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/manage_threading.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/forcerec.h"
  48 #include "gromacs/mdtypes/inputrec.h"
  49 #include "gromacs/pbcutil/mshift.h"
  50 #include "gromacs/pbcutil/pbc.h"
  51 #include "gromacs/topology/mtop_util.h"
  52 #include "gromacs/topology/topology.h"
  53 #include "gromacs/utility/gmxassert.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 /* TODO: Add a routine that collects the initial setup of the algorithms.
  57  *
  58  * The final solution should be an MD algorithm base class with methods
  59  * for initialization and atom-data setup.
  60  */
  61 void mdAlgorithmsSetupAtomData(const t_commrec  *cr,
  62                                const t_inputrec *ir,
  63                                const gmx_mtop_t &top_global,
  64                                gmx_localtop_t   *top,
  65                                t_forcerec       *fr,
  66                                t_graph         **graph,
  67                                gmx::MDAtoms     *mdAtoms,
  68                                gmx::Constraints *constr,
  69                                gmx_vsite_t      *vsite,
  70                                gmx_shellfc_t    *shellfc)
  71 {
  72     bool  usingDomDec = DOMAINDECOMP(cr);
  73
  74     int   numAtomIndex, numHomeAtoms;
  75     int  *atomIndex;
  76
  77     if (usingDomDec)
  78     {
  79         numAtomIndex = dd_natoms_mdatoms(cr->dd);
  80         atomIndex    = cr->dd->globalAtomIndices.data();
  81         numHomeAtoms = dd_numHomeAtoms(*cr->dd);
  82     }
  83     else
  84     {
  85         numAtomIndex = -1;
  86         atomIndex    = nullptr;
  87         numHomeAtoms = top_global.natoms;
  88     }
  89     atoms2md(&top_global, ir, numAtomIndex, atomIndex, numHomeAtoms, mdAtoms);
  90
  91     auto mdatoms = mdAtoms->mdatoms();
  92     if (usingDomDec)
  93     {
  94         dd_sort_local_top(cr->dd, mdatoms, top);
  95     }
  96     else
  97     {
  98         gmx_mtop_generate_local_top(top_global, top, ir->efep != efepNO);
  99     }
 100
 101     if (vsite)
 102     {
 103         if (usingDomDec)
 104         {
 105             /* The vsites were already assigned by the domdec topology code.
 106              * We only need to do the thread division here.
 107              */
 108             split_vsites_over_threads(top->idef.il, top->idef.iparams,
 109                                       mdatoms, vsite);
 110         }
 111         else
 112         {
 113             set_vsite_top(vsite, top, mdatoms);
 114         }
 115     }
 116
 117     if (!usingDomDec && ir->ePBC != epbcNONE && !fr->bMolPBC)
 118     {
 119         GMX_ASSERT(graph != nullptr, "We use a graph with PBC (no periodic mols) and without DD");
 120
 121         *graph = mk_graph(nullptr, &(top->idef), 0, top_global.natoms, FALSE, FALSE);
 122     }
 123     else if (graph != nullptr)
 124     {
 125         *graph = nullptr;
 126     }
 127
 128     /* Note that with DD only flexible constraints, not shells, are supported
 129      * and these don't require setup in make_local_shells().
 130      *
 131      * TODO: This should only happen in ShellFCElement (it is called directly by the modular
 132      *       simulator ShellFCElement already, but still used here by legacy simulators)
 133      */
 134     if (!usingDomDec && shellfc)
 135     {
 136         make_local_shells(cr, mdatoms, shellfc);
 137     }
 138
 139     setup_bonded_threading(fr->bondedThreading,
 140                            fr->natoms_force,
 141                            fr->gpuBonded != nullptr,
 142                            top->idef);
 143
 144     if (EEL_PME(fr->ic->eeltype) && (cr->duty & DUTY_PME))
 145     {
 146         /* This handles the PP+PME rank case where fr->pmedata is valid.
 147          * For PME-only ranks, gmx_pmeonly() has its own call to gmx_pme_reinit_atoms().
 148          */
 149         const int numPmeAtoms = numHomeAtoms - fr->n_tpi;
 150         gmx_pme_reinit_atoms(fr->pmedata, numPmeAtoms, mdatoms->chargeA);
 151     }
 152
 153     if (constr)
 154     {
 155         constr->setConstraints(*top, *mdatoms);
 156     }
 157 }