This class contains a lattice representation of a materials blend with the ability to simulate phase separation and perform a variety of structural analyses. More...

#include <Morphology.h>

Public Member Functions
	Morphology ()
	Default constructor that creates a Morphology object with the default parameters and an empty lattice. More...

	Morphology (const Parameters &params, const int id)
	This constructor creates a Morphology object with a 3D lattice with a size defined by the input dimensions (length, width, height). More...

	Morphology (const Lattice &input_lattice, const Parameters &params, const int id)
	This constructor creates a Morphology object with a 3D lattice defined by the input Lattice object. More...

virtual	~Morphology ()
	This is the default virtual destructor. More...

void	calculateAnisotropies ()
	Calculates the domain size anisotropy of each phase. More...

void	calculateCorrelationDistances ()
	Calculates the correlation length data and the domain size using the input parameter options. More...

void	calculateDepthDependentData ()
	Calculates the lattice depth dependent (z-direction) characteristics of the morphology. More...

double	calculateInterfacialAreaVolumeRatio () const
	Calculates the interfacial area in units of lattice units squared. More...

void	calculateInterfacialDistanceHistogram ()
	Calculates the interfacial distance histograms, which gives the fraction of sites at a specified distance from the interface. More...

double	calculateInterfacialVolumeFraction () const
	Calculates the fraction of sites adjacent to an interface. More...

void	calculateMixFractions ()
	Calculates the volume fraction of each type site in the lattice to the total number of sites. More...

bool	calculateTortuosity (const char site_type, const bool enable_reduced_memory)
	Calculates the tortuosity histogram for the specified site type. More...

void	createBilayerMorphology ()
	Creates a split bilayer morphology in the z-direction. More...

void	createCheckerboardMorphology ()
	Creates a 3D checkerboard morphology. More...

void	createRandomMorphology (const std::vector< double > &mix_fractions)
	Creates a randomly mixed morphology with the specified blend ratios. More...

void	executeIsingSwapping (const int num_MCsteps, const double interaction_energy1, const double interaction_energy2, const bool enable_growth_pref, const int growth_direction, const double additional_interaction)
	Executes the Ising site swapping processes with the specified parameters for a given mumber of iterations. More...

void	executeMixing (const double interfacial_width, const double interfacial_conc)
	Executes interfacial mixing with a specified interfacial width and interfacial mixing concentration. More...

void	executeSmoothing (const double smoothing_threshold, const int rescale_factor)
	Executes a smoothing algorithm that smooths out rough domain interfaces and removes small islands and island sites. More...

std::vector< double >	getCorrelationData (const char site_type) const
	Returns a vector containing the pair-pair autocorrelation function data for the specified site type. More...

std::vector< double >	getDepthCompositionData (const char site_type) const
	Returns a vector containing the film depth dependent blend composition data in the z-direction. More...

std::vector< double >	getDepthDomainSizeData (const char site_type) const
	Returns a vector containing the film depth dependent domain size data in the z-direction. More...

std::vector< double >	getDepthIVData () const
	Returns a vector containing the film depth dependent interfacial volume fraction data in the z-direction. More...

double	getDomainSize (const char site_type) const
	Returns the domain size determined for the specified site type. More...

double	getDomainAnisotropy (const char site_type) const
	Returns the domain anisotropy determined for the specified site type. More...

int	getHeight () const
	Gets the height or z-direction size of the lattice. More...

int	getID () const
	Gets the ID number of the Morphology object. More...

std::vector< std::pair< double, int > >	getInterfacialDistanceHistogram (const char site_type) const
	Returns a vector containing the interfacial distance probability histogram data for the specified site type. More...

double	getIslandVolumeFraction (const char site_type) const
	Returns the island volume for the specified site type. More...

int	getLength () const
	Returns the length or x-direction size of the lattice. More...

double	getMixFraction (const char site_type) const
	Returns the mix fraction for the specified site type. More...

std::vector< double >	getTortuosityData (const char site_type) const
	Returns a vector containing the end-to-end tortuosity data for the specified site type. More...

double	getUnitSize () const
	Returns the lattice unit size in units of nm. More...

int	getWidth () const
	Returns the width or y-direction size of the lattice. More...

