src/tools/gmx_vanhove.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <string.h>
  40 #include <ctype.h>
  41 #include <math.h>
  42
  43 #include "sysstuff.h"
  44 #include "smalloc.h"
  45 #include "macros.h"
  46 #include "statutil.h"
  47 #include "maths.h"
  48 #include "futil.h"
  49 #include "index.h"
  50 #include "copyrite.h"
  51 #include "typedefs.h"
  52 #include "xvgr.h"
  53 #include "gstat.h"
  54 #include "tpxio.h"
  55 #include "vec.h"
  56 #include "matio.h"
  57 #include "gmx_ana.h"
  58
  59
  60 int gmx_vanhove(int argc,char *argv[])
  61 {
  62   const char *desc[] = {
  63     "g_vanhove computes the Van Hove correlation function.",
  64     "The Van Hove G(r,t) is the probability that a particle that is at r0",
  65     "at time zero can be found at position r0+r at time t.",
  66     "g_vanhove determines G not for a vector r, but for the length of r.",
  67     "Thus it gives the probability that a particle moves a distance of r",
  68     "in time t.",
  69     "Jumps across the periodic boundaries are removed.",
  70     "Corrections are made for scaling due to isotropic",
  71     "or anisotropic pressure coupling.",
  72     "[PAR]",
  73     "With option [TT]-om[tt] the whole matrix can be written as a function",
  74     "of t and r or as a function of sqrt(t) and r (option [TT]-sqrt[tt]).",
  75     "[PAR]",
  76     "With option [TT]-or[tt] the Van Hove function is plotted for one",
  77     "or more values of t. Option [TT]-nr[tt] sets the number of times,",
  78     "option [TT]-fr[tt] the number spacing between the times.",
  79     "The binwidth is set with option [TT]-rbin[tt]. The number of bins",
  80     "is determined automatically.",
  81     "[PAR]",
  82     "With option [TT]-ot[tt] the integral up to a certain distance",
  83     "(option [TT]-rt[tt]) is plotted as a function of time.",
  84     "[PAR]",
  85     "For all frames that are read the coordinates of the selected particles",
  86     "are stored in memory. Therefore the program may use a lot of memory.",
  87     "For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
  88     "This is because the calculation scales as the number of frames times",
  89     "[TT]-fm[tt] or [TT]-ft[tt].",
  90     "Note that with the [TT]-dt[tt] option the memory usage and calculation",
  91     "time can be reduced."
  92   };
  93   static int fmmax=0,ftmax=0,nlev=81,nr=1,fshift=0;
  94   static real sbin=0,rmax=2,rbin=0.01,mmax=0,rint=0;
  95   t_pargs pa[] = {
  96     { "-sqrt",    FALSE, etREAL,{&sbin},
  97       "Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)" },
  98     { "-fm",      FALSE, etINT, {&fmmax},
  99       "Number of frames in the matrix, 0 is plot all" },
 100     { "-rmax",    FALSE, etREAL, {&rmax},
 101       "Maximum r in the matrix (nm)" },
 102     { "-rbin",    FALSE, etREAL, {&rbin},
 103       "Binwidth in the matrix and for -or (nm)" },
 104     { "-mmax",    FALSE, etREAL, {&mmax},
 105       "Maximum density in the matrix, 0 is calculate (1/nm)" },
 106     { "-nlevels" ,FALSE, etINT,  {&nlev},
 107       "Number of levels in the matrix" },
 108     { "-nr",      FALSE, etINT, {&nr},
 109       "Number of curves for the -or output" },
 110     { "-fr",      FALSE, etINT, {&fshift},
 111       "Frame spacing for the -or output" },
 112     { "-rt",      FALSE, etREAL, {&rint},
 113       "Integration limit for the -ot output (nm)" },
 114     { "-ft",      FALSE, etINT, {&ftmax},
 115       "Number of frames in the -ot output, 0 is plot all" }
 116   };
 117 #define NPA asize(pa)
 118
 119   t_filenm fnm[] = {
 120     { efTRX, NULL, NULL,  ffREAD },
 121     { efTPS, NULL, NULL,  ffREAD },
 122     { efNDX, NULL, NULL,  ffOPTRD },
 123     { efXPM, "-om", "vanhove", ffOPTWR },
 124     { efXVG, "-or", "vanhove_r", ffOPTWR },
 125     { efXVG, "-ot", "vanhove_t", ffOPTWR }
 126   };
 127 #define NFILE asize(fnm)
 128
 129   output_env_t oenv;
 130   const char *matfile,*otfile,*orfile;
 131   char     title[256];
 132   t_topology top;
