if( comm.Get_rank()==0 ) {
+ // the number of replica is added to file name to distingwish replica.
+ FILE *outlog2 = fopen("replica.out", "a");
+ fprintf(outlog2, "%*d", 8, (int)getStep()/interval);
+ fprintf(outlog2, "%16.6e ", work);
+ fprintf(outlog2, "%16.6e ", weight);
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ fprintf(outlog2, "%17.8f", fict_ave[i]);
+ }
+ fprintf(outlog2," \n");
+ fclose(outlog2);
+ }
+
+ // reset mean force
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ ffict[i] = 0.0;
+ fict_ave[i] = 0.0;
+ }
+
+} // update
+
+/**
+ \brief update fictitious variables by NVE mechanics.
+ \details This function updates ficitious variables by one NVE-MFD step using mean forces
+ and flattening coefficient and free energy.
+ */
+void LogMFD::updateNVE() {
+ const double dt = delta_t;
+
+ // get latest free energy and flattening coefficient
+ flog = calcFlog();
+ const double clog = calcClog();
+
+ // update all ficitious variables by one MFD step
+ for( unsigned i=0; i<getNumberOfArguments(); ++i ) {
+ // update velocity (full step)
+ vfict[i]+=clog*ffict[i]*dt/mfict[i];
+ // update position (full step)
+ fict[i]+=vfict[i]*dt;
+ }
+} // updateNVE
+
+/**
+ \brief update fictitious variables by NVT mechanics.
+ \details This function updates ficitious variables by one NVT-MFD step using mean forces
+ and flattening coefficient and free energy.
+ */
+void LogMFD::updateNVT() {
+ const double dt = delta_t;
+ const double nkt = getNumberOfArguments()*kbt;
+
+ // backup vfict
+ std::vector<double> vfict_backup(getNumberOfArguments());
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ vfict_backup[i] = vfict[i];
+ }
+
+ const int niter=5;
+ for(unsigned j=0; j<niter; ++j) {
+ // get latest free energy and flattening coefficient
+ flog = calcFlog();
+ const double clog = calcClog();
+
+ // restore vfict from vfict_backup
+ for(unsigned l=0; l<getNumberOfArguments(); ++l) {
+ vfict[l] = vfict_backup[l];
+ }
+
+ // evolve vfict from vfict_backup by dt/2
+ for(unsigned m=0; m<getNumberOfArguments(); ++m) {
+ vfict[m] *= exp(-0.25*dt*veta);
+ vfict[m] += 0.5*dt*clog*ffict[m]/mfict[m];
+ vfict[m] *= exp(-0.25*dt*veta);
+ }
+ }
+
+ // get latest free energy and flattening coefficient
+ flog = calcFlog();
+ const double clog = calcClog();
+
+ // evolve vfict by dt/2, and evolve fict by dt
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ vfict[i] *= exp(-0.25*dt*veta);
+ vfict[i] += 0.5*dt*clog*ffict[i]/mfict[i];
+ vfict[i] *= exp(-0.25*dt*veta);
+ fict[i] += dt*vfict[i];
+ }
+
+ // evolve xeta and veta by dt
+ xeta += 0.5*dt*veta;
+ const double ekin = calcEkin();
+ veta += dt*(2.0*ekin-nkt)/meta;
+ xeta += 0.5*dt*veta;
+} // updateNVT
+
+/**
+ \brief update fictitious variables by VS mechanics.
+ \details This function updates ficitious variables by one VS-MFD step using mean forces
+ and flattening coefficient and free energy.
+ */
+void LogMFD::updateVS() {
+ const double dt = delta_t;
+ const double nkt = getNumberOfArguments()*kbt;
+
+ // get latest free energy and flattening coefficient
+ flog = calcFlog();
+ const double clog = calcClog();
+
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ // update velocity (full step)
+ vfict[i] += clog*ffict[i]*dt/mfict[i];
+ }
+
+ const double ekin = calcEkin();
+ const double svs = sqrt(nkt/ekin/2);
+
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ // update position (full step)
+ vfict[i] *= svs;
+ fict[i] += vfict[i]*dt;
+ }
+
+ // evolve VS potential
+ phivs += nkt*std::log(svs);
+} // updateVS
+
+/**
+ \brief calculate mean force for fictitious variables.
