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