Model that implements the linked cell algorithm. More...

#include <LinkedCells.h>

Inheritance diagram for LinkedCells:

Collaboration diagram for LinkedCells:

Public Member Functions
	LinkedCells (Force &force, double deltaT, std::array< double, 3 > domainSize, double rCutOff, FileHandler::outputFormat outputFormat, BoundarySet boundaryConditions, bool gravityOn, std::array< double, 3 > g={}, MembraneParameters membraneParameters=MembraneParameters{}, enumsStructs::ParallelizationStrategy parallelizationStrategy=enumsStructs::ParallelizationStrategy::none)
	Contruct a new Linked Cells model. More...

void	step (int iteration) override
	Perform one time step in the linked cells model. More...

void	updateForcesOptimized ()
	Implements the optimization we presented as our second idea. At the moment this is dead code, because we did not have time yet to make it compatible with our current program structure and only integrated it once when doing the time measurements. More...

void	initializeForces () override
	Calculate forces at the beginning of the simulation that the old force is not 0. More...

Public Member Functions inherited from Model
virtual	~Model ()=default
	Virtual default constructor to guarantee appropriate memory clean up. More...

void	plot (int iteration, std::string &baseName)
	Write current state of the model to a file. More...

void	addCuboid (const std::array< double, 3 > &position, unsigned N1, unsigned N2, unsigned N3, double h, double mass, const std::array< double, 3 > &initVelocity, int dimensions, double brownianMotionAverageVelocity, double epsilon=5, double sigma=1, bool fixed=false)
	Add a cuboid structure to this model. More...

void	addDisc (const std::array< double, 3 > &center, const std::array< double, 3 > &initVelocity, int N, double h, double mass, int dimensions, double brownianMotionAverageVelocity, double epsilon=5, double sigma=1, bool fixed=false)
	Add a 2D disc structure to this model. More...

void	addSphere (const std::array< double, 3 > &center, const std::array< double, 3 > &initVelocity, int N, double h, double mass, int dimensions, double brownianMotionAverageVelocity, double epsilon=5, double sigma=1, bool fixed=false)
	Add a 3D sphere structure to this model. More...

void	addParticle (Particle &p)
	Add a single particle to this model. More...

void	addViaFile (std::string &filepath, FileHandler::inputFormat inputFormat)
	Add new particles / particle structures to the model via a file. More...

void	saveState ()
	Export the current state of all molecules to a txt file for using them in a new simulation. More...

void	updateForces () const
	Helper method to calculate the force between all particles. More...

ParticleContainer &	getParticles () const
	Get the Particles of this model. More...

Private Member Functions
void	processBoundaryForces ()
	Apply forces to all particles in boundary cells according to the specified boundary conditions. More...

void	processHaloCells ()
	Process all particles which have left the domain at the end of a simulation step according to the specified boundary conditions. More...

void	pullMarkedParticles ()
	Apply to all particles that are marked a constant force. More...

void	updateForcesMembrane ()
	Calculate forces between particles in a membrane structure. More...

Private Attributes
bool	membraneSetting

bool	pull

int	pullingActiveUntil

std::array< double, 3 >	pullingForce {}

std::unique_ptr< Force >	forceBetweenDiagonalNeighborsInMembrane

std::unique_ptr< Force >	forceBetweenDirectNeighborsInMembrane

enumsStructs::ParallelizationStrategy	parallelizationStrategy

LinkedCellsContainer	particles

std::vector< std::pair< Side, enumsStructs::BoundaryCondition > >	boundarySettings

Additional Inherited Members
Protected Member Functions inherited from Model
	Model (ParticleContainer &particles, Force &force, double deltaT, FileHandler::outputFormat outputFormat, bool gravityOn, std::array< double, 3 > g={})
	Constructor for this model. Cannot be called from any other class but classes that extend this class, because this class is a base class and should not be instantiated. More...

void	updatePositions () const
	Helper method to calculate the position of all particles. More...

void	updateVelocities () const
	Helper method to calculate the velocity of all particles. More...

void	applyGravity ()
	Add a gravitational force of g * m along the y-axis to each particle inside the simulation domain. More...

Protected Attributes inherited from Model
ParticleContainer &	particles

Force &	force

double	deltaT

bool	gravityOn

std::array< double, 3 >	g

Detailed Description

Model that implements the linked cell algorithm.

