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/constr.h"
  44 #include "gromacs/mdlib/mdatoms.h"
  45 #include "gromacs/mdlib/shellfc.h"
  46 #include "gromacs/mdlib/vsite.h"
  47 #include "gromacs/mdtypes/commrec.h"
  48 #include "gromacs/mdtypes/forcerec.h"
  49 #include "gromacs/mdtypes/inputrec.h"
  50 #include "gromacs/pbcutil/mshift.h"
  51 #include "gromacs/pbcutil/pbc.h"
  52 #include "gromacs/topology/mtop_util.h"
  53 #include "gromacs/topology/topology.h"
  54 #include "gromacs/utility/gmxassert.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 /* TODO: Add a routine that collects the initial setup of the algorithms.
  58  *
  59  * The final solution should be an MD algorithm base class with methods
  60  * for initialization and atom-data setup.
  61  */
  62
  63 void mdAlgorithmsSetupAtomData(const t_commrec   *cr,
  64                                const t_inputrec  *ir,
  65                                const gmx_mtop_t  *top_global,
  66                                gmx_localtop_t    *top,
  67                                t_forcerec        *fr,
  68                                t_graph          **graph,
  69                                gmx::MDAtoms      *mdAtoms,
  70                                gmx::Constraints  *constr,
  71                                gmx_vsite_t       *vsite,
  72                                gmx_shellfc_t     *shellfc)
  73 {
  74     bool  usingDomDec = DOMAINDECOMP(cr);
  75
  76     int   numAtomIndex, numHomeAtoms;
  77     int  *atomIndex;
  78
  79     if (usingDomDec)
  80     {
  81         numAtomIndex = dd_natoms_mdatoms(cr->dd);
  82         atomIndex    = cr->dd->globalAtomIndices.data();
  83         numHomeAtoms = dd_numHomeAtoms(*cr->dd);
  84     }
  85     else
  86     {
  87         numAtomIndex = -1;
  88         atomIndex    = nullptr;
  89         numHomeAtoms = top_global->natoms;
  90     }
  91     atoms2md(top_global, ir, numAtomIndex, atomIndex, numHomeAtoms, mdAtoms);
  92
  93     auto mdatoms = mdAtoms->mdatoms();
  94     if (usingDomDec)
  95     {
  96         dd_sort_local_top(cr->dd, mdatoms, top);
  97     }
  98     else
  99     {
 100         /* Currently gmx_generate_local_top allocates and returns a pointer.
 101          * We should implement a more elegant solution.
 102          */
 103         gmx_localtop_t *tmpTop;
 104
 105         tmpTop = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
 106         *top   = *tmpTop;
 107         sfree(tmpTop);
 108     }
 109
 110     if (vsite)
 111     {
 112         if (usingDomDec)
 113         {
 114             /* The vsites were already assigned by the domdec topology code.
 115              * We only need to do the thread division here.
 116              */
 117             split_vsites_over_threads(top->idef.il, top->idef.iparams,
 118                                       mdatoms, vsite);
 119         }
 120         else
 121         {
 122             set_vsite_top(vsite, top, mdatoms);
 123         }
 124     }
 125
 126     if (!usingDomDec && ir->ePBC != epbcNONE && !fr->bMolPBC)
 127     {
 128         GMX_ASSERT(graph != nullptr, "We use a graph with PBC (no periodic mols) and without DD");
 129
 130         *graph = mk_graph(nullptr, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
 131     }
 132     else if (graph != nullptr)
 133     {
 134         *graph = nullptr;
 135     }
 136
 137     /* Note that with DD only flexible constraints, not shells, are supported
 138      * and these don't require setup in make_local_shells().
 139      */
 140     if (!usingDomDec && shellfc)
 141     {
 142         make_local_shells(cr, mdatoms, shellfc);
 143     }
 144
 145     setup_bonded_threading(fr->bondedThreading,
 146                            fr->natoms_force,
 147                            &top->idef);
 148
 149     gmx_pme_reinit_atoms(fr->pmedata, numHomeAtoms, mdatoms->chargeA);
 150     /* This handles the PP+PME rank case where fr->pmedata is valid.
 151      * For PME-only ranks, gmx_pmeonly() has its own call to gmx_pme_reinit_atoms().
 152      * TODO: this only handles the GPU logic so far, should handle CPU as well.
 153      * TODO: this also does not account for TPI.
 154      */
 155
 156     if (constr)
 157     {
 158         constr->setConstraints(*top, *mdatoms);
 159     }
 160 }