Simulation Class Reference

This class represents the simulation of the Cellular Potts Model. More...

#include <Simulation.hpp>

Public Member Functions
	Simulation (int length_box, int number_of_steps, std::vector< std::vector< float > > J, std::vector< float > lambda_surface, std::vector< float > lambda_length, std::vector< float > lambda_chemotaxis, float kT)
	Construct a new Simulation:: Simulation object.
	~Simulation ()
	Destructor of the simulation.
int	get_length_box ()
	Get the length of the box This function returns the size of the lattice.
int	get_number_of_cases ()
	Get the number of cases This function returns the number of cases in the lattice.
int	get_number_of_steps ()
	Get the number of steps This function returns the number of steps of the simulation.
int	get_number_of_cells ()
	Get the number of cells This function returns the number of cells in the simulation.
std::vector< Cell * >	get_cells_array ()
	Get the cells array This function returns the array of cells.
std::vector< std::vector< int > >	get_lattice ()
	Get the lattice This function returns the lattice of the simulation.
std::vector< std::vector< float > >	get_J ()
	Get the J matrix This function returns the J matrix of the simulation.
std::vector< float >	get_lambda_surface ()
	Get the lambda surface vector This function returns the lambda surface vector of the simulation.
void	set_cells_array (std::vector< Cell * > cells_array)
	Set the cells array This function sets the cells array of the simulation.
void	set_lattice (std::vector< std::vector< int > > lattice)
	Set the lattice This function sets the lattice of the simulation.
void	initialize_lattice (bool is_periodic)
	Initialize the lattice.
void	display_lattice ()
	Display the lattice.
Cell *	create_cell (int type, int target_surface, float target_length, sf::Color color)
	Create a cell.
void	add_cell_to_lattice (Cell *c, int safe_distance)
	Add a cell to the lattice.
void	remove_cell_from_lattice (Cell *c)
	Remove a cell from the lattice.
void	updateCellsLength ()
void	write_header (std::ofstream &file)
	Write the header of the data file to save the simulation.
void	write_tail (std::ofstream &file, float total_time)
	Write the tail of the data file to save the simulation.
void	save_lattice (std::ofstream &file, int step, float time)
	Save the lattice to the data file.
float	calculate_energy_of_two_sites (int x1, int y1, int x2, int y2)
	Calculate the energy of two sites.
float	calculate_energy_of_site (int x, int y)
	Calculate the energy of a site.
float	calculate_total_hamiltonian ()
bool	is_connectivity_broken (int x_trial, int y_trial, int cell_id)
	Check if the connectivity is broken at a site.
float	calculate_local_hamiltonian (int x_trial, int y_trial, int cell_id_trial, int x, int y, int cell_id)
	Calculate the local Hamiltonian of the simulation.
void	metropolis_algorithm (int x, int y, int x_trial, int y_trial, float delta_H)
std::vector< int >	monte_carlo_step ()
	Monte Carlo step of the simulation.
void	simulation_step ()
void	run_simulation ()
	Run the simulation.
void	run_and_save_simulation (int nb_save, const char *filename)
	Run the simulation and save the data.
void	run_simulation_sfml (const char *filename)
	Run the simulation with SFML rendering.
void	run_simulation_sfml_diff (const char *filename)
	Run the simulation with SFML rendering and diffusion.
void	updateCellShape (int x, int y, sf::RectangleShape &shape)
	Update the shape of the cell.

Detailed Description

This class represents the simulation of the Cellular Potts Model.

This class contains all the methods and attributes to run a simulation of the Cellular Potts Model.

Constructor & Destructor Documentation

Simulation()

Simulation::Simulation	(	int	length_box,
		int	number_of_steps,
		std::vector< std::vector< float > >	J,
		std::vector< float >	lambda_surface,
		std::vector< float >	lambda_length,
		std::vector< float >	lambda_chemotaxis,
		float	kT
	)

Construct a new Simulation:: Simulation object.

This constructor initializes the simulation with the parameters given.

Parameters

length_box	the size of the lattice
number_of_steps	the number of steps of the simulation
J	the J matrix
lambda_surface	the lambda surface vector
lambda_length	the lambda length vector
lambda_chemotaxis	the lambda chemotaxis vector
kT	the temperature

~Simulation()

Simulation::~Simulation

(

)

Destructor of the simulation.

This destructor cleans up the dynamically allocated cells. Not that much to do here as almost everything is in an array.

