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43 #include "gromacs/fileio/strdb.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/random/random.h"
46 #include "gromacs/topology/topology.h"
47 #include "gromacs/utility/cstringutil.h"
48 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/utility/gmxomp.h"
51 #include "gromacs/utility/smalloc.h"
53 void check_binwidth(real binwidth)
55 real smallest_bin = 0.1;
56 if (binwidth < smallest_bin)
58 gmx_fatal(FARGS, "Binwidth shouldnt be smaller then smallest bond length (H-H bond ~0.1nm) in a box");
62 void check_mcover(real mcover)
66 gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
68 else if ((mcover < 0)&(mcover != -1))
70 gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
78 void normalize_probability(int n, double *a)
82 for (i = 0; i < n; i++)
86 for (i = 0; i < n; i++)
92 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn)
94 /* read nsfactor.dat */
102 gmx_neutron_atomic_structurefactors_t *gnsf;
106 /* allocate memory for structure */
108 snew(gnsf->atomnm, nralloc);
109 snew(gnsf->p, nralloc);
110 snew(gnsf->n, nralloc);
111 snew(gnsf->slength, nralloc);
113 gnsf->nratoms = line_no;
115 while (get_a_line(fp, line, STRLEN))
118 if (sscanf(line, "%s %d %d %lf", atomnm, &p, &n, &slength) == 4)
120 gnsf->atomnm[i] = gmx_strdup(atomnm);
123 gnsf->slength[i] = slength;
125 gnsf->nratoms = line_no;
126 if (line_no == nralloc)
129 srenew(gnsf->atomnm, nralloc);
130 srenew(gnsf->p, nralloc);
131 srenew(gnsf->n, nralloc);
132 srenew(gnsf->slength, nralloc);
137 fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n",
141 srenew(gnsf->atomnm, gnsf->nratoms);
142 srenew(gnsf->p, gnsf->nratoms);
143 srenew(gnsf->n, gnsf->nratoms);
144 srenew(gnsf->slength, gnsf->nratoms);
148 return (gmx_neutron_atomic_structurefactors_t *) gnsf;
151 gmx_sans_t *gmx_sans_init (t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf)
153 gmx_sans_t *gsans = NULL;
155 /* Try to assing scattering length from nsfactor.dat */
157 snew(gsans->slength, top->atoms.nr);
158 /* copy topology data */
160 for (i = 0; i < top->atoms.nr; i++)
162 for (j = 0; j < gnsf->nratoms; j++)
164 if (top->atoms.atom[i].atomnumber == gnsf->p[j])
166 /* we need special case for H and D */
167 if (top->atoms.atom[i].atomnumber == 1)
169 if (top->atoms.atom[i].m == 1.008000)
171 gsans->slength[i] = gnsf->slength[0];
175 gsans->slength[i] = gnsf->slength[1];
180 gsans->slength[i] = gnsf->slength[j];
186 return (gmx_sans_t *) gsans;
189 gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram (
201 gmx_radial_distribution_histogram_t *pr = NULL;
209 gmx_rng_t *trng = NULL;
211 gmx_int64_t mc = 0, max;
212 gmx_rng_t rng = NULL;
214 /* allocate memory for pr */
216 /* set some fields */
217 pr->binwidth = binwidth;
220 * create max dist rvec
221 * dist = box[xx] + box[yy] + box[zz]
223 rvec_add(box[XX], box[YY], dist);
224 rvec_add(box[ZZ], dist, dist);
228 pr->grn = (int)floor(rmax/pr->binwidth)+1;
229 rmax = pr->grn*pr->binwidth;
231 snew(pr->gr, pr->grn);
235 /* Special case for setting automaticaly number of mc iterations to 1% of total number of direct iterations */
238 max = (gmx_int64_t)floor(0.5*0.01*isize*(isize-1));
242 max = (gmx_int64_t)floor(0.5*mcover*isize*(isize-1));
244 rng = gmx_rng_init(seed);
246 nthreads = gmx_omp_get_max_threads();
248 snew(trng, nthreads);
249 for (i = 0; i < nthreads; i++)
251 snew(tgr[i], pr->grn);
252 trng[i] = gmx_rng_init(gmx_rng_uniform_uint32(rng));
254 #pragma omp parallel shared(tgr,trng,mc) private(tid,i,j)
256 tid = gmx_omp_get_thread_num();
257 /* now starting parallel threads */
259 for (mc = 0; mc < max; mc++)
261 i = (int)floor(gmx_rng_uniform_real(trng[tid])*isize);
262 j = (int)floor(gmx_rng_uniform_real(trng[tid])*isize);
265 tgr[tid][(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]];
269 /* collecting data from threads */
270 for (i = 0; i < pr->grn; i++)
272 for (j = 0; j < nthreads; j++)
274 pr->gr[i] += tgr[j][i];
277 /* freeing memory for tgr and destroying trng */
278 for (i = 0; i < nthreads; i++)
281 gmx_rng_destroy(trng[i]);
286 for (mc = 0; mc < max; mc++)
288 i = (int)floor(gmx_rng_uniform_real(rng)*isize);
289 j = (int)floor(gmx_rng_uniform_real(rng)*isize);
292 pr->gr[(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]];
296 gmx_rng_destroy(rng);
301 nthreads = gmx_omp_get_max_threads();
302 /* Allocating memory for tgr arrays */
304 for (i = 0; i < nthreads; i++)
306 snew(tgr[i], pr->grn);
308 #pragma omp parallel shared(tgr) private(tid,i,j)
310 tid = gmx_omp_get_thread_num();
311 /* starting parallel threads */
313 for (i = 0; i < isize; i++)
315 for (j = 0; j < i; j++)
317 tgr[tid][(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]];
321 /* collecating data for pr->gr */
322 for (i = 0; i < pr->grn; i++)
324 for (j = 0; j < nthreads; j++)
326 pr->gr[i] += tgr[j][i];
329 /* freeing memory for tgr */
330 for (i = 0; i < nthreads; i++)
336 for (i = 0; i < isize; i++)
338 for (j = 0; j < i; j++)
340 pr->gr[(int)floor(sqrt(distance2(x[index[i]], x[index[j]]))/binwidth)] += gsans->slength[index[i]]*gsans->slength[index[j]];
346 /* normalize if needed */
349 normalize_probability(pr->grn, pr->gr);
352 snew(pr->r, pr->grn);
353 for (i = 0; i < pr->grn; i++)
355 pr->r[i] = (pr->binwidth*i+pr->binwidth*0.5);
358 return (gmx_radial_distribution_histogram_t *) pr;
361 gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step)
363 gmx_static_structurefactor_t *sq = NULL;
367 sq->qn = (int)floor((end_q-start_q)/q_step);
370 for (i = 0; i < sq->qn; i++)
372 sq->q[i] = start_q+i*q_step;
378 for (i = 1; i < sq->qn; i++)
380 for (j = 0; j < pr->grn; j++)
382 sq->s[i] += (pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]);
384 sq->s[i] /= sq->q[i];
389 for (i = 0; i < sq->qn; i++)
391 for (j = 0; j < pr->grn; j++)
393 sq->s[i] += (pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]);
395 sq->s[i] /= sq->q[i];
399 return (gmx_static_structurefactor_t *) sq;