src/gromacs/gmxana/nsfactor.cpp

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  36 #include "gmxpre.h"
  37
  38 #include "nsfactor.h"
  39
  40 #include "config.h"
  41
  42 #include <cmath>
  43 #include <cstring>
  44
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/random/threefry.h"
  47 #include "gromacs/random/uniformintdistribution.h"
  48 #include "gromacs/topology/topology.h"
  49 #include "gromacs/utility/basedefinitions.h"
  50 #include "gromacs/utility/cstringutil.h"
  51 #include "gromacs/utility/exceptions.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/futil.h"
  54 #include "gromacs/utility/gmxomp.h"
  55 #include "gromacs/utility/smalloc.h"
  56 #include "gromacs/utility/strdb.h"
  57
  58 void check_binwidth(real binwidth)
  59 {
  60     real smallest_bin = 0.1;
  61     if (binwidth < smallest_bin)
  62     {
  63         gmx_fatal(FARGS,
  64                   "Binwidth shouldn't be smaller then smallest bond length (H-H bond ~0.1nm) in a "
  65                   "box");
  66     }
  67 }
  68
  69 void check_mcover(real mcover)
  70 {
  71     if (mcover > 1.0)
  72     {
  73         gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
  74     }
  75     else if ((mcover < 0) && (mcover != -1))
  76     {
  77         gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
  78     }
  79     else
  80     {
  81         return;
  82     }
  83 }
  84
  85 void normalize_probability(int n, double* a)
  86 {
  87     int    i;
  88     double norm = 0.0;
  89     for (i = 0; i < n; i++)
  90     {
  91         norm += a[i];
  92     }
  93     for (i = 0; i < n; i++)
  94     {
  95         a[i] /= norm;
  96     }
  97 }
  98
  99 gmx_neutron_atomic_structurefactors_t* gmx_neutronstructurefactors_init(const char* datfn)
 100 {
 101     /* read nsfactor.dat */
 102     char                                   line[STRLEN];
 103     int                                    nralloc = 10;
 104     int                                    n, p;
 105     int                                    i, line_no;
 106     char                                   atomnm[8];
 107     double                                 slength;
 108     gmx_neutron_atomic_structurefactors_t* gnsf;
 109
 110     gmx::FilePtr fp = gmx::openLibraryFile(datfn);
 111     line_no         = 0;
 112     /* allocate memory for structure */
 113     snew(gnsf, nralloc);
 114     snew(gnsf->atomnm, nralloc);
 115     snew(gnsf->p, nralloc);
 116     snew(gnsf->n, nralloc);
 117     snew(gnsf->slength, nralloc);
 118
 119     gnsf->nratoms = line_no;
 120
 121     while (get_a_line(fp.get(), line, STRLEN))
 122     {
 123         i = line_no;
 124         if (sscanf(line, "%s %d %d %lf", atomnm, &p, &n, &slength) == 4)
 125         {
 126             gnsf->atomnm[i]  = gmx_strdup(atomnm);
 127             gnsf->n[i]       = n;
 128             gnsf->p[i]       = p;
 129             gnsf->slength[i] = slength;
 130             line_no++;
 131             gnsf->nratoms = line_no;
 132             if (line_no == nralloc)
 133             {
 134                 nralloc++;
 135                 srenew(gnsf->atomnm, nralloc);
 136                 srenew(gnsf->p, nralloc);
 137                 srenew(gnsf->n, nralloc);
 138                 srenew(gnsf->slength, nralloc);
 139             }
 140         }
 141         else
 142         {
 143             fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n", datfn, line_no);
 144         }
 145     }
 146     srenew(gnsf->atomnm, gnsf->nratoms);
 147     srenew(gnsf->p, gnsf->nratoms);
 148     srenew(gnsf->n, gnsf->nratoms);
 149     srenew(gnsf->slength, gnsf->nratoms);
 150
 151     return gnsf;
 152 }
 153
 154 gmx_sans_t* gmx_sans_init(const t_topology* top, gmx_neutron_atomic_structurefactors_t* gnsf)
 155 {
 156     gmx_sans_t* gsans = nullptr;
 157     int         i, j;
 158     /* Try to assing scattering length from nsfactor.dat */
 159     snew(gsans, 1);
 160     snew(gsans->slength, top->atoms.nr);
 161     /* copy topology data */
 162     gsans->top = top;
 163     for (i = 0; i < top->atoms.nr; i++)
 164     {
 165         for (j = 0; j < gnsf->nratoms; j++)
 166         {
 167             if (top->atoms.atom[i].atomnumber == gnsf->p[j])
 168             {
 169                 /* we need special case for H and D */
 170                 if (top->atoms.atom[i].atomnumber == 1)
 171                 {
 172                     if (top->atoms.atom[i].m == 1.008000)
 173                     {
 174                         gsans->slength[i] = gnsf->slength[0];
 175                     }
 176                     else
 177                     {
 178                         gsans->slength[i] = gnsf->slength[1];
 179                     }
 180                 }
 181                 else
 182                 {
 183                     gsans->slength[i] = gnsf->slength[j];
 184                 }
 185             }
 186         }
 187     }
 188
 189     return gsans;
 190 }
 191
 192 gmx_radial_distribution_histogram_t* calc_radial_distribution_histogram(gmx_sans_t*  gsans,
 193                                                                         rvec*        x,
 194                                                                         matrix       box,
 195                                                                         const int*   index,
 196                                                                         int          isize,
 197                                                                         double       binwidth,
 198                                                                         gmx_bool     bMC,
 199                                                                         gmx_bool     bNORM,
 200                                                                         real         mcover,
 201                                                                         unsigned int seed)
 202 {
 203     gmx_radial_distribution_histogram_t* pr = nullptr;
 204     rvec                                 dist;
 205     double                               rmax;
 206     int                                  i, j;
 207 #if GMX_OPENMP
 208     double**                  tgr;
 209     int                       tid;
 210     int                       nthreads;
 211     gmx::DefaultRandomEngine* trng = nullptr;
 212 #endif
 213     int64_t                  mc_max;
 214     gmx::DefaultRandomEngine rng(seed);
 215
 216     /* allocate memory for pr */
 217     snew(pr, 1);
 218     /* set some fields */
 219     pr->binwidth = binwidth;
 220
 221     /*
 222      * create max dist rvec
 223      * dist = box[xx] + box[yy] + box[zz]
 224      */
 225     rvec_add(box[XX], box[YY], dist);
 226     rvec_add(box[ZZ], dist, dist);
 227
 228     rmax = norm(dist);
 229
 230     pr->grn = static_cast<int>(std::floor(rmax / pr->binwidth) + 1);
 231
 232     snew(pr->gr, pr->grn);
 233
 234     if (bMC)
 235     {
 236         /* Special case for setting automaticaly number of mc iterations to 1% of total number of direct iterations */
 237         if (mcover == -1)
 238         {
 239             mc_max = static_cast<int64_t>(std::floor(0.5 * 0.01 * isize * (isize - 1)));
 240         }
 241         else
 242         {
 243             mc_max = static_cast<int64_t>(std::floor(0.5 * mcover * isize * (isize - 1)));
 244         }
 245 #if GMX_OPENMP
 246         nthreads = gmx_omp_get_max_threads();
 247         snew(tgr, nthreads);
 248         trng = new gmx::DefaultRandomEngine[nthreads];
 249         for (i = 0; i < nthreads; i++)
 250         {
 251             snew(tgr[i], pr->grn);
 252             trng[i].seed(rng());
 253         }
 254 #    pragma omp parallel shared(tgr, trng) private(tid, i, j)
 255         {
 256             gmx::UniformIntDistribution<int> tdist(0, isize - 1);
 257             tid = gmx_omp_get_thread_num();
 258             /* now starting parallel threads */
 259 #    pragma omp for
 260             for (int64_t mc = 0; mc < mc_max; mc++)
 261             {
 262                 try
 263                 {
 264                     i = tdist(trng[tid]); // [0,isize-1]
 265                     j = tdist(trng[tid]); // [0,isize-1]
 266                     if (i != j)
 267                     {
 268                         tgr[tid][static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 269                                 gsans->slength[index[i]] * gsans->slength[index[j]];
 270                     }
 271                 }
 272                 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 273             }
 274         }
 275         /* collecting data from threads */
 276         for (i = 0; i < pr->grn; i++)
 277         {
 278             for (j = 0; j < nthreads; j++)
 279             {
