src/tools/gmx_rotacf.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 #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 "index.h"
  49 #include "macros.h"
  50 #include "gmx_fatal.h"
  51 #include "xvgr.h"
  52 #include "gstat.h"
  53 #include "vec.h"
  54 #include "gmx_ana.h"
  55
  56
  57 int gmx_rotacf(int argc,char *argv[])
  58 {
  59   const char *desc[] = {
  60     "g_rotacf calculates the rotational correlation function",
  61     "for molecules. Three atoms (i,j,k) must be given in the index",
  62     "file, defining two vectors ij and jk. The rotational acf",
  63     "is calculated as the autocorrelation function of the vector",
  64     "n = ij x jk, i.e. the cross product of the two vectors.",
  65     "Since three atoms span a plane, the order of the three atoms",
  66     "does not matter. Optionally, controlled by the -d switch, you can",
  67     "calculate the rotational correlation function for linear molecules",
  68     "by specifying two atoms (i,j) in the index file.",
  69     "[PAR]",
  70     "EXAMPLES[PAR]",
  71     "g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
  72     "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[PAR]",
  73     "This will calculate the rotational correlation function using a first",
  74     "order Legendre polynomial of the angle of a vector defined by the index",
  75     "file. The correlation function will be fitted from 2.5 ps till 20.0 ps",
  76     "to a two parameter exponential.",
  77
  78
  79     ""
  80   };
  81   static bool bVec    = FALSE,bAver=TRUE;
  82
  83   t_pargs pa[] = {
  84     { "-d",   FALSE, etBOOL, {&bVec},
  85       "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
  86     { "-aver",FALSE, etBOOL, {&bAver},
  87       "Average over molecules" }
  88   };
  89
  90   t_trxstatus *status;
  91   int        isize;
  92   atom_id    *index;
  93   char       *grpname;
  94   rvec       *x,*x_s;
  95   matrix     box;
  96   real       **c1;
  97   rvec       xij,xjk,n;
  98   int        i,m,teller,n_alloc,natoms,nvec,ai,aj,ak;
  99   unsigned long mode;
 100   real       t,t0,t1,dt;
 101   t_topology *top;
 102   int        ePBC;
 103   t_filenm   fnm[] = {
 104     { efTRX, "-f", NULL,  ffREAD  },
 105     { efTPX, NULL, NULL,  ffREAD },
 106     { efNDX, NULL, NULL,  ffREAD  },
 107     { efXVG, "-o", "rotacf",  ffWRITE }
 108   };
 109 #define NFILE asize(fnm)
 110   int     npargs;
 111   t_pargs *ppa;
 112
 113   output_env_t oenv;
 114
 115   CopyRight(stderr,argv[0]);
 116   npargs = asize(pa);
 117   ppa    = add_acf_pargs(&npargs,pa);
 118
 119   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 120                     NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
 121
 122   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 123
 124   if (bVec)
 125     nvec = isize/2;
 126   else
 127     nvec = isize/3;
 128
 129   if (((isize % 3) != 0) && !bVec)
 130     gmx_fatal(FARGS,"number of index elements not multiple of 3, "
 131                 "these can not be atom triplets\n");
 132   if (((isize % 2) != 0) && bVec)
 133     gmx_fatal(FARGS,"number of index elements not multiple of 2, "
 134                 "these can not be atom doublets\n");
 135
 136   top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
 137
 138   snew(c1,nvec);
 139   for (i=0; (i<nvec); i++)
 140     c1[i]=NULL;
 141   n_alloc=0;
 142
 143   natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 144   snew(x_s,natoms);
 145
 146   /* Start the loop over frames */
 147   t1 = t0 = t;
 148   teller  = 0;
 149   do {
 150     if (teller >= n_alloc) {
 151       n_alloc+=100;
 152       for (i=0; (i<nvec); i++)
 153         srenew(c1[i],DIM*n_alloc);
 154     }
 155     t1 = t;
 156
 157     /* Remove periodicity */
 158     rm_pbc(&(top->idef),ePBC,natoms,box,x,x_s);
 159
 160     /* Compute crossproducts for all vectors, if triplets.
 161      * else, just get the vectors in case of doublets.
 162      */
 163     if (bVec == FALSE) {
 164       for (i=0; (i<nvec); i++) {
 165         ai=index[3*i];
 166         aj=index[3*i+1];
 167         ak=index[3*i+2];
 168         rvec_sub(x_s[ai],x_s[aj],xij);
 169         rvec_sub(x_s[aj],x_s[ak],xjk);
 170         cprod(xij,xjk,n);
 171         for(m=0; (m<DIM); m++)
 172           c1[i][DIM*teller+m]=n[m];
 173       }
 174     }
 175     else {
 176       for (i=0; (i<nvec); i++) {
 177         ai=index[2*i];
 178         aj=index[2*i+1];
 179         rvec_sub(x_s[ai],x_s[aj],n);
 180         for(m=0; (m<DIM); m++)
 181           c1[i][DIM*teller+m]=n[m];
 182       }
 183     }
 184     /* Increment loop counter */
 185     teller++;
 186   } while (read_next_x(oenv,status,&t,natoms,x,box));
 187   close_trj(status);
 188   fprintf(stderr,"\nDone with trajectory\n");
 189
 190   /* Autocorrelation function */
 191   if (teller < 2)
 192     fprintf(stderr,"Not enough frames for correlation function\n");
 193   else {
 194     dt=(t1 - t0)/(teller-1);
 195
 196     mode = eacVector;
 197
 198     do_autocorr(ftp2fn(efXVG,NFILE,fnm),oenv,"Rotational Correlation Function",
 199                 teller,nvec,c1,dt,mode,bAver);
 200   }
 201
 202   do_view(oenv,ftp2fn(efXVG,NFILE,fnm),NULL);
 203
 204   thanx(stderr);
 205
 206   return 0;
 207 }