diff --git a/CHANGES/v2.2.txt b/CHANGES/v2.2.txt
index 8133601a2377a433d174762313cd8322591a8cb9..b8ff918f5893ae1fc39708ee6ad31ea994a71cac 100644
--- a/CHANGES/v2.2.txt
+++ b/CHANGES/v2.2.txt
@@ -116,6 +116,8 @@ For users:
asks for too many atoms, see \issue{185}.
- Optimisations (activation of the dependencies, secondary structures, DRMSD)
- Fixed a performance regression with RMSD=OPTIMAL-FAST
+- Fixed a bug in the normalization of kernel functions (relevant for \ref HISTOGRAM).
+- Updated patch for gromacs 5.1
For developers:
- Fixed a bug in the interpretation of cmd strings. Namely, an erroneous string was not triggering an error.
diff --git a/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt
index 3ff4b77ec68178f49e84e6b9a60dea750d784c94..2af9fdf862dea3a884a4aaf07865bb85b43cc9ba 100644
--- a/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt
+++ b/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt
@@ -73,7 +73,7 @@ if(GMX_USE_TNG)
"TNG >= 1.6.0 not found. "
"You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
endif()
- include_directories(${TNG_IO_INCLUDE_DIRS})
+ include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
endif()
if(NOT GMX_EXTERNAL_TNG)
include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
@@ -83,7 +83,7 @@ if(GMX_USE_TNG)
if (HAVE_ZLIB)
list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(${ZLIB_INCLUDE_DIRS})
+ include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
endif()
endif()
else()
@@ -199,13 +199,17 @@ else()
endif()
set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
+target_link_libraries(libgromacs ${PLUMED_LOAD})
+
target_link_libraries(libgromacs
${EXTRAE_LIBRARIES}
${GMX_EXTRA_LIBRARIES}
${TNG_IO_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
${XML_LIBRARIES}
- ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES} ${PLUMED_LOAD})
+ ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES})
+
+
set_target_properties(libgromacs PROPERTIES
OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
SOVERSION ${LIBRARY_SOVERSION_MAJOR}
diff --git a/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt.preplumed
index 26d7111383d96c659540fb93926fc9026e74ec4f..467b0be4c1abb18c0a53a96ed052353a608d4a0f 100644
--- a/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt.preplumed
+++ b/patches/gromacs-5.1.2.diff/src/gromacs/CMakeLists.txt.preplumed
@@ -71,7 +71,7 @@ if(GMX_USE_TNG)
"TNG >= 1.6.0 not found. "
"You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
endif()
- include_directories(${TNG_IO_INCLUDE_DIRS})
+ include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
endif()
if(NOT GMX_EXTERNAL_TNG)
include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
@@ -81,7 +81,7 @@ if(GMX_USE_TNG)
if (HAVE_ZLIB)
list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(${ZLIB_INCLUDE_DIRS})
+ include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
endif()
endif()
else()
diff --git a/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp
index 4c552329584542397e34e6645e136882d4925374..dade566c5e3836dc572000709101488bf1cc4ffa 100644
--- a/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp
@@ -3,7 +3,7 @@
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
@@ -184,7 +184,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_int64_t step, step_rel;
double elapsed_time;
double t, t0, lam0[efptNR];
- gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+ gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
bBornRadii, bStartingFromCpt;
@@ -354,11 +354,6 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
}
- if (bRerunMD && fr->cutoff_scheme == ecutsVERLET && ir->opts.ngener > 1 && usingGpu(fr->nbv))
- {
- gmx_fatal(FARGS, "The Verlet scheme on GPUs does not support energy groups, so your rerun should probably use a .tpr file without energy groups, or mdrun -nb auto");
- }
-
if (DEFORM(*ir))
{
tMPI_Thread_mutex_lock(&deform_init_box_mutex);
@@ -551,6 +546,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
gmx_fatal(FARGS, "nstexpanded should be divisible by nstcalclr");
}
+ nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
}
if (repl_ex_nst > 0)
{
@@ -976,7 +972,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bBornRadii = TRUE;
}
- do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+ /* do_log triggers energy and virial calculation. Because this leads
+ * to different code paths, forces can be different. Thus for exact
+ * continuation we should avoid extra log output.
+ * Note that the || bLastStep can result in non-exact continuation
+ * beyond the last step. But we don't consider that to be an issue.
