From f1d63ad36e03dc74a4e7c0ecb9191b59080c212a Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Wed, 22 Jun 2016 09:46:29 +0200
Subject: [PATCH] GMX2016 patch updated
---
...beta1.config => gromacs-2016-beta2.config} | 0
.../src/gromacs/CMakeLists.txt | 32 ++---------
.../src/gromacs/CMakeLists.txt.preplumed | 32 ++---------
.../src/gromacs/mdlib/force.cpp | 0
.../src/gromacs/mdlib/force.cpp.preplumed | 0
.../src/gromacs/mdlib/minimize.cpp | 54 +++++++++++++------
.../src/gromacs/mdlib/minimize.cpp.preplumed | 54 +++++++++++++------
.../src/programs/mdrun/md.cpp | 4 ++
.../src/programs/mdrun/md.cpp.preplumed | 0
.../src/programs/mdrun/mdrun.cpp | 11 ++--
.../src/programs/mdrun/mdrun.cpp.preplumed | 11 ++--
.../src/programs/mdrun/repl_ex.cpp | 17 ++++--
.../src/programs/mdrun/repl_ex.cpp.preplumed | 17 ++++--
.../src/programs/mdrun/runner.cpp | 5 +-
.../src/programs/mdrun/runner.cpp.preplumed | 5 +-
15 files changed, 134 insertions(+), 108 deletions(-)
rename patches/{gromacs-2016-beta1.config => gromacs-2016-beta2.config} (100%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/gromacs/CMakeLists.txt (88%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/gromacs/CMakeLists.txt.preplumed (88%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/gromacs/mdlib/force.cpp (100%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/gromacs/mdlib/force.cpp.preplumed (100%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/gromacs/mdlib/minimize.cpp (98%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/gromacs/mdlib/minimize.cpp.preplumed (98%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/md.cpp (99%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/md.cpp.preplumed (100%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/mdrun.cpp (98%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/mdrun.cpp.preplumed (98%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/repl_ex.cpp (98%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/repl_ex.cpp.preplumed (98%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/runner.cpp (99%)
rename patches/{gromacs-2016-beta1.diff => gromacs-2016-beta2.diff}/src/programs/mdrun/runner.cpp.preplumed (99%)
diff --git a/patches/gromacs-2016-beta1.config b/patches/gromacs-2016-beta2.config
similarity index 100%
rename from patches/gromacs-2016-beta1.config
rename to patches/gromacs-2016-beta2.config
diff --git a/patches/gromacs-2016-beta1.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt
similarity index 88%
rename from patches/gromacs-2016-beta1.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt
index 2f8a59296..a9f3b4fd3 100644
--- a/patches/gromacs-2016-beta1.diff/src/gromacs/CMakeLists.txt
+++ b/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt
@@ -71,35 +71,6 @@ function (gmx_write_installed_header_list)
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
endfunction()
-if(GMX_USE_TNG)
- option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
- OFF)
- # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
- if(GMX_EXTERNAL_TNG)
- find_package(TNG_IO 1.6.0)
- if(NOT TNG_IO_FOUND)
- message(FATAL_ERROR
- "TNG >= 1.6.0 not found. "
- "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
- endif()
- include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
- endif()
- if(NOT GMX_EXTERNAL_TNG)
- include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
- tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
- list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
- tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
-
- if (HAVE_ZLIB)
- list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
- endif()
- endif()
-else()
- # We still need to get tng/tng_io_fwd.h from somewhere!
- include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
-endif()
-
add_subdirectory(gmxlib)
add_subdirectory(mdlib)
add_subdirectory(listed-forces)
@@ -152,6 +123,9 @@ list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOU
tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
+list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
+tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+
configure_file(version.h.cmakein version.h)
gmx_install_headers(
analysisdata.h
diff --git a/patches/gromacs-2016-beta1.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 88%
rename from patches/gromacs-2016-beta1.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt.preplumed
index edc051fe8..ab9d64df4 100644
--- a/patches/gromacs-2016-beta1.diff/src/gromacs/CMakeLists.txt.preplumed
+++ b/patches/gromacs-2016-beta2.diff/src/gromacs/CMakeLists.txt.preplumed
@@ -69,35 +69,6 @@ function (gmx_write_installed_header_list)
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
endfunction()
-if(GMX_USE_TNG)
- option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
- OFF)
- # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
- if(GMX_EXTERNAL_TNG)
- find_package(TNG_IO 1.6.0)
- if(NOT TNG_IO_FOUND)
- message(FATAL_ERROR
- "TNG >= 1.6.0 not found. "
- "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
- endif()
- include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
- endif()
- if(NOT GMX_EXTERNAL_TNG)
- include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
- tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
- list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
- tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
-
- if (HAVE_ZLIB)
- list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
- endif()
- endif()
-else()
- # We still need to get tng/tng_io_fwd.h from somewhere!
- include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
-endif()
-
add_subdirectory(gmxlib)
add_subdirectory(mdlib)
add_subdirectory(listed-forces)
@@ -150,6 +121,9 @@ list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOU
tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
+list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
+tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+
configure_file(version.h.cmakein version.h)
gmx_install_headers(
analysisdata.h
diff --git a/patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp
similarity index 98%
rename from patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp
index 3ce783281..b60b80991 100644
--- a/patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/minimize.cpp
+++ b/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp
@@ -614,8 +614,10 @@ static void write_em_traj(FILE *fplog, t_commrec *cr,
}
}
-//! Do one minimization step
-static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
+//! \brief Do one minimization step
+//
+// \returns true when the step succeeded, false when a constraint error occurred
+static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
gmx_bool bMolPBC,
em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
gmx_constr_t constr, gmx_localtop_t *top,
@@ -630,6 +632,8 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
real dvdl_constr;
int nthreads gmx_unused;
+ bool validStep = true;
+
s1 = &ems1->s;
s2 = &ems2->s;
@@ -744,13 +748,23 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
{
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
- constrain(NULL, TRUE, TRUE, constr, &top->idef,
- ir, cr, count, 0, 1.0, md,
- s1->x, s2->x, NULL, bMolPBC, s2->box,
- s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
+ validStep =
+ constrain(NULL, TRUE, TRUE, constr, &top->idef,
+ ir, cr, count, 0, 1.0, md,
+ s1->x, s2->x, NULL, bMolPBC, s2->box,
+ s2->lambda[efptBONDED], &dvdl_constr,
+ NULL, NULL, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
+
+ // We should move this check to the different minimizers
+ if (!validStep && ir->eI != eiSteep)
+ {
+ gmx_fatal(FARGS, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
+ EI(ir->eI), EI(eiSteep), EI(ir->eI));
+ }
}
+
+ return validStep;
}
//! Prepare EM for using domain decomposition parallellization
@@ -2635,18 +2649,28 @@ double do_steep(FILE *fplog, t_commrec *cr,
bAbort = (nsteps >= 0) && (count == nsteps);
/* set new coordinates, except for first step */
+ bool validStep = true;
if (count > 0)
{
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
- s_min, stepsize, s_min->f, s_try,
- constr, top, nrnb, wcycle, count);
+ validStep =
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
+ s_min, stepsize, s_min->f, s_try,
+ constr, top, nrnb, wcycle, count);
}
- evaluate_energy(fplog, cr,
- top_global, s_try, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, count, count == 0);
+ if (validStep)
+ {
+ evaluate_energy(fplog, cr,
+ top_global, s_try, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, count, count == 0);
+ }
+ else
+ {
+ // Signal constraint error during stepping with energy=inf
+ s_try->epot = std::numeric_limits<real>::infinity();
+ }
if (MASTER(cr))
{
diff --git a/patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 98%
rename from patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
index 5a2056940..55200ce0a 100644
--- a/patches/gromacs-2016-beta1.diff/src/gromacs/mdlib/minimize.cpp.preplumed
+++ b/patches/gromacs-2016-beta2.diff/src/gromacs/mdlib/minimize.cpp.preplumed
@@ -570,8 +570,10 @@ static void write_em_traj(FILE *fplog, t_commrec *cr,
}
}
-//! Do one minimization step
-static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
+//! \brief Do one minimization step
+//
+// \returns true when the step succeeded, false when a constraint error occurred
+static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
gmx_bool bMolPBC,
em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
gmx_constr_t constr, gmx_localtop_t *top,
@@ -586,6 +588,8 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
real dvdl_constr;
int nthreads gmx_unused;
+ bool validStep = true;
+
s1 = &ems1->s;
s2 = &ems2->s;
@@ -700,13 +704,23 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
{
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
- constrain(NULL, TRUE, TRUE, constr, &top->idef,
- ir, cr, count, 0, 1.0, md,
- s1->x, s2->x, NULL, bMolPBC, s2->box,
- s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
+ validStep =
+ constrain(NULL, TRUE, TRUE, constr, &top->idef,
+ ir, cr, count, 0, 1.0, md,
+ s1->x, s2->x, NULL, bMolPBC, s2->box,
+ s2->lambda[efptBONDED], &dvdl_constr,
+ NULL, NULL, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
+
+ // We should move this check to the different minimizers
+ if (!validStep && ir->eI != eiSteep)
+ {
+ gmx_fatal(FARGS, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
+ EI(ir->eI), EI(eiSteep), EI(ir->eI));
+ }
}
+
+ return validStep;
}
//! Prepare EM for using domain decomposition parallellization
@@ -2561,18 +2575,28 @@ double do_steep(FILE *fplog, t_commrec *cr,
bAbort = (nsteps >= 0) && (count == nsteps);
/* set new coordinates, except for first step */
+ bool validStep = true;
if (count > 0)
{
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
- s_min, stepsize, s_min->f, s_try,
- constr, top, nrnb, wcycle, count);
+ validStep =
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
+ s_min, stepsize, s_min->f, s_try,
+ constr, top, nrnb, wcycle, count);
}
- evaluate_energy(fplog, cr,
- top_global, s_try, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, count, count == 0);
+ if (validStep)
+ {
+ evaluate_energy(fplog, cr,
+ top_global, s_try, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, count, count == 0);
+ }
+ else
+ {
+ // Signal constraint error during stepping with energy=inf
+ s_try->epot = std::numeric_limits<real>::infinity();
+ }
if (MASTER(cr))
{
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp
similarity index 99%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp
index 2bd872565..19cea9f69 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp
@@ -1165,6 +1165,8 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* PLUMED */
plumedNeedsEnergy=0;
if(plumedswitch){
+ int pversion=0;
+ plumed_cmd(plumedmain,"getApiVersion",&pversion);
long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
plumed_cmd(plumedmain,"setPositions",&state->x[0][0]);
plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[0]);
@@ -1172,6 +1174,8 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
plumed_cmd(plumedmain,"prepareCalc",NULL);
plumed_cmd(plumedmain,"setStopFlag",&plumedWantsToStop);
+ int checkp=0; if(bCPT) checkp=1;
+ if(pversion>3) plumed_cmd(plumedmain,"doCheckPoint",&checkp);
plumed_cmd(plumedmain,"setForces",&f[0][0]);
plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
clear_mat(plumed_vir);
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/md.cpp.preplumed
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp
similarity index 98%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp
index 55f3529fa..3efc27c46 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/mdrun.cpp
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp
@@ -141,10 +141,11 @@ int gmx_mdrun(int argc, char *argv[])
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
- "For each different tabulated interaction type the table file name is",
- "modified in a different way: before the file extension an underscore is",
- "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
- "and finally the table number of the interaction type.[PAR]",
+ "For each different tabulated interaction type used, a table file name must",
+ "be given. For the topology to work, a file name given here must match a",
+ "character sequence before the file extension. That sequence is: an underscore,",
+ "then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
+ "and finally the matching table number index used in the topology.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [REF].mdp[ref] file.[PAR]",
@@ -246,7 +247,7 @@ int gmx_mdrun(int argc, char *argv[])
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRDMULT },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 98%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp.preplumed
index 9458dfbf9..e56c4a145 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/mdrun.cpp.preplumed
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/mdrun.cpp.preplumed
@@ -134,10 +134,11 @@ int gmx_mdrun(int argc, char *argv[])
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
- "For each different tabulated interaction type the table file name is",
- "modified in a different way: before the file extension an underscore is",
- "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
- "and finally the table number of the interaction type.[PAR]",
+ "For each different tabulated interaction type used, a table file name must",
+ "be given. For the topology to work, a file name given here must match a",
+ "character sequence before the file extension. That sequence is: an underscore,",
+ "then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
+ "and finally the matching table number index used in the topology.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [REF].mdp[ref] file.[PAR]",
@@ -239,7 +240,7 @@ int gmx_mdrun(int argc, char *argv[])
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRDMULT },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp
similarity index 98%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp
index 2b870b96d..70d9f30b8 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/repl_ex.cpp
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp
@@ -976,6 +976,8 @@ test_for_replica_exchange(FILE *fplog,
pind[i] = re->ind[i];
}
+ rng.restart( step, 0 );
+
/* PLUMED */
int plumed_test_exchange_pattern=0;
/* END PLUMED */
@@ -985,10 +987,13 @@ test_for_replica_exchange(FILE *fplog,
/* multiple random switch exchange */
int nself = 0;
- rng.restart( step, 0 );
for (i = 0; i < re->nex + nself; i++)
{
+ // For now this is superfluous, but just in case we ever add more
+ // calls in different branches it is safer to always reset the distribution.
+ uniformNreplDist.reset();
+
/* randomly select a pair */
/* in theory, could reduce this by identifying only which switches had a nonneglibible
probability of occurring (log p > -100) and only operate on those switches */
@@ -1033,7 +1038,10 @@ test_for_replica_exchange(FILE *fplog,
{
prob[0] = exp(-delta);
}
- /* roll a number to determine if accepted */
+ // roll a number to determine if accepted. For now it is superfluous to
+ // reset, but just in case we ever add more calls in different branches
+ // it is safer to always reset the distribution.
+ uniformRealDist.reset();
bEx[0] = uniformRealDist(rng) < prob[0];
}
re->prob_sum[0] += prob[0];
@@ -1116,7 +1124,10 @@ test_for_replica_exchange(FILE *fplog,
{
prob[i] = exp(-delta);
}
- /* roll a number to determine if accepted */
+ // roll a number to determine if accepted. For now it is superfluous to
+ // reset, but just in case we ever add more calls in different branches
+ // it is safer to always reset the distribution.
+ uniformRealDist.reset();
bEx[i] = uniformRealDist(rng) < prob[i];
}
re->prob_sum[i] += prob[i];
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 98%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp.preplumed
index ab12fc4f1..a3d89573f 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/repl_ex.cpp.preplumed
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/repl_ex.cpp.preplumed
@@ -961,15 +961,20 @@ test_for_replica_exchange(FILE *fplog,
pind[i] = re->ind[i];
}
+ rng.restart( step, 0 );
+
if (bMultiEx)
{
/* multiple random switch exchange */
int nself = 0;
- rng.restart( step, 0 );
for (i = 0; i < re->nex + nself; i++)
{
+ // For now this is superfluous, but just in case we ever add more
+ // calls in different branches it is safer to always reset the distribution.
+ uniformNreplDist.reset();
+
/* randomly select a pair */
/* in theory, could reduce this by identifying only which switches had a nonneglibible
probability of occurring (log p > -100) and only operate on those switches */
@@ -1014,7 +1019,10 @@ test_for_replica_exchange(FILE *fplog,
{
prob[0] = exp(-delta);
}
- /* roll a number to determine if accepted */
+ // roll a number to determine if accepted. For now it is superfluous to
+ // reset, but just in case we ever add more calls in different branches
+ // it is safer to always reset the distribution.
+ uniformRealDist.reset();
bEx[0] = uniformRealDist(rng) < prob[0];
}
re->prob_sum[0] += prob[0];
@@ -1060,7 +1068,10 @@ test_for_replica_exchange(FILE *fplog,
{
prob[i] = exp(-delta);
}
- /* roll a number to determine if accepted */
+ // roll a number to determine if accepted. For now it is superfluous to
+ // reset, but just in case we ever add more calls in different branches
+ // it is safer to always reset the distribution.
+ uniformRealDist.reset();
bEx[i] = uniformRealDist(rng) < prob[i];
}
re->prob_sum[i] += prob[i];
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp
similarity index 99%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/runner.cpp
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp
index d642a42e2..b8550c39e 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/runner.cpp
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp
@@ -989,7 +989,8 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
cr, ddxyz, &npme,
inputrec, state, &bReadEkin,
(Flags & MD_APPENDFILES),
- (Flags & MD_APPENDFILESSET));
+ (Flags & MD_APPENDFILESSET),
+ (Flags & MD_REPRODUCIBLE));
if (bReadEkin)
{
@@ -1159,7 +1160,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
init_forcerec(fplog, fr, fcd, inputrec, mtop, cr, box,
opt2fn("-table", nfile, fnm),
opt2fn("-tablep", nfile, fnm),
- opt2fn("-tableb", nfile, fnm),
+ getFilenm("-tableb", nfile, fnm),
nbpu_opt,
FALSE,
pforce);
diff --git a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp.preplumed
similarity index 99%
rename from patches/gromacs-2016-beta1.diff/src/programs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp.preplumed
index 3294776ff..ddc5895c9 100644
--- a/patches/gromacs-2016-beta1.diff/src/programs/mdrun/runner.cpp.preplumed
+++ b/patches/gromacs-2016-beta2.diff/src/programs/mdrun/runner.cpp.preplumed
@@ -983,7 +983,8 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
cr, ddxyz, &npme,
inputrec, state, &bReadEkin,
(Flags & MD_APPENDFILES),
- (Flags & MD_APPENDFILESSET));
+ (Flags & MD_APPENDFILESSET),
+ (Flags & MD_REPRODUCIBLE));
if (bReadEkin)
{
@@ -1153,7 +1154,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
init_forcerec(fplog, fr, fcd, inputrec, mtop, cr, box,
opt2fn("-table", nfile, fnm),
opt2fn("-tablep", nfile, fnm),
- opt2fn("-tableb", nfile, fnm),
+ getFilenm("-tableb", nfile, fnm),
nbpu_opt,
FALSE,
pforce);
--
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