Bug Summary

File:gromacs/gmxlib/topsort.c
Location:line 134, column 13
Description:Value stored to 'bPert' 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) 2001-2008, 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
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.
25 *
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.
33 *
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.
36 */
37
38#ifdef HAVE_CONFIG_H1
39#include <config.h>
40#endif
41
42#include "typedefs.h"
43#include "topsort.h"
44#include "gromacs/utility/smalloc.h"
45#include "gromacs/utility/fatalerror.h"
46
47static gmx_bool ip_pert(int ftype, const t_iparams *ip)
48{
49 gmx_bool bPert;
50 int i;
51
52 if (NRFPB(ftype)(interaction_function[(ftype)].nrfpB) == 0)
53 {
54 return FALSE0;
55 }
56
57 switch (ftype)
58 {
59 case F_BONDS:
60 case F_G96BONDS:
61 case F_HARMONIC:
62 case F_ANGLES:
63 case F_G96ANGLES:
64 case F_IDIHS:
65 bPert = (ip->harmonic.rA != ip->harmonic.rB ||
66 ip->harmonic.krA != ip->harmonic.krB);
67 break;
68 case F_MORSE:
69 bPert = (ip->morse.b0A != ip->morse.b0B ||
70 ip->morse.cbA != ip->morse.cbB ||
71 ip->morse.betaA != ip->morse.betaB);
72 break;
73 case F_RESTRBONDS:
74 bPert = (ip->restraint.lowA != ip->restraint.lowB ||
75 ip->restraint.up1A != ip->restraint.up1B ||
76 ip->restraint.up2A != ip->restraint.up2B ||
77 ip->restraint.kA != ip->restraint.kB);
78 break;
79 case F_UREY_BRADLEY:
80 bPert = (ip->u_b.thetaA != ip->u_b.thetaB ||
81 ip->u_b.kthetaA != ip->u_b.kthetaB ||
82 ip->u_b.r13A != ip->u_b.r13B ||
83 ip->u_b.kUBA != ip->u_b.kUBB);
84 break;
85 case F_PDIHS:
86 case F_PIDIHS:
87 case F_ANGRES:
88 case F_ANGRESZ:
89 bPert = (ip->pdihs.phiA != ip->pdihs.phiB ||
90 ip->pdihs.cpA != ip->pdihs.cpB);
91 break;
92 case F_RBDIHS:
93 bPert = FALSE0;
94 for (i = 0; i < NR_RBDIHS6; i++)
95 {
96 if (ip->rbdihs.rbcA[i] != ip->rbdihs.rbcB[i])
97 {
98 bPert = TRUE1;
99 }
100 }
101 break;
102 case F_TABBONDS:
103 case F_TABBONDSNC:
104 case F_TABANGLES:
105 case F_TABDIHS:
106 bPert = (ip->tab.kA != ip->tab.kB);
107 break;
108 case F_POSRES:
109 bPert = FALSE0;
110 for (i = 0; i < DIM3; i++)
111 {
112 if (ip->posres.pos0A[i] != ip->posres.pos0B[i] ||
113 ip->posres.fcA[i] != ip->posres.fcB[i])
114 {
115 bPert = TRUE1;
116 }
117 }
118 break;
119 case F_DIHRES:
120 bPert = ((ip->dihres.phiA != ip->dihres.phiB) ||
121 (ip->dihres.dphiA != ip->dihres.dphiB) ||
122 (ip->dihres.kfacA != ip->dihres.kfacB));
123 break;
124 case F_LJ14:
125 bPert = (ip->lj14.c6A != ip->lj14.c6B ||
126 ip->lj14.c12A != ip->lj14.c12B);
127 break;
128 case F_CMAP:
129 bPert = FALSE0;
130 break;
131 case F_RESTRANGLES:
132 case F_RESTRDIHS:
133 case F_CBTDIHS:
134 bPert = FALSE0;
Value stored to 'bPert' is never read
135 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/topsort.c"
, 135, "Function type %s does not support currentely free energy calculations",
136 interaction_function[ftype].longname);
137 default:
138 bPert = FALSE0;
139 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/topsort.c"
, 139, "Function type %s not implemented in ip_pert",
140 interaction_function[ftype].longname);
141 }
142
143 return bPert;
144}
145
146static gmx_bool ip_q_pert(int ftype, const t_iatom *ia,
147 const t_iparams *ip, const real *qA, const real *qB)
148{
149 /* 1-4 interactions do not have the charges stored in the iparams list,
150 * so we need a separate check for those.