+ \details This function calculates mean forces by averaging forces accumulated during one MFD step,
+ update work variables done by fictitious variables by one MFD step,
+ calculate weight variable of this replica for LogPD.
+*/
+void LogMFD::calcMeanForce() {
+ // cale temporal mean force for each CV
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ ffict[i] /= interval;
+ // average of diff (getArgument(i)-fict[i])
+ fict_ave[i] /= interval;
+ // average of getArgument(i)
+ fict_ave[i] += fict[i];
+
+ // correct fict_ave so that it is inside [min:max].
+ fict_ave[i] = fictValue[i]->bringBackInPbc(fict_ave[i]);
+ }
+
+ // accumulate work, it was initialized as 0.0
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ work -= ffict[i] * vfict[i] * delta_t; // modified sign
+ }
+
+ // for replica parallel
+ if( multi_sim_comm.Get_size()>1 ) {
+ // find the minimum work among all replicas
+ double work_min = work;
+ multi_sim_comm.Min(work_min);
+
+ // weight of this replica.
+ // here, work is reduced by work_min to avoid all exp(-work/kbt)s disconverge
+ if( kbt == 0.0 ) {
+ weight = work==work_min ? 1.0 : 0.0;
+ }
+ else {
+ weight = exp(-(work-work_min)/kbt);
+ }
+
+ // normalize the weight
+ double sum_weight = weight;
+ multi_sim_comm.Sum(sum_weight);
+ weight /= sum_weight;
+
+ // weighting force of this replica
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ ffict[i] *= weight;
+ }
+
+ // mean forces of all replica.
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ multi_sim_comm.Sum(ffict[i]);
+ }
+ // now, mean force is obtained.
+ }
+} // calcMeanForce
+
+/**
+ \brief calculate kinetic energy of fictitious variables.
+ \retval kinetic energy.
+ \details This function calculates sum of kinetic energy of all fictitious variables.
+ */
+double LogMFD::calcEkin() {
+ double ekin=0.0;
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+ ekin += mfict[i]*vfict[i]*vfict[i]*0.5;
+ }
+ return ekin;
+} // calcEkin
+
+/**
+ \brief calculate free energy of fictitious variables.
+ \retval free energy.
+ \details This function calculates free energy by using invariant of canonical mechanics.
+ */
+double LogMFD::calcFlog() {
+ const double nkt = getNumberOfArguments()*kbt;
+ const double ekin = calcEkin();
+ double pot;
+
+ if( false ) {
+ }
+ else if (thermostat == "NVE") {
+ pot = hlog - ekin;
+ }
+ else if (thermostat == "NVT") {
+ const double ekin_bath = 0.5*veta*veta*meta+xeta*nkt;
+ pot = hlog - ekin - ekin_bath;
+ }
+ else if (thermostat == "VS") {
+ pot = phivs;
+ }
+ else {
+ pot = 0.0; // never occurs
+ }
+
+ return TAMD ? pot : sgn(pot)*expm1(fabs(pot)/gamma)/alpha;
+} // calcFlog
+
+/**
+ \brief calculate coefficient for flattening.
+ \retval flattering coefficient.
+ \details This function returns 1.0 for TAMD, flattening coefficient for LogMFD.
