return 0;
}
+ std::unique_ptr<df_history_t> localDFHistory = nullptr;
if (*dfhistPtr == nullptr)
{
- snew(*dfhistPtr, 1);
+ localDFHistory = std::make_unique<df_history_t>();
+ *dfhistPtr = localDFHistory.get();
(*dfhistPtr)->nlambda = nlambda;
init_df_history(*dfhistPtr, nlambda);
}
init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
- if (ir->bExpanded)
+ if (ir->bExpanded && !useModularSimulator)
{
snew(state->dfhist, 1);
init_df_history(state->dfhist, ir->fepvals->n_lambda);
--- /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.
+ */
+/*! \internal \file
+ * \brief Defines the expanded ensemble element for the modular simulator
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ * \ingroup module_modularsimulator
+ */
+
+#include "gmxpre.h"
+
+#include "expandedensembleelement.h"
+
+#include "gromacs/domdec/distribute.h"
+#include "gromacs/mdlib/expanded.h"
+#include "gromacs/mdlib/stat.h"
+#include "gromacs/mdtypes/checkpointdata.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/fatalerror.h"
+
+#include "energydata.h"
+#include "simulatoralgorithm.h"
+
+namespace gmx
+{
+
+void ExpandedEnsembleElement::apply(Step step, bool doLambdaStep, bool doLog)
+{
+ if (doLambdaStep)
+ {
+ const int newFepState =
+ expandedEnsembleUpdateLambdaState(fplog_,
+ inputrec_,
+ energyData_->enerdata(),
+ freeEnergyPerturbationData_->currentFEPState(),
+ dfhist_.get(),
+ step);
+ // Set new state at next step
+ fepStateSetting_->setNewState(newFepState, step + 1);
+ }
+ if (doLog)
+ {
+ /* only needed if doing expanded ensemble */
+ PrintFreeEnergyInfoToFile(fplog_,
+ inputrec_->fepvals.get(),
+ inputrec_->expandedvals.get(),
+ inputrec_->bSimTemp ? inputrec_->simtempvals.get() : nullptr,
+ dfhist_.get(),
+ freeEnergyPerturbationData_->currentFEPState(),
+ inputrec_->nstlog,
+ step);
+ }
+}
+
+void ExpandedEnsembleElement::elementSetup()
+{
+ // Check nstexpanded here, because the grompp check was broken (#2714)
+ if (inputrec_->expandedvals->nstexpanded % inputrec_->nstcalcenergy != 0)
+ {
+ gmx_fatal(FARGS,
+ "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
+ }
+ init_expanded_ensemble(restoredFromCheckpoint_, inputrec_, dfhist_.get());
+}
+
+void ExpandedEnsembleElement::scheduleTask(Step step, Time /*unused*/, const RegisterRunFunction& registerRunFunction)
+{
+ const bool isFirstStep = (step == initialStep_);
+ const bool doLambdaStep = (do_per_step(step, frequency_) && !isFirstStep);
+ const bool doLog = (isMasterRank_ && step == nextLogWritingStep_ && (fplog_ != nullptr));
+
+ if (doLambdaStep || doLog)
+ {
+ registerRunFunction([this, step, doLambdaStep, doLog]() { apply(step, doLambdaStep, doLog); });
+ }
+ if (doLambdaStep)
+ {
+ // We'll compute a new lambda state and want it applied for next step
+ fepStateSetting_->signalSettingStep(step + 1);
+ }
+}
+
+namespace
+{
+/*!
+ * \brief Enum describing the contents FreeEnergyPerturbationData::Element writes to modular checkpoint
+ *
+ * When changing the checkpoint content, add a new element just above Count, and adjust the
+ * checkpoint functionality.
+ */
+enum class CheckpointVersion
+{
+ Base, //!< First version of modular checkpointing
+ Count //!< Number of entries. Add new versions right above this!
