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35 /*! \inpublicapi \file
37 * Implements nblib tpr reading
39 * \author Victor Holanda <victor.holanda@cscs.ch>
40 * \author Joe Jordan <ejjordan@kth.se>
41 * \author Prashanth Kanduri <kanduri@cscs.ch>
42 * \author Sebastian Keller <keller@cscs.ch>
45 #include "nblib/tpr.h"
47 #include "gromacs/fileio/tpxio.h"
48 #include "gromacs/gmxlib/network.h"
49 #include "gromacs/listed_forces/listed_forces.h"
50 #include "gromacs/mdtypes/forcerec.h"
51 #include "gromacs/mdlib/mdatoms.h"
52 #include "gromacs/mdlib/forcerec.h"
53 #include "gromacs/mdtypes/commrec.h"
54 #include "gromacs/mdtypes/iforceprovider.h"
55 #include "gromacs/mdtypes/inputrec.h"
56 #include "gromacs/mdtypes/mdatom.h"
57 #include "gromacs/mdtypes/simulation_workload.h"
58 #include "gromacs/mdtypes/state.h"
59 #include "gromacs/topology/mtop_util.h"
60 #include "gromacs/topology/topology.h"
61 #include "gromacs/utility/logger.h"
62 #include "nblib/box.h"
67 TprReader::TprReader(std::string filename)
69 t_inputrec inputRecord;
71 gmx_mtop_t molecularTopology;
72 gmx::SimulationWorkload simulationWorkload;
74 // If the file does not exist, this function will throw
75 PartialDeserializedTprFile partialDeserializedTpr =
76 read_tpx_state(filename.c_str(), &inputRecord, &globalState, &molecularTopology);
79 t_forcerec forceRecord;
81 gmx::ForceProviders forceProviders;
82 forceRecord.forceProviders = &forceProviders;
83 init_forcerec(nullptr,
93 gmx::ArrayRef<const std::string>{},
96 nonbondedParameters_ = makeNonBondedParameterLists(molecularTopology.ffparams.atnr,
97 molecularTopology.ffparams.iparams,
98 forceRecord.haveBuckingham);
100 gmx_localtop_t localtop(molecularTopology.ffparams);
101 gmx_mtop_generate_local_top(molecularTopology, &localtop, false);
102 exclusionListElements_ = std::vector<int>(localtop.excls.elementsView().begin(),
103 localtop.excls.elementsView().end());
104 exclusionListRanges_ = std::vector<int>(localtop.excls.listRangesView().begin(),
105 localtop.excls.listRangesView().end());
107 int ntopatoms = molecularTopology.natoms;
108 std::unique_ptr<gmx::MDAtoms> mdAtoms =
109 gmx::makeMDAtoms(nullptr, molecularTopology, inputRecord, false);
110 atoms2md(molecularTopology, inputRecord, -1, {}, ntopatoms, mdAtoms.get());
111 update_mdatoms(mdAtoms->mdatoms(), inputRecord.fepvals->init_lambda);
112 auto numParticles = mdAtoms->mdatoms()->nr;
113 charges_.resize(numParticles);
114 particleTypeIdOfAllParticles_.resize(numParticles);
115 inverseMasses_.resize(numParticles);
116 for (int i = 0; i < numParticles; i++)
118 charges_[i] = mdAtoms->mdatoms()->chargeA[i];
119 particleTypeIdOfAllParticles_[i] = mdAtoms->mdatoms()->typeA[i];
120 inverseMasses_[i] = mdAtoms->mdatoms()->invmass[i];
122 particleInteractionFlags_ = forceRecord.atomInfo;
124 if (TRICLINIC(globalState.box))
126 throw InputException("Only rectangular unit-cells are supported here");
128 boxX_ = globalState.box[XX][XX];
129 boxY_ = globalState.box[YY][YY];
130 boxZ_ = globalState.box[ZZ][ZZ];
131 coordinates_.assign(globalState.x.begin(), globalState.x.end());
132 velocities_.assign(globalState.v.begin(), globalState.v.end());
135 Box TprReader::getBox() const
137 return Box(boxX_, boxY_, boxZ_);