cleaned up old files that don't matter

13 files changed, 0 insertions, 2186 deletions

diff --git a/src/beta_scales.c b/src/beta_scales.c
deleted file mode 100644
index 8cbc5d1..0000000
--- a/src/beta_scales.c
+++ /dev/null
@@ -1,21 +0,0 @@
-
-#include "fracture.h"
-
-double beta_scaling_flat(double beta, double x, double y) { return beta; }
-
-double beta_mag(double beta) {
-	double aa = -7.52579;
-	double bb = 9.63706;
-	double cc = 0.692515;
-	double dd = -2.47638;
-
-	return gsl_sf_exp(aa + bb * gsl_sf_erf(cc * (gsl_sf_log(beta) - dd)));
-}
-
-double beta_scaling_gaus(double beta, double x, double y) {
-	double sigma = 0.25;
-	double nu_f = 1.56;
-	double betap = beta * gsl_sf_exp((gsl_pow_2(x - 0.5) + gsl_pow_2(y - 0.5)) /
-																	 (2 * sigma * 2 * nu_f));
-	return betap;
-}
diff --git a/src/bin_values.c b/src/bin_values.c
deleted file mode 100644
index 70009c1..0000000
--- a/src/bin_values.c
+++ /dev/null
@@ -1,23 +0,0 @@
-
-#include "fracture.h"
-
-double *bin_values(graph_t *network, unsigned int width, double *values) {
-	double *binned = calloc(pow(width, 2), sizeof(double));
-	unsigned int *num_binned = calloc(pow(width, 2), sizeof(unsigned int));
-	for (unsigned int i = 0; i < network->ne; i++) {
-		if (values[i] != 0) {
-			unsigned int x = ((int)(network->ex[2 * i] * width)) % width;
-			unsigned int y = ((int)(network->ex[2 * i + 1] * width)) % width;
-			binned[width * x + y] += fabs(values[i]);
-			num_binned[width * x + y]++;
-		}
-	}
-
-	for (unsigned int i = 0; i < pow(width, 2); i++) {
-		if (num_binned[i] != 0) {
-			binned[i] /= num_binned[i];
-		}
-	}
-
-	return binned;
-}
diff --git a/src/compare_voronoi_fracture.c b/src/compare_voronoi_fracture.c
deleted file mode 100644
index 91fdcea..0000000
--- a/src/compare_voronoi_fracture.c
+++ /dev/null
@@ -1,124 +0,0 @@
-
-
-#include "fracture.h"
-
-int main(int argc, char *argv[]) {
-	int opt;
-
-	// defining variables to be (potentially) set by command line flags
-	unsigned int N, L, filename_len;
-	double beta, inf, cutoff;
-	bound_t boundary;
-
-	filename_len = 100;
-
-	N = 100;
-	L = 16;
-	beta = .3;
-	inf = 1e10;
-	cutoff = 1e-10;
-	boundary = FREE_BOUND;
-
-	int boundary_int;
-	char boundc2 = 'f';
-
-	while ((opt = getopt(argc, argv, "n:L:b:B:dcoNsCrt")) != -1) {
-		switch (opt) {
-			case 'n':
-				N = atoi(optarg);
-				break;
-			case 'L':
-				L = atoi(optarg);
-				break;
-			case 'b':
-				beta = atof(optarg);
-				break;
-			case 'B':
-				boundary_int = atoi(optarg);
-				switch (boundary_int) {
-					case 0:
-						boundary = FREE_BOUND;
-						boundc2 = 'f';
-						break;
-					case 1:
-						boundary = CYLINDER_BOUND;
-						boundc2 = 'c';
-						break;
-					default:
-						printf("boundary specifier must be 0 (FREE_BOUND) or 1 (CYLINDER_BOUND).\n");
-				}
-				break;
-			default: /* '?' */
-				exit(EXIT_FAILURE);
-		}
-	}
-
-	char *break_filename = (char *)malloc(filename_len * sizeof(char));
-	snprintf(break_filename, filename_len, "breaks_v_vc_%c_%u_%g.txt", boundc2, L, beta);
-	FILE *break_out = fopen(break_filename, "a");
-	free(break_filename);
-
-
-	// start cholmod
-	cholmod_common c;
-	CHOL_F(start)(&c);
-
-	(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-
-
-	graph_t *network = ini_voro_graph(L, false, boundary, genfunc_hyperuniform, &c);
-	net_t *perm_voltage_instance = create_instance(network, inf, true, true, &c);
-	net_t *perm_current_instance = create_instance(network, inf, false, true, &c);
-	double *fuse_thres = gen_fuse_thres(network->ne, network->ex, beta, beta_scaling_flat);
-	net_t *voltage_instance = copy_instance(perm_voltage_instance, &c);
-	net_t *current_instance = copy_instance(perm_current_instance, &c);
-	data_t *breaking_data_voltage = fracture_network(voltage_instance, fuse_thres, &c, cutoff);
-	data_t *breaking_data_current = fracture_network(current_instance, fuse_thres, &c, cutoff);
-	free_instance(voltage_instance, &c);
-	free_instance(current_instance, &c);
-	free_instance(perm_voltage_instance, &c);
-	free_instance(perm_current_instance, &c);
-	free(fuse_thres);
-
-	FILE *net_out = fopen("network.txt", "w");
-	for (unsigned int j = 0; j < network->nv; j++) {
-		fprintf(net_out, "%f %f ", network->vx[2 * j],
-						network->vx[2 * j + 1]);
-	}
-	fprintf(net_out, "\n");
-	for (unsigned int j = 0; j < network->ne; j++) {
