#include "gmxpre.h"
#include <cmath>
#include <algorithm>
#include <memory>
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selection.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 "gromacs/utility/smalloc.h"
#include "gromacs/utility/vec.h"
#include "gromacs/utility/vectypes.h"
#include "selelem.h"
#include "selmethod.h"
#include "selmethod_impl.h"

Include dependency graph for sm_insolidangle.cpp:

Description

Implements the insolidangle selection method.

Todo:: The implementation could be optimized quite a bit.

Todo:: Move the covered fraction stuff somewhere else and make it more generic (along the lines it is handled in selection.h and trajana.h in the old C API).

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

Classes
struct	t_partition_item
	Internal data structure for the `insolidangle` selection method. More...

struct	partition
	Internal data structure for the `insolidangle` selection method. More...

struct	spheresurfacebin
	Internal data structure for the `insolidangle` selection method. More...

struct	methoddata_insolidangle
	Data structure for the `insolidangle` selection method. More...

Typedefs
typedef struct partition	t_partition
	Internal data structure for the `insolidangle` selection method. More...

typedef struct spheresurfacebin	t_spheresurfacebin
	Internal data structure for the `insolidangle` selection method. More...

typedef struct methoddata_insolidangle	t_methoddata_insolidangle
	Data structure for the `insolidangle` selection method. More...

Functions
static void *	init_data_insolidangle (int npar, gmx_ana_selparam_t *param)
	Allocates data for the `insolidangle` selection method. More...

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

static void	free_data_insolidangle (void *data)
	Frees the data allocated for the `insolidangle` selection method. More...

static void	init_frame_insolidangle (const gmx::SelMethodEvalContext &context, void *data)
	Initializes the evaluation of the `insolidangle` selection method for a frame. More...

static bool	accept_insolidangle (rvec x, const t_pbc pbc, void data)
	Internal helper function for evaluate_insolidangle(). More...

static void	evaluate_insolidangle (const gmx::SelMethodEvalContext &context, gmx_ana_pos_t pos, gmx_ana_selvalue_t out, void *data)
	Evaluates the `insolidangle` selection method. More...

static real	sph_distc (rvec x1, rvec x2)
	Calculates the distance between unit vectors. More...

static int	find_partition_bin (t_partition *p, real value)
	Does a binary search on a `t_partition` to find a bin for a value. More...

static int	find_surface_bin (t_methoddata_insolidangle *surf, rvec x)
	Finds a bin that corresponds to a location on the unit sphere surface. More...

static void	clear_surface_points (t_methoddata_insolidangle *surf)
	Clears/initializes the bins on the unit sphere surface. More...

static void	free_surface_points (t_methoddata_insolidangle *surf)
	Frees memory allocated for storing the reference points in the surface bins. More...

static void	add_surface_point (t_methoddata_insolidangle *surf, int tbin, int pbin, rvec x)
	Adds a reference point to a given bin. More...

static void	mark_surface_covered (t_methoddata_insolidangle *surf, int tbin, int pbin)
	Marks a bin as completely covered. More...

static void	update_surface_bin (t_methoddata_insolidangle *surf, int tbin, real phi, real pdelta1, real pdelta2, real pdeltamax, rvec x)
	Helper function for store_surface_point() to update a single zenith angle bin. More...

static void	store_surface_point (t_methoddata_insolidangle *surf, rvec x)
	Adds a single reference point and updates the surface bins. More...

static void	optimize_surface_points (t_methoddata_insolidangle *surf)
	Optimizes the surface bins for faster searching. More...

static real	estimate_covered_fraction (t_methoddata_insolidangle *surf)
	Estimates the area covered by the reference cones. More...

static bool	is_surface_covered (t_methoddata_insolidangle *surf, rvec x)
	Checks whether a point lies within a solid angle. More...

bool	_gmx_selelem_can_estimate_cover (const gmx::SelectionTreeElement &sel)
	Returns true if the covered fraction of the selection can be calculated. More...

real	_gmx_selelem_estimate_coverfrac (const gmx::SelectionTreeElement &sel)
	Returns the covered fraction of the selection for the current frame. More...

Variables
static gmx_ana_selparam_t	smparams_insolidangle []
	Parameters for the `insolidangle` selection method. More...

static const char *const	help_insolidangle []
	Help text for the `insolidangle` selection method. More...

gmx_ana_selmethod_t	sm_insolidangle
	Selection method data for the `insolidangle` method. More...

