src/tools/gmx_bond.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 #include "sysstuff.h"
  41 #include "typedefs.h"
  42 #include "smalloc.h"
  43 #include "macros.h"
  44 #include "vec.h"
  45 #include "pbc.h"
  46 #include "xvgr.h"
  47 #include "copyrite.h"
  48 #include "gmx_fatal.h"
  49 #include "futil.h"
  50 #include "statutil.h"
  51 #include "index.h"
  52 #include "gmx_statistics.h"
  53 #include "tpxio.h"
  54 #include "gmx_ana.h"
  55
  56
  57 static void make_dist_leg(FILE *fp,int gnx,atom_id index[],t_atoms *atoms,
  58                           const output_env_t oenv)
  59 {
  60   char **leg;
  61   int  i;
  62
  63   snew(leg,gnx/2);
  64   for(i=0; i<gnx; i+=2) {
  65     snew(leg[i/2],256);
  66     sprintf(leg[i/2],"%s %s%d - %s %s%d",
  67             *(atoms->atomname[index[i]]),
  68             *(atoms->resinfo[atoms->atom[index[i]].resind].name),
  69             atoms->resinfo[atoms->atom[index[i]].resind].nr,
  70             *(atoms->atomname[index[i+1]]),
  71             *(atoms->resinfo[atoms->atom[index[i+1]].resind].name),
  72             atoms->resinfo[atoms->atom[index[i+1]].resind].nr);
  73   }
  74   xvgr_legend(fp,gnx/2,(const char**)leg,oenv);
  75   for(i=0; i<gnx/2; i++)
  76     sfree(leg[i]);
  77   sfree(leg);
  78 }
  79
  80 static void do_bonds(FILE *log,const char *fn,const char *fbond,
  81                      const char *fdist, int gnx,atom_id index[],
  82                      real blen,real tol,gmx_bool bAver,
  83                      t_topology *top,int ePBC,gmx_bool bAverDist,
  84                      const output_env_t oenv)
  85 {
  86 #define MAXTAB 1000
  87   FILE   *out,*outd=NULL;
  88   int    *btab=NULL;
  89   real   b0=0,b1,db=0;
  90   real   bond,bav;
  91   gmx_stats_t b_one=NULL,*b_all=NULL;
  92   /*real   mean, mean2, sqrdev2, sigma2;
  93     int    counter;*/
  94   rvec   *x;
  95   rvec   dx;
  96   t_trxstatus *status;
  97   int    natoms;
  98   matrix box;
  99   real   t,fac;
 100   int    bind,i,nframes,i0,i1;
 101   t_pbc  pbc;
 102   int    N;
 103   real   aver,sigma,error;
 104
 105   if (!bAver) {
 106     snew(b_all,gnx/2);
 107     for(i=0; (i<gnx/2); i++)
 108       b_all[i] = gmx_stats_init();
 109   }
 110   else {
 111     b_one = gmx_stats_init();
 112     snew(btab,MAXTAB+1);
 113   }
 114
 115   natoms=read_first_x(oenv,&status,fn,&t,&x,box);
 116   if (natoms == 0)
 117     gmx_fatal(FARGS,"No atoms in trajectory!");
 118
 119   if (fdist) {
 120     outd = xvgropen(fdist,bAverDist ? "Average distance" : "Distances",
 121                     "Time (ps)","Distance (nm)",oenv);
 122     if (!bAverDist)
 123       make_dist_leg(outd,gnx,index,&(top->atoms),oenv);
 124   }
 125
 126   nframes=0;
 127   do {
 128     set_pbc(&pbc,ePBC,box);
 129     if (fdist)
 130       fprintf(outd," %8.4f",t);
 131     nframes++; /* count frames */
 132     bav = 0.0;
 133     for(i=0; (i<gnx); i+=2) {
 134       pbc_dx(&pbc,x[index[i]],x[index[i+1]],dx);
 135       bond   = norm(dx);
 136       if (bAverDist)
 137         bav += bond;
 138       else if (fdist)
 139         fprintf(outd," %.3f",bond);
 140       if (bAver) {
 141         gmx_stats_add_point(b_one,t,bond,0,0);
 142         if (db == 0) {
 143           if (blen == -1) {
 144             b0 = 0;
 145             b1 = 0.2;
 146             db = (b1-b0)/MAXTAB;
 147           }
 148           else {
 149             b0   = (1.0-tol)*blen;
 150             b1   = (1.0+tol)*blen;
 151             db   = (2.0*(b1-b0))/MAXTAB;
 152           }
 153         }
 154         bind = (int)((bond-b0)/db+0.5);
 155         if ((bind >= 0) && (bind <= MAXTAB))
 156           btab[bind]++;
 157         else {
 158           /*
 159             printf("bond: %4d-%4d bond=%10.5e, dx=(%10.5e,%10.5e,%10.5e)\n",
 160             index[i],index[i+1],bond,dx[XX],dx[YY],dx[ZZ]);
 161           */
 162         }
 163       }
 164       else {
 165         gmx_stats_add_point(b_all[i/2],t,bond,0,0);
 166       }
 167     }
 168     if (bAverDist)
 169       fprintf(outd," %.5f",bav*2.0/gnx);
 170     if (fdist)
 171       fprintf(outd,"\n");
 172   } while (read_next_x(oenv,status,&t,natoms,x,box));
 173   close_trj(status);
 174
 175   if (fdist)
 176     ffclose(outd);
 177
 178   /*
 179     mean = mean / counter;
 180     mean2 = mean2 / counter;
 181     sqrdev2 = (mean2 - mean*mean);
 182     sigma2 = sqrdev2*counter / (counter - 1);
 183   */
 184   /* For definitions see "Weet wat je meet" */
 185   if (bAver) {
 186     printf("\n");
 187     gmx_stats_get_npoints(b_one,&N);
 188     printf("Total number of samples               : %d\n",N);
