src/gromacs/gmxana/nsfactor.cpp

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   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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             INTEL_DIAGNOSTIC_IGNORE(593)
 260 #    pragma omp for
 261             for (int64_t mc = 0; mc < mc_max; mc++)
 262             {
 263                 try
 264                 {
 265                     i = tdist(trng[tid]); // [0,isize-1]
 266                     j = tdist(trng[tid]); // [0,isize-1]
 267                     if (i != j)
 268                     {
 269                         tgr[tid][static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 270                                 gsans->slength[index[i]] * gsans->slength[index[j]];
 271                     }
 272                 }
 273                 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 274             }
 275         }
 276         INTEL_DIAGNOSTIC_RESET
 277         /* collecting data from threads */
 278         for (i = 0; i < pr->grn; i++)
 279         {
 280             for (j = 0; j < nthreads; j++)
 281             {
 282                 pr->gr[i] += tgr[j][i];
 283             }
 284         }
 285         /* freeing memory for tgr and destroying trng */
 286         for (i = 0; i < nthreads; i++)
 287         {
 288             sfree(tgr[i]);
 289         }
 290         sfree(tgr);
 291         delete[] trng;
 292 #else
 293         gmx::UniformIntDistribution<int> dist(0, isize - 1);
 294         for (int64_t mc = 0; mc < mc_max; mc++)
 295         {
 296             i = dist(rng); // [0,isize-1]
 297             j = dist(rng); // [0,isize-1]
 298             if (i != j)
 299             {
 300                 pr->gr[static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 301                         gsans->slength[index[i]] * gsans->slength[index[j]];
 302             }
 303         }
 304 #endif
 305     }
 306     else
 307     {
 308 #if GMX_OPENMP
 309         nthreads = gmx_omp_get_max_threads();
 310         /* Allocating memory for tgr arrays */
 311         snew(tgr, nthreads);
 312         for (i = 0; i < nthreads; i++)
 313         {
 314             snew(tgr[i], pr->grn);
 315         }
 316 #    pragma omp parallel shared(tgr) private(tid, i, j)
 317         {
 318             tid = gmx_omp_get_thread_num();
 319 /* starting parallel threads */
 320 #    pragma omp for
 321             for (i = 0; i < isize; i++)
 322             {
 323                 try
 324                 {
 325                     for (j = 0; j < i; j++)
 326                     {
 327                         tgr[tid][static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 328                                 gsans->slength[index[i]] * gsans->slength[index[j]];
 329                     }
 330                 }
 331                 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 332             }
 333         }
 334         /* collecating data for pr->gr */
 335         for (i = 0; i < pr->grn; i++)
 336         {
 337             for (j = 0; j < nthreads; j++)
 338             {
 339                 pr->gr[i] += tgr[j][i];
 340             }
 341         }
 342         /* freeing memory for tgr */
 343         for (i = 0; i < nthreads; i++)
 344         {
 345             sfree(tgr[i]);
 346         }
 347         sfree(tgr);
 348 #else
 349         for (i = 0; i < isize; i++)
 350         {
 351             for (j = 0; j < i; j++)
 352             {
 353                 pr->gr[static_cast<int>(std::floor(std::sqrt(distance2(x[index[i]], x[index[j]])) / binwidth))] +=
 354                         gsans->slength[index[i]] * gsans->slength[index[j]];
 355             }
 356         }
 357 #endif
 358     }
 359
 360     /* normalize if needed */
 361     if (bNORM)
 362     {
 363         normalize_probability(pr->grn, pr->gr);
 364     }
 365
 366     snew(pr->r, pr->grn);
 367     for (i = 0; i < pr->grn; i++)
 368     {
 369         pr->r[i] = (pr->binwidth * i + pr->binwidth * 0.5);
 370     }
 371
 372     return pr;
 373 }
 374
 375 gmx_static_structurefactor_t* convert_histogram_to_intensity_curve(gmx_radial_distribution_histogram_t* pr,
 376                                                                    double start_q,
 377                                                                    double end_q,
 378                                                                    double q_step)
 379 {
 380     gmx_static_structurefactor_t* sq = nullptr;
 381     int                           i, j;
 382     /* init data */
 383     snew(sq, 1);
 384     sq->qn = static_cast<int>(std::floor((end_q - start_q) / q_step));
 385     snew(sq->q, sq->qn);
 386     snew(sq->s, sq->qn);
 387     for (i = 0; i < sq->qn; i++)
 388     {
 389         sq->q[i] = start_q + i * q_step;
 390     }
 391
 392     if (start_q == 0.0)
 393     {
 394         sq->s[0] = 1.0;
 395         for (i = 1; i < sq->qn; i++)
 396         {
 397             for (j = 0; j < pr->grn; j++)
 398             {
 399                 sq->s[i] += (pr->gr[j] / pr->r[j]) * std::sin(sq->q[i] * pr->r[j]);
 400             }
 401             sq->s[i] /= sq->q[i];
 402         }
 403     }
 404     else
 405     {
 406         for (i = 0; i < sq->qn; i++)
 407         {
 408             for (j = 0; j < pr->grn; j++)
 409             {
 410                 sq->s[i] += (pr->gr[j] / pr->r[j]) * std::sin(sq->q[i] * pr->r[j]);
 411             }
 412             sq->s[i] /= sq->q[i];
 413         }
 414     }
 415
 416     return sq;
 417 }