simulation_interacting.cpp File Reference

#include <iostream>
#include <vector>
#include <fstream>
#include <cmath>
#include <sstream>
#include <algorithm>
#include <cstring>
#include <ctime>
#include <thread>
#include "GlobalRandomVariables.h"
#include "GlobalVariables.h"
#include "Funz_C.h"
#include "Funz_C_Par.h"
#include "Funz_C_Inter.h"
#include "E_Coli.h"
#include "ParameterEstimation_E_Coli.h"
#include "CV_rExp_tExp.h"
#include "LoadBar.hpp"
#include "Manipulation_Matrix.h"
#include "constants.h"

Macros
#define	max(a, b)   ( ((a) > (b)) ? (a) : (b) )
#define	min(a, b)   ( ((a) < (b)) ? (a) : (b) )

Functions
int	SolveHeat2D_Neumann2 (double **U, double **Q, double n_t, double r, int n_x, int n_y, double dt, double kd_, double &f_max)
void	timestamp ()
int	Stima_tempo (int n_c, int n_val_termine, int &j_cel_finale, int &j_cel_inizio, time_t timer1)
int	initial_position (int j, double *x, double *x0, double Raggio, int num_dist, int &cont_dist_5, int delta_dist_cont, double Delta_delta_dist)
void	funz_clear ()
void	funz_clearAll ()
void	loadbar (unsigned int x, unsigned int n, unsigned int w)
int	simulation_interacting (vector< E_coli * > batterio, double T_f, Funz_C *f, double *x_0, double dt, int n_c, double Raggio, int delta_dist, int num_dist, int const_salv, string *names_files_Ecoli_mod, string names_indice_mod, string *names_files_tau_mod, string names_file_dyn_mod, string *names_info_mod, int cont_gen_sim, double &f_max)

Macro Definition Documentation

#define max	(		a,
			b
	)		( ((a) > (b)) ? (a) : (b) )

#define min	(		a,
			b
	)		( ((a) < (b)) ? (a) : (b) )

Function Documentation

void funz_clear

(

)

This function clear the terminal (different command according to the system)

void funz_clearAll

(

)

int initial_position	(	int	j,
		double *	x,
		double *	x0,
		double	Raggio,
		int	num_dist,
		int &	cont_dist_5,
		int	delta_dist_cont,
		double	Delta_delta_dist
	)

This function set the initial position. What it does is: if the distribution is the n. 5, then update the new center, otherwise it calls dist_iniz(x,x0,Raggio,num_dist).

Parameters

x[]	position of pacterium (to be set)
x0[]	initial position, set in the menu
R	radius distribution
type	of distribution, see menu

Returns

if the initial position change return 1, otherwise 0. If the position didn't change the initial condition for this bacterium are the same as the previous one, so we don't have to perform initial-condition calculation.

void loadbar	(	unsigned int	x,
		unsigned int	n,
		unsigned int	w
	)

int simulation_interacting	(	vector< E_coli * >	batterio,
		double	T_f,
		Funz_C *	f,
		double *	x_0,
		double	dt,
		int	n_c,
		double	Raggio,
		int	delta_dist,
		int	num_dist,
		int	const_salv,
		string *	names_files_Ecoli_mod,
		string	names_indice_mod,
		string *	names_files_tau_mod,
		string	names_file_dyn_mod,
		string *	names_info_mod,
		int	cont_gen_sim,
		double &	f_max
	)

Function that performs the actual simulation of population interacting with the ligand

(double)n_t;

int SolveHeat2D_Neumann2	(	double **	U,
		double **	Q,
		double	n_t,
		double	r,
		int	n_x,
		int	n_y,
		double	dt,
		double	kd_,
		double &	f_max
	)

This function solve the 2D Heat Equation with Neumann boundary using the he Alternating Direction Implicit (ADI) method.

Parameters

U	pointer to the matrix of solution
Q	pointer to the matrix of source/sink of Equation
n_t	number of iteration of the solver
n_x,n_y	number grid points (in x and y)
dt	time step
kd_,r	parameters of the finite laplacian

int Stima_tempo	(	int	n_c,
		int	n_val_termine,
		int &	j_cel_finale,
		int &	j_cel_inizio,
		time_t	timer1
	)

This function extimate the time to finish the simulation

void timestamp

(

)