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Searched refs:globalAtomIndices (Results 1 – 25 of 34) sorted by relevance

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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/tests/
H A Dupdategroupscog.cpp119 std::vector<int> globalAtomIndices(numAtoms); in TEST() local
122 globalAtomIndices[i] = i; in TEST()
132 std::swap(globalAtomIndices[a1], globalAtomIndices[a2]); in TEST()
137 updateGroupsCog.addCogs(globalAtomIndices, positions); in TEST()
144 cogPerAtom[globalAtomIndices[i]] = updateGroupsCog.cogForAtom(i); in TEST()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/
H A Dupdategroupscog.cpp80 void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices, in addCogs() argument
86 GMX_RELEASE_ASSERT(globalAtomIndices.ssize() >= localAtomBegin, in addCogs()
90 cogIndices_.reserve(globalAtomIndices.size()); in addCogs()
93 for (gmx::index localAtom = localAtomBegin; localAtom < globalAtomIndices.ssize(); localAtom++) in addCogs()
95 const int globalAtom = globalAtomIndices[localAtom]; in addCogs()
H A Dupdategroupscog.h91 …void addCogs(gmx::ArrayRef<const int> globalAtomIndices, gmx::ArrayRef<const gmx::RVec> coordinate…
H A Dupdate.cpp1171 v, f, step, seed, DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr); in do_update_sd()
1394 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr); in update_sd_second_half()
1531 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr); in update_coords()
H A Dconstr.cpp297 ii = dd->globalAtomIndices[i]; in write_constr_pdb()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/domdec/
H A Dmdsetup.cpp102 usingDomDec ? cr->dd->globalAtomIndices : std::vector<int>(), numHomeAtoms, mdAtoms); in mdAlgorithmsSetupAtomData()
H A Ddomdec_specatomcomm.cpp528 dd->globalAtomIndices.resize(nat_tot_specat + spas->nrecv); in setup_specat_communication()
531 … spac->ibuf.size(), dd->globalAtomIndices.data() + nat_tot_specat, spas->nrecv); in setup_specat_communication()
555 ga2la_specat->insert_or_assign(dd->globalAtomIndices[i], i); in setup_specat_communication()
H A Ddomdec_struct.h222 std::vector<int> globalAtomIndices; member
H A Ddomdec_topology.cpp200 gmx::ArrayRef<const int> globalAtomIndices, in flagInteractionsForType() argument
211 const int a0 = globalAtomIndices[ia[1]]; in flagInteractionsForType()
237 if (globalAtomIndices[ia[1 + a]] in flagInteractionsForType()
281 cr->dd->globalAtomIndices, isAssigned); in printMissingInteractionsMolblock()
1288 const int i_gl = dd->globalAtomIndices[i]; in make_bondeds_zone()
1343 a_gl = dd->globalAtomIndices[at]; in make_exclusions_zone()
1364 … intermolecularExclusionGroup.end(), dd->globalAtomIndices[at]) in make_exclusions_zone()
H A Ddump.cpp176 int ii = dd->globalAtomIndices[i]; in write_dd_pdb()
H A Ddomdec_constraints.cpp250 int a_gl = dd->globalAtomIndices[a]; in atoms_to_settles()
330 int a_gl = dd->globalAtomIndices[a]; in atoms_to_constraints()
H A Dredistribute.cpp134 gmx::ArrayRef<const int> globalAtomIndices, in clear_and_mark_ind() argument
143 ga2la->erase(globalAtomIndices[a]); in clear_and_mark_ind()
732 clear_and_mark_ind(move, dd->globalAtomIndices, dd->ga2la, moved); in dd_redistribute_cg()
H A Dpartition.cpp484 std::vector<int>& globalAtomIndices = dd->globalAtomIndices; in make_dd_indices() local
494 globalAtomIndices.resize(a); in make_dd_indices()
518 globalAtomIndices.push_back(cg_gl); in make_dd_indices()
537 int globalAtomIndex = dd->globalAtomIndices[a]; in check_index_consistency()
569 if (dd->globalAtomIndices[a] != i) in check_index_consistency()
574 dd->rank, i + 1, a + 1, dd->globalAtomIndices[a] + 1); in check_index_consistency()
591 dd->rank, where, a + 1, dd->globalAtomIndices[a] + 1); in check_index_consistency()
616 ga2la.erase(dd->globalAtomIndices[i]); in clearDDStateIndices()
H A Ddistribute.cpp510 dd->globalAtomIndices.resize(dd->comm->atomRanges.numHomeAtoms()); in distributeAtomGroups()
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdlib/
H A Dforce.cpp191 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork); in do_force_lowlevel()
H A Dforce.cpp.preplumed185 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/
H A Dmd.cpp647 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
845 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
960 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
H A Dminimize.cpp303 a_max = cr->dd->globalAtomIndices[la_max]; in get_f_norm_max()
535 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in init_em()
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/
H A Dmd.cpp739 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
909 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
1033 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
H A Dminimize.cpp324 a_max = cr->dd->globalAtomIndices[la_max]; in get_f_norm_max()
518 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in init_em()
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/
H A Dmd.cpp722 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
923 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
1037 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in do_md()
H A Dminimize.cpp314 a_max = cr->dd->globalAtomIndices[la_max]; in get_f_norm_max()
514 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in init_em()
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdlib/
H A Dforce.cpp347 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, in do_force_lowlevel()
H A Dforce.cpp.preplumed341 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/
H A Dshellfc.cpp585 shells.push_back(shfc->shell_gl[ind[dd->globalAtomIndices[i]]]); in make_local_shells()

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