2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team,
6 * check out http://www.gromacs.org for more information.
7 * Copyright (c) 2012, by the GROMACS development team, led by
8 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
9 * others, as listed in the AUTHORS file in the top-level source
10 * directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
56 typedef struct gmx_rmpbc {
64 static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc,int ePBC,int natoms)
72 || gpbc->idef->ntypes <= 0)
78 for(i=0; i<gpbc->ngraph; i++)
80 if (natoms == gpbc->graph[i].natoms)
87 /* We'd like to check with the number of atoms in the topology,
88 * but we don't have that available.
89 * So we check against the number of atoms that gmx_rmpbc_init
92 if (natoms > gpbc->natoms_init)
94 gmx_fatal(FARGS,"Structure or trajectory file has more atoms (%d) than the topology (%d)",natoms,gpbc->natoms_init);
97 srenew(gpbc->graph,gpbc->ngraph);
98 gr = &gpbc->graph[gpbc->ngraph-1];
100 gr->gr = mk_graph(NULL,gpbc->idef,0,natoms,FALSE,FALSE);
106 gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef,int ePBC,int natoms,
113 gpbc->natoms_init = natoms;
115 /* This sets pbc when we now it,
116 * otherwise we guess it from the instantaneous box in the trajectory.
121 if (gpbc->idef->ntypes <= 0)
125 "WARNING: If there are molecules in the input trajectory file\n"
126 " that are broken across periodic boundaries, they\n"
127 " cannot be made whole (or treated as whole) without\n"
128 " you providing a run input file.\n\n");
134 void gmx_rmpbc_done(gmx_rmpbc_t gpbc)
140 for(i=0; i<gpbc->ngraph; i++)
142 done_graph(gpbc->graph[i].gr);
144 if (gpbc->graph != NULL)
151 static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc,matrix box)
153 if (NULL != gpbc && gpbc->ePBC >= 0)
159 return guess_ePBC(box);
163 void gmx_rmpbc(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[])
168 ePBC = gmx_rmpbc_ePBC(gpbc,box);
169 gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
172 mk_mshift(stdout,gr,ePBC,box,x);
173 shift_self(gr,box,x);
177 void gmx_rmpbc_copy(gmx_rmpbc_t gpbc,int natoms,matrix box,rvec x[],rvec x_s[])
183 ePBC = gmx_rmpbc_ePBC(gpbc,box);
184 gr = gmx_rmpbc_get_graph(gpbc,ePBC,natoms);
187 mk_mshift(stdout,gr,ePBC,box,x);
188 shift_x(gr,box,x,x_s);
192 for(i=0; i<natoms; i++)
194 copy_rvec(x[i],x_s[i]);
199 void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc,t_trxframe *fr)
204 if (fr->bX && fr->bBox)
206 ePBC = gmx_rmpbc_ePBC(gpbc,fr->box);
207 gr = gmx_rmpbc_get_graph(gpbc,ePBC,fr->natoms);
210 mk_mshift(stdout,gr,ePBC,fr->box,fr->x);
211 shift_self(gr,fr->box,fr->x);
216 void rm_gropbc(t_atoms *atoms,rvec x[],matrix box)
221 /* check periodic boundary */
222 for(n=1;(n<atoms->nr);n++)
224 for(m=DIM-1; m>=0; m--)
226 dist = x[n][m]-x[n-1][m];
227 if (fabs(dist) > 0.9*box[m][m])
233 x[n][d] -= box[m][d];
240 x[n][d] += box[m][d];