 133   int      ePBC;
 134   matrix   boxtop,box,*sbox,avbox,corr;
 135   rvec     *xtop,*x,**sx;
 136   int      status,isize,nalloc,nallocn,natom;
 137   atom_id  *index;
 138   char     *grpname;
 139   int      nfr,f,ff,i,m,mat_nx=0,nbin=0,bin,mbin,fbin;
 140   real     *time,t,invbin=0,rmax2=0,rint2=0,d2;
 141   real     invsbin=0,matmax,normfac,dt,*tickx,*ticky;
 142   char     buf[STRLEN],**legend;
 143   real     **mat=NULL;
 144   int      *pt=NULL,**pr=NULL,*mcount=NULL,*tcount=NULL,*rcount=NULL;
 145   FILE     *fp;
 146   t_rgb    rlo={1,1,1}, rhi={0,0,0};
 147
 148   CopyRight(stderr,argv[0]);
 149
 150   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 151                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 152
 153   matfile = opt2fn_null("-om",NFILE,fnm);
 154   if (opt2parg_bSet("-fr",NPA,pa))
 155     orfile  = opt2fn("-or",NFILE,fnm);
 156   else
 157     orfile  = opt2fn_null("-or",NFILE,fnm);
 158   if (opt2parg_bSet("-rt",NPA,pa))
 159     otfile  = opt2fn("-ot",NFILE,fnm);
 160   else
 161     otfile  = opt2fn_null("-ot",NFILE,fnm);
 162
 163   if (!matfile && !otfile && !orfile) {
 164     fprintf(stderr,
 165             "For output set one (or more) of the output file options\n");
 166     exit(0);
 167   }
 168
 169   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,boxtop,
 170                 FALSE);
 171   get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 172
 173   nalloc = 0;
 174   time = NULL;
 175   sbox = NULL;
 176   sx   = NULL;
 177   clear_mat(avbox);
 178
 179   natom=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 180   nfr = 0;
 181   do {
 182     if (nfr >= nalloc) {
 183       nalloc += 100;
 184       srenew(time,nalloc);
 185       srenew(sbox,nalloc);
 186       srenew(sx,nalloc);
 187     }
 188
 189     time[nfr] = t;
 190     copy_mat(box,sbox[nfr]);
 191     /* This assumes that the off-diagonal box elements
 192      * are not affected by jumps across the periodic boundaries.
 193      */
 194     m_add(avbox,box,avbox);
 195     snew(sx[nfr],isize);
 196     for(i=0; i<isize; i++)
 197      copy_rvec(x[index[i]],sx[nfr][i]);
 198
 199     nfr++;
 200   } while (read_next_x(oenv,status,&t,natom,x,box));
 201
 202   /* clean up */
 203   sfree(x);
 204   close_trj(status);
 205
 206   fprintf(stderr,"Read %d frames\n",nfr);
 207
 208   dt = (time[nfr-1] - time[0])/(nfr - 1);
 209   /* Some ugly rounding to get nice nice times in the output */
 210   dt = (int)(10000.0*dt + 0.5)/10000.0;
 211
 212   invbin = 1.0/rbin;
 213
 214   if (matfile) {
 215     if (fmmax <= 0 || fmmax >= nfr)
 216       fmmax = nfr - 1;
 217     snew(mcount,fmmax);
 218     nbin = (int)(rmax*invbin + 0.5);
 219     if (sbin == 0) {
 220       mat_nx = fmmax + 1;
 221     } else {
 222       invsbin = 1.0/sbin;
 223       mat_nx = sqrt(fmmax*dt)*invsbin + 1;
 224     }
 225     snew(mat,mat_nx);
 226     for(f=0; f<mat_nx; f++)
 227       snew(mat[f],nbin);
 228     rmax2 = sqr(nbin*rbin);
 229     /* Initialize time zero */
 230     mat[0][0] = nfr*isize;
 231     mcount[0] += nfr;
 232   } else {
 233     fmmax = 0;
 234   }
 235
 236   if (orfile) {
 237     snew(pr,nr);
 238     nalloc = 0;
 239     snew(rcount,nr);
 240   }
 241
 242   if (otfile) {
 243     if (ftmax <= 0)
 244       ftmax = nfr - 1;
 245     snew(tcount,ftmax);
 246     snew(pt,nfr);
 247     rint2 = rint*rint;
 248     /* Initialize time zero */
 249     pt[0] = nfr*isize;
 250     tcount[0] += nfr;
 251   } else {
 252     ftmax = 0;
 253   }
 254
 255   msmul(avbox,1.0/nfr,avbox);
 256   for(f=0; f<nfr; f++) {
 257     if (f % 100 == 0)
 258       fprintf(stderr,"\rProcessing frame %d",f);
 259     /* Scale all the configuration to the average box */
 260     m_inv_ur0(sbox[f],corr);
 261     mmul_ur0(avbox,corr,corr);
 262     for(i=0; i<isize; i++) {
 263       mvmul_ur0(corr,sx[f][i],sx[f][i]);
 264       if (f > 0) {
 265         /* Correct for periodic jumps */
 266         for(m=DIM-1; m>=0; m--) {
 267           while(sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
 268             rvec_dec(sx[f][i],avbox[m]);
 269           while(sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
 270             rvec_inc(sx[f][i],avbox[m]);
 271         }
 272       }
 273     }
 274     for(ff=0; ff<f; ff++) {
 275       fbin = f - ff;
 276       if (fbin <= fmmax || fbin <= ftmax) {
 277         if (sbin == 0)
 278           mbin = fbin;
 279         else
 280           mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
 281         for(i=0; i<isize; i++) {
 282           d2 = distance2(sx[f][i],sx[ff][i]);
 283           if (mbin < mat_nx && d2 < rmax2) {
 284             bin = (int)(sqrt(d2)*invbin + 0.5);
 285             if (bin < nbin) {
 286               mat[mbin][bin] += 1;
 287             }
 288           }
 289           if (fbin <= ftmax && d2 <= rint2)
 290             pt[fbin]++;
 291         }
 292         if (matfile)
 293           mcount[mbin]++;
 294         if (otfile)
 295           tcount[fbin]++;
 296       }
 297     }
 298     if (orfile) {
 299       for(fbin=0; fbin<nr; fbin++) {
 300         ff = f - (fbin + 1)*fshift;
 301         if (ff >= 0) {
 302           for(i=0; i<isize; i++) {
 303             d2 = distance2(sx[f][i],sx[ff][i]);
 304             bin = (int)(sqrt(d2)*invbin);
 305             if (bin >= nalloc) {
 306               nallocn = 10*(bin/10) + 11;
 307               for(m=0; m<nr; m++) {
 308                 srenew(pr[m],nallocn);
 309                 for(i=nalloc; i<nallocn; i++)
 310                   pr[m][i] = 0;
 311               }
 312               nalloc = nallocn;
 313             }
 314             pr[fbin][bin]++;
 315           }
 316           rcount[fbin]++;
 317         }
 318       }
 319     }
 320   }
 321   fprintf(stderr,"\n");
 322
 323   if (matfile) {
 324     matmax = 0;
 325     for(f=0; f<mat_nx; f++) {
 326       normfac = 1.0/(mcount[f]*isize*rbin);
 327       for(i=0; i<nbin; i++) {
 328         mat[f][i] *= normfac;
 329         if (mat[f][i] > matmax && (f!=0 || i!=0))
 330           matmax = mat[f][i];
 331       }
 332     }
 333     fprintf(stdout,"Value at (0,0): %.3f, maximum of the rest %.3f\n",
 334             mat[0][0],matmax);
 335     if (mmax > 0)
 336       matmax = mmax;
 337     snew(tickx,mat_nx);
 338     for(f=0; f<mat_nx; f++) {
 339       if (sbin == 0)
 340         tickx[f] = f*dt;
 341       else
 342         tickx[f] = f*sbin;
 343     }
 344     snew(ticky,nbin+1);
 345     for(i=0; i<=nbin; i++)
 346       ticky[i] = i*rbin;
 347     fp = ffopen(matfile,"w");
 348     write_xpm(fp,MAT_SPATIAL_Y,"Van Hove function","G (1/nm)",
 349               sbin==0 ? "time (ps)" : "sqrt(time) (ps^1/2)","r (nm)",
 350               mat_nx,nbin,tickx,ticky,mat,0,matmax,rlo,rhi,&nlev);
 351     ffclose(fp);
 352   }
 353
 354   if (orfile) {
 355     fp = xvgropen(orfile,"Van Hove function","r (nm)","G (nm\\S-1\\N)",oenv);
 356     fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
 357     snew(legend,nr);
 358     for(fbin=0; fbin<nr; fbin++) {
 359       sprintf(buf,"%g ps",(fbin + 1)*fshift*dt);
 360       legend[fbin] = strdup(buf);
 361     }
 362     xvgr_legend(fp,nr,legend,oenv);
 363     for(i=0; i<nalloc; i++) {
 364       fprintf(fp,"%g",i*rbin);
 365       for(fbin=0; fbin<nr; fbin++)
 366         fprintf(fp," %g",
 367                 (real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i==0 ? 0.5 : 1)));
 368       fprintf(fp,"\n");
 369     }
 370     ffclose(fp);
 371   }
 372
 373   if (otfile) {
 374     sprintf(buf,"Probability of moving less than %g nm",rint);
 375     fp = xvgropen(otfile,buf,"t (ps)","",oenv);
 376     fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
 377     for(f=0; f<=ftmax; f++)
 378       fprintf(fp,"%g %g\n",f*dt,(real)pt[f]/(tcount[f]*isize));
 379     ffclose(fp);
 380   }
 381
 382   do_view(oenv, matfile,NULL);
 383   do_view(oenv, orfile,NULL);
 384   do_view(oenv, otfile,NULL);
 385
 386   thanx(stderr);
 387
 388   return 0;
 389 }