src/tools/gmx_nmens.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40 #include <string.h>
  41
  42 #include "statutil.h"
  43 #include "sysstuff.h"
  44 #include "typedefs.h"
  45 #include "smalloc.h"
  46 #include "macros.h"
  47 #include "gmx_fatal.h"
  48 #include "vec.h"
  49 #include "copyrite.h"
  50 #include "futil.h"
  51 #include "statutil.h"
  52 #include "index.h"
  53 #include "pdbio.h"
  54 #include "tpxio.h"
  55 #include "txtdump.h"
  56 #include "physics.h"
  57 #include "random.h"
  58 #include "eigio.h"
  59 #include "gmx_ana.h"
  60
  61
  62 int gmx_nmens(int argc,char *argv[])
  63 {
  64   const char *desc[] = {
  65     "[TT]g_nmens[tt] generates an ensemble around an average structure",
  66     "in a subspace which is defined by a set of normal modes (eigenvectors).",
  67     "The eigenvectors are assumed to be mass-weighted.",
  68     "The position along each eigenvector is randomly taken from a Gaussian",
  69     "distribution with variance kT/eigenvalue.[PAR]",
  70     "By default the starting eigenvector is set to 7, since the first six",
  71     "normal modes are the translational and rotational degrees of freedom."
  72   };
  73   static int  nstruct=100,first=7,last=-1,seed=-1;
  74   static real temp=300.0;
  75   t_pargs pa[] = {
  76     { "-temp",  FALSE, etREAL, {&temp},
  77       "Temperature in Kelvin" },
  78     { "-seed", FALSE, etINT, {&seed},
  79       "Random seed, -1 generates a seed from time and pid" },
  80     { "-num", FALSE, etINT, {&nstruct},
  81       "Number of structures to generate" },
  82     { "-first", FALSE, etINT, {&first},
  83       "First eigenvector to use (-1 is select)" },
  84     { "-last",  FALSE, etINT, {&last},
  85       "Last eigenvector to use (-1 is till the last)" }
  86   };
  87 #define NPA asize(pa)
  88
  89   t_trxstatus *out;
  90   int        status,trjout;
  91   t_topology top;
  92   int        ePBC;
  93   t_atoms    *atoms;
  94   rvec       *xtop,*xref,*xav,*xout1,*xout2;
  95   gmx_bool       bDMR,bDMA,bFit;
  96   int        nvec,*eignr=NULL;
  97   rvec       **eigvec=NULL;
  98   matrix     box;
  99   real       *eigval,totmass,*invsqrtm,t,disp;
 100   int        natoms,neigval;
 101   char       *grpname,title[STRLEN];
 102   const char *indexfile;
 103   int        i,j,d,s,v;
 104   int        nout,*iout,noutvec,*outvec;
 105   atom_id    *index;
 106   real       rfac,invfr,rhalf,jr;
 107   int *      eigvalnr;
 108   output_env_t oenv;
 109
 110   unsigned long      jran;
 111   const unsigned long im = 0xffff;
 112   const unsigned long ia = 1093;
 113   const unsigned long ic = 18257;
 114
 115
 116   t_filenm fnm[] = {
 117     { efTRN, "-v",    "eigenvec",    ffREAD  },
 118     { efXVG, "-e",    "eigenval",    ffREAD  },
 119     { efTPS, NULL,    NULL,          ffREAD },
 120     { efNDX, NULL,    NULL,          ffOPTRD },
 121     { efTRO, "-o",    "ensemble",    ffWRITE }
 122   };
 123 #define NFILE asize(fnm)
 124
 125   CopyRight(stderr,argv[0]);
 126   parse_common_args(&argc,argv,PCA_BE_NICE,
 127                     NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL,&oenv);
 128
 129   indexfile=ftp2fn_null(efNDX,NFILE,fnm);
 130
 131   read_eigenvectors(opt2fn("-v",NFILE,fnm),&natoms,&bFit,
 132                     &xref,&bDMR,&xav,&bDMA,&nvec,&eignr,&eigvec,&eigval);
 133
 134   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,bDMA);
 135   atoms=&top.atoms;
 136
 137   printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n",natoms);
 138   get_index(atoms,indexfile,1,&i,&index,&grpname);
 139   if (i!=natoms)
 140     gmx_fatal(FARGS,"you selected a group with %d elements instead of %d",
 141                 i,natoms);
 142   printf("\n");
 143
 144   snew(invsqrtm,natoms);
 145   if (bDMA) {
 146     for(i=0; (i<natoms); i++)
 147       invsqrtm[i] = gmx_invsqrt(atoms->atom[index[i]].m);
 148   } else {
 149     for(i=0; (i<natoms); i++)
 150       invsqrtm[i]=1.0;
 151   }
 152
 153   if (last==-1)
 154       last=natoms*DIM;
 155   if (first>-1)
 156   {
 157       /* make an index from first to last */
 158       nout=last-first+1;
 159       snew(iout,nout);
 160       for(i=0; i<nout; i++)
 161           iout[i]=first-1+i;
 162   }
 163   else
 164   {
 165       printf("Select eigenvectors for output, end your selection with 0\n");
 166       nout=-1;
 167       iout=NULL;
 168       do {
 169           nout++;
 170           srenew(iout,nout+1);
 171           if(1 != scanf("%d",&iout[nout]))
 172           {
 173               gmx_fatal(FARGS,"Error reading user input");
 174           }
 175           iout[nout]--;
 176       } while (iout[nout]>=0);
 177       printf("\n");
 178   }
 179
 180   /* make an index of the eigenvectors which are present */
 181   snew(outvec,nout);
 182   noutvec=0;
 183   for(i=0; i<nout; i++)
 184   {
 185       j=0;
 186       while ((j<nvec) && (eignr[j]!=iout[i]))
 187           j++;
 188       if ((j<nvec) && (eignr[j]==iout[i]))
 189       {
 190           outvec[noutvec] = j;
 191           iout[noutvec] = iout[i];
 192           noutvec++;
 193       }
 194   }
 195
 196   fprintf(stderr,"%d eigenvectors selected for output\n",noutvec);
 197
 198   if (seed == -1)
 199     seed = make_seed();
 200   fprintf(stderr,"Using seed %d and a temperature of %g K\n",seed,temp);
 201
 202   snew(xout1,natoms);
 203   snew(xout2,atoms->nr);
 204   out=open_trx(ftp2fn(efTRO,NFILE,fnm),"w");
 205   jran = (unsigned long)((real)im*rando(&seed));
 206   for(s=0; s<nstruct; s++) {
 207     for(i=0; i<natoms; i++)
 208       copy_rvec(xav[i],xout1[i]);
 209     for(j=0; j<noutvec; j++) {
 210       v = outvec[j];
 211       /* (r-0.5) n times:  var_n = n * var_1 = n/12
 212          n=4:  var_n = 1/3, so multiply with 3 */
 213
 214       rfac  = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
 215       rhalf = 2.0*rfac;
 216       rfac  = rfac/(real)im;
 217
 218       jran = (jran*ia+ic) & im;
 219       jr = (real)jran;
 220       jran = (jran*ia+ic) & im;
 221       jr += (real)jran;
 222       jran = (jran*ia+ic) & im;
 223       jr += (real)jran;
 224       jran = (jran*ia+ic) & im;
 225       jr += (real)jran;
 226       disp = rfac * jr - rhalf;
 227
 228       for(i=0; i<natoms; i++)
 229           for(d=0; d<DIM; d++)
 230               xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
 231     }
 232     for(i=0; i<natoms; i++)
 233         copy_rvec(xout1[i],xout2[index[i]]);
 234     t = s+1;
 235     write_trx(out,natoms,index,atoms,0,t,box,xout2,NULL,NULL);
 236     fprintf(stderr,"\rGenerated %d structures",s+1);
 237   }
 238   fprintf(stderr,"\n");
 239   close_trx(out);
 240
 241   return 0;
 242 }
 243