From d51fa13b0d99e6d2ba0c7e05e80af72205ba12c7 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Wed, 2 Oct 2019 10:33:02 +0200
Subject: [PATCH] gromacs 2019.4
---
...acs-2019.2.config => gromacs-2019.4.config} | 0
.../src/gromacs/CMakeLists.txt | 0
.../src/gromacs/CMakeLists.txt.preplumed | 0
.../src/gromacs/mdlib/force.cpp | 0
.../src/gromacs/mdlib/force.cpp.preplumed | 0
.../src/gromacs/mdrun/legacymdrunoptions.cpp | 0
.../mdrun/legacymdrunoptions.cpp.preplumed | 0
.../src/gromacs/mdrun/legacymdrunoptions.h | 0
.../mdrun/legacymdrunoptions.h.preplumed | 0
.../src/gromacs/mdrun/md.cpp | 18 +++++++++++++++---
.../src/gromacs/mdrun/md.cpp.preplumed | 18 +++++++++++++++---
.../src/gromacs/mdrun/minimize.cpp | 11 +++++++++--
.../src/gromacs/mdrun/minimize.cpp.preplumed | 11 +++++++++--
.../src/gromacs/mdrun/replicaexchange.cpp | 0
.../mdrun/replicaexchange.cpp.preplumed | 0
.../src/gromacs/mdrun/replicaexchange.h | 0
.../gromacs/mdrun/replicaexchange.h.preplumed | 0
.../src/gromacs/mdrun/runner.cpp | 0
.../src/gromacs/mdrun/runner.cpp.preplumed | 0
19 files changed, 48 insertions(+), 10 deletions(-)
rename patches/{gromacs-2019.2.config => gromacs-2019.4.config} (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/CMakeLists.txt (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/CMakeLists.txt.preplumed (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdlib/force.cpp (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdlib/force.cpp.preplumed (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/legacymdrunoptions.cpp (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/legacymdrunoptions.h (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/legacymdrunoptions.h.preplumed (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/md.cpp (98%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/md.cpp.preplumed (98%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/minimize.cpp (99%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/minimize.cpp.preplumed (99%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/replicaexchange.cpp (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/replicaexchange.cpp.preplumed (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/replicaexchange.h (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/replicaexchange.h.preplumed (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/runner.cpp (100%)
rename patches/{gromacs-2019.2.diff => gromacs-2019.4.diff}/src/gromacs/mdrun/runner.cpp.preplumed (100%)
diff --git a/patches/gromacs-2019.2.config b/patches/gromacs-2019.4.config
similarity index 100%
rename from patches/gromacs-2019.2.config
rename to patches/gromacs-2019.4.config
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2019.4.diff/src/gromacs/CMakeLists.txt
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2019.4.diff/src/gromacs/CMakeLists.txt
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/CMakeLists.txt.preplumed
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2019.4.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2019.4.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.h
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.h
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/md.cpp
similarity index 98%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/md.cpp
index 887526a8d..0c649e918 100644
--- a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp
+++ b/patches/gromacs-2019.4.diff/src/gromacs/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) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019, 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.
@@ -792,6 +792,11 @@ void gmx::Integrator::do_md()
/* Determine whether or not to do Neighbour Searching */
bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
+ /* Note that the stopHandler will cause termination at nstglobalcomm
+ * steps. Since this concides with nstcalcenergy, nsttcouple and/or
+ * nstpcouple steps, we have computed the half-step kinetic energy
+ * of the previous step and can always output energies at the last step.
+ */
bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
/* do_log triggers energy and virial calculation. Because this leads
@@ -1442,9 +1447,16 @@ void gmx::Integrator::do_md()
{
// Organize to do inter-simulation signalling on steps if
// and when algorithms require it.
- bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
+ const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
+
+ // With leap-frog we also need to compute the half-step
+ // kinetic energy at the step before we need to write
+ // the full-step kinetic energy
+ const bool needEkinAtNextStep =
+ (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) ||
+ step_rel + 1 == ir->nsteps));
- if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)) || doInterSimSignal)
+ if (bGStat || needEkinAtNextStep || doInterSimSignal)
{
// Since we're already communicating at this step, we
// can propagate intra-simulation signals. Note that
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/md.cpp.preplumed
similarity index 98%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/md.cpp.preplumed
index a49a15df5..f0a634fc6 100644
--- a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/md.cpp.preplumed
+++ b/patches/gromacs-2019.4.diff/src/gromacs/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) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019, 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.
@@ -729,6 +729,11 @@ void gmx::Integrator::do_md()
/* Determine whether or not to do Neighbour Searching */
bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
+ /* Note that the stopHandler will cause termination at nstglobalcomm
+ * steps. Since this concides with nstcalcenergy, nsttcouple and/or
+ * nstpcouple steps, we have computed the half-step kinetic energy
+ * of the previous step and can always output energies at the last step.
+ */
bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
/* do_log triggers energy and virial calculation. Because this leads
@@ -1245,9 +1250,16 @@ void gmx::Integrator::do_md()
{
// Organize to do inter-simulation signalling on steps if
// and when algorithms require it.
- bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
+ const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
+
+ // With leap-frog we also need to compute the half-step
+ // kinetic energy at the step before we need to write
+ // the full-step kinetic energy
+ const bool needEkinAtNextStep =
+ (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) ||
+ step_rel + 1 == ir->nsteps));
- if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)) || doInterSimSignal)
+ if (bGStat || needEkinAtNextStep || doInterSimSignal)
{
// Since we're already communicating at this step, we
// can propagate intra-simulation signals. Note that
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/minimize.cpp
similarity index 99%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/minimize.cpp
index 6fb913acd..f4d0d562f 100644
--- a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp
+++ b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/minimize.cpp
@@ -2688,8 +2688,15 @@ Integrator::do_steep()
}
}
- /* Determine new step */
- stepsize = ustep/s_min->fmax;
+ // If the force is very small after finishing minimization,
+ // we risk dividing by zero when calculating the step size.
+ // So we check first if the minimization has stopped before
+ // trying to obtain a new step size.
+ if (!bDone)
+ {
+ /* Determine new step */
+ stepsize = ustep/s_min->fmax;
+ }
/* Check if stepsize is too small, with 1 nm as a characteristic length */
#if GMX_DOUBLE
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/minimize.cpp.preplumed
similarity index 99%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/minimize.cpp.preplumed
index 77421a32a..427ec5444 100644
--- a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/minimize.cpp.preplumed
+++ b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/minimize.cpp.preplumed
@@ -2613,8 +2613,15 @@ Integrator::do_steep()
}
}
- /* Determine new step */
- stepsize = ustep/s_min->fmax;
+ // If the force is very small after finishing minimization,
+ // we risk dividing by zero when calculating the step size.
+ // So we check first if the minimization has stopped before
+ // trying to obtain a new step size.
+ if (!bDone)
+ {
+ /* Determine new step */
+ stepsize = ustep/s_min->fmax;
+ }
/* Check if stepsize is too small, with 1 nm as a characteristic length */
#if GMX_DOUBLE
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.cpp
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.cpp
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.h
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.h
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/runner.cpp
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/runner.cpp
diff --git a/patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp.preplumed b/patches/gromacs-2019.4.diff/src/gromacs/mdrun/runner.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2019.2.diff/src/gromacs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2019.4.diff/src/gromacs/mdrun/runner.cpp.preplumed
--
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