+};
+constexpr auto c_currentVersion = CheckpointVersion(int(CheckpointVersion::Count) - 1);
+} // namespace
+
+template<CheckpointDataOperation operation>
+void ExpandedEnsembleElement::doCheckpointData(CheckpointData<operation>* checkpointData)
+{
+ checkpointVersion(checkpointData, "ExpandedEnsembleElement version", c_currentVersion);
+
+ dfhist_->doCheckpoint<operation>(checkpointData->subCheckpointData("dfhist"),
+ inputrec_->expandedvals->elamstats);
+}
+
+void ExpandedEnsembleElement::saveCheckpointState(std::optional<WriteCheckpointData> checkpointData,
+ const t_commrec* cr)
+{
+ if (MASTER(cr))
+ {
+ doCheckpointData<CheckpointDataOperation::Write>(&checkpointData.value());
+ }
+}
+
+void ExpandedEnsembleElement::restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData,
+ const t_commrec* cr)
+{
+ if (MASTER(cr))
+ {
+ doCheckpointData<CheckpointDataOperation::Read>(&checkpointData.value());
+ }
+ if (DOMAINDECOMP(cr))
+ {
+ dd_distribute_dfhist(cr->dd, dfhist_.get());
+ }
+ restoredFromCheckpoint_ = true;
+}
+
+const std::string& ExpandedEnsembleElement::clientID()
+{
+ return identifier_;
+}
+
+std::optional<SignallerCallback> ExpandedEnsembleElement::registerLoggingCallback()
+{
+ if (isMasterRank_)
+ {
+ return [this](Step step, Time /*unused*/) { nextLogWritingStep_ = step; };
+ }
+ else
+ {
+ return std::nullopt;
+ }
+}
+
+ExpandedEnsembleElement::ExpandedEnsembleElement(bool isMasterRank,
+ Step initialStep,
+ int frequency,
+ const EnergyData* energyData,
+ const FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ FILE* fplog,
+ const t_inputrec* inputrec) :
+ fepStateSetting_(freeEnergyPerturbationData->enableExternalFepStateSetting()),
+ isMasterRank_(isMasterRank),
+ initialStep_(initialStep),
+ frequency_(frequency),
+ nextLogWritingStep_(-1),
+ dfhist_(std::make_unique<df_history_t>()),
+ restoredFromCheckpoint_(false),
+ energyData_(energyData),
+ freeEnergyPerturbationData_(freeEnergyPerturbationData),
+ fplog_(fplog),
+ inputrec_(inputrec)
+{
+ init_df_history(dfhist_.get(), inputrec_->fepvals->n_lambda);
+}
+
+ISimulatorElement* ExpandedEnsembleElement::getElementPointerImpl(
+ LegacySimulatorData* legacySimulatorData,
+ ModularSimulatorAlgorithmBuilderHelper* builderHelper,
+ StatePropagatorData gmx_unused* statePropagatorData,
+ EnergyData* energyData,
+ FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
+ ObservablesReducer* /*observablesReducer*/)
+{
+ return builderHelper->storeElement(std::make_unique<ExpandedEnsembleElement>(
+ MASTER(legacySimulatorData->cr),
+ legacySimulatorData->inputrec->init_step,
+ legacySimulatorData->inputrec->expandedvals->nstexpanded,
+ energyData,
+ freeEnergyPerturbationData,
+ legacySimulatorData->fplog,
+ legacySimulatorData->inputrec));
+}
+
+} // 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.
+ */
+/*! \internal \file
+ * \brief Declares the expanded ensemble element for the modular simulator
+ *
+ * \author Pascal Merz <pascal.merz@me.com>
+ * \ingroup module_modularsimulator
+ *
+ * This header is only used within the modular simulator module
+ */
+
+#ifndef GMX_MODULARSIMULATOR_EXPANDEDENSEMBLEELEMENT_H
+#define GMX_MODULARSIMULATOR_EXPANDEDENSEMBLEELEMENT_H
+
+#include "freeenergyperturbationdata.h"
+
+struct df_history_t;
+struct t_inputrec;
+
+namespace gmx
+{
+enum class CheckpointDataOperation;
+class EnergyData;
+class GlobalCommunicationHelper;
+class LegacySimulatorData;
+class MDAtoms;
+class ModularSimulatorAlgorithmBuilderHelper;
+class ObservablesReducer;
+class StatePropagatorData;
+
+/*! \internal
+ * \ingroup module_modularsimulator
+ * \brief The expanded ensemble element
+ *
+ * This element periodically attempts Monte Carlo moves in lambda
+ * space and sets the new lambda state in FreeEnergyPerturbationData::Element.
