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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;
66 /** Allocates data for the \p permute selection modifier. */
68 init_data_permute(int npar, gmx_ana_selparam_t *param);
69 /** Initializes data for the \p permute selection modifier. */
71 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
72 /** Initializes output for the \p permute selection modifier. */
74 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
75 /** Frees the memory allocated for the \p permute selection modifier. */
77 free_data_permute(void *data);
78 /** Evaluates the \p permute selection modifier. */
80 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
81 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
83 /** Parameters for the \p permute selection modifier. */
84 static gmx_ana_selparam_t smparams_permute[] = {
85 {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
86 {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
89 /** Help text for the \p permute selection modifier. */
90 static const char *help_permute[] = {
91 "PERMUTING SELECTIONS[PAR]",
93 "[TT]permute P1 ... PN[tt][PAR]",
95 "By default, all selections are evaluated such that the atom indices are",
96 "returned in ascending order. This can be changed by appending",
97 "[TT]permute P1 P2 ... PN[tt] to an expression.",
98 "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
99 "This keyword permutes each N-position block in the selection such that",
100 "the i'th position in the block becomes Pi'th.",
101 "Note that it is the positions that are permuted, not individual atoms.",
102 "A fatal error occurs if the size of the selection is not a multiple of n.",
103 "It is only possible to permute the whole selection expression, not any",
104 "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
108 /** \internal Selection method data for the \p permute modifier. */
109 gmx_ana_selmethod_t sm_permute = {
110 "permute", POS_VALUE, SMETH_MODIFIER,
111 asize(smparams_permute), smparams_permute,
115 &init_output_permute,
120 {"permute P1 ... PN", asize(help_permute), help_permute},
124 * \param[in] npar Not used (should be 2).
125 * \param[in,out] param Method parameters (should point to a copy of
126 * \ref smparams_permute).
127 * \returns Pointer to the allocated data (\p t_methoddata_permute).
129 * Allocates memory for a \p t_methoddata_permute structure.
132 init_data_permute(int npar, gmx_ana_selparam_t *param)
134 t_methoddata_permute *data;
137 param[0].val.u.p = &data->p;
142 * \param[in] top Not used.
143 * \param[in] npar Not used (should be 2).
144 * \param[in] param Method parameters (should point to \ref smparams_permute).
145 * \param[in] data Should point to a \p t_methoddata_permute.
146 * \returns 0 if the input permutation is valid, -1 on error.
149 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
151 t_methoddata_permute *d = (t_methoddata_permute *)data;
154 d->n = param[1].val.nr;
155 d->perm = param[1].val.u.i;
156 if (d->p.nr % d->n != 0)
158 GMX_THROW(gmx::InconsistentInputError(
159 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
161 snew(d->rperm, d->n);
162 for (i = 0; i < d->n; ++i)
166 for (i = 0; i < d->n; ++i)
169 if (d->perm[i] < 0 || d->perm[i] >= d->n)
171 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
173 if (d->rperm[d->perm[i]] >= 0)
175 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
177 d->rperm[d->perm[i]] = i;
182 * \param[in] top Topology data structure.
183 * \param[in,out] out Pointer to output data structure.
184 * \param[in,out] data Should point to \c t_methoddata_permute.
187 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data)
189 t_methoddata_permute *d = (t_methoddata_permute *)data;
192 out->u.p->m.type = d->p.m.type;
193 gmx_ana_pos_reserve_for_append(out->u.p, d->p.nr, d->p.m.b.nra,
194 d->p.v != NULL, d->p.f != NULL);
195 gmx_ana_pos_empty_init(out->u.p);
196 for (i = 0; i < d->p.nr; i += d->n)
198 for (j = 0; j < d->n; ++j)
201 gmx_ana_pos_append_init(out->u.p, &d->p, b);
207 * \param data Data to free (should point to a \p t_methoddata_permute).
209 * Frees the memory allocated for \c t_methoddata_permute.
212 free_data_permute(void *data)
214 t_methoddata_permute *d = (t_methoddata_permute *)data;
221 * \param[in] top Not used.
222 * \param[in] fr Not used.
223 * \param[in] pbc Not used.
224 * \param[in] p Positions to permute (should point to \p data->p).
225 * \param[out] out Output data structure (\p out->u.p is used).
226 * \param[in] data Should point to a \p t_methoddata_permute.
227 * \returns 0 if \p p could be permuted, -1 on error.
229 * Returns -1 if the size of \p p is not divisible by the number of
230 * elements in the permutation.
233 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
234 gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
236 t_methoddata_permute *d = (t_methoddata_permute *)data;
240 if (d->p.nr % d->n != 0)
242 GMX_THROW(gmx::InconsistentInputError(
243 gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
245 gmx_ana_pos_empty(out->u.p);
246 for (i = 0; i < d->p.nr; i += d->n)
248 for (j = 0; j < d->n; ++j)
251 refid = d->p.m.refid[b];
254 /* De-permute the reference ID */
255 refid = refid - (refid % d->n) + d->perm[refid % d->n];
257 gmx_ana_pos_append(out->u.p, p, b, refid);
260 gmx_ana_pos_append_finish(out->u.p);