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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"
65 const InteractionDefinitions* interactionDefinitions;
74 static t_graph* gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, PbcType pbcType, int natoms)
79 if (pbcType == PbcType::No || nullptr == gpbc || nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)
85 for (i = 0; i < gpbc->ngraph; i++)
87 if (natoms == gpbc->graph[i].natoms)
94 /* We'd like to check with the number of atoms in the topology,
95 * but we don't have that available.
96 * So we check against the number of atoms that gmx_rmpbc_init
99 if (natoms > gpbc->natoms_init)
102 "Structure or trajectory file has more atoms (%d) than the topology (%d)",
103 natoms, gpbc->natoms_init);
106 srenew(gpbc->graph, gpbc->ngraph);
107 gr = &gpbc->graph[gpbc->ngraph - 1];
109 if (gpbc->interactionDefinitions)
111 gr->gr = mk_graph(nullptr, *gpbc->interactionDefinitions, 0, natoms, FALSE, FALSE);
115 gr->gr = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
122 gmx_rmpbc_t gmx_rmpbc_init(const InteractionDefinitions& idef, PbcType pbcType, int natoms)
128 gpbc->natoms_init = natoms;
130 /* This sets pbc when we now it,
131 * otherwise we guess it from the instantaneous box in the trajectory.
133 gpbc->pbcType = pbcType;
135 gpbc->interactionDefinitions = &idef;
140 gmx_rmpbc_t gmx_rmpbc_init(const t_idef* idef, PbcType pbcType, int natoms)
146 gpbc->natoms_init = natoms;
148 /* This sets pbc when we now it,
149 * otherwise we guess it from the instantaneous box in the trajectory.
151 gpbc->pbcType = pbcType;
154 if (gpbc->idef->ntypes <= 0)
158 "WARNING: If there are molecules in the input trajectory file\n"
159 " that are broken across periodic boundaries, they\n"
160 " cannot be made whole (or treated as whole) without\n"
161 " you providing a run input file.\n\n");
167 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
173 for (i = 0; i < gpbc->ngraph; i++)
175 done_graph(gpbc->graph[i].gr);
176 sfree(gpbc->graph[i].gr);
178 if (gpbc->graph != nullptr)
186 static PbcType gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
188 if (nullptr != gpbc && gpbc->pbcType != PbcType::Unset)
190 return gpbc->pbcType;
194 return guessPbcType(box);
198 void gmx_rmpbc(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[])
203 pbcType = gmx_rmpbc_ePBC(gpbc, box);
204 gr = gmx_rmpbc_get_graph(gpbc, pbcType, natoms);
207 mk_mshift(stdout, gr, pbcType, box, x);
208 shift_self(gr, box, x);
212 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc, int natoms, const matrix box, rvec x[], rvec x_s[])
218 pbcType = gmx_rmpbc_ePBC(gpbc, box);
219 gr = gmx_rmpbc_get_graph(gpbc, pbcType, natoms);
222 mk_mshift(stdout, gr, pbcType, box, x);
223 shift_x(gr, box, x, x_s);
227 for (i = 0; i < natoms; i++)
229 copy_rvec(x[i], x_s[i]);
234 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe* fr)
239 if (fr->bX && fr->bBox)
241 pbcType = gmx_rmpbc_ePBC(gpbc, fr->box);
242 gr = gmx_rmpbc_get_graph(gpbc, pbcType, fr->natoms);
245 mk_mshift(stdout, gr, pbcType, fr->box, fr->x);
246 shift_self(gr, fr->box, fr->x);
251 void rm_gropbc(const t_atoms* atoms, rvec x[], const matrix box)
256 /* check periodic boundary */
257 for (n = 1; (n < atoms->nr); n++)
259 for (m = DIM - 1; m >= 0; m--)
261 dist = x[n][m] - x[n - 1][m];
262 if (std::abs(dist) > 0.9 * box[m][m])
266 for (d = 0; d <= m; d++)
268 x[n][d] -= box[m][d];
273 for (d = 0; d <= m; d++)
275 x[n][d] += box[m][d];