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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"
69 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
76 || nullptr == gpbc->idef
77 || 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)
99 gmx_fatal(FARGS, "Structure or trajectory file has more atoms (%d) than the topology (%d)", natoms, gpbc->natoms_init);
102 srenew(gpbc->graph, gpbc->ngraph);
103 gr = &gpbc->graph[gpbc->ngraph-1];
105 gr->gr = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
111 gmx_rmpbc_t gmx_rmpbc_init(const t_idef *idef, int ePBC, int natoms)
117 gpbc->natoms_init = natoms;
119 /* This sets pbc when we now it,
120 * otherwise we guess it from the instantaneous box in the trajectory.
125 if (gpbc->idef->ntypes <= 0)
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");
138 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
144 for (i = 0; i < gpbc->ngraph; i++)
146 done_graph(gpbc->graph[i].gr);
147 sfree(gpbc->graph[i].gr);
149 if (gpbc->graph != nullptr)
157 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
159 if (nullptr != gpbc && gpbc->ePBC >= 0)
165 return guess_ePBC(box);
169 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
174 ePBC = gmx_rmpbc_ePBC(gpbc, box);
175 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
178 mk_mshift(stdout, gr, ePBC, box, x);
179 shift_self(gr, box, x);
183 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
189 ePBC = gmx_rmpbc_ePBC(gpbc, box);
190 gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
193 mk_mshift(stdout, gr, ePBC, box, x);
194 shift_x(gr, box, x, x_s);
198 for (i = 0; i < natoms; i++)
200 copy_rvec(x[i], x_s[i]);
205 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr)
210 if (fr->bX && fr->bBox)
212 ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
213 gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
216 mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
217 shift_self(gr, fr->box, fr->x);
222 void rm_gropbc(const t_atoms *atoms, rvec x[], const matrix box)
227 /* check periodic boundary */
228 for (n = 1; (n < atoms->nr); n++)
230 for (m = DIM-1; m >= 0; m--)
232 dist = x[n][m]-x[n-1][m];
233 if (std::abs(dist) > 0.9*box[m][m])
237 for (d = 0; d <= m; d++)
239 x[n][d] -= box[m][d];
244 for (d = 0; d <= m; d++)
246 x[n][d] += box[m][d];