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44 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/topology/index.h"
52 #include "gromacs/pbcutil/rmpbc.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trxio.h"
61 calc_principal_axes(t_topology * top,
70 sub_xcm(x, n, index, top->atoms.atom, xcm, FALSE);
71 principal_comp(n, index, top->atoms.atom, x, axes, inertia);
74 int gmx_principal(int argc, char *argv[])
76 const char *desc[] = {
77 "[THISMODULE] calculates the three principal axes of inertia for a group",
78 "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
79 "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
80 "contains the x/y/z components of the first (major) principal axis for",
81 "each frame, and similarly for the middle and minor axes in paxis2.dat",
84 static gmx_bool foo = FALSE;
87 { "-foo", FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
96 char *grpname, title[256];
97 int i, j, m, gnx, nam, mol;
106 gmx_rmpbc_t gpbc = NULL;
110 { efTRX, "-f", NULL, ffREAD },
111 { efTPS, NULL, NULL, ffREAD },
112 { efNDX, NULL, NULL, ffOPTRD },
113 { efDAT, "-a1", "paxis1", ffWRITE },
114 { efDAT, "-a2", "paxis2", ffWRITE },
115 { efDAT, "-a3", "paxis3", ffWRITE },
116 { efDAT, "-om", "moi", ffWRITE }
118 #define NFILE asize(fnm)
120 if (!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))
127 axis1 = gmx_ffopen(opt2fn("-a1", NFILE, fnm), "w");
128 axis2 = gmx_ffopen(opt2fn("-a2", NFILE, fnm), "w");
129 axis3 = gmx_ffopen(opt2fn("-a3", NFILE, fnm), "w");
130 fmoi = gmx_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);
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[XX][YY], axes[XX][ZZ]);
147 fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
148 fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], 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, x, box));
153 gmx_rmpbc_done(gpbc);