+ */
+class ExpandedEnsembleElement final : public ISimulatorElement, public ICheckpointHelperClient, public ILoggingSignallerClient
+{
+public:
+ //! Constructor
+ explicit ExpandedEnsembleElement(bool isMasterRank,
+ Step initialStep,
+ int frequency,
+ const EnergyData* energyData,
+ const FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ FILE* fplog,
+ const t_inputrec* inputrec);
+
+ //! Attempt lambda MC step and write log
+ void scheduleTask(Step step, Time time, const RegisterRunFunction& registerRunFunction) override;
+ //! Set up FEP history object
+ void elementSetup() override;
+ //! No teardown needed
+ void elementTeardown() override{};
+
+ //! ICheckpointHelperClient write checkpoint implementation
+ void saveCheckpointState(std::optional<WriteCheckpointData> checkpointData, const t_commrec* cr) override;
+ //! ICheckpointHelperClient read checkpoint implementation
+ void restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData, const t_commrec* cr) override;
+ //! ICheckpointHelperClient key implementation
+ const std::string& clientID() override;
+
+ /*! \brief Factory method implementation
+ *
+ * \param legacySimulatorData Pointer allowing access to simulator level data
+ * \param builderHelper ModularSimulatorAlgorithmBuilder helper object
+ * \param statePropagatorData Pointer to the \c StatePropagatorData object
+ * \param energyData Pointer to the \c EnergyData object
+ * \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
+ * \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
+ * \param observablesReducer Pointer to the \c ObservablesReducer object
+ *
+ * \return Pointer to the element to be added. Element needs to have been stored using \c storeElement
+ */
+ static ISimulatorElement* getElementPointerImpl(LegacySimulatorData* legacySimulatorData,
+ ModularSimulatorAlgorithmBuilderHelper* builderHelper,
+ StatePropagatorData* statePropagatorData,
+ EnergyData* energyData,
+ FreeEnergyPerturbationData* freeEnergyPerturbationData,
+ GlobalCommunicationHelper* globalCommunicationHelper,
+ ObservablesReducer* observablesReducer);
+
+private:
+ //! Use expanded ensemble to determine new FEP state or write log
+ void apply(Step step, bool doLambdaStep, bool doLog);
+
+ //! Helper object allowing to set new FEP state
+ FepStateSetting* fepStateSetting_;
+
+ //! Whether this runs on master
+ const bool isMasterRank_;
+ //! The initial Step
+ const Step initialStep_;
+ //! The frequency of lambda MC steps
+ const int frequency_;
+
+ //! ILoggingSignallerClient implementation
+ std::optional<SignallerCallback> registerLoggingCallback() override;
+ //! The next logging step
+ Step nextLogWritingStep_;
+
+ //! The free energy sampling history
+ std::unique_ptr<df_history_t> dfhist_;
+
+ //! CheckpointHelper identifier
+ const std::string identifier_ = "ExpandedEnsembleElement";
+ //! Helper function to read from / write to CheckpointData
+ template<CheckpointDataOperation operation>
+ void doCheckpointData(CheckpointData<operation>* checkpointData);
+ //! Whether this object was restored from checkpoint
+ bool restoredFromCheckpoint_;
+
+ // TODO: Clarify relationship to data objects and find a more robust alternative to raw pointers (#3583)
+ //! Pointer to the energy data
+ const EnergyData* energyData_;
+ //! Pointer to the free energy perturbation data
+ const FreeEnergyPerturbationData* freeEnergyPerturbationData_;
+
+ // Access to ISimulator data
+ //! Handles logging.
+ FILE* fplog_;
+ //! Contains user input mdp options.
+ const t_inputrec* inputrec_;
+};
+
+} // namespace gmx
+
+#endif // GMX_MODULARSIMULATOR_EXPANDEDENSEMBLEELEMENT_H
#include "andersentemperaturecoupling.h"
#include "computeglobalselement.h"
#include "constraintelement.h"
+#include "expandedensembleelement.h"
#include "firstorderpressurecoupling.h"
#include "forceelement.h"
#include "mttk.h"
builder->add<ConstraintsElement<ConstraintVariable::Velocities>>();
}
builder->add<ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>>();
+ // Here, we have x / v / f at the full time step
builder->add<StatePropagatorData::Element>();
+ if (legacySimulatorData_->inputrec->bExpanded)
+ {
+ builder->add<ExpandedEnsembleElement>();
+ }
if (legacySimulatorData_->inputrec->etc == TemperatureCoupling::VRescale
|| legacySimulatorData_->inputrec->etc == TemperatureCoupling::Berendsen)
{
}
// We have a full state at time t here
builder->add<StatePropagatorData::Element>();
+ if (legacySimulatorData_->inputrec->bExpanded)
+ {
+ builder->add<ExpandedEnsembleElement>();
+ }
// Propagate extended system variables from t to t+dt/2
if (legacySimulatorData_->inputrec->epc == PressureCoupling::Mttk)
isInputCompatible =
isInputCompatible
&& conditionalAssert(!doRerun, "Rerun is not supported by the modular simulator.");
- isInputCompatible =
- isInputCompatible
- && conditionalAssert(inputrec->efep == FreeEnergyPerturbationType::No
- || inputrec->efep == FreeEnergyPerturbationType::Yes
- || inputrec->efep == FreeEnergyPerturbationType::SlowGrowth,
- "Expanded ensemble free energy calculation is not "
- "supported by the modular simulator.");
isInputCompatible = isInputCompatible
&& conditionalAssert(!inputrec->bPull,
"Pulling is not supported by the modular simulator.");
isInputCompatible
&& conditionalAssert(!inputrec->bSimTemp,
"Simulated tempering is not supported by the modular simulator.");
- isInputCompatible = isInputCompatible
- && conditionalAssert(!inputrec->bExpanded,
- "Expanded ensemble simulations are not supported by "
- "the modular simulator.");
isInputCompatible =
isInputCompatible
&& conditionalAssert(!doEssentialDynamics,
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff