src/tools/g_gyrate.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 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
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  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
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  31  */
  32 static char *SRCID_g_gyrate_c = "$Id$";
  33 #include <math.h>
  34 #include <string.h>
  35 #include "statutil.h"
  36 #include "sysstuff.h"
  37 #include "typedefs.h"
  38 #include "smalloc.h"
  39 #include "macros.h"
  40 #include "vec.h"
  41 #include "pbc.h"
  42 #include "copyrite.h"
  43 #include "futil.h"
  44 #include "statutil.h"
  45 #include "rdgroup.h"
  46 #include "mshift.h"
  47 #include "xvgr.h"
  48 #include "princ.h"
  49 #include "rmpbc.h"
  50 #include "txtdump.h"
  51 #include "tpxio.h"
  52
  53 real calc_gyro(rvec x[],int gnx,atom_id index[],t_atom atom[],real tm,
  54                rvec gvec,rvec d,bool bQ,bool bRot)
  55 {
  56   int    i,ii,m;
  57   real   gyro,dx2,m0;
  58   matrix trans;
  59   rvec   comp;
  60
  61   if (bRot) {
  62     principal_comp(gnx,index,atom,x,trans,d);
  63     for(m=0; (m<DIM); m++)
  64       d[m]=sqrt(d[m]/tm);
  65 #ifdef DEBUG
  66     pr_rvecs(stderr,0,"trans",trans,DIM);
  67 #endif
  68     /* rotate_atoms(gnx,index,x,trans); */
  69   }
  70   clear_rvec(comp);
  71   for(i=0; (i<gnx); i++) {
  72     ii=index[i];
  73     if (bQ)
  74       m0=fabs(atom[ii].q);
  75     else
  76       m0=atom[ii].m;
  77     for(m=0; (m<DIM); m++) {
  78       dx2=x[ii][m]*x[ii][m];
  79       comp[m]+=dx2*m0;
  80     }
  81   }
  82   gyro=comp[XX]+comp[YY]+comp[ZZ];
  83
  84   for(m=0; (m<DIM); m++)
  85     gvec[m]=sqrt((gyro-comp[m])/tm);
  86
  87   return sqrt(gyro/tm);
  88 }
  89
  90 int main(int argc,char *argv[])
  91 {
  92   static char *desc[] = {
  93     "g_gyrate computes the radius of gyration of a group of atoms",
  94     "and the radii of gyration about the x, y and z axes,"
  95     "as a function of time. The atoms are explicitly mass weighted."
  96   };
  97   static bool bQ=FALSE,bRot=FALSE;
  98   t_pargs pa[] = {
  99     { "-q", FALSE, etBOOL, {&bQ},
 100       "Use absolute value of the charge of an atom as weighting factor instead of mass" },
 101     { "-p", FALSE, etBOOL, {&bRot},
 102       "Calculate the radii of gyration about the principal axes." }
 103   };
 104   FILE       *out;
 105   int        status;
 106   t_topology top;
 107   rvec       *x,*x_s;
 108   rvec       xcm,gvec;
 109   rvec       d;         /* eigenvalues of inertia tensor */
 110   matrix     box;
 111   real       t,tm,gyro;
 112   int        natoms;
 113   char       *grpname,title[256];
 114   int        i,j,gnx;
 115   atom_id    *index;
 116   char       *leg[] = { "Rg", "RgX", "RgY", "RgZ" };
 117 #define NLEG asize(leg)
 118   t_filenm fnm[] = {
 119     { efTRX, "-f", NULL, ffREAD },
 120     { efTPS, NULL, NULL, ffREAD },
 121     { efXVG, NULL, "gyrate", ffWRITE },
 122     { efNDX, NULL, NULL, ffOPTRD }
 123   };
 124 #define NFILE asize(fnm)
 125
 126   CopyRight(stderr,argv[0]);
 127   parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
 128                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
 129   clear_rvec(d);
 130
 131   for(i=1; (i<argc); i++) {
 132     if (strcmp(argv[i],"-q") == 0) {
 133       bQ=TRUE;
 134       fprintf(stderr,"Will print radius normalised by charge\n");
 135     }
 136     else if (strcmp(argv[i],"-r") == 0) {
 137       bRot=TRUE;
 138       fprintf(stderr,"Will rotate system along principal axes\n");
 139     }
 140   }
 141   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&x,NULL,box,TRUE);
 142   get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
 143
 144   natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 145   snew(x_s,natoms);
 146
 147   j=0;
 148   if (bQ)
 149     out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
 150                  "Radius of Charge","Time (ps)","Rg (nm)");
 151   else
 152     out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
 153                  "Radius of gyration","Time (ps)","Rg (nm)");
 154   if (bRot)
 155     fprintf(out,"@ subtitle \"Axes are principal component axes\"\n");
 156   xvgr_legend(out,NLEG,leg);
 157   do {
 158     rm_pbc(&top.idef,natoms,box,x,x_s);
 159     tm=sub_xcm(x_s,gnx,index,top.atoms.atom,xcm,bQ);
 160     gyro=calc_gyro(x_s,gnx,index,top.atoms.atom,tm,gvec,d,bQ,bRot);
 161
 162     if (bRot) {
 163       fprintf(out,"%10g  %10g  %10g  %10g  %10g\n",
 164               t,gyro,d[XX],d[YY],d[ZZ]); }
 165     else {
 166       fprintf(out,"%10g  %10g  %10g  %10g  %10g\n",
 167               t,gyro,gvec[XX],gvec[YY],gvec[ZZ]); }
 168     j++;
 169   } while(read_next_x(status,&t,natoms,x,box));
 170   close_trj(status);
 171
 172   fclose(out);
 173
 174   do_view(ftp2fn(efXVG,NFILE,fnm),"-nxy");
 175
 176   thanx(stderr);
 177
 178   return 0;
 179 }