std::vector< Morphology >	importTomogramMorphologyFile ()
	Imports the tomogram dataset specified in the parameter file. More...

bool	importMorphologyFile (std::ifstream &infile)
	Imports the Ising_OPV morphology text file given by the specified input filestream. More...

void	outputCompositionMaps (std::ofstream &outfile) const
	Outputs the areal composition map data to the specified output filestream. More...

void	outputCorrelationData (std::ofstream &outfile) const
	Outputs the domain autocorrelation function data to the specified output filestream. More...

void	outputDepthDependentData (std::ofstream &outfile) const
	Outputs the lattice depth dependent (z-direction) characteristics to the specified output filestream. More...

void	outputMorphologyFile (std::ofstream &outfile, const bool enable_export_compressed) const
	Outputs the morphology data to a file specified by the output filestream. More...

void	outputMorphologyCrossSection (std::ofstream &outfile) const
	Outputs a cross-section of the morphology at the x=Length/2 plane to the specified output filestream. More...

void	outputTortuosityMaps (std::ofstream &outfile) const
	Outputs the areal end-to-end tortuosity map data to the specified output filestream. More...

void	setParameters (const Parameters &params)
	Sets the parameters of the Morphology class using the input Parameters object. More...

void	shrinkLattice (const int rescale_factor)
	Shrinks the existing lattice by a fraction of 1 over the integer rescale_factor value. More...

void	stretchLattice (const int rescale_factor)
	Stretches the existing lattice by a integer rescale_factor value. More...

Detailed Description

This class contains a lattice representation of a materials blend with the ability to simulate phase separation and perform a variety of structural analyses.

The class makes use of the Lattice class to store the morphology data, and phase separation simulations are implemented using an Ising-based method. Morphological descriptors such as thh domain size, interfacial area, tortuosity, and more can be calculated for a given morphology.

Copyright: MIT License. For more information, see the LICENSE file that accompanies this software package.

Author: Michael C. Heiber

Date: 2014-2019

Constructor & Destructor Documentation

◆ Morphology() [1/3]

Ising_OPV::Morphology::Morphology ( )

Default constructor that creates a Morphology object with the default parameters and an empty lattice.

Warning: An empty Morphology object should not be used without defining a lattice.

◆ Morphology() [2/3]

Ising_OPV::Morphology::Morphology	(	const Parameters &	params,
		const int	id
	)

This constructor creates a Morphology object with a 3D lattice with a size defined by the input dimensions (length, width, height).

Two-dimensional periodic boundaries in the x- and y- directions are implemented by default, but periodic boundaries in the z-direction can also be enabled upon construction. Morphology objects are also tagged with an integer identification number.

Parameters

params	is the Parameters object that contains all parameters needed by the Morphology class.
id	is the input integer ID number that will be assigned to the Morphology object.

◆ Morphology() [3/3]

Ising_OPV::Morphology::Morphology	(	const Lattice &	input_lattice,
		const Parameters &	params,
		const int	id
	)

This constructor creates a Morphology object with a 3D lattice defined by the input Lattice object.

Parameters

input_lattice	is the input Lattice object that will be used to create the Morphology.
params	is the Parameters object that contains all parameters needed by the Morphology class.
id	is the input integer ID number that will be assigned to the Morphology object.

◆ ~Morphology()

Ising_OPV::Morphology::~Morphology ( )

virtual

This is the default virtual destructor.

Member Function Documentation

◆ calculateAnisotropies()

void Ising_OPV::Morphology::calculateAnisotropies ( )

Calculates the domain size anisotropy of each phase.

◆ calculateCorrelationDistances()

void Ising_OPV::Morphology::calculateCorrelationDistances ( )

Calculates the correlation length data and the domain size using the input parameter options.

◆ calculateDepthDependentData()

void Ising_OPV::Morphology::calculateDepthDependentData ( )

Calculates the lattice depth dependent (z-direction) characteristics of the morphology.

Calculates the depth dependent composition, interfacial volume fraction, and domain size.

◆ calculateInterfacialAreaVolumeRatio()

double Ising_OPV::Morphology::calculateInterfacialAreaVolumeRatio ( ) const

Calculates the interfacial area in units of lattice units squared.