The linked-cells algorithm is significantly faster than the direct sum algorithm. It reduces the time complexity from O(n²) to O(n). The following plot shows some benchmarks.

Benchmarks

Constructor & Destructor Documentation

◆ LinkedCells()

LinkedCells::LinkedCells	(	Force &	force,
		double	deltaT,
		std::array< double, 3 >	domainSize,
		double	rCutOff,
		FileHandler::outputFormat	outputFormat,
		BoundarySet	boundaryConditions,
		bool	gravityOn,
		std::array< double, 3 >	g = `{}`,
		MembraneParameters	membraneParameters = `MembraneParameters{}`,
		enumsStructs::ParallelizationStrategy	parallelizationStrategy = `enumsStructs::ParallelizationStrategy::none`
	)

Contruct a new Linked Cells model.

Parameters

force	Force to use.
deltaT	Discretisation step.
domainSize	Domain size.
rCutOff	Cutoff radius.
outputFormat	Output format.
boundaryConditions	Boundary conditions.
gravityOn	Toggle gravity on or off.
g	Gravitational factor.
membraneParameters	Contains specification if a membrane is simulated
parallelizationStrategy	Strategy to use for parallelization.

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Member Function Documentation

◆ initializeForces()

void LinkedCells::initializeForces ( )

overridevirtual

Calculate forces at the beginning of the simulation that the old force is not 0.

Implements Model.

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◆ processBoundaryForces()

void LinkedCells::processBoundaryForces ( )

private

Apply forces to all particles in boundary cells according to the specified boundary conditions.

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◆ processHaloCells()

void LinkedCells::processHaloCells ( )

private

Process all particles which have left the domain at the end of a simulation step according to the specified boundary conditions.

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◆ pullMarkedParticles()

void LinkedCells::pullMarkedParticles ( )

private

Apply to all particles that are marked a constant force.

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◆ step()

void LinkedCells::step ( int iteration )

overridevirtual

Perform one time step in the linked cells model.

Parameters

iteration Current iteration the simulator is in.

Implements Model.

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◆ updateForcesMembrane()

void LinkedCells::updateForcesMembrane ( )

private

Calculate forces between particles in a membrane structure.

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◆ updateForcesOptimized()

void LinkedCells::updateForcesOptimized ( )

Implements the optimization we presented as our second idea. At the moment this is dead code, because we did not have time yet to make it compatible with our current program structure and only integrated it once when doing the time measurements.

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Member Data Documentation

◆ boundarySettings

std::vector<std::pair<Side, enumsStructs::BoundaryCondition> > LinkedCells::boundarySettings

private

Definition of the boundary condition for each side.

◆ forceBetweenDiagonalNeighborsInMembrane

std::unique_ptr<Force> LinkedCells::forceBetweenDiagonalNeighborsInMembrane

private

◆ forceBetweenDirectNeighborsInMembrane

std::unique_ptr<Force> LinkedCells::forceBetweenDirectNeighborsInMembrane

private

◆ membraneSetting

bool LinkedCells::membraneSetting

private

◆ parallelizationStrategy

enumsStructs::ParallelizationStrategy LinkedCells::parallelizationStrategy

private

◆ particles

LinkedCellsContainer LinkedCells::particles

private

This model uses the LinkedCellsContainer to store its particles

◆ pull

bool LinkedCells::pull

private

◆ pullingActiveUntil

int LinkedCells::pullingActiveUntil

private

◆ pullingForce

std::array<double, 3> LinkedCells::pullingForce {}

private

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

/home/runner/work/MolSim/MolSim/src/models/linkedCells/LinkedCells.h
/home/runner/work/MolSim/MolSim/src/models/linkedCells/LinkedCells.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LinkedCells()

Member Function Documentation

◆ initializeForces()

◆ processBoundaryForces()

◆ processHaloCells()

◆ pullMarkedParticles()

◆ step()

◆ updateForcesMembrane()

◆ updateForcesOptimized()

Member Data Documentation

◆ boundarySettings

◆ forceBetweenDiagonalNeighborsInMembrane

◆ forceBetweenDirectNeighborsInMembrane

◆ membraneSetting

◆ parallelizationStrategy

◆ particles

◆ pull

◆ pullingActiveUntil

◆ pullingForce