ProRadialDistributionFunction computes radial distribution function (RDF). More...

#include <pro_radial_distribution_function.h>

Inheritance diagram for ProRadialDistributionFunction:

Collaboration diagram for ProRadialDistributionFunction:

Public Member Functions
	ProRadialDistributionFunction (const ElPtr &targets, const ElPtr &box)
	Constructor of ProRadialDistributionFunction class for a snapshot of simulation. More...

	ProRadialDistributionFunction (const Vec< std::pair< ElPtr, ElPtr >> &pairs)
	Constructor of ProThicknessProfile class for multiple snapshots of simulation. More...

virtual void	prepare () override
	Resize number_traj, volume_traj and counts_traj. More...

virtual void	finish () override
	Compute rdf and rdf_traj from number_traj, volume_traj and counts_traj. More...

void	set_bin (double bin_width_, int n_bins_)
	Set width and number of bins in the distance axis. Each bin is a spherical shell of which center is positioned at a reference particle. More...

void	bin_from_r_to_r_plus_dr (bool bin_from_r_=true)
	By default, the bins are [0, 0.5dr), [0.5dr, 1.5dr), ...* . If this method is called without a parameter, the bins are set as [0, dr), [dr, 2dr), ...* . More...

void	beyond_half_box_length (bool beyond_half_=true)
	Use a sample including particles of which distance from a reference particle are larger than half the simulation box length. More...

const ArrayXd	get_r_axis ()
	Get a one-dimensional array of distance, [0, dr, 2dr, ... ]*, where dr is width of a bin. More...

const ArrayXd &	get_rdf ()
	Get the radial distribution function as a one-dimensional array. More...

const Vec< ArrayXd > &	get_rdf_traj ()
	Get a sequence of radial distribution functions as list of one-dimensional arrays. More...

Public Member Functions inherited from Processor
	Processor ()=default
	Constructor of Processor class (default).

virtual bool	run ()
	Run analysis using i th Generator object in generators, where i = i_generator. More...

void	startup ()
	Startup this Processor object. More...

Protected Member Functions
virtual void	run_impl (const int index) override
	Implementation of analysis using an element of generators. More...

Protected Member Functions inherited from Processor
template<class GEN >
void	register_generator (const ShPtr< GEN > &gen)

template<class GEN >
void	register_generators (const Vec< ShPtr< GEN >> &gens)

virtual void	use_generator_at (const int i)
	Call Generator::generate_data of i th Generator object in generators. More...

virtual void	finish_using_generator_at (const int i)
	Call Generator::finish_using_generated_data of i* th Generator object in generators. More...

Protected Attributes
int	n_bins = 1

double	bin_width = 1.0

bool	bin_from_r = false

bool	beyond_half = false

ArrayXd	rdf

Vec< ArrayXd >	rdf_traj

Vec< int >	number_traj

Vec< double >	volume_traj

Vec< ArrayXi >	counts_traj

Protected Attributes inherited from Processor
int	n_generators

Vec< ShPtr< Generator > >	generators

Detailed Description

ProRadialDistributionFunction computes radial distribution function (RDF).

An object of this class makes a one-dimensional array of radial distribution function of particles (can be atoms, beads, molecules ...). Each element of the array corresponds to a ratio of local density at distance r to global density, where r is distance from a reference particle. The local density at r defined as a division of the number of particles in a spherical shell with radius of r by volume of the spherical shell.

List of radial distribution functions is also computed for a multiple snapshots of a simulation.

Note that a particle which is one of special bonds of a reference particle is excluded from a sample used for computing radial distribution function. About special bonds, please see AddSpecialBonds class.

About usage in Python, please see pybind::py_pro_radial_distribution_function.

Definition at line 37 of file pro_radial_distribution_function.h.

Constructor & Destructor Documentation

◆ ProRadialDistributionFunction() [1/2]

ProRadialDistributionFunction::ProRadialDistributionFunction	(	const ElPtr &	targets,
		const ElPtr &	box
	)

Constructor of ProRadialDistributionFunction class for a snapshot of simulation.

Parameters

targets

An Element object for particles (can be atoms, beads, molecules...).

