message(FATAL_ERROR "To build GROMACS with CP2K Interface both CP2K_DIR and CP2K_LINKER_FLAGS should be defined")
endif()
+ # Add directory with libcp2k.h into system include directories
+ include_directories(SYSTEM "${CP2K_DIR}/../../../src/start")
+
# Add libcp2k and DBCSR for linking
set(CMAKE_CXX_STANDARD_LIBRARIES "${CMAKE_CXX_STANDARD_LIBRARIES} -Wl,--allow-multiple-definition -L${CP2K_DIR} -lcp2k -L${CP2K_DIR}/exts/dbcsr -ldbcsr")
qmmmtopologypreprocessor.cpp
)
+# If we have libcp2k linked then compile qmmmforceprovider.cpp
+# In other case compile stub implementation qmmmforceprovider_stub.cpp
+if (GMX_CP2K)
+gmx_add_libgromacs_sources(
+ qmmmforceprovider.cpp
+ )
+else()
+gmx_add_libgromacs_sources(
+ qmmmforceprovider_stub.cpp
+ )
+endif()
+
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
--- /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
+ * Implements force provider for QMMM
+ *
+ * \author Dmitry Morozov <dmitry.morozov@jyu.fi>
+ * \author Christian Blau <blau@kth.se>
+ * \ingroup module_applied_forces
+ */
+
+#include "gmxpre.h"
+
+#include "qmmmforceprovider.h"
+
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/units.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
+
+#include <libcp2k.h>
+
+namespace gmx
+{
+
+QMMMForceProvider::QMMMForceProvider(const QMMMParameters& parameters,
+ const LocalAtomSet& localQMAtomSet,
+ const LocalAtomSet& localMMAtomSet,
+ PbcType pbcType,
+ const MDLogger& logger) :
+ parameters_(parameters),
+ qmAtoms_(localQMAtomSet),
+ mmAtoms_(localMMAtomSet),
+ pbcType_(pbcType),
+ logger_(logger),
+ box_{ { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 } }
+{
+}
+
+QMMMForceProvider::~QMMMForceProvider()
+{
+ if (force_env_ != -1)
+ {
+ cp2k_destroy_force_env(force_env_);
+ if (GMX_LIB_MPI)
+ {
+ cp2k_finalize_without_mpi();
+ }
+ else
+ {
+ cp2k_finalize();
+ }
+ }
+}
+
+bool QMMMForceProvider::isQMAtom(index globalAtomIndex)
+{
+ return std::find(qmAtoms_.globalIndex().begin(), qmAtoms_.globalIndex().end(), globalAtomIndex)
+ != qmAtoms_.globalIndex().end();
+}
+
+void QMMMForceProvider::appendLog(const std::string& msg)
+{
+ GMX_LOG(logger_.info).asParagraph().appendText(msg);
+}
+
+void QMMMForceProvider::initCP2KForceEnvironment(const t_commrec& cr)
+{
+ // Check that we have filename either defined in KVT or deduced from *.tpr name
+ GMX_RELEASE_ASSERT(parameters_.qmFileNameBase_.empty(),
+ "Names of CP2K input/output files is not defined in QMMMParameters");
+
+
+ // Names of CP2K Input and Output files
+ const std::string cp2kInputName = parameters_.qmFileNameBase_ + ".inp";
+ const std::string cp2kPdbName = parameters_.qmFileNameBase_ + ".pdb";
+ const std::string cp2kOutputName = parameters_.qmFileNameBase_ + ".out";
+
+ // Write CP2K input if we are Master
+ if (MASTER(&cr))
+ {
+ // In the CP2K Input we need to substitute placeholder with the actuall *.pdb file name
+ TextWriter::writeFileFromString(
+ cp2kInputName, formatString(parameters_.qmInput_.c_str(), cp2kPdbName.c_str()));
+
+ // Write *.pdb with point charges for CP2K
+ TextWriter::writeFileFromString(cp2kPdbName, parameters_.qmPdb_);
+ }
+
+ // Check if we have external MPI library
+ if (GMX_LIB_MPI)
+ {
+ /* Attempt to init CP2K and create force environment in case we have an external MPI library.
+ * _without_mpi - means that libcp2k will not call MPI_Init() itself,
+ * but rather expects it to be called already
+ */
+ cp2k_init_without_mpi();
+
+ // Here #if (GMX_LIB_MPI) needed because of MPI_Comm_c2f() usage
+ // TODO: Probably there should be more elegant solution
+#if GMX_LIB_MPI
+ cp2k_create_force_env_comm(
+ &force_env_, cp2kInputName.c_str(), cp2kOutputName.c_str(), MPI_Comm_c2f(cr.mpi_comm_mysim));
+#endif
+ }
+ else
+ {
+
+ // If we have thread-MPI or no-MPI then we should initialize CP2P differently
+ if (cr.nnodes > 1)
+ {
+ // CP2K could not use thread-MPI parallelization. In case -ntmpi > 1 throw an error.
+ std::string msg =
+ "Using GROMACS with CP2K requires the GROMACS build to be configured "
+ "with an MPI library or to use a single thread-MPI rank (-ntmpi 1). "
+ "In the latter case, manual use of -ntomp is also advisable when "
+ "the node has many cores to fill them with threads.";
+ GMX_THROW(NotImplementedError(msg.c_str()));
+ }
+
+ // Attempt to init CP2K and create force environment
+ cp2k_init();
+ cp2k_create_force_env(&force_env_, cp2kInputName.c_str(), cp2kOutputName.c_str());
+ }
+
+ // Set flag of successful initialization
+ isCp2kLibraryInitialized_ = true;
+
+} // namespace gmx
+
+void QMMMForceProvider::calculateForces(const ForceProviderInput& fInput, ForceProviderOutput* fOutput)
+{
+ // Total number of atoms in the system
+ size_t numAtoms = qmAtoms_.numAtomsGlobal() + mmAtoms_.numAtomsGlobal();
+
+ // Save box
+ copy_mat(fInput.box_, box_);
+
+ // Initialize PBC
+ t_pbc pbc;
+ set_pbc(&pbc, pbcType_, box_);
+
+ /*
+ * 1) If calculateForce called first time, then we need to init CP2K,
+ * as it was not possible during QMMMForceProvider constructor
+ * due to absence of full communication record at that point.
+ */
+ if (!isCp2kLibraryInitialized_)
+ {
+ try
+ {
+ initCP2KForceEnvironment(fInput.cr_);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+
+ /*
+ * 2) We need to gather fInput.x_ in case of MPI / DD setup
+ */
+
+ // x - coordinates (gathered across nodes in case of DD)
+ std::vector<RVec> x(numAtoms, RVec({ 0.0, 0.0, 0.0 }));
+
+ // Fill cordinates of local QM atoms and add translation
+ for (size_t i = 0; i < qmAtoms_.numAtomsLocal(); i++)
+ {
+ x[qmAtoms_.globalIndex()[qmAtoms_.collectiveIndex()[i]]] =
+ fInput.x_[qmAtoms_.localIndex()[i]] + parameters_.qmTrans_;
+ }
+
+ // Fill cordinates of local MM atoms and add translation
+ for (size_t i = 0; i < mmAtoms_.numAtomsLocal(); i++)
+ {
+ x[mmAtoms_.globalIndex()[mmAtoms_.collectiveIndex()[i]]] =
+ fInput.x_[mmAtoms_.localIndex()[i]] + parameters_.qmTrans_;
+ }
+
+ // If we are in MPI / DD conditions then gather coordinates over nodes
+ if (havePPDomainDecomposition(&fInput.cr_))
+ {
+ gmx_sum(3 * numAtoms, x.data()->as_vec(), &fInput.cr_);
+ }
+
+ // Put all atoms into the central box (they might be shifted out of it because of the translation)
+ put_atoms_in_box(pbcType_, fInput.box_, ArrayRef<RVec>(x));
+
+ /*
+ * 3) Cast data to double format of libcp2k
+ * update coordinates and box in CP2K and perform QM calculation
+ */
+ // x_d - coordinates casted to linear dobule vector for CP2K with parameters_.qmTrans_ added
+ std::vector<double> x_d(3 * numAtoms, 0.0);
+ for (size_t i = 0; i < numAtoms; i++)
+ {
+ x_d[3 * i] = static_cast<double>((x[i][XX]) / c_bohr2Nm);
+ x_d[3 * i + 1] = static_cast<double>((x[i][YY]) / c_bohr2Nm);
+ x_d[3 * i + 2] = static_cast<double>((x[i][ZZ]) / c_bohr2Nm);
+ }
+
+ // box_d - box_ casted to linear dobule vector for CP2K
+ std::vector<double> box_d(9);
+ for (size_t i = 0; i < DIM; i++)
+ {
+ box_d[3 * i] = static_cast<double>(box_[0][i] / c_bohr2Nm);
+ box_d[3 * i + 1] = static_cast<double>(box_[1][i] / c_bohr2Nm);
+ box_d[3 * i + 2] = static_cast<double>(box_[2][i] / c_bohr2Nm);
+ }
+
+ // Update coordinates and box in CP2K
+ cp2k_set_positions(force_env_, x_d.data(), 3 * numAtoms);
+ cp2k_set_cell(force_env_, box_d.data());
+
+ // Run CP2K calculation
+ cp2k_calc_energy_force(force_env_);
+
+ /*
+ * 4) Get output data
+ * We need to fill only local part into fOutput
+ */
+
+ // Only master process should add QM + QMMM energy
+ if (MASTER(&fInput.cr_))
+ {
+ double qmEner = 0.0;
+ cp2k_get_potential_energy(force_env_, &qmEner);
+ fOutput->enerd_.term[F_EQM] += qmEner * c_hartree2Kj * c_avogadro;
+ }
+
+ // Get Forces they are in Hartree/Bohr and will be converted to kJ/mol/nm
+ std::vector<double> cp2kForce(3 * numAtoms, 0.0);
+ cp2k_get_forces(force_env_, cp2kForce.data(), 3 * numAtoms);
+
+ // Fill forces on QM atoms first
+ for (size_t i = 0; i < qmAtoms_.numAtomsLocal(); i++)
+ {
+ fOutput->forceWithVirial_.force_[qmAtoms_.localIndex()[i]][XX] +=
+ static_cast<real>(cp2kForce[3 * qmAtoms_.globalIndex()[qmAtoms_.collectiveIndex()[i]]])
+ * c_hartreeBohr2Md;
+
+ fOutput->forceWithVirial_.force_[qmAtoms_.localIndex()[i]][YY] +=
+ static_cast<real>(cp2kForce[3 * qmAtoms_.globalIndex()[qmAtoms_.collectiveIndex()[i]] + 1])
+ * c_hartreeBohr2Md;
+
+ fOutput->forceWithVirial_.force_[qmAtoms_.localIndex()[i]][ZZ] +=
+ static_cast<real>(cp2kForce[3 * qmAtoms_.globalIndex()[qmAtoms_.collectiveIndex()[i]] + 2])
+ * c_hartreeBohr2Md;
+ }
+
+ // Filll forces on MM atoms then
+ for (size_t i = 0; i < mmAtoms_.numAtomsLocal(); i++)
+ {
+ fOutput->forceWithVirial_.force_[mmAtoms_.localIndex()[i]][XX] +=
+ static_cast<real>(cp2kForce[3 * mmAtoms_.globalIndex()[mmAtoms_.collectiveIndex()[i]]])
+ * c_hartreeBohr2Md;
+
+ fOutput->forceWithVirial_.force_[mmAtoms_.localIndex()[i]][YY] +=
+ static_cast<real>(cp2kForce[3 * mmAtoms_.globalIndex()[mmAtoms_.collectiveIndex()[i]] + 1])
+ * c_hartreeBohr2Md;
+
+ fOutput->forceWithVirial_.force_[mmAtoms_.localIndex()[i]][ZZ] +=
+ static_cast<real>(cp2kForce[3 * mmAtoms_.globalIndex()[mmAtoms_.collectiveIndex()[i]] + 2])
+ * c_hartreeBohr2Md;
+ }
+};
+
+} // 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 force provider for QMMM
+ *
+ * \author Dmitry Morozov <dmitry.morozov@jyu.fi>
+ * \author Christian Blau <blau@kth.se>
+ * \ingroup module_applied_forces
+ */
+#ifndef GMX_APPLIED_FORCES_QMMMFORCEPROVIDER_H
+#define GMX_APPLIED_FORCES_QMMMFORCEPROVIDER_H
+
+#include "gromacs/domdec/localatomset.h"
+#include "gromacs/mdtypes/forceoutput.h"
+#include "gromacs/mdtypes/iforceprovider.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/logger.h"
+
+#include "qmmmtypes.h"
+
+namespace gmx
+{
+
+#ifdef __clang__
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wunused-private-field"
+#endif
+
+//! Type for CP2K force environment handle
+typedef int force_env_t;
+
+/*! \internal \brief
+ * Implements IForceProvider for QM/MM.
+ */
+class QMMMForceProvider final : public IForceProvider
+{
+public:
+ QMMMForceProvider(const QMMMParameters& parameters,
+ const LocalAtomSet& localQMAtomSet,
+ const LocalAtomSet& localMMAtomSet,
+ PbcType pbcType,
+ const MDLogger& logger);
+
+ //! Destruct force provider for QMMM and finalize libcp2k
+ ~QMMMForceProvider();
+
+ /*!\brief Calculate forces of QMMM.
+ * \param[in] fInput input for force provider
+ * \param[out] fOutput output for force provider
+ */
+ void calculateForces(const ForceProviderInput& fInput, ForceProviderOutput* fOutput) override;
+
+private:
+ //! Write message to the log
+ void appendLog(const std::string& msg);
+
+ /*!\brief Check if atom belongs to the global index of qmAtoms_
+ * \param[in] globalAtomIndex global index of the atom to check
+ */
+ bool isQMAtom(index globalAtomIndex);
+
+ /*!\brief Initialization of QM program.
+ * \param[in] cr connection record structure
+ */
+ void initCP2KForceEnvironment(const t_commrec& cr);
+
+ const QMMMParameters& parameters_;
+ const LocalAtomSet& qmAtoms_;
+ const LocalAtomSet& mmAtoms_;
+ const PbcType pbcType_;
+ const MDLogger& logger_;
+
+ //! Internal copy of PBC box
+ matrix box_;
+
+ //! Flag wether initCP2KForceEnvironment() has been called already
+ bool isCp2kLibraryInitialized_ = false;
+
+ //! CP2K force environment handle
+ force_env_t force_env_ = -1;
+};
+
+#ifdef __clang__
+# pragma clang diagnostic pop
+#endif
+
+} // namespace gmx
+
+#endif // GMX_APPLIED_FORCES_QMMMFORCEPROVIDER_H
--- /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
+ * Stub implementation of QMMMForceProvider
+ * Compiled in case if CP2K is not linked
+ *
+ * \author Dmitry Morozov <dmitry.morozov@jyu.fi>
+ * \author Christian Blau <blau@kth.se>
+ * \ingroup module_applied_forces
+ */
+
+#include "gmxpre.h"
+
+#include "qmmmforceprovider.h"
+
+#include "gromacs/utility/exceptions.h"
+
+namespace gmx
+{
+
+
+#ifdef __clang__
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wmissing-noreturn"
+#endif
+
+QMMMForceProvider::QMMMForceProvider(const QMMMParameters& parameters,
+ const LocalAtomSet& localQMAtomSet,
+ const LocalAtomSet& localMMAtomSet,
+ PbcType pbcType,
+ const MDLogger& logger) :
+ parameters_(parameters),
+ qmAtoms_(localQMAtomSet),
+ mmAtoms_(localMMAtomSet),
+ pbcType_(pbcType),
+ logger_(logger),
+ box_{ { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.0 } }
+{
+ GMX_THROW(
+ InternalError("CP2K has not been linked into GROMACS, QMMM simulation is not "
+ "possible.\nPlease, reconfigure GROMACS with -DGMX_CP2K=ON\n"));
+}
+
+QMMMForceProvider::~QMMMForceProvider() {}
+
+// NOLINTNEXTLINE(readability-convert-member-functions-to-static)
+bool QMMMForceProvider::isQMAtom(index /*globalAtomIndex*/)
+{
+ GMX_THROW(
+ InternalError("CP2K has not been linked into GROMACS, QMMM simulation is not "
