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39 #include "gromacs/domdec/domdec.h"
40 #include "gromacs/domdec/domdec_struct.h"
41 #include "gromacs/ewald/pme.h"
42 #include "gromacs/listed_forces/listed_forces.h"
43 #include "gromacs/mdlib/constr.h"
44 #include "gromacs/mdlib/mdatoms.h"
45 #include "gromacs/mdlib/vsite.h"
46 #include "gromacs/mdtypes/commrec.h"
47 #include "gromacs/mdtypes/forcebuffers.h"
48 #include "gromacs/mdtypes/forcerec.h"
49 #include "gromacs/mdtypes/inputrec.h"
50 #include "gromacs/mdtypes/interaction_const.h"
51 #include "gromacs/mdtypes/mdatom.h"
52 #include "gromacs/pbcutil/pbc.h"
53 #include "gromacs/topology/mtop_util.h"
54 #include "gromacs/topology/topology.h"
55 #include "gromacs/utility/arrayref.h"
56 #include "gromacs/utility/gmxassert.h"
57 #include "gromacs/utility/smalloc.h"
62 /* TODO: Add a routine that collects the initial setup of the algorithms.
64 * The final solution should be an MD algorithm base class with methods
65 * for initialization and atom-data setup.
67 void mdAlgorithmsSetupAtomData(const t_commrec* cr,
68 const t_inputrec& inputrec,
69 const gmx_mtop_t& top_global,
75 VirtualSitesHandler* vsite,
76 gmx_shellfc_t* shellfc)
78 bool usingDomDec = DOMAINDECOMP(cr);
86 numAtomIndex = dd_natoms_mdatoms(*cr->dd);
87 numHomeAtoms = dd_numHomeAtoms(*cr->dd);
88 numTotalAtoms = dd_natoms_mdatoms(*cr->dd);
93 numHomeAtoms = top_global.natoms;
94 numTotalAtoms = top_global.natoms;
99 force->resize(numTotalAtoms);
105 usingDomDec ? cr->dd->globalAtomIndices : std::vector<int>(),
109 t_mdatoms* mdatoms = mdAtoms->mdatoms();
112 dd_sort_local_top(*cr->dd, mdatoms, top);
116 gmx_mtop_generate_local_top(top_global, top, inputrec.efep != FreeEnergyPerturbationType::No);
121 vsite->setVirtualSites(top->idef.il,
124 gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr));
127 /* Note that with DD only flexible constraints, not shells, are supported
128 * and these don't require setup in make_local_shells().
130 * TODO: This should only happen in ShellFCElement (it is called directly by the modular
131 * simulator ShellFCElement already, but still used here by legacy simulators)
133 if (!usingDomDec && shellfc)
135 make_local_shells(cr, *mdatoms, shellfc);
138 for (auto& listedForces : fr->listedForces)
140 listedForces.setup(top->idef, fr->natoms_force, fr->listedForcesGpu != nullptr);
143 if (EEL_PME(fr->ic->eeltype) && (cr->duty & DUTY_PME))
145 /* This handles the PP+PME rank case where fr->pmedata is valid.
146 * For PME-only ranks, gmx_pmeonly() has its own call to gmx_pme_reinit_atoms().
148 const int numPmeAtoms = numHomeAtoms - fr->n_tpi;
149 gmx_pme_reinit_atoms(fr->pmedata,
151 mdatoms->chargeA ? gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr)
152 : gmx::ArrayRef<real>{},
153 mdatoms->chargeB ? gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr)
154 : gmx::ArrayRef<real>{});
159 constr->setConstraints(top,
162 gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
163 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
164 mdatoms->nMassPerturbed != 0,
166 mdatoms->cFREEZE ? gmx::arrayRefFromArray(mdatoms->cFREEZE, mdatoms->nr)
167 : gmx::ArrayRef<const unsigned short>());