◆ calculateInterfacialDistanceHistogram()

void Ising_OPV::Morphology::calculateInterfacialDistanceHistogram ( )

Calculates the interfacial distance histograms, which gives the fraction of sites at a specified distance from the interface.

◆ calculateInterfacialVolumeFraction()

double Ising_OPV::Morphology::calculateInterfacialVolumeFraction ( ) const

Calculates the fraction of sites adjacent to an interface.

◆ calculateMixFractions()

void Ising_OPV::Morphology::calculateMixFractions ( )

Calculates the volume fraction of each type site in the lattice to the total number of sites.

◆ calculateTortuosity()

bool Ising_OPV::Morphology::calculateTortuosity	(	const char	site_type,
		const bool	enable_reduced_memory
	)

Calculates the tortuosity histogram for the specified site type.

For all type 1 sites, the shortest paths through other type 1 sites to the boundary at z=0 is calculated. For all type 2 sites, the shortest pathes through other type 2 sites to the boundary at z=Height-1 is calculated. The shortest paths are calculated using Dijkstra's algorithm.

Parameters

site_type	specifies which site type to perform the tortuosity calculation on.
enable_reduced_memory	allows users to choose to use a slower algorithm that uses less RAM.

◆ createBilayerMorphology()

void Ising_OPV::Morphology::createBilayerMorphology ( )

Creates a split bilayer morphology in the z-direction.

◆ createCheckerboardMorphology()

void Ising_OPV::Morphology::createCheckerboardMorphology ( )

Creates a 3D checkerboard morphology.

◆ createRandomMorphology()

void Ising_OPV::Morphology::createRandomMorphology ( const std::vector< double > & mix_fractions )

Creates a randomly mixed morphology with the specified blend ratios.

Parameters

mix_fractions is a vector that specifies the blend ratio of each site type.

◆ executeIsingSwapping()

void Ising_OPV::Morphology::executeIsingSwapping	(	const int	num_MCsteps,
		const double	interaction_energy1,
		const double	interaction_energy2,
		const bool	enable_growth_pref,
		const int	growth_direction,
		const double	additional_interaction
	)

Executes the Ising site swapping processes with the specified parameters for a given mumber of iterations.

This function uses the bond formation algorithm to determine the energy change in the system that results from swapping two neighboring sites. Positive values for the interaction energies result in a driving force for phase separation.

Parameters

num_MCsteps	is the number of Monte Carlo steps to execute, where the number of steps is defined by the total number of iterations divided by the total lattice volume.
interaction_energy1	defines the energetic difference between like-like and unlike-unlike interactions for type 1 sites in units of kT.
interaction_energy2	defines the energetic difference between like-like and unlike-unlike interactions for type 2 sites in units of kT.
enable_growth_pref	is a boolean option that allows users to enable preferential interations in one of the pricipal lattice directions.
growth_direction	is an integer used when directional interactions are enabled and specifies the direction with a modified interaction energy, with 1 = x-direction, 2 = y-direction, and 3 = z-direction.
additional_interaction	is used when directional interactions are enabled and specifies the additional interaction energy with sites in the specified direction.

◆ executeMixing()

void Ising_OPV::Morphology::executeMixing	(	const double	interfacial_width,
		const double	interfacial_conc
	)

Executes interfacial mixing with a specified interfacial width and interfacial mixing concentration.

Random swapping of type 1 and type 2 sites near the interface is done to produce an mixed interfaction region with a controlled width and blend ratio.

Parameters

interfacial_width	specifies the desired width of the mixed interfacial region.
interfacial_conc	specified the desired blend ratio of mixed interfacial region.

◆ executeSmoothing()

void Ising_OPV::Morphology::executeSmoothing	(	const double	smoothing_threshold,
		const int	rescale_factor
	)

Executes a smoothing algorithm that smooths out rough domain interfaces and removes small islands and island sites.

Smoothing is done by determining a roughness factor for each site that is given by the fraction of surrounding sites that are a different type. Sites with a roughness factor is greater than the specified smoothing_threshold are switched to the opposite type. A rescale dependent smoothing process is executed when the rescale factor is greater than 2.

