sm_distance.cpp File Reference

#include "gmxpre.h"
#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selparam.h"
#include "gromacs/selection/selvalue.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/real.h"
#include "selmethod.h"
#include "selmethod_impl.h"

Include dependency graph for sm_distance.cpp:

Description

Implements distance-based selection methods.

This file implements the distance, mindistance and within selection methods.

Author

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

Classes
struct	t_methoddata_distance
	Data structure for distance-based selection method. More...

Functions
static void *	init_data_common (int npar, gmx_ana_selparam_t *param)
	Allocates data for distance-based selection methods. More...
static void	init_common (const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data)
	Initializes a distance-based selection method. More...
static void	free_data_common (void *data)
	Frees the data allocated for a distance-based selection method. More...
static void	init_frame_common (const gmx::SelMethodEvalContext &context, void *data)
	Initializes the evaluation of a distance-based within selection method for a frame. More...
static void	evaluate_distance (const gmx::SelMethodEvalContext &, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
	Evaluates the distance selection method. More...
static void	evaluate_within (const gmx::SelMethodEvalContext &, gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
	Evaluates the within selection method. More...

Variables
static gmx_ana_selparam_t	smparams_distance []
	Parameters for the distance selection method. More...
static gmx_ana_selparam_t	smparams_mindistance []
	Parameters for the mindistance selection method. More...
static gmx_ana_selparam_t	smparams_within []
	Parameters for the within selection method. More...
static const char	helptitle_distance [] = "Selecting based on distance"
	Help title for distance selection methods.
static const char *const	help_distance []
	Help text for distance selection methods. More...
gmx_ana_selmethod_t	sm_distance
	Selection method data for the distance method. More...
gmx_ana_selmethod_t	sm_mindistance
	Selection method data for the distance method. More...
gmx_ana_selmethod_t	sm_within
	Selection method data for the within method. More...

Function Documentation

static void evaluate_distance ( const gmx::SelMethodEvalContext &  , gmx_ana_pos_t *  pos, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the distance selection method.

See sel_updatefunc_pos() for description of the parameters. data should point to a t_methoddata_distance.

Calculates the distance of each position from t_methoddata_distance::p and puts them in out->u.r.

static void evaluate_within ( const gmx::SelMethodEvalContext &  , gmx_ana_pos_t *  pos, gmx_ana_selvalue_t *  out, void *  data  )

static

Evaluates the within selection method.

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

Finds the atoms that are closer than the defined cutoff to t_methoddata_distance::xref and puts them in out.g.

static void free_data_common ( void *  data )

static

Frees the data allocated for a distance-based selection method.

Parameters

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

Frees the memory allocated for t_methoddata_distance::xref and t_methoddata_distance::nb.

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

static

Initializes a distance-based selection method.

Parameters

top	Not used.
npar	Not used (should be 2).
param	Method parameters (should point to one of the distance parameter arrays).
data	Pointer to t_methoddata_distance to initialize.

Returns

0 on success, a non-zero error code on failure.

Initializes the neighborhood search data structure (t_methoddata_distance::nb). Also checks that the cutoff is valid.

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

static

Allocates data for distance-based selection methods.

Parameters

[in]	npar	Not used (should be 2).
[in,out]	param	Method parameters (should point to one of the distance parameter arrays).

Returns

Pointer to the allocated data (t_methoddata_distance).

Allocates memory for a t_methoddata_distance structure and initializes the parameter as follows:

• the first parameter defines the value for t_methoddata_distance::cutoff.
• the second parameter defines the reference positions and the value is stored in t_methoddata_distance::p.

static void init_frame_common ( const gmx::SelMethodEvalContext &  context, void *  data  )

static

Initializes the evaluation of a distance-based within selection method for a frame.

Parameters

[in]	context	Evaluation context.
	data	Should point to a t_methoddata_distance.

Returns

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

Initializes the neighborhood search for the current frame.

Variable Documentation

const char* const help_distance[]

static

Initial value:

= {
    "::",
    "",
    "  distance from POS [cutoff REAL]",
    "  mindistance from POS_EXPR [cutoff REAL]",
    "  within REAL of POS_EXPR",
    "",
    "[TT]distance[tt] and [TT]mindistance[tt] calculate the distance from the",
    "given position(s), the only difference being in that [TT]distance[tt]",
    "only accepts a single position, while any number of positions can be",
    "given for [TT]mindistance[tt], which then calculates the distance to the",
    "closest position.",
    "[TT]within[tt] directly selects atoms that are within [TT]REAL[tt] of",
    "[TT]POS_EXPR[tt].[PAR]",

    "For the first two keywords, it is possible to specify a cutoff to speed",
    "up the evaluation: all distances above the specified cutoff are",
    "returned as equal to the cutoff.",
}

Help text for distance selection methods.

gmx_ana_selmethod_t sm_distance

Initial value:

= {
    "distance",
    REAL_VALUE,
     4 ,
    asize(smparams_distance),
    smparams_distance,
    &init_data_common,
    nullptr,
    &init_common,
    nullptr,
    &free_data_common,
    &init_frame_common,
    nullptr,
    &evaluate_distance,
    { "distance from POS [cutoff REAL]", helptitle_distance, asize(help_distance), help_distance },
}

Selection method data for the distance method.

gmx_ana_selmethod_t sm_mindistance

Initial value:

= {
    "mindistance",
    REAL_VALUE,
     4 ,
    asize(smparams_mindistance),
    smparams_mindistance,
    &init_data_common,
    nullptr,
    &init_common,
    nullptr,
    &free_data_common,
    &init_frame_common,
    nullptr,
    &evaluate_distance,
    { "mindistance from POS_EXPR [cutoff REAL]", helptitle_distance, asize(help_distance), help_distance },
}

Selection method data for the distance method.

gmx_ana_selmethod_t sm_within

Initial value:

= {
    "within",
    GROUP_VALUE,
     4 ,
    asize(smparams_within),
    smparams_within,
    &init_data_common,
    nullptr,
    &init_common,
    nullptr,
    &free_data_common,
    &init_frame_common,
    nullptr,
    &evaluate_within,
    { "within REAL of POS_EXPR", helptitle_distance, asize(help_distance), help_distance },
}

Selection method data for the within method.

gmx_ana_selparam_t smparams_distance[]

static

Initial value:

= {
    { "cutoff", { REAL_VALUE, 1, { nullptr } }, nullptr,  2  },
    { "from", { POS_VALUE, 1, { nullptr } }, nullptr,  4  },
}

Parameters for the distance selection method.

gmx_ana_selparam_t smparams_mindistance[]

static

Initial value:

= {
    { "cutoff", { REAL_VALUE, 1, { nullptr } }, nullptr,  2  },
    { "from", { POS_VALUE, -1, { nullptr } }, nullptr,  4  |  16  },
}

Parameters for the mindistance selection method.

gmx_ana_selparam_t smparams_within[]

static

Initial value:

= {
    { nullptr, { REAL_VALUE, 1, { nullptr } }, nullptr, 0 },
    { "of", { POS_VALUE, -1, { nullptr } }, nullptr,  4  |  16  },
}

Parameters for the within selection method.