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64 calc_principal_axes(t_topology * top,
73 sub_xcm(x,n,index,top->atoms.atom,xcm,FALSE);
74 principal_comp(n,index,top->atoms.atom,x,axes,inertia);
77 int gmx_principal(int argc,char *argv[])
79 const char *desc[] = {
80 "g_principal calculates the three principal axes of inertia for a group",
83 static bool foo = FALSE;
86 { "-foo", FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
95 char *grpname,title[256];
96 int i,j,m,gnx,nam,mol;
105 gmx_rmpbc_t gpbc=NULL;
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 }
117 #define NFILE asize(fnm)
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);
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");
129 read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,NULL,NULL,box,TRUE);
131 get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
133 natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
135 gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
139 gmx_rmpbc(gpbc,natoms,box,x);
141 calc_principal_axes(&top,x,index,gnx,axes,moi);
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]);
148 while(read_next_x(oenv,status,&t,natoms,x,box));
150 gmx_rmpbc_done(gpbc);