Required property

id : integer
x : float
y : float
z : float
mass : float (for deformation)
I_xx : float (for deformation)
I_yy : float (for deformation)
I_zz : float (for deformation)
I_xy : float (for deformation)
I_xz : float (for deformation)
I_yz : float (for deformation)
special-bonds : array of integers (optional)

box

An Element object for a simulation box.

Required property

lo_x : float
lo_y : float
lo_z : float
hi_x : float
hi_y : float
hi_z : float

A GenDict object is constructed taking the targets and box, and then put into generators by register_generator.

Definition at line 20 of file pro_radial_distribution_function.cpp.

Here is the call graph for this function:

◆ ProRadialDistributionFunction() [2/2]

ProRadialDistributionFunction::ProRadialDistributionFunction ( const Vec< std::pair< ElPtr, ElPtr >> & pairs )

Constructor of ProThicknessProfile class for multiple snapshots of simulation.

Parameters

pairs

List of pairs of two Element objects: the first object is for particles and the second object is for a simulation box. If each Element object has an array data, all the array should have the same length.

Required property (first)

id : integer
x : float
y : float
z : float
mass : float (for deformation)
I_xx : float (for deformation)
I_yy : float (for deformation)
I_zz : float (for deformation)
I_xy : float (for deformation)
I_xz : float (for deformation)
I_yz : float (for deformation)
special-bonds : array of integers (optional)

Required property (second)

lo_x : float
lo_y : float
lo_z : float
hi_x : float
hi_y : float
hi_z : float

GenDict objects are constructed taking each element of the pairs, and then put into generators by register_generators.

Definition at line 30 of file pro_radial_distribution_function.cpp.

Here is the call graph for this function:

Member Function Documentation

◆ beyond_half_box_length()

void ProRadialDistributionFunction::beyond_half_box_length ( bool beyond_half_ = true )

Use a sample including particles of which distance from a reference particle are larger than half the simulation box length.

Parameters

beyond_half_ A boolean, whether to use particles beyond half the simulation box from a reference particle (default is true). This parameter is assigned to beyond_half.

Returns: None.

Definition at line 246 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ bin_from_r_to_r_plus_dr()

void ProRadialDistributionFunction::bin_from_r_to_r_plus_dr ( bool bin_from_r_ = true )

By default, the bins are [0, 0.5*dr), [0.5*dr, 1.5*dr), ... . If this method is called without a parameter, the bins are set as [0, dr), [dr, 2*dr), ... .

Parameters

bin_from_r_ A boolean, whether to use bin of which inner radius is r and outer radius is r+dr (default is true). This parameter is assigned to bin_from_r.

Returns: None.

Definition at line 238 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ finish()

void ProRadialDistributionFunction::finish ( )

overridevirtual

Compute rdf and rdf_traj from number_traj, volume_traj and counts_traj.

Returns: None.

Note that rdf and an average over elements in rdf_traj are identical only when volume of the simulation box and the number of particles are unchanged during the simulation.

Reimplemented from Processor.

Reimplemented in ProRadialDistributionFunctionWithDeformation.

Definition at line 172 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ get_r_axis()

const ArrayXd ProRadialDistributionFunction::get_r_axis ( )

Get a one-dimensional array of distance, [0, dr, 2*dr, ... ], where dr is width of a bin.

Returns: ArrayXd (Numpy-Array in Python).

Definition at line 254 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ get_rdf()

const ArrayXd & ProRadialDistributionFunction::get_rdf ( )

Get the radial distribution function as a one-dimensional array.

Returns: rdf.

Definition at line 268 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ get_rdf_traj()

const Vec< ArrayXd > & ProRadialDistributionFunction::get_rdf_traj ( )

Get a sequence of radial distribution functions as list of one-dimensional arrays.

Returns: rdf_traj.

Definition at line 275 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ prepare()

void ProRadialDistributionFunction::prepare ( )

overridevirtual

Resize number_traj, volume_traj and counts_traj.

Returns: None.

Reimplemented from Processor.

Reimplemented in ProRadialDistributionFunctionWithDeformation.

Definition at line 163 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

◆ run_impl()

void ProRadialDistributionFunction::run_impl ( const int index )

overrideprotectedvirtual

Implementation of analysis using an element of generators.

Parameters

index An index in generators for a Generator object to be analyzed.

Returns: None.