-		fprintf(net_out, "%u %u ", network->ev[2 * j],
-						network->ev[2 * j + 1]);
-	}
-	fprintf(net_out, "\n");
-	for (unsigned int j = 0; j < network->dnv; j++) {
-		fprintf(net_out, "%f %f ", network->dvx[2 * j],
-						network->dvx[2 * j + 1]);
-	}
-	fprintf(net_out, "\n");
-	for (unsigned int j = 0; j < network->ne; j++) {
-		fprintf(net_out, "%u %u ", network->dev[2 * j],
-						network->dev[2 * j + 1]);
-	}
-
-	free_net(network, &c);
-
-	for (unsigned int j = 0; j < breaking_data_voltage->num_broken; j++) {
-		fprintf(break_out, "%u %g %g ", breaking_data_voltage->break_list[j],
-						breaking_data_voltage->extern_field[j], breaking_data_voltage->conductivity[j]);
-	}
-	fprintf(break_out, "\n");
-	for (unsigned int j = 0; j < breaking_data_current->num_broken; j++) {
-		fprintf(break_out, "%u %g %g ", breaking_data_current->break_list[j],
-						breaking_data_current->extern_field[j], breaking_data_current->conductivity[j]);
-	}
-	fprintf(break_out, "\n");
-
-	free_break_data(breaking_data_voltage);
-	free_break_data(breaking_data_current);
-	fclose(break_out);
-
-	CHOL_F(finish)(&c);
-
-	return 0;
-}
diff --git a/src/course_grain_square.c b/src/course_grain_square.c
deleted file mode 100644
index 6587e83..0000000
--- a/src/course_grain_square.c
+++ /dev/null
@@ -1,168 +0,0 @@
-
-#include "fracture.h"
-
-int main(int argc, char *argv[]) {
-	int opt;
-
-	// defining variables to be (potentially) set by command line flags
-	int num = 100;
-	int width = 16;
-	double beta = .3;
-	bool save_clusters = false;
-	bool voltage_bound = false;
-	bool output_break_data = false;
-
-	while ((opt = getopt(argc, argv, "n:w:b:cVo")) != -1) {
-		switch (opt) {
-		case 'n':
-			num = atoi(optarg);
-			break;
-		case 'w':
-			width = atoi(optarg);
-			break;
-		case 'b':
-			beta = atof(optarg);
-			break;
-		case 'c':
-			save_clusters = true;
-			break;
-		case 'V':
-			voltage_bound = true;
-			break;
-		case 'o':
-			output_break_data = true;
-			break;
-		default: /* '?' */
-			exit(EXIT_FAILURE);
-		}
-	}
-
-	FILE *break_out;
-	if (output_break_data) {
-		char *break_filename = (char *)malloc(100 * sizeof(char));
-		snprintf(break_filename, 100, "breaks_%d_%.3f_%d.txt", width, beta, num);
-		break_out = fopen(break_filename, "w");
-		free(break_filename);
-	}
-
-	bool periodic = true;
-	double inf = 1;
-	double cutoff = 1e-10;
-
-	// start cholmod
-	cholmod_common c;
-	CHOL_F(start)(&c);
-
-	/* if we use voltage boundary conditions, the laplacian matrix is positive
-	 * definite and we can use a supernodal LL decomposition.  otherwise we need
-	 * to use the simplicial LDL decomposition
-	 */
-	if (voltage_bound) {
-		(&c)->supernodal = CHOLMOD_SUPERNODAL;
-	} else {
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	}
-
-	graph_t *network = ini_square_network(width, periodic, false, &c);
-	graph_t *network_p = ini_square_network(width / 2, periodic, false, &c);
-	net_t *perm_instance = create_instance(network, inf, voltage_bound, true, &c);
-	unsigned int c_dist_size = network->dnv;
-	unsigned int c_p_dist_size = network_p->dnv;
-
-	// define arrays for saving cluster and avalanche distributions
-	unsigned int *cluster_size_dist =
-			(unsigned int *)calloc(c_dist_size, sizeof(unsigned int));
-	unsigned int *cluster_p_size_dist =
-			(unsigned int *)calloc(c_p_dist_size, sizeof(unsigned int));
-
-	printf("\n");
-	for (int DUMB = 0; DUMB < num; DUMB++) {
-		printf("\033[F\033[JCOURSEGRAIN_SQUARE: %0*d / %d\n", (int)log10(num) + 1,
-					 DUMB + 1, num);
-
-		data_t *breaking_data = NULL;
-		net_t *instance = NULL;
-		while (breaking_data == NULL) {
-			double *fuse_thres = gen_fuse_thres(
-					network->ne, network->ex, beta, beta_scaling_flat);
-			instance = copy_instance(perm_instance, &c);
-			breaking_data = fracture_network(instance, fuse_thres, &c, cutoff);
-			free_instance(instance, &c);
-			free(fuse_thres);
-		}
-
-		unsigned int min_pos = 0;
-		double min_val = DBL_MAX;
-
-		for (unsigned int j = 0; j < breaking_data->num_broken; j++) {
-			double val = fabs(breaking_data->extern_field[j]);
-			if (val < min_val) {
-				min_pos = j;
-				min_val = val;
-			}
-			if (val > 10 * min_val)
-				break;
-		}
-
-		net_t *tmp_instance = copy_instance(perm_instance, &c);
-
-		for (unsigned int i = 0; i < breaking_data->num_broken; i++) {
