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67 calc_principal_axes(t_topology * top,
76 sub_xcm(x,n,index,top->atoms.atom,xcm,FALSE);
77 principal_comp(n,index,top->atoms.atom,x,axes,inertia);
80 int gmx_principal(int argc,char *argv[])
82 const char *desc[] = {
83 "[TT]g_principal[tt] calculates the three principal axes of inertia for a group",
86 static gmx_bool foo = FALSE;
89 { "-foo", FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
98 char *grpname,title[256];
99 int i,j,m,gnx,nam,mol;
108 gmx_rmpbc_t gpbc=NULL;
112 { efTRX, "-f", NULL, ffREAD },
113 { efTPS, NULL, NULL, ffREAD },
114 { efNDX, NULL, NULL, ffOPTRD },
115 { efDAT, "-a1", "axis1", ffWRITE },
116 { efDAT, "-a2", "axis2", ffWRITE },
117 { efDAT, "-a3", "axis3", ffWRITE },
118 { efDAT, "-om", "moi", ffWRITE }
120 #define NFILE asize(fnm)
122 CopyRight(stderr,argv[0]);
123 parse_common_args(&argc,argv,
124 PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
125 NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
127 axis1=ffopen(opt2fn("-a1",NFILE,fnm),"w");
128 axis2=ffopen(opt2fn("-a2",NFILE,fnm),"w");
129 axis3=ffopen(opt2fn("-a3",NFILE,fnm),"w");
130 fmoi =ffopen(opt2fn("-om",NFILE,fnm),"w");
132 read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,NULL,NULL,box,TRUE);
134 get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
136 natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
138 gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
142 gmx_rmpbc(gpbc,natoms,box,x);
144 calc_principal_axes(&top,x,index,gnx,axes,moi);
146 fprintf(axis1,"%15.10f %15.10f %15.10f %15.10f\n",t,axes[XX][XX],axes[YY][XX],axes[ZZ][XX]);
147 fprintf(axis2,"%15.10f %15.10f %15.10f %15.10f\n",t,axes[XX][YY],axes[YY][YY],axes[ZZ][YY]);
148 fprintf(axis3,"%15.10f %15.10f %15.10f %15.10f\n",t,axes[XX][ZZ],axes[YY][ZZ],axes[ZZ][ZZ]);
149 fprintf(fmoi, "%15.10f %15.10f %15.10f %15.10f\n",t,moi[XX],moi[YY],moi[ZZ]);
151 while(read_next_x(oenv,status,&t,natoms,x,box));
153 gmx_rmpbc_done(gpbc);