src/gromacs/gmxana/nsfactor.cpp

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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, "Binwidth shouldn't be smaller then smallest bond length (H-H bond ~0.1nm) in a box");
  62     }
  63 }
  64
  65 void check_mcover(real mcover)
  66 {
  67     if (mcover > 1.0)
  68     {
  69         gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
  70     }
  71     else if ((mcover < 0)&(mcover != -1))
  72     {
  73         gmx_fatal(FARGS, "mcover should be -1 or (0,1]");
  74     }
  75     else
  76     {
  77         return;
  78     }
  79 }
  80
  81 void normalize_probability(int n, double *a)
  82 {
  83     int    i;
  84     double norm = 0.0;
  85     for (i = 0; i < n; i++)
  86     {
  87         norm += a[i];
  88     }
  89     for (i = 0; i < n; i++)
  90     {
  91         a[i] /= norm;
  92     }
  93 }
  94
  95 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn)
  96 {
  97     /* read nsfactor.dat */
  98     FILE    *fp;
  99     char     line[STRLEN];
 100     int      nralloc = 10;
 101     int      n, p;
 102     int      i, line_no;
 103     char     atomnm[8];
 104     double   slength;
 105     gmx_neutron_atomic_structurefactors_t   *gnsf;
 106
 107     fp      = libopen(datfn);
 108     line_no = 0;
 109     /* allocate memory for structure */
 110     snew(gnsf, nralloc);
 111     snew(gnsf->atomnm, nralloc);
 112     snew(gnsf->p, nralloc);
 113     snew(gnsf->n, nralloc);
 114     snew(gnsf->slength, nralloc);
 115
 116     gnsf->nratoms = line_no;
 117
 118     while (get_a_line(fp, line, STRLEN))
 119     {
 120         i = line_no;
 121         if (sscanf(line, "%s %d %d %lf", atomnm, &p, &n, &slength) == 4)
 122         {
 123             gnsf->atomnm[i]  = gmx_strdup(atomnm);
 124             gnsf->n[i]       = n;
 125             gnsf->p[i]       = p;
 126             gnsf->slength[i] = slength;
 127             line_no++;
 128             gnsf->nratoms = line_no;
 129             if (line_no == nralloc)
 130             {
 131                 nralloc++;
 132                 srenew(gnsf->atomnm, nralloc);
 133                 srenew(gnsf->p, nralloc);
 134                 srenew(gnsf->n, nralloc);
 135                 srenew(gnsf->slength, nralloc);
 136             }
 137         }
 138         else
 139         {
 140             fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n",
 141                     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     fclose(fp);
 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 (
 193         gmx_sans_t        *gsans,
 194         rvec              *x,
 195         matrix             box,
 196         const int         *index,
 197         int                isize,
 198         double             binwidth,
 199         gmx_bool           bMC,
 200         gmx_bool           bNORM,
 201         real               mcover,
 202         unsigned int       seed)
 203 {
 204     gmx_radial_distribution_histogram_t    *pr = nullptr;
 205     rvec                                    dist;
 206     double                                  rmax;
 207     int                                     i, j;
 208 #if GMX_OPENMP
 209     double                                **tgr;
 210     int                                     tid;
 211     int                                     nthreads;
 212     gmx::DefaultRandomEngine               *trng = nullptr;
 213 #endif
 214     int64_t                                 mc  = 0, mc_max;
 215     gmx::DefaultRandomEngine                rng(seed);
 216
 217     /* allocate memory for pr */
 218     snew(pr, 1);
 219     /* set some fields */
 220     pr->binwidth = binwidth;
 221
 222     /*
 223      * create max dist rvec
 224      * dist = box[xx] + box[yy] + box[zz]
 225      */
 226     rvec_add(box[XX], box[YY], dist);
 227     rvec_add(box[ZZ], dist, dist);
 228
 229     rmax = norm(dist);
 230
 231     pr->grn = static_cast<int>(std::floor(rmax/pr->binwidth)+1);
 232
 233     snew(pr->gr, pr->grn);
 234
 235     if (bMC)
 236     {
 237         /* Special case for setting automaticaly number of mc iterations to 1% of total number of direct iterations */
 238         if (mcover == -1)
 239         {
 240             mc_max = static_cast<int64_t>(std::floor(0.5*0.01*isize*(isize-1)));
 241         }
 242         else
 243         {
 244             mc_max = static_cast<int64_t>(std::floor(0.5*mcover*isize*(isize-1)));
 245         }
 246 #if GMX_OPENMP
 247         nthreads = gmx_omp_get_max_threads();
 248         snew(tgr, nthreads);
 249         trng = new gmx::DefaultRandomEngine[nthreads];
 250         for (i = 0; i < nthreads; i++)
 251         {
 252             snew(tgr[i], pr->grn);
 253             trng[i].seed(rng());
 254         }
 255         #pragma omp parallel shared(tgr,trng,mc) private(tid,i,j)
 256         {
 257             gmx::UniformIntDistribution<int> tdist(0, isize-1);
 258             tid = gmx_omp_get_thread_num();
 259             /* now starting parallel threads */
 260             #pragma omp for
 261             for (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))] += 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 (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))] += 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))] += 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))] += gsans->slength[index[i]]*gsans->slength[index[j]];
 350             }
 351         }
 352 #endif
 353     }
 354
 355     /* normalize if needed */
 356     if (bNORM)
 357     {
 358         normalize_probability(pr->grn, pr->gr);
 359     }
 360
 361     snew(pr->r, pr->grn);
 362     for (i = 0; i < pr->grn; i++)
 363     {
 364         pr->r[i] = (pr->binwidth*i+pr->binwidth*0.5);
 365     }
 366
 367     return pr;
 368 }
 369
 370 gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step)
 371 {
 372     gmx_static_structurefactor_t    *sq = nullptr;
 373     int         i, j;
 374     /* init data */
 375     snew(sq, 1);
 376     sq->qn = static_cast<int>(std::floor((end_q-start_q)/q_step));
 377     snew(sq->q, sq->qn);
 378     snew(sq->s, sq->qn);
 379     for (i = 0; i < sq->qn; i++)
 380     {
 381         sq->q[i] = start_q+i*q_step;
 382     }
 383
 384     if (start_q == 0.0)
 385     {
 386         sq->s[0] = 1.0;
 387         for (i = 1; i < sq->qn; i++)
 388         {
 389             for (j = 0; j < pr->grn; j++)
 390             {
 391                 sq->s[i] += (pr->gr[j]/pr->r[j])*std::sin(sq->q[i]*pr->r[j]);
 392             }
 393             sq->s[i] /= sq->q[i];
 394         }
 395     }
 396     else
 397     {
 398         for (i = 0; i < sq->qn; i++)
 399         {
 400             for (j = 0; j < pr->grn; j++)
 401             {
 402                 sq->s[i] += (pr->gr[j]/pr->r[j])*std::sin(sq->q[i]*pr->r[j]);
 403             }
 404             sq->s[i] /= sq->q[i];
 405         }
 406     }
 407
 408     return sq;
 409 }