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) 2012,2013, 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.
53 #include "gmx_fatal.h"
60 int gmx_rotacf(int argc,char *argv[])
62 const char *desc[] = {
63 "[TT]g_rotacf[tt] calculates the rotational correlation function",
64 "for molecules. Atom triplets (i,j,k) must be given in the index",
65 "file, defining two vectors ij and jk. The rotational ACF",
66 "is calculated as the autocorrelation function of the vector",
67 "n = ij x jk, i.e. the cross product of the two vectors.",
68 "Since three atoms span a plane, the order of the three atoms",
69 "does not matter. Optionally, by invoking the [TT]-d[tt] switch, you can",
70 "calculate the rotational correlation function for linear molecules",
71 "by specifying atom pairs (i,j) in the index file.",
74 "[TT]g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
75 "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[tt][PAR]",
76 "This will calculate the rotational correlation function using a first",
77 "order Legendre polynomial of the angle of a vector defined by the index",
78 "file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
79 "to a two-parameter exponential."
81 static gmx_bool bVec = FALSE,bAver=TRUE;
84 { "-d", FALSE, etBOOL, {&bVec},
85 "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
86 { "-aver",FALSE, etBOOL, {&bAver},
87 "Average over molecules" }
98 int i,m,teller,n_alloc,natoms,nvec,ai,aj,ak;
101 gmx_rmpbc_t gpbc=NULL;
105 { efTRX, "-f", NULL, ffREAD },
106 { efTPX, NULL, NULL, ffREAD },
107 { efNDX, NULL, NULL, ffREAD },
108 { efXVG, "-o", "rotacf", ffWRITE }
110 #define NFILE asize(fnm)
116 CopyRight(stderr,argv[0]);
118 ppa = add_acf_pargs(&npargs,pa);
120 parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
121 NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
123 rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
130 if (((isize % 3) != 0) && !bVec)
131 gmx_fatal(FARGS,"number of index elements not multiple of 3, "
132 "these can not be atom triplets\n");
133 if (((isize % 2) != 0) && bVec)
134 gmx_fatal(FARGS,"number of index elements not multiple of 2, "
135 "these can not be atom doublets\n");
137 top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
140 for (i=0; (i<nvec); i++)
144 natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
147 gpbc = gmx_rmpbc_init(&(top->idef),ePBC,natoms,box);
149 /* Start the loop over frames */
153 if (teller >= n_alloc) {
155 for (i=0; (i<nvec); i++)
156 srenew(c1[i],DIM*n_alloc);
160 /* Remove periodicity */
161 gmx_rmpbc_copy(gpbc,natoms,box,x,x_s);
163 /* Compute crossproducts for all vectors, if triplets.
164 * else, just get the vectors in case of doublets.
167 for (i=0; (i<nvec); i++) {
171 rvec_sub(x_s[ai],x_s[aj],xij);
172 rvec_sub(x_s[aj],x_s[ak],xjk);
174 for(m=0; (m<DIM); m++)
175 c1[i][DIM*teller+m]=n[m];
179 for (i=0; (i<nvec); i++) {
182 rvec_sub(x_s[ai],x_s[aj],n);
183 for(m=0; (m<DIM); m++)
184 c1[i][DIM*teller+m]=n[m];
187 /* Increment loop counter */
189 } while (read_next_x(oenv,status,&t,natoms,x,box));
191 fprintf(stderr,"\nDone with trajectory\n");
193 gmx_rmpbc_done(gpbc);
196 /* Autocorrelation function */
198 fprintf(stderr,"Not enough frames for correlation function\n");
200 dt=(t1 - t0)/(teller-1);
204 do_autocorr(ftp2fn(efXVG,NFILE,fnm),oenv,"Rotational Correlation Function",
205 teller,nvec,c1,dt,mode,bAver);
208 do_view(oenv,ftp2fn(efXVG,NFILE,fnm),NULL);