+ */
+double LogMFD::calcClog() {
+ return TAMD ? 1.0 : alpha*gamma/(alpha*fabs(flog)+1.0);
+} // calcClog
+
+} // logmfd
+} // PLMD
diff --git a/src/logmfd/Makefile b/src/logmfd/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..e69a015a6cda91f5465b64507a1ee53a2c671a18
--- /dev/null
+++ b/src/logmfd/Makefile
@@ -0,0 +1,3 @@
+USE=core tools bias
+# generic makefile
+include ../maketools/make.module
diff --git a/src/logmfd/module.type b/src/logmfd/module.type
new file mode 100644
index 0000000000000000000000000000000000000000..de832730330473a1870bd368868640da677460ae
--- /dev/null
+++ b/src/logmfd/module.type
@@ -0,0 +1 @@
+default-off
diff --git a/src/tools/Communicator.cpp b/src/tools/Communicator.cpp
index fe83076b3b05ef0f1bc036d0acfd258b2fcba4b9..bc2e047426aa391db22148fc4860e8d5cfd1d8fe 100644
--- a/src/tools/Communicator.cpp
+++ b/src/tools/Communicator.cpp
@@ -34,20 +34,12 @@ Communicator::Communicator()
{
}
-// cppcheck complains about this:
-// Member variable 'Communicator::communicator' is not initialized in the constructor
-// this is a false positive so I suppress it
-// cppcheck-suppress uninitMemberVar
Communicator::Communicator(const Communicator&pc) {
Set_comm(pc.communicator);
}
Communicator::Status Communicator::StatusIgnore;
-// cppcheck complains about this:
-// Member variable 'Communicator::communicator' is not assigned a value in 'Communicator::operator='
-// this is a false positive so I suppress it
-// cppcheck-suppress operatorEqVarError
Communicator& Communicator::operator=(const Communicator&pc) {
if (this != &pc) {
Set_comm(pc.communicator);
@@ -139,6 +131,30 @@ void Communicator::Sum(Data data) {
#endif
}
+void Communicator::Prod(Data data) {
+#if defined(__PLUMED_HAS_MPI)
+ if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_PROD,communicator);
+#else
+ (void) data;
+#endif
+}
+
+void Communicator::Max(Data data) {
+#if defined(__PLUMED_HAS_MPI)
+ if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_MAX,communicator);
+#else
+ (void) data;
+#endif
+}
+
+void Communicator::Min(Data data) {
+#if defined(__PLUMED_HAS_MPI)
+ if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_MIN,communicator);
+#else
+ (void) data;
+#endif
+}
+
Communicator::Request Communicator::Isend(ConstData data,int source,int tag) {
Request req;
#ifdef __PLUMED_HAS_MPI
diff --git a/src/tools/Communicator.h b/src/tools/Communicator.h
index 97cc60fb8c0b5bba02c8472db3915da3119ed954..eaf93054125b3265c9d8dec9f2d452698e933b07 100644
--- a/src/tools/Communicator.h
+++ b/src/tools/Communicator.h
@@ -175,6 +175,24 @@ public:
template <class T> void Sum(T*buf,int count) {Sum(Data(buf,count));}
/// Wrapper for MPI_Allreduce with MPI_SUM (reference)
template <class T> void Sum(T&buf) {Sum(Data(buf));}
+/// Wrapper for MPI_Allreduce with MPI_PROD (data struct)
+ void Prod(Data);
+/// Wrapper for MPI_Allreduce with MPI_PROD (pointer)
+ template <class T> void Prod(T*buf,int count) {Prod(Data(buf,count));}
+/// Wrapper for MPI_Allreduce with MPI_PROD (reference)
+ template <class T> void Prod(T&buf) {Prod(Data(buf));}
+/// Wrapper for MPI_Allreduce with MPI_MAX (data struct)
+ void Max(Data);
+/// Wrapper for MPI_Allreduce with MPI_MAX (pointer)
+ template <class T> void Max(T*buf,int count) {Max(Data(buf,count));}
