src/tools/gmx_principal.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 "vec.h"
  48 #include "pbc.h"
  49 #include "copyrite.h"
  50 #include "futil.h"
  51 #include "statutil.h"
  52 #include "index.h"
  53 #include "mshift.h"
  54 #include "xvgr.h"
  55 #include "princ.h"
  56 #include "rmpbc.h"
  57 #include "txtdump.h"
  58 #include "tpxio.h"
  59 #include "gstat.h"
  60 #include "gmx_ana.h"
  61
  62
  63 void
  64 calc_principal_axes(t_topology *   top,
  65                                         rvec *         x,
  66                                         atom_id *      index,
  67                                         int            n,
  68                                         matrix         axes,
  69                     rvec           inertia)
  70 {
  71         rvec   xcm;
  72
  73         sub_xcm(x,n,index,top->atoms.atom,xcm,FALSE);
  74         principal_comp(n,index,top->atoms.atom,x,axes,inertia);
  75 }
  76
  77 int gmx_principal(int argc,char *argv[])
  78 {
  79   const char *desc[] = {
  80     "[TT]g_principal[tt] calculates the three principal axes of inertia for a group",
  81     "of atoms.",
  82   };
  83   static gmx_bool foo = FALSE;
  84
  85   t_pargs pa[] = {
  86           { "-foo",      FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
  87   };
  88   t_trxstatus *status;
  89   t_topology top;
  90   int        ePBC;
  91   real       t;
  92   rvec *     x;
  93
  94   int        natoms;
  95   char       *grpname,title[256];
  96   int        i,j,m,gnx,nam,mol;
  97   atom_id    *index;
  98   rvec       a1,a2,a3,moi;
  99   FILE *     axis1;
 100   FILE *     axis2;
 101   FILE *     axis3;
 102   FILE *     fmoi;
 103   matrix     axes,box;
 104   output_env_t oenv;
 105   gmx_rmpbc_t  gpbc=NULL;
 106
 107
 108   t_filenm fnm[] = {
 109     { efTRX, "-f",   NULL,       ffREAD },
 110     { efTPS, NULL,   NULL,       ffREAD },
 111     { efNDX, NULL,   NULL,       ffOPTRD },
 112     { efDAT, "-a1",  "axis1",    ffWRITE },
 113         { efDAT, "-a2",  "axis2",    ffWRITE },
 114         { efDAT, "-a3",  "axis3",    ffWRITE },
 115     { efDAT, "-om",  "moi",      ffWRITE }
 116   };
 117 #define NFILE asize(fnm)
 118
 119   CopyRight(stderr,argv[0]);
 120   parse_common_args(&argc,argv,
 121                     PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
 122                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 123
 124   axis1=ffopen(opt2fn("-a1",NFILE,fnm),"w");
 125   axis2=ffopen(opt2fn("-a2",NFILE,fnm),"w");
 126   axis3=ffopen(opt2fn("-a3",NFILE,fnm),"w");
 127   fmoi =ffopen(opt2fn("-om",NFILE,fnm),"w");
 128
 129   read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,NULL,NULL,box,TRUE);
 130
 131   get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
 132
 133   natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 134
 135   gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
 136
 137   do
 138   {
 139     gmx_rmpbc(gpbc,natoms,box,x);
 140
 141           calc_principal_axes(&top,x,index,gnx,axes,moi);
 142
 143           fprintf(axis1,"%15.10f     %15.10f  %15.10f  %15.10f\n",t,axes[XX][XX],axes[YY][XX],axes[ZZ][XX]);
 144           fprintf(axis2,"%15.10f     %15.10f  %15.10f  %15.10f\n",t,axes[XX][YY],axes[YY][YY],axes[ZZ][YY]);
 145           fprintf(axis3,"%15.10f     %15.10f  %15.10f  %15.10f\n",t,axes[XX][ZZ],axes[YY][ZZ],axes[ZZ][ZZ]);
 146           fprintf(fmoi,  "%15.10f     %15.10f  %15.10f  %15.10f\n",t,moi[XX],moi[YY],moi[ZZ]);
 147   }
 148   while(read_next_x(oenv,status,&t,natoms,x,box));
 149
 150   gmx_rmpbc_done(gpbc);
 151
 152
 153   close_trj(status);
 154   ffclose(axis1);
 155   ffclose(axis2);
 156   ffclose(axis3);
 157   ffclose(fmoi);
 158
 159   thanx(stderr);
 160
 161   return 0;
 162 }