 280                 pr->gr[i] += tgr[j][i];
 281             }
 282         }
 283         /* freeing memory for tgr and destroying trng */
 284         for (i = 0; i < nthreads; i++)
 285         {
 286             sfree(tgr[i]);
 287         }
 288         sfree(tgr);
 289         delete[] trng;
 290 #else
 291         gmx::UniformIntDistribution<int> dist(0, isize - 1);
 292         for (int64_t mc = 0; mc < mc_max; mc++)
 293         {
 294             i = dist(rng); // [0,isize-1]
 295             j = dist(rng); // [0,isize-1]
 296             if (i != j)
 297             {
 298                 pr->gr[static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 299                         gsans->slength[index[i]] * gsans->slength[index[j]];
 300             }
 301         }
 302 #endif
 303     }
 304     else
 305     {
 306 #if GMX_OPENMP
 307         nthreads = gmx_omp_get_max_threads();
 308         /* Allocating memory for tgr arrays */
 309         snew(tgr, nthreads);
 310         for (i = 0; i < nthreads; i++)
 311         {
 312             snew(tgr[i], pr->grn);
 313         }
 314 #    pragma omp parallel shared(tgr) private(tid, i, j)
 315         {
 316             tid = gmx_omp_get_thread_num();
 317 /* starting parallel threads */
 318 #    pragma omp for
 319             for (i = 0; i < isize; i++)
 320             {
 321                 try
 322                 {
 323                     for (j = 0; j < i; j++)
 324                     {
 325                         tgr[tid][static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 326                                 gsans->slength[index[i]] * gsans->slength[index[j]];
 327                     }
 328                 }
 329                 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 330             }
 331         }
 332         /* collecating data for pr->gr */
 333         for (i = 0; i < pr->grn; i++)
 334         {
 335             for (j = 0; j < nthreads; j++)
 336             {
 337                 pr->gr[i] += tgr[j][i];
 338             }
 339         }
 340         /* freeing memory for tgr */
 341         for (i = 0; i < nthreads; i++)
 342         {
 343             sfree(tgr[i]);
 344         }
 345         sfree(tgr);
 346 #else
 347         for (i = 0; i < isize; i++)
 348         {
 349             for (j = 0; j < i; j++)
 350             {
 351                 pr->gr[static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 352                         gsans->slength[index[i]] * gsans->slength[index[j]];
 353             }
 354         }
 355 #endif
 356     }
 357
 358     /* normalize if needed */
 359     if (bNORM)
 360     {
 361         normalize_probability(pr->grn, pr->gr);
 362     }
 363
 364     snew(pr->r, pr->grn);
 365     for (i = 0; i < pr->grn; i++)
 366     {
 367         pr->r[i] = (pr->binwidth * i + pr->binwidth * 0.5);
 368     }
 369
 370     return pr;
 371 }
 372
 373 gmx_static_structurefactor_t* convert_histogram_to_intensity_curve(gmx_radial_distribution_histogram_t* pr,
 374                                                                    double start_q,
 375                                                                    double end_q,
 376                                                                    double q_step)
 377 {
 378     gmx_static_structurefactor_t* sq = nullptr;
 379     int                           i, j;
 380     /* init data */
 381     snew(sq, 1);
 382     sq->qn = static_cast<int>(std::floor((end_q - start_q) / q_step));
 383     snew(sq->q, sq->qn);
 384     snew(sq->s, sq->qn);
 385     for (i = 0; i < sq->qn; i++)
 386     {
 387         sq->q[i] = start_q + i * q_step;
 388     }
 389
 390     if (start_q == 0.0)
 391     {
 392         sq->s[0] = 1.0;
 393         for (i = 1; i < sq->qn; i++)
 394         {
 395             for (j = 0; j < pr->grn; j++)
 396             {
 397                 sq->s[i] += (pr->gr[j] / pr->r[j]) * std::sin(sq->q[i] * pr->r[j]);
 398             }
 399             sq->s[i] /= sq->q[i];
 400         }
 401     }
 402     else
 403     {
 404         for (i = 0; i < sq->qn; i++)
 405         {
 406             for (j = 0; j < pr->grn; j++)
 407             {
 408                 sq->s[i] += (pr->gr[j] / pr->r[j]) * std::sin(sq->q[i] * pr->r[j]);
 409             }
 410             sq->s[i] /= sq->q[i];
 411         }
 412     }
 413
 414     return sq;
 415 }