To be compatible with multithreading computation, class members should not be modified in this method. If modification of some members is necessary, please consider defining them as Vec, and modifying only their i th element, where i = index.

I am sorry to say that the best documentation for this method is its source code...

Implements Processor.

Reimplemented in ProRadialDistributionFunctionWithDeformation.

Definition at line 46 of file pro_radial_distribution_function.cpp.

Here is the call graph for this function:

◆ set_bin()

void ProRadialDistributionFunction::set_bin	(	double	bin_width_,
		int	n_bins_
	)

Set width and number of bins in the distance axis. Each bin is a spherical shell of which center is positioned at a reference particle.

Parameters

bin_width_	Width of a bin. This parameter is assigned to bin_width.
n_bins_	Number of bins. This parameter is assigned to n_bins.

Returns: None.

Definition at line 228 of file pro_radial_distribution_function.cpp.

Here is the caller graph for this function:

Member Data Documentation

◆ beyond_half

bool ProRadialDistributionFunction::beyond_half = false

protected

If this member is false (default), a particle of which distance from a reference particle are larger than half the simulation box length is excluded from a sample used for computing radial distribution function. Such particles can be included in the sample for a case of small simulation box.

Definition at line 68 of file pro_radial_distribution_function.h.

◆ bin_from_r

bool ProRadialDistributionFunction::bin_from_r = false

protected

If this member is true, the bins are [0, dr), [dr, 2*dr), ..., [(n_bins-1)*dr, n_bins*dr). If this member is false, the bins are [0, 0.5*dr), [0.5*dr, 1.5*dr), ..., [(n_bins-1.5)*dr, (n_bins-0.5)*dr). Default is false.

Definition at line 59 of file pro_radial_distribution_function.h.

◆ bin_width

double ProRadialDistributionFunction::bin_width = 1.0

protected

Width of a bin. The maximum distance in a domain, where the radial distribution function is computed, is given as a product of n_bins (if bin_from_r is true) and bin_width.

Definition at line 52 of file pro_radial_distribution_function.h.

◆ counts_traj

Vec<ArrayXi> ProRadialDistributionFunction::counts_traj

protected

List consisting of temporary numbers of particles in a spherical shell with radius of r, where r is distance from a reference particle. Indices in this list corresponds those in generators.

Definition at line 94 of file pro_radial_distribution_function.h.

◆ n_bins

int ProRadialDistributionFunction::n_bins = 1

protected

Number of bins in the distance axis. The maximum distance in a domain, where the radial distribution function is computed, is given as a product of n_bins (if bin_from_r is true) and bin_width.

Definition at line 45 of file pro_radial_distribution_function.h.

◆ number_traj

Vec<int> ProRadialDistributionFunction::number_traj

protected

List consisting of temporary numbers of particles. Indices in this list corresponds those in generators.

Definition at line 82 of file pro_radial_distribution_function.h.

◆ rdf

ArrayXd ProRadialDistributionFunction::rdf

protected

A one-dimensional array of the radial distribution function.

Definition at line 72 of file pro_radial_distribution_function.h.

◆ rdf_traj

Vec<ArrayXd> ProRadialDistributionFunction::rdf_traj

protected

List consisting of temporary radial distribution functions. Indices in this list corresponds those in generators.

Definition at line 77 of file pro_radial_distribution_function.h.

◆ volume_traj

Vec<double> ProRadialDistributionFunction::volume_traj

protected

List consisting of temporary volumes of the simulation box. Indices in this list corresponds those in generators.

Definition at line 87 of file pro_radial_distribution_function.h.

The documentation for this class was generated from the following files:

src/processors/pro_radial_distribution_function.h
src/processors/pro_radial_distribution_function.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProRadialDistributionFunction() [1/2]

◆ ProRadialDistributionFunction() [2/2]

Member Function Documentation

◆ beyond_half_box_length()

◆ bin_from_r_to_r_plus_dr()

◆ finish()

◆ get_r_axis()

◆ get_rdf()

◆ get_rdf_traj()

◆ prepare()

◆ run_impl()

◆ set_bin()

Member Data Documentation

◆ beyond_half

◆ bin_from_r

◆ bin_width

◆ counts_traj

◆ n_bins

◆ number_traj

◆ rdf

◆ rdf_traj

◆ volume_traj