src/tools/gmx_vanhove.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Green Red Orange Magenta Azure Cyan Skyblue
  34  */
  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      isize,nalloc,nallocn,natom;
 137   t_trxstatus *status;
 138   atom_id  *index;
 139   char     *grpname;
 140   int      nfr,f,ff,i,m,mat_nx=0,nbin=0,bin,mbin,fbin;
 141   real     *time,t,invbin=0,rmax2=0,rint2=0,d2;
 142   real     invsbin=0,matmax,normfac,dt,*tickx,*ticky;
 143   char     buf[STRLEN],**legend;
 144   real     **mat=NULL;
 145   int      *pt=NULL,**pr=NULL,*mcount=NULL,*tcount=NULL,*rcount=NULL;
 146   FILE     *fp;
 147   t_rgb    rlo={1,1,1}, rhi={0,0,0};
 148
 149   CopyRight(stderr,argv[0]);
 150
 151   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 152                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 153
 154   matfile = opt2fn_null("-om",NFILE,fnm);
 155   if (opt2parg_bSet("-fr",NPA,pa))
 156     orfile  = opt2fn("-or",NFILE,fnm);
 157   else
 158     orfile  = opt2fn_null("-or",NFILE,fnm);
 159   if (opt2parg_bSet("-rt",NPA,pa))
 160     otfile  = opt2fn("-ot",NFILE,fnm);
 161   else
 162     otfile  = opt2fn_null("-ot",NFILE,fnm);
 163
 164   if (!matfile && !otfile && !orfile) {
 165     fprintf(stderr,
 166             "For output set one (or more) of the output file options\n");
 167     exit(0);
 168   }
 169
 170   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,boxtop,
 171                 FALSE);
 172   get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 173
 174   nalloc = 0;
 175   time = NULL;
 176   sbox = NULL;
 177   sx   = NULL;
 178   clear_mat(avbox);
 179
 180   natom=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 181   nfr = 0;
 182   do {
 183     if (nfr >= nalloc) {
 184       nalloc += 100;
 185       srenew(time,nalloc);
 186       srenew(sbox,nalloc);
 187       srenew(sx,nalloc);
 188     }
 189
 190     time[nfr] = t;
 191     copy_mat(box,sbox[nfr]);
 192     /* This assumes that the off-diagonal box elements
 193      * are not affected by jumps across the periodic boundaries.
 194      */
 195     m_add(avbox,box,avbox);
 196     snew(sx[nfr],isize);
 197     for(i=0; i<isize; i++)
 198      copy_rvec(x[index[i]],sx[nfr][i]);
 199
 200     nfr++;
 201   } while (read_next_x(oenv,status,&t,natom,x,box));
 202
 203   /* clean up */
 204   sfree(x);
 205   close_trj(status);
 206
 207   fprintf(stderr,"Read %d frames\n",nfr);
 208
 209   dt = (time[nfr-1] - time[0])/(nfr - 1);
 210   /* Some ugly rounding to get nice nice times in the output */
 211   dt = (int)(10000.0*dt + 0.5)/10000.0;
 212
 213   invbin = 1.0/rbin;
 214
 215   if (matfile) {
 216     if (fmmax <= 0 || fmmax >= nfr)
 217       fmmax = nfr - 1;
 218     snew(mcount,fmmax);
 219     nbin = (int)(rmax*invbin + 0.5);
 220     if (sbin == 0) {
 221       mat_nx = fmmax + 1;
 222     } else {
 223       invsbin = 1.0/sbin;
 224       mat_nx = sqrt(fmmax*dt)*invsbin + 1;
 225     }
 226     snew(mat,mat_nx);
 227     for(f=0; f<mat_nx; f++)
 228       snew(mat[f],nbin);
 229     rmax2 = sqr(nbin*rbin);
 230     /* Initialize time zero */
 231     mat[0][0] = nfr*isize;
 232     mcount[0] += nfr;
 233   } else {
 234     fmmax = 0;
 235   }
 236
 237   if (orfile) {
 238     snew(pr,nr);
 239     nalloc = 0;
 240     snew(rcount,nr);
 241   }
 242
 243   if (otfile) {
 244     if (ftmax <= 0)
 245       ftmax = nfr - 1;
 246     snew(tcount,ftmax);
 247     snew(pt,nfr);
 248     rint2 = rint*rint;
 249     /* Initialize time zero */
 250     pt[0] = nfr*isize;
 251     tcount[0] += nfr;
 252   } else {
 253     ftmax = 0;
 254   }
 255
 256   msmul(avbox,1.0/nfr,avbox);
 257   for(f=0; f<nfr; f++) {
 258     if (f % 100 == 0)
 259       fprintf(stderr,"\rProcessing frame %d",f);
 260     /* Scale all the configuration to the average box */
 261     m_inv_ur0(sbox[f],corr);
 262     mmul_ur0(avbox,corr,corr);
 263     for(i=0; i<isize; i++) {
 264       mvmul_ur0(corr,sx[f][i],sx[f][i]);
 265       if (f > 0) {
 266         /* Correct for periodic jumps */
 267         for(m=DIM-1; m>=0; m--) {
 268           while(sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
 269             rvec_dec(sx[f][i],avbox[m]);
 270           while(sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
 271             rvec_inc(sx[f][i],avbox[m]);
 272         }
 273       }
 274     }
 275     for(ff=0; ff<f; ff++) {
 276       fbin = f - ff;
 277       if (fbin <= fmmax || fbin <= ftmax) {
 278         if (sbin == 0)
 279           mbin = fbin;
 280         else
 281           mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
 282         for(i=0; i<isize; i++) {
 283           d2 = distance2(sx[f][i],sx[ff][i]);
 284           if (mbin < mat_nx && d2 < rmax2) {
 285             bin = (int)(sqrt(d2)*invbin + 0.5);
 286             if (bin < nbin) {
 287               mat[mbin][bin] += 1;
 288             }
 289           }
 290           if (fbin <= ftmax && d2 <= rint2)
 291             pt[fbin]++;
 292         }
 293         if (matfile)
 294           mcount[mbin]++;
 295         if (otfile)
 296           tcount[fbin]++;
 297       }
 298     }
 299     if (orfile) {
 300       for(fbin=0; fbin<nr; fbin++) {
 301         ff = f - (fbin + 1)*fshift;
 302         if (ff >= 0) {
 303           for(i=0; i<isize; i++) {
 304             d2 = distance2(sx[f][i],sx[ff][i]);
 305             bin = (int)(sqrt(d2)*invbin);
 306             if (bin >= nalloc) {
 307               nallocn = 10*(bin/10) + 11;
 308               for(m=0; m<nr; m++) {
 309                 srenew(pr[m],nallocn);
 310                 for(i=nalloc; i<nallocn; i++)
 311                   pr[m][i] = 0;
 312               }
 313               nalloc = nallocn;
 314             }
 315             pr[fbin][bin]++;
 316           }
 317           rcount[fbin]++;
 318         }
 319       }
 320     }
 321   }
 322   fprintf(stderr,"\n");
 323
 324   if (matfile) {
 325     matmax = 0;
 326     for(f=0; f<mat_nx; f++) {
 327       normfac = 1.0/(mcount[f]*isize*rbin);
 328       for(i=0; i<nbin; i++) {
 329         mat[f][i] *= normfac;
 330         if (mat[f][i] > matmax && (f!=0 || i!=0))
 331           matmax = mat[f][i];
 332       }
 333     }
 334     fprintf(stdout,"Value at (0,0): %.3f, maximum of the rest %.3f\n",
 335             mat[0][0],matmax);
 336     if (mmax > 0)
 337       matmax = mmax;
 338     snew(tickx,mat_nx);
 339     for(f=0; f<mat_nx; f++) {
 340       if (sbin == 0)
 341         tickx[f] = f*dt;
 342       else
 343         tickx[f] = f*sbin;
 344     }
 345     snew(ticky,nbin+1);
 346     for(i=0; i<=nbin; i++)
 347       ticky[i] = i*rbin;
 348     fp = ffopen(matfile,"w");
 349     write_xpm(fp,MAT_SPATIAL_Y,"Van Hove function","G (1/nm)",
 350               sbin==0 ? "time (ps)" : "sqrt(time) (ps^1/2)","r (nm)",
 351               mat_nx,nbin,tickx,ticky,mat,0,matmax,rlo,rhi,&nlev);
 352     ffclose(fp);
 353   }
 354
 355   if (orfile) {
 356     fp = xvgropen(orfile,"Van Hove function","r (nm)","G (nm\\S-1\\N)",oenv);
 357     fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
 358     snew(legend,nr);
 359     for(fbin=0; fbin<nr; fbin++) {
 360       sprintf(buf,"%g ps",(fbin + 1)*fshift*dt);
 361       legend[fbin] = strdup(buf);
 362     }
 363     xvgr_legend(fp,nr,(const char**)legend,oenv);
 364     for(i=0; i<nalloc; i++) {
 365       fprintf(fp,"%g",i*rbin);
 366       for(fbin=0; fbin<nr; fbin++)
 367         fprintf(fp," %g",
 368                 (real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i==0 ? 0.5 : 1)));
 369       fprintf(fp,"\n");
 370     }
 371     ffclose(fp);
 372   }
 373
 374   if (otfile) {
 375     sprintf(buf,"Probability of moving less than %g nm",rint);
 376     fp = xvgropen(otfile,buf,"t (ps)","",oenv);
 377     fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
 378     for(f=0; f<=ftmax; f++)
 379       fprintf(fp,"%g %g\n",f*dt,(real)pt[f]/(tcount[f]*isize));
 380     ffclose(fp);
 381   }
 382
 383   do_view(oenv, matfile,NULL);
 384   do_view(oenv, orfile,NULL);
 385   do_view(oenv, otfile,NULL);
 386
 387   thanx(stderr);
 388
 389   return 0;
 390 }