| File: | gromacs/gmxana/nsfactor.c |
| Location: | line 228, column 5 |
| Description: | Value stored to 'rmax' is never read |
| 1 | /* |
| 2 | * This file is part of the GROMACS molecular simulation package. |
| 3 | * |
| 4 | * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by |
| 5 | * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, |
| 6 | * and including many others, as listed in the AUTHORS file in the |
| 7 | * top-level source directory and at http://www.gromacs.org. |
| 8 | * |
| 9 | * GROMACS is free software; you can redistribute it and/or |
| 10 | * modify it under the terms of the GNU Lesser General Public License |
| 11 | * as published by the Free Software Foundation; either version 2.1 |
| 12 | * of the License, or (at your option) any later version. |
| 13 | * |
| 14 | * GROMACS is distributed in the hope that it will be useful, |
| 15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 17 | * Lesser General Public License for more details. |
| 18 | * |
| 19 | * You should have received a copy of the GNU Lesser General Public |
| 20 | * License along with GROMACS; if not, see |
| 21 | * http://www.gnu.org/licenses, or write to the Free Software Foundation, |
| 22 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
| 23 | * |
| 24 | * If you want to redistribute modifications to GROMACS, please |
| 25 | * consider that scientific software is very special. Version |
| 26 | * control is crucial - bugs must be traceable. We will be happy to |
| 27 | * consider code for inclusion in the official distribution, but |
| 28 | * derived work must not be called official GROMACS. Details are found |
| 29 | * in the README & COPYING files - if they are missing, get the |
| 30 | * official version at http://www.gromacs.org. |
| 31 | * |
| 32 | * To help us fund GROMACS development, we humbly ask that you cite |
| 33 | * the research papers on the package. Check out http://www.gromacs.org. |
| 34 | */ |
| 35 | #ifdef HAVE_CONFIG_H1 |
| 36 | #include <config.h> |
| 37 | #endif |
| 38 | |
| 39 | #include <string.h> |
| 40 | |
| 41 | #include "gromacs/math/vec.h" |
| 42 | #include "nsfactor.h" |
| 43 | |
| 44 | #include "gromacs/utility/futil.h" |
| 45 | #include "gromacs/fileio/strdb.h" |
| 46 | #include "gromacs/random/random.h" |
| 47 | #include "gromacs/utility/cstringutil.h" |
| 48 | #include "gromacs/utility/fatalerror.h" |
| 49 | #include "gromacs/utility/gmxomp.h" |
| 50 | #include "gromacs/utility/smalloc.h" |
| 51 | |
| 52 | void check_binwidth(real binwidth) |
| 53 | { |
| 54 | real smallest_bin = 0.1; |
| 55 | if (binwidth < smallest_bin) |
| 56 | { |
| 57 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 57, "Binwidth shouldnt be smaller then smallest bond length (H-H bond ~0.1nm) in a box"); |
| 58 | } |
| 59 | } |
| 60 | |
| 61 | void check_mcover(real mcover) |
| 62 | { |
| 63 | if (mcover > 1.0) |
| 64 | { |
| 65 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 65, "mcover should be -1 or (0,1]"); |
| 66 | } |
| 67 | else if ((mcover < 0)&(mcover != -1)) |
| 68 | { |
| 69 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 69, "mcover should be -1 or (0,1]"); |
| 70 | } |
| 71 | else |
| 72 | { |
| 73 | return; |
| 74 | } |
| 75 | } |
| 76 | |
| 77 | void normalize_probability(int n, double *a) |
| 78 | { |
| 79 | int i; |
| 80 | double norm = 0.0; |
| 81 | for (i = 0; i < n; i++) |
| 82 | { |
| 83 | norm += a[i]; |
| 84 | } |
| 85 | for (i = 0; i < n; i++) |
| 86 | { |
| 87 | a[i] /= norm; |
| 88 | } |
| 89 | } |
| 90 | |
| 91 | gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn) |
| 92 | { |
| 93 | /* read nsfactor.dat */ |
| 94 | FILE *fp; |
| 95 | char line[STRLEN4096]; |
| 96 | int nralloc = 10; |
| 97 | int n, p; |
| 98 | int i, line_no; |
| 99 | char atomnm[8]; |
| 100 | double slength; |
| 101 | gmx_neutron_atomic_structurefactors_t *gnsf; |
| 102 | |
| 103 | fp = libopen(datfn); |
| 104 | line_no = 0; |
| 105 | /* allocate memory for structure */ |
| 106 | snew(gnsf, nralloc)(gnsf) = save_calloc("gnsf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 106, (nralloc), sizeof(*(gnsf))); |
| 107 | snew(gnsf->atomnm, nralloc)(gnsf->atomnm) = save_calloc("gnsf->atomnm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 107, (nralloc), sizeof(*(gnsf->atomnm))); |
| 108 | snew(gnsf->p, nralloc)(gnsf->p) = save_calloc("gnsf->p", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 108, (nralloc), sizeof(*(gnsf->p))); |
| 109 | snew(gnsf->n, nralloc)(gnsf->n) = save_calloc("gnsf->n", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 109, (nralloc), sizeof(*(gnsf->n))); |
| 110 | snew(gnsf->slength, nralloc)(gnsf->slength) = save_calloc("gnsf->slength", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 110, (nralloc), sizeof(*(gnsf->slength))); |
| 111 | |
| 112 | gnsf->nratoms = line_no; |
| 113 | |
| 114 | while (get_a_line(fp, line, STRLEN4096)) |
| 115 | { |
| 116 | i = line_no; |
| 117 | if (sscanf(line, "%s %d %d %lf", atomnm, &p, &n, &slength) == 4) |
| 118 | { |
| 119 | gnsf->atomnm[i] = strdup(atomnm)(__extension__ (__builtin_constant_p (atomnm) && ((size_t )(const void *)((atomnm) + 1) - (size_t)(const void *)(atomnm ) == 1) ? (((const char *) (atomnm))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (atomnm) + 1; char *__retval = (char *) malloc (__len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, atomnm, __len ); __retval; })) : __strdup (atomnm))); |
| 120 | gnsf->n[i] = n; |
| 121 | gnsf->p[i] = p; |
| 122 | gnsf->slength[i] = slength; |
| 123 | line_no++; |
| 124 | gnsf->nratoms = line_no; |
| 125 | if (line_no == nralloc) |
| 126 | { |
| 127 | nralloc++; |
| 128 | srenew(gnsf->atomnm, nralloc)(gnsf->atomnm) = save_realloc("gnsf->atomnm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 128, (gnsf->atomnm), (nralloc), sizeof(*(gnsf->atomnm ))); |
| 129 | srenew(gnsf->p, nralloc)(gnsf->p) = save_realloc("gnsf->p", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 129, (gnsf->p), (nralloc), sizeof(*(gnsf->p))); |
| 130 | srenew(gnsf->n, nralloc)(gnsf->n) = save_realloc("gnsf->n", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 130, (gnsf->n), (nralloc), sizeof(*(gnsf->n))); |
| 131 | srenew(gnsf->slength, nralloc)(gnsf->slength) = save_realloc("gnsf->slength", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 131, (gnsf->slength), (nralloc), sizeof(*(gnsf->slength ))); |
| 132 | } |
| 133 | } |
| 134 | else |
| 135 | { |
| 136 | fprintf(stderrstderr, "WARNING: Error in file %s at line %d ignored\n", |
| 137 | datfn, line_no); |
| 138 | } |
| 139 | } |