Parameters

smoothing_threshold	is the numerical parameter used to adjust how aggressive the smoothing should be.
rescale_factor	specifies whether the smoothing algorithm should be adjust to account for prior lattice rescaling by giving the rescaling factor used.

◆ getCorrelationData()

vector< double > Ising_OPV::Morphology::getCorrelationData ( const char site_type ) const

Returns a vector containing the pair-pair autocorrelation function data for the specified site type.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: a copy of the data vector.

◆ getDepthCompositionData()

vector< double > Ising_OPV::Morphology::getDepthCompositionData ( const char site_type ) const

Returns a vector containing the film depth dependent blend composition data in the z-direction.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: a copy of the data vector.

◆ getDepthDomainSizeData()

vector< double > Ising_OPV::Morphology::getDepthDomainSizeData ( const char site_type ) const

Returns a vector containing the film depth dependent domain size data in the z-direction.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: a copy of the data vector.

◆ getDepthIVData()

vector< double > Ising_OPV::Morphology::getDepthIVData ( ) const

Returns a vector containing the film depth dependent interfacial volume fraction data in the z-direction.

Returns: a copy of the data vector.

◆ getDomainAnisotropy()

double Ising_OPV::Morphology::getDomainAnisotropy ( const char site_type ) const

Returns the domain anisotropy determined for the specified site type.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: zero if the calculateAnisotropy function has not been called.; the domain anisotropy calculated from the direction dependent correlation function data.

◆ getDomainSize()

double Ising_OPV::Morphology::getDomainSize ( const char site_type ) const

Returns the domain size determined for the specified site type.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: -1 if the calculateCorrelationDistance function has not been called.; the domain size calculated from the correlation function data.

◆ getHeight()

int Ising_OPV::Morphology::getHeight ( ) const

Gets the height or z-direction size of the lattice.

Returns: an integer representing the height or z-direction size of the lattice.

◆ getID()

int Ising_OPV::Morphology::getID ( ) const

Gets the ID number of the Morphology object.

Returns: the integer ID number.

◆ getInterfacialDistanceHistogram()

vector< pair< double, int > > Ising_OPV::Morphology::getInterfacialDistanceHistogram ( const char site_type ) const

Returns a vector containing the interfacial distance probability histogram data for the specified site type.

The histogram bins are distances given by the vector index + 1 in lattice units.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: a copy of the data vector.

◆ getIslandVolumeFraction()

double Ising_OPV::Morphology::getIslandVolumeFraction ( const char site_type ) const

Returns the island volume for the specified site type.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: -1 if the calculateTortuosity function has not been called.; the volume fraction of island sites not connected to the top or bottom surface (z-dimension).

◆ getLength()

int Ising_OPV::Morphology::getLength ( ) const

Returns the length or x-direction size of the lattice.

Returns: an integer representing the length or x-direction size of the lattice.

◆ getMixFraction()

double Ising_OPV::Morphology::getMixFraction ( const char site_type ) const

Returns the mix fraction for the specified site type.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: -1 if the calculateMixFractions function has not been called.; the volumetric blend ratio of the specified site type.

◆ getTortuosityData()

vector< double > Ising_OPV::Morphology::getTortuosityData ( const char site_type ) const

Returns a vector containing the end-to-end tortuosity data for the specified site type.

Parameters

site_type specifies for which site type the data should be retrieved.

Returns: a copy of the data vector.

◆ getUnitSize()

double Ising_OPV::Morphology::getUnitSize ( ) const

Returns the lattice unit size in units of nm.

◆ getWidth()

int Ising_OPV::Morphology::getWidth ( ) const

Returns the width or y-direction size of the lattice.

Returns: an integer representing the width or y-direction size of the lattice.

◆ importMorphologyFile()

bool Ising_OPV::Morphology::importMorphologyFile ( std::ifstream & infile )

Imports the Ising_OPV morphology text file given by the specified input filestream.

Parameters

infile is the already open input filestream pointing to an Ising_OPV morphology file.

Returns: false if there is an error during file import.; true if morphology file import is sucessful.

◆ importTomogramMorphologyFile()

vector< Morphology > Ising_OPV::Morphology::importTomogramMorphologyFile ( )

Imports the tomogram dataset specified in the parameter file.

