src/gromacs/pbcutil/rmpbc.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "rmpbc.h"
  41
  42 #include <cmath>
  43 #include <cstdlib>
  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 {
  59     int      natoms;
  60     t_graph* gr;
  61 } rmpbc_graph_t;
  62
  63 struct gmx_rmpbc
  64 {
  65     const t_idef*  idef;
  66     int            natoms_init;
  67     int            ePBC;
  68     int            ngraph;
  69     rmpbc_graph_t* graph;
  70 };
  71
  72 static t_graph* gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
  73 {
  74     int            i;
  75     rmpbc_graph_t* gr;
  76
  77     if (ePBC == epbcNONE || nullptr == gpbc || nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)
  78     {
  79         return nullptr;
  80     }
  81
  82     gr = nullptr;
  83     for (i = 0; i < gpbc->ngraph; i++)
  84     {
  85         if (natoms == gpbc->graph[i].natoms)
  86         {
  87             gr = &gpbc->graph[i];
  88         }
  89     }
  90     if (gr == nullptr)
  91     {
  92         /* We'd like to check with the number of atoms in the topology,
  93          * but we don't have that available.
  94          * So we check against the number of atoms that gmx_rmpbc_init
  95          * was called with.
  96          */
  97         if (natoms > gpbc->natoms_init)
  98         {
  99             gmx_fatal(FARGS,
 100                       "Structure or trajectory file has more atoms (%d) than the topology (%d)",
 101                       natoms, gpbc->natoms_init);
 102         }
 103         gpbc->ngraph++;
 104         srenew(gpbc->graph, gpbc->ngraph);
 105         gr         = &gpbc->graph[gpbc->ngraph - 1];
 106         gr->natoms = natoms;
 107         gr->gr     = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
 108     }
 109
 110     return gr->gr;
 111 }
 112
 113 gmx_rmpbc_t gmx_rmpbc_init(const t_idef* idef, int ePBC, int natoms)
 114 {
 115     gmx_rmpbc_t gpbc;
 116
 117     snew(gpbc, 1);
 118
 119     gpbc->natoms_init = natoms;
 120
 121     /* This sets pbc when we now it,
 122      * otherwise we guess it from the instantaneous box in the trajectory.
 123      */
 124     gpbc->ePBC = ePBC;
 125
 126     gpbc->idef = idef;
 127     if (gpbc->idef->ntypes <= 0)
 128     {
 129         fprintf(stderr,
 130                 "\n"
 131                 "WARNING: If there are molecules in the input trajectory file\n"
 132                 "         that are broken across periodic boundaries, they\n"
 133                 "         cannot be made whole (or treated as whole) without\n"
 134                 "         you providing a run input file.\n\n");
 135     }
 136
 137     return gpbc;
 138 }
 139
 140 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
 141 {
 142     int i;
 143
 144     if (nullptr != gpbc)
 145     {
 146         for (i = 0; i < gpbc->ngraph; i++)
 147         {
 148             done_graph(gpbc->graph[i].gr);
 149             sfree(gpbc->graph[i].gr);
 150         }
 151         if (gpbc->graph != nullptr)
 152         {
 153             sfree(gpbc->graph);
 154         }
 155         sfree(gpbc);
 156     }
 157 }
 158
 159 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
 160 {
 161     if (nullptr != gpbc && gpbc->ePBC >= 0)
 162     {
 163         return gpbc->ePBC;
 164     }
 165     else
 166     {
 167         return guess_ePBC(box);
 168     }
 169 }
 170
 171 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
 172 {
 173     int      ePBC;
 174     t_graph* gr;
 175
 176     ePBC = gmx_rmpbc_ePBC(gpbc, box);
 177     gr   = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
 178     if (gr != nullptr)
 179     {
 180         mk_mshift(stdout, gr, ePBC, box, x);
 181         shift_self(gr, box, x);
 182     }
 183 }
 184
 185 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
 186 {
 187     int      ePBC;
 188     t_graph* gr;
 189     int      i;
 190
 191     ePBC = gmx_rmpbc_ePBC(gpbc, box);
 192     gr   = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
 193     if (gr != nullptr)
 194     {
 195         mk_mshift(stdout, gr, ePBC, box, x);
 196         shift_x(gr, box, x, x_s);
 197     }
 198     else
 199     {
 200         for (i = 0; i < natoms; i++)
 201         {
 202             copy_rvec(x[i], x_s[i]);
 203         }
 204     }
 205 }
 206
 207 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe* fr)
 208 {
 209     int      ePBC;
 210     t_graph* gr;
 211
 212     if (fr->bX && fr->bBox)
 213     {
 214         ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
 215         gr   = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
 216         if (gr != nullptr)
 217         {
 218             mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
 219             shift_self(gr, fr->box, fr->x);
 220         }
 221     }
 222 }
 223
 224 void rm_gropbc(const t_atoms* atoms, rvec x[], const matrix box)
 225 {
 226     real dist;
 227     int  n, m, d;
 228
 229     /* check periodic boundary */
 230     for (n = 1; (n < atoms->nr); n++)
 231     {
 232         for (m = DIM - 1; m >= 0; m--)
 233         {
 234             dist = x[n][m] - x[n - 1][m];
 235             if (std::abs(dist) > 0.9 * box[m][m])
 236             {
 237                 if (dist > 0)
 238                 {
 239                     for (d = 0; d <= m; d++)
 240                     {
 241                         x[n][d] -= box[m][d];
 242                     }
 243                 }
 244                 else
 245                 {
 246                     for (d = 0; d <= m; d++)
 247                     {
 248                         x[n][d] += box[m][d];
 249                     }
 250                 }
 251             }
 252         }
 253     }
 254 }