-			break_edge(tmp_instance, breaking_data->break_list[i], &c);
-		}
-
-		unsigned int *tmp_cluster_dist = get_cluster_dist(tmp_instance, &c);
-		for (unsigned int i = 0; i < network->dnv; i++) {
-			cluster_size_dist[i] += tmp_cluster_dist[i];
-		}
-		free(tmp_cluster_dist);
-
-		net_t *instance_p = coursegrain_square(tmp_instance, network_p, &c);
-
-		unsigned int *tmp_cluster_p_dist = get_cluster_dist(instance_p, &c);
-		for (unsigned int i = 0; i < network_p->dnv; i++) {
-			cluster_p_size_dist[i] += tmp_cluster_p_dist[i];
-		}
-		free(tmp_cluster_p_dist);
-
-		free_instance(tmp_instance, &c);
-		free_instance(instance_p, &c);
-		if (output_break_data) {
-			for (unsigned int i = 0; i < breaking_data->num_broken; i++) {
-				fprintf(break_out, "%u %f ", breaking_data->break_list[i],
-								breaking_data->extern_field[i]);
-			}
-			fprintf(break_out, "\n");
-		}
-		free(breaking_data->break_list);
-		free(breaking_data->extern_field);
-		free(breaking_data);
-	}
-
-	printf("\033[F\033[JCURRENT_SCALING: COMPLETE");
-
-	if (save_clusters) {
-		FILE *cluster_out = get_file("cluster", width, 0, beta, 1, 1, num, false);
-		for (int i = 0; i < c_dist_size; i++) {
-			fprintf(cluster_out, "%u ", cluster_size_dist[i]);
-		}
-		fprintf(cluster_out, "\n");
-		for (int i = 0; i < c_p_dist_size; i++) {
-			fprintf(cluster_out, "%u ", cluster_p_size_dist[i]);
-		}
-		fclose(cluster_out);
-	}
-
-	if (output_break_data) {
-		fclose(break_out);
-	}
-
-	free(cluster_size_dist);
-	free(cluster_p_size_dist);
-	free_instance(perm_instance, &c);
-	free_net(network, &c);
-	free_net(network_p, &c);
-
-	CHOL_F(finish)(&c);
-
-	return 0;
-}
diff --git a/src/coursegrain.c b/src/coursegrain.c
deleted file mode 100644
index 3e9db1a..0000000
--- a/src/coursegrain.c
+++ /dev/null
@@ -1,40 +0,0 @@
-
-#include "fracture.h"
-
-net_t *coursegrain_square(net_t *instance, graph_t *network_p, cholmod_common *c) {
-	unsigned int width = sqrt(instance->graph->ne);
-	assert(width % 4 == 0);
-
-	net_t *instance_p = create_instance(network_p, instance->inf, 1,
-																			instance->voltage_bound, true, c);
-
-	unsigned int width_p = width / 2;
-	bool *fuses = instance->fuses;
-
-	for (unsigned int i = 0; i < network_p->ne; i++) {
-		int xp = i / width_p;
-		int yp = i % width_p;
-		unsigned int x1 = 2 * xp;
-		unsigned int y1 = (2 * yp - 1) % width;
-		unsigned int x2 = 2 * xp;
-		unsigned int y2 = 2 * yp;
-		unsigned int x3 = 2 * xp + 1;
-		unsigned int y3 = (2 * yp - 1) % width;
-		unsigned int x4 = 2 * xp + 1;
-		unsigned int y4 = 2 * yp;
-		bool f1 = fuses[width * x1 + y1];
-		bool f2 = fuses[width * x2 + y2];
-		bool f3 = fuses[width * x3 + y3];
-		bool f4 = fuses[width * x4 + y4];
-
-		if ((f1 && f2) || (f3 && f4)) {
-			//		instance_p->fuses[i] = true;
-			//		instance_p->num_remaining_edges--;
-			break_edge(instance_p, i, c);
-		}
-	}
-
-	// fin_instance(instance_p, c);
-
-	return instance_p;
-}
diff --git a/src/current_scaling.c b/src/current_scaling.c
deleted file mode 100644
index ef36b0e..0000000
--- a/src/current_scaling.c
+++ /dev/null
@@ -1,300 +0,0 @@
-
-#include "fracture.h"
-
-int main(int argc, char *argv[]) {
-	int opt;
-
-	// defining variables to be (potentially) set by command line flags
-	int iter = 1;
-	int num = 100;
-	int width = 16;
-	double crack_len = 8;
-	double beta = .3;
-	double inf = 1e-8;
-	double cutoff = 1e-8;
-	bool beta_shift = false;
-	bool supplied_bound = false;
-	bool ash_beta = false;
-	char *bound_file;
-	bool voltage_bound = false;
-	bool use_first = false;
-	bool save_stress = false;
-	bool save_bound = false;
-	bool save_damage = false;
-	bool save_strength = false;
-
-	while ((opt = getopt(argc, argv, "n:w:b:l:i:Bf:aVFsSed")) != -1) {
-		switch (opt) {
-		case 'n':
-			num = atoi(optarg);
-			break;
-		case 'w':
-			width = atoi(optarg);
-			break;
-		case 'b':
-			beta = atof(optarg);
-			break;
-		case 'l':
-			crack_len = atof(optarg);
-			break;
-		case 'i':
-			iter = atoi(optarg);
-			break;
-		case 'B':
-			beta_shift = true;
-			break;
-		case 'a':
-			ash_beta = true;
-			break;
-		case 'V':
-			voltage_bound = true;
-			break;
-		case 'F':
-			use_first = true;
-			break;
-		case 's':
-			save_stress = true;
-			break;
-		case 'd':
-			save_damage = true;
-			break;
-		case 'e':
-			save_bound = true;
-			break;
-		case 'S':
-			save_strength = true;
-			break;
-		case 'f':
-			supplied_bound = true;
-			bound_file = optarg;
-			break;
-		default: /* '?' */
-			exit(EXIT_FAILURE);
-		}
-	}
-
-	// start cholmod
-	cholmod_common c;
-	CHOL_F(start)(&c);
-
-	/* if we use voltage boundary conditions, the laplacian matrix is positive
-	 * definite and we can use a supernodal LL decomposition.  otherwise we need
-	 * to use the simplicial LDL decomposition
-	 */
-	if (voltage_bound) {
-		(&c)->supernodal = CHOLMOD_SUPERNODAL;
-	} else {
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	}
-
-	graph_t *network = ini_square_network(width, false, true, &c);
-	net_t *perm_instance =
-			create_instance(network, inf, voltage_bound, false, &c);
-	gen_crack(perm_instance, crack_len, &c);
-	finish_instance(perm_instance, &c);
-
-	if (voltage_bound) {
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-		net_t *tmp_instance = create_instance(network, inf, false, false, &c);
-		gen_crack(tmp_instance, crack_len, &c);
-		finish_instance(tmp_instance, &c);
-		double *voltage = get_voltage(tmp_instance, &c);
-
-		for (int i = 0; i < network->num_bounds; i++) {
-			for (int j = 0; j < network->bound_inds[i + 1] - network->bound_inds[i];
-					 j++) {
-				((double *)perm_instance->boundary_cond
-						 ->x)[network->bound_verts[network->bound_inds[i] + j]] =
-						voltage[network->bound_verts[network->bound_inds[i] + j]];
-			}
-		}
-		(&c)->supernodal = CHOLMOD_SUPERNODAL;
-	}
-
-	if (supplied_bound) {
-		FILE *bound_f = fopen(bound_file, "r");
-		for (int i = 0; i < network->nv; i++) {
-			double tmp;
-			fscanf(bound_f, "%lg ", &tmp);
-			((double *)perm_instance->boundary_cond->x)[i] = tmp;
-		}
-
-		((double *)perm_instance->boundary_cond->x)[network->nv] = 0;
-		((double *)perm_instance->boundary_cond->x)[network->nv + 1] = 0;
-		fclose(bound_f);
-	}
-
-	printf("\n");
-	for (int DUMB2 = 0; DUMB2 < iter; DUMB2++) {
-
-		double *strength;
-		if (save_strength) {
-			strength = (double *)malloc(num * sizeof(double));
-		}
-
-		double *damage;
-		if (save_damage) {
-			damage = (double *)calloc(network->ne, sizeof(double));
-		}
-		double *avg_current = (double *)calloc(network->ne, sizeof(double));
-		unsigned int *num_current_skipped =
-				(unsigned int *)calloc(network->ne, sizeof(unsigned int));
-		double *avg_voltage = (double *)calloc(network->nv, sizeof(double));
-		unsigned int *num_voltage_skipped =
-				(unsigned int *)calloc(network->nv, sizeof(unsigned int));
-
-		for (int DUMB = 0; DUMB < num; DUMB++) {
-			printf("\033[F\033[JCURRENT_SCALING: ITERATION %0*d: %0*d / %d\n",
-						 (int)log10(iter) + 1, DUMB2 + 1, (int)log10(num) + 1, DUMB + 1,
-						 num);
-
-			data_t *breaking_data = NULL;
-			while (breaking_data == NULL) {
-				double *fuse_thres = gen_fuse_thres(
-						network->ne, network->ex, beta, beta_scaling_flat);
-				net_t *instance = copy_instance(perm_instance, &c);
-				breaking_data = fracture_network(instance, fuse_thres, &c, cutoff);
-				free_instance(instance, &c);
-				free(fuse_thres);
-			}
-
-			unsigned int min_pos = 0;
-			double min_val = DBL_MAX;
-
-			for (unsigned int j = 0; j < breaking_data->num_broken; j++) {
-				double val = fabs(breaking_data->extern_field[j]);
-				if (val < min_val) {
-					min_pos = j;
-					min_val = val;
-				}
-			}
-
-			if (save_strength) {
-				strength[DUMB] = fabs(breaking_data->extern_field[min_pos]);
-			}
-
-			net_t *tmp_instance = copy_instance(perm_instance, &c);
-
-			unsigned int until = min_pos;
-			if (use_first)
-				until = 1;
-			for (unsigned int i = 0; i < until; i++) {
-				break_edge(tmp_instance, breaking_data->break_list[i], &c);
-				if (save_damage) {
-					damage[breaking_data->break_list[i]] += 1. / num;
-				}
-			}
-
-			double *voltage = get_voltage(tmp_instance, &c);
-			double *current = get_current(tmp_instance, &c);
-
-			for (unsigned int i = 0; i < network->ne; i++) {
-				avg_current[i] += current[i];
-				if (current[i] == 0)
-					num_current_skipped[i]++;
-			}
-
-			for (unsigned int i = 0; i < network->nv; i++) {
-				if (tmp_instance->marks[i] == tmp_instance->marks[network->nv]) {
-					avg_voltage[i] += voltage[i];
-				} else {
-					num_voltage_skipped[i]++;
-				}
-			}
-
-			free(current);
-			free(voltage);
-			free_instance(tmp_instance, &c);
-			free(breaking_data->break_list);
-			free(breaking_data->extern_field);
-			free(breaking_data);
-		}
-
-		for (int i = 0; i < network->ne; i++) {
-			if (num_current_skipped[i] < num) {
-				avg_current[i] /= num - num_current_skipped[i];
-			}
-		}
-
-		for (int i = 0; i < network->nv; i++) {
-			if (num_voltage_skipped[i] < num) {
-				avg_voltage[i] /= num - num_voltage_skipped[i];
-			}
-		}
-
-		double *avg_field;
-		if (voltage_bound)
-			avg_field = avg_voltage;
-		else
-			avg_field = avg_current;
-
-		update_boundary(perm_instance, avg_field);
-
-		if (save_stress) {
-			char *c_filename = (char *)malloc(100 * sizeof(char));
-			snprintf(c_filename, 100, "current_%d_%g_%d_%g.txt", width, crack_len,
-							 iter, beta);
-			FILE *outfile = fopen(c_filename, "w");
-			for (int i = 0; i < network->ne; i++) {
-				fprintf(outfile, "%g ", avg_current[i]);
-			}
-			fclose(outfile);
-			free(c_filename);
-		}
-
-		if (save_damage) {
-			char *c_filename = (char *)malloc(100 * sizeof(char));
-			snprintf(c_filename, 100, "damage_%d_%g_%d_%g.txt", width, crack_len,
-							 iter, beta);
-			FILE *outfile = fopen(c_filename, "w");
-			for (int i = 0; i < network->ne; i++) {
-				fprintf(outfile, "%g ", damage[i]);
-			}
-			fclose(outfile);
-			free(c_filename);
-		}
-
-		if (save_strength) {
-			char *s_filename = (char *)malloc(100 * sizeof(char));
-			snprintf(s_filename, 100, "strength_%d_%g_%d_%g.txt", width, crack_len, iter, beta);
-			FILE *f = fopen(s_filename, "a");
-			for (int i = 0; i < num; i++) {
-				fprintf(f, "%g ", strength[i]);
-			}
-			fclose(f);
-			free(s_filename);
-		}
-
-		if (save_bound) {
-			char *b_filename = (char *)malloc(100 * sizeof(char));
-			snprintf(b_filename, 100, "bounds_%d_%g_%d_%g.txt", width, crack_len,
-							 iter, beta);
-			FILE *outfile = fopen(b_filename, "w");
-			for (int i = 0; i < network->nv; i++) {
-				fprintf(outfile, "%g ", ((double *)perm_instance->boundary_cond->x)[i]);
-			}
-			fclose(outfile);
-			free(b_filename);
-		}
-
-		free(avg_current);
-		free(avg_voltage);
-		if (save_damage) free(damage);
-		free(num_current_skipped);
-		free(num_voltage_skipped);
-		if (save_strength) {
-			free(strength);
-		}
-
-		printf(
-				"\033[F\033[JCURRENT_SCALING: ITERATION %0*d COMPLETE, BETA = %.2f\n\n",
-				(int)log10(iter) + 1, DUMB2 + 1, beta);
-	}
-
-	free_instance(perm_instance, &c);
-	free_net(network, &c);
-
-	CHOL_F(finish)(&c);
-
-	return 0;
-}
diff --git a/src/get_file.c b/src/get_file.c
deleted file mode 100644
index 9141631..0000000
--- a/src/get_file.c
+++ /dev/null
@@ -1,38 +0,0 @@
-
-#include "fracture.h"
-
-FILE *get_file(const char *prefix, unsigned int width, unsigned int crack,
-							 double beta, unsigned int iter, unsigned int num_iter,
-							 unsigned int num, bool read) {
-	int prefix_len = strlen(prefix);
-	int width_len = 1 + (int)log10(width);
-	int crack_len;
-	if (crack != 0) {
-		crack_len = 1 + (int)log10(crack);
-	} else {
-		crack_len = 1;
-	}
-	int beta_len;
-	if (beta > 1) {
-		beta_len = 1 + (int)log10(beta) + 3;
-	} else {
-		beta_len = 4;
-	}
-	int iter_len = 1 + (int)log10(num_iter);
-	int num_len = 1 + (int)log10(num);
-	int num_underscores = 5;
-
-	int len = prefix_len + width_len + crack_len + beta_len + iter_len + num_len +
-						num_underscores + 4;
-
-	char filename[len + 1];
-	snprintf(filename, sizeof(filename), "%s_%u_%u_%.2f_%0*u_%u.txt", prefix,
-					 width, crack, beta, iter_len, iter + 1, num);
-
-	char *mode = "w";
-	if (read) {
-		mode = "r";
-	}
-	FILE *file = fopen(filename, mode);
-	return file;
-}
diff --git a/src/homo_square_fracture.c b/src/homo_square_fracture.c
deleted file mode 100644
index b301136..0000000
--- a/src/homo_square_fracture.c
+++ /dev/null
@@ -1,418 +0,0 @@
-
-
-#include "fracture.h"
-
-int main(int argc, char *argv[]) {
-	int opt;
-
-	// defining variables to be (potentially) set by command line flags
-	unsigned int N, L, filename_len;
-	double beta, inf, cutoff;
-	bound_t boundary;
-	bool include_breaking, save_cluster_dist, use_voltage_boundaries, save_network,
-			 save_crit_stress, save_toughness, save_corr, save_conductivity,
-			 save_damage;
-
-	filename_len = 100;
-
-	N = 100;
-	L = 16;
-	beta = .3;
-	inf = 1e-8;
-	cutoff = 1e-10;
-	boundary = FREE_BOUND;
-	include_breaking = false;
-	save_cluster_dist = false;
-	use_voltage_boundaries = false;
-	save_network = false;
-	save_crit_stress = false;
-	save_damage = false;
-	save_corr = false;
-	save_conductivity = false;
-	save_toughness = false;
-
-	int boundary_int;
-	char boundc2 = 'f';
-
-	while ((opt = getopt(argc, argv, "n:L:b:B:dVcoNsCrt")) != -1) {
-		switch (opt) {
-			case 'n':
-				N = atoi(optarg);
-				break;
-			case 'L':
-				L = atoi(optarg);
-				break;
-			case 'b':
-				beta = atof(optarg);
-				break;
-			case 'B':
-				boundary_int = atoi(optarg);
-				switch (boundary_int) {
-					case 0:
-						boundary = FREE_BOUND;
-						boundc2 = 'f';
-						break;
-					case 1:
-						boundary = CYLINDER_BOUND;
-						boundc2 = 'c';
-						break;
-					case 2:
-						boundary = TORUS_BOUND;
-						use_voltage_boundaries = true;
-						boundc2 = 't';
-						break;
-					default:
-						printf("boundary specifier must be 0 (FREE_BOUND), 1 (CYLINDER_BOUND), or 2 (TORUS_BOUND).\n");
-				}
-				break;
-			case 'd':
-				save_damage = true;
-				break;
-			case 'V':
-				use_voltage_boundaries = true;
-				break;
-			case 'c':
-				save_cluster_dist = true;
-				break;
-			case 'o':
-				include_breaking = true;
-				break;
-			case 'N':
-				save_network = true;
-				break;
-			case 's':
-				save_crit_stress = true;
-				break;
-			case 'C':
-				save_corr = true;
-				break;
-			case 'r':
-				save_conductivity = true;
-				inf = 1;
-				break;
-			case 't':
-				save_toughness = true;
-				break;
-			default: /* '?' */
-				exit(EXIT_FAILURE);
-		}
-	}
-
-	char boundc;
-	if (use_voltage_boundaries) boundc = 'v';
-	else boundc = 'c';
-
-	FILE *break_out;
-	if (include_breaking) {
-		char *break_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(break_filename, filename_len, "breaks_s_%c_%c_%u_%g.txt", boundc, boundc2, L, beta);
-		break_out = fopen(break_filename, "a");
-		free(break_filename);
-	}
-
-	// start cholmod
-	cholmod_common c;
-	CHOL_F(start)(&c);
-
-	/* if we use voltage boundary conditions, the laplacian matrix is positive
-	 * definite and we can use a supernodal LL decomposition.  otherwise we need
-	 * to use the simplicial LDL decomposition
-	 */
-	if (use_voltage_boundaries) {
-		//(&c)->supernodal = CHOLMOD_SUPERNODAL;
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	} else {
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	}
-
-
-	graph_t *network = ini_square_network(L, boundary, false, &c);
-	net_t *perm_instance = create_instance(network, inf, use_voltage_boundaries, true, &c);
-	unsigned int c_dist_size = network->dnv;
-	unsigned int a_dist_size = network->nv;
-
-	// define arrays for saving cluster and avalanche distributions
-	unsigned int *cluster_size_dist;
-	unsigned int *avalanche_size_dist;
-	char *c_filename;
-	if (save_cluster_dist) {
-		cluster_size_dist =
-				(unsigned int *)calloc(c_dist_size, sizeof(unsigned int));
-		avalanche_size_dist =
-				(unsigned int *)calloc(a_dist_size, sizeof(unsigned int));
-
-		c_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(c_filename, filename_len, "cstr_s_%c_%c_%d_%g.txt", boundc, boundc2, L, beta);
-
-		FILE *cluster_out = fopen(c_filename, "r");
-
-		if (cluster_out != NULL) {
-			for (unsigned int i = 0; i < c_dist_size; i++) {
-				unsigned int tmp;
-				fscanf(cluster_out, "%u ", &tmp);
-				cluster_size_dist[i] = tmp;
-			}
-			fscanf(cluster_out, "\n");
-			for (unsigned int i = 0; i < a_dist_size; i++) {
-				unsigned int tmp;
-				fscanf(cluster_out, "%u ", &tmp);
-				avalanche_size_dist[i] = tmp;
-			}
-			fclose(cluster_out);
-		}
-	}
-
-	double *crit_stress;
-	if (save_crit_stress) {
-		crit_stress = (double *)malloc(N * sizeof(double));
-	}
-
-	double *avg_corr;
-	unsigned int **dists = NULL;
-	if (save_corr) {
-		avg_corr = (double *)calloc(c_dist_size, sizeof(double));
-	}
-
-	double *conductivity;
-	if (save_conductivity) {
-		conductivity = (double *)malloc(N * sizeof(double));
-	}
-
-	double *damage;
-	if (save_damage) {
-		damage = (double *)malloc(N * sizeof(double));
-	}
-
-	double *toughness;
-	if (save_toughness) {
-		toughness = (double *)malloc(N * sizeof(double));
-	}
-
-
-	printf("\n");
-	for (unsigned int i = 0; i < N; i++) {
-		printf("\033[F\033[JFRACTURE: %0*d / %d\n", (int)log10(N) + 1, i + 1, N);
-
-		double *fuse_thres = gen_fuse_thres(network->ne, network->ex, beta, beta_scaling_flat);
-		net_t *instance = copy_instance(perm_instance, &c);
