Bug Summary

File:gromacs/gmxana/gmx_rotacf.c
Location:line 161, column 5
Description:Value stored to 't1' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
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.
10 *
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.
15 *
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.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
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24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
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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
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36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <math.h>
42#include <string.h>
43
44#include "physics.h"
45#include "typedefs.h"
46#include "gromacs/utility/smalloc.h"
47#include "gromacs/utility/futil.h"
48#include "gromacs/commandline/pargs.h"
49#include "index.h"
50#include "macros.h"
51#include "gromacs/utility/fatalerror.h"
52#include "gstat.h"
53#include "gromacs/math/vec.h"
54#include "viewit.h"
55#include "gmx_ana.h"
56#include "gromacs/fileio/trxio.h"
57
58
59int gmx_rotacf(int argc, char *argv[])
60{
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.",
71 "[PAR]",
72 "EXAMPLES[PAR]",
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."
79 };
80 static gmx_bool bVec = FALSE0, bAver = TRUE1;
81
82 t_pargs pa[] = {
83 { "-d", FALSE0, etBOOL, {&bVec},
84 "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
85 { "-aver", FALSE0, etBOOL, {&bAver},
86 "Average over molecules" }
87 };
88
89 t_trxstatus *status;
90 int isize;
91 atom_id *index;
92 char *grpname;
93 rvec *x, *x_s;
94 matrix box;
95 real **c1;
96 rvec xij, xjk, n;
97 int i, m, teller, n_alloc, natoms, nvec, ai, aj, ak;
98 unsigned long mode;
99 real t, t0, t1, dt;
100 gmx_rmpbc_t gpbc = NULL((void*)0);
101 t_topology *top;
102 int ePBC;
103 t_filenm fnm[] = {
104 { efTRX, "-f", NULL((void*)0), ffREAD1<<1 },
105 { efTPX, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
106 { efNDX, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
107 { efXVG, "-o", "rotacf", ffWRITE1<<2 }
108 };
109#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
110 int npargs;
111 t_pargs *ppa;
112
113 output_env_t oenv;
114
115 npargs = asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])));
116 ppa = add_acf_pargs(&npargs, pa);
117
118 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW(1<<5) | PCA_CAN_TIME((1<<6) | (1<<7) | (1<<14)) | PCA_BE_NICE(1<<13),
119 NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, npargs, ppa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
120 {
121 return 0;
122 }
123
124 rd_index(ftp2fn(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), 1, &isize, &index, &grpname);
125
126 if (bVec)
127 {
128 nvec = isize/2;
129 }
130 else
131 {
132 nvec = isize/3;
133 }
134
135 if (((isize % 3) != 0) && !bVec)
136 {
137 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotacf.c"
, 137, "number of index elements not multiple of 3, "
138 "these can not be atom triplets\n");
139 }
140 if (((isize % 2) != 0) && bVec)
141 {
142 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotacf.c"
, 142, "number of index elements not multiple of 2, "
143 "these can not be atom doublets\n");
144 }
145
146 top = read_top(ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &ePBC);
147
148 snew(c1, nvec)(c1) = save_calloc("c1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotacf.c"
, 148, (nvec), sizeof(*(c1)));
149 for (i = 0; (i < nvec); i++)
150 {
151 c1[i] = NULL((void*)0);
152 }
153 n_alloc = 0;
154
155 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &t, &x, box);
156 snew(x_s, natoms)(x_s) = save_calloc("x_s", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotacf.c"
, 156, (natoms), sizeof(*(x_s)));
157
158 gpbc = gmx_rmpbc_init(&(top->idef), ePBC, natoms);
159
160 /* Start the loop over frames */
161 t1 = t0 = t;
Value stored to 't1' is never read
162 teller = 0;
163 do
164 {
165 if (teller >= n_alloc)
166 {
167 n_alloc += 100;
168 for (i = 0; (i < nvec); i++)
169 {
170 srenew(c1[i], DIM*n_alloc)(c1[i]) = save_realloc("c1[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_rotacf.c"
, 170, (c1[i]), (3*n_alloc), sizeof(*(c1[i])));
171 }
172 }
173 t1 = t;
174
175 /* Remove periodicity */
176 gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
177
178 /* Compute crossproducts for all vectors, if triplets.
179 * else, just get the vectors in case of doublets.
180 */
181 if (bVec == FALSE0)
182 {
183 for (i = 0; (i < nvec); i++)
184 {
185 ai = index[3*i];
186 aj = index[3*i+1];
187 ak = index[3*i+2];
188 rvec_sub(x_s[ai], x_s[aj], xij);
189 rvec_sub(x_s[aj], x_s[ak], xjk);
190 cprod(xij, xjk, n);
191 for (m = 0; (m < DIM3); m++)
192 {
193 c1[i][DIM3*teller+m] = n[m];
194 }
195 }
196 }
197 else
198 {
199 for (i = 0; (i < nvec); i++)
200 {
201 ai = index[2*i];
202 aj = index[2*i+1];
203 rvec_sub(x_s[ai], x_s[aj], n);
204 for (m = 0; (m < DIM3); m++)
205 {
206 c1[i][DIM3*teller+m] = n[m];
207 }
208 }
209 }
210 /* Increment loop counter */
211 teller++;
212 }
213 while (read_next_x(oenv, status, &t, x, box));
214 close_trj(status);
215 fprintf(stderrstderr, "\nDone with trajectory\n");
216
217 gmx_rmpbc_done(gpbc);
218
219
220 /* Autocorrelation function */
221 if (teller < 2)
222 {
223 fprintf(stderrstderr, "Not enough frames for correlation function\n");
224 }
225 else
226 {
227 dt = (t1 - t0)/(teller-1);
228
229 mode = eacVector(1<<2);
230
231 do_autocorr(ftp2fn(efXVG, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), oenv, "Rotational Correlation Function",
232 teller, nvec, c1, dt, mode, bAver);
233 }
234
235 do_view(oenv, ftp2fn(efXVG, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), NULL((void*)0));
236
237 return 0;
238}