src/gmxlib/rmpbc.c

   1 /*
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   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
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  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include "sysstuff.h"
  43 #include "typedefs.h"
  44 #include "smalloc.h"
  45 #include "mshift.h"
  46 #include "pbc.h"
  47 #include "gstat.h"
  48 #include "futil.h"
  49 #include "vec.h"
  50
  51 typedef struct {
  52     int     natoms;
  53     t_graph *gr;
  54 } rmpbc_graph_t;
  55
  56 typedef struct gmx_rmpbc {
  57     t_idef        *idef;
  58     int           natoms_init;
  59     int           ePBC;
  60     int           ngraph;
  61     rmpbc_graph_t *graph;
  62 } koeiepoep;
  63
  64 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc,int ePBC,int natoms)
  65 {
  66     int           i;
  67     rmpbc_graph_t *gr;
  68
  69     if (ePBC == epbcNONE
  70         || NULL == gpbc
  71         || NULL == gpbc->idef
  72         || gpbc->idef->ntypes <= 0)
  73     {
  74         return NULL;
  75     }
  76
  77     gr = NULL;
  78     for(i=0; i<gpbc->ngraph; i++)
  79     {
  80         if (natoms == gpbc->graph[i].natoms)
  81         {
  82             gr = &gpbc->graph[i];
  83         }
  84     }
  85     if (gr == NULL)
  86     {
  87         /* We'd like to check with the number of atoms in the topology,
  88          * but we don't have that available.
  89          * So we check against the number of atoms that gmx_rmpbc_init
  90          * was called with.
  91          */
  92         if (natoms > gpbc->natoms_init)
  93         {
  94             gmx_fatal(FARGS,"Structure or trajectory file has more atoms (%d) than the topology (%d)",natoms,gpbc->natoms_init);
  95         }
  96         gpbc->ngraph++;
  97         srenew(gpbc->graph,gpbc->ngraph);
  98         gr = &gpbc->graph[gpbc->ngraph-1];
  99         gr->natoms = natoms;
 100         gr->gr     = mk_graph(NULL,gpbc->idef,0,natoms,FALSE,FALSE);
 101     }
 102
 103     return gr->gr;
 104 }
 105
 106 gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
 107                            matrix box)
 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         }
 144         if (gpbc->graph != NULL)
 145         {
 146             sfree(gpbc->graph);
 147         }
 148     }
 149 }
 150
 151 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc,matrix box)
 152 {
 153     if (NULL != gpbc && gpbc->ePBC >= 0)
 154     {
 155         return gpbc->ePBC;
 156     }
 157     else
 158     {
 159         return guess_ePBC(box);
 160     }
 161 }
 162
 163 void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[])
 164 {
 165     int     ePBC;
 166     t_graph *gr;
 167
 168     ePBC = gmx_rmpbc_ePBC(gpbc,box);
 169     gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
 170     if (gr != NULL)
 171     {
 172         mk_mshift(stdout,gr,ePBC,box,x);
 173         shift_self(gr,box,x);
 174     }
 175 }
 176
 177 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],rvec x_s[])
 178 {
 179     int     ePBC;
 180     t_graph *gr;
 181     int     i;
 182
 183     ePBC = gmx_rmpbc_ePBC(gpbc,box);
 184     gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
 185     if (gr != NULL)
 186     {
 187         mk_mshift(stdout,gr,ePBC,box,x);
 188         shift_x(gr,box,x,x_s);
 189     }
 190     else
 191     {
 192         for(i=0; i<natoms; i++)
 193         {
 194             copy_rvec(x[i],x_s[i]);
 195         }
 196     }
 197 }
 198
 199 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr)
 200 {
 201     int     ePBC;
 202     t_graph *gr;
 203
 204     if (fr->bX && fr->bBox)
 205     {
 206         ePBC = gmx_rmpbc_ePBC(gpbc,fr->box);
 207         gr = gmx_rmpbc_get_graph(gpbc,ePBC,fr->natoms);
 208         if (gr != NULL)
 209         {
 210             mk_mshift(stdout,gr,ePBC,fr->box,fr->x);
 211             shift_self(gr,fr->box,fr->x);
 212         }
 213     }
 214 }
 215
 216 void rm_gropbc(t_atoms *atoms,rvec x[],matrix box)
 217 {
 218     real dist;
 219     int  n,m,d;
 220
 221     /* check periodic boundary */
 222     for(n=1;(n<atoms->nr);n++)
 223     {
 224         for(m=DIM-1; m>=0; m--)
 225         {
 226             dist = x[n][m]-x[n-1][m];
 227             if (fabs(dist) > 0.9*box[m][m])
 228             {
 229                 if ( dist >  0 )
 230                 {
 231                     for(d=0; d<=m; d++)
 232                     {
 233                         x[n][d] -= box[m][d];
 234                     }
 235                 }
 236                 else
 237                 {
 238                     for(d=0; d<=m; d++)
 239                     {
 240                         x[n][d] += box[m][d];
 241                     }
 242                 }
 243             }
 244         }
 245     }
 246 }
 247