| 140 | srenew(gnsf->atomnm, gnsf->nratoms)(gnsf->atomnm) = save_realloc("gnsf->atomnm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 140, (gnsf->atomnm), (gnsf->nratoms), sizeof(*(gnsf-> atomnm))); |
| 141 | srenew(gnsf->p, gnsf->nratoms)(gnsf->p) = save_realloc("gnsf->p", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 141, (gnsf->p), (gnsf->nratoms), sizeof(*(gnsf->p) )); |
| 142 | srenew(gnsf->n, gnsf->nratoms)(gnsf->n) = save_realloc("gnsf->n", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 142, (gnsf->n), (gnsf->nratoms), sizeof(*(gnsf->n) )); |
| 143 | srenew(gnsf->slength, gnsf->nratoms)(gnsf->slength) = save_realloc("gnsf->slength", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 143, (gnsf->slength), (gnsf->nratoms), sizeof(*(gnsf-> slength))); |
| 144 | |
| 145 | fclose(fp); |
| 146 | |
| 147 | return (gmx_neutron_atomic_structurefactors_t *) gnsf; |
| 148 | } |
| 149 | |
| 150 | gmx_sans_t *gmx_sans_init (t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf) |
| 151 | { |
| 152 | gmx_sans_t *gsans = NULL((void*)0); |
| 153 | int i, j; |
| 154 | /* Try to assing scattering length from nsfactor.dat */ |
| 155 | snew(gsans, 1)(gsans) = save_calloc("gsans", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 155, (1), sizeof(*(gsans))); |
| 156 | snew(gsans->slength, top->atoms.nr)(gsans->slength) = save_calloc("gsans->slength", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 156, (top->atoms.nr), sizeof(*(gsans->slength))); |
| 157 | /* copy topology data */ |
| 158 | gsans->top = top; |
| 159 | for (i = 0; i < top->atoms.nr; i++) |
| 160 | { |
| 161 | for (j = 0; j < gnsf->nratoms; j++) |
| 162 | { |
| 163 | if (top->atoms.atom[i].atomnumber == gnsf->p[j]) |
| 164 | { |
| 165 | /* we need special case for H and D */ |
| 166 | if (top->atoms.atom[i].atomnumber == 1) |
| 167 | { |
| 168 | if (top->atoms.atom[i].m == 1.008000) |
| 169 | { |
| 170 | gsans->slength[i] = gnsf->slength[0]; |
| 171 | } |
| 172 | else |
| 173 | { |
| 174 | gsans->slength[i] = gnsf->slength[1]; |
| 175 | } |
| 176 | } |
| 177 | else |
| 178 | { |
| 179 | gsans->slength[i] = gnsf->slength[j]; |
| 180 | } |
| 181 | } |
| 182 | } |
| 183 | } |
| 184 | |
| 185 | return (gmx_sans_t *) gsans; |
| 186 | } |
| 187 | |
| 188 | gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram ( |
| 189 | gmx_sans_t *gsans, |
| 190 | rvec *x, |
| 191 | matrix box, |
| 192 | atom_id *index, |
| 193 | int isize, |
| 194 | double binwidth, |
| 195 | gmx_bool bMC, |
| 196 | gmx_bool bNORM, |
| 197 | real mcover, |
| 198 | unsigned int seed) |
| 199 | { |
| 200 | gmx_radial_distribution_histogram_t *pr = NULL((void*)0); |
| 201 | rvec dist; |
| 202 | double rmax; |
| 203 | int i, j; |
| 204 | #ifdef GMX_OPENMP |
| 205 | double **tgr; |
| 206 | int tid; |
| 207 | int nthreads; |
| 208 | gmx_rng_t *trng = NULL((void*)0); |
| 209 | #endif |
| 210 | gmx_int64_t mc = 0, max; |
| 211 | gmx_rng_t rng = NULL((void*)0); |
| 212 | |
| 213 | /* allocate memory for pr */ |
| 214 | snew(pr, 1)(pr) = save_calloc("pr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 214, (1), sizeof(*(pr))); |
| 215 | /* set some fields */ |
| 216 | pr->binwidth = binwidth; |
| 217 | |
| 218 | /* |
| 219 | * create max dist rvec |
| 220 | * dist = box[xx] + box[yy] + box[zz] |
| 221 | */ |
| 222 | rvec_add(box[XX0], box[YY1], dist); |
| 223 | rvec_add(box[ZZ2], dist, dist); |
