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37 * Implements the \p permute selection modifier.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
42 #include "gromacs/legacyheaders/macros.h"
43 #include "gromacs/legacyheaders/smalloc.h"
44 #include "gromacs/legacyheaders/vec.h"
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 /** Number of elements in the permutation. */
60 /** Array describing the permutation. */
62 /** Array that has the permutation reversed. */
64 } t_methoddata_permute;
67 * Allocates data for the \p permute selection modifier.
69 * \param[in] npar Not used (should be 2).
70 * \param[in,out] param Method parameters (should point to a copy of
71 * \ref smparams_permute).
72 * \returns Pointer to the allocated data (\p t_methoddata_permute).
74 * Allocates memory for a \p t_methoddata_permute structure.
77 init_data_permute(int npar, gmx_ana_selparam_t *param);
79 * Initializes data for the \p permute selection modifier.
81 * \param[in] top Not used.
82 * \param[in] npar Not used (should be 2).
83 * \param[in] param Method parameters (should point to \ref smparams_permute).
84 * \param[in] data Should point to a \p t_methoddata_permute.
85 * \returns 0 if the input permutation is valid, -1 on error.
88 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
90 * Initializes output for the \p permute selection modifier.
92 * \param[in] top Topology data structure.
93 * \param[in,out] out Pointer to output data structure.
94 * \param[in,out] data Should point to \c t_methoddata_permute.
97 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
98 /** Frees the memory allocated for the \p permute selection modifier. */
100 free_data_permute(void *data);
103 * Evaluates the \p permute selection modifier.
105 * \param[in] top Not used.
106 * \param[in] fr Not used.
107 * \param[in] pbc Not used.
108 * \param[in] p Positions to permute (should point to \p data->p).
109 * \param[out] out Output data structure (\p out->u.p is used).
110 * \param[in] data Should point to a \p t_methoddata_permute.
111 * \returns 0 if \p p could be permuted, -1 on error.
113 * Returns -1 if the size of \p p is not divisible by the number of
114 * elements in the permutation.
116 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
117 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
119 /** Parameters for the \p permute selection modifier. */
120 static gmx_ana_selparam_t smparams_permute[] = {
121 {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
122 {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
125 /** Help text for the \p permute selection modifier. */
126 static const char *help_permute[] = {
127 "PERMUTING SELECTIONS[PAR]",
129 "[TT]permute P1 ... PN[tt][PAR]",
131 "By default, all selections are evaluated such that the atom indices are",
132 "returned in ascending order. This can be changed by appending",
133 "[TT]permute P1 P2 ... PN[tt] to an expression.",
134 "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
135 "This keyword permutes each N-position block in the selection such that",
136 "the i'th position in the block becomes Pi'th.",
137 "Note that it is the positions that are permuted, not individual atoms.",
138 "A fatal error occurs if the size of the selection is not a multiple of n.",
139 "It is only possible to permute the whole selection expression, not any",
140 "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
144 /** Selection method data for the \p permute modifier. */
145 gmx_ana_selmethod_t sm_permute = {
146 "permute", POS_VALUE, SMETH_MODIFIER,
147 asize(smparams_permute), smparams_permute,
151 &init_output_permute,
156 {"permute P1 ... PN", asize(help_permute), help_permute},
160 init_data_permute(int /* npar */, gmx_ana_selparam_t *param)
162 t_methoddata_permute *data = new t_methoddata_permute();
166 param[0].val.u.p = &data->p;
171 init_permute(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
173 t_methoddata_permute *d = (t_methoddata_permute *)data;
176 d->n = param[1].val.nr;
177 d->perm = param[1].val.u.i;
178 if (d->p.count() % d->n != 0)
180 GMX_THROW(gmx::InconsistentInputError(
181 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
183 snew(d->rperm, d->n);
184 for (i = 0; i < d->n; ++i)
188 for (i = 0; i < d->n; ++i)
191 if (d->perm[i] < 0 || d->perm[i] >= d->n)
193 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
195 if (d->rperm[d->perm[i]] >= 0)
197 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
199 d->rperm[d->perm[i]] = i;
204 init_output_permute(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
206 t_methoddata_permute *d = (t_methoddata_permute *)data;
209 out->u.p->m.type = d->p.m.type;
210 gmx_ana_pos_reserve_for_append(out->u.p, d->p.count(), d->p.m.b.nra,
211 d->p.v != NULL, d->p.f != NULL);
212 gmx_ana_pos_empty_init(out->u.p);
213 for (i = 0; i < d->p.count(); i += d->n)
215 for (j = 0; j < d->n; ++j)
218 gmx_ana_pos_append_init(out->u.p, &d->p, b);
224 * \param data Data to free (should point to a \p t_methoddata_permute).
226 * Frees the memory allocated for \c t_methoddata_permute.
229 free_data_permute(void *data)
231 t_methoddata_permute *d = (t_methoddata_permute *)data;
238 evaluate_permute(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
239 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
241 t_methoddata_permute *d = (t_methoddata_permute *)data;
245 if (d->p.count() % d->n != 0)
247 GMX_THROW(gmx::InconsistentInputError(
248 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
250 gmx_ana_pos_empty(out->u.p);
251 for (i = 0; i < d->p.count(); i += d->n)
253 for (j = 0; j < d->n; ++j)
256 refid = d->p.m.refid[b];
259 /* De-permute the reference ID */
260 refid = refid - (refid % d->n) + d->perm[refid % d->n];
262 gmx_ana_pos_append(out->u.p, p, b, refid);
265 gmx_ana_pos_append_finish(out->u.p);