src/gmxlib/rmpbc.c

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