simulationstate.cpp
topologyhelpers.cpp
topology.cpp
+ tpr.cpp
virials.cpp
)
particletype.h
simulationstate.h
topology.h
+ tpr.h
vector.h
DESTINATION include/nblib)
endif()
#include "nblib/pbc.hpp"
#include "nblib/systemdescription.h"
#include "nblib/topology.h"
+#include "nblib/tpr.h"
#include "nblib/virials.h"
namespace nblib
options);
}
+std::unique_ptr<GmxNBForceCalculatorCpu> setupGmxForceCalculatorCpu(TprReader& tprReader,
+ const NBKernelOptions& options)
+{
+ return std::make_unique<GmxNBForceCalculatorCpu>(tprReader.particleTypeIdOfAllParticles_,
+ tprReader.nonbondedParameters_,
+ tprReader.charges_,
+ tprReader.particleInteractionFlags_,
+ tprReader.exclusionListRanges_,
+ tprReader.exclusionListElements_,
+ options);
+}
+
} // namespace nblib
{
struct NBKernelOptions;
class Topology;
+struct TprReader;
class GmxNBForceCalculatorCpu final
{
std::unique_ptr<GmxNBForceCalculatorCpu> setupGmxForceCalculatorCpu(const Topology& topology,
const NBKernelOptions& options);
+//! Sets up and returns a GmxForceCalculatorCpu based on a TPR file as input
+std::unique_ptr<GmxNBForceCalculatorCpu> setupGmxForceCalculatorCpu(TprReader& tprReader,
+ const NBKernelOptions& options);
+
} // namespace nblib
#endif // NBLIB_GMXCALCULATORCPU_H
molecules.cpp
nbnxmsetup.cpp
topology.cpp
+ tpr.cpp
virials.cpp
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * 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
+ * This implements TPR reading tests
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#include <gtest/gtest.h>
+
+#include "nblib/tpr.h"
+
+#include "gromacs/tools/convert_tpr.h"
+
+#include "nblib/gmxcalculatorcpu.h"
+#include "nblib/tests/testsystems.h"
+#include "nblib/tests/testhelpers.h"
+
+#include "programs/mdrun/tests/moduletest.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/simulationdatabase.h"
+
+namespace nblib
+{
+namespace test
+{
+
+//! Test fixture for running the utils needed for reading TPR files from simulation database
+class TprReaderTest : public gmx::test::MdrunTestFixture
+{
+public:
+ //! Returns a TprReader object populated with the given files in the simulation database
+ TprReader makeTPRfromSimulationDatabase(const std::string& filename)
+ {
+ gmx::test::CommandLine caller;
+ runner_.useTopGroAndNdxFromDatabase(filename);
+ auto mdpFieldValues = gmx::test::prepareMdpFieldValues(filename.c_str(), "md", "no", "no");
+ mdpFieldValues["init-lambda-state"] = "0";
+ mdpFieldValues["constraints"] = "none"; // constraints not supported in NBLIB
+ runner_.useStringAsMdpFile(gmx::test::prepareMdpFileContents(mdpFieldValues));
+ runner_.callGrompp(caller);
+
+ return TprReader(runner_.tprFileName_);
+ }
+};
+
+TEST_F(TprReaderTest, SimDBTprIsCreated)
+{
+ EXPECT_NO_THROW(makeTPRfromSimulationDatabase("argon12"));
+}
+
+TEST_F(TprReaderTest, Spc2Reads)
+{
+ TprReader tprReader = makeTPRfromSimulationDatabase("spc2");
+
+ EXPECT_NO_THROW(tprReader.coordinates_.size());
+}
+
+TEST_F(TprReaderTest, ArgonImportedDataIsCorrect)
+{
+ TprReader tprReader = makeTPRfromSimulationDatabase("argon12");
+ RefDataChecker dataImportTest(5e-5);
+
+ // check number of coordinates in the system
+ EXPECT_EQ(tprReader.coordinates_.size(), 12);
+
+ // check coordinates
+ dataImportTest.testArrays<Vec3>(tprReader.coordinates_, "coordinates");
+
+ // check number of velocities in the system
+ EXPECT_EQ(tprReader.velocities_.size(), 12);
