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41 #include "gromacs/fileio/trx.h"
42 #include "gromacs/math/vec.h"
43 #include "gromacs/pbcutil/mshift.h"
44 #include "gromacs/pbcutil/pbc.h"
45 #include "gromacs/topology/atoms.h"
46 #include "gromacs/topology/idef.h"
47 #include "gromacs/utility/fatalerror.h"
48 #include "gromacs/utility/futil.h"
49 #include "gromacs/utility/smalloc.h"
64 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
72 || gpbc->idef->ntypes <= 0)
78 for (i = 0; i < gpbc->ngraph; i++)
80 if (natoms == gpbc->graph[i].natoms)
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
92 if (natoms > gpbc->natoms_init)
94 gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
97 srenew(gpbc->graph, gpbc->ngraph);
98 gr = &gpbc->graph[gpbc->ngraph-1];
100 gr->gr = mk_graph(NULL, gpbc->idef, 0, natoms, FALSE, FALSE);
106 gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef, int ePBC, int natoms)
112 gpbc->natoms_init = natoms;
114 /* This sets pbc when we now it,
115 * otherwise we guess it from the instantaneous box in the trajectory.
120 if (gpbc->idef->ntypes <= 0)
124 "WARNING: If there are molecules in the input trajectory file\n"
125 " that are broken across periodic boundaries, they\n"
126 " cannot be made whole (or treated as whole) without\n"
127 " you providing a run input file.\n\n");
133 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
139 for (i = 0; i < gpbc->ngraph; i++)
141 done_graph(gpbc->graph[i].gr);
142 sfree(gpbc->graph[i].gr);
144 if (gpbc->graph != NULL)
152 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, matrix box)
154 if (NULL != gpbc && gpbc->ePBC >= 0)
160 return guess_ePBC(box);
164 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, matrix box, rvec x[])
169 ePBC = gmx_rmpbc_ePBC(gpbc, box);
170 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
173 mk_mshift(stdout, gr, ePBC, box, x);
174 shift_self(gr, box, x);
178 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, matrix box, rvec x[], rvec x_s[])
184 ePBC = gmx_rmpbc_ePBC(gpbc, box);
185 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
188 mk_mshift(stdout, gr, ePBC, box, x);
189 shift_x(gr, box, x, x_s);
193 for (i = 0; i < natoms; i++)
195 copy_rvec(x[i], x_s[i]);
200 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
205 if (fr->bX && fr->bBox)
207 ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
208 gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
211 mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
212 shift_self(gr, fr->box, fr->x);
217 void rm_gropbc(t_atoms *atoms, rvec x[], matrix box)
222 /* check periodic boundary */
223 for (n = 1; (n < atoms->nr); n++)
225 for (m = DIM-1; m >= 0; m--)
227 dist = x[n][m]-x[n-1][m];
228 if (fabs(dist) > 0.9*box[m][m])
232 for (d = 0; d <= m; d++)
234 x[n][d] -= box[m][d];
239 for (d = 0; d <= m; d++)
241 x[n][d] += box[m][d];