From: Mark Abraham Date: Thu, 3 Jun 2021 08:26:22 +0000 (+0200) Subject: Convert atomInfo to int64_t X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=59f107b0b9b7146eb1c29915feef4ce32679247f;p=alexxy%2Fgromacs.git Convert atomInfo to int64_t This ensures we can use bits from a 64-bit range if we ever need that. Or easily switch to 32-bit range if that's advantageous. Refs #4004 --- diff --git a/api/nblib/forcecalculator.cpp b/api/nblib/forcecalculator.cpp index e9811f46fb..06a52872b4 100644 --- a/api/nblib/forcecalculator.cpp +++ b/api/nblib/forcecalculator.cpp @@ -70,9 +70,9 @@ void ForceCalculator::compute(gmx::ArrayRef coordinates, gmx::ArrayR gmxForceCalculator_->compute(coordinates, forces); } -void ForceCalculator::updatePairList(gmx::ArrayRef particleInfoAllVdW, - gmx::ArrayRef coordinates, - const Box& box) +void ForceCalculator::updatePairList(gmx::ArrayRef particleInfoAllVdW, + gmx::ArrayRef coordinates, + const Box& box) { gmxForceCalculator_->setParticlesOnGrid(particleInfoAllVdW, coordinates, box); } diff --git a/api/nblib/forcecalculator.h b/api/nblib/forcecalculator.h index ca7173aa2c..8a16c945e2 100644 --- a/api/nblib/forcecalculator.h +++ b/api/nblib/forcecalculator.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2020, by the GROMACS development team, led by + * 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. @@ -99,9 +99,9 @@ public: * \param coordinates The coordinates to be placed on grids * \param[in] box The system simulation box */ - void updatePairList(gmx::ArrayRef particleInfoAllVdW, - gmx::ArrayRef coordinates, - const Box& box); + void updatePairList(gmx::ArrayRef particleInfoAllVdW, + gmx::ArrayRef coordinates, + const Box& box); private: //! GROMACS force calculator to compute forces diff --git a/api/nblib/gmxcalculator.cpp b/api/nblib/gmxcalculator.cpp index 751ed51518..81e740f7c0 100644 --- a/api/nblib/gmxcalculator.cpp +++ b/api/nblib/gmxcalculator.cpp @@ -87,7 +87,7 @@ void GmxForceCalculator::compute(gmx::ArrayRef coordinateInput, nbv_->atomdata_add_nbat_f_to_f(gmx::AtomLocality::All, forceOutput); } -void GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef particleInfoAllVdw, +void GmxForceCalculator::setParticlesOnGrid(gmx::ArrayRef particleInfoAllVdw, gmx::ArrayRef coordinates, const Box& box) { diff --git a/api/nblib/gmxcalculator.h b/api/nblib/gmxcalculator.h index b5cd04382d..71a56ebb08 100644 --- a/api/nblib/gmxcalculator.h +++ b/api/nblib/gmxcalculator.h @@ -1,7 +1,7 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2020, by the GROMACS development team, led by + * 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. @@ -94,7 +94,7 @@ public: void compute(gmx::ArrayRef coordinateInput, gmx::ArrayRef forceOutput); //! Puts particles on a grid based on bounds specified by the box (for every NS step) - void setParticlesOnGrid(gmx::ArrayRef particleInfoAllVdw, + void setParticlesOnGrid(gmx::ArrayRef particleInfoAllVdw, gmx::ArrayRef coordinates, const Box& box); diff --git a/api/nblib/gmxsetup.h b/api/nblib/gmxsetup.h index 4b61b2e77e..3382cf17ec 100644 --- a/api/nblib/gmxsetup.h +++ b/api/nblib/gmxsetup.h @@ -121,7 +121,7 @@ private: std::vector nonbondedParameters_; //! Particle info where all particles are marked to have Van der Waals interactions - std::vector particleInfoAllVdw_; + std::vector particleInfoAllVdw_; //! GROMACS force calculator to compute forces std::unique_ptr gmxForceCalculator_; diff --git a/src/gromacs/domdec/domdec_constraints.cpp b/src/gromacs/domdec/domdec_constraints.cpp index 9a6813dfe2..6be77ec4b2 100644 --- a/src/gromacs/domdec/domdec_constraints.cpp +++ b/src/gromacs/domdec/domdec_constraints.cpp @@ -223,7 +223,7 @@ static void walk_out(int con, /*! \brief Looks up SETTLE constraints for a range of charge-groups */ static void atoms_to_settles(gmx_domdec_t* dd, const gmx_mtop_t& mtop, - const int* atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef> at2settle_mt, int cg_start, int cg_end, @@ -298,7 +298,7 @@ static void atoms_to_settles(gmx_domdec_t* dd, /*! \brief Looks up constraint for the local atoms */ static void atoms_to_constraints(gmx_domdec_t* dd, const gmx_mtop_t& mtop, - const int* atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef> at2con_mt, int nrec, InteractionList* ilc_local, @@ -399,7 +399,7 @@ static void atoms_to_constraints(gmx_domdec_t* dd, int dd_make_local_constraints(gmx_domdec_t* dd, int at_start, const struct gmx_mtop_t& mtop, - const int* atomInfo, + gmx::ArrayRef atomInfo, gmx::Constraints* constr, int nrec, gmx::ArrayRef il_local) diff --git a/src/gromacs/domdec/domdec_constraints.h b/src/gromacs/domdec/domdec_constraints.h index 81390a8f99..b2e366d3d8 100644 --- a/src/gromacs/domdec/domdec_constraints.h +++ b/src/gromacs/domdec/domdec_constraints.h @@ -64,7 +64,7 @@ void dd_clear_local_constraint_indices(gmx_domdec_t* dd); int dd_make_local_constraints(struct gmx_domdec_t* dd, int at_start, const struct gmx_mtop_t& mtop, - const int* atomInfo, + gmx::ArrayRef atomInfo, gmx::Constraints* constr, int nrec, gmx::ArrayRef il_local); diff --git a/src/gromacs/domdec/domdec_internal.h b/src/gromacs/domdec/domdec_internal.h index 0c30bf2551..40e6744461 100644 --- a/src/gromacs/domdec/domdec_internal.h +++ b/src/gromacs/domdec/domdec_internal.h @@ -189,6 +189,8 @@ typedef struct gmx_domdec_sort std::vector moved; /**< Integer buffer for sorting */ std::vector intBuffer; + /**< Int64 buffer for sorting */ + std::vector int64Buffer; } gmx_domdec_sort_t; /*! \brief Manages atom ranges and order for the local state atom vectors */ diff --git a/src/gromacs/domdec/localtopology.cpp b/src/gromacs/domdec/localtopology.cpp index ac2bb05500..ea4a68c725 100644 --- a/src/gromacs/domdec/localtopology.cpp +++ b/src/gromacs/domdec/localtopology.cpp @@ -706,7 +706,7 @@ static void make_exclusions_zone(ArrayRef globalAtomInd gmx_domdec_zones_t* zones, ArrayRef molblockIndices, const std::vector& moltype, - const int* atomInfo, + gmx::ArrayRef atomInfo, ListOfLists* lexcls, int iz, int at_start, @@ -781,7 +781,7 @@ static void make_exclusions_zone(ArrayRef globalAtomInd static int make_local_bondeds_excls(gmx_domdec_t* dd, gmx_domdec_zones_t* zones, const gmx_mtop_t& mtop, - const int* atomInfo, + ArrayRef atomInfo, const bool checkDistanceMultiBody, const ivec rcheck, const gmx_bool checkDistanceTwoBody, @@ -1001,7 +1001,7 @@ int dd_make_local_top(gmx_domdec_t* dd, int numBondedInteractionsToReduce = make_local_bondeds_excls(dd, zones, mtop, - fr->atomInfo.data(), + fr->atomInfo, checkDistanceMultiBody, rcheck, checkDistanceTwoBody, diff --git a/src/gromacs/domdec/partition.cpp b/src/gromacs/domdec/partition.cpp index cbf0fe493f..46cef19234 100644 --- a/src/gromacs/domdec/partition.cpp +++ b/src/gromacs/domdec/partition.cpp @@ -481,7 +481,7 @@ static void dd_set_atominfo(gmx::ArrayRef index_gl, int cg0, int cg1, { gmx::ArrayRef atomInfoForEachMoleculeBlock = fr->atomInfoForEachMoleculeBlock; - gmx::ArrayRef atomInfo = fr->atomInfo; + gmx::ArrayRef atomInfo = fr->atomInfo; for (int cg = cg0; cg < cg1; cg++) { @@ -1344,7 +1344,7 @@ static void merge_cg_buffers(int nce gmx::ArrayRef x, gmx::ArrayRef recv_vr, gmx::ArrayRef atomInfoForEachMoleculeBlock, - gmx::ArrayRef