+
+ // check velocities
+ dataImportTest.testArrays<Vec3>(tprReader.velocities_, "velocities");
+
+ // check box
+ EXPECT_TRUE(tprReader.getBox() == Box(6.05449));
+
+ // check non-bonded params
+ dataImportTest.testArrays<real>(tprReader.nonbondedParameters_, "nbparams");
+
+ // check exclusion elements
+ dataImportTest.testArrays<int>(tprReader.exclusionListElements_, "exclusion elements");
+
+ // check exclusion ranges
+ dataImportTest.testArrays<int>(tprReader.exclusionListRanges_, "exclusion ranges");
+}
+
+TEST_F(TprReaderTest, FCfromTprDataWorks)
+{
+ auto options = NBKernelOptions();
+ options.nbnxmSimd = SimdKernels::SimdNo;
+ options.coulombType = CoulombType::Cutoff;
+
+ TprReader tprReader = makeTPRfromSimulationDatabase("argon12");
+
+ auto forceCalculatorTpr = setupGmxForceCalculatorCpu(tprReader, options);
+
+ std::vector<Vec3> forceOutputTpr(tprReader.coordinates_.size(), Vec3{ 0, 0, 0 });
+
+ forceCalculatorTpr->updatePairlist(tprReader.coordinates_, tprReader.getBox());
+ forceCalculatorTpr->compute(tprReader.coordinates_, tprReader.getBox(), forceOutputTpr);
+
+ RefDataChecker forcesOutputTest;
+ forcesOutputTest.testArrays<Vec3>(forceOutputTpr, "Argon forces");
+}
+
+} // namespace test
+
+} // namespace nblib
--- /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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib tpr reading
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+
+#include "nblib/tpr.h"
+
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/listed_forces/listed_forces.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/iforceprovider.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/simulation_workload.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/logger.h"
+#include "nblib/box.h"
+
+namespace nblib
+{
+
+TprReader::TprReader(std::string filename)
+{
+ t_inputrec inputRecord;
+ t_state globalState;
+ gmx_mtop_t molecularTopology;
+ gmx::SimulationWorkload simulationWorkload;
+
+ // If the file does not exist, this function will throw
+ PartialDeserializedTprFile partialDeserializedTpr =
+ read_tpx_state(filename.c_str(), &inputRecord, &globalState, &molecularTopology);
+
+ // init commrec
+ MPI_Comm simulationCommunicator = MPI_COMM_WORLD;
+ CommrecHandle crHandle = init_commrec(simulationCommunicator);
+ t_commrec* commrec = crHandle.get();
+ assert((commrec != nullptr) && "Must have valid commrec");
+
+ // init forcerec
+ t_forcerec forceRecord;
+ gmx::ForceProviders forceProviders;
+ forceRecord.forceProviders = &forceProviders;
+ init_forcerec(nullptr,
+ gmx::MDLogger(),
+ simulationWorkload,
+ &forceRecord,
+ inputRecord,
+ molecularTopology,
+ commrec,
+ globalState.box,
+ nullptr,
+ nullptr,
+ gmx::ArrayRef<const std::string>{},
+ -1);
+
+ nonbondedParameters_ = makeNonBondedParameterLists(molecularTopology.ffparams.atnr,
+ molecularTopology.ffparams.iparams,
+ forceRecord.haveBuckingham);
+
+ gmx_localtop_t localtop(molecularTopology.ffparams);
+ gmx_mtop_generate_local_top(molecularTopology, &localtop, false);
+ exclusionListElements_ = std::vector<int>(localtop.excls.elementsView().begin(),
+ localtop.excls.elementsView().end());
+ exclusionListRanges_ = std::vector<int>(localtop.excls.listRangesView().begin(),
+ localtop.excls.listRangesView().end());
+
+ int ntopatoms = molecularTopology.natoms;
+ std::unique_ptr<gmx::MDAtoms> mdAtoms =
