src/tools/gmx_angle.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38 #include <math.h>
  39 #include <string.h>
  40
  41 #include "sysstuff.h"
  42 #include "physics.h"
  43 #include "typedefs.h"
  44 #include "smalloc.h"
  45 #include "futil.h"
  46 #include "statutil.h"
  47 #include "copyrite.h"
  48 #include "vec.h"
  49 #include "index.h"
  50 #include "macros.h"
  51 #include "gmx_fatal.h"
  52 #include "xvgr.h"
  53 #include "gstat.h"
  54 #include "trnio.h"
  55 #include "gmx_ana.h"
  56
  57
  58 static void dump_dih_trn(int nframes,int nangles,real **dih,const char *fn,
  59                          real dt)
  60 {
  61   int    i,j,k,l,m,na,trn;
  62   rvec   *x;
  63   matrix box = {{2,0,0},{0,2,0},{0,0,2}};
  64
  65   na = (nangles*2);
  66   if ((na % 3) != 0)
  67     na = 1+na/3;
  68   else
  69     na = na/3;
  70   printf("There are %d dihedrals. Will fill %d atom positions with cos/sin\n",
  71          nangles,na);
  72   snew(x,na);
  73   trn = open_trn(fn,"w");
  74   for(i=0; (i<nframes); i++) {
  75     k = l = 0;
  76     for(j=0; (j<nangles); j++) {
  77       for(m=0; (m<2); m++) {
  78         x[k][l] = (m == 0) ? cos(dih[j][i]) : sin(dih[j][i]);
  79         l++;
  80         if (l == DIM) {
  81           l = 0;
  82           k++;
  83         }
  84       }
  85     }
  86     fwrite_trn(trn,i,(real)i*dt,0,box,na,x,NULL,NULL);
  87   }
  88   close_trn(trn);
  89   sfree(x);
  90 }
  91
  92 int gmx_g_angle(int argc,char *argv[])
  93 {
  94   static const char *desc[] = {
  95     "g_angle computes the angle distribution for a number of angles",
  96     "or dihedrals. This way you can check whether your simulation",
  97     "is correct. With option -ov you can plot the average angle of",
  98     "a group of angles as a function of time. With the -all option",
  99     "the first graph is the average, the rest are the individual angles.[PAR]",
 100     "With the -of option g_angle also calculates the fraction of trans",
 101     "dihedrals (only for dihedrals) as function of time, but this is",
 102     "probably only fun for a selected few.[PAR]",
 103     "With option -oc a dihedral correlation function is calculated.[PAR]",
 104     "It should be noted that the indexfile should contain",
 105     "atom-triples for angles or atom-quadruplets for dihedrals.",
 106     "If this is not the case, the program will crash.[PAR]",
 107     "With option [TT]-or[tt] a trajectory file is dumped containing cos and"
 108     "sin of selected dihedral angles which subsequently can be used as",
 109     "input for a PCA analysis using [TT]g_covar[tt]."
 110   };
 111   static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
 112   static bool bALL=FALSE,bChandler=FALSE,bAverCorr=FALSE,bPBC=TRUE;
 113   static real binwidth=1;
 114   t_pargs pa[] = {
 115     { "-type", FALSE, etENUM, {opt},
 116       "Type of angle to analyse" },
 117     { "-all",    FALSE,  etBOOL, {&bALL},
 118       "Plot all angles separately in the averages file, in the order of appearance in the index file." },
 119     { "-binwidth", FALSE, etREAL, {&binwidth},
 120       "binwidth (degrees) for calculating the distribution" },
 121     { "-periodic", FALSE, etBOOL, {&bPBC},
 122       "Print dihedral angles modulo 360 degrees" },
 123     { "-chandler", FALSE,  etBOOL, {&bChandler},
 124       "Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60." },
 125     { "-avercorr", FALSE,  etBOOL, {&bAverCorr},
 126       "Average the correlation functions for the individual angles/dihedrals" }
 127   };
 128   static const char *bugs[] = {
 129     "Counting transitions only works for dihedrals with multiplicity 3"
 130   };
 131
 132   FILE       *out;
 133   real       tmp,dt;
 134   int        status,isize;
 135   atom_id    *index;
 136   char       *grpname;
 137   real       maxang,Jc,S2,norm_fac,maxstat;
 138   unsigned long mode;
 139   int        nframes,maxangstat,mult,*angstat;
 140   int        i,j,total,nangles,natoms,nat2,first,last,angind;
 141   bool       bAver,bRb,bPeriodic,
 142     bFrac,          /* calculate fraction too?  */
 143     bTrans,         /* worry about transtions too? */
