Abstract base class for any model for molecule simulation. More...

#include <Model.h>

Inheritance diagram for Model:

Collaboration diagram for Model:

Public Member Functions
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...

virtual void	step (int iteration)=0
	Perform one single step in the simulation. More...

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

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

Protected Member Functions
	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
ParticleContainer &	particles

Force &	force

double	deltaT

bool	gravityOn

std::array< double, 3 >	g

Private Attributes
FileHandler	fileHandler

FileHandler::outputFormat	outputFormat

Friends
class	DefaultThermostat

class	Thermostat

class	FlowThermostat

Detailed Description

Abstract base class for any model for molecule simulation.

Each specific model should extend this class. At the moment there are two different models: -Direct Sum -Linked Cells

Constructor & Destructor Documentation

◆ Model()

Model::Model	(	ParticleContainer &	particles,
		Force &	force,
		double	deltaT,
		FileHandler::outputFormat	outputFormat,
		bool	gravityOn,
		std::array< double, 3 >	g = `{}`
	)

protected

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.

Parameters

particles	Particle container of the model. This parameter is instantiated with the appropriated container by the derived models.
force	Force to use in the simulation.
deltaT	Duration of one time step. Small time step will result in a better simulation, but will demand more computational resources.
outputFormat	Format of the output file. Supported formats are vtk and xyz.
gravityOn	Toggle gravtiy on or of
g	Gravity factor

◆ ~Model()

virtual Model::~Model ( )

virtualdefault

Virtual default constructor to guarantee appropriate memory clean up.

Member Function Documentation

◆ addCuboid()

void Model::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.

Parameters

position	The coordinates of the lower left front-side corner.
N1	Number of particles in dimension N1.
N2	Number of particles in dimension N2.
N3	Number of particles in dimension N3.
h	Distance of the particles (mesh width of the grid).
mass	Mass of one particle.
initVelocity	Initial velocity of the of the particles.
dimensions	Number of dimensions to which the Brownian Motion will be added. Valid values are 0, 1, 2 and 3.
brownianMotionAverageVelocity
epsilon	Leonard Jones parameter epsilon
sigma	Leonard Jones parameter sigma
fixed	Fix particles.

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◆ addDisc()

void Model::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.

Parameters

center	The coordinates of the center of the disc.
initVelocity	Initial velocity of the of the particles.
N	Number of particles along the radius, including the particle in the center.
h	Distance of the particles (mesh width of the grid).
mass	Mass of one particle.
dimensions	Number of dimensions to which the Brownian Motion will be added. Valid values are 0, 1, 2 and 3.
brownianMotionAverageVelocity	Constant, specifying the average velocity of the Brownian Motion.
epsilon	Leonard Jones parameter epsilon
sigma	Leonard Jones parameter sigma
fixed	Fix particles.

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◆ addParticle()

void Model::addParticle ( Particle & p )

Add a single particle to this model.

Parameters

p	Particle to add to this model.

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◆ addSphere()

void Model::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.

Parameters

center	The coordinates of the center of the disc.
initVelocity	Initial velocity of the of the particles.
N	Number of particles along the radius, including the particle in the center.
h	Distance of the particles (mesh width of the grid).
mass	Mass of one particle.
dimensions	Number of dimensions to which the Brownian Motion will be added. Valid values are 0, 1, 2 and 3.
brownianMotionAverageVelocity	Constant, specifying the average velocity of the Brownian Motion.
epsilon	Leonard Jones parameter epsilon
sigma	Leonard Jones parameter sigma
fixed	Fix particles.

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◆ addViaFile()

void Model::addViaFile	(	std::string &	filepath,
		FileHandler::inputFormat	inputFormat
	)

Add new particles / particle structures to the model via a file.

Parameters

filepath	Path to the file. Example: ../input/eingabe-sonne.txt
inputFormat	Format of the input file (txt, xml)

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◆ applyGravity()

void Model::applyGravity ( )

protected

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

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◆ getParticles()

ParticleContainer& Model::getParticles ( ) const

inline

Get the Particles of this model.

Returns: Particles stored in this model.

Should be only used for testing purposes.

◆ initializeForces()

virtual void Model::initializeForces ( )

pure virtual

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

Implemented in LinkedCells, and DirectSum.

◆ plot()

void Model::plot	(	int	iteration,
		std::string &	baseName
	)

Write current state of the model to a file.

Parameters

iteration	Current iteration.
baseName	Base name of the output file.

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◆ saveState()

void Model::saveState ( )

Export the current state of all molecules to a txt file for using them in a new simulation.

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◆ step()

virtual void Model::step ( int iteration )

pure virtual

Perform one single step in the simulation.

@parameter Current iteration the simulator is in.

Each step consists of force, velocity and position updates. For each concrete model the exact implementation might differ.

Implemented in LinkedCells, and DirectSum.

◆ updateForces()

void Model::updateForces ( ) const

Helper method to calculate the force between all particles.

After each time step the forces acting between the particles have changed due to their new positions, so they have to be recalculated. This method uses Newtons third law of motion to simplify calculations and make them more efficient.

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◆ updatePositions()

void Model::updatePositions ( ) const

protected

Helper method to calculate the position of all particles.

After each time step positions of all particles with velocities unequal to zero have to be updated.

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◆ updateVelocities()

void Model::updateVelocities ( ) const

protected

Helper method to calculate the velocity of all particles.

After each time step the velocity of each particle may have changed due to forces that act between the particles.

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Friends And Related Function Documentation

◆ DefaultThermostat

friend class DefaultThermostat

friend

◆ FlowThermostat

friend class FlowThermostat

friend

◆ Thermostat

friend class Thermostat

friend

Member Data Documentation

◆ deltaT

double Model::deltaT

protected

◆ fileHandler

FileHandler Model::fileHandler

private

◆ force

Force& Model::force

protected

◆ g

std::array<double, 3> Model::g

protected

◆ gravityOn

bool Model::gravityOn

protected

◆ outputFormat

FileHandler::outputFormat Model::outputFormat

private

◆ particles

ParticleContainer& Model::particles

protected

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

/home/runner/work/MolSim/MolSim/src/models/Model.h
/home/runner/work/MolSim/MolSim/src/models/Model.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Model()

◆ ~Model()

Member Function Documentation

◆ addCuboid()

◆ addDisc()

◆ addParticle()

◆ addSphere()

◆ addViaFile()

◆ applyGravity()

◆ getParticles()

◆ initializeForces()

◆ plot()

◆ saveState()

◆ step()

◆ updateForces()

◆ updatePositions()

◆ updateVelocities()

Friends And Related Function Documentation

◆ DefaultThermostat

◆ FlowThermostat

◆ Thermostat

Member Data Documentation

◆ deltaT

◆ fileHandler

◆ force

◆ g

◆ gravityOn

◆ outputFormat

◆ particles