src/gromacs/domdec/mdsetup.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "mdsetup.h"
  38
  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/gmxassert.h"
  56 #include "gromacs/utility/smalloc.h"
  57
  58 namespace gmx
  59 {
  60
  61 /* TODO: Add a routine that collects the initial setup of the algorithms.
  62  *
  63  * The final solution should be an MD algorithm base class with methods
  64  * for initialization and atom-data setup.
  65  */
  66 void mdAlgorithmsSetupAtomData(const t_commrec*     cr,
  67                                const t_inputrec*    ir,
  68                                const gmx_mtop_t&    top_global,
  69                                gmx_localtop_t*      top,
  70                                t_forcerec*          fr,
  71                                ForceBuffers*        force,
  72                                MDAtoms*             mdAtoms,
  73                                Constraints*         constr,
  74                                VirtualSitesHandler* vsite,
  75                                gmx_shellfc_t*       shellfc)
  76 {
  77     bool usingDomDec = DOMAINDECOMP(cr);
  78
  79     int numAtomIndex;
  80     int numHomeAtoms;
  81     int numTotalAtoms;
  82
  83     if (usingDomDec)
  84     {
  85         numAtomIndex  = dd_natoms_mdatoms(cr->dd);
  86         numHomeAtoms  = dd_numHomeAtoms(*cr->dd);
  87         numTotalAtoms = dd_natoms_mdatoms(cr->dd);
  88     }
  89     else
  90     {
  91         numAtomIndex  = -1;
  92         numHomeAtoms  = top_global.natoms;
  93         numTotalAtoms = top_global.natoms;
  94     }
  95
  96     if (force != nullptr)
  97     {
  98         force->resize(numTotalAtoms);
  99     }
 100
 101     atoms2md(&top_global, ir, numAtomIndex,
 102              usingDomDec ? cr->dd->globalAtomIndices : std::vector<int>(), numHomeAtoms, mdAtoms);
 103
 104     auto mdatoms = mdAtoms->mdatoms();
 105     if (usingDomDec)
 106     {
 107         dd_sort_local_top(cr->dd, mdatoms, top);
 108     }
 109     else
 110     {
 111         gmx_mtop_generate_local_top(top_global, top, ir->efep != efepNO);
 112     }
 113
 114     if (vsite)
 115     {
 116         vsite->setVirtualSites(top->idef.il, *mdatoms);
 117     }
 118
 119     /* Note that with DD only flexible constraints, not shells, are supported
 120      * and these don't require setup in make_local_shells().
 121      *
 122      * TODO: This should only happen in ShellFCElement (it is called directly by the modular
 123      *       simulator ShellFCElement already, but still used here by legacy simulators)
 124      */
 125     if (!usingDomDec && shellfc)
 126     {
 127         make_local_shells(cr, mdatoms, shellfc);
 128     }
 129
 130     for (auto& listedForces : fr->listedForces)
 131     {
 132         listedForces.setup(top->idef, fr->natoms_force, fr->gpuBonded != nullptr);
 133     }
 134
 135     if (EEL_PME(fr->ic->eeltype) && (cr->duty & DUTY_PME))
 136     {
 137         /* This handles the PP+PME rank case where fr->pmedata is valid.
 138          * For PME-only ranks, gmx_pmeonly() has its own call to gmx_pme_reinit_atoms().
 139          */
 140         const int numPmeAtoms = numHomeAtoms - fr->n_tpi;
 141         gmx_pme_reinit_atoms(fr->pmedata, numPmeAtoms, mdatoms->chargeA, mdatoms->chargeB);
 142     }
 143
 144     if (constr)
 145     {
 146         constr->setConstraints(top, mdatoms->nr, mdatoms->homenr, mdatoms->massT, mdatoms->invmass,
 147                                mdatoms->nMassPerturbed != 0, mdatoms->lambda, mdatoms->cFREEZE);
 148     }
 149 }
 150
 151 } // namespace gmx