 144     bCorr;          /* correlation function ? */
 145   real       t,aa,aver,aver2,aversig,fraction;       /* fraction trans dihedrals */
 146   double     tfrac=0;
 147   char       title[256];
 148   real       **dih=NULL;          /* mega array with all dih. angles at all times*/
 149   char       buf[80];
 150   real       *time,*trans_frac,*aver_angle;
 151   t_filenm   fnm[] = {
 152     { efTRX, "-f", NULL,  ffREAD  },
 153     { efNDX, NULL, "angle",  ffREAD  },
 154     { efXVG, "-od", "angdist",  ffWRITE },
 155     { efXVG, "-ov", "angaver",  ffOPTWR },
 156     { efXVG, "-of", "dihfrac",  ffOPTWR },
 157     { efXVG, "-ot", "dihtrans", ffOPTWR },
 158     { efXVG, "-oh", "trhisto",  ffOPTWR },
 159     { efXVG, "-oc", "dihcorr",  ffOPTWR },
 160     { efTRR, "-or", NULL,       ffOPTWR }
 161   };
 162 #define NFILE asize(fnm)
 163   int     npargs;
 164   t_pargs *ppa;
 165   output_env_t oenv;
 166
 167   CopyRight(stderr,argv[0]);
 168   npargs = asize(pa);
 169   ppa    = add_acf_pargs(&npargs,pa);
 170   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 171                     NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs,
 172                     &oenv);
 173
 174   mult   = 4;
 175   maxang = 360.0;
 176   bRb    = FALSE;
 177   switch(opt[0][0]) {
 178   case 'a':
 179     mult   = 3;
 180     maxang = 180.0;
 181     break;
 182   case 'd':
 183     break;
 184   case 'i':
 185     break;
 186   case 'r':
 187     bRb = TRUE;
 188     break;
 189   }
 190
 191   if (opt2bSet("-or",NFILE,fnm)) {
 192     if (mult != 4)
 193       gmx_fatal(FARGS,"Can not combine angles with trn dump");
 194     else
 195       please_cite(stdout,"Mu2005a");
 196   }
 197
 198   /* Calculate bin size */
 199   maxangstat=(int)(maxang/binwidth+0.5);
 200   binwidth=maxang/maxangstat;
 201
 202   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 203   nangles=isize/mult;
 204   if ((isize % mult) != 0)
 205     gmx_fatal(FARGS,"number of index elements not multiple of %d, "
 206                 "these can not be %s\n",
 207                 mult,(mult==3) ? "angle triplets" : "dihedral quadruplets");
 208
 209
 210   /* Check whether specific analysis has to be performed */
 211   bCorr=opt2bSet("-oc",NFILE,fnm);
 212   bAver=opt2bSet("-ov",NFILE,fnm);
 213   bTrans=opt2bSet("-ot",NFILE,fnm);
 214   bFrac=opt2bSet("-of",NFILE,fnm);
 215
 216   if (bChandler && !bCorr)
 217     bCorr=TRUE;
 218
 219   if (bFrac && !bRb) {
 220     fprintf(stderr,"Warning:"
 221             " calculating fractions as defined in this program\n"
 222             "makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
 223     bFrac = FALSE;
 224   }
 225
 226   if ( (bTrans || bFrac || bCorr) && mult==3)
 227     gmx_fatal(FARGS,"Can only do transition, fraction or correlation\n"
 228                 "on dihedrals. Select -d\n");
 229
 230   /*
 231    * We need to know the nr of frames so we can allocate memory for an array
 232    * with all dihedral angles at all timesteps. Works for me.
 233    */
 234   if (bTrans || bCorr  || bALL || opt2bSet("-or",NFILE,fnm))
 235     snew(dih,nangles);
 236
 237   snew(angstat,maxangstat);
 238
 239   read_ang_dih(ftp2fn(efTRX,NFILE,fnm),(mult == 3),
 240                bALL || bCorr || bTrans || opt2bSet("-or",NFILE,fnm),
 241                bRb,bPBC,maxangstat,angstat,
 242                &nframes,&time,isize,index,&trans_frac,&aver_angle,dih,
 243                oenv);
 244
 245   dt=(time[nframes-1]-time[0])/(nframes-1);
 246
 247   if (bAver) {
 248     sprintf(title,"Average Angle: %s",grpname);
 249     out=xvgropen(opt2fn("-ov",NFILE,fnm),
 250                  title,"Time (ps)","Angle (degrees)",oenv);
 251     for(i=0; (i<nframes); i++) {
 252       fprintf(out,"%10.5f  %8.3f",time[i],aver_angle[i]*RAD2DEG);
 253       if (bALL) {
 254         for(j=0; (j<nangles); j++)
 255           if (bPBC) {
 256             real dd = dih[j][i];
 257             fprintf(out,"  %8.3f",atan2(sin(dd),cos(dd))*RAD2DEG);
 258           }
 259           else
 260             fprintf(out,"  %8.3f",dih[j][i]*RAD2DEG);
 261       }
 262       fprintf(out,"\n");
 263     }
 264     ffclose(out);
 265   }
 266   if (opt2bSet("-or",NFILE,fnm))
