/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/tests/ |
H A D | updategroupscog.cpp | 119 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()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
H A D | updategroupscog.cpp | 80 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()
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H A D | updategroupscog.h | 91 …void addCogs(gmx::ArrayRef<const int> globalAtomIndices, gmx::ArrayRef<const gmx::RVec> coordinate…
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H A D | update.cpp | 1171 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()
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H A D | constr.cpp | 297 ii = dd->globalAtomIndices[i]; in write_constr_pdb()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/domdec/ |
H A D | mdsetup.cpp | 102 usingDomDec ? cr->dd->globalAtomIndices : std::vector<int>(), numHomeAtoms, mdAtoms); in mdAlgorithmsSetupAtomData()
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H A D | domdec_specatomcomm.cpp | 528 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()
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H A D | domdec_struct.h | 222 std::vector<int> globalAtomIndices; member
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H A D | domdec_topology.cpp | 200 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()
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H A D | dump.cpp | 176 int ii = dd->globalAtomIndices[i]; in write_dd_pdb()
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H A D | domdec_constraints.cpp | 250 int a_gl = dd->globalAtomIndices[a]; in atoms_to_settles() 330 int a_gl = dd->globalAtomIndices[a]; in atoms_to_constraints()
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H A D | redistribute.cpp | 134 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()
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H A D | partition.cpp | 484 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()
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H A D | distribute.cpp | 510 dd->globalAtomIndices.resize(dd->comm->atomRanges.numHomeAtoms()); in distributeAtomGroups()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdlib/ |
H A D | force.cpp | 191 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork); in do_force_lowlevel()
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H A D | force.cpp.preplumed | 185 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, stepWork);
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/ |
H A D | md.cpp | 647 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()
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H A D | minimize.cpp | 303 a_max = cr->dd->globalAtomIndices[la_max]; in get_f_norm_max() 535 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in init_em()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/ |
H A D | md.cpp | 739 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()
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H A D | minimize.cpp | 324 a_max = cr->dd->globalAtomIndices[la_max]; in get_f_norm_max() 518 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in init_em()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/ |
H A D | md.cpp | 722 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()
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H A D | minimize.cpp | 314 a_max = cr->dd->globalAtomIndices[la_max]; in get_f_norm_max() 514 plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data()); in init_em()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdlib/ |
H A D | force.cpp | 347 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr, in do_force_lowlevel()
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H A D | force.cpp.preplumed | 341 DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/ |
H A D | shellfc.cpp | 585 shells.push_back(shfc->shell_gl[ind[dd->globalAtomIndices[i]]]); in make_local_shells()
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