atomInfo) + gmx::ArrayRef atomInfo) { gmx_domdec_ind_t *ind, *ind_p; int p, cell, c, cg, cg0, cg1, cg_gl; @@ -1580,7 +1580,7 @@ static void get_zone_pulse_groups(gmx_domdec_t* dd, gmx_bool bDist2B, gmx_bool bDistMB, gmx::ArrayRef coordinates, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, std::vector* localAtomGroups, dd_comm_setup_work_t* work) { @@ -2599,7 +2599,7 @@ static void dd_sort_state(gmx_domdec_t* dd, t_forcerec* fr, t_state* state) /* Reorder the global cg index */ orderVector(cgsort, dd->globalAtomGroupIndices, &sort->intBuffer); /* Reorder the atom info */ - orderVector(cgsort, fr->atomInfo, &sort->intBuffer); + orderVector(cgsort, fr->atomInfo, &sort->int64Buffer); /* Set the home atom number */ dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, dd->numHomeAtoms); @@ -3236,7 +3236,7 @@ void dd_partition_system(FILE* fplog, n = dd_make_local_constraints(dd, n, top_global, - fr->atomInfo.data(), + fr->atomInfo, constr, inputrec.nProjOrder, top_local->idef.il); diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp index 1862b75125..3cbb1124e7 100644 --- a/src/gromacs/mdlib/forcerec.cpp +++ b/src/gromacs/mdlib/forcerec.cpp @@ -288,7 +288,7 @@ makeAtomInfoForEachMoleculeBlock(const gmx_mtop_t& mtop, const t_forcerec* fr) for (int a = 0; a < molt.atoms.nr; a++) { const t_atom& atom = molt.atoms.atom[a]; - int& atomInfo = atomInfoOfMoleculeBlock.atomInfo[moleculeOffsetInBlock + a]; + int64_t& atomInfo = atomInfoOfMoleculeBlock.atomInfo[moleculeOffsetInBlock + a]; /* Store the energy group in atomInfo */ int gid = getGroupType(mtop.groups, @@ -345,12 +345,12 @@ makeAtomInfoForEachMoleculeBlock(const gmx_mtop_t& mtop, const t_forcerec* fr) return atomInfoForEachMoleculeBlock; } -static std::vector expandAtomInfo(const int nmb, - gmx::ArrayRef atomInfoForEachMoleculeBlock) +static std::vector expandAtomInfo(const int nmb, + gmx::ArrayRef atomInfoForEachMoleculeBlock) { const int numAtoms = atomInfoForEachMoleculeBlock[nmb - 1].indexOfLastAtomInMoleculeBlock; - std::vector atomInfo(numAtoms); + std::vector atomInfo(numAtoms); int mb = 0; for (int a = 0; a < numAtoms; a++) diff --git a/src/gromacs/mdtypes/atominfo.h b/src/gromacs/mdtypes/atominfo.h index 013ea6cb56..8697dc2501 100644 --- a/src/gromacs/mdtypes/atominfo.h +++ b/src/gromacs/mdtypes/atominfo.h @@ -49,7 +49,7 @@ namespace gmx { -/*! \brief Constants whose bit describes properties of atoms in +/*! \brief Constants whose bit describes a property of an atom in * AtomInfoWithinMoleculeBlock.atomInfo. * * No bit should exceed 1 << 63, so that it fits into a 64-bit @@ -59,16 +59,16 @@ namespace gmx * here, reserving bits 0-7 for the energy-group ID. */ //! \{ -static constexpr int sc_atomInfo_FreeEnergyPerturbation = 1 << 15; -static constexpr int sc_atomInfo_Exclusion = 1 << 17; -static constexpr int sc_atomInfo_Constraint = 1 << 20; -static constexpr int sc_atomInfo_Settle = 1 << 21; -static constexpr int sc_atomInfo_BondCommunication = 1 << 22; -static constexpr int sc_atomInfo_HasVdw = 1 << 23; -static constexpr int sc_atomInfo_HasCharge = 1 << 24; +static constexpr int64_t sc_atomInfo_FreeEnergyPerturbation = 1 << 15; +static constexpr int64_t sc_atomInfo_Exclusion = 1 << 17; +static constexpr int64_t sc_atomInfo_Constraint = 1 << 20; +static constexpr int64_t sc_atomInfo_Settle = 1 << 21; +static constexpr int64_t sc_atomInfo_BondCommunication = 1 << 22; +static constexpr int64_t sc_atomInfo_HasVdw = 1 << 23; +static constexpr int64_t sc_atomInfo_HasCharge = 1 << 24; //! \} //! The first 8 bits are reserved for energy-group ID -static constexpr int