src/tools/g_rotacf.c

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * Green Red Orange Magenta Azure Cyan Skyblue
  35  */
  36 #include <math.h>
  37 #include <string.h>
  38 #include "sysstuff.h"
  39 #include "physics.h"
  40 #include "typedefs.h"
  41 #include "smalloc.h"
  42 #include "futil.h"
  43 #include "statutil.h"
  44 #include "copyrite.h"
  45 #include "index.h"
  46 #include "macros.h"
  47 #include "fatal.h"
  48 #include "xvgr.h"
  49 #include "gstat.h"
  50 #include "vec.h"
  51
  52 int gmx_rotacf(int argc,char *argv[])
  53 {
  54   static char *desc[] = {
  55     "g_rotacf calculates the rotational correlation function",
  56     "for molecules. Three atoms (i,j,k) must be given in the index",
  57     "file, defining two vectors ij and jk. The rotational acf",
  58     "is calculated as the autocorrelation function of the vector",
  59     "n = ij x jk, i.e. the cross product of the two vectors.",
  60     "Since three atoms span a plane, the order of the three atoms",
  61     "does not matter. Optionally, controlled by the -d switch, you can",
  62     "calculate the rotational correlation function for linear molecules",
  63     "by specifying two atoms (i,j) in the index file.",
  64     "[PAR]",
  65     "EXAMPLES[PAR]",
  66     "g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
  67     "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[PAR]",
  68     "This will calculate the rotational correlation function using a first",
  69     "order Legendre polynomial of the angle of a vector defined by the index",
  70     "file. The correlation function will be fitted from 2.5 ps till 20.0 ps",
  71     "to a two parameter exponential",
  72
  73
  74     ""
  75   };
  76   static bool bVec    = FALSE,bAver=TRUE;
  77
  78   t_pargs pa[] = {
  79     { "-d",   FALSE, etBOOL, {&bVec},
  80       "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
  81     { "-aver",FALSE, etBOOL, {&bAver},
  82       "Average over molecules" }
  83   };
  84
  85   int        status,isize;
  86   atom_id    *index;
  87   char       *grpname;
  88   rvec       *x,*x_s;
  89   matrix     box;
  90   real       **c1;
  91   rvec       xij,xjk,n;
  92   int        i,m,teller,n_alloc,natoms,nvec,ai,aj,ak;
  93   unsigned long mode;
  94   real       t,t0,t1,dt;
  95   t_topology *top;
  96   t_filenm   fnm[] = {
  97     { efTRX, "-f", NULL,  ffREAD  },
  98     { efTPX, NULL, NULL,  ffREAD },
  99     { efNDX, NULL, NULL,  ffREAD  },
 100     { efXVG, "-o", "rotacf",  ffWRITE }
 101   };
 102 #define NFILE asize(fnm)
 103   int     npargs;
 104   t_pargs *ppa;
 105
 106   CopyRight(stderr,argv[0]);
 107   npargs = asize(pa);
 108   ppa    = add_acf_pargs(&npargs,pa);
 109
 110   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 111                     NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
 112
 113   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 114
 115   if (bVec)
 116     nvec = isize/2;
 117   else
 118     nvec = isize/3;
 119
 120   if (((isize % 3) != 0) && !bVec)
 121     fatal_error(0,"number of index elements not multiple of 3, "
 122                 "these can not be atom triplets\n");
 123   if (((isize % 2) != 0) && bVec)
 124     fatal_error(0,"number of index elements not multiple of 2, "
 125                 "these can not be atom doublets\n");
 126
 127   top=read_top(ftp2fn(efTPX,NFILE,fnm));
 128
 129   snew(c1,nvec);
 130   for (i=0; (i<nvec); i++)
 131     c1[i]=NULL;
 132   n_alloc=0;
 133
 134   natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 135   snew(x_s,natoms);
 136
 137   /* Start the loop over frames */
 138   t1 = t0 = t;
 139   teller  = 0;
 140   do {
 141     if (teller >= n_alloc) {
 142       n_alloc+=100;
 143       for (i=0; (i<nvec); i++)
 144         srenew(c1[i],DIM*n_alloc);
 145     }
 146     t1 = t;
 147
 148     /* Remove periodicity */
 149     rm_pbc(&(top->idef),natoms,box,x,x_s);
 150
 151     /* Compute crossproducts for all vectors, if triplets.
 152      * else, just get the vectors in case of doublets.
 153      */
 154     if (bVec == FALSE) {
 155       for (i=0; (i<nvec); i++) {
 156         ai=index[3*i];
 157         aj=index[3*i+1];
 158         ak=index[3*i+2];
 159         rvec_sub(x_s[ai],x_s[aj],xij);
 160         rvec_sub(x_s[aj],x_s[ak],xjk);
 161         oprod(xij,xjk,n);
 162         for(m=0; (m<DIM); m++)
 163           c1[i][DIM*teller+m]=n[m];
 164       }
 165     }
 166     else {
 167       for (i=0; (i<nvec); i++) {
 168         ai=index[2*i];
 169         aj=index[2*i+1];
 170         rvec_sub(x_s[ai],x_s[aj],n);
 171         for(m=0; (m<DIM); m++)
 172           c1[i][DIM*teller+m]=n[m];
 173       }
 174     }
 175     /* Increment loop counter */
 176     teller++;
 177   } while (read_next_x(status,&t,natoms,x,box));
 178   close_trj(status);
 179   fprintf(stderr,"\nDone with trajectory\n");
 180
 181   /* Autocorrelation function */
 182   if (teller < 2)
 183     fprintf(stderr,"Not enough frames for correlation function\n");
 184   else {
 185     dt=(t1 - t0)/(teller-1);
 186
 187     mode = eacVector;
 188
 189     do_autocorr(ftp2fn(efXVG,NFILE,fnm),"Rotational Correlation Function",
 190                 teller,nvec,c1,dt,mode,bAver);
 191   }
 192
 193   do_view(ftp2fn(efXVG,NFILE,fnm),NULL);
 194
 195   thanx(stderr);
 196
 197   return 0;
 198 }