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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"
72 static t_graph* gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
77 if (ePBC == epbcNONE || nullptr == gpbc || nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)
83 for (i = 0; i < gpbc->ngraph; i++)
85 if (natoms == gpbc->graph[i].natoms)
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
97 if (natoms > gpbc->natoms_init)
100 "Structure or trajectory file has more atoms (%d) than the topology (%d)",
101 natoms, gpbc->natoms_init);
104 srenew(gpbc->graph, gpbc->ngraph);
105 gr = &gpbc->graph[gpbc->ngraph - 1];
107 gr->gr = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
113 gmx_rmpbc_t gmx_rmpbc_init(const t_idef* idef, int ePBC, int natoms)
119 gpbc->natoms_init = natoms;
121 /* This sets pbc when we now it,
122 * otherwise we guess it from the instantaneous box in the trajectory.
127 if (gpbc->idef->ntypes <= 0)
131 "WARNING: If there are molecules in the input trajectory file\n"
132 " that are broken across periodic boundaries, they\n"
133 " cannot be made whole (or treated as whole) without\n"
134 " you providing a run input file.\n\n");
140 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
146 for (i = 0; i < gpbc->ngraph; i++)
148 done_graph(gpbc->graph[i].gr);
149 sfree(gpbc->graph[i].gr);
151 if (gpbc->graph != nullptr)
159 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
161 if (nullptr != gpbc && gpbc->ePBC >= 0)
167 return guess_ePBC(box);
171 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
176 ePBC = gmx_rmpbc_ePBC(gpbc, box);
177 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
180 mk_mshift(stdout, gr, ePBC, box, x);
181 shift_self(gr, box, x);
185 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
191 ePBC = gmx_rmpbc_ePBC(gpbc, box);
192 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
195 mk_mshift(stdout, gr, ePBC, box, x);
196 shift_x(gr, box, x, x_s);
200 for (i = 0; i < natoms; i++)
202 copy_rvec(x[i], x_s[i]);
207 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe* fr)
212 if (fr->bX && fr->bBox)
214 ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
215 gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
218 mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
219 shift_self(gr, fr->box, fr->x);
224 void rm_gropbc(const t_atoms* atoms, rvec x[], const matrix box)
229 /* check periodic boundary */
230 for (n = 1; (n < atoms->nr); n++)
232 for (m = DIM - 1; m >= 0; m--)
234 dist = x[n][m] - x[n - 1][m];
235 if (std::abs(dist) > 0.9 * box[m][m])
239 for (d = 0; d <= m; d++)
241 x[n][d] -= box[m][d];
246 for (d = 0; d <= m; d++)
248 x[n][d] += box[m][d];