First commit.

.github/AUTHORS.md

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+## Author(s)
+-[Jeremy Vachier](https://github.com/jvachier)

.github/CONTRIBUTORS.md

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+# Contributor(s)
+
+## Main contributor(s)
+-[Jeremy Vachier](https://github.com/jvachier)

.github/pull_request_template.md

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+## Describe your changes
+
+## Issue ticket number and link
+
+## Checklist before requesting a review
+- [ ] I have performed a self-review of my code
+- [ ] If it is a core feature, I have added thorough tests.
+- [ ] Do we need to implement analytics?
+- [ ] Will this be part of a product update? If yes, please write one phrase about this update.

.gitignore

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+# Ignore Mac system files
+.DS_store
+.dSYM
+
+# Ignore all csv files
+*.csv
+
+# Ignore all png files
+*.png
+
+# Ignore all text files
+*.txt
+
+# Ignore specific file
+test.mp4
+
+# Ignore all executable files
+*.o
+*.out
+
+# Ignore jupyter checkpoints
+*.ipynb_checkpoints

src/Makefile

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+CC = g++-13
+CFLAGS = -Wall -g -fopenmp
+
+abp_2D_confine: abp_2D_confine.o print_file.o reflective_boundary_conditions.o circular_reflective_boundary_conditions.o initialization.o update_position.o check_nooverlap.o
+	$(CC) $(CFLAGS) -o abp_2D_confine.out abp_2D_confine.o print_file.o reflective_boundary_conditions.o circular_reflective_boundary_conditions.o initialization.o update_position.o check_nooverlap.o
+
+abp_2D_confine.o: abp_2D_confine.cpp
+	$(CC) -c abp_2D_confine.cpp
+
+print_file.o: print_file.cpp
+	$(CC) -c print_file.cpp
+
+reflective_boundary_conditions.o: reflective_boundary_conditions.cpp
+	$(CC) -c reflective_boundary_conditions.cpp
+
+circular_reflective_boundary_conditions.o: circular_reflective_boundary_conditions.cpp
+	$(CC) -c circular_reflective_boundary_conditions.cpp
+
+initialization.o: initialization.cpp
+	$(CC) -c initialization.cpp
+
+update_position.o: update_position.cpp
+	$(CC) -c update_position.cpp
+
+check_nooverlap.o: check_nooverlap.cpp
+	$(CC) -c check_nooverlap.cpp
+
+clean:
+	rm *.o