+ gmx::makeMDAtoms(nullptr, molecularTopology, inputRecord, false);
+ atoms2md(molecularTopology, inputRecord, -1, {}, ntopatoms, mdAtoms.get());
+ update_mdatoms(mdAtoms->mdatoms(), inputRecord.fepvals->init_lambda);
+ auto numParticles = mdAtoms->mdatoms()->nr;
+ charges_.resize(numParticles);
+ particleTypeIdOfAllParticles_.resize(numParticles);
+ inverseMasses_.resize(numParticles);
+ for (int i = 0; i < numParticles; i++)
+ {
+ charges_[i] = mdAtoms->mdatoms()->chargeA[i];
+ particleTypeIdOfAllParticles_[i] = mdAtoms->mdatoms()->typeA[i];
+ inverseMasses_[i] = mdAtoms->mdatoms()->invmass[i];
+ }
+ particleInteractionFlags_ = forceRecord.atomInfo;
+
+ if (TRICLINIC(globalState.box))
+ {
+ throw InputException("Only rectangular unit-cells are supported here");
+ }
+ boxX_ = globalState.box[XX][XX];
+ boxY_ = globalState.box[YY][YY];
+ boxZ_ = globalState.box[ZZ][ZZ];
+ coordinates_.assign(globalState.x.begin(), globalState.x.end());
+ velocities_.assign(globalState.v.begin(), globalState.v.end());
+}
+
+Box TprReader::getBox() const
+{
+ return Box(boxX_, boxY_, boxZ_);
+}
+
+} // namespace nblib
--- /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.
+ */
+/*! \inpublicapi \file
+ * \brief
+ * Implements nblib tpr reading
+ *
+ * \author Victor Holanda <victor.holanda@cscs.ch>
+ * \author Joe Jordan <ejjordan@kth.se>
+ * \author Prashanth Kanduri <kanduri@cscs.ch>
+ * \author Sebastian Keller <keller@cscs.ch>
+ */
+#ifndef NBLIB_TPR_H
+#define NBLIB_TPR_H
+
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "nblib/basicdefinitions.h"
+#include "nblib/box.h"
+#include "nblib/vector.h"
+#include "nblib/topology.h"
+
+namespace nblib
+{
+template<typename T>
+struct ExclusionLists;
+class Box;
+
+/*! \brief Reads in data from tpr which can be used in construction of force calculators
+ *
+ * This object reads data such as topology and coordinates from a tpr file, with the
+ * intent of using that data for construction of nblib force calculator objects. To
+ * allow for maximum flexibility in the calling code, it is the responsibility of the
+ * caller to, e.g., make copies if they want to preserve initial state information or
+ * use the data to construct multiple force calculator objects.
+ */
+struct TprReader
+{
+public:
+ TprReader(std::string filename);
+
+ //! Particle info where all particles are marked to have Van der Waals interactions
+ std::vector<int64_t> particleInteractionFlags_;
+ //! particle type id of all particles
+ std::vector<int> particleTypeIdOfAllParticles_;
+ //! Storage for parameters for short range interactions.
+ std::vector<real> nonbondedParameters_;
+ //! electrostatic charges
+ std::vector<real> charges_;
+ //! inverse masses
+ std::vector<real> inverseMasses_;
+ //! stores information about particles pairs to be excluded from the non-bonded force
+ //! calculation exclusion list ranges
+ std::vector<int> exclusionListRanges_;
+ //! exclusion list elements
+ std::vector<int> exclusionListElements_;
+ //! coordinates
+ std::vector<Vec3> coordinates_;
+ //! velocities
+ std::vector<Vec3> velocities_;
+ //! listed forces data
+ ListedInteractionData listedInteractionData_;
+
+ //! bounding box of particle coordinates
+ [[nodiscard]] Box getBox() const;
+
+private:
+ real boxX_;
+ real boxY_;
+ real boxZ_;
+};
+
+} // namespace nblib
+#endif // NBLIB_TPR_H
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff