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/*
* 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,
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* 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
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* consider code for inclusion in the official distribution, but
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* 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.
*/
/*! \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 <filesystem>
#include "listed_forces/conversionscommon.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/math/paddedvector.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.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/pbcutil/pbc.h"
#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/vectypes.h"
#include "nblib/box.h"
#include "nblib/exception.h"
#include "nblib/listed_forces/bondtypes.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, &inputRecord, &globalState, &molecularTopology);
// init forcerec
t_forcerec forceRecord;
gmx::MpiComm mpiComm = gmx::MpiComm(gmx::MpiComm::SingleRank{});
t_commrec commrec(mpiComm, mpiComm, nullptr);
gmx::ForceProviders forceProviders;
forceRecord.forceProviders = &forceProviders;
init_forcerec(nullptr,
gmx::MDLogger(),
simulationWorkload,
&forceRecord,
inputRecord,
molecularTopology,
&commrec,
nullptr,
globalState.box,
nullptr,
nullptr,
gmx::ArrayRef<const std::string>{},
-1,
std::nullopt);
nonbondedParameters_ = makeNonBondedParameterLists(molecularTopology.ffparams.atnr,
false,
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());
const double initMassLambda =
(inputRecord.efep == FreeEnergyPerturbationType::No
? 0.0
: inputRecord.fepvals->initialLambda(FreeEnergyPerturbationCouplingType::Mass));
update_mdatoms(mdAtoms->mdatoms(), initMassLambda);
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());
// Copy listed interactions data
int listedInteractionCount = gmx_mtop_interaction_count(molecularTopology, IF_BOND)
+ gmx_mtop_interaction_count(molecularTopology, IF_PAIR)
+ gmx_mtop_interaction_count(molecularTopology, IF_DIHEDRAL);
if (listedInteractionCount != 0)
{
InteractionDefinitions interactionDefinitions = localtop.idef;
listedInteractionData_ = convertToNblibInteractions(interactionDefinitions);
}
}
Box TprReader::getBox() const
{
return Box(boxX_, boxY_, boxZ_);
}
} // namespace nblib
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