src/gromacs/mdlib/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/mdatoms.h"
  44 #include "gromacs/mdlib/shellfc.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
  62 void mdAlgorithmsSetupAtomData(t_commrec         *cr,
  63                                const t_inputrec  *ir,
  64                                const gmx_mtop_t  *top_global,
  65                                gmx_localtop_t    *top,
  66                                t_forcerec        *fr,
  67                                t_graph          **graph,
  68                                gmx::MDAtoms      *mdAtoms,
  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->gatindex;
  81         numHomeAtoms = cr->dd->nat_home;
  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         /* Currently gmx_generate_local_top allocates and returns a pointer.
  99          * We should implement a more elegant solution.
 100          */
 101         gmx_localtop_t *tmpTop;
 102
 103         tmpTop = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
 104         *top   = *tmpTop;
 105         sfree(tmpTop);
 106     }
 107
 108     if (vsite)
 109     {
 110         if (usingDomDec)
 111         {
 112             /* The vsites were already assigned by the domdec topology code.
 113              * We only need to do the thread division here.
 114              */
 115             split_vsites_over_threads(top->idef.il, top->idef.iparams,
 116                                       mdatoms, vsite);
 117         }
 118         else
 119         {
 120             set_vsite_top(vsite, top, mdatoms);
 121         }
 122     }
 123
 124     if (!usingDomDec && ir->ePBC != epbcNONE && !fr->bMolPBC)
 125     {
 126         GMX_ASSERT(graph != NULL, "We use a graph with PBC (no periodic mols) and without DD");
 127
 128         *graph = mk_graph(nullptr, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
 129     }
 130     else if (graph != nullptr)
 131     {
 132         *graph = nullptr;
 133     }
 134
 135     /* Note that with DD only flexible constraints, not shells, are supported
 136      * and these don't require setup in make_local_shells().
 137      */
 138     if (!usingDomDec && shellfc)
 139     {
 140         make_local_shells(cr, mdatoms, shellfc);
 141     }
 142
 143     setup_bonded_threading(fr, &top->idef);
 144
 145     gmx_pme_reinit_atoms(fr->pmedata, numHomeAtoms, mdatoms->chargeA);
 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      * TODO: this only handles the GPU logic so far, should handle CPU as well.
 149      * TODO: this also does not account for TPI.
 150      */
 151 }