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54 typedef struct gmx_rmpbc {
62 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc,int ePBC,int natoms)
70 || gpbc->idef->ntypes <= 0)
76 for(i=0; i<gpbc->ngraph; i++)
78 if (natoms == gpbc->graph[i].natoms)
85 /* We'd like to check with the number of atoms in the topology,
86 * but we don't have that available.
87 * So we check against the number of atoms that gmx_rmpbc_init
90 if (natoms > gpbc->natoms_init)
92 gmx_fatal(FARGS,"Structure or trajectory file has more atoms (%d) than the topology (%d)",natoms,gpbc->natoms_init);
95 srenew(gpbc->graph,gpbc->ngraph);
96 gr = &gpbc->graph[gpbc->ngraph-1];
98 gr->gr = mk_graph(NULL,gpbc->idef,0,natoms,FALSE,FALSE);
104 gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
111 gpbc->natoms_init = natoms;
113 /* This sets pbc when we now it,
114 * otherwise we guess it from the instantaneous box in the trajectory.
119 if (gpbc->idef->ntypes <= 0)
123 "WARNING: If there are molecules in the input trajectory file\n"
124 " that are broken across periodic boundaries, they\n"
125 " cannot be made whole (or treated as whole) without\n"
126 " you providing a run input file.\n\n");
132 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
138 for(i=0; i<gpbc->ngraph; i++)
140 done_graph(gpbc->graph[i].gr);
142 if (gpbc->graph != NULL)
149 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc,matrix box)
151 if (NULL != gpbc && gpbc->ePBC >= 0)
157 return guess_ePBC(box);
161 void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[])
166 ePBC = gmx_rmpbc_ePBC(gpbc,box);
167 gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
170 mk_mshift(stdout,gr,ePBC,box,x);
171 shift_self(gr,box,x);
175 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],rvec x_s[])
181 ePBC = gmx_rmpbc_ePBC(gpbc,box);
182 gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
185 mk_mshift(stdout,gr,ePBC,box,x);
186 shift_x(gr,box,x,x_s);
190 for(i=0; i<natoms; i++)
192 copy_rvec(x[i],x_s[i]);
197 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr)
202 if (fr->bX && fr->bBox)
204 ePBC = gmx_rmpbc_ePBC(gpbc,fr->box);
205 gr = gmx_rmpbc_get_graph(gpbc,ePBC,fr->natoms);
208 mk_mshift(stdout,gr,ePBC,fr->box,fr->x);
209 shift_self(gr,fr->box,fr->x);
214 void rm_gropbc(t_atoms *atoms,rvec x[],matrix box)
219 /* check periodic boundary */
220 for(n=1;(n<atoms->nr);n++)
222 for(m=DIM-1; m>=0; m--)
224 dist = x[n][m]-x[n-1][m];
225 if (fabs(dist) > 0.9*box[m][m])
231 x[n][d] -= box[m][d];
238 x[n][d] += box[m][d];