Returns

void

Member Function Documentation

add_cell_to_lattice()

void Simulation::add_cell_to_lattice	(	Cell *	c,
		int	safe_distance
	)

Add a cell to the lattice.

Parameters

c	the cell to add
safe_distance	the safe distance : distance from the end of the lattice where the cell can be added.

Returns

void

Note

Here this only works if the cell has a surface energy. If not, only one case is added, and the cell might be deleted with monte carlo steps.

This function adds a cell to the lattice at a random position. The cell is added to the lattice and its position is updated. Only one case is added, and then the cell will add the other cases in the lattice with the surface energy.

calculate_energy_of_site()

float Simulation::calculate_energy_of_site	(	int	x,
		int	y
	)

Calculate the energy of a site.

Parameters

x	x coordinate of the site
y	y coordinate of the site

Returns

the energy of the site

This function calculates the energy of a site with its neighbors. The energy is calculated with the J matrix.

calculate_energy_of_two_sites()

float Simulation::calculate_energy_of_two_sites	(	int	x1,
		int	y1,
		int	x2,
		int	y2
	)

Calculate the energy of two sites.

Parameters

x1	x coordinate of the first site
y1	y coordinate of the first site
x2	x coordinate of the second site
y2	y coordinate of the second site

Returns

the energy of the two sites

Note

The energy is calculated with the J matrix

This function calculates the energy of two sites with the J matrix. The energy is calculated with the kronecker delta.

calculate_local_hamiltonian()

float Simulation::calculate_local_hamiltonian	(	int	x_trial,
		int	y_trial,
		int	cell_id_trial,
		int	x,
		int	y,
		int	cell_id
	)

Calculate the local Hamiltonian of the simulation.

Parameters

x_trial	the x coordinate of the trial site
y_trial	the y coordinate of the trial site
cell_id_trial	the id of the cell in the trial site
x	the x coordinate of the site
y	the y coordinate of the site
cell_id	the id of the cell in the site

Returns

float the local Hamiltonian of the simulation

This function calculates the local Hamiltonian of the simulation. The local Hamiltonian is the energy of the site and the energy of the site of its neighbors. This is not the total hamiltonian and is a simplification to calculate the change in energy.

create_cell()

Cell * Simulation::create_cell	(	int	type,
		int	target_surface,
		float	target_length,
		sf::Color	color
	)

Create a cell.

Parameters

type	the type of the cell
surface	the surface of the cell
target_surface	the target surface of the cell
target_length	the target length of the cell
color	the color of the cell

Returns

the created cell

Note

The cell is added to the cells array m_cells_array

This function creates a cell with the given parameters and adds it to the cells array.

display_lattice()

void Simulation::display_lattice

(

)

Display the lattice.

Returns

void

Note

This function is used for debug

This function displays the lattice in the console.

get_cells_array()

std::vector< Cell * > Simulation::get_cells_array

(

)

Get the cells array This function returns the array of cells.

Returns

std::vector<Cell*> the cells array

get_J()

std::vector< std::vector< float > > Simulation::get_J

(

)

Get the J matrix This function returns the J matrix of the simulation.

Returns

std::vector<std::vector <float>> the J matrix

get_lambda_surface()

std::vector< float > Simulation::get_lambda_surface

(

)

Get the lambda surface vector This function returns the lambda surface vector of the simulation.

Returns

std::vector<float> the lambda surface vector

get_lattice()

std::vector< std::vector< int > > Simulation::get_lattice

(

)

Get the lattice This function returns the lattice of the simulation.

Returns

std::vector<std::vector<int>> the lattice

get_length_box()

int Simulation::get_length_box

(

)

Get the length of the box This function returns the size of the lattice.

Returns

int the length of the box

get_number_of_cases()

int Simulation::get_number_of_cases

(

)

Get the number of cases This function returns the number of cases in the lattice.

Returns

int the number of cases

get_number_of_cells()

int Simulation::get_number_of_cells

(

)

Get the number of cells This function returns the number of cells in the simulation.

Returns

int the number of cells

get_number_of_steps()

int Simulation::get_number_of_steps

(

)

Get the number of steps This function returns the number of steps of the simulation.

Returns

int the number of steps

initialize_lattice()

void Simulation::initialize_lattice

(

bool

is_periodic = true

)

Initialize the lattice.

