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