| 224 | |
| 225 | rmax = norm(dist); |
| 226 | |
| 227 | pr->grn = (int)floor(rmax/pr->binwidth)+1; |
| 228 | rmax = pr->grn*pr->binwidth; |
Value stored to 'rmax' is never read | |
| 229 | |
| 230 | snew(pr->gr, pr->grn)(pr->gr) = save_calloc("pr->gr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 230, (pr->grn), sizeof(*(pr->gr))); |
| 231 | |
| 232 | if (bMC) |
| 233 | { |
| 234 | /* Special case for setting automaticaly number of mc iterations to 1% of total number of direct iterations */ |
| 235 | if (mcover == -1) |
| 236 | { |
| 237 | max = (gmx_int64_t)floor(0.5*0.01*isize*(isize-1)); |
| 238 | } |
| 239 | else |
| 240 | { |
| 241 | max = (gmx_int64_t)floor(0.5*mcover*isize*(isize-1)); |
| 242 | } |
| 243 | rng = gmx_rng_init(seed); |
| 244 | #ifdef GMX_OPENMP |
| 245 | nthreads = gmx_omp_get_max_threads(); |
| 246 | snew(tgr, nthreads)(tgr) = save_calloc("tgr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 246, (nthreads), sizeof(*(tgr))); |
| 247 | snew(trng, nthreads)(trng) = save_calloc("trng", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 247, (nthreads), sizeof(*(trng))); |
| 248 | for (i = 0; i < nthreads; i++) |
| 249 | { |
| 250 | snew(tgr[i], pr->grn)(tgr[i]) = save_calloc("tgr[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 250, (pr->grn), sizeof(*(tgr[i]))); |
| 251 | trng[i] = gmx_rng_init(gmx_rng_uniform_uint32(rng)); |
| 252 | } |
| 253 | #pragma omp parallel shared(tgr,trng,mc) private(tid,i,j) |
| 254 | { |
| 255 | tid = gmx_omp_get_thread_num(); |
| 256 | /* now starting parallel threads */ |
| 257 | #pragma omp for |
| 258 | for (mc = 0; mc < max; mc++) |
| 259 | { |
| 260 | i = (int)floor(gmx_rng_uniform_real(trng[tid])*isize); |
| 261 | j = (int)floor(gmx_rng_uniform_real(trng[tid])*isize); |
| 262 | if (i != j) |
| 263 | { |
| 264 | tgr[tid][(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]]; |
| 265 | } |
| 266 | } |
| 267 | } |
| 268 | /* collecting data from threads */ |
| 269 | for (i = 0; i < pr->grn; i++) |
| 270 | { |
| 271 | for (j = 0; j < nthreads; j++) |
| 272 | { |
| 273 | pr->gr[i] += tgr[j][i]; |
| 274 | } |
| 275 | } |
| 276 | /* freeing memory for tgr and destroying trng */ |
| 277 | for (i = 0; i < nthreads; i++) |
| 278 | { |
| 279 | sfree(tgr[i])save_free("tgr[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 279, (tgr[i])); |
| 280 | gmx_rng_destroy(trng[i]); |
| 281 | } |
| 282 | sfree(tgr)save_free("tgr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 282, (tgr)); |
| 283 | sfree(trng)save_free("trng", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 283, (trng)); |
| 284 | #else |
| 285 | for (mc = 0; mc < max; mc++) |
| 286 | { |
| 287 | i = (int)floor(gmx_rng_uniform_real(rng)*isize); |
| 288 | j = (int)floor(gmx_rng_uniform_real(rng)*isize); |
| 289 | if (i != j) |
| 290 | { |
| 291 | pr->gr[(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]]; |
| 292 | } |
| 293 | } |
| 294 | #endif |
| 295 | gmx_rng_destroy(rng); |
| 296 | } |
| 297 | else |
| 298 | { |
| 299 | #ifdef GMX_OPENMP |
| 300 | nthreads = gmx_omp_get_max_threads(); |
| 301 | /* Allocating memory for tgr arrays */ |
| 302 | snew(tgr, nthreads)(tgr) = save_calloc("tgr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 302, (nthreads), sizeof(*(tgr))); |
| 303 | for (i = 0; i < nthreads; i++) |
| 304 | { |
| 305 | snew(tgr[i], pr->grn)(tgr[i]) = save_calloc("tgr[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 305, (pr->grn), sizeof(*(tgr[i]))); |
| 306 | } |
| 307 | #pragma omp parallel shared(tgr) private(tid,i,j) |
| 308 | { |
| 309 | tid = gmx_omp_get_thread_num(); |
| 310 | /* starting parallel threads */ |
| 311 | #pragma omp for |
| 312 | for (i = 0; i < isize; i++) |
| 313 | { |
| 314 | for (j = 0; j < i; j++) |
| 315 | { |
| 316 | tgr[tid][(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]]; |
| 317 | } |
| 318 | } |
| 319 | } |
| 320 | /* collecating data for pr->gr */ |
| 321 | for (i = 0; i < pr->grn; i++) |
| 322 | { |
| 323 | for (j = 0; j < nthreads; j++) |
| 324 | { |
| 325 | pr->gr[i] += tgr[j][i]; |
| 326 | } |
| 327 | } |
| 328 | /* freeing memory for tgr */ |
| 329 | for (i = 0; i < nthreads; i++) |
| 330 | { |
| 331 | sfree(tgr[i])save_free("tgr[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 331, (tgr[i])); |
| 332 | } |
| 333 | sfree(tgr)save_free("tgr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 333, (tgr)); |
| 334 | #else |
| 335 | for (i = 0; i < isize; i++) |
| 336 | { |
| 337 | for (j = 0; j < i; j++) |
| 338 | { |
| 339 | pr->gr[(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]]; |
| 340 | } |
| 341 | } |
| 342 | #endif |
| 343 | } |
| 344 | |
| 345 | /* normalize if needed */ |
| 346 | if (bNORM) |
| 347 | { |
| 348 | normalize_probability(pr->grn, pr->gr); |
| 349 | } |
| 350 | |
| 351 | snew(pr->r, pr->grn)(pr->r) = save_calloc("pr->r", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 351, (pr->grn), sizeof(*(pr->r))); |
| 352 | for (i = 0; i < pr->grn; i++) |
| 353 | { |
| 354 | pr->r[i] = (pr->binwidth*i+pr->binwidth*0.5); |
| 355 | } |
| 356 | |
| 357 | return (gmx_radial_distribution_histogram_t *) pr; |
| 358 | } |
| 359 | |
| 360 | gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step) |
| 361 | { |
| 362 | gmx_static_structurefactor_t *sq = NULL((void*)0); |
| 363 | int i, j; |
| 364 | /* init data */ |
| 365 | snew(sq, 1)(sq) = save_calloc("sq", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 365, (1), sizeof(*(sq))); |
| 366 | sq->qn = (int)floor((end_q-start_q)/q_step); |
| 367 | snew(sq->q, sq->qn)(sq->q) = save_calloc("sq->q", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 367, (sq->qn), sizeof(*(sq->q))); |
| 368 | snew(sq->s, sq->qn)(sq->s) = save_calloc("sq->s", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/nsfactor.c" , 368, (sq->qn), sizeof(*(sq->s))); |
| 369 | for (i = 0; i < sq->qn; i++) |
| 370 | { |
| 371 | sq->q[i] = start_q+i*q_step; |
| 372 | } |
| 373 | |
| 374 | if (start_q == 0.0) |
| 375 | { |
| 376 | sq->s[0] = 1.0; |
| 377 | for (i = 1; i < sq->qn; i++) |
| 378 | { |
| 379 | for (j = 0; j < pr->grn; j++) |
| 380 | { |
| 381 | sq->s[i] += (pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]); |
| 382 | } |
| 383 | sq->s[i] /= sq->q[i]; |
| 384 | } |
| 385 | } |
| 386 | else |
| 387 | { |
| 388 | for (i = 0; i < sq->qn; i++) |
| 389 | { |
| 390 | for (j = 0; j < pr->grn; j++) |
| 391 | { |
| 392 | sq->s[i] += (pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]); |
| 393 | } |
| 394 | sq->s[i] /= sq->q[i]; |
| 395 | } |
| 396 | } |
| 397 | |
| 398 | return (gmx_static_structurefactor_t *) sq; |
| 399 | } |