hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp

@@ -0,0 +1,224 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2021- The GROMACS Authors
+ * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+ * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ *
+ * 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
+ * https://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 https://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out https://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)
+    {
+        real realFepState = 0; /* PLUMED */ 
+        const int newFepState =
+                expandedEnsembleUpdateLambdaState(fplog_,
+                                                  inputrec_,
+                                                  energyData_->enerdata(),
+                                                  freeEnergyPerturbationData_->currentFEPState(),
+                                                  dfhist_.get(),
+                                                  step,
+                                                  &realFepState); /* PLUMED */
+        // 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_ && !restoredFromCheckpoint_);
+    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 (haveDDAtomOrdering(*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

plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/modularsimulator/expandedensembleelement.cpp.preplumed

@@ -0,0 +1,222 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2021- The GROMACS Authors
+ * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+ * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ *
+ * 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
+ * https://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 https://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out https://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_ && !restoredFromCheckpoint_);
+    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 (haveDDAtomOrdering(*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

plumed/_lib/lib/plumed/patches/gromacs-2023.5.config

@@ -0,0 +1,43 @@
+
+
+function plumed_preliminary_test(){
+# check if the README contains the word GROMACS and if gromacs has been already configured
+  grep -q GROMACS README 1>/dev/null 2>/dev/null
+}
+
+function plumed_patch_info(){
+cat << EOF
+PLUMED can be incorporated into gromacs using the standard patching procedure.
+Patching must be done in the gromacs root directory  _before_ the cmake command is invoked.
+
+PLUMED is not compatible with the internal multi-threading implementation of GROMACS so you need
+to configure gromacs as
+
+cmake -DGMX_THREAD_MPI=OFF and add -DGMX_MPI=ON if you want to use MPI.  
+
+On clusters you may want to patch gromacs using the static version of plumed, in this case
+building gromacs can result in multiple errors. One possible solution is to configure gromacs
+with these additional options:
+
+cmake -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
+
+To enable PLUMED in a gromacs simulation one should use
+mdrun with an extra -plumed flag. The flag can be used to
+specify the name of the PLUMED input file, e.g.:
+
+gmx mdrun -plumed plumed.dat
+
+For more information on gromacs you should visit http://www.gromacs.org
+
+EOF
+}
+
+plumed_before_patch(){
+  plumed_patch_info
+  
+  mv cmake/gmxVersionInfo.cmake cmake/gmxVersionInfo.cmake.preplumed
+  awk -v version="$PLUMED_VERSION" '/^set\(GMX_VERSION_STRING_OF_FORK/{gsub(/""/, "plumed-" version)}; {print}' cmake/gmxVersionInfo.cmake.preplumed > cmake/gmxVersionInfo.cmake
+}
+
+PLUMED_PREPLUMED_IGNORE=cmake/gmxVersionInfo.cmake
+