#include "gromacs/mdlib/update_vv.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdrunutility/freeenergy.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdrunutility/printtime.h"
matrix lastbox;
int lamnew = 0;
/* for FEP */
- int nstfep = 0;
double cycles;
real saved_conserved_quantity = 0;
real last_ekin = 0;
}
}
- if (ir->efep != FreeEnergyPerturbationType::No)
- {
- /* Set free energy calculation frequency as the greatest common
- * denominator of nstdhdl and repl_ex_nst. */
- nstfep = ir->fepvals->nstdhdl;
- if (ir->bExpanded)
- {
- nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
- }
- if (useReplicaExchange)
- {
- nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
- }
- if (ir->bDoAwh)
- {
- nstfep = std::gcd(ir->awhParams->nstSampleCoord(), nstfep);
- }
- }
+ const int nstfep = computeFepPeriod(*ir, replExParams);
/* Be REALLY careful about what flags you set here. You CANNOT assume
* this is the first step, since we might be restarting from a checkpoint,
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2019,2020,2021, 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.
add_library(mdrunutility INTERFACE)
gmx_add_libgromacs_sources(
+ freeenergy.cpp
handlerestart.cpp
logging.cpp
multisim.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, 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.
+ *
+ * GROMACS 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 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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 GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief Defines helper functions for mdrun pertaining to free energy calculations.
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ * \ingroup module_mdrunutility
+ * \inlibraryapi
+ */
+
+#include "gmxpre.h"
+
+#include "freeenergy.h"
+
+#include <numeric>
+
+#include "gromacs/mdrun/replicaexchange.h"
+#include "gromacs/mdtypes/awh_params.h"
+#include "gromacs/mdtypes/inputrec.h"
+
+namespace gmx
+{
+
+int computeFepPeriod(const t_inputrec& inputrec, const ReplicaExchangeParameters& replExParams)
+{
+ if (inputrec.efep == FreeEnergyPerturbationType::No)
+ {
+ return 0;
+ }
+
+ // Set free energy calculation period as the greatest common
+ // denominator of nstdhdl, nstexpanded, replica exchange interval,
+ // and AWH nstSampleCoord.
+ int nstfep = inputrec.fepvals->nstdhdl;
+ if (inputrec.bExpanded)
+ {
+ nstfep = std::gcd(inputrec.expandedvals->nstexpanded, nstfep);
+ }
+ if (replExParams.exchangeInterval > 0)
+ {
+ nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
+ }
+ if (inputrec.bDoAwh)
+ {
+ nstfep = std::gcd(inputrec.awhParams->nstSampleCoord(), nstfep);
+ }
+ return nstfep;
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, 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.
+ *
+ * GROMACS 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 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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 GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief Declares helper functions for mdrun pertaining to free energy calculations.
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ * \ingroup module_mdrunutility
+ * \inlibraryapi
+ */
+
+#ifndef GMX_MDRUNUTILITY_FREEENERGY_H
+#define GMX_MDRUNUTILITY_FREEENERGY_H
+
+struct ReplicaExchangeParameters;
+struct t_inputrec;
+
+namespace gmx
+{
+
+/*! \brief Compute the period at which FEP calculation is performed
+ *
+ * This harmonizes the free energy calculation period specified by
+ * `nstdhdl` with the periods specified by expanded ensemble,
+ * replica exchange, and AWH.
+ *
+ * \param inputrec The input record
+ * \param replExParams The replica exchange parameters
+ * \return The period required by the involved algorithms
+ */
+int computeFepPeriod(const t_inputrec& inputrec, const ReplicaExchangeParameters& replExParams);
+
+} // namespace gmx
+
+#endif // GMX_MDRUNUTILITY_FREEENERGY_H
#include "gromacs/mdlib/stat.h"
#include "gromacs/mdrun/replicaexchange.h"
#include "gromacs/mdrun/shellfc.h"
+#include "gromacs/mdrunutility/freeenergy.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/printtime.h"
#include "gromacs/mdtypes/commrec.h"
}
}
addSignaller(energySignallerBuilder_.build(
- inputrec->nstcalcenergy, inputrec->fepvals->nstdhdl, inputrec->nstpcouple, virialMode));
+ inputrec->nstcalcenergy,
+ computeFepPeriod(*inputrec, legacySimulatorData_->replExParams),
+ inputrec->nstpcouple,
+ virialMode));
addSignaller(trajectorySignallerBuilder_.build(inputrec->nstxout,
inputrec->nstvout,
inputrec->nstfout,
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff