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 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
45 #include "gromacs/utility/futil.h"
46 #include "gromacs/topology/index.h"
49 #include "gromacs/math/vec.h"
52 #include "gromacs/fileio/trxio.h"
54 #include "gromacs/commandline/pargs.h"
55 #include "gromacs/pbcutil/rmpbc.h"
56 #include "gromacs/utility/fatalerror.h"
57 #include "gromacs/utility/smalloc.h"
59 int gmx_rotacf(int argc, char *argv[])
61 const char *desc[] = {
62 "[THISMODULE] calculates the rotational correlation function",
63 "for molecules. Atom triplets (i,j,k) must be given in the index",
64 "file, defining two vectors ij and jk. The rotational ACF",
65 "is calculated as the autocorrelation function of the vector",
66 "n = ij x jk, i.e. the cross product of the two vectors.",
67 "Since three atoms span a plane, the order of the three atoms",
68 "does not matter. Optionally, by invoking the [TT]-d[tt] switch, you can",
69 "calculate the rotational correlation function for linear molecules",
70 "by specifying atom pairs (i,j) in the index file.",
73 "[TT]gmx rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
74 "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[tt][PAR]",
75 "This will calculate the rotational correlation function using a first",
76 "order Legendre polynomial of the angle of a vector defined by the index",
77 "file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
78 "to a two-parameter exponential."
80 static gmx_bool bVec = FALSE, bAver = TRUE;
83 { "-d", FALSE, etBOOL, {&bVec},
84 "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
85 { "-aver", FALSE, etBOOL, {&bAver},
86 "Average over molecules" }
97 int i, m, teller, n_alloc, natoms, nvec, ai, aj, ak;
100 gmx_rmpbc_t gpbc = NULL;
104 { efTRX, "-f", NULL, ffREAD },
105 { efTPX, NULL, NULL, ffREAD },
106 { efNDX, NULL, NULL, ffREAD },
107 { efXVG, "-o", "rotacf", ffWRITE }
109 #define NFILE asize(fnm)
116 ppa = add_acf_pargs(&npargs, pa);
118 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
119 NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
124 rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
135 if (((isize % 3) != 0) && !bVec)
137 gmx_fatal(FARGS, "number of index elements not multiple of 3, "
138 "these can not be atom triplets\n");
140 if (((isize % 2) != 0) && bVec)
142 gmx_fatal(FARGS, "number of index elements not multiple of 2, "
143 "these can not be atom doublets\n");
146 top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
149 for (i = 0; (i < nvec); i++)
155 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
158 gpbc = gmx_rmpbc_init(&(top->idef), ePBC, natoms);
160 /* Start the loop over frames */
165 if (teller >= n_alloc)
168 for (i = 0; (i < nvec); i++)
170 srenew(c1[i], DIM*n_alloc);
175 /* Remove periodicity */
176 gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
178 /* Compute crossproducts for all vectors, if triplets.
179 * else, just get the vectors in case of doublets.
183 for (i = 0; (i < nvec); i++)
188 rvec_sub(x_s[ai], x_s[aj], xij);
189 rvec_sub(x_s[aj], x_s[ak], xjk);
191 for (m = 0; (m < DIM); m++)
193 c1[i][DIM*teller+m] = n[m];
199 for (i = 0; (i < nvec); i++)
203 rvec_sub(x_s[ai], x_s[aj], n);
204 for (m = 0; (m < DIM); m++)
206 c1[i][DIM*teller+m] = n[m];
210 /* Increment loop counter */
213 while (read_next_x(oenv, status, &t, x, box));
215 fprintf(stderr, "\nDone with trajectory\n");
217 gmx_rmpbc_done(gpbc);
220 /* Autocorrelation function */
223 fprintf(stderr, "Not enough frames for correlation function\n");
227 dt = (t1 - t0)/(teller-1);
231 do_autocorr(ftp2fn(efXVG, NFILE, fnm), oenv, "Rotational Correlation Function",
232 teller, nvec, c1, dt, mode, bAver);
235 do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);