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44 #include "gromacs/math/vec.h"
45 #include "gromacs/random/threefry.h"
46 #include "gromacs/random/uniformintdistribution.h"
47 #include "gromacs/topology/topology.h"
48 #include "gromacs/utility/cstringutil.h"
49 #include "gromacs/utility/exceptions.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/futil.h"
52 #include "gromacs/utility/gmxomp.h"
53 #include "gromacs/utility/smalloc.h"
54 #include "gromacs/utility/strdb.h"
56 void check_binwidth(real binwidth)
58 real smallest_bin = 0.1;
59 if (binwidth < smallest_bin)
61 gmx_fatal(FARGS, "Binwidth shouldn't be smaller then smallest bond length (H-H bond ~0.1nm) in a box");
65 void check_mcover(real mcover)
69 gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
71 else if ((mcover < 0) && (mcover != -1))
73 gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
81 void normalize_probability(int n, double *a)
85 for (i = 0; i < n; i++)
89 for (i = 0; i < n; i++)
95 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn)
97 /* read nsfactor.dat */
105 gmx_neutron_atomic_structurefactors_t *gnsf;
109 /* allocate memory for structure */
111 snew(gnsf->atomnm, nralloc);
112 snew(gnsf->p, nralloc);
113 snew(gnsf->n, nralloc);
114 snew(gnsf->slength, nralloc);
116 gnsf->nratoms = line_no;
118 while (get_a_line(fp, line, STRLEN))
121 if (sscanf(line, "%s %d %d %lf", atomnm, &p, &n, &slength) == 4)
123 gnsf->atomnm[i] = gmx_strdup(atomnm);
126 gnsf->slength[i] = slength;
128 gnsf->nratoms = line_no;
129 if (line_no == nralloc)
132 srenew(gnsf->atomnm, nralloc);
133 srenew(gnsf->p, nralloc);
134 srenew(gnsf->n, nralloc);
135 srenew(gnsf->slength, nralloc);
140 fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n",
144 srenew(gnsf->atomnm, gnsf->nratoms);
145 srenew(gnsf->p, gnsf->nratoms);
146 srenew(gnsf->n, gnsf->nratoms);
147 srenew(gnsf->slength, gnsf->nratoms);
154 gmx_sans_t *gmx_sans_init (const t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf)
156 gmx_sans_t *gsans = nullptr;
158 /* Try to assing scattering length from nsfactor.dat */
160 snew(gsans->slength, top->atoms.nr);
161 /* copy topology data */
163 for (i = 0; i < top->atoms.nr; i++)
165 for (j = 0; j < gnsf->nratoms; j++)
167 if (top->atoms.atom[i].atomnumber == gnsf->p[j])
169 /* we need special case for H and D */
170 if (top->atoms.atom[i].atomnumber == 1)
172 if (top->atoms.atom[i].m == 1.008000)
174 gsans->slength[i] = gnsf->slength[0];
178 gsans->slength[i] = gnsf->slength[1];
183 gsans->slength[i] = gnsf->slength[j];
192 gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram (
204 gmx_radial_distribution_histogram_t *pr = nullptr;
212 gmx::DefaultRandomEngine *trng = nullptr;
214 int64_t mc = 0, mc_max;
215 gmx::DefaultRandomEngine rng(seed);
217 /* allocate memory for pr */
219 /* set some fields */
220 pr->binwidth = binwidth;
223 * create max dist rvec
224 * dist = box[xx] + box[yy] + box[zz]
226 rvec_add(box[XX], box[YY], dist);
227 rvec_add(box[ZZ], dist, dist);
231 pr->grn = static_cast<int>(std::floor(rmax/pr->binwidth)+1);
233 snew(pr->gr, pr->grn);
237 /* Special case for setting automaticaly number of mc iterations to 1% of total number of direct iterations */
240 mc_max = static_cast<int64_t>(std::floor(0.5*0.01*isize*(isize-1)));
244 mc_max = static_cast<int64_t>(std::floor(0.5*mcover*isize*(isize-1)));
247 nthreads = gmx_omp_get_max_threads();
249 trng = new gmx::DefaultRandomEngine[nthreads];
250 for (i = 0; i < nthreads; i++)
252 snew(tgr[i], pr->grn);
255 #pragma omp parallel shared(tgr,trng,mc) private(tid,i,j)
257 gmx::UniformIntDistribution<int> tdist(0, isize-1);
258 tid = gmx_omp_get_thread_num();
259 /* now starting parallel threads */
261 for (mc = 0; mc < mc_max; mc++)
265 i = tdist(trng[tid]); // [0,isize-1]
266 j = tdist(trng[tid]); // [0,isize-1]
269 tgr[tid][static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]]))/binwidth))] += gsans->slength[index[i]]*gsans->slength[index[j]];
272 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
275 /* collecting data from threads */
276 for (i = 0; i < pr->grn; i++)
278 for (j = 0; j < nthreads; j++)
280 pr->gr[i] += tgr[j][i];
283 /* freeing memory for tgr and destroying trng */
284 for (i = 0; i < nthreads; i++)
291 gmx::UniformIntDistribution<int> dist(0, isize-1);
292 for (mc = 0; mc < mc_max; mc++)
294 i = dist(rng); // [0,isize-1]
295 j = dist(rng); // [0,isize-1]
298 pr->gr[static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]]))/binwidth))] += gsans->slength[index[i]]*gsans->slength[index[j]];
306 nthreads = gmx_omp_get_max_threads();
307 /* Allocating memory for tgr arrays */
309 for (i = 0; i < nthreads; i++)
311 snew(tgr[i], pr->grn);
313 #pragma omp parallel shared(tgr) private(tid,i,j)
315 tid = gmx_omp_get_thread_num();
316 /* starting parallel threads */
318 for (i = 0; i < isize; i++)
322 for (j = 0; j < i; j++)
324 tgr[tid][static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]]))/binwidth))] += gsans->slength[index[i]]*gsans->slength[index[j]];
327 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
330 /* collecating data for pr->gr */
331 for (i = 0; i < pr->grn; i++)
333 for (j = 0; j < nthreads; j++)
335 pr->gr[i] += tgr[j][i];
338 /* freeing memory for tgr */
339 for (i = 0; i < nthreads; i++)
345 for (i = 0; i < isize; i++)
347 for (j = 0; j < i; j++)
349 pr->gr[static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]]))/binwidth))] += gsans->slength[index[i]]*gsans->slength[index[j]];
355 /* normalize if needed */
358 normalize_probability(pr->grn, pr->gr);
361 snew(pr->r, pr->grn);
362 for (i = 0; i < pr->grn; i++)
364 pr->r[i] = (pr->binwidth*i+pr->binwidth*0.5);
370 gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step)
372 gmx_static_structurefactor_t *sq = nullptr;
376 sq->qn = static_cast<int>(std::floor((end_q-start_q)/q_step));
379 for (i = 0; i < sq->qn; i++)
381 sq->q[i] = start_q+i*q_step;
387 for (i = 1; i < sq->qn; i++)
389 for (j = 0; j < pr->grn; j++)
391 sq->s[i] += (pr->gr[j]/pr->r[j])*std::sin(sq->q[i]*pr->r[j]);
393 sq->s[i] /= sq->q[i];
398 for (i = 0; i < sq->qn; i++)
400 for (j = 0; j < pr->grn; j++)
402 sq->s[i] += (pr->gr[j]/pr->r[j])*std::sin(sq->q[i]*pr->r[j]);
404 sq->s[i] /= sq->q[i];