#include "gmxpre.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selparam.h"
#include "gromacs/selection/selvalue.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "keywords.h"
#include "poscalc.h"
#include "selelem.h"
#include "selmethod.h"
#include "selmethod_impl.h"

Include dependency graph for sm_position.cpp:

Description

Implements position evaluation selection methods.

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

Classes
struct	t_methoddata_pos
	Data structure for position keyword evaluation. More...

Functions
static void *	init_data_pos (int npar, gmx_ana_selparam_t *param)
	Allocates data for position evaluation selection methods. More...

static void	set_poscoll_pos (gmx::PositionCalculationCollection pcc, void data)
	Sets the position calculation collection for position evaluation selection methods. More...

static void	init_kwpos (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes position evaluation keywords. More...

static void	init_cog (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes the `cog` selection method. More...

static void	init_com (const gmx_mtop_t top, int npar, gmx_ana_selparam_t param, void *data)
	Initializes the `cog` selection method. More...

static void	init_output_pos (const gmx_mtop_t top, gmx_ana_selvalue_t out, void *data)
	Initializes output for position evaluation selection methods. More...

static void	free_data_pos (void *data)
	Frees the data allocated for position evaluation selection methods. More...

static void	evaluate_pos (const gmx::SelMethodEvalContext &context, gmx_ana_index_t , gmx_ana_selvalue_t out, void *data)
	Evaluates position evaluation selection methods. More...

bool	_gmx_selelem_is_default_kwpos (const gmx::SelectionTreeElement &sel)
	Returns whether the selection element is a default position keyword. More...

static void	set_pos_method_flags (gmx_ana_selmethod_t method, t_methoddata_pos d)
	Updates selection method flags about required topology information. More...

void	_gmx_selelem_set_kwpos_type (gmx::SelectionTreeElement sel, const char type)
	Sets the position type for position keyword evaluation. More...

void	_gmx_selelem_set_kwpos_flags (gmx::SelectionTreeElement *sel, int flags)
	Sets the flags for position keyword evaluation. More...

Variables
static gmx_ana_selparam_t	smparams_keyword_pos []
	Parameters for position keyword evaluation. More...

static gmx_ana_selparam_t	smparams_com []
	Parameters for the `cog` and `com` selection methods. More...

gmx_ana_selmethod_t	sm_keyword_pos
	Selection method data for position keyword evaluation. More...

gmx_ana_selmethod_t	sm_cog
	Selection method data for the `cog` method. More...

gmx_ana_selmethod_t	sm_com
	Selection method data for the `com` method. More...

Function Documentation

bool _gmx_selelem_is_default_kwpos ( const gmx::SelectionTreeElement & sel )

Returns whether the selection element is a default position keyword.

Parameters

[in] sel Selection element to query.

Returns: true if sel represents a position keyword evaluation that uses the default (implicit) position keyword.

This method only works before the selection has been compiled.

void _gmx_selelem_set_kwpos_flags	(	gmx::SelectionTreeElement *	sel,
		int	flags
	)

Sets the flags for position keyword evaluation.

Parameters

[in,out]	sel	Selection element to initialize.
[in]	flags	Default completion flags (see PositionCalculationCollection::typeFromEnum()).

Initializes the flags for position evaluation. If called multiple times, the first setting takes effect, and later calls are neglected.

void _gmx_selelem_set_kwpos_type	(	gmx::SelectionTreeElement *	sel,
		const char *	type
	)

Sets the position type for position keyword evaluation.

Parameters

[in,out]	sel	Selection element to initialize.
[in]	type	One of the enum values acceptable for PositionCalculationCollection::typeFromEnum().

Initializes the reference position type for position evaluation. If called multiple times, the first setting takes effect, and later calls are neglected.

static void evaluate_pos	(	const gmx::SelMethodEvalContext &	context,
		gmx_ana_index_t *	,
		gmx_ana_selvalue_t *	out,
		void *	data
	)

static

Evaluates position evaluation selection methods.

See sel_updatefunc() for description of the parameters. data should point to a t_methoddata_pos.

Calculates the positions using t_methoddata_pos::pc for the index group in t_methoddata_pos::g and stores the results in out->u.p.

static void free_data_pos ( void * data )

static

Frees the data allocated for position evaluation selection methods.

Parameters

data	Data to free (should point to a `t_methoddata_pos`).

Frees the memory allocated for t_methoddata_pos::g and t_methoddata_pos::pc.

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

static

Initializes the cog selection method.

Parameters

[in]	top	Topology data structure.
[in]	npar	Not used.
[in]	param	Not used.
[in,out]	data	Should point to `t_methoddata_pos`.

Returns: 0 on success, a non-zero error code on error.

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

static

Initializes the cog selection method.

Parameters

[in]	top	Topology data structure.
[in]	npar	Not used.
[in]	param	Not used.
[in,out]	data	Should point to `t_methoddata_pos`.

Returns: 0 on success, a non-zero error code on error.

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

static

Allocates data for position evaluation selection methods.

Parameters

[in]	npar	Should be 1 or 2.
[in,out]	param	Method parameters (should point to smparams_keyword_pos or smparams_com).

Returns: Pointer to the allocated data (t_methoddata_pos).

Allocates memory for a t_methoddata_pos structure and initializes the first parameter to define the value for t_methoddata_pos::g. If a second parameter is present, it is used for setting the t_methoddata_pos::bPBC flag.

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

static

Initializes position evaluation keywords.

Parameters

[in]	top	Not used.
[in]	npar	Not used.
[in]	param	Not used.
[in,out]	data	Should point to `t_methoddata_pos`.

Returns: 0 on success, a non-zero error code on error.

The t_methoddata_pos::type field should have been initialized externally using _gmx_selelem_set_kwpos_type().

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

static

Initializes output for position evaluation selection methods.

Parameters

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

Returns: 0 for success.

static void set_pos_method_flags	(	gmx_ana_selmethod_t *	method,
		t_methoddata_pos *	d
	)

static

Updates selection method flags about required topology information.

Sets the flags to require topology and/or masses if the position calculation requires them.

static void set_poscoll_pos	(	gmx::PositionCalculationCollection *	pcc,
		void *	data
	)

static

Sets the position calculation collection for position evaluation selection methods.

Parameters

[in]	pcc	Position calculation collection to use.
[in,out]	data	Should point to `t_methoddata_pos`.

Variable Documentation

gmx_ana_selmethod_t sm_cog

Initial value:

= {
    "cog",
    POS_VALUE,
     4  |  8 ,
    asize(smparams_com),
    smparams_com,
    &init_data_pos,
    &set_poscoll_pos,
    &init_cog,
    &init_output_pos,
    &free_data_pos,
    nullptr,
    &evaluate_pos,
    nullptr,
    { "cog of ATOM_EXPR [pbc]", nullptr, 0, nullptr },
}

Selection method data for the cog method.

gmx_ana_selmethod_t sm_com

Initial value:

= {
    "com",
    POS_VALUE,
     2  |  4  |  8 ,
    asize(smparams_com),
    smparams_com,
    &init_data_pos,
    &set_poscoll_pos,
    &init_com,
    &init_output_pos,
    &free_data_pos,
    nullptr,
    &evaluate_pos,
    nullptr,
    { "com of ATOM_EXPR [pbc]", nullptr, 0, nullptr },
}

Selection method data for the com method.

gmx_ana_selmethod_t sm_keyword_pos

Initial value:

= {
    "kw_pos",
    POS_VALUE,
     4  |  16  |  128 ,
    asize(smparams_keyword_pos),
    smparams_keyword_pos,
    &init_data_pos,
    &set_poscoll_pos,
    &init_kwpos,
    &init_output_pos,
    &free_data_pos,
    nullptr,
    &evaluate_pos,
    nullptr,
    { nullptr, nullptr, 0, nullptr },
}

Selection method data for position keyword evaluation.

gmx_ana_selparam_t smparams_com[]

static

Initial value:

= {
    { "of", { GROUP_VALUE, 1, { nullptr } }, nullptr,  4  },
    { "pbc", { NO_VALUE, 0, { nullptr } }, nullptr, 0 },
}

Parameters for the cog and com selection methods.

gmx_ana_selparam_t smparams_keyword_pos[]

static

Initial value:

= {
    { nullptr, { GROUP_VALUE, 1, { nullptr } }, nullptr,  4  },
}

Parameters for position keyword evaluation.

Description

Classes

Functions

Variables

Function Documentation

Variable Documentation