src/abp_3D_confine.cpp

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+/*
+ * Author: Jeremy Vachier
+ * Purpose: ABP 3D confine in a square using an Euler-Mayurama algorithm
+ * Language: C++
+ * Date: 2023
+ * Compilation line to use pragma: g++ name.cpp -fopenmp -o name.o (on mac run g++-12 ; 12 latest version obtain using brew list gcc)
+ * Compilation line to use pragma, simd (vectorization) and tuple: g++ -O3 -std=c++17 name.cpp -fopenmp -o name.o
+ */
+
+#include <iostream>
+#include <random>
+#include <cstring>
+#include <stdio.h>
+#include <cmath>
+#include <time.h>
+#include <omp.h> //import library to use pragma
+#include <tuple> //to output multiple components of a function
+
+#include "print_file.h"
+#include "reflective_boundary_conditions.h"
+#include "circular_reflective_boundary_conditions.h"
+#include "initialization.h"
+#include "update_position.h"
+#include "check_nooverlap.h"
+
+#define PI 3.141592653589793
+#define N_thread 6
+
+using namespace std;
+
+int main(int argc, char *argv[])
+{
+	// File
+	FILE *datacsv;
+	FILE *parameter;
+	parameter = fopen("parameter.txt", "r");
+	datacsv = fopen("./data/simulation.csv", "w");
+
+	// check if the file parameter is exist
+	if (parameter == NULL)
+	{
+		printf("no such file.");
+		return 0;
+	}
+
+	// read the parameters from the file
+	double epsilon, delta, Dt, De, vs;
+	double F, R, Wall;
+	int Particles;
+	char name[100];
+	char key1[] = "circular";
+	char key2[] = "squared";
+
+	bool flag = false;
+
+	printf("Select confinement geometry, either squared or circular:");
+	scanf("%s", &name);
+
+	while (flag == false)
+	{
+		if ((strcmp(name, key1) == 0) or (strcmp(name, key2) == 0))
+		{
+			flag = true;
+		}
+		else
+		{
+			printf("You have not selected the correct, please select again\n");
+			printf("Select confinement geometry, either squared or circular:");
+			scanf("%s", &name);
+			flag = false;
+		}
+	}
+	fscanf(parameter, "%lf\t%lf\t%d\t%lf\t%lf\t%lf\t%lf\n", &epsilon, &delta, &Particles, &Dt, &De, &vs, &Wall);
+	printf("%lf\t%lf\t%d\t%lf\t%lf\t%lf\t%lf\n", epsilon, delta, Particles, Dt, De, vs, Wall);
+
+	double *x = (double *)malloc(Particles * sizeof(double)); // x-position
+	double *y = (double *)malloc(Particles * sizeof(double)); // y-position
+
+	// parameters
+	const int N = 1E6; // number of iterations
+	const int L = 1.0; // particle size
+
+	// initialization of the random generator
+	random_device rdev;
+	default_random_engine generator(rdev()); // random seed -> rdev
+	// default_random_engine generator(1); //same seed
+
+	// Distributions Gaussian
+	normal_distribution<double> Gaussdistribution(0.0, 1.0);
+	// Distribution Uniform for initialization
+	uniform_real_distribution<double> distribution(-Wall, Wall);
+	// uniform_real_distribution<double> distribution_e(0.0,360.0*PI / 180.0); // directly in radian
+	uniform_real_distribution<double> distribution_e(0.0, 360.0);
+
+	double xi_px; // noise for x-position
+	double xi_py; // noise for y-position
+	double xi_e;  // noise ortientation
+	double x_x;	  // used to initialize
+	double y_y;	  // used to initialize
+	int i, j, k;
+
+	double phi = 0.0;
+	double prefactor_e = sqrt(2.0 * delta * De);
+	double prefactor_xi_px = sqrt(2.0 * delta * Dt);
+	double prefactor_xi_py = sqrt(2.0 * delta * Dt);
+	double prefactor_interaction = epsilon * 48.0;
+	double r = 5.0 * L;
+
+	clock_t tStart = clock(); // check time for one trajectory
+
+	fprintf(datacsv, "Particles,x-position,y-position,time,%s\n", name);
+
+	// initialization position and activity
+	initialization(
+		x, y, Particles,
+		generator, distribution);
+
+	check_nooverlap(
+		x, y, Particles,
+		R, L,
+		generator, distribution);
+	printf("Initialization done.\n");
+
+	// Time evoultion
+	int time;
+	for (time = 0; time < N; time++)
+	{
+		update_position(
+			x, y, phi, prefactor_e, Particles,
+			delta, De, Dt, xi_e, xi_px,
+			xi_py, vs, prefactor_xi_px, prefactor_xi_py,
+			r, R, F, prefactor_interaction,
+			generator, Gaussdistribution, distribution_e);
+		if (strcmp(name, key1) == 0)
+		{
+			circular_reflective_boundary_conditions(
+				x, y, Particles,
+				Wall, L);
+		}
+		if (strcmp(name, key2) == 0)
+		{
+			reflective_boundary_conditions(
+				x, y, Particles,
+				Wall, L);
+		}
+
+		if (time % 100 == 0 && time >= 0)
+		{
+			print_file(
+				x, y,
+				Particles, time,
+				datacsv);
+		}
+	}
+
+	printf("Time taken: %.2fs\n", (double)(clock() - tStart) / CLOCKS_PER_SEC); // time for one trajectory
+
+	free(x);
+	free(y);
+
+	fclose(datacsv);
+	return 0;
+}