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) 2012,2014,2015, 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.
37 /* This file is completely threadsafe - keep it that way! */
44 #include "gromacs/legacyheaders/txtdump.h"
45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/linearalgebra/nrjac.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/utility/smalloc.h"
50 static void m_op(matrix mat, rvec x)
55 for (m = 0; (m < DIM); m++)
57 xp[m] = mat[m][XX]*x[XX]+mat[m][YY]*x[YY]+mat[m][ZZ]*x[ZZ];
59 fprintf(stderr, "x %8.3f %8.3f %8.3f\n", x[XX], x[YY], x[ZZ]);
60 fprintf(stderr, "xp %8.3f %8.3f %8.3f\n", xp[XX], xp[YY], xp[ZZ]);
61 fprintf(stderr, "fac %8.3f %8.3f %8.3f\n", xp[XX]/x[XX], xp[YY]/x[YY],
68 static void ptrans(char *s, real **inten, real d[], real e[])
72 for (m = 1; (m < NDIM); m++)
78 fprintf(stderr, "%8s %8.3f %8.3f %8.3f, norm:%8.3f, d:%8.3f, e:%8.3f\n",
79 s, x, y, z, std::sqrt(n), d[m], e[m]);
81 fprintf(stderr, "\n");
84 void t_trans(matrix trans, real d[], real **ev)
88 for (j = 0; (j < DIM); j++)
94 fprintf(stderr, "d[%d]=%g\n", j, d[j+1]);
99 void principal_comp(int n, atom_id index[], t_atom atom[], rvec x[],
100 matrix trans, rvec d)
102 int i, j, ai, m, nrot;
104 double **inten, dd[NDIM], tvec[NDIM], **ev;
112 for (i = 0; (i < NDIM); i++)
114 snew(inten[i], NDIM);
122 for (i = 0; (i < NDIM); i++)
124 for (m = 0; (m < NDIM); m++)
129 for (i = 0; (i < n); i++)
136 inten[0][0] += mm*(sqr(ry)+sqr(rz));
137 inten[1][1] += mm*(sqr(rx)+sqr(rz));
138 inten[2][2] += mm*(sqr(rx)+sqr(ry));
139 inten[1][0] -= mm*(ry*rx);
140 inten[2][0] -= mm*(rx*rz);
141 inten[2][1] -= mm*(rz*ry);
143 inten[0][1] = inten[1][0];
144 inten[0][2] = inten[2][0];
145 inten[1][2] = inten[2][1];
147 ptrans("initial", inten, dd, e);
150 for (i = 0; (i < DIM); i++)
152 for (m = 0; (m < DIM); m++)
154 trans[i][m] = inten[i][m];
158 /* Call numerical recipe routines */
159 jacobi(inten, 3, dd, ev, &nrot);
161 ptrans("jacobi", ev, dd, e);
164 /* Sort eigenvalues in ascending order */
166 if (std::abs(dd[i+1]) < std::abs(dd[i])) { \
168 for (j = 0; (j < NDIM); j++) { tvec[j] = ev[j][i]; } \
170 for (j = 0; (j < NDIM); j++) { ev[j][i] = ev[j][i+1]; } \
172 for (j = 0; (j < NDIM); j++) { ev[j][i+1] = tvec[j]; } \
178 ptrans("swap", ev, dd, e);
179 t_trans(trans, dd, ev);
182 for (i = 0; (i < DIM); i++)
185 for (m = 0; (m < DIM); m++)
187 trans[i][m] = ev[m][i];
191 for (i = 0; (i < NDIM); i++)
200 void rotate_atoms(int gnx, atom_id *index, rvec x[], matrix trans)
205 for (i = 0; (i < gnx); i++)
207 ii = index ? index[i] : i;
211 x[ii][XX] = trans[XX][XX]*xt+trans[XX][YY]*yt+trans[XX][ZZ]*zt;
212 x[ii][YY] = trans[YY][XX]*xt+trans[YY][YY]*yt+trans[YY][ZZ]*zt;
213 x[ii][ZZ] = trans[ZZ][XX]*xt+trans[ZZ][YY]*yt+trans[ZZ][ZZ]*zt;
217 real calc_xcm(rvec x[], int gnx, atom_id *index, t_atom *atom, rvec xcm,
225 for (i = 0; (i < gnx); i++)
227 ii = index ? index[i] : i;
232 m0 = std::abs(atom[ii].q);
244 for (m = 0; (m < DIM); m++)
246 xcm[m] += m0*x[ii][m];
249 for (m = 0; (m < DIM); m++)
257 real sub_xcm(rvec x[], int gnx, atom_id *index, t_atom atom[], rvec xcm,
263 tm = calc_xcm(x, gnx, index, atom, xcm, bQ);
264 for (i = 0; (i < gnx); i++)
266 ii = index ? index[i] : i;
267 rvec_dec(x[ii], xcm);
272 void add_xcm(rvec x[], int gnx, atom_id *index, rvec xcm)
276 for (i = 0; (i < gnx); i++)
278 ii = index ? index[i] : i;
279 rvec_inc(x[ii], xcm);
283 void orient_princ(t_atoms *atoms, int isize, atom_id *index,
284 int natoms, rvec x[], rvec *v, rvec d)
290 calc_xcm(x, isize, index, atoms->atom, xcm, FALSE);
291 for (i = 0; i < natoms; i++)
295 principal_comp(isize, index, atoms->atom, x, trans, prcomp);
298 copy_rvec(prcomp, d);
301 /* Check whether this trans matrix mirrors the molecule */
304 for (m = 0; (m < DIM); m++)
306 trans[ZZ][m] = -trans[ZZ][m];
309 rotate_atoms(natoms, NULL, x, trans);
312 rotate_atoms(natoms, NULL, v, trans);
315 for (i = 0; i < natoms; i++)