src/gromacs/pbcutil/rmpbc.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "rmpbc.h"
  40
  41 #include <stdlib.h>
  42
  43 #include <cmath>
  44
  45 #include <algorithm>
  46
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/pbcutil/mshift.h"
  49 #include "gromacs/pbcutil/pbc.h"
  50 #include "gromacs/topology/atoms.h"
  51 #include "gromacs/topology/idef.h"
  52 #include "gromacs/trajectory/trajectoryframe.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 typedef struct {
  58     int      natoms;
  59     t_graph *gr;
  60 } rmpbc_graph_t;
  61
  62 struct gmx_rmpbc {
  63     const t_idef  *idef;
  64     int            natoms_init;
  65     int            ePBC;
  66     int            ngraph;
  67     rmpbc_graph_t *graph;
  68 };
  69
  70 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
  71 {
  72     int            i;
  73     rmpbc_graph_t *gr;
  74
  75     if (ePBC == epbcNONE
  76         || nullptr == gpbc
  77         || nullptr == gpbc->idef
  78         || gpbc->idef->ntypes <= 0)
  79     {
  80         return nullptr;
  81     }
  82
  83     gr = nullptr;
  84     for (i = 0; i < gpbc->ngraph; i++)
  85     {
  86         if (natoms == gpbc->graph[i].natoms)
  87         {
  88             gr = &gpbc->graph[i];
  89         }
  90     }
  91     if (gr == nullptr)
  92     {
  93         /* We'd like to check with the number of atoms in the topology,
  94          * but we don't have that available.
  95          * So we check against the number of atoms that gmx_rmpbc_init
  96          * was called with.
  97          */
  98         if (natoms > gpbc->natoms_init)
  99         {
 100             gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
 101         }
 102         gpbc->ngraph++;
 103         srenew(gpbc->graph, gpbc->ngraph);
 104         gr         = &gpbc->graph[gpbc->ngraph-1];
 105         gr->natoms = natoms;
 106         gr->gr     = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
 107     }
 108
 109     return gr->gr;
 110 }
 111
 112 gmx_rmpbc_t gmx_rmpbc_init(const t_idef *idef, int ePBC, int natoms)
 113 {
 114     gmx_rmpbc_t gpbc;
 115
 116     snew(gpbc, 1);
 117
 118     gpbc->natoms_init = natoms;
 119
 120     /* This sets pbc when we now it,
 121      * otherwise we guess it from the instantaneous box in the trajectory.
 122      */
 123     gpbc->ePBC = ePBC;
 124
 125     gpbc->idef = idef;
 126     if (gpbc->idef->ntypes <= 0)
 127     {
 128         fprintf(stderr,
 129                 "\n"
 130                 "WARNING: If there are molecules in the input trajectory file\n"
 131                 "         that are broken across periodic boundaries, they\n"
 132                 "         cannot be made whole (or treated as whole) without\n"
 133                 "         you providing a run input file.\n\n");
 134     }
 135
 136     return gpbc;
 137 }
 138
 139 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
 140 {
 141     int i;
 142
 143     if (nullptr != gpbc)
 144     {
 145         for (i = 0; i < gpbc->ngraph; i++)
 146         {
 147             done_graph(gpbc->graph[i].gr);
 148             sfree(gpbc->graph[i].gr);
 149         }
 150         if (gpbc->graph != nullptr)
 151         {
 152             sfree(gpbc->graph);
 153         }
 154         sfree(gpbc);
 155     }
 156 }
 157
 158 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
 159 {
 160     if (nullptr != gpbc && gpbc->ePBC >= 0)
 161     {
 162         return gpbc->ePBC;
 163     }
 164     else
 165     {
 166         return guess_ePBC(box);
 167     }
 168 }
 169
 170 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
 171 {
 172     int      ePBC;
 173     t_graph *gr;
 174
 175     ePBC = gmx_rmpbc_ePBC(gpbc, box);
 176     gr   = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
 177     if (gr != nullptr)
 178     {
 179         mk_mshift(stdout, gr, ePBC, box, x);
 180         shift_self(gr, box, x);
 181     }
 182 }
 183
 184 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
 185 {
 186     int      ePBC;
 187     t_graph *gr;
 188     int      i;
 189
 190     ePBC = gmx_rmpbc_ePBC(gpbc, box);
 191     gr   = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
 192     if (gr != nullptr)
 193     {
 194         mk_mshift(stdout, gr, ePBC, box, x);
 195         shift_x(gr, box, x, x_s);
 196     }
 197     else
 198     {
 199         for (i = 0; i < natoms; i++)
 200         {
 201             copy_rvec(x[i], x_s[i]);
 202         }
 203     }
 204 }
 205
 206 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
 207 {
 208     int      ePBC;
 209     t_graph *gr;
 210
 211     if (fr->bX && fr->bBox)
 212     {
 213         ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
 214         gr   = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
 215         if (gr != nullptr)
 216         {
 217             mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
 218             shift_self(gr, fr->box, fr->x);
 219         }
 220     }
 221 }
 222
 223 void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box)
 224 {
 225     real dist;
 226     int  n, m, d;
 227
 228     /* check periodic boundary */
 229     for (n = 1; (n < atoms->nr); n++)
 230     {
 231         for (m = DIM-1; m >= 0; m--)
 232         {
 233             dist = x[n][m]-x[n-1][m];
 234             if (std::abs(dist) > 0.9*box[m][m])
 235             {
 236                 if (dist >  0)
 237                 {
 238                     for (d = 0; d <= m; d++)
 239                     {
 240                         x[n][d] -= box[m][d];
 241                     }
 242                 }
 243                 else
 244                 {
 245                     for (d = 0; d <= m; d++)
 246                     {
 247                         x[n][d] += box[m][d];
 248                     }
 249                 }
 250             }
 251         }
 252     }
 253 }