sc_atomInfo_EnergyGroupIdMask = 0b11111111; +static constexpr int64_t sc_atomInfo_EnergyGroupIdMask = 0b11111111; /*! \brief Contains information about each atom in a molecule block of * the global topology. */ @@ -94,7 +94,7 @@ struct AtomInfoWithinMoleculeBlock * * The vector needs to be indexed accordingly. */ - std::vector atomInfo; + std::vector atomInfo; }; } // namespace gmx diff --git a/src/gromacs/mdtypes/forcerec.h b/src/gromacs/mdtypes/forcerec.h index 838988ce35..8abdadfa9f 100644 --- a/src/gromacs/mdtypes/forcerec.h +++ b/src/gromacs/mdtypes/forcerec.h @@ -191,7 +191,7 @@ struct t_forcerec /* Information about atom properties for the molecule blocks in the global topology */ std::vector atomInfoForEachMoleculeBlock; /* Information about atom properties for local and non-local atoms */ - std::vector atomInfo; + std::vector atomInfo; std::vector shift_vec; diff --git a/src/gromacs/nbnxm/atomdata.cpp b/src/gromacs/nbnxm/atomdata.cpp index 4ccf58e213..8fd0569df2 100644 --- a/src/gromacs/nbnxm/atomdata.cpp +++ b/src/gromacs/nbnxm/atomdata.cpp @@ -861,13 +861,13 @@ static void nbnxn_atomdata_mask_fep(nbnxn_atomdata_t* nbat, const Nbnxm::GridSet } /* Copies the energy group indices to a reordered and packed array */ -static void copy_egp_to_nbat_egps(const int* a, - int na, - int na_round, - int na_c, - int bit_shift, - ArrayRef atomInfo, - int* atomInfoNb) +static void copy_egp_to_nbat_egps(const int* a, + int na, + int na_round, + int na_c, + int bit_shift, + ArrayRef atomInfo, + int* atomInfoNb) { int i = 0, j = 0; for (; i < na; i += na_c) @@ -894,7 +894,7 @@ static void copy_egp_to_nbat_egps(const int* a, /* Set the energy group indices for atoms in nbnxn_atomdata_t */ static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t::Params* params, const Nbnxm::GridSet& gridSet, - ArrayRef atomInfo) + ArrayRef atomInfo) { if (params->nenergrp == 1) { @@ -923,11 +923,11 @@ static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t::Params* params, } /* Sets all required atom parameter data in nbnxn_atomdata_t */ -void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat, - const Nbnxm::GridSet& gridSet, - ArrayRef atomTypes, - ArrayRef atomCharges, - ArrayRef atomInfo) +void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat, + const Nbnxm::GridSet& gridSet, + ArrayRef atomTypes, + ArrayRef atomCharges, + ArrayRef atomInfo) { nbnxn_atomdata_t::Params& params = nbat->paramsDeprecated(); diff --git a/src/gromacs/nbnxm/atomdata.h b/src/gromacs/nbnxm/atomdata.h index 23b0759abb..50c4d5f311 100644 --- a/src/gromacs/nbnxm/atomdata.h +++ b/src/gromacs/nbnxm/atomdata.h @@ -328,11 +328,11 @@ enum }; //! Sets the atomdata after pair search -void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat, - const Nbnxm::GridSet& gridSet, - gmx::ArrayRef atomTypes, - gmx::ArrayRef atomCharges, - gmx::ArrayRef atomInfo); +void nbnxn_atomdata_set(nbnxn_atomdata_t* nbat, + const Nbnxm::GridSet& gridSet, + gmx::ArrayRef atomTypes, + gmx::ArrayRef atomCharges, + gmx::ArrayRef atomInfo); //! Copy the shift vectors to nbat void nbnxn_atomdata_copy_shiftvec(bool dynamic_box, gmx::ArrayRef shift_vec, nbnxn_atomdata_t* nbat); diff --git a/src/gromacs/nbnxm/benchmark/bench_setup.cpp b/src/gromacs/nbnxm/benchmark/bench_setup.cpp index e45db48ca3..88faac52a1 100644 --- a/src/gromacs/nbnxm/benchmark/bench_setup.cpp +++ b/src/gromacs/nbnxm/benchmark/bench_setup.cpp @@ -220,7 +220,7 @@ static std::unique_ptr setupNbnxmForBenchInstance(const Kern const rvec lowerCorner = { 0, 0, 0 }; const rvec upperCorner = { system.box[XX][XX], system.box[YY][YY], system.box[ZZ][ZZ] }; - gmx::ArrayRef