Parameters

is_periodic

if the lattice is periodic

Returns

void

This function initializes the lattice with zeros. If the lattice is not periodic, it adds walls to the lattice (represented by cells with id -1).

is_connectivity_broken()

bool Simulation::is_connectivity_broken	(	int	x_trial,
		int	y_trial,
		int	cell_id
	)

Check if the connectivity is broken at a site.

Parameters

x_trial	x coordinate of the site
y_trial	y coordinate of the site
cell_id	the id of the cell to check the connectivity

This function checks if the connectivity is broken at a site. The site is locally disconnected if the connectivity loss exceeds 2. The connectivity loss is calculated with the kronecker delta.

monte_carlo_step()

std::vector< int > Simulation::monte_carlo_step

(

)

Monte Carlo step of the simulation.

Returns

the coordinate and id of the changed cell

Note

The Monte Carlo step is a Metropolis algorithm

This function performs a Monte Carlo step of the simulation. It takes a random site and a random move. It calculates the energy difference of the move and decides if the move is accepted with the Metropolis algorithm.

remove_cell_from_lattice()

void Simulation::remove_cell_from_lattice

(

Cell *

c

)

Remove a cell from the lattice.

Parameters

c	the cell to remove

Returns

void

This function removes a cell from the lattice. The cell is removed from the lattice and its position is cleared.

run_and_save_simulation()

void Simulation::run_and_save_simulation	(	int	nb_save,
		const char *	filename
	)

Run the simulation and save the data.

Parameters

nb_save	the number of saves
filename	the name of the file to save the data

Returns

void

This function runs the simulation and saves the data. It performs a Monte Carlo step for each step of the simulation and saves the data every nb_save steps.

run_simulation()

void Simulation::run_simulation

(

)

Run the simulation.

Returns

void

This function runs the simulation. It performs a Monte Carlo step for each step of the simulation.

run_simulation_sfml()

void Simulation::run_simulation_sfml

(

const char *

filename

)

Run the simulation with SFML rendering.

Parameters

filename

the name of the file to save the data

Returns

void

This function runs the simulation with SFML rendering. It performs a Monte Carlo step for each step of the simulation and renders the lattice with SFML.

run_simulation_sfml_diff()

void Simulation::run_simulation_sfml_diff

(

const char *

filename

)

Run the simulation with SFML rendering and diffusion.

Parameters

filename

the name of the file to save the data

This function runs the simulation with SFML rendering and diffusion. It performs a Monte Carlo step for each step of the simulation and renders the lattice with SFML. It also updates the concentration matrix with the diffusion equation.

save_lattice()

void Simulation::save_lattice	(	std::ofstream &	file,
		int	step,
		float	time
	)

Save the lattice to the data file.

Parameters

file	the file to save the simulation
step	the step of the simulation
time	the time of the simulation

Returns

void

This function saves the lattice to the data file. It writes the step, the time, the lattice, and the concentration matrix.

set_cells_array()

void Simulation::set_cells_array

(

std::vector< Cell * >

cells_array

)

Set the cells array This function sets the cells array of the simulation.

Parameters

cells_array

the cells array

set_lattice()

void Simulation::set_lattice

(

std::vector< std::vector< int > >

lattice

)

Set the lattice This function sets the lattice of the simulation.

Parameters

lattice

the lattice

updateCellShape()

void Simulation::updateCellShape	(	int	x,
		int	y,
		sf::RectangleShape &	shape
	)

Update the shape of the cell.

Parameters

x	x coordinate of the cell
y	y coordinate of the cell
shape	the shape of the cell

Returns

void

This function updates the shape of the cell. It sets the color of the cell according to the cell type.

write_header()

void Simulation::write_header

(

std::ofstream &

file

)

Write the header of the data file to save the simulation.

Parameters

file	the file to save the simulation

Returns

void

This function writes the header of the data file to save the simulation. It writes the date and time, the simulation parameters, the J matrix, the lambda vectors, the Hamiltonian terms,

write_tail()

void Simulation::write_tail	(	std::ofstream &	file,
		float	total_time
	)

Write the tail of the data file to save the simulation.

Parameters

file	the file to save the simulation
total_time	the total time of the simulation

Returns

void

This function writes the tail of the data file to save the simulation. It writes the date and time, the total time of the simulation.

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

• /home/faroth/cpm/include/Simulation.hpp
• /home/faroth/cpm/src/Simulation.cpp