Laboratoire RDP » Biophysics Team » Cell Division Rule

#include "compute_cell_areas.h"

#include "compute_areas.h"

#include "compute_lengths.h"

#include "compute_barycenters.h"

#include "step.h"

#include <stdio.h>

#include <math.h>

#include "minimize_BFGS.h"

#include "minimize_steepest_descent.h"

#include "growth_and_chemistry.h"

#include "compute_stress_periclinal.h"

#include "compute_stress_anticlinal.h"

#include "compute_cell_walls.h"

#include <gsl/gsl_odeiv2.h>

#include <gsl/gsl_errno.h>

#include "compute_energy_and_forces.h"

#include "compute_center_of_mass.h"

#include "save_data.h"

#include "compute_shapes.h"

#include <cstdlib>

#include "constants.h"

/* this function performs a time step (growth and chemistry, then mechanics) */

void step(double *vertices, int vertices_number, int *cells_vertices, int *vertices_number_in_each_cell, int cell_number, int *wall_vertices, int wall_number, int *cell_walls,

          double *barycenters, double *shapes, double *targets, double *lengths, double *target_lengths, double *areas, double *cell_areas, double *forces, double *stress_periclinal, double *stress_anticlinal,

          int *boundary, double *growth_rate, double *relative_pressure){

/* minimization of energy: move the vertices in order to make the energy as small as possible, i.e. in order to make cells

   as close as possible of their targets */

//printf("step1\n");

minimize_BFGS(vertices_number, cell_number, vertices, cells_vertices, vertices_number_in_each_cell, barycenters, shapes, targets, areas, cell_areas, wall_vertices, wall_number, lengths, target_lengths, boundary, relative_pressure);

compute_cell_walls(vertices, cells_vertices, vertices_number_in_each_cell, cell_number, cell_walls, wall_vertices, wall_number);

compute_areas(vertices, cells_vertices, vertices_number_in_each_cell, cell_number, areas);

compute_cell_areas(vertices, cells_vertices, vertices_number_in_each_cell, cell_number, areas, cell_areas); //printf("step2\n");int bug[1]={0};

compute_barycenters(vertices, vertices_number, cells_vertices, vertices_number_in_each_cell, cell_number, barycenters);

compute_shapes(vertices, cells_vertices, vertices_number_in_each_cell, cell_number, barycenters, shapes);

compute_lengths(vertices, wall_vertices, wall_number, lengths);

for (int i=0; i<cell_number;i++){

    compute_stress_periclinal(i, vertices, vertices_number_in_each_cell, cell_number, stress_periclinal, shapes, targets, cell_areas, wall_vertices, cell_walls, lengths, target_lengths);

}

for (int i=0; i<wall_number;i++){

    compute_stress_anticlinal(i, vertices, vertices_number_in_each_cell, cell_number, stress_anticlinal, wall_vertices, cell_walls, lengths, target_lengths);

}

//for (int i=0; i<cell_number;i++){ stress_periclinal[3*i]=0; stress_periclinal[3*i+1]=0; stress_periclinal[3*i+2]=0;

//    for (int j=vertices_number_in_each_cell[i]; j<vertices_number_in_each_cell[i+1];j++){

//        stress_periclinal[3*i]+=stress_anticlinal[3*cell_walls[j]]; stress_periclinal[3*i+1]+=stress_anticlinal[3*cell_walls[j]+1]; stress_periclinal[3*i+2]+=stress_anticlinal[3*cell_walls[j]+2];

//    }

//}

        /* save the data */

//if ((iteration%100)==0 /*|| iteration==51*/){

//    FILE *f=NULL; char file_name[256];

//    sprintf(file_name,"results/boundary/results_%i/%i_%i_%i.txt",m,(int)threshold_division,((m/4)%4),iteration); f=fopen(file_name,"w+");

//    //sprintf(file_name,"results/ablation/%i_%i_%i_%i.txt",(int)threshold_division,(m/4)%300,m%4,iteration); f=fopen(file_name,"w+");

//    //sprintf(file_name,"results/isotropic/%i_%i_%i.txt",(int)threshold_division,m/2,iteration); f=fopen(file_name,"w+");

//    //sprintf(file_name,"results/results_%i/%i.txt",m,iteration); f=fopen(file_name,"w+");

//    save_data(f, vertices_number, vertices, cell_number, vertices_number_in_each_cell, cells_vertices, wall_number, barycenters, stress_periclinal, stress_anticlinal,  boundary, cell_areas, lengths,shapes, targets, growth_rate, cell_walls);

//    fclose(f);

//}

/* center the tissue */

//double center[2]={0,0};

//for (int i=0;i<cell_number;i++){center[0]+=barycenters[2*i]; center[1]+=barycenters[2*i+1];}

//center[0]/=cell_number; center[1]/=cell_number;

//for (int i=0;i<cell_number;i++){barycenters[2*i]-=center[0]; barycenters[2*i+1]-=center[1];}

//for (int i=0;i<vertices_number;i++){vertices[2*i]-=center[0]; vertices[2*i+1]-=center[1];}

    /* resolution of growth */

double noise[cell_number];

for (int i=0; i<cell_number;i++){

    noise[i]=1.+noise_amplitude*(2.*(double)(rand())/(double)RAND_MAX-1.);

}

struct parameters_list2 {int cell_number; int *cells_vertices; int *vertices_number_in_each_cell; double *shapes; double *lengths; double *cell_areas; double *barycenters;

                         int *cell_walls; int wall_number; int *boundary; int *wall_vertices; double *vertices; double *growth_rate; double *noise;};

struct parameters_list2 parameters2;

parameters2.cell_number=cell_number;

parameters2.cells_vertices=cells_vertices;

parameters2.vertices_number_in_each_cell=vertices_number_in_each_cell;

parameters2.shapes=shapes;

parameters2.lengths=lengths;

parameters2.cell_areas=cell_areas;

parameters2.barycenters=barycenters;

parameters2.cell_walls=cell_walls;

parameters2.wall_number=wall_number;

parameters2.boundary=boundary;

parameters2.wall_vertices=wall_vertices;

parameters2.vertices=vertices;

parameters2.growth_rate=growth_rate;

parameters2.noise=noise;

void *pparameters2=&parameters2;

int system_size=3*cell_number+wall_number;

double x[system_size];

for (int i=0;i<3*cell_number;i++){ x[i]=targets[i];}

for (int i=0;i<wall_number;i++){ x[3*cell_number+i]=target_lengths[i];}

gsl_odeiv2_system sys={growth_and_chemistry, NULL, system_size, pparameters2};

gsl_odeiv2_driver *d=gsl_odeiv2_driver_alloc_y_new (&sys, gsl_odeiv2_step_rk2, 1.e-3, 1.e-3, 0.);

int s; double t=0.0;

s=gsl_odeiv2_driver_apply(d, &t, 1.e1, x);

//printf("résolution croissance/chimie: %d\n",s);

//printf("test\n");

for (int i=0;i<3*cell_number;i++){ targets[i]=x[i];}

for (int i=0;i<wall_number;i++){ target_lengths[i]=x[3*cell_number+i];}

gsl_odeiv2_driver_free(d);

}