1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
8 *
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
13 *
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
18 *
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
23 *
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
31 *
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
34 */
35 /*! \internal \file
36 * \brief
37 * Implements routines in boxutilities.h.
38 *
39 * Utility functions for handling boxes.
40 */
41 #include "gmxpre.h"
42
43 #include "boxutilities.h"
44
45 #include <algorithm>
46
47 #include "gromacs/math/utilities.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/math/vectypes.h"
50
do_box_rel(int ndim,const matrix deform,matrix box_rel,matrix b,bool bInit)51 void do_box_rel(int ndim, const matrix deform, matrix box_rel, matrix b, bool bInit)
52 {
53 for (int d = YY; d <= ZZ; ++d)
54 {
55 for (int d2 = XX; d2 < ndim; ++d2)
56 {
57 /* We need to check if this box component is deformed
58 * or if deformation of another component might cause
59 * changes in this component due to box corrections.
60 */
61 if (deform[d][d2] == 0
62 && !(d == ZZ && d2 == XX && deform[d][YY] != 0 && (b[YY][d2] != 0 || deform[YY][d2] != 0)))
63 {
64 if (bInit)
65 {
66 box_rel[d][d2] = b[d][d2] / b[XX][XX];
67 }
68 else
69 {
70 b[d][d2] = b[XX][XX] * box_rel[d][d2];
71 }
72 }
73 }
74 }
75 }
76
77 namespace gmx
78 {
79
80 namespace
81 {
82
83 //! Whether two box elements are equal (with a tolerance).
boxElementEqual(real element1,real element2)84 bool boxElementEqual(real element1, real element2)
85 {
86 // Compare with a relative tolerance (for big boxes) and with
87 // an absolute tolerance (small boxes are generally not specified with very
88 // high number of decimals).
89 return gmx_within_tol(element1, element2, 10 * GMX_REAL_EPS) || std::fabs(element1 - element2) < 1e-3;
90 }
91
92 } // namespace
93
boxesAreEqual(const matrix box1,const matrix box2)94 bool boxesAreEqual(const matrix box1, const matrix box2)
95 {
96 return boxElementEqual(box1[XX][XX], box2[XX][XX]) && boxElementEqual(box1[YY][XX], box2[YY][XX])
97 && boxElementEqual(box1[YY][YY], box2[YY][YY])
98 && boxElementEqual(box1[ZZ][XX], box2[ZZ][XX]) && boxElementEqual(box1[ZZ][YY], box2[ZZ][YY])
99 && boxElementEqual(box1[ZZ][ZZ], box2[ZZ][ZZ]);
100 }
101
boxIsZero(const matrix box)102 bool boxIsZero(const matrix box)
103 {
104 return boxElementEqual(box[XX][XX], 0.0) && boxElementEqual(box[YY][XX], 0.0)
105 && boxElementEqual(box[YY][YY], 0.0) && boxElementEqual(box[ZZ][XX], 0.0)
106 && boxElementEqual(box[ZZ][YY], 0.0) && boxElementEqual(box[ZZ][ZZ], 0.0);
107 }
108
109 } // namespace gmx
110