+/// Wrapper for MPI_Allreduce with MPI_MAX (reference)
+ template <class T> void Max(T&buf) {Max(Data(buf));}
+/// Wrapper for MPI_Allreduce with MPI_MIN (data struct)
+ void Min(Data);
+/// Wrapper for MPI_Allreduce with MPI_MIN (pointer)
+ template <class T> void Min(T*buf,int count) {Min(Data(buf,count));}
+/// Wrapper for MPI_Allreduce with MPI_MIN (reference)
+ template <class T> void Min(T&buf) {Min(Data(buf));}
/// Wrapper for MPI_Bcast (data struct)
void Bcast(Data,int);
diff --git a/src/tools/HistogramBead.cpp b/src/tools/HistogramBead.cpp
index 87ede128d25d2780965a050975ff376e70d692be..2a92b58bce572d9b16b2ca61b22416e11770eda9 100644
--- a/src/tools/HistogramBead.cpp
+++ b/src/tools/HistogramBead.cpp
@@ -139,7 +139,10 @@ void HistogramBead::generateBins( const std::string& params, std::vector<std::st
void HistogramBead::set( const std::string& params, std::string& errormsg ) {
std::vector<std::string> data=Tools::getWords(params);
- if(data.size()<1) errormsg="No input has been specified";
+ if(data.size()<1) {
+ errormsg="No input has been specified";
+ return;
+ }
std::string name=data[0]; const double DP2CUTOFF=6.25;
if(name=="GAUSSIAN") { type=gaussian; cutoff=sqrt(2.0*DP2CUTOFF); }
diff --git a/src/tools/IFile.cpp b/src/tools/IFile.cpp
index a9e436a3e4e3f3f96f85c3a7d4622452cc072add..1a3fcdf38d8700dafed1c9ff56f6e953825f4c78 100644
--- a/src/tools/IFile.cpp
+++ b/src/tools/IFile.cpp
@@ -64,7 +64,8 @@ IFile& IFile::advanceField() {
bool done=false;
while(!done) {
getline(line);
- if(!*this) {return *this;}
+// using explicit conversion not to confuse cppcheck 1.86
+ if(!bool(*this)) {return *this;}
std::vector<std::string> words=Tools::getWords(line);
if(words.size()>=2 && words[0]=="#!" && words[1]=="FIELDS") {
fields.clear();
@@ -124,7 +125,8 @@ IFile& IFile::open(const std::string&path) {
IFile& IFile::scanFieldList(std::vector<std::string>&s) {
if(!inMiddleOfField) advanceField();
- if(!*this) return *this;
+// using explicit conversion not to confuse cppcheck 1.86
+ if(!bool(*this)) return *this;
s.clear();
for(unsigned i=0; i<fields.size(); i++)
s.push_back(fields[i].name);
@@ -141,7 +143,8 @@ bool IFile::FieldExist(const std::string& s) {
IFile& IFile::scanField(const std::string&name,std::string&str) {
if(!inMiddleOfField) advanceField();
- if(!*this) return *this;
+// using explicit conversion not to confuse cppcheck 1.86
+ if(!bool(*this)) return *this;
unsigned i=findField(name);
str=fields[i].value;
fields[i].read=true;
diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp
index b76e3c2d486cf1c346bb5eb6ef9836948801c51f..f9bad7065d5fe061024c4792b4861fbc3a6f5165 100644
--- a/src/tools/SwitchingFunction.cpp
+++ b/src/tools/SwitchingFunction.cpp
@@ -184,7 +184,10 @@ void SwitchingFunction::registerKeywords( Keywords& keys ) {
void SwitchingFunction::set(const std::string & definition,std::string& errormsg) {
vector<string> data=Tools::getWords(definition);
- if( data.size()<1 ) errormsg="missing all input for switching function";
+ if( data.size()<1 ) {
+ errormsg="missing all input for switching function";
+ return;
+ }
string name=data[0];
data.erase(data.begin());
invr0=0.0;
diff --git a/src/ves/FermiSwitchingFunction.cpp b/src/ves/FermiSwitchingFunction.cpp
index a53ab6f6a3f444ab6a2886dd1a761c00ccab97a0..f0695c4e801f206936cfe3f7a5a4457afc1432d9 100644
