src/tools/g_angle.c

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * GRowing Old MAkes el Chrono Sweat
  28  */
  29 static char *SRCID_g_angle_c = "$Id$";
  30
  31 #include <math.h>
  32 #include <string.h>
  33 #include "sysstuff.h"
  34 #include "physics.h"
  35 #include "typedefs.h"
  36 #include "smalloc.h"
  37 #include "futil.h"
  38 #include "statutil.h"
  39 #include "copyrite.h"
  40 #include "rdgroup.h"
  41 #include "macros.h"
  42 #include "fatal.h"
  43 #include "xvgr.h"
  44 #include "gstat.h"
  45
  46 int main(int argc,char *argv[])
  47 {
  48   static char *desc[] = {
  49     "g_angle computes the angle distribution for a number of angles",
  50     "or dihedrals. This way you can check whether your simulation",
  51     "is correct. With option -ov you can plot the average angle of",
  52     "a group of angles as a function of time. With the -all option",
  53     "the first graph is the average, the rest are the individual angles.[PAR]",
  54     "With the -of option g_angle also calculates the fraction of trans",
  55     "dihedrals (only for dihedrals) as function of time, but this is",
  56     "probably only fun for a selected few.[PAR]",
  57     "With option -oc a dihedral correlation function is calculated.[PAR]",
  58     "It should be noted that the indexfile should contain",
  59     "atom-triples for angles or atom-quadruplets for dihedrals.",
  60     "If this is not the case, the program will crash."
  61   };
  62   static char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
  63   static bool bALL=FALSE,bChandler=FALSE,bAverCorr=FALSE;
  64   static real binwidth=1;
  65   t_pargs pa[] = {
  66     { "-type", FALSE, etENUM, {opt},
  67       "Type of angle to analyse" },
  68     { "-all",    FALSE,  etBOOL, {&bALL},
  69       "Plot all angles separately in the averages file, in the order of appearance in the index file." },
  70     { "-binwidth", FALSE, etREAL, {&binwidth},
  71       "binwidth (degrees) for calculating the distribution" },
  72     { "-chandler", FALSE,  etBOOL, {&bChandler},
  73       "Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60." },
  74     { "-avercorr", FALSE,  etBOOL, {&bAverCorr},
  75       "Average the correlation functions for the individual angles/dihedrals" }
  76   };
  77   static char *bugs[] = {
  78     "Counting transitions only works for dihedrals with multiplicity 3"
  79   };
  80
  81   FILE       *out;
  82   real       tmp,dt;
  83   int        status,isize;
  84   atom_id    *index;
  85   char       *grpname;
  86   real       maxang,Jc,S2,norm_fac,maxstat;
  87   unsigned long mode;
  88   int        nframes,maxangstat,mult,*angstat;
  89   int        i,j,total,nangles,natoms,nat2,first,last,angind;
  90   bool       bAver,bRb,bPeriodic,
  91     bFrac,          /* calculate fraction too?  */
  92     bTrans,         /* worry about transtions too? */
  93     bCorr;          /* correlation function ? */
  94   real       t,aa,aver,fraction;       /* fraction trans dihedrals */
  95   double     tfrac=0;
  96   char       title[256];
  97   real       **dih=NULL;          /* mega array with all dih. angles at all times*/
  98   char       buf[80];
  99   real       *time,*trans_frac,*aver_angle;
 100   t_filenm   fnm[] = {
 101     { efTRX, "-f", NULL,  ffREAD  },
 102     { efTPX, NULL, NULL,  ffREAD  },
 103     { efNDX, NULL, "angle",  ffREAD  },
 104     { efXVG, "-od", "angdist",  ffWRITE },
 105     { efXVG, "-ov", "angaver",  ffOPTWR },
 106     { efXVG, "-of", "dihfrac",  ffOPTWR },
 107     { efXVG, "-ot", "dihtrans", ffOPTWR },
 108     { efXVG, "-oh", "trhisto",  ffOPTWR },
 109     { efXVG, "-oc", "dihcorr",  ffOPTWR }
 110   };
 111 #define NFILE asize(fnm)
 112   int     npargs;
 113   t_pargs *ppa;
 114
 115   CopyRight(stderr,argv[0]);
 116   npargs = asize(pa);
 117   ppa    = add_acf_pargs(&npargs,pa);
 118   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
 119                     NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs);
 120
 121   mult   = 4;
 122   maxang = 360.0;
 123   bRb    = FALSE;
 124   switch(opt[0][0]) {
 125   case 'a':
 126     mult   = 3;
 127     maxang = 180.0;
 128     break;
 129   case 'd':
 130     break;
 131   case 'i':
 132     break;
 133   case 'r':
 134     bRb = TRUE;
 135     break;
 136   }
 137
 138   /* Calculate bin size */
 139   maxangstat=(int)(maxang/binwidth+0.5);
 140   binwidth=maxang/maxangstat;
 141
 142   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 143   nangles=isize/mult;
 144   if ((isize % mult) != 0)
 145     fatal_error(0,"number of index elements not multiple of %d, "
 146                 "these can not be %s\n",
 147                 mult,(mult==3) ? "angle triplets" : "dihedral quadruplets");
 148
 149
 150   /* Check whether specific analyses have to be performed */
 151   bCorr=opt2bSet("-oc",NFILE,fnm);
 152   bAver=opt2bSet("-ov",NFILE,fnm);
 153   bTrans=opt2bSet("-ot",NFILE,fnm);
 154   bFrac=opt2bSet("-of",NFILE,fnm);
 155
 156   if (bChandler && !bCorr)
 157     bCorr=TRUE;
 158
 159   if (bFrac && !bRb) {
 160     fprintf(stderr,"Warning:"
 161             " calculating fractions as defined in this program\n"
 162             "makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
 163     bFrac = FALSE;
 164   }
 165
 166   if ( (bTrans || bFrac || bCorr) && mult==3)
 167     fatal_error(0,"Can only do transition, fraction or correlation\n"
 168                 "on dihedrals. Select -d\n");
 169
 170   /*
 171    * We need to know the nr of frames so we can allocate memory for an array
 172    * with all dihedral angles at all timesteps. Works for me.
 173    */
 174   if (bTrans || bCorr  || bALL)
 175     snew(dih,nangles);
 176
 177   snew(angstat,maxangstat);
 178
 179   read_ang_dih(ftp2fn(efTRX,NFILE,fnm),ftp2fn(efTPX,NFILE,fnm),(mult == 3),
 180                bALL || bCorr || bTrans,bRb,maxangstat,angstat,
 181                &nframes,&time,isize,index,&trans_frac,&aver_angle,dih);
 182
 183   dt=(time[nframes-1]-time[0])/(nframes-1);
 184
 185   if (bAver) {
 186     sprintf(title,"Average Angle: %s",grpname);
 187     out=xvgropen(opt2fn("-ov",NFILE,fnm),
 188                  title,"Time (ps)","Angle (degrees)");
 189     for(i=0; (i<nframes); i++) {
 190       fprintf(out,"%10.5f  %8.3f",time[i],aver_angle[i]*RAD2DEG);
 191       if (bALL)
 192         for(j=0; (j<nangles); j++)
 193           fprintf(out,"  %8.3f",dih[j][i]*RAD2DEG);
 194       fprintf(out,"\n");
 195     }
 196     fclose(out);
 197   }
 198
 199   if (bFrac) {
 200     sprintf(title,"Trans fraction: %s",grpname);
 201     out=xvgropen(opt2fn("-of",NFILE,fnm),
 202                   title,"Time (ps)","Fraction");
 203     tfrac = 0.0;
 204     for(i=0; (i<nframes); i++) {
 205       fprintf(out,"%10.5f  %10.3f\n",time[i],trans_frac[i]);
 206       tfrac += trans_frac[i];
 207     }
 208     fclose(out);
 209
 210     tfrac/=nframes;
 211     fprintf(stderr,"Average trans fraction: %g\n",tfrac);
 212   }
 213   sfree(trans_frac);
 214
 215   if (bTrans)
 216     ana_dih_trans(opt2fn("-ot",NFILE,fnm),opt2fn("-oh",NFILE,fnm),
 217                   dih,nframes,nangles,grpname,time[0],dt,bRb);
 218
 219   if (bCorr) {
 220     /* Autocorrelation function */
 221     if (nframes < 2)
 222       fprintf(stderr,"Not enough frames for correlation function\n");
 223     else {
 224
 225       if (bChandler) {
 226         real dval,sixty=DEG2RAD*60;
 227         bool bTest;
 228
 229         for(i=0; (i<nangles); i++)
 230           for(j=0; (j<nframes); j++) {
 231             dval = dih[i][j];
 232             if (bRb)
 233               bTest=(dval > -sixty) && (dval < sixty);
 234             else
 235               bTest=(dval < -sixty) || (dval > sixty);
 236             if (bTest)
 237               dih[i][j] = dval-tfrac;
 238             else
 239               dih[i][j] = -tfrac;
 240           }
 241       }
 242       if (bChandler)
 243         mode = eacNormal;
 244       else
 245         mode = eacCos;
 246       do_autocorr(opt2fn("-oc",NFILE,fnm),"Dihedral Autocorrelation Function",
 247                   nframes,nangles,dih,dt,mode,bAverCorr);
 248     }
 249   }
 250
 251
 252   /* Determine the non-zero part of the distribution */
 253   for(first=0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
 254     ;
 255   for(last=maxangstat-1; (last > 0) && (angstat[last-1] == 0) ; last--)
 256     ;
 257
 258   aver=0;
 259   for(i=0; (i<nframes); i++)
 260     aver+=aver_angle[i];
 261   aver/=nframes;
 262
 263   fprintf(stderr,"Found points in the range from %d to %d (max %d), "
 264           "average %g\n",
 265           first,last,maxangstat,aver*RAD2DEG);
 266
 267   if (mult == 3)
 268     sprintf(title,"Angle Distribution: %s",grpname);
 269   else {
 270     sprintf(title,"Dihedral Distribution: %s",grpname);
 271
 272     calc_distribution_props(maxangstat,angstat,-180.0,0,NULL,&S2);
 273     fprintf(stderr,"Order parameter S^2 = %g\n",S2);
 274   }
 275
 276   bPeriodic=(mult==4) && (first==0) && (last==maxangstat-1);
 277
 278   out=xvgropen(opt2fn("-od",NFILE,fnm),title,"Degrees","");
 279   fprintf(out,"@    subtitle \"average angle: %g\\So\\N\"\n",aver*RAD2DEG);
 280   norm_fac=1.0/(nangles*nframes*binwidth);
 281   if (bPeriodic) {
 282     maxstat=0;
 283     for(i=first; (i<=last); i++)
 284       maxstat=max(maxstat,angstat[i]*norm_fac);
 285     fprintf(out,"@with g0\n");
 286     fprintf(out,"@    world xmin -180\n");
 287     fprintf(out,"@    world xmax  180\n");
 288     fprintf(out,"@    world ymin 0\n");
 289     fprintf(out,"@    world ymax %g\n",maxstat*1.05);
 290     fprintf(out,"@    xaxis  tick major 60\n");
 291     fprintf(out,"@    xaxis  tick minor 30\n");
 292     fprintf(out,"@    yaxis  tick major 0.005\n");
 293     fprintf(out,"@    yaxis  tick minor 0.0025\n");
 294   }
 295   for(i=first; (i<=last); i++)
 296     fprintf(out,"%10g  %10f\n",i*binwidth+180.0-maxang,angstat[i]*norm_fac);
 297   if ( bPeriodic )
 298     /* print first bin again as last one */
 299     fprintf(out,"%10g  %10f\n",180.0,angstat[0]*norm_fac);
 300
 301   fclose(out);
 302
 303   xvgr_file(opt2fn("-od",NFILE,fnm),NULL);
 304   if (bAver)
 305     xvgr_file(opt2fn("-ov",NFILE,fnm),"-nxy");
 306
 307   thanx(stdout);
 308
 309   return 0;
 310 }