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47 #include "gromacs/math/vec.h"
48 #include "gromacs/pbcutil/mshift.h"
49 #include "gromacs/pbcutil/pbc.h"
50 #include "gromacs/topology/atoms.h"
51 #include "gromacs/topology/idef.h"
52 #include "gromacs/trajectory/trajectoryframe.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/futil.h"
55 #include "gromacs/utility/smalloc.h"
70 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
78 || gpbc->idef->ntypes <= 0)
84 for (i = 0; i < gpbc->ngraph; i++)
86 if (natoms == gpbc->graph[i].natoms)
93 /* We'd like to check with the number of atoms in the topology,
94 * but we don't have that available.
95 * So we check against the number of atoms that gmx_rmpbc_init
98 if (natoms > gpbc->natoms_init)
100 gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
103 srenew(gpbc->graph, gpbc->ngraph);
104 gr = &gpbc->graph[gpbc->ngraph-1];
106 gr->gr = mk_graph(NULL, gpbc->idef, 0, natoms, FALSE, FALSE);
112 gmx_rmpbc_t gmx_rmpbc_init(const t_idef *idef, int ePBC, int natoms)
118 gpbc->natoms_init = natoms;
120 /* This sets pbc when we now it,
121 * otherwise we guess it from the instantaneous box in the trajectory.
126 if (gpbc->idef->ntypes <= 0)
130 "WARNING: If there are molecules in the input trajectory file\n"
131 " that are broken across periodic boundaries, they\n"
132 " cannot be made whole (or treated as whole) without\n"
133 " you providing a run input file.\n\n");
139 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
145 for (i = 0; i < gpbc->ngraph; i++)
147 done_graph(gpbc->graph[i].gr);
148 sfree(gpbc->graph[i].gr);
150 if (gpbc->graph != NULL)
158 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
160 if (NULL != gpbc && gpbc->ePBC >= 0)
166 return guess_ePBC(box);
170 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
175 ePBC = gmx_rmpbc_ePBC(gpbc, box);
176 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
179 mk_mshift(stdout, gr, ePBC, box, x);
180 shift_self(gr, box, x);
184 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
190 ePBC = gmx_rmpbc_ePBC(gpbc, box);
191 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
194 mk_mshift(stdout, gr, ePBC, box, x);
195 shift_x(gr, box, x, x_s);
199 for (i = 0; i < natoms; i++)
201 copy_rvec(x[i], x_s[i]);
206 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
211 if (fr->bX && fr->bBox)
213 ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
214 gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
217 mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
218 shift_self(gr, fr->box, fr->x);
223 void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box)
228 /* check periodic boundary */
229 for (n = 1; (n < atoms->nr); n++)
231 for (m = DIM-1; m >= 0; m--)
233 dist = x[n][m]-x[n-1][m];
234 if (std::abs(dist) > 0.9*box[m][m])
238 for (d = 0; d <= m; d++)
240 x[n][d] -= box[m][d];
245 for (d = 0; d <= m; d++)
247 x[n][d] += box[m][d];