--- a/src/ves/FermiSwitchingFunction.cpp
+++ b/src/ves/FermiSwitchingFunction.cpp
@@ -41,7 +41,10 @@ void FermiSwitchingFunction::registerKeywords( Keywords& keys ) {
void FermiSwitchingFunction::set(const std::string& definition,std::string& errormsg) {
std::vector<std::string> data=Tools::getWords(definition);
- if( data.size()<1 ) errormsg="missing all input for switching function";
+ if( data.size()<1 ) {
+ errormsg="missing all input for switching function";
+ return;
+ }
std::string name=data[0];
data.erase(data.begin());
if(name!="FERMI") {errormsg="only FERMI is supported";}
diff --git a/src/ves/MD_LinearExpansionPES.cpp b/src/ves/MD_LinearExpansionPES.cpp
index 153bc0d5be6b5fadcca8b5384ca44c28bc8cb56e..233c2b69f80254f18aef88e6ffe0d3b7a87bb8b8 100644
--- a/src/ves/MD_LinearExpansionPES.cpp
+++ b/src/ves/MD_LinearExpansionPES.cpp
@@ -237,8 +237,8 @@ int MD_LinearExpansionPES::main( FILE* in, FILE* out, PLMD::Communicator& pc) {
parse("nstep",nsteps);
double tstep;
parse("tstep",tstep);
- //
- double temp;
+ // initialize to solve a cppcheck 1.86 warning
+ double temp=0.0;
std::vector<double> temps_vec(0);
parseVector("temperature",temps_vec);
if(temps_vec.size()==1) {
diff --git a/user-doc/LOGMFDMOD.md b/user-doc/LOGMFDMOD.md
new file mode 100644
index 0000000000000000000000000000000000000000..f7f460163fe55d1d7c322093001a1566d7221bec
--- /dev/null
+++ b/user-doc/LOGMFDMOD.md
@@ -0,0 +1,26 @@
+\page LOGMFDMOD xxxxxxxx
+
+<!--
+description: xxxxxxxxx
+authors: xxxxxxxxx
+reference: xxxxxxxxxx
+-->
+
+## Overview
+
+xxxxxxxxx
+
+## Installation
+This module is not installed by default. Add '\-\-enable-modules=logmfd' to your './configure' command when building PLUMED to enable these features.
+
+## Usage
+Currently, all features of the LOGMFD module are included in a single LOGMFD bias function: \ref LOGMFD
+
+## Module Contents
+- \subpage LOGMFDMODBias
+
+\page LOGMFDMODBias Biases Documentation
+
+The following list contains descriptions of biases developed for the PLUMED-LOGMFD module. They can be used in combination with other biases outside of the LOGMFD module.
+
+@LOGMFDMOD_BIAS@
diff --git a/user-doc/Miscelaneous.md b/user-doc/Miscelaneous.md
index 80684c75724e4ca58b4c094051e47f1caf06d1d1..d53c840e2f675a81e2c1fd554f2bffd73e9758a2 100644
--- a/user-doc/Miscelaneous.md
+++ b/user-doc/Miscelaneous.md
@@ -144,14 +144,14 @@ autocompletion should be installed. Otherwise, configure will look for the prese
and, in case it is installed on the same prefix as PLUMED, also PLUMED autocompletion will be installed.
Finally, if none of these two conditions are satisfied, autocompletion will not be enabled. You will
have to change your bashrc file once adding the following lines:
-Now look at these lines:
\verbatim
_plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";}
complete -F _plumed -o default plumed
\endverbatim
-This is what you are expected to do if for instance you have multiple versions of PLUMED installed
-concurrently using separate env modules.
-The command `plumed completion` just writes on its standard output the body of a bash function.
+The command `plumed completion` just writes on its standard output the body of a bash function that is
+then used by bash to construct the autocompletion.