-		data_t *breaking_data = fracture_network(instance, fuse_thres, &c, cutoff);
-		free_instance(instance, &c);
-		free(fuse_thres);
-
-		unsigned int max_pos = 0;
-		double max_val = 0;
-
-		for (unsigned int j = 0; j < breaking_data->num_broken; j++) {
-			double val = breaking_data->extern_field[j];
-
-			if (val > max_val) {
-				max_pos = j;
-				max_val = val;
-			}
-		}
-
-		if (save_crit_stress) {
-			crit_stress[i] =
-					breaking_data->extern_field[max_pos];
-		}
-
-		net_t *tmp_instance = copy_instance(perm_instance, &c);
-
-		unsigned int av_size = 0;
-		double cur_val = DBL_MAX;
-		for (unsigned int j = 0; j < max_pos; j++) {
-			break_edge(tmp_instance, breaking_data->break_list[j], &c);
-
-			double val = fabs(breaking_data->extern_field[j]);
-			if (save_cluster_dist) {
-				if (val < cur_val) {
-					av_size++;
-				}
-
-				if (val > cur_val) {
-					avalanche_size_dist[av_size]++;
-					av_size = 0;
-					cur_val = val;
-				}
-			}
-		}
-
-		if (save_conductivity) {
-			if (!use_voltage_boundaries) {
-				double *tmp_voltage = get_voltage(tmp_instance, &c);
-				conductivity[i] = 1/fabs(tmp_voltage[tmp_instance->graph->nv + 1] - tmp_voltage[tmp_instance->graph->nv]);
-				free(tmp_voltage);
-			} else {
-				conductivity[i] = breaking_data->conductivity[max_pos];
-			}
-		}
-
-		if (save_toughness) {
-			double tmp_toughness = 0;
-			if (max_pos > 0) {
-				double sigma1 = breaking_data->extern_field[0];
-				double epsilon1 = sigma1 / breaking_data->conductivity[0];
-				for (unsigned int j = 0; j < max_pos - 1; j++) {
-					double sigma2 = breaking_data->extern_field[j+1];
-					double epsilon2 = sigma2 / breaking_data->conductivity[j+1];
-					if (epsilon2 > epsilon1) {
-						tmp_toughness += (sigma1 + sigma2) * (epsilon2 - epsilon1) / 2;
-						sigma1 = sigma2; epsilon1 = epsilon2;
-					}
-				}
-			}
-			toughness[i] = tmp_toughness;
-		}
-
-		if (save_damage) {
-			damage[i] = ((double)max_pos) / tmp_instance->graph->ne;
-		}
-
-		if (save_cluster_dist) {
-			unsigned int *tmp_cluster_dist = get_cluster_dist(tmp_instance, &c);
-			for (unsigned int j = 0; j < tmp_instance->graph->dnv; j++) {
-				cluster_size_dist[j] += tmp_cluster_dist[j];
-			}
-			free(tmp_cluster_dist);
-		}
-
-		if (save_corr) {
-			double *tmp_corr = get_corr(tmp_instance, dists, &c);
-			for (unsigned int j = 0; j < tmp_instance->graph->dnv; j++) {
-				avg_corr[i] += tmp_corr[j] / N;
-			}
-			free(tmp_corr);
-		}
-
-		if (save_network) {
-			FILE *net_out = fopen("network.txt", "w");
-			for (unsigned int j = 0; j < network->nv; j++) {
-				fprintf(net_out, "%f %f ", network->vx[2 * j],
-								tmp_instance->graph->vx[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->graph->ne; j++) {
-				fprintf(net_out, "%u %u ", tmp_instance->graph->ev[2 * j],
-								tmp_instance->graph->ev[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->graph->dnv; j++) {
-				fprintf(net_out, "%f %f ", tmp_instance->graph->dvx[2 * j],
-								tmp_instance->graph->dvx[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->graph->ne; j++) {
-				fprintf(net_out, "%u %u ", tmp_instance->graph->dev[2 * j],
-								tmp_instance->graph->dev[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->graph->ne; j++) {
-				fprintf(net_out, "%d ", tmp_instance->fuses[j]);
-			}
-			fclose(net_out);
-		}
-
-		free_instance(tmp_instance, &c);
-
-		if (include_breaking) {
-			for (unsigned int j = 0; j < breaking_data->num_broken; j++) {
-				fprintf(break_out, "%u %g %g ", breaking_data->break_list[j],
-								breaking_data->extern_field[j], breaking_data->conductivity[j]);
-			}
-			fprintf(break_out, "\n");
-		}
-
-		free_break_data(breaking_data);
-	}
-
-	printf("\033[F\033[JFRACTURE: COMPLETE\n");
-
-	free_instance(perm_instance, &c);
-	free_net(network, &c);
-
-	if (save_cluster_dist) {
-		FILE *cluster_out = fopen(c_filename, "w");
-
-		for (int i = 0; i < c_dist_size; i++) {
-			fprintf(cluster_out, "%u ", cluster_size_dist[i]);
-		}
-		fprintf(cluster_out, "\n");
-		for (int i = 0; i < a_dist_size; i++) {
-			fprintf(cluster_out, "%u ", avalanche_size_dist[i]);
-		}
-		fclose(cluster_out);
-
-		free(c_filename);
-		free(cluster_size_dist);
-		free(avalanche_size_dist);
-	}
-
-	if (save_corr) {