+ */
+ do_log = do_per_step(step, ir->nstlog) || (bFirstStep && !bStateFromCP) || bLastStep;
do_verbose = bVerbose &&
(step % stepout == 0 || bFirstStep || bLastStep);
@@ -1147,21 +1149,18 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
but the virial needs to be calculated on both the current step and the 'next' step. Future
reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
- bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
- bCalcVir = bCalcEner ||
+ /* TODO: This is probably not what we want, we will write to energy file one step after nstcalcenergy steps. */
+ bCalcEnerStep = do_per_step(step - 1, ir->nstcalcenergy);
+ bCalcVir = bCalcEnerStep ||
(ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
}
else
{
- bCalcEner = do_per_step(step, ir->nstcalcenergy);
- bCalcVir = bCalcEner ||
+ bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
+ bCalcVir = bCalcEnerStep ||
(ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
}
-
- /* Do we need global communication ? */
- bGStat = (bCalcVir || bCalcEner || bStopCM ||
- do_per_step(step, nstglobalcomm) ||
- (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)));
+ bCalcEner = bCalcEnerStep;
do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
@@ -1169,9 +1168,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
bCalcVir = TRUE;
bCalcEner = TRUE;
- bGStat = TRUE;
}
+ /* Do we need global communication ? */
+ bGStat = (bCalcVir || bCalcEner || bStopCM ||
+ do_per_step(step, nstglobalcomm) ||
+ (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)));
+
/* these CGLO_ options remain the same throughout the iteration */
cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
(bGStat ? CGLO_GSTAT : 0)
@@ -1353,6 +1356,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
| (bTemp ? CGLO_TEMPERATURE : 0)
| (bPres ? CGLO_PRESSURE : 0)
| (bPres ? CGLO_CONSTRAINT : 0)
+ | (bStopCM ? CGLO_STOPCM : 0)
| CGLO_SCALEEKIN
);
/* explanation of above:
@@ -1455,8 +1459,8 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Check if IMD step and do IMD communication, if bIMD is TRUE. */
bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
- /* kludge -- virial is lost with restart for NPT control. Must restart */
- if (bStartingFromCpt && bVV)
+ /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
+ if (bStartingFromCpt && bTrotter)
{
copy_mat(state->svir_prev, shake_vir);
copy_mat(state->fvir_prev, force_vir);
@@ -1531,26 +1535,21 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gs.sig[eglsCHKPT] = 1;
}
- /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
- if (EI_VV(ir->eI))
+ /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen controlled
+ in preprocessing */
+
+ if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
{
- if (!bInitStep)
- {
- update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
- }
- if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+ gmx_bool bIfRandomize;
+ bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
+ /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
+ if (constr && bIfRandomize)
{
- gmx_bool bIfRandomize;
- bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
- /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
- if (constr && bIfRandomize)
- {
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
- }
+ update_constraints(fplog, step, NULL, ir, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir,
+ cr, nrnb, wcycle, upd, constr,
+ TRUE, bCalcVir);
}
}
/* ######### START SECOND UPDATE STEP ################# */
@@ -1780,36 +1779,32 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Output stuff */
if (MASTER(cr))
{
- gmx_bool do_dr, do_or;
-
if (fplog && do_log && bDoExpanded)
{
/* only needed if doing expanded ensemble */
PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
&state_global->dfhist, state->fep_state, ir->nstlog, step);
}
- if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+ if (bCalcEner)
{
- if (bCalcEner)
- {
- upd_mdebin(mdebin, bDoDHDL, TRUE,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, lastbox,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot, constr);
- }
- else
- {
- upd_mdebin_step(mdebin);
- }
+ upd_mdebin(mdebin, bDoDHDL, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+ }
+ else
+ {
+ upd_mdebin_step(mdebin);
+ }
- do_dr = do_per_step(step, ir->nstdisreout);
- do_or = do_per_step(step, ir->nstorireout);
+ gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
+ gmx_bool do_or = do_per_step(step, ir->nstorireout);
+
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ step, t,
+ eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
- step, t,
- eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
- }
if (ir->bPull)
{
pull_print_output(ir->pull_work, step, t);
@@ -1947,7 +1942,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* until after load balancing completes,
* e.g. https://gerrit.gromacs.org/#/c/4964/2 */
gmx_fatal(FARGS, "PME tuning was still active when attempting to "
- "reset mdrun counters at step " GMX_PRId64 ". Try "
+ "reset mdrun counters at step %" GMX_PRId64 ". Try "
"resetting counters later in the run, e.g. with gmx "
"mdrun -resetstep.", step);
}
diff --git a/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed
index 4f33d897e950a2793d76d963e8451ed0d6c8dd96..ce25ac7e90d312d3671b4f1ccd495775caeee445 100644
--- a/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed
+++ b/patches/gromacs-5.1.2.diff/src/programs/mdrun/md.cpp.preplumed
@@ -3,7 +3,7 @@
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
@@ -174,7 +174,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_int64_t step, step_rel;
double elapsed_time;
double t, t0, lam0[efptNR];
- gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+ gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
bBornRadii, bStartingFromCpt;
@@ -338,11 +338,6 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
}
- if (bRerunMD && fr->cutoff_scheme == ecutsVERLET && ir->opts.ngener > 1 && usingGpu(fr->nbv))
- {
- gmx_fatal(FARGS, "The Verlet scheme on GPUs does not support energy groups, so your rerun should probably use a .tpr file without energy groups, or mdrun -nb auto");
- }
-
if (DEFORM(*ir))
{
tMPI_Thread_mutex_lock(&deform_init_box_mutex);
@@ -535,6 +530,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
gmx_fatal(FARGS, "nstexpanded should be divisible by nstcalclr");
}
+ nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
}
if (repl_ex_nst > 0)
{
@@ -914,7 +910,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
bBornRadii = TRUE;
}
- do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+ /* do_log triggers energy and virial calculation. Because this leads
+ * to different code paths, forces can be different. Thus for exact
+ * continuation we should avoid extra log output.
+ * Note that the || bLastStep can result in non-exact continuation
+ * beyond the last step. But we don't consider that to be an issue.
+ */
+ do_log = do_per_step(step, ir->nstlog) || (bFirstStep && !bStateFromCP) || bLastStep;
do_verbose = bVerbose &&
(step % stepout == 0 || bFirstStep || bLastStep);
@@ -1001,21 +1003,18 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
but the virial needs to be calculated on both the current step and the 'next' step. Future
reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
- bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
- bCalcVir = bCalcEner ||
+ /* TODO: This is probably not what we want, we will write to energy file one step after nstcalcenergy steps. */
+ bCalcEnerStep = do_per_step(step - 1, ir->nstcalcenergy);
+ bCalcVir = bCalcEnerStep ||
(ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
}
else
{
- bCalcEner = do_per_step(step, ir->nstcalcenergy);
- bCalcVir = bCalcEner ||
+ bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
+ bCalcVir = bCalcEnerStep ||
(ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
}
-
- /* Do we need global communication ? */
- bGStat = (bCalcVir || bCalcEner || bStopCM ||
- do_per_step(step, nstglobalcomm) ||
- (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)));
+ bCalcEner = bCalcEnerStep;
do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
@@ -1023,9 +1022,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
{
bCalcVir = TRUE;
bCalcEner = TRUE;
- bGStat = TRUE;
}
+ /* Do we need global communication ? */
+ bGStat = (bCalcVir || bCalcEner || bStopCM ||
+ do_per_step(step, nstglobalcomm) ||
+ (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)));
+
/* these CGLO_ options remain the same throughout the iteration */
cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
(bGStat ? CGLO_GSTAT : 0)
@@ -1172,6 +1175,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
| (bTemp ? CGLO_TEMPERATURE : 0)
| (bPres ? CGLO_PRESSURE : 0)
| (bPres ? CGLO_CONSTRAINT : 0)
+ | (bStopCM ? CGLO_STOPCM : 0)
| CGLO_SCALEEKIN
);
/* explanation of above:
@@ -1274,8 +1278,8 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Check if IMD step and do IMD communication, if bIMD is TRUE. */
bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
- /* kludge -- virial is lost with restart for NPT control. Must restart */
- if (bStartingFromCpt && bVV)
+ /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
+ if (bStartingFromCpt && bTrotter)
{
copy_mat(state->svir_prev, shake_vir);
copy_mat(state->fvir_prev, force_vir);
@@ -1350,26 +1354,21 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
gs.sig[eglsCHKPT] = 1;
}
- /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
- if (EI_VV(ir->eI))
+ /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen controlled
+ in preprocessing */
+
+ if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
{
- if (!bInitStep)
- {
- update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
- }
- if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+ gmx_bool bIfRandomize;
+ bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
+ /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
+ if (constr && bIfRandomize)
{
- gmx_bool bIfRandomize;
- bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
- /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
- if (constr && bIfRandomize)
- {
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
- }
+ update_constraints(fplog, step, NULL, ir, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir,
+ cr, nrnb, wcycle, upd, constr,
+ TRUE, bCalcVir);
}
}
/* ######### START SECOND UPDATE STEP ################# */
@@ -1599,36 +1598,32 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* Output stuff */
if (MASTER(cr))
{
- gmx_bool do_dr, do_or;
-
if (fplog && do_log && bDoExpanded)
{
/* only needed if doing expanded ensemble */
PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
&state_global->dfhist, state->fep_state, ir->nstlog, step);
}
- if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+ if (bCalcEner)
{
- if (bCalcEner)
- {
- upd_mdebin(mdebin, bDoDHDL, TRUE,
- t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, lastbox,
- shake_vir, force_vir, total_vir, pres,
- ekind, mu_tot, constr);
- }
- else
- {
- upd_mdebin_step(mdebin);
- }
+ upd_mdebin(mdebin, bDoDHDL, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+ }
+ else
+ {
+ upd_mdebin_step(mdebin);
+ }
- do_dr = do_per_step(step, ir->nstdisreout);
- do_or = do_per_step(step, ir->nstorireout);
+ gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
+ gmx_bool do_or = do_per_step(step, ir->nstorireout);
+
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ step, t,
+ eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
- step, t,
- eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
- }
if (ir->bPull)
{
pull_print_output(ir->pull_work, step, t);
@@ -1766,7 +1761,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
* until after load balancing completes,
* e.g. https://gerrit.gromacs.org/#/c/4964/2 */
gmx_fatal(FARGS, "PME tuning was still active when attempting to "
- "reset mdrun counters at step " GMX_PRId64 ". Try "
+ "reset mdrun counters at step %" GMX_PRId64 ". Try "
"resetting counters later in the run, e.g. with gmx "
"mdrun -resetstep.", step);
}