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 broken molecules in the trajectory file,\n"
 124                 "         they can not be made whole without a run input file\n\n");
 125     }
 126
 127     return gpbc;
 128 }
 129
 130 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
 131 {
 132     int i;
 133
 134     if (NULL != gpbc)
 135     {
 136         for(i=0; i<gpbc->ngraph; i++)
 137         {
 138             done_graph(gpbc->graph[i].gr);
 139         }
 140         if (gpbc->graph != NULL)
 141         {
 142             sfree(gpbc->graph);
 143         }
 144     }
 145 }
 146
 147 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc,matrix box)
 148 {
 149     if (NULL != gpbc && gpbc->ePBC >= 0)
 150     {
 151         return gpbc->ePBC;
 152     }
 153     else
 154     {
 155         return guess_ePBC(box);
 156     }
 157 }
 158
 159 void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[])
 160 {
 161     int     ePBC;
 162     t_graph *gr;
 163
 164     ePBC = gmx_rmpbc_ePBC(gpbc,box);
 165     gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
 166     if (gr != NULL)
 167     {
 168         mk_mshift(stdout,gr,ePBC,box,x);
 169         shift_x(gr,box,x,x);
 170     }
 171 }
 172
 173 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],rvec x_s[])
 174 {
 175     int     ePBC;
 176     t_graph *gr;
 177     int     i;
 178
 179     ePBC = gmx_rmpbc_ePBC(gpbc,box);
 180     gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
 181     if (gr != NULL)
 182     {
 183         mk_mshift(stdout,gr,ePBC,box,x);
 184         shift_x(gr,box,x,x_s);
 185     }
 186     else
 187     {
 188         for(i=0; i<natoms; i++)
 189         {
 190             copy_rvec(x[i],x_s[i]);
 191         }
 192     }
 193 }
 194
 195 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr)
 196 {
 197     int     ePBC;
 198     t_graph *gr;
 199
 200     if (fr->bX && fr->bBox)
 201     {
 202         ePBC = gmx_rmpbc_ePBC(gpbc,fr->box);
 203         gr = gmx_rmpbc_get_graph(gpbc,ePBC,fr->natoms);
 204         if (gr != NULL)
 205         {
 206             mk_mshift(stdout,gr,ePBC,fr->box,fr->x);
 207             shift_x(gr,fr->box,fr->x,fr->x);
 208         }
 209     }
 210 }
 211
 212 void rm_gropbc(t_atoms *atoms,rvec x[],matrix box)
 213 {
 214     real dist;
 215     int  n,m,d;
 216
 217     /* check periodic boundary */
 218     for(n=1;(n<atoms->nr);n++)
 219     {
 220         for(m=DIM-1; m>=0; m--)
 221         {
 222             dist = x[n][m]-x[n-1][m];
 223             if (fabs(dist) > 0.9*box[m][m])
 224             {
 225                 if ( dist >  0 )
 226                 {
 227                     for(d=0; d<=m; d++)
 228                     {
 229                         x[n][d] -= box[m][d];
 230                     }
 231                 }
 232                 else
 233                 {
 234                     for(d=0; d<=m; d++)
 235                     {
 236                         x[n][d] += box[m][d];
 237                     }
 238                 }
 239             }
 240         }
 241     }
 242 }
 243