atomInfo; + gmx::ArrayRef atomInfo; if (options.useHalfLJOptimization) { atomInfo = system.atomInfoOxygenVdw; diff --git a/src/gromacs/nbnxm/benchmark/bench_system.h b/src/gromacs/nbnxm/benchmark/bench_system.h index f5e0bdd746..56b49a82cc 100644 --- a/src/gromacs/nbnxm/benchmark/bench_system.h +++ b/src/gromacs/nbnxm/benchmark/bench_system.h @@ -78,9 +78,9 @@ struct BenchmarkSystem //! Storage for atom partial charges. std::vector charges; //! Atom info where all atoms are marked to have Van der Waals interactions - std::vector atomInfoAllVdw; + std::vector atomInfoAllVdw; //! Atom info where only oxygen atoms are marked to have Van der Waals interactions - std::vector atomInfoOxygenVdw; + std::vector atomInfoOxygenVdw; //! Information about exclusions. ListOfLists excls; //! Storage for atom positions. diff --git a/src/gromacs/nbnxm/grid.cpp b/src/gromacs/nbnxm/grid.cpp index bfd143a0a9..75b44dfdcb 100644 --- a/src/gromacs/nbnxm/grid.cpp +++ b/src/gromacs/nbnxm/grid.cpp @@ -798,12 +798,12 @@ static void print_bbsizes_supersub(FILE* fp, const Grid& grid) * * Sorts atoms on LJ coefficients: !=0 first, ==0 at the end. */ -static void sort_cluster_on_flag(int numAtomsInCluster, - int atomStart, - int atomEnd, - gmx::ArrayRef atomInfo, - gmx::ArrayRef order, - int* flags) +static void sort_cluster_on_flag(int numAtomsInCluster, + int atomStart, + int atomEnd, + gmx::ArrayRef atomInfo, + gmx::ArrayRef order, + int* flags) { constexpr int c_maxNumAtomsInCluster = 8; int sort1[c_maxNumAtomsInCluster]; @@ -879,7 +879,7 @@ void Grid::fillCell(GridSetData* gridSetData, nbnxn_atomdata_t* nbat, int atomStart, int atomEnd, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, BoundingBox gmx_unused* bb_work_aligned) { @@ -1025,7 +1025,7 @@ void Grid::fillCell(GridSetData* gridSetData, void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData, int dd_zone, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, nbnxn_atomdata_t* nbat, const gmx::Range columnRange, @@ -1100,7 +1100,7 @@ void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData, /* Spatially sort the atoms within one grid column */ void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData, int dd_zone, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, nbnxn_atomdata_t* nbat, const gmx::Range columnRange, @@ -1370,7 +1370,7 @@ void Grid::setCellIndices(int ddZone, GridSetData* gridSetData, gmx::ArrayRef gridWork, const gmx::Range atomRange, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, const int numAtomsMoved, nbnxn_atomdata_t* nbat) diff --git a/src/gromacs/nbnxm/grid.h b/src/gromacs/nbnxm/grid.h index 5c669446cd..19e440f548 100644 --- a/src/gromacs/nbnxm/grid.h +++ b/src/gromacs/nbnxm/grid.h @@ -349,7 +349,7 @@ public: GridSetData* gridSetData, gmx::ArrayRef gridWork, gmx::Range atomRange, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, int numAtomsMoved, nbnxn_atomdata_t* nbat); @@ -375,14 +375,14 @@ private: nbnxn_atomdata_t* nbat, int atomStart, int atomEnd, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, BoundingBox gmx_unused* bb_work_aligned); //! Spatially sort the atoms within the given column range, for CPU geometry void sortColumnsCpuGeometry(GridSetData* gridSetData, int dd_zone, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, nbnxn_atomdata_t* nbat, gmx::Range columnRange, @@ -391,7 +391,7 @@ private: //! Spatially sort the atoms within the given column range, for GPU geometry void sortColumnsGpuGeometry(GridSetData* gridSetData, int dd_zone, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, nbnxn_atomdata_t* nbat, gmx::Range columnRange, diff --git a/src/gromacs/nbnxm/gridset.cpp b/src/gromacs/nbnxm/gridset.cpp index 07d5f9a042..c3a1a7ec26 100644 --- a/src/gromacs/nbnxm/gridset.cpp +++ b/src/gromacs/nbnxm/gridset.cpp @@ -152,7 +152,7 @@ void GridSet::putOnGrid(const matrix box, const gmx::UpdateGroupsCog* updateGroupsCog, const gmx::Range atomRange, real atomDensity, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, const int numAtomsMoved, const int* move, diff --git a/src/gromacs/nbnxm/gridset.h b/src/gromacs/nbnxm/gridset.h index 340a673f5e..be9b5237dd 100644 --- a/src/gromacs/nbnxm/gridset.h +++ b/src/gromacs/nbnxm/gridset.h @@ -126,7 +126,7 @@ public: const gmx::UpdateGroupsCog* updateGroupsCog, gmx::Range atomRange, real atomDensity, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, int numAtomsMoved, const int* move, diff --git a/src/gromacs/nbnxm/nbnxm.cpp b/src/gromacs/nbnxm/nbnxm.cpp index e0aae3761f..dca77313ed 100644 --- a/src/gromacs/nbnxm/nbnxm.cpp +++ b/src/gromacs/nbnxm/nbnxm.cpp @@ -64,7 +64,7 @@ void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet, const gmx::UpdateGroupsCog* updateGroupsCog, gmx::Range atomRange, real atomDensity, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, int numAtomsMoved, const int* move) @@ -86,7 +86,7 @@ void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet, /* Calls nbnxn_put_on_grid for all non-local domains */ void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv, const struct gmx_domdec_zones_t* zones, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x) { for (int zone = 1; zone < zones->n; zone++) @@ -138,9 +138,9 @@ void nonbonded_verlet_t::setLocalAtomOrder() const pairSearch_->setLocalAtomOrder(); } -void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef atomTypes, - gmx::ArrayRef atomCharges, - gmx::ArrayRef atomInfo) const +void nonbonded_verlet_t::setAtomProperties(gmx::ArrayRef atomTypes, + gmx::ArrayRef atomCharges, + gmx::ArrayRef atomInfo) const { nbnxn_atomdata_set(nbat.get(), pairSearch_->gridSet(), atomTypes, atomCharges, atomInfo); } diff --git a/src/gromacs/nbnxm/nbnxm.h b/src/gromacs/nbnxm/nbnxm.h index 545f85ef4a..e3e90d9238 100644 --- a/src/gromacs/nbnxm/nbnxm.h +++ b/src/gromacs/nbnxm/nbnxm.h @@ -314,9 +314,9 @@ public: t_nrnb* nrnb) const; //! Updates all the atom properties in Nbnxm - void setAtomProperties(gmx::ArrayRef atomTypes, - gmx::ArrayRef atomCharges, - gmx::ArrayRef atomInfo) const; + void setAtomProperties(gmx::ArrayRef atomTypes, + gmx::ArrayRef atomCharges, + gmx::ArrayRef atomInfo) const; /*!\brief Convert the coordinates to NBNXM format for the given locality. * @@ -491,7 +491,7 @@ void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet, const gmx::UpdateGroupsCog* updateGroupsCog, gmx::Range atomRange, real atomDensity, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, int numAtomsMoved, const int* move); @@ -503,7 +503,7 @@ void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet, */ void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nb_verlet, const struct gmx_domdec_zones_t* zones, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x); /*! \brief Check if GROMACS has been built with GPU support. diff --git a/src/gromacs/nbnxm/pairsearch.h b/src/gromacs/nbnxm/pairsearch.h index 7da87cf5c3..1bb1898d98 100644 --- a/src/gromacs/nbnxm/pairsearch.h +++ b/src/gromacs/nbnxm/pairsearch.h @@ -185,7 +185,7 @@ public: const gmx::UpdateGroupsCog* updateGroupsCog, gmx::Range atomRange, real atomDensity, - gmx::ArrayRef atomInfo, + gmx::ArrayRef atomInfo, gmx::ArrayRef x, int numAtomsMoved, const int* move,