+ "possible.\nPlease, reconfigure GROMACS with -DGMX_CP2K=ON\n"));
+}
+
+// NOLINTNEXTLINE(readability-convert-member-functions-to-static)
+void QMMMForceProvider::appendLog(const std::string& /*msg*/)
+{
+ GMX_THROW(
+ InternalError("CP2K has not been linked into GROMACS, QMMM simulation is not "
+ "possible.\nPlease, reconfigure GROMACS with -DGMX_CP2K=ON\n"));
+}
+
+// NOLINTNEXTLINE(readability-convert-member-functions-to-static)
+void QMMMForceProvider::initCP2KForceEnvironment(const t_commrec& /*cr*/)
+{
+ GMX_THROW(
+ InternalError("CP2K has not been linked into GROMACS, QMMM simulation is not "
+ "possible.\nPlease, reconfigure GROMACS with -DGMX_CP2K=ON\n"));
+}
+
+void QMMMForceProvider::calculateForces(const ForceProviderInput& /*fInput*/, ForceProviderOutput* /*fOutput*/)
+{
+ GMX_THROW(
+ InternalError("CP2K has not been linked into GROMACS, QMMM simulation is not "
+ "possible.\nPlease, reconfigure GROMACS with -DGMX_CP2K=ON\n"));
+};
+
+#ifdef __clang__
+# pragma clang diagnostic pop
+#endif
+
+} // namespace gmx
//! symbols of the elements in periodic table
const std::vector<std::string> periodic_system = {
- "X ", "H ", "He ", "Li ", "Be ", "B ", "C ", "N ", "O ", "F ", "Ne ", "Na ", "Mg ",
- "Al ", "Si ", "P ", "S ", "Cl ", "Ar ", "K ", "Ca ", "Sc ", "Ti ", "V ", "Cr ", "Mn ",
- "Fe ", "Co ", "Ni ", "Cu ", "Zn ", "Ga ", "Ge ", "As ", "Se ", "Br ", "Kr "
+ "X ", "H ", "He ", "Li ", "Be ", "B ", "C ", "N ", "O ", "F ", "Ne ", "Na ",
+ "Mg ", "Al ", "Si ", "P ", "S ", "Cl ", "Ar ", "K ", "Ca ", "Sc ", "Ti ", "V ",
+ "Cr ", "Mn ", "Fe ", "Co ", "Ni ", "Cu ", "Zn ", "Ga ", "Ge ", "As ", "Se ", "Br ",
+ "Kr ", "Rb ", "Sr ", "Y ", "Zr ", "Nb ", "Mo ", "Tc ", "Ru ", "Rh ", "Pd ", "Ag ",
+ "Cd ", "In ", "Sn ", "Sb ", "Te ", "I ", "Xe ", "Cs ", "Ba ", "La ", "Ce ", "Pr ",
+ "Nd ", "Pm ", "Sm ", "Eu ", "Gd ", "Tb ", "Dy ", "Ho ", "Er ", "Tm ", "Yb ", "Lu ",
+ "Hf ", "Ta ", "W ", "Re ", "Os ", "Ir ", "Pt ", "Au ", "Hg ", "Tl ", "Pb ", "Bi ",
+ "Po ", "At ", "Rn ", "Fr ", "Ra ", "Ac ", "Th ", "Pa ", "U ", "Np ", "Pu ", "Am ",
+ "Cm ", "Bk ", "Cf ", "Es ", "Fm ", "Md ", "No ", "Lr ", "Rf ", "Db ", "Sg ", "Bh ",
+ "Hs ", "Mt ", "Ds ", "Rg ", "Cn ", "Nh ", "Fl ", "Mc ", "Lv ", "Ts ", "Og "
};
/*! \internal
int qmMult_ = 1;
//! Method used for QM calculation (default DFT with PBE functional)
QMMMQMMethod qmMethod_ = QMMMQMMethod::PBE;
- //! String containing name of the input file for CP2K (default "topol-qmmm.inp")
- std::string qmInputFileName_ = "topol-qmmm.inp";
- //! String containing name of the PDB file for CP2K input (default "topol-qmmm.pdb")
- std::string qmPdbFileName_ = "topol-qmmm.pdb";
+ /*! \brief String containing name of the CP2K files (*.inp, *.out, *.pdb)
+ * default value empty, means will be deduced from *.tpr name during mdrun
+ */
+ std::string qmFileNameBase_;
