src/gromacs/mdlib/mdsetup.cpp

   1 /*
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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/listed-forces/manage-threading.h"
  42 #include "gromacs/mdlib/mdatoms.h"
  43 #include "gromacs/mdlib/shellfc.h"
  44 #include "gromacs/mdlib/vsite.h"
  45 #include "gromacs/mdtypes/commrec.h"
  46 #include "gromacs/mdtypes/forcerec.h"
  47 #include "gromacs/mdtypes/inputrec.h"
  48 #include "gromacs/pbcutil/mshift.h"
  49 #include "gromacs/pbcutil/pbc.h"
  50 #include "gromacs/topology/mtop_util.h"
  51 #include "gromacs/topology/topology.h"
  52 #include "gromacs/utility/gmxassert.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 /* TODO: Add a routine that collects the initial setup of the algorithms.
  56  *
  57  * The final solution should be an MD algorithm base class with methods
  58  * for initialization and atom-data setup.
  59  */
  60
  61 void mdAlgorithmsSetupAtomData(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                                t_mdatoms         *mdatoms,
  68                                gmx_vsite_t       *vsite,
  69                                gmx_shellfc_t     *shellfc)
  70 {
  71     bool  usingDomDec = DOMAINDECOMP(cr);
  72
  73     int   numAtomIndex, numHomeAtoms;
  74     int  *atomIndex;
  75
  76     if (usingDomDec)
  77     {
  78         numAtomIndex = dd_natoms_mdatoms(cr->dd);
  79         atomIndex    = cr->dd->gatindex;
  80         numHomeAtoms = cr->dd->nat_home;
  81     }
  82     else
  83     {
  84         numAtomIndex = -1;
  85         atomIndex    = nullptr;
  86         numHomeAtoms = top_global->natoms;
  87     }
  88     atoms2md(top_global, ir, numAtomIndex, atomIndex, numHomeAtoms, mdatoms);
  89
  90     if (usingDomDec)
  91     {
  92         dd_sort_local_top(cr->dd, mdatoms, top);
  93     }
  94     else
  95     {
  96         /* Currently gmx_generate_local_top allocates and returns a pointer.
  97          * We should implement a more elegant solution.
  98          */
  99         gmx_localtop_t *tmpTop;
 100
 101         tmpTop = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
 102         *top   = *tmpTop;
 103         sfree(tmpTop);
 104     }
 105
 106     if (vsite)
 107     {
 108         if (usingDomDec)
 109         {
 110             /* The vsites were already assigned by the domdec topology code.
 111              * We only need to do the thread division here.
 112              */
 113             split_vsites_over_threads(top->idef.il, top->idef.iparams,
 114                                       mdatoms, FALSE, vsite);
 115         }
 116         else
 117         {
 118             set_vsite_top(vsite, top, mdatoms, cr);
 119         }
 120     }
 121
 122     if (!usingDomDec && ir->ePBC != epbcNONE && !fr->bMolPBC)
 123     {
 124         GMX_ASSERT(graph != NULL, "We use a graph with PBC (no periodic mols) and without DD");
 125
 126         *graph = mk_graph(nullptr, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
 127     }
 128     else if (graph != nullptr)
 129     {
 130         *graph = nullptr;
 131     }
 132
 133     /* Note that with DD only flexible constraints, not shells, are supported
 134      * and these don't require setup in make_local_shells().
 135      */
 136     if (!usingDomDec && shellfc)
 137     {
 138         make_local_shells(cr, mdatoms, shellfc);
 139     }
 140
 141     setup_bonded_threading(fr, &top->idef);
 142 }