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39 #include "gromacs/pbcutil/rmpbc.h"
43 #include "gromacs/fileio/trx.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/pbcutil/mshift.h"
46 #include "gromacs/pbcutil/pbc.h"
47 #include "gromacs/topology/atoms.h"
48 #include "gromacs/topology/idef.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/smalloc.h"
66 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
74 || gpbc->idef->ntypes <= 0)
80 for (i = 0; i < gpbc->ngraph; i++)
82 if (natoms == gpbc->graph[i].natoms)
89 /* We'd like to check with the number of atoms in the topology,
90 * but we don't have that available.
91 * So we check against the number of atoms that gmx_rmpbc_init
94 if (natoms > gpbc->natoms_init)
96 gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
99 srenew(gpbc->graph, gpbc->ngraph);
100 gr = &gpbc->graph[gpbc->ngraph-1];
102 gr->gr = mk_graph(NULL, gpbc->idef, 0, natoms, FALSE, FALSE);
108 gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef, int ePBC, int natoms)
114 gpbc->natoms_init = natoms;
116 /* This sets pbc when we now it,
117 * otherwise we guess it from the instantaneous box in the trajectory.
122 if (gpbc->idef->ntypes <= 0)
126 "WARNING: If there are molecules in the input trajectory file\n"
127 " that are broken across periodic boundaries, they\n"
128 " cannot be made whole (or treated as whole) without\n"
129 " you providing a run input file.\n\n");
135 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
141 for (i = 0; i < gpbc->ngraph; i++)
143 done_graph(gpbc->graph[i].gr);
144 sfree(gpbc->graph[i].gr);
146 if (gpbc->graph != NULL)
154 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, matrix box)
156 if (NULL != gpbc && gpbc->ePBC >= 0)
162 return guess_ePBC(box);
166 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, matrix box, rvec x[])
171 ePBC = gmx_rmpbc_ePBC(gpbc, box);
172 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
175 mk_mshift(stdout, gr, ePBC, box, x);
176 shift_self(gr, box, x);
180 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, matrix box, rvec x[], rvec x_s[])
186 ePBC = gmx_rmpbc_ePBC(gpbc, box);
187 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
190 mk_mshift(stdout, gr, ePBC, box, x);
191 shift_x(gr, box, x, x_s);
195 for (i = 0; i < natoms; i++)
197 copy_rvec(x[i], x_s[i]);
202 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
207 if (fr->bX && fr->bBox)
209 ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
210 gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
213 mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
214 shift_self(gr, fr->box, fr->x);
219 void rm_gropbc(t_atoms *atoms, rvec x[], matrix box)
224 /* check periodic boundary */
225 for (n = 1; (n < atoms->nr); n++)
227 for (m = DIM-1; m >= 0; m--)
229 dist = x[n][m]-x[n-1][m];
230 if (fabs(dist) > 0.9*box[m][m])
234 for (d = 0; d <= m; d++)
236 x[n][d] -= box[m][d];
241 for (d = 0; d <= m; d++)
243 x[n][d] += box[m][d];