src/tools/g_nmens.c

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  36 #include <math.h>
  37 #include <string.h>
  38 #include "statutil.h"
  39 #include "sysstuff.h"
  40 #include "typedefs.h"
  41 #include "smalloc.h"
  42 #include "macros.h"
  43 #include "fatal.h"
  44 #include "vec.h"
  45 #include "copyrite.h"
  46 #include "futil.h"
  47 #include "statutil.h"
  48 #include "index.h"
  49 #include "pdbio.h"
  50 #include "tpxio.h"
  51 #include "txtdump.h"
  52 #include "physics.h"
  53 #include "random.h"
  54 #include "eigio.h"
  55
  56 int read_eigval(char *fn,int nmax,real eigval[])
  57 {
  58   FILE *fp;
  59   char line[STRLEN];
  60   int  n,num;
  61   double dbl;
  62   bool bEndOfSet;
  63
  64   n=0;
  65   fp = ffopen(fn,"r");
  66   bEndOfSet = FALSE;
  67   while (fgets(line,STRLEN-1,fp) && !bEndOfSet) {
  68     bEndOfSet = (line[0] == '&');
  69     if ((line[0] != '#') && (line[0] != '@') && !bEndOfSet) {
  70       if ((sscanf(line,"%d %lf",&num,&dbl) != 2) || ((num < 1) || (num > nmax)))
  71 fprintf(stderr,"Invalid line in %s: '%s'\n",fn,line);
  72       else {
  73         eigval[num-1] = dbl;
  74         n++;
  75       }
  76     }
  77   }
  78   fclose(fp);
  79
  80   return n;
  81 }
  82
  83 int gmx_nmens(int argc,char *argv[])
  84 {
  85   static char *desc[] = {
  86     "[TT]g_nmens[tt] generates an ensemble around an average structure",
  87     "in a subspace which is defined by a set of normal modes (eigenvectors).",
  88     "The eigenvectors are assumed to be mass-weighted.",
  89     "The position along each eigenvector is randomly taken from a Gaussian",
  90     "distribution with variance kT/eigenvalue.[PAR]",
  91     "By default the starting eigenvector is set to 7, since the first six",
  92     "normal modes are the translational and rotational degrees of freedom."
  93   };
  94   static int  nstruct=100,first=7,last=-1,seed=-1;
  95   static real temp=300.0;
  96   t_pargs pa[] = {
  97     { "-temp",  FALSE, etREAL, {&temp},
  98       "Temperature in Kelvin" },
  99     { "-seed", FALSE, etINT, {&seed},
 100       "Random seed, -1 generates a seed from time and pid" },
 101     { "-num", FALSE, etINT, {&nstruct},
 102       "Number of structures to generate" },
 103     { "-first", FALSE, etINT, {&first},
 104       "First eigenvector to use (-1 is select)" },
 105     { "-last",  FALSE, etINT, {&last},
 106       "Last eigenvector to use (-1 is till the last)" }
 107   };
 108 #define NPA asize(pa)
 109
 110   int        out;
 111   int        status,trjout;
 112   t_topology top;
 113   t_atoms    *atoms;
 114   rvec       *xtop,*xref,*xav,*xout1,*xout2;
 115   bool       bDMR,bDMA,bFit;
 116   int        nvec,*eignr=NULL;
 117   rvec       **eigvec=NULL;
 118   matrix     box;
 119   real       *eigval,totmass,*invsqrtm,t,disp;
 120   int        natoms,neigval;
 121   char       *grpname,*indexfile,title[STRLEN];
 122   int        i,j,d,s,v;
 123   int        nout,*iout,noutvec,*outvec;
 124   atom_id    *index;
 125   real       rfac,invfr,rhalf,jr;
 126   unsigned long      jran;
 127   const unsigned long im = 0xffff;
 128   const unsigned long ia = 1093;
 129   const unsigned long ic = 18257;
 130
 131   t_filenm fnm[] = {
 132     { efTRN, "-v",    "eigenvec",    ffREAD  },
 133     { efXVG, "-e",    "eigenval",    ffREAD  },
 134     { efTPS, NULL,    NULL,          ffREAD },
 135     { efNDX, NULL,    NULL,          ffOPTRD },
 136     { efTRX, "-o",    "ensemble",    ffWRITE }
 137   };
 138 #define NFILE asize(fnm)
 139
 140   CopyRight(stderr,argv[0]);
