sm_permute.cpp File Reference

#include "gmxpre.h"
#include <string>
#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selparam.h"
#include "gromacs/selection/selvalue.h"
#include "gromacs/topology/block.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "selmethod.h"
#include "selmethod_impl.h"

Include dependency graph for sm_permute.cpp:

Description

Implements the permute selection modifier.

Author

Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
struct	methoddata_permute
	Data structure for the permute selection modifier. More...

Typedefs
typedef struct methoddata_permute	t_methoddata_permute
	Data structure for the permute selection modifier. More...

Functions
static void *	init_data_permute (int npar, gmx_ana_selparam_t *param)
	Allocates data for the permute selection modifier. More...
static void	init_permute (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data)
	Initializes data for the permute selection modifier. More...
static void	init_output_permute (const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data)
	Initializes output for the permute selection modifier. More...
static void	free_data_permute (void *data)
	Frees the memory allocated for the permute selection modifier. More...
static void	evaluate_permute (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
	Evaluates the permute selection modifier. More...

Variables
static gmx_ana_selparam_t	smparams_permute []
	Parameters for the permute selection modifier. More...
static const char *const	help_permute []
	Help text for the permute selection modifier. More...
gmx_ana_selmethod_t	sm_permute
	Selection method data for the permute modifier. More...

Typedef Documentation

typedef struct methoddata_permute t_methoddata_permute

Data structure for the permute selection modifier.

Function Documentation

static void evaluate_permute ( const gmx::SelMethodEvalContext &  context, gmx_ana_pos_t *  p, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the permute selection modifier.

Parameters

[in]	context	Not used.
[in]	p	Positions to permute (should point to data->p).
[out]	out	Output data structure (out->u.p is used).
[in]	data	Should point to a t_methoddata_permute.

Throws if the size of p is not divisible by the number of elements in the permutation.

static void free_data_permute ( void *  data )

static

Frees the memory allocated for the permute selection modifier.

Parameters

data	Data to free (should point to a t_methoddata_permute).

Frees the memory allocated for t_methoddata_permute.

static void * init_data_permute ( int  npar, gmx_ana_selparam_t *  param  )

static

Allocates data for the permute selection modifier.

Parameters

[in]	npar	Not used (should be 2).
[in,out]	param	Method parameters (should point to a copy of smparams_permute).

Returns

Pointer to the allocated data (t_methoddata_permute).

Allocates memory for a t_methoddata_permute structure.

static void init_output_permute ( const gmx_mtop_t *  top, gmx_ana_selvalue_t *  out, void *  data  )

static

Initializes output for the permute selection modifier.

Parameters

[in]	top	Topology data structure.
[in,out]	out	Pointer to output data structure.
[in,out]	data	Should point to t_methoddata_permute.

static void init_permute ( const gmx_mtop_t *  top, int  npar, gmx_ana_selparam_t *  param, void *  data  )

static

Initializes data for the permute selection modifier.

Parameters

[in]	top	Not used.
[in]	npar	Not used (should be 2).
[in]	param	Method parameters (should point to smparams_permute).
[in]	data	Should point to a t_methoddata_permute.

Returns

0 if the input permutation is valid, -1 on error.

Variable Documentation

const char* const help_permute[]

static

Initial value:

= {
    "::",
    "",
    "  permute P1 ... PN",
    "",
    "By default, all selections are evaluated such that the atom indices are",
    "returned in ascending order. This can be changed by appending",
    "[TT]permute P1 P2 ... PN[tt] to an expression.",
    "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
    "This keyword permutes each N-position block in the selection such that",
    "the i'th position in the block becomes Pi'th.",
    "Note that it is the positions that are permuted, not individual atoms.",
    "A fatal error occurs if the size of the selection is not a multiple of n.",
    "It is only possible to permute the whole selection expression, not any",
    "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
    "a selection.",
}

Help text for the permute selection modifier.

gmx_ana_selmethod_t sm_permute

Initial value:

= {
    "permute",
    POS_VALUE,
     256 ,
    asize(smparams_permute),
    smparams_permute,
    &init_data_permute,
    nullptr,
    &init_permute,
    &init_output_permute,
    &free_data_permute,
    nullptr,
    nullptr,
    &evaluate_permute,
    { "POSEXPR permute P1 ... PN", "Permuting selections", asize(help_permute), help_permute },
}

Selection method data for the permute modifier.

gmx_ana_selparam_t smparams_permute[]

static

Initial value:

= {
    { nullptr, { POS_VALUE, -1, { nullptr } }, nullptr,  4  |  16  },
    { nullptr, { INT_VALUE, -1, { nullptr } }, nullptr,  16  },
}

Parameters for the permute selection modifier.