151 */
152 return (ip_pert(ftype, ip+ia[0]) ||
153 (ftype == F_LJ14 && (qA[ia[1]] != qB[ia[1]] ||
154 qA[ia[2]] != qB[ia[2]])));
155}
156
157gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop)
158{
159 const gmx_ffparams_t *ffparams;
160 int i, ftype;
161 int mb;
162 t_atom *atom;
163 t_ilist *il;
164 t_iatom *ia;
165 gmx_bool bPert;
166
167 ffparams = &mtop->ffparams;
168
169 /* Loop over all the function types and compare the A/B parameters */
170 bPert = FALSE0;
171 for (i = 0; i < ffparams->ntypes; i++)
172 {
173 ftype = ffparams->functype[i];
174 if (interaction_function[ftype].flags & IF_BOND1)
175 {
176 if (ip_pert(ftype, &ffparams->iparams[i]))
177 {
178 bPert = TRUE1;
179 }
180 }
181 }
182
183 /* Check perturbed charges for 1-4 interactions */
184 for (mb = 0; mb < mtop->nmolblock; mb++)
185 {
186 atom = mtop->moltype[mtop->molblock[mb].type].atoms.atom;
187 il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_LJ14];
188 ia = il->iatoms;
189 for (i = 0; i < il->nr; i += 3)
190 {
191 if (atom[ia[i+1]].q != atom[ia[i+1]].qB ||
192 atom[ia[i+2]].q != atom[ia[i+2]].qB)
193 {
194 bPert = TRUE1;
195 }
196 }
197 }
198
199 return bPert;
200}
201
202void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB)
203{
204 int ftype, nral, i, ic, ib, a;
205 t_iparams *iparams;
206 t_ilist *ilist;
207 t_iatom *iatoms;
208 gmx_bool bPert;
209 t_iatom *iabuf;
210 int iabuf_nalloc;
211
212 if (qB == NULL((void*)0))
213 {
214 qB = qA;
215 }
216
217 iabuf_nalloc = 0;
218 iabuf = NULL((void*)0);
219
220 iparams = idef->iparams;
221
222 for (ftype = 0; ftype < F_NRE; ftype++)
223 {
224 if (interaction_function[ftype].flags & IF_BOND1)
225 {
226 ilist = &idef->il[ftype];
227 iatoms = ilist->iatoms;
228 nral = NRAL(ftype)(interaction_function[(ftype)].nratoms);
229 ic = 0;
230 ib = 0;
231 i = 0;
232 while (i < ilist->nr)
233 {
234 /* Check if this interaction is perturbed */
235 if (ip_q_pert(ftype, iatoms+i, iparams, qA, qB))
236 {
237 /* Copy to the perturbed buffer */
238 if (ib + 1 + nral > iabuf_nalloc)
239 {
240 iabuf_nalloc = over_alloc_large(ib+1+nral)(int)(1.19*(ib+1+nral) + 1000);
241 srenew(iabuf, iabuf_nalloc)(iabuf) = save_realloc("iabuf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/topsort.c"
, 241, (iabuf), (iabuf_nalloc), sizeof(*(iabuf)));
242 }
243 for (a = 0; a < 1+nral; a++)
244 {
245 iabuf[ib++] = iatoms[i++];
246 }
247 }
248 else
249 {
250 /* Copy in place */
251 for (a = 0; a < 1+nral; a++)
252 {
253 iatoms[ic++] = iatoms[i++];
254 }
255 }
256 }
257 /* Now we now the number of non-perturbed interactions */
258 ilist->nr_nonperturbed = ic;
259
260 /* Copy the buffer with perturbed interactions to the ilist */
261 for (a = 0; a < ib; a++)
262 {
263 iatoms[ic++] = iabuf[a];
264 }
265
266 if (debug)
267 {
268 fprintf(debug, "%s non-pert %d pert %d\n",
269 interaction_function[ftype].longname,
270 ilist->nr_nonperturbed,
271 ilist->nr-ilist->nr_nonperturbed);
272 }
273 }
274 }
275
276 sfree(iabuf)save_free("iabuf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/topsort.c"
, 276, (iabuf));
277
278 idef->ilsort = ilsortFE_SORTED;
279}