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33 * Implements the \p permute selection modifier.
35 * \author Teemu Murtola <teemu.murtola@cbr.su.se>
36 * \ingroup module_selection
46 #include "gromacs/selection/position.h"
47 #include "gromacs/selection/selmethod.h"
48 #include "gromacs/utility/exceptions.h"
49 #include "gromacs/utility/stringutil.h"
52 * Data structure for the \p permute selection modifier.
56 /** Positions to permute. */
58 /** Group to receive the output permutation. */
60 /** Number of elements in the permutation. */
62 /** Array describing the permutation. */
64 /** Array that has the permutation reversed. */
66 } t_methoddata_permute;
68 /** Allocates data for the \p permute selection modifier. */
70 init_data_permute(int npar, gmx_ana_selparam_t *param);
71 /** Initializes data for the \p permute selection modifier. */
73 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
74 /** Initializes output for the \p permute selection modifier. */
76 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
77 /** Frees the memory allocated for the \p permute selection modifier. */
79 free_data_permute(void *data);
80 /** Evaluates the \p permute selection modifier. */
82 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
83 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
85 /** Parameters for the \p permute selection modifier. */
86 static gmx_ana_selparam_t smparams_permute[] = {
87 {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
88 {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
91 /** Help text for the \p permute selection modifier. */
92 static const char *help_permute[] = {
93 "PERMUTING SELECTIONS[PAR]",
95 "[TT]permute P1 ... PN[tt][PAR]",
97 "By default, all selections are evaluated such that the atom indices are",
98 "returned in ascending order. This can be changed by appending",
99 "[TT]permute P1 P2 ... PN[tt] to an expression.",
100 "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
101 "This keyword permutes each N-position block in the selection such that",
102 "the i'th position in the block becomes Pi'th.",
103 "Note that it is the positions that are permuted, not individual atoms.",
104 "A fatal error occurs if the size of the selection is not a multiple of n.",
105 "It is only possible to permute the whole selection expression, not any",
106 "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
110 /** \internal Selection method data for the \p permute modifier. */
111 gmx_ana_selmethod_t sm_permute = {
112 "permute", POS_VALUE, SMETH_MODIFIER,
113 asize(smparams_permute), smparams_permute,
117 &init_output_permute,
122 {"permute P1 ... PN", asize(help_permute), help_permute},
126 * \param[in] npar Not used (should be 2).
127 * \param[in,out] param Method parameters (should point to a copy of
128 * \ref smparams_permute).
129 * \returns Pointer to the allocated data (\p t_methoddata_permute).
131 * Allocates memory for a \p t_methoddata_permute structure.
134 init_data_permute(int npar, gmx_ana_selparam_t *param)
136 t_methoddata_permute *data;
139 param[0].val.u.p = &data->p;
144 * \param[in] top Not used.
145 * \param[in] npar Not used (should be 2).
146 * \param[in] param Method parameters (should point to \ref smparams_permute).
147 * \param[in] data Should point to a \p t_methoddata_permute.
148 * \returns 0 if the input permutation is valid, -1 on error.
151 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
153 t_methoddata_permute *d = (t_methoddata_permute *)data;
156 gmx_ana_index_reserve(&d->g, d->p.g->isize);
157 d->n = param[1].val.nr;
158 d->perm = param[1].val.u.i;
159 if (d->p.nr % d->n != 0)
161 GMX_THROW(gmx::InconsistentInputError(
162 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
164 snew(d->rperm, d->n);
165 for (i = 0; i < d->n; ++i)
169 for (i = 0; i < d->n; ++i)
172 if (d->perm[i] < 0 || d->perm[i] >= d->n)
174 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
176 if (d->rperm[d->perm[i]] >= 0)
178 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
180 d->rperm[d->perm[i]] = i;
185 * \param[in] top Topology data structure.
186 * \param[in,out] out Pointer to output data structure.
187 * \param[in,out] data Should point to \c t_methoddata_permute.
190 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data)
192 t_methoddata_permute *d = (t_methoddata_permute *)data;
195 gmx_ana_pos_copy(out->u.p, &d->p, true);
196 gmx_ana_pos_set_evalgrp(out->u.p, &d->g);
198 gmx_ana_pos_empty_init(out->u.p);
199 for (i = 0; i < d->p.nr; i += d->n)
201 for (j = 0; j < d->n; ++j)
204 gmx_ana_pos_append_init(out->u.p, &d->g, &d->p, b);
210 * \param data Data to free (should point to a \p t_methoddata_permute).
212 * Frees the memory allocated for \c t_methoddata_permute.
215 free_data_permute(void *data)
217 t_methoddata_permute *d = (t_methoddata_permute *)data;
219 gmx_ana_index_deinit(&d->g);
224 * \param[in] top Not used.
225 * \param[in] fr Not used.
226 * \param[in] pbc Not used.
227 * \param[in] p Positions to permute (should point to \p data->p).
228 * \param[out] out Output data structure (\p out->u.p is used).
229 * \param[in] data Should point to a \p t_methoddata_permute.
230 * \returns 0 if \p p could be permuted, -1 on error.
232 * Returns -1 if the size of \p p is not divisible by the number of
233 * elements in the permutation.
236 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
237 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
239 t_methoddata_permute *d = (t_methoddata_permute *)data;
243 if (d->p.nr % d->n != 0)
245 GMX_THROW(gmx::InconsistentInputError(
246 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
249 gmx_ana_pos_empty(out->u.p);
250 for (i = 0; i < d->p.nr; i += d->n)
252 for (j = 0; j < d->n; ++j)
255 refid = d->p.m.refid[b];
258 /* De-permute the reference ID */
259 refid = refid - (refid % d->n) + d->perm[refid % d->n];
261 gmx_ana_pos_append(out->u.p, &d->g, p, b, refid);
264 gmx_ana_pos_append_finish(out->u.p);