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37 * Implements the \p permute selection modifier.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
44 #include "gromacs/math/vec.h"
45 #include "gromacs/selection/position.h"
46 #include "gromacs/utility/arraysize.h"
47 #include "gromacs/utility/exceptions.h"
48 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/utility/stringutil.h"
51 #include "selmethod.h"
52 #include "selmethod-impl.h"
55 * Data structure for the \p permute selection modifier.
59 /** Positions to permute. */
61 /** Number of elements in the permutation. */
63 /** Array describing the permutation. */
65 /** Array that has the permutation reversed. */
67 } t_methoddata_permute
;
70 * Allocates data for the \p permute selection modifier.
72 * \param[in] npar Not used (should be 2).
73 * \param[in,out] param Method parameters (should point to a copy of
74 * \ref smparams_permute).
75 * \returns Pointer to the allocated data (\p t_methoddata_permute).
77 * Allocates memory for a \p t_methoddata_permute structure.
80 init_data_permute(int npar
, gmx_ana_selparam_t
*param
);
82 * Initializes data for the \p permute selection modifier.
84 * \param[in] top Not used.
85 * \param[in] npar Not used (should be 2).
86 * \param[in] param Method parameters (should point to \ref smparams_permute).
87 * \param[in] data Should point to a \p t_methoddata_permute.
88 * \returns 0 if the input permutation is valid, -1 on error.
91 init_permute(const gmx_mtop_t
*top
, int npar
, gmx_ana_selparam_t
*param
, void *data
);
93 * Initializes output for the \p permute selection modifier.
95 * \param[in] top Topology data structure.
96 * \param[in,out] out Pointer to output data structure.
97 * \param[in,out] data Should point to \c t_methoddata_permute.
100 init_output_permute(const gmx_mtop_t
*top
, gmx_ana_selvalue_t
*out
, void *data
);
101 /** Frees the memory allocated for the \p permute selection modifier. */
103 free_data_permute(void *data
);
105 * Evaluates the \p permute selection modifier.
107 * \param[in] context 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.
112 * Throws if the size of \p p is not divisible by the number of
113 * elements in the permutation.
116 evaluate_permute(const gmx::SelMethodEvalContext
&context
,
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 {nullptr, {POS_VALUE
, -1, {nullptr}}, nullptr, SPAR_DYNAMIC
| SPAR_VARNUM
},
122 {nullptr, {INT_VALUE
, -1, {nullptr}}, nullptr, SPAR_VARNUM
},
125 /** Help text for the \p permute selection modifier. */
126 static const char *const help_permute
[] = {
129 " permute P1 ... PN",
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 {"POSEXPR permute P1 ... PN",
157 "Permuting selections", asize(help_permute
), help_permute
},
161 init_data_permute(int /* npar */, gmx_ana_selparam_t
*param
)
163 t_methoddata_permute
*data
= new t_methoddata_permute();
165 data
->perm
= nullptr;
166 data
->rperm
= nullptr;
167 param
[0].val
.u
.p
= &data
->p
;
172 init_permute(const gmx_mtop_t
* /* top */, int /* npar */, gmx_ana_selparam_t
*param
, void *data
)
174 t_methoddata_permute
*d
= static_cast<t_methoddata_permute
*>(data
);
177 d
->n
= param
[1].val
.nr
;
178 d
->perm
= param
[1].val
.u
.i
;
179 if (d
->p
.count() % d
->n
!= 0)
181 GMX_THROW(gmx::InconsistentInputError(
182 gmx::formatString("The number of positions to be permuted is not divisible by %d", d
->n
)));
184 snew(d
->rperm
, d
->n
);
185 for (i
= 0; i
< d
->n
; ++i
)
189 for (i
= 0; i
< d
->n
; ++i
)
192 if (d
->perm
[i
] < 0 || d
->perm
[i
] >= d
->n
)
194 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
196 if (d
->rperm
[d
->perm
[i
]] >= 0)
198 GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
200 d
->rperm
[d
->perm
[i
]] = i
;
205 init_output_permute(const gmx_mtop_t
* /* top */, gmx_ana_selvalue_t
*out
, void *data
)
207 t_methoddata_permute
*d
= static_cast<t_methoddata_permute
*>(data
);
210 out
->u
.p
->m
.type
= d
->p
.m
.type
;
211 gmx_ana_pos_reserve_for_append(out
->u
.p
, d
->p
.count(), d
->p
.m
.b
.nra
,
212 d
->p
.v
!= nullptr, d
->p
.f
!= nullptr);
213 gmx_ana_pos_empty_init(out
->u
.p
);
214 for (i
= 0; i
< d
->p
.count(); i
+= d
->n
)
216 for (j
= 0; j
< d
->n
; ++j
)
219 gmx_ana_pos_append_init(out
->u
.p
, &d
->p
, b
);
225 * \param data Data to free (should point to a \p t_methoddata_permute).
227 * Frees the memory allocated for \c t_methoddata_permute.
230 free_data_permute(void *data
)
232 t_methoddata_permute
*d
= static_cast<t_methoddata_permute
*>(data
);
239 evaluate_permute(const gmx::SelMethodEvalContext
& /*context*/,
240 gmx_ana_pos_t
* /*p*/, gmx_ana_selvalue_t
*out
, void *data
)
242 t_methoddata_permute
*d
= static_cast<t_methoddata_permute
*>(data
);
246 if (d
->p
.count() % d
->n
!= 0)
248 GMX_THROW(gmx::InconsistentInputError(
249 gmx::formatString("The number of positions to be permuted is not divisible by %d", d
->n
)));
251 gmx_ana_pos_empty(out
->u
.p
);
252 for (i
= 0; i
< d
->p
.count(); i
+= d
->n
)
254 for (j
= 0; j
< d
->n
; ++j
)
257 refid
= d
->p
.m
.refid
[b
];
260 /* De-permute the reference ID */
261 refid
= refid
- (refid
% d
->n
) + d
->perm
[refid
% d
->n
];
263 gmx_ana_pos_append(out
->u
.p
, &d
->p
, b
, refid
);
266 gmx_ana_pos_append_finish(out
->u
.p
);