ProMeanSquareDisplacement computes mean square displacement (MSD). More...

#include <pro_mean_square_displacement.h>

Inheritance diagram for ProMeanSquareDisplacement:

Collaboration diagram for ProMeanSquareDisplacement:

Public Member Functions
	ProMeanSquareDisplacement (const Vec< ElPtr > &elems)
	Constructor of ProMeanSquareDisplacement class. More...

virtual void	prepare () override
	Set initial positions and resize displacement2_traj. More...

virtual void	finish () override
	Fill displacement2_array with values of displacement2_traj, and calculate mean_square_displacement by averaging over columns of displacement2_array. More...

void	set_dimension (bool include_x, bool include_y, bool include_z)
	Specify dimensions to be considered. By default, the mean square displacement is computed in three dimensions. To compute the mean square displacement in xy place, for example, the third parameter of this method must be set to `false`. More...

void	without_drift_correction (bool without_drift_correction_=true)
	Disable to correct a drift of center of mass of the simulation system. More...

const ArrayXXd &	get_displacement2_array ()
	Get computed time series of squared displacements from initial position for each target as a two-dimensional array: each row corresponds to each snapshot of the simulation and each column corresponds to each target. More...

const ArrayXd &	get_mean_square_displacement ()
	Get time series of the mean square displacement as a one-dimensional array. Each element of the array corresponds to each snapshot of the simulation. 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...

Private Member Functions
void	extract_positions (ArrayXXd &positions, const ElPtr &elem)
	Extract position vectors from an Element object. More...

Private Attributes
bool	drift_correction = true

Vec< bool >	dimension = {true, true, true}

ArrayXXd	initial_rs

Vec< RowArrayXd >	displacement2_traj

ArrayXXd	displacement2_array

ArrayXd	mean_square_displacement

Additional Inherited Members
Protected Attributes inherited from Processor
int	n_generators

Vec< ShPtr< Generator > >	generators

Detailed Description

ProMeanSquareDisplacement computes mean square displacement (MSD).

An object of this class makes a two-dimensional array of squared displacements from initial position for each target (can be an atom, bead, molecule...) over a simulation trajectory. Each row of the array corresponds to each snapshot of a simulation, and each column of the array corresponds to each target. By averaging over columns of the array, the object of this class also makes a one-dimensional array for the mean square displacement.

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

Definition at line 29 of file pro_mean_square_displacement.h.

Constructor & Destructor Documentation

◆ ProMeanSquareDisplacement()

ProMeanSquareDisplacement::ProMeanSquareDisplacement ( const Vec< ElPtr > & elems )

Constructor of ProMeanSquareDisplacement class.

Parameters

elems

List of Element objects for atoms, beads, molecules... If each Element object has an array data, all the array should have the same length.

Required property

id : integer
xu : float
yu : float
zu : float
mass : float (for drift correction)

Element objects in the elems are put into generators by register_generators.

Definition at line 16 of file pro_mean_square_displacement.cpp.

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Member Function Documentation

◆ extract_positions()

void ProMeanSquareDisplacement::extract_positions	(	ArrayXXd &	positions,
		const ElPtr &	elem
	)

private

Extract position vectors from an Element object.

Parameters

positions	Mutable reference of a two-dimensional array whose rows are position vectors.
elem	This method extracts position vectors from this Element object.

Returns: None.

Definition at line 24 of file pro_mean_square_displacement.cpp.

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◆ finish()

void ProMeanSquareDisplacement::finish ( )

overridevirtual

Fill displacement2_array with values of displacement2_traj, and calculate mean_square_displacement by averaging over columns of displacement2_array.

Returns: None.

Each row of displacement2_array corresponds to each element of displacement2_traj.

Reimplemented from Processor.

Definition at line 82 of file pro_mean_square_displacement.cpp.

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◆ get_displacement2_array()

const ArrayXXd & ProMeanSquareDisplacement::get_displacement2_array ( )

Get computed time series of squared displacements from initial position for each target as a two-dimensional array: each row corresponds to each snapshot of the simulation and each column corresponds to each target.

Returns: displacement2_array.

Definition at line 127 of file pro_mean_square_displacement.cpp.

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◆ get_mean_square_displacement()

const ArrayXd & ProMeanSquareDisplacement::get_mean_square_displacement ( )

Get time series of the mean square displacement as a one-dimensional array. Each element of the array corresponds to each snapshot of the simulation.

Returns: mean_square_displacement.

Definition at line 134 of file pro_mean_square_displacement.cpp.

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◆ prepare()

void ProMeanSquareDisplacement::prepare ( )

overridevirtual

Set initial positions and resize displacement2_traj.

Returns: None.

Reimplemented from Processor.

Definition at line 71 of file pro_mean_square_displacement.cpp.

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◆ run_impl()

void ProMeanSquareDisplacement::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 48 of file pro_mean_square_displacement.cpp.

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◆ set_dimension()

void ProMeanSquareDisplacement::set_dimension	(	bool	include_x,
		bool	include_y,
		bool	include_z
	)

Specify dimensions to be considered. By default, the mean square displacement is computed in three dimensions. To compute the mean square displacement in xy place, for example, the third parameter of this method must be set to false.

Parameters

include_x	A boolean, whether component in the x direction is included in squared displacement. This parameter is stored as the first element of dimension.
include_y	A boolean, whether component in the y direction is included in squared displacement. This parameter is stored as the second element of dimension.
include_z	A boolean, whether component in the z direction is included in squared displacement. This parameter is stored as the third element of dimension.

Returns: None.

Definition at line 109 of file pro_mean_square_displacement.cpp.

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◆ without_drift_correction()

void ProMeanSquareDisplacement::without_drift_correction ( bool without_drift_correction_ = true )

Disable to correct a drift of center of mass of the simulation system.

Parameters

without_drift_correction_ Whether disable the drift correction or not (default is true). Negation of this parameter is assigned to drift_correction.

Returns: None.

Definition at line 119 of file pro_mean_square_displacement.cpp.

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Member Data Documentation

◆ dimension

Vec<bool> ProMeanSquareDisplacement::dimension = {true, true, true}

private

Dimensions to be considered in computing squared displacements. Three elements of this member corresponds to x, y, and z direction, respectively. Only if an element of this member is true, displacement in the corresponding direction is added to resulted displacement. Default is true for all the direction.

Definition at line 46 of file pro_mean_square_displacement.h.

◆ displacement2_array

ArrayXXd ProMeanSquareDisplacement::displacement2_array

private

A two-dimensional array of squared displacements from initial position for each target over a simulation trajectory. Each column corresponds to time series of the squared displacement for each target, and each row corresponds to each element of generators (snapshot of simulation).

Definition at line 65 of file pro_mean_square_displacement.h.

◆ displacement2_traj

Vec<RowArrayXd> ProMeanSquareDisplacement::displacement2_traj

private

List in which RowArrayXd objects of computed squared displacements of each target are stored. Indices in this list corresponds those in generators.

Definition at line 57 of file pro_mean_square_displacement.h.

◆ drift_correction

bool ProMeanSquareDisplacement::drift_correction = true

private

Whether to correct a drift of center of mass of the simulation system (default is true). If the initial structure of the simulation has some biases of position or velocity, drift of the simulation system (translational displacement of center of mass of the system) can occur and, as the result, distort the mean square displacement.

Definition at line 38 of file pro_mean_square_displacement.h.

◆ initial_rs

ArrayXXd ProMeanSquareDisplacement::initial_rs

private

Initial positions of targets. The first element of generators is used for the initial positions.

Definition at line 51 of file pro_mean_square_displacement.h.

◆ mean_square_displacement

ArrayXd ProMeanSquareDisplacement::mean_square_displacement

private

The mean square displacement. Each element corresponds to each element of generators (snapshot of simulation).

Definition at line 71 of file pro_mean_square_displacement.h.

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

src/processors/pro_mean_square_displacement.h
src/processors/pro_mean_square_displacement.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProMeanSquareDisplacement()

Member Function Documentation

◆ extract_positions()

◆ finish()

◆ get_displacement2_array()

◆ get_mean_square_displacement()

◆ prepare()

◆ run_impl()

◆ set_dimension()

◆ without_drift_correction()

Member Data Documentation

◆ dimension

◆ displacement2_array

◆ displacement2_traj

◆ drift_correction

◆ initial_rs

◆ mean_square_displacement