//! String containing whole CP2K input which can be stored inside *.tpr
std::string qmInput_;
//! String containing PDB file for CP2K input which can be stored inside *.tpr
std::string qmPdb_;
//! Matrix that contains vectors defining QM box
matrix qmBox_;
- //! Matrix that contains vectors defining QM box
+ //! Translation vector to center QM subsystem inside the QM Box
RVec qmTrans_;
//! Constructor with default initializers for arrays
CPP_SOURCE_FILES
qmmminputgenerator.cpp
qmmmtopologypreprocessor.cpp
+ qmmmforceprovider.cpp
)
+
+# For QMMMForceProvider test we need to define wether libcp2k linked
+if (GMX_CP2K)
+ set_source_files_properties(qmmmforceprovider.cpp PROPERTIES COMPILE_DEFINITIONS GMX_CP2K=1)
+else()
+ set_source_files_properties(qmmmforceprovider.cpp PROPERTIES COMPILE_DEFINITIONS GMX_CP2K=0)
+endif()
--- /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
+ * Tests for QMMMForceProvider class for QMMM MDModule
+ *
+ * \author Dmitry Morozov <dmitry.morozov@jyu.fi>
+ * \ingroup module_applied_forces
+ */
+#include "gmxpre.h"
+
+#include "gromacs/applied_forces/qmmm/qmmmforceprovider.h"
+
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/domdec/localatomsetmanager.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/gmxpreprocess/grompp.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_lookup.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/textwriter.h"
+#include "testutils/cmdlinetest.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+
+namespace gmx
+{
+
+class QMMMForceProviderTest : public ::testing::Test
+{
+public:
+ void setDefaultParameters()
+ {
+ parameters_.active_ = true;
+ std::vector<gmx::index> qmIndicies = { 0, 1, 2 };
+ std::vector<gmx::index> mmIndicies = { 3, 4, 5 };
+ LocalAtomSet set1 = atomSetManager_.add(ArrayRef<const gmx::index>(qmIndicies));
+ LocalAtomSet set2 = atomSetManager_.add(ArrayRef<const gmx::index>(mmIndicies));
+ qmAtomSet_ = std::make_unique<LocalAtomSet>(set1);
+ mmAtomSet_ = std::make_unique<LocalAtomSet>(set2);
+ }
+
+protected:
+ QMMMParameters parameters_;
+ LocalAtomSetManager atomSetManager_;
+ std::unique_ptr<LocalAtomSet> qmAtomSet_;
+ std::unique_ptr<LocalAtomSet> mmAtomSet_;
+ PbcType pbcType_;
+ MDLogger logger_;
+};
+
+TEST_F(QMMMForceProviderTest, CanConstructOrNot)
+{
+ setDefaultParameters();
+
+ // GMX_CP2K is defined in CMakeList.txt trough set_source_files_properties()
+ if (GMX_CP2K)
+ {
+ // if libcp2k linked then we do not expect throws
+ EXPECT_NO_THROW(QMMMForceProvider forceProvider(
+ parameters_, *qmAtomSet_, *mmAtomSet_, pbcType_, logger_));
+ }
+ else
+ {
+ // if libcp2k not linked then we expect throw from constructor
+ EXPECT_ANY_THROW(QMMMForceProvider forceProvider(
+ parameters_, *qmAtomSet_, *mmAtomSet_, pbcType_, logger_));
+ }
+}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff