src/gromacs/gmxlib/rmpbc.c

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