Function Documentation

bool _gmx_selelem_can_estimate_cover ( const gmx::SelectionTreeElement & sel )

Returns true if the covered fraction of the selection can be calculated.

Parameters

[in] sel Selection element to query.

Returns: true if the covered fraction can be estimated for sel with _gmx_selelem_estimate_coverfrac(), false otherwise.

real _gmx_selelem_estimate_coverfrac ( const gmx::SelectionTreeElement & sel )

Returns the covered fraction of the selection for the current frame.

Parameters

[in] sel Selection for which the fraction should be calculated.

Returns: Fraction of angles covered by the selection (between zero and one).

The return value is undefined if _gmx_selelem_can_estimate_cover() returns false. Should be called after gmx_ana_evaluate_selections() has been called for the frame.

static bool accept_insolidangle	(	rvec	x,
		const t_pbc *	pbc,
		void *	data
	)

static

Internal helper function for evaluate_insolidangle().

Parameters

[in]	x	Test point.
[in]	pbc	PBC data (if NULL, no PBC are used).
[in]	data	Pointer to a `t_methoddata_insolidangle` data structure.

Returns: true if x is within the solid angle, false otherwise.

static void add_surface_point	(	t_methoddata_insolidangle *	surf,
		int	tbin,
		int	pbin,
		rvec	x
	)

static

Adds a reference point to a given bin.

Parameters

[in,out]	surf	Surface data structure.
[in]	tbin	Bin number in the zenith angle direction.
[in]	pbin	Bin number in the azimuthal angle direction.
[in]	x	Point to store.

static void clear_surface_points ( t_methoddata_insolidangle * surf )

static

Clears/initializes the bins on the unit sphere surface.

Parameters

[in,out] surf Surface data structure.

Clears the reference points from the bins and (re)initializes the edges of the azimuthal bins.

static real estimate_covered_fraction ( t_methoddata_insolidangle * surf )

static

Estimates the area covered by the reference cones.

Parameters

[in] surf Surface data structure.

Returns: An estimate for the area covered by the reference points.

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

static

Evaluates the insolidangle selection method.

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

Calculates which atoms in g are within the solid angle spanned by t_methoddata_insolidangle::span and centered at t_methoddata_insolidangle::center, and stores the result in out->u.g.

static int find_partition_bin	(	t_partition *	p,
		real	value
	)

static

Does a binary search on a t_partition to find a bin for a value.

Parameters

[in]	p	Partition to search.
[in]	value	Value to search for.

Returns: The partition index in p that contains value.

If value is outside the range of p, the first/last index is returned. Otherwise, the return value i satisfies p->p[i].left<=value and p->p[i+1].left>value

static int find_surface_bin	(	t_methoddata_insolidangle *	surf,
		rvec	x
	)

static

Finds a bin that corresponds to a location on the unit sphere surface.

Parameters

[in]	surf	Surface data structure to search.
[in]	x	Unit vector to find.

Returns: The bin index that contains x.

The return value is an index to the surf->bin array.

static void free_data_insolidangle ( void * data )

static

Frees the data allocated for the insolidangle selection method.

Parameters

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

Frees the memory allocated for t_methoddata_insolidangle::center and t_methoddata_insolidangle::span, as well as the memory for the internal bin structure.

static void free_surface_points ( t_methoddata_insolidangle * surf )

static

Frees memory allocated for storing the reference points in the surface bins.

Parameters

[in,out] surf Surface data structure.

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

static

Allocates data for the insolidangle selection method.

Parameters

[in]	npar	Not used (should be 3).
[in,out]	param	Method parameters (should point to smparams_insolidangle).

Returns: Pointer to the allocated data (t_methoddata_insolidangle).

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

center defines the value for t_methoddata_insolidangle::center.
span defines the value for t_methoddata_insolidangle::span.
cutoff defines the value for t_methoddata_insolidangle::angcut.

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

static

Initializes the evaluation of the insolidangle selection method for a frame.

Parameters

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

Creates a lookup structure that enables fast queries of whether a point is within the solid angle or not.

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

static

Initializes the insolidangle selection method.

Parameters

top	Not used.
npar	Not used.
param	Not used.
data	Pointer to t_methoddata_insolidangle to initialize.

Converts t_methoddata_insolidangle::angcut to radians and allocates and allocates memory for the bins used during the evaluation.

static bool is_surface_covered	(	t_methoddata_insolidangle *	surf,
		rvec	x
	)

static

Checks whether a point lies within a solid angle.

Parameters

[in]	surf	Surface data structure to search.
[in]	x	Unit vector to check.

Returns: true if x is within the solid angle, false otherwise.

static void mark_surface_covered	(	t_methoddata_insolidangle *	surf,
		int	tbin,
		int	pbin
	)

static

Marks a bin as completely covered.

Parameters

[in,out]	surf	Surface data structure.
[in]	tbin	Bin number in the zenith angle direction.
[in]	pbin	Bin number in the azimuthal angle direction.

static void optimize_surface_points ( t_methoddata_insolidangle * surf )

static

Optimizes the surface bins for faster searching.

Parameters

[in,out] surf Surface data structure.

Currently, this function does nothing.

static real sph_distc	(	rvec	x1,
		rvec	x2
	)

static

Calculates the distance between unit vectors.

Parameters

[in]	x1	Unit vector 1.
[in]	x2	Unit vector 2.

Returns: Minus the dot product of x1 and x2.

This function is used internally to calculate the distance between the unit vectors x1 and x2 to find out whether x2 is within the cone centered at x1. Currently, the cosine of the angle is used for efficiency, and the minus is there to make it behave like a normal distance (larger values mean longer distances).

static void store_surface_point	(	t_methoddata_insolidangle *	surf,
		rvec	x
	)

static

Adds a single reference point and updates the surface bins.

Parameters

[in,out]	surf	Surface data structure.
[in]	x	Point to store (should have unit length).

Finds all the bins covered by the cone centered at x and calls update_surface_bin() to update them.

static void update_surface_bin	(	t_methoddata_insolidangle *	surf,
		int	tbin,
		real	phi,
		real	pdelta1,
		real	pdelta2,
		real	pdeltamax,
		rvec	x
	)

static

Helper function for store_surface_point() to update a single zenith angle bin.

Parameters

[in,out]	surf	Surface data structure.
[in]	tbin	Bin number in the zenith angle direction.
[in]	phi	Azimuthal angle of `x`.
[in]	pdelta1	Width of the cone at the lower edge of `tbin`.
[in]	pdelta2	Width of the cone at the uppper edge of `tbin`.
[in]	pdeltamax	Max. width of the cone inside `tbin`.
[in]	x	Point to store (should have unit length).

Variable Documentation

const char* const help_insolidangle[]

static

Initial value:

= {
    "::",
    "",
    "  insolidangle center POS span POS_EXPR [cutoff REAL]",
    "",
    "This keyword selects atoms that are within [TT]REAL[tt] degrees",
    "(default=5) of any position in [TT]POS_EXPR[tt] as seen from [TT]POS[tt]",
    "a position expression that evaluates to a single position), i.e., atoms",
    "in the solid angle spanned by the positions in [TT]POS_EXPR[tt] and",
    "centered at [TT]POS[tt].[PAR]",
    "Technically, the solid angle is constructed as a union of small cones",
    "whose tip is at [TT]POS[tt] and the axis goes through a point in",
    "[TT]POS_EXPR[tt]. There is such a cone for each position in",
    "[TT]POS_EXPR[tt], and point is in the solid angle if it lies within any",
    "of these cones. The cutoff determines the width of the cones.",
}

Help text for the insolidangle selection method.

gmx_ana_selmethod_t sm_insolidangle

Initial value:

= {
    "insolidangle",
    GROUP_VALUE,
     4 ,
    asize(smparams_insolidangle),
    smparams_insolidangle,
    &init_data_insolidangle,
    nullptr,
    &init_insolidangle,
    nullptr,
    &free_data_insolidangle,
    &init_frame_insolidangle,
    nullptr,
    &evaluate_insolidangle,
    { "insolidangle center POS span POS_EXPR [cutoff REAL]",
      "Selecting atoms in a solid angle",
      asize(help_insolidangle),
      help_insolidangle },
}

Selection method data for the insolidangle method.

gmx_ana_selparam_t smparams_insolidangle[]

static

Initial value:

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

Parameters for the insolidangle selection method.

Description

Classes

Typedefs

Functions

Variables

Function Documentation

Variable Documentation