src/gromacs/gmxana/nsfactor.cpp

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