ProThicknessProfile computes thickness profile of a film consisting of particles (can be atoms, beads, molecules...). More...

#include <pro_thickness_profile.h>

Inheritance diagram for ProThicknessProfile:

Collaboration diagram for ProThicknessProfile:

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

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

virtual void	prepare () override
	Resize conditions and profiles. More...

void	set_grid (int nx_, int ny_)
	Specify the number of grids in the x and y directions. More...

void	set_offset (double offset_)
	Specify the offset for thickness (height). More...

void	shift_half_delta (bool shift_half_=true)
	Increment coordinates of the grid points by half the grid width. By default, grids in the x direction are set as x_0, x_0+dx, x_0+2dx, ...* , where x_0 is the minimum x coordinate in the simulation box and dx is the grid width. If this method is called without a parameter, the grids are set as x_0+0.5dx, x_0+1.5dx, x_0+2.5dx, ...* . More...

const Vec< Json > &	get_conditions ()
	Get computation conditions (origin of computed area, grid width and the number of grads) used by this object as list of dictionary. More...

const Vec< ArrayXXd > &	get_profiles ()
	Get a sequence of two-dimensional profile of film thickness as list of two-dimensional arrays. Row and column of each array is for the x and y direction, respectively. More...

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

virtual void	finish ()
	Finish analysis. More...

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...

Private Attributes
int	nx = 1

int	ny = 1

bool	shift_half = false

double	offset = 0.0

Vec< Json >	conditions

Vec< ArrayXXd >	profiles

Additional Inherited Members
Protected Attributes inherited from Processor
int	n_generators

Vec< ShPtr< Generator > >	generators

Detailed Description

ProThicknessProfile computes thickness profile of a film consisting of particles (can be atoms, beads, molecules...).

An object of this class makes list of two-dimensional arrays: each array is a two-dimensional profile of film thickness for each snapshot of the simulation. Row and column of each array is for the x and y direction, respectively. The thickness is measured in the z direction.

Note that each particle is assumed to have a radius, and an excluded volume defined by the radius. Film thickness at point of (x, y) is defined as the highest z* coordinate inside excluded volume of any of the particles.

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

Definition at line 32 of file pro_thickness_profile.h.

Constructor & Destructor Documentation

◆ ProThicknessProfile() [1/2]

ProThicknessProfile::ProThicknessProfile	(	const ElPtr &	atoms,
		const ElPtr &	box
	)

Constructor of ProThicknessProfile class for a snapshot of simulation.

Parameters

atoms

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

Required property

x : float
y : float
z : float
radius : float

box

An Element object for a simulation box.

Required property

lo_x : float
lo_y : float
hi_x : float
hi_y : float

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

Definition at line 13 of file pro_thickness_profile.cpp.

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◆ ProThicknessProfile() [2/2]

ProThicknessProfile::ProThicknessProfile ( 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 forming a film 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)

x : float
y : float
z : float
radius : float

Required property (second)

lo_x : float
lo_y : float
hi_x : float
hi_y : float

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

Definition at line 23 of file pro_thickness_profile.cpp.

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Member Function Documentation

◆ get_conditions()

const Vec< Json > & ProThicknessProfile::get_conditions ( )

Get computation conditions (origin of computed area, grid width and the number of grads) used by this object as list of dictionary.

Returns: conditions.

Definition at line 174 of file pro_thickness_profile.cpp.

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◆ get_profiles()

const Vec< ArrayXXd > & ProThicknessProfile::get_profiles ( )

Get a sequence of two-dimensional profile of film thickness as list of two-dimensional arrays. Row and column of each array is for the x and y direction, respectively.

Returns: profiles.

Definition at line 181 of file pro_thickness_profile.cpp.

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◆ prepare()

void ProThicknessProfile::prepare ( )

overridevirtual

Resize conditions and profiles.

Returns: None.

Reimplemented from Processor.

Definition at line 140 of file pro_thickness_profile.cpp.

◆ run_impl()

void ProThicknessProfile::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.

Definition at line 39 of file pro_thickness_profile.cpp.

◆ set_grid()

void ProThicknessProfile::set_grid	(	int	nx_,
		int	ny_
	)

Specify the number of grids in the x and y directions.

Parameters

nx_	The number of grids in the x direction. This parameter is assigned to nx.
ny_	The number of grids in the y direction. This parameter is assigned to ny.

Returns: None.

Definition at line 148 of file pro_thickness_profile.cpp.

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◆ set_offset()

void ProThicknessProfile::set_offset ( double offset_ )

Specify the offset for thickness (height).

Parameters

offset_ Film thickness is calculated after subtracting this value from z coordinate of particles. This parameter is assigned to offset.

Returns: None.

Definition at line 158 of file pro_thickness_profile.cpp.

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◆ shift_half_delta()

void ProThicknessProfile::shift_half_delta ( bool shift_half_ = true )

Increment coordinates of the grid points by half the grid width. By default, grids in the x direction are set as x_0, x_0+dx, x_0+2*dx, ... , where x_0 is the minimum x coordinate in the simulation box and dx is the grid width. If this method is called without a parameter, the grids are set as x_0+0.5*dx, x_0+1.5*dx, x_0+2.5*dx, ... .

Parameters

shift_half_ A boolean, whether to shift the grid points or not (default is true). This parameter is assigned to shift_half.

Returns: None.

Definition at line 166 of file pro_thickness_profile.cpp.

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Member Data Documentation

◆ conditions

Vec<Json> ProThicknessProfile::conditions

private

Computation conditions (origin of computed area, grid width and the number of grads) used by this object are stored here. If the simulation box is unchanged during the simulation, every element of this member is identical.

Definition at line 63 of file pro_thickness_profile.h.

◆ nx

int ProThicknessProfile::nx = 1

private

The number of grids in x direction.

Definition at line 36 of file pro_thickness_profile.h.

◆ ny

int ProThicknessProfile::ny = 1

private

The number of grids in y direction.

Definition at line 40 of file pro_thickness_profile.h.

◆ offset

double ProThicknessProfile::offset = 0.0

private

Calculate film thickness after subtracting a value of this member from z coordinate of the particles. Default is 0.

Definition at line 56 of file pro_thickness_profile.h.

◆ profiles

Vec<ArrayXXd> ProThicknessProfile::profiles

private

Time series (if a simulation trajectory is used as an input) of two-dimensional profile of film thickness. Indices in this list corresponds those in generators.

Definition at line 69 of file pro_thickness_profile.h.

◆ shift_half

bool ProThicknessProfile::shift_half = false

private

Whether to shift grids at which film thickness is computed. If this member is false, grids in the x direction are set as x_0, x_0+dx, x_0+2*dx, ..., x_0+(nx-1)*dx, where x_0 is the minimum x coordinate in the simulation box and dx is the grid width. If this member is true, grids in the x direction are set as x_0+0.5*dx, x_0+1.5*dx, x_0+2.5*dx, ..., x_0+(nx-0.5)*dx. Default is false.

Definition at line 51 of file pro_thickness_profile.h.

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

src/processors/pro_thickness_profile.h
src/processors/pro_thickness_profile.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProThicknessProfile() [1/2]

◆ ProThicknessProfile() [2/2]

Member Function Documentation

◆ get_conditions()

◆ get_profiles()

◆ prepare()

◆ run_impl()

◆ set_grid()

◆ set_offset()

◆ shift_half_delta()

Member Data Documentation

◆ conditions

◆ nx

◆ ny

◆ offset

◆ profiles

◆ shift_half