-		char *corr_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(corr_filename, filename_len, "corr_s_%c_%c_%d_%g.txt", boundc, boundc2, L,
-						 beta);
-		FILE *corr_file = fopen(corr_filename, "w");
-		for (unsigned int i = 0; i < c_dist_size; i++) {
-			fprintf(corr_file, "%g ", avg_corr[i]);
-		}
-		fclose(corr_file);
-		free(corr_filename);
-		free(avg_corr);
-	}
-
-	if (save_conductivity) {
-		char *cond_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(cond_filename, filename_len, "cond_s_%c_%c_%d_%g.txt", boundc, boundc2, L, beta);
-		FILE *cond_file = fopen(cond_filename, "a");
-		for (unsigned int i = 0; i < N; i++) {
-			fprintf(cond_file, "%g ", conductivity[i]);
-		}
-		fclose(cond_file);
-		free(cond_filename);
-		free(conductivity);
-	}
-
-	if (save_toughness) {
-		char *tough_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(tough_filename, filename_len, "tuff_s_%c_%c_%d_%g.txt", boundc, boundc2, L, beta);
-		FILE *tough_file = fopen(tough_filename, "a");
-		for (unsigned int i = 0; i < N; i++) {
-			fprintf(tough_file, "%g ", toughness[i]);
-		}
-		fclose(tough_file);
-		free(tough_filename);
-		free(toughness);
-	}
-
-	if (save_damage) {
-		char *hdam_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(hdam_filename, filename_len, "damg_s_%c_%c_%d_%g.txt", boundc, boundc2, L, beta);
-		FILE *hdam_file = fopen(hdam_filename, "a");
-		for (unsigned int i = 0; i < N; i++) {
-			fprintf(hdam_file, "%g ", damage[i]);
-		}
-		fclose(hdam_file);
-		free(hdam_filename);
-		free(damage);
-	}
-
-	if (include_breaking) {
-		fclose(break_out);
-	}
-
-	if (save_crit_stress) {
-		char *a_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(a_filename, filename_len, "strs_s_%c_%c_%d_%g.txt", boundc, boundc2, L, beta);
-		FILE *a_file = fopen(a_filename, "a");
-		for (int i = 0; i < N; i++) {
-			fprintf(a_file, "%g ", crit_stress[i]);
-		}
-		fclose(a_file);
-		free(a_filename);
-		free(crit_stress);
-	}
-
-	CHOL_F(finish)(&c);
-
-	return 0;
-}
diff --git a/src/homo_voronoi_fracture.c b/src/homo_voronoi_fracture.c
deleted file mode 100644
index 85a9c2b..0000000
--- a/src/homo_voronoi_fracture.c
+++ /dev/null
@@ -1,405 +0,0 @@
-
-
-#include "fracture.h"
-
-int main(int argc, char *argv[]) {
-	int opt;
-
-	// defining variables to be (potentially) set by command line flags
-	uint8_t filename_len;
-	uint32_t N;
-	uint_t L;
-	double beta, inf, cutoff;
-	bool include_breaking, save_cluster_dist, use_voltage_boundaries, use_dual, save_network,
-			 save_crit_stress, save_toughness, save_conductivity,
-			 save_damage;
-	bound_t boundary;
-
-	filename_len = 100;
-
-	N = 100;
-	L = 16;
-	beta = .3;
-	inf = 1e10;
-	cutoff = 1e-9;
-	boundary = FREE_BOUND;
-	include_breaking = false;
-	save_cluster_dist = false;
-	use_voltage_boundaries = false;
-	use_dual = false;
-	save_network = false;
-	save_crit_stress = false;
-	save_damage = false;
-	save_conductivity = false;
-	save_toughness = false;
-
-	uint8_t bound_i;
-	char boundc2 = 'f';
-
-	while ((opt = getopt(argc, argv, "n:L:b:B:dVcoNsCrtD")) != -1) {
-		switch (opt) {
-			case 'n':
-				N = atoi(optarg);
-				break;
-			case 'L':
-				L = atoi(optarg);
-				break;
-			case 'b':
-				beta = atof(optarg);
-				break;
-			case 'B':
-				bound_i = atoi(optarg);
-				switch (bound_i) {
-					case 0:
-						boundary = FREE_BOUND;
-						boundc2 = 'f';
-						break;
-					case 1:
-						boundary = CYLINDER_BOUND;
-						boundc2 = 'c';
-						break;
-					case 2:
-						boundary = TORUS_BOUND;
-						use_voltage_boundaries = true;
-						boundc2 = 't';
-						break;
-					case 3:
-						boundary = EMBEDDED_BOUND;
-						boundc2 = 'e';
-						use_dual = true;
-						break;
-					default:
-						printf("boundary specifier must be 0 (FREE_BOUND), 1 (CYLINDER_BOUND), or 2 (TORUS_BOUND).\n");
-						exit(EXIT_FAILURE);
-				}
-				break;
-			case 'd':
-				save_damage = true;
-				break;
-			case 'V':
-				use_voltage_boundaries = true;
-				break;
-			case 'D':
-				use_dual = true;
-				break;
-			case 'c':
-				save_cluster_dist = true;
-				break;
-			case 'o':
-				include_breaking = true;
-				break;
-			case 'N':
-				save_network = true;
-				break;
-			case 's':
-				save_crit_stress = true;
-				break;
-			case 'r':
-				save_conductivity = true;
-				//inf = 1;
-				break;
-			case 't':
-				save_toughness = true;
-				break;
-			default: /* '?' */
-				exit(EXIT_FAILURE