 189     gmx_stats_get_ase(b_one,&aver,&sigma,&error);
 190     printf("Mean                                  : %g\n",aver);
 191     printf("Standard deviation of the distribution: %g\n",sigma);
 192     printf("Standard deviation of the mean        : %g\n",error);
 193     gmx_stats_done(b_one);
 194     sfree(b_one);
 195
 196     out=xvgropen(fbond,"Bond Stretching Distribution",
 197                  "Bond Length (nm)","",oenv);
 198
 199     for(i0=0;      ((i0 < MAXTAB) && (btab[i0]==0)); i0++)
 200       ;
 201     i0=max(0,i0-1);
 202     for(i1=MAXTAB; ((i1 > 0)      && (btab[i1]==0)); i1--)
 203       ;
 204     i1=min(MAXTAB,i1+1);
 205
 206     if (i0 >= i1)
 207       gmx_fatal(FARGS,"No distribution... (i0 = %d, i1 = %d)? ? ! ! ? !",i0,i1);
 208
 209     fac=2.0/(nframes*gnx*db);
 210     for(i=i0; (i<=i1); i++)
 211       fprintf(out,"%8.5f  %8.5f\n",b0+i*db,btab[i]*fac);
 212     ffclose(out);
 213   }
 214   else {
 215     fprintf(log,"%5s  %5s  %8s  %8s\n","i","j","b_aver","sigma");
 216     for(i=0; (i<gnx/2); i++) {
 217       gmx_stats_get_ase(b_all[i],&aver,&sigma,NULL);
 218       fprintf(log,"%5u  %5u  %8.5f  %8.5f\n",1+index[2*i],1+index[2*i+1],
 219               aver,sigma);
 220       gmx_stats_done(b_all[i]);
 221       sfree(b_all[i]);
 222     }
 223     sfree(b_all);
 224   }
 225 }
 226
 227 int gmx_bond(int argc,char *argv[])
 228 {
 229   const char *desc[] = {
 230     "[TT]g_bond[tt] makes a distribution of bond lengths. If all is well a",
 231     "Gaussian distribution should be made when using a harmonic potential.",
 232     "Bonds are read from a single group in the index file in order i1-j1",
 233     "i2-j2 through in-jn.[PAR]",
 234     "[TT]-tol[tt] gives the half-width of the distribution as a fraction",
 235     "of the bondlength ([TT]-blen[tt]). That means, for a bond of 0.2",
 236     "a tol of 0.1 gives a distribution from 0.18 to 0.22.[PAR]",
 237     "Option [TT]-d[tt] plots all the distances as a function of time.",
 238     "This requires a structure file for the atom and residue names in",
 239     "the output. If however the option [TT]-averdist[tt] is given (as well",
 240     "or separately) the average bond length is plotted instead."
 241   };
 242   const char *bugs[] = {
 243     "It should be possible to get bond information from the topology."
 244   };
 245   static real blen=-1.0,tol=0.1;
 246   static gmx_bool bAver=TRUE,bAverDist=TRUE;
 247   t_pargs pa[] = {
 248     { "-blen", FALSE, etREAL, {&blen},
 249       "Bond length. By default length of first bond" },
 250     { "-tol",  FALSE, etREAL, {&tol},
 251       "Half width of distribution as fraction of blen" },
 252     { "-aver", FALSE, etBOOL, {&bAver},
 253       "Average bond length distributions" },
 254     { "-averdist", FALSE, etBOOL, {&bAverDist},
 255       "Average distances (turns on [TT]-d[tt])" }
 256   };
 257   FILE      *fp;
 258   char      *grpname;
 259   const char *fdist;
 260   int       gnx;
 261   atom_id   *index;
 262   char      title[STRLEN];
 263   t_topology top;
 264   int       ePBC=-1;
 265   rvec      *x;
 266   matrix    box;
 267   output_env_t oenv;
 268
 269   t_filenm fnm[] = {
 270     { efTRX, "-f", NULL, ffREAD  },
 271     { efNDX, NULL, NULL, ffREAD  },
 272     { efTPS, NULL, NULL, ffOPTRD },
 273     { efXVG, "-o", "bonds", ffWRITE },
 274     { efLOG, NULL, "bonds", ffOPTWR },
 275     { efXVG, "-d", "distance", ffOPTWR }
 276   };
 277 #define NFILE asize(fnm)
 278
 279   CopyRight(stderr,argv[0]);
 280   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE ,
 281                     NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs,
 282                     &oenv);
 283
 284   if (bAverDist)
 285     fdist = opt2fn("-d",NFILE,fnm);
 286   else {
 287     fdist = opt2fn_null("-d",NFILE,fnm);
 288     if (fdist)
 289       read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x,NULL,box,
 290                     FALSE);
 291   }
 292
 293   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
 294   if ( !even(gnx) )
 295     fprintf(stderr,"WARNING: odd number of atoms (%d) in group!\n",gnx);
 296   fprintf(stderr,"Will gather information on %d bonds\n",gnx/2);
 297
 298   if (!bAver)
 299     fp = ftp2FILE(efLOG,NFILE,fnm,"w");
 300   else
 301     fp = NULL;
 302
 303   do_bonds(fp,ftp2fn(efTRX,NFILE,fnm),opt2fn("-o",NFILE,fnm),fdist,gnx,index,
 304            blen,tol,bAver,&top,ePBC,bAverDist,oenv);
 305
 306   do_view(oenv,opt2fn("-o",NFILE,fnm),"-nxy");
 307   do_view(oenv,opt2fn_null("-d",NFILE,fnm),"-nxy");
 308
 309   thanx(stderr);
 310
 311   return 0;
 312 }
 313