2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
44 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/utility/smalloc.h"
51 #include "gromacs/fileio/futil.h"
58 #include "gromacs/fileio/tpxio.h"
59 #include "gromacs/fileio/trxio.h"
65 calc_principal_axes(t_topology * top,
74 sub_xcm(x, n, index, top->atoms.atom, xcm, FALSE);
75 principal_comp(n, index, top->atoms.atom, x, axes, inertia);
78 int gmx_principal(int argc, char *argv[])
80 const char *desc[] = {
81 "[THISMODULE] calculates the three principal axes of inertia for a group",
82 "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
83 "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
84 "contains the x/y/z components of the first (major) principal axis for",
85 "each frame, and similarly for the middle and minor axes in paxis2.dat",
88 static gmx_bool foo = FALSE;
91 { "-foo", FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
100 char *grpname, title[256];
101 int i, j, m, gnx, nam, mol;
103 rvec a1, a2, a3, moi;
110 gmx_rmpbc_t gpbc = NULL;
114 { efTRX, "-f", NULL, ffREAD },
115 { efTPS, NULL, NULL, ffREAD },
116 { efNDX, NULL, NULL, ffOPTRD },
117 { efDAT, "-a1", "paxis1", ffWRITE },
118 { efDAT, "-a2", "paxis2", ffWRITE },
119 { efDAT, "-a3", "paxis3", ffWRITE },
120 { efDAT, "-om", "moi", ffWRITE }
122 #define NFILE asize(fnm)
124 if (!parse_common_args(&argc, argv,
125 PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
126 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
131 axis1 = gmx_ffopen(opt2fn("-a1", NFILE, fnm), "w");
132 axis2 = gmx_ffopen(opt2fn("-a2", NFILE, fnm), "w");
133 axis3 = gmx_ffopen(opt2fn("-a3", NFILE, fnm), "w");
134 fmoi = gmx_ffopen(opt2fn("-om", NFILE, fnm), "w");
136 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box, TRUE);
138 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
140 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
142 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
146 gmx_rmpbc(gpbc, natoms, box, x);
148 calc_principal_axes(&top, x, index, gnx, axes, moi);
150 fprintf(axis1, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[XX][XX], axes[XX][YY], axes[XX][ZZ]);
151 fprintf(axis2, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[YY][XX], axes[YY][YY], axes[YY][ZZ]);
152 fprintf(axis3, "%15.10f %15.10f %15.10f %15.10f\n", t, axes[ZZ][XX], axes[ZZ][YY], axes[ZZ][ZZ]);
153 fprintf(fmoi, "%15.10f %15.10f %15.10f %15.10f\n", t, moi[XX], moi[YY], moi[ZZ]);
155 while (read_next_x(oenv, status, &t, x, box));
157 gmx_rmpbc_done(gpbc);