 141   parse_common_args(&argc,argv,PCA_BE_NICE,
 142                     NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
 143
 144   indexfile=ftp2fn_null(efNDX,NFILE,fnm);
 145
 146   read_eigenvectors(opt2fn("-v",NFILE,fnm),&natoms,&bFit,
 147                     &xref,&bDMR,&xav,&bDMA,&nvec,&eignr,&eigvec);
 148
 149   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&xtop,NULL,box,bDMA);
 150   atoms=&top.atoms;
 151
 152   printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n",natoms);
 153   get_index(atoms,indexfile,1,&i,&index,&grpname);
 154   if (i!=natoms)
 155     fatal_error(0,"you selected a group with %d elements instead of %d",
 156                 i,natoms);
 157   printf("\n");
 158
 159   snew(eigval,DIM*natoms);
 160   neigval=read_eigval(ftp2fn(efXVG,NFILE,fnm),DIM*natoms,eigval);
 161   fprintf(stderr,"Read %d eigenvalues\n",neigval);
 162
 163   snew(invsqrtm,natoms);
 164   if (bDMA) {
 165     for(i=0; (i<natoms); i++)
 166       invsqrtm[i] = invsqrt(atoms->atom[index[i]].m);
 167   } else {
 168     for(i=0; (i<natoms); i++)
 169       invsqrtm[i]=1.0;
 170   }
 171
 172   if (last==-1)
 173     last=natoms*DIM;
 174   if (first>-1) {
 175     /* make an index from first to last */
 176     nout=last-first+1;
 177     snew(iout,nout);
 178     for(i=0; i<nout; i++)
 179       iout[i]=first-1+i;
 180   } else {
 181     printf("Select eigenvectors for output, end your selection with 0\n");
 182     nout=-1;
 183     iout=NULL;
 184     do {
 185       nout++;
 186       srenew(iout,nout+1);
 187       scanf("%d",&iout[nout]);
 188       iout[nout]--;
 189     } while (iout[nout]>=0);
 190     printf("\n");
 191   }
 192   /* make an index of the eigenvectors which are present */
 193   snew(outvec,nout);
 194   noutvec=0;
 195   for(i=0; i<nout; i++) {
 196     j=0;
 197     while ((j<nvec) && (eignr[j]!=iout[i]))
 198       j++;
 199     if ((j<nvec) && (eignr[j]==iout[i])) {
 200       outvec[noutvec] = j;
 201       iout[noutvec] = iout[i];
 202       noutvec++;
 203     }
 204   }
 205   fprintf(stderr,"%d eigenvectors selected for output\n",noutvec);
 206
 207   if (seed == -1)
 208     seed = make_seed();
 209   fprintf(stderr,"Using seed %d and a temperature of %g K\n",seed,temp);
 210
 211   snew(xout1,natoms);
 212   snew(xout2,atoms->nr);
 213   out=open_trx(ftp2fn(efTRX,NFILE,fnm),"w");
 214   jran = (unsigned long)((real)im*rando(&seed));
 215   for(s=0; s<nstruct; s++) {
 216     for(i=0; i<natoms; i++)
 217       copy_rvec(xav[i],xout1[i]);
 218     for(j=0; j<noutvec; j++) {
 219       v = outvec[j];
 220       /* (r-0.5) n times:  var_n = n * var_1 = n/12
 221          n=4:  var_n = 1/3, so multiply with 3 */
 222
 223       rfac  = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
 224       rhalf = 2.0*rfac;
 225       rfac  = rfac/(real)im;
 226
 227       jran = (jran*ia+ic) & im;
 228       jr = (real)jran;
 229       jran = (jran*ia+ic) & im;
 230       jr += (real)jran;
 231       jran = (jran*ia+ic) & im;
 232       jr += (real)jran;
 233       jran = (jran*ia+ic) & im;
 234       jr += (real)jran;
 235       disp = rfac * jr - rhalf;
 236
 237       for(i=0; i<natoms; i++)
 238         for(d=0; d<DIM; d++)
 239           xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
 240     }
 241     for(i=0; i<natoms; i++)
 242       copy_rvec(xout1[i],xout2[index[i]]);
 243     t = s+1;
 244     write_trx(out,natoms,index,atoms,0,t,box,xout2,NULL);
 245     fprintf(stderr,"\rGenerated %d structures",s+1);
 246   }
 247   fprintf(stderr,"\n");
 248   close_trx(out);
 249
 250   return 0;
 251 }
 252