src/gromacs/pbcutil/rmpbc.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "rmpbc.h"
  40
  41 #include <cmath>
  42 #include <cstdlib>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/pbcutil/mshift.h"
  48 #include "gromacs/pbcutil/pbc.h"
  49 #include "gromacs/topology/atoms.h"
  50 #include "gromacs/topology/idef.h"
  51 #include "gromacs/trajectory/trajectoryframe.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/futil.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 typedef struct {
  57     int      natoms;
  58     t_graph *gr;
  59 } rmpbc_graph_t;
  60
  61 struct gmx_rmpbc {
  62     const t_idef  *idef;
  63     int            natoms_init;
  64     int            ePBC;
  65     int            ngraph;
  66     rmpbc_graph_t *graph;
  67 };
  68
  69 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
  70 {
  71     int            i;
  72     rmpbc_graph_t *gr;
  73
  74     if (ePBC == epbcNONE
  75         || nullptr == gpbc
  76         || nullptr == gpbc->idef
  77         || gpbc->idef->ntypes <= 0)
  78     {
  79         return nullptr;
  80     }
  81
  82     gr = nullptr;
  83     for (i = 0; i < gpbc->ngraph; i++)
  84     {
  85         if (natoms == gpbc->graph[i].natoms)
  86         {
  87             gr = &gpbc->graph[i];
  88         }
  89     }
  90     if (gr == nullptr)
  91     {
  92         /* We'd like to check with the number of atoms in the topology,
  93          * but we don't have that available.
  94          * So we check against the number of atoms that gmx_rmpbc_init
  95          * was called with.
  96          */
  97         if (natoms > gpbc->natoms_init)
  98         {
  99             gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
 100         }
 101         gpbc->ngraph++;
 102         srenew(gpbc->graph, gpbc->ngraph);
 103         gr         = &gpbc->graph[gpbc->ngraph-1];
 104         gr->natoms = natoms;
 105         gr->gr     = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
 106     }
 107
 108     return gr->gr;
 109 }
 110
 111 gmx_rmpbc_t gmx_rmpbc_init(const t_idef *idef, int ePBC, int natoms)
 112 {
 113     gmx_rmpbc_t gpbc;
 114
 115     snew(gpbc, 1);
 116
 117     gpbc->natoms_init = natoms;
 118
 119     /* This sets pbc when we now it,
 120      * otherwise we guess it from the instantaneous box in the trajectory.
 121      */
 122     gpbc->ePBC = ePBC;
 123
 124     gpbc->idef = idef;
 125     if (gpbc->idef->ntypes <= 0)
 126     {
 127         fprintf(stderr,
 128                 "\n"
 129                 "WARNING: If there are molecules in the input trajectory file\n"
 130                 "         that are broken across periodic boundaries, they\n"
 131                 "         cannot be made whole (or treated as whole) without\n"
 132                 "         you providing a run input file.\n\n");
 133     }
 134
 135     return gpbc;
 136 }
 137
 138 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
 139 {
 140     int i;
 141
 142     if (nullptr != gpbc)
 143     {
 144         for (i = 0; i < gpbc->ngraph; i++)
 145         {
 146             done_graph(gpbc->graph[i].gr);
 147             sfree(gpbc->graph[i].gr);
 148         }
 149         if (gpbc->graph != nullptr)
 150         {
 151             sfree(gpbc->graph);
 152         }
 153         sfree(gpbc);
 154     }
 155 }
 156
 157 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
 158 {
 159     if (nullptr != gpbc && gpbc->ePBC >= 0)
 160     {
 161         return gpbc->ePBC;
 162     }
 163     else
 164     {
 165         return guess_ePBC(box);
 166     }
 167 }
 168
 169 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
 170 {
 171     int      ePBC;
 172     t_graph *gr;
 173
 174     ePBC = gmx_rmpbc_ePBC(gpbc, box);
 175     gr   = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
 176     if (gr != nullptr)
 177     {
 178         mk_mshift(stdout, gr, ePBC, box, x);
 179         shift_self(gr, box, x);
 180     }
 181 }
 182
 183 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
 184 {
 185     int      ePBC;
 186     t_graph *gr;
 187     int      i;
 188
 189     ePBC = gmx_rmpbc_ePBC(gpbc, box);
 190     gr   = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
 191     if (gr != nullptr)
 192     {
 193         mk_mshift(stdout, gr, ePBC, box, x);
 194         shift_x(gr, box, x, x_s);
 195     }
 196     else
 197     {
 198         for (i = 0; i < natoms; i++)
 199         {
 200             copy_rvec(x[i], x_s[i]);
 201         }
 202     }
 203 }
 204
 205 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
 206 {
 207     int      ePBC;
 208     t_graph *gr;
 209
 210     if (fr->bX && fr->bBox)
 211     {
 212         ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
 213         gr   = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
 214         if (gr != nullptr)
 215         {
 216             mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
 217             shift_self(gr, fr->box, fr->x);
 218         }
 219     }
 220 }
 221
 222 void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box)
 223 {
 224     real dist;
 225     int  n, m, d;
 226
 227     /* check periodic boundary */
 228     for (n = 1; (n < atoms->nr); n++)
 229     {
 230         for (m = DIM-1; m >= 0; m--)
 231         {
 232             dist = x[n][m]-x[n-1][m];
 233             if (std::abs(dist) > 0.9*box[m][m])
 234             {
 235                 if (dist >  0)
 236                 {
 237                     for (d = 0; d <= m; d++)
 238                     {
 239                         x[n][d] -= box[m][d];
 240                     }
 241                 }
 242                 else
 243                 {
 244                     for (d = 0; d <= m; d++)
 245                     {
 246                         x[n][d] += box[m][d];
 247                     }
 248                 }
 249             }
 250         }
 251     }
 252 }