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   int        status,isize;
  91   atom_id    *index;
  92   char       *grpname;
  93   rvec       *x,*x_s;
  94   matrix     box;
  95   real       **c1;
  96   rvec       xij,xjk,n;
  97   int        i,m,teller,n_alloc,natoms,nvec,ai,aj,ak;
  98   unsigned long mode;
  99   real       t,t0,t1,dt;
 100   t_topology *top;
 101   int        ePBC;
 102   t_filenm   fnm[] = {
 103     { efTRX, "-f", NULL,  ffREAD  },
 104     { efTPX, NULL, NULL,  ffREAD },
 105     { efNDX, NULL, NULL,  ffREAD  },
 106     { efXVG, "-o", "rotacf",  ffWRITE }
 107   };
 108 #define NFILE asize(fnm)
 109   int     npargs;
 110   t_pargs *ppa;
 111
 112   output_env_t oenv;
 113
 114   CopyRight(stderr,argv[0]);
 115   npargs = asize(pa);
 116   ppa    = add_acf_pargs(&npargs,pa);
 117
 118   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 119                     NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
 120
 121   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 122
 123   if (bVec)
 124     nvec = isize/2;
 125   else
 126     nvec = isize/3;
 127
 128   if (((isize % 3) != 0) && !bVec)
 129     gmx_fatal(FARGS,"number of index elements not multiple of 3, "
 130                 "these can not be atom triplets\n");
 131   if (((isize % 2) != 0) && bVec)
 132     gmx_fatal(FARGS,"number of index elements not multiple of 2, "
 133                 "these can not be atom doublets\n");
 134
 135   top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
 136
 137   snew(c1,nvec);
 138   for (i=0; (i<nvec); i++)
 139     c1[i]=NULL;
 140   n_alloc=0;
 141
 142   natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 143   snew(x_s,natoms);
 144
 145   /* Start the loop over frames */
 146   t1 = t0 = t;
 147   teller  = 0;
 148   do {
 149     if (teller >= n_alloc) {
 150       n_alloc+=100;
 151       for (i=0; (i<nvec); i++)
 152         srenew(c1[i],DIM*n_alloc);
 153     }
 154     t1 = t;
 155
 156     /* Remove periodicity */
 157     rm_pbc(&(top->idef),ePBC,natoms,box,x,x_s);
 158
 159     /* Compute crossproducts for all vectors, if triplets.
 160      * else, just get the vectors in case of doublets.
 161      */
 162     if (bVec == FALSE) {
 163       for (i=0; (i<nvec); i++) {
 164         ai=index[3*i];
 165         aj=index[3*i+1];
 166         ak=index[3*i+2];
 167         rvec_sub(x_s[ai],x_s[aj],xij);
 168         rvec_sub(x_s[aj],x_s[ak],xjk);
 169         cprod(xij,xjk,n);
 170         for(m=0; (m<DIM); m++)
 171           c1[i][DIM*teller+m]=n[m];
 172       }
 173     }
 174     else {
 175       for (i=0; (i<nvec); i++) {
 176         ai=index[2*i];
 177         aj=index[2*i+1];
 178         rvec_sub(x_s[ai],x_s[aj],n);
 179         for(m=0; (m<DIM); m++)
 180           c1[i][DIM*teller+m]=n[m];
 181       }
 182     }
 183     /* Increment loop counter */
 184     teller++;
 185   } while (read_next_x(oenv,status,&t,natoms,x,box));
 186   close_trj(status);
 187   fprintf(stderr,"\nDone with trajectory\n");
 188
 189   /* Autocorrelation function */
 190   if (teller < 2)
 191     fprintf(stderr,"Not enough frames for correlation function\n");
 192   else {
 193     dt=(t1 - t0)/(teller-1);
 194
 195     mode = eacVector;
 196
 197     do_autocorr(ftp2fn(efXVG,NFILE,fnm),oenv,"Rotational Correlation Function",
 198                 teller,nvec,c1,dt,mode,bAver);
 199   }
 200
 201   do_view(oenv,ftp2fn(efXVG,NFILE,fnm),NULL);
 202
 203   thanx(stderr);
 204
 205   return 0;
 206 }