2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
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.
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.
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.
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.
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.
37 * Implements the \p permute selection modifier.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "gromacs/legacyheaders/macros.h"
45 #include "gromacs/math/vec.h"
46 #include "gromacs/selection/position.h"
47 #include "gromacs/utility/exceptions.h"
48 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/utility/stringutil.h"
51 #include "selmethod.h"
54 * Data structure for the \p permute selection modifier.
58 /** Positions to permute. */
60 /** Number of elements in the permutation. */
62 /** Array describing the permutation. */
64 /** Array that has the permutation reversed. */
66 } t_methoddata_permute;
69 * Allocates data for the \p permute selection modifier.
71 * \param[in] npar Not used (should be 2).
72 * \param[in,out] param Method parameters (should point to a copy of
73 * \ref smparams_permute).
74 * \returns Pointer to the allocated data (\p t_methoddata_permute).
76 * Allocates memory for a \p t_methoddata_permute structure.
79 init_data_permute(int npar, gmx_ana_selparam_t *param);
81 * Initializes data for the \p permute selection modifier.
83 * \param[in] top Not used.
84 * \param[in] npar Not used (should be 2).
85 * \param[in] param Method parameters (should point to \ref smparams_permute).
86 * \param[in] data Should point to a \p t_methoddata_permute.
87 * \returns 0 if the input permutation is valid, -1 on error.
90 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
92 * Initializes output for the \p permute selection modifier.
94 * \param[in] top Topology data structure.
95 * \param[in,out] out Pointer to output data structure.
96 * \param[in,out] data Should point to \c t_methoddata_permute.
99 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
100 /** Frees the memory allocated for the \p permute selection modifier. */
102 free_data_permute(void *data);
105 * Evaluates the \p permute selection modifier.
107 * \param[in] top Not used.
108 * \param[in] fr Not used.
109 * \param[in] pbc Not used.
110 * \param[in] p Positions to permute (should point to \p data->p).
111 * \param[out] out Output data structure (\p out->u.p is used).
112 * \param[in] data Should point to a \p t_methoddata_permute.
113 * \returns 0 if \p p could be permuted, -1 on error.
115 * Returns -1 if the size of \p p is not divisible by the number of
116 * elements in the permutation.
118 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
119 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
121 /** Parameters for the \p permute selection modifier. */
122 static gmx_ana_selparam_t smparams_permute[] = {
123 {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
124 {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
127 /** Help text for the \p permute selection modifier. */
128 static const char *help_permute[] = {
129 "PERMUTING SELECTIONS[PAR]",
131 "[TT]permute P1 ... PN[tt][PAR]",
133 "By default, all selections are evaluated such that the atom indices are",
134 "returned in ascending order. This can be changed by appending",
135 "[TT]permute P1 P2 ... PN[tt] to an expression.",
136 "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
137 "This keyword permutes each N-position block in the selection such that",
138 "the i'th position in the block becomes Pi'th.",
139 "Note that it is the positions that are permuted, not individual atoms.",
140 "A fatal error occurs if the size of the selection is not a multiple of n.",
141 "It is only possible to permute the whole selection expression, not any",
142 "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
146 /** Selection method data for the \p permute modifier. */
147 gmx_ana_selmethod_t sm_permute = {
148 "permute", POS_VALUE, SMETH_MODIFIER,
149 asize(smparams_permute), smparams_permute,
153 &init_output_permute,
158 {"permute P1 ... PN", asize(help_permute), help_permute},
162 init_data_permute(int /* npar */, gmx_ana_selparam_t *param)
164 t_methoddata_permute *data = new t_methoddata_permute();
168 param[0].val.u.p = &data->p;
173 init_permute(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
175 t_methoddata_permute *d = (t_methoddata_permute *)data;
178 d->n = param[1].val.nr;
179 d->perm = param[1].val.u.i;
180 if (d->p.count() % d->n != 0)
182 GMX_THROW(gmx::InconsistentInputError(
183 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
185 snew(d->rperm, d->n);
186 for (i = 0; i < d->n; ++i)
190 for (i = 0; i < d->n; ++i)
193 if (d->perm[i] < 0 || d->perm[i] >= d->n)
195 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
197 if (d->rperm[d->perm[i]] >= 0)
199 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
201 d->rperm[d->perm[i]] = i;
206 init_output_permute(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
208 t_methoddata_permute *d = (t_methoddata_permute *)data;
211 out->u.p->m.type = d->p.m.type;
212 gmx_ana_pos_reserve_for_append(out->u.p, d->p.count(), d->p.m.b.nra,
213 d->p.v != NULL, d->p.f != NULL);
214 gmx_ana_pos_empty_init(out->u.p);
215 for (i = 0; i < d->p.count(); i += d->n)
217 for (j = 0; j < d->n; ++j)
220 gmx_ana_pos_append_init(out->u.p, &d->p, b);
226 * \param data Data to free (should point to a \p t_methoddata_permute).
228 * Frees the memory allocated for \c t_methoddata_permute.
231 free_data_permute(void *data)
233 t_methoddata_permute *d = (t_methoddata_permute *)data;
240 evaluate_permute(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
241 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
243 t_methoddata_permute *d = (t_methoddata_permute *)data;
247 if (d->p.count() % d->n != 0)
249 GMX_THROW(gmx::InconsistentInputError(
250 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
252 gmx_ana_pos_empty(out->u.p);
253 for (i = 0; i < d->p.count(); i += d->n)
255 for (j = 0; j < d->n; ++j)
258 refid = d->p.m.refid[b];
261 /* De-permute the reference ID */
262 refid = refid - (refid % d->n) + d->perm[refid % d->n];
264 gmx_ana_pos_append(out->u.p, p, b, refid);
267 gmx_ana_pos_append_finish(out->u.p);