src/tools/nsfactor.c

   1 /*
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <ctype.h>
  40 #include <string.h>
  41 #include "futil.h"
  42 #include "gmx_random.h"
  43 #include "smalloc.h"
  44 #include "sysstuff.h"
  45 #include "strdb.h"
  46 #include "vec.h"
  47 #include "nsfactor.h"
  48
  49 #ifdef GMX_OPENMP
  50 #include <omp.h>
  51 #endif
  52
  53 void check_binwidth(real binwidth) {
  54     real smallest_bin=0.1;
  55     if (binwidth<smallest_bin)
  56         gmx_fatal(FARGS,"Binwidth shouldnt be smaller then smallest bond length (H-H bond ~0.1nm) in a box");
  57 }
  58
  59 void check_mcover(real mcover) {
  60     if (mcover>1.0) {
  61         gmx_fatal(FARGS,"mcover should be -1 or (0,1]");
  62     } else if ((mcover<0)&(mcover != -1)) {
  63         gmx_fatal(FARGS,"mcover should be -1 or (0,1]");
  64     } else {
  65         return;
  66     }
  67 }
  68
  69 void normalize_probability(int n,double *a){
  70     int i;
  71     double norm=0.0;
  72     for (i=0;i<n;i++) norm +=a[i];
  73     for (i=0;i<n;i++) a[i]/=norm;
  74 }
  75
  76 gmx_nentron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn) {
  77     /* read nsfactor.dat */
  78     FILE    *fp;
  79     char    line[STRLEN];
  80     int     nralloc=10;
  81     int     n,p;
  82     int     i, line_no;
  83     char    atomnm[8];
  84     double  slength;
  85     gmx_nentron_atomic_structurefactors_t   *gnsf;
  86
  87     fp=libopen(datfn);
  88     line_no = 0;
  89     /* allocate memory for structure */
  90     snew(gnsf,nralloc);
  91     snew(gnsf->atomnm,nralloc);
  92     snew(gnsf->p,nralloc);
  93     snew(gnsf->n,nralloc);
  94     snew(gnsf->slength,nralloc);
  95
  96     gnsf->nratoms=line_no;
  97
  98     while(get_a_line(fp,line,STRLEN)) {
  99         i=line_no;
 100         if (sscanf(line,"%s %d %d %lf",atomnm,&p,&n,&slength) == 4) {
 101             gnsf->atomnm[i]=strdup(atomnm);
 102             gnsf->n[i]=n;
 103             gnsf->p[i]=p;
 104             gnsf->slength[i]=slength;
 105             line_no++;
 106             gnsf->nratoms=line_no;
 107             if (line_no==nralloc){
 108                 nralloc++;
 109                 srenew(gnsf->atomnm,nralloc);
 110                 srenew(gnsf->p,nralloc);
 111                 srenew(gnsf->n,nralloc);
 112                 srenew(gnsf->slength,nralloc);
 113             }
 114         } else
 115             fprintf(stderr,"WARNING: Error in file %s at line %d ignored\n",
 116                     datfn,line_no);
 117     }
 118     srenew(gnsf->atomnm,gnsf->nratoms);
 119     srenew(gnsf->p,gnsf->nratoms);
 120     srenew(gnsf->n,gnsf->nratoms);
 121     srenew(gnsf->slength,gnsf->nratoms);
 122
 123     fclose(fp);
 124
 125     return (gmx_nentron_atomic_structurefactors_t *) gnsf;
 126 }
 127
 128 gmx_sans_t *gmx_sans_init (t_topology *top, gmx_nentron_atomic_structurefactors_t *gnsf) {
 129     gmx_sans_t    *gsans=NULL;
 130     int     i,j;
 131     /* Try to assing scattering length from nsfactor.dat */
 132     snew(gsans,1);
 133     snew(gsans->slength,top->atoms.nr);
 134     /* copy topology data */
 135     gsans->top = top;
 136     for(i=0;i<top->atoms.nr;i++) {
 137         for(j=0;j<gnsf->nratoms;j++) {
 138             if(top->atoms.atom[i].atomnumber == gnsf->p[j]) {
 139                 /* we need special case for H and D */
 140                 if(top->atoms.atom[i].atomnumber == 1) {
 141                     if(top->atoms.atom[i].m == 1.008000) {
 142                         gsans->slength[i] = gnsf->slength[0];
 143                     } else
 144                         gsans->slength[i] = gnsf->slength[1];
 145                 } else
 146                     gsans->slength[i] = gnsf->slength[j];
 147             }
 148         }
 149     }
 150
 151     return (gmx_sans_t *) gsans;
 152 }
 153
 154 gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram (
 155                             gmx_sans_t *gsans,
 156                             rvec *x,
 157                             matrix box,
 158                             atom_id *index,
 159                             int isize,
 160                             double binwidth,
 161                             gmx_bool bMC,
 162                             real mcover,
 163                             unsigned int seed) {
 164     gmx_radial_distribution_histogram_t    *pr=NULL;
 165     rvec            dist;
 166     double          rmax;
 167     int             i,j;
 168 #ifdef GMX_OPENMP
 169     double          **tgr;
 170     int             tid;
 171     int             nthreads;
 172     gmx_rng_t       *trng=NULL;
 173 #endif
 174     gmx_large_int_t mc=0,max;
 175     gmx_rng_t       rng=NULL;
 176
 177     /* allocate memory for pr */
 178     snew(pr,1);
 179     /* set some fields */
 180     pr->binwidth=binwidth;
 181
 182     /*
 183     * create max dist rvec
 184     * dist = box[xx] + box[yy] + box[zz]
 185     */
 186     rvec_add(box[XX],box[YY],dist);
 187     rvec_add(box[ZZ],dist,dist);
 188
 189     rmax=norm(dist);
 190
 191     pr->grn=(int)floor(rmax/pr->binwidth)+1;
 192     rmax=pr->grn*pr->binwidth;
 193
 194     snew(pr->gr,pr->grn);
 195
 196     if(bMC) {
 197         /* Special case for setting automaticaly number of mc iterations to 1% of total number of direct iterations */
 198         if (mcover==-1) {
 199             max=(gmx_large_int_t)floor(0.5*0.01*isize*(isize-1));
 200         } else {
 201             max=(gmx_large_int_t)floor(0.5*mcover*isize*(isize-1));
 202         }
 203         rng=gmx_rng_init(seed);
 204 #ifdef GMX_OPENMP
 205         nthreads = omp_get_max_threads();
 206         snew(tgr,nthreads);
 207         snew(trng,nthreads);
 208         for(i=0;i<nthreads;i++){
 209             snew(tgr[i],pr->grn);
 210             trng[i]=gmx_rng_init(gmx_rng_uniform_uint32(rng));
 211         }
 212         #pragma omp parallel shared(tgr,trng,mc) private(tid,i,j)
 213         {
 214             tid = omp_get_thread_num();
 215             /* now starting parallel threads */
 216             #pragma omp for
 217             for(mc=0;mc<max;mc++) {
 218                 i=(int)floor(gmx_rng_uniform_real(trng[tid])*isize);
 219                 j=(int)floor(gmx_rng_uniform_real(trng[tid])*isize);
 220                 if(i!=j) {
 221                     tgr[tid][(int)floor(sqrt(distance2(x[index[i]],x[index[j]]))/binwidth)]+=gsans->slength[index[i]]*gsans->slength[index[j]];
 222                 }
 223             }
 224         }
 225         /* collecting data from threads */
 226         for(i=0;i<pr->grn;i++) {
 227             for(j=0;j<nthreads;j++) {
 228                 pr->gr[i] += tgr[j][i];
 229             }
 230         }
 231         /* freeing memory for tgr and destroying trng */
 232         for(i=0;i<nthreads;i++) {
 233             sfree(tgr[i]);
 234             gmx_rng_destroy(trng[i]);
 235         }
 236         sfree(tgr);
 237         sfree(trng);
 238 #else
 239         for(mc=0;mc<max;mc++) {
 240             i=(int)floor(gmx_rng_uniform_real(rng)*isize);
 241             j=(int)floor(gmx_rng_uniform_real(rng)*isize);
 242             if(i!=j)
 243                 pr->gr[(int)floor(sqrt(distance2(x[index[i]],x[index[j]]))/binwidth)]+=gsans->slength[index[i]]*gsans->slength[index[j]];
 244         }
 245 #endif
 246         gmx_rng_destroy(rng);
 247     } else {
 248 #ifdef GMX_OPENMP
 249         nthreads = omp_get_max_threads();
 250         /* Allocating memory for tgr arrays */
 251         snew(tgr,nthreads);
 252         for(i=0;i<nthreads;i++) {
 253             snew(tgr[i],pr->grn);
 254         }
 255         #pragma omp parallel shared(tgr) private(tid,i,j)
 256         {
 257             tid = omp_get_thread_num();
 258             /* starting parallel threads */
 259             #pragma omp for
 260             for(i=0;i<isize;i++) {
 261                 for(j=0;j<i;j++) {
 262                     tgr[tid][(int)floor(sqrt(distance2(x[index[i]],x[index[j]]))/binwidth)]+=gsans->slength[index[i]]*gsans->slength[index[j]];
 263                 }
 264             }
 265         }
 266         /* collecating data for pr->gr */
 267         for(i=0;i<pr->grn;i++) {
 268             for(j=0;j<nthreads;j++) {
 269                 pr->gr[i] += tgr[j][i];
 270             }
 271         }
 272         /* freeing memory for tgr */
 273         for(i=0;i<nthreads;i++) {
 274             sfree(tgr[i]);
 275         }
 276         sfree(tgr);
 277 #else
 278         for(i=0;i<isize;i++) {
 279             for(j=0;j<i;j++) {
 280                 pr->gr[(int)floor(sqrt(distance2(x[index[i]],x[index[j]]))/binwidth)]+=gsans->slength[index[i]]*gsans->slength[index[j]];
 281             }
 282         }
 283 #endif
 284     }
 285
 286     /* normalize */
 287     normalize_probability(pr->grn,pr->gr);
 288     snew(pr->r,pr->grn);
 289     for(i=0;i<pr->grn;i++)
 290         pr->r[i]=(pr->binwidth*i+pr->binwidth*0.5);
 291
 292     return (gmx_radial_distribution_histogram_t *) pr;
 293 }
 294
 295 gmx_static_structurefator_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step) {
 296     gmx_static_structurefator_t    *sq=NULL;
 297     int         i,j;
 298     /* init data */
 299     snew(sq,1);
 300     sq->qn=(int)floor((end_q-start_q)/q_step);
 301     snew(sq->q,sq->qn);
 302     snew(sq->s,sq->qn);
 303     for(i=0;i<sq->qn;i++)
 304         sq->q[i]=start_q+i*q_step;
 305
 306     if(start_q==0.0) {
 307         sq->s[0]=1.0;
 308         for(i=1;i<sq->qn;i++) {
 309             for(j=0;j<pr->grn;j++)
 310                 sq->s[i]+=(pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]);
 311             sq->s[i] /= sq->q[i];
 312         }
 313     } else {
 314         for(i=0;i<sq->qn;i++) {
 315             for(j=0;j<pr->grn;j++)
 316                 sq->s[i]+=(pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]);
 317             sq->s[i] /= sq->q[i];
 318         }
 319     }
 320
 321     return (gmx_static_structurefator_t *) sq;
 322 }