+The `--no-mpi` flag makes it more likely that the command can be executed correctly e.g. when you are on the login node of a cluster and
+PLUMED was compiled with MPI but the login node does not support MPI. In other cases, it is harmless.
The `-o default` options will make sure that if `plumed --no-mpi completion` returns an error the default bash completion
will be used. This is what will happen if you load an older PLUMED version for which the `completion` command is not available yet.
In future PLUMED versions the `plumed completion` command might return more sophisticated functions. You should
diff --git a/user-doc/Performances.md b/user-doc/Performances.md
index a963d9c626edc32593b780977f811d1d7d62c82e..b4dad4c1c01ee5f51fa3a2c62fd2d76ecde773b0 100644
--- a/user-doc/Performances.md
+++ b/user-doc/Performances.md
@@ -230,8 +230,8 @@ At last, try to reduce the number of residues in the calculation.
In case you are using a lot of \ref CUSTOM functions or \ref switchingfunction "switching functions",
notice that these functionalities depend on the lepton library included in PLUMED.
-This library replace libmatheval since PLUMED 2.5, and by itself it is significantly faster than libmatheval.
-However, you can make it even faster using a [just-in-time compilater](https://github.com/asmjit/asmjit.git).
+This library replaces libmatheval since PLUMED 2.5, and by itself it is significantly faster than libmatheval.
+However, you can make it even faster using a [just-in-time compiler](https://github.com/asmjit/asmjit.git).
Currently, this is an experimental feature, so use it with care.
In order to enable it you should first install asmjit.
@@ -285,7 +285,10 @@ PLUMED: 4A 2 dfast 108 0.135210 0.
...
\endverbatim
-Notice the usage of `x2` as a variable for the switching function (see \ref switchingfunction).
+Notice the usage of `x2` as a variable for the switching function (see \ref switchingfunction), which
+avoids an unnecessary square root calculation (this is done automatically by the hard-coded switching functions
+when you use only even powers). The asmjit calculation (`dfast`) takes less than 10% more than the hard-coded
+one (`c`).
\page Time Time your Input
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 16689de15f47bc218c37c7f4263478cf0bff2121..c9465b58b091362e0ed6c4c9009280734f1bf2f8 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -2819,5 +2819,34 @@ year = {2017},
doi = {10.1021/acs.jctc.6b00691}
}
+@article{MorishitaLogMFD,
+author = {Morishita, T. and Itoh, S. G. and Okumura, H. and Mikami, M.},
+title = {Free-energy calculation via mean-force dynamics using a logarithmic energy landscape},
+journal = {Physical Review E},
+volume = {85},
+pages = {066702},
+year = {2012},
+doi = {10.1103/PhysRevE.85.066702}
+}
+
+@article{MorishitaLogPD,
+author = {Morishita, T. and Yonezawa, Y and Ito, A. M.},
+title = {Free energy reconstruction from logarithmic mean-force dynamics using multiple nonequilibrium trajectories},
+journal = {Journal of Chemical Theory and Computation},
+volume = {13},
+pages = {3106},
+year = {2017},
+doi = {10.1021/acs.jctc.7b00252}
+}
+
+@article{MorishitaVsLogMFD,
+author = {Morishita, T. and Nakamura, T and Shinoda, W and Ito, A. M.},
+title = {Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction},
+journal = {Chemical Physics Letter},
+volume = {706},
+pages = {633},
+year = {2018}
+}
+
@Comment{jabref-meta: databaseType:bibtex;}
diff --git a/user-doc/extract b/user-doc/extract
index e2a74f5dd1611948ba6b22972708bf0da118f8a5..cd92173fd2aacc983a2ce71c2733677e47a47a29 100755
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -48,7 +48,7 @@ EOF
cat << EOF
-\note This command line tool is implemented as a shell script. It's help message is pasted below:
+\note This command line tool is implemented as a shell script. Its help message is pasted below:
\verbatim
EOF