Returns: a vector of Morphology objects that consists of a series of subsections of the original tomogram data.

◆ outputCompositionMaps()

void Ising_OPV::Morphology::outputCompositionMaps ( std::ofstream & outfile ) const

Outputs the areal composition map data to the specified output filestream.

Parameters

outfile is the already open output filestream.

◆ outputCorrelationData()

void Ising_OPV::Morphology::outputCorrelationData ( std::ofstream & outfile ) const

Outputs the domain autocorrelation function data to the specified output filestream.

Parameters

outfile is the already open output filestream.

◆ outputDepthDependentData()

void Ising_OPV::Morphology::outputDepthDependentData ( std::ofstream & outfile ) const

Outputs the lattice depth dependent (z-direction) characteristics to the specified output filestream.

Outputs the depth dependent composition, interfacial volume fraction, and domain size.

Parameters

outfile is the already open output filestream.

◆ outputMorphologyCrossSection()

void Ising_OPV::Morphology::outputMorphologyCrossSection ( std::ofstream & outfile ) const

Outputs a cross-section of the morphology at the x=Length/2 plane to the specified output filestream.

Parameters

outfile is the already open output filestream.

◆ outputMorphologyFile()

void Ising_OPV::Morphology::outputMorphologyFile	(	std::ofstream &	outfile,
		const bool	enable_export_compressed
	)		const

Outputs the morphology data to a file specified by the output filestream.

The user can specify whether to use the compressed format or not.

Parameters

outfile	is the already open output filestream.
enable_export_compressed	is a boolean option that allows users to choose whether the output morphology file uses the compressed format or not.

◆ outputTortuosityMaps()

void Ising_OPV::Morphology::outputTortuosityMaps ( std::ofstream & outfile ) const

Outputs the areal end-to-end tortuosity map data to the specified output filestream.

Parameters

outfile is the already open output filestream.

◆ setParameters()

void Ising_OPV::Morphology::setParameters ( const Parameters & params )

Sets the parameters of the Morphology class using the input Parameters object.

Parameters

params is the Parameters object that contains all parameters needed by the Morphology class.

◆ shrinkLattice()

void Ising_OPV::Morphology::shrinkLattice ( const int rescale_factor )

Shrinks the existing lattice by a fraction of 1 over the integer rescale_factor value.

Each of the original lattice dimensions must be divisible by the rescale factor. The original lattice is overwritten by the newly created smaller lattice.

◆ stretchLattice()

void Ising_OPV::Morphology::stretchLattice ( const int rescale_factor )

Stretches the existing lattice by a integer rescale_factor value.

The original lattice is overwritten by the newly created larger lattice.

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

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ Morphology() [1/3]

◆ Morphology() [2/3]

◆ Morphology() [3/3]

◆ ~Morphology()

Member Function Documentation

◆ calculateAnisotropies()

◆ calculateCorrelationDistances()

◆ calculateDepthDependentData()

◆ calculateInterfacialAreaVolumeRatio()

◆ calculateInterfacialDistanceHistogram()

◆ calculateInterfacialVolumeFraction()

◆ calculateMixFractions()

◆ calculateTortuosity()

◆ createBilayerMorphology()

◆ createCheckerboardMorphology()

◆ createRandomMorphology()

◆ executeIsingSwapping()

◆ executeMixing()

◆ executeSmoothing()

◆ getCorrelationData()

◆ getDepthCompositionData()

◆ getDepthDomainSizeData()

◆ getDepthIVData()

◆ getDomainAnisotropy()

◆ getDomainSize()

◆ getHeight()

◆ getID()

◆ getInterfacialDistanceHistogram()

◆ getIslandVolumeFraction()

◆ getLength()

◆ getMixFraction()

◆ getTortuosityData()

◆ getUnitSize()

◆ getWidth()

◆ importMorphologyFile()

◆ importTomogramMorphologyFile()

◆ outputCompositionMaps()

◆ outputCorrelationData()

◆ outputDepthDependentData()

◆ outputMorphologyCrossSection()

◆ outputMorphologyFile()

◆ outputTortuosityMaps()

◆ setParameters()

◆ shrinkLattice()

◆ stretchLattice()