 267     dump_dih_trn(nframes,nangles,dih,opt2fn("-or",NFILE,fnm),dt);
 268
 269   if (bFrac) {
 270     sprintf(title,"Trans fraction: %s",grpname);
 271     out=xvgropen(opt2fn("-of",NFILE,fnm),
 272                   title,"Time (ps)","Fraction",oenv);
 273     tfrac = 0.0;
 274     for(i=0; (i<nframes); i++) {
 275       fprintf(out,"%10.5f  %10.3f\n",time[i],trans_frac[i]);
 276       tfrac += trans_frac[i];
 277     }
 278     ffclose(out);
 279
 280     tfrac/=nframes;
 281     fprintf(stderr,"Average trans fraction: %g\n",tfrac);
 282   }
 283   sfree(trans_frac);
 284
 285   if (bTrans)
 286     ana_dih_trans(opt2fn("-ot",NFILE,fnm),opt2fn("-oh",NFILE,fnm),
 287                   dih,nframes,nangles,grpname,time[0],dt,bRb,oenv);
 288
 289   if (bCorr) {
 290     /* Autocorrelation function */
 291     if (nframes < 2)
 292       fprintf(stderr,"Not enough frames for correlation function\n");
 293     else {
 294
 295       if (bChandler) {
 296         real dval,sixty=DEG2RAD*60;
 297         bool bTest;
 298
 299         for(i=0; (i<nangles); i++)
 300           for(j=0; (j<nframes); j++) {
 301             dval = dih[i][j];
 302             if (bRb)
 303               bTest=(dval > -sixty) && (dval < sixty);
 304             else
 305               bTest=(dval < -sixty) || (dval > sixty);
 306             if (bTest)
 307               dih[i][j] = dval-tfrac;
 308             else
 309               dih[i][j] = -tfrac;
 310           }
 311       }
 312       if (bChandler)
 313         mode = eacNormal;
 314       else
 315         mode = eacCos;
 316       do_autocorr(opt2fn("-oc",NFILE,fnm), oenv,
 317                   "Dihedral Autocorrelation Function",
 318                   nframes,nangles,dih,dt,mode,bAverCorr);
 319     }
 320   }
 321
 322
 323   /* Determine the non-zero part of the distribution */
 324   for(first=0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
 325     ;
 326   for(last=maxangstat-1; (last > 0) && (angstat[last-1] == 0) ; last--)
 327     ;
 328
 329   aver=aver2=0;
 330   for(i=0; (i<nframes); i++) {
 331     aver  += RAD2DEG*aver_angle[i];
 332     aver2 += sqr(RAD2DEG*aver_angle[i]);
 333   }
 334   aver   /= (real) nframes;
 335   aver2  /= (real) nframes;
 336   aversig = sqrt(aver2-sqr(aver));
 337   printf("Found points in the range from %d to %d (max %d)\n",
 338          first,last,maxangstat);
 339   printf(" < angle >  = %g\n",aver);
 340   printf("< angle^2 > = %g\n",aver2);
 341   printf("Std. Dev.   = %g\n",aversig);
 342
 343   if (mult == 3)
 344     sprintf(title,"Angle Distribution: %s",grpname);
 345   else {
 346     sprintf(title,"Dihedral Distribution: %s",grpname);
 347
 348     calc_distribution_props(maxangstat,angstat,-180.0,0,NULL,&S2);
 349     fprintf(stderr,"Order parameter S^2 = %g\n",S2);
 350   }
 351
 352   bPeriodic=(mult==4) && (first==0) && (last==maxangstat-1);
 353
 354   out=xvgropen(opt2fn("-od",NFILE,fnm),title,"Degrees","",oenv);
 355   if (output_env_get_print_xvgr_codes(oenv))
 356     fprintf(out,"@    subtitle \"average angle: %g\\So\\N\"\n",aver);
 357   norm_fac=1.0/(nangles*nframes*binwidth);
 358   if (bPeriodic) {
 359     maxstat=0;
 360     for(i=first; (i<=last); i++)
 361       maxstat=max(maxstat,angstat[i]*norm_fac);
 362     fprintf(out,"@with g0\n");
 363     fprintf(out,"@    world xmin -180\n");
 364     fprintf(out,"@    world xmax  180\n");
 365     fprintf(out,"@    world ymin 0\n");
 366     fprintf(out,"@    world ymax %g\n",maxstat*1.05);
 367     fprintf(out,"@    xaxis  tick major 60\n");
 368     fprintf(out,"@    xaxis  tick minor 30\n");
 369     fprintf(out,"@    yaxis  tick major 0.005\n");
 370     fprintf(out,"@    yaxis  tick minor 0.0025\n");
 371   }
 372   for(i=first; (i<=last); i++)
 373     fprintf(out,"%10g  %10f\n",i*binwidth+180.0-maxang,angstat[i]*norm_fac);
 374   if ( bPeriodic )
 375     /* print first bin again as last one */
 376     fprintf(out,"%10g  %10f\n",180.0,angstat[0]*norm_fac);
 377
 378   ffclose(out);
 379
 380   do_view(oenv,opt2fn("-od",NFILE,fnm),"-nxy");
 381   if (bAver)
 382     do_view(oenv,opt2fn("-ov",NFILE,fnm),"-nxy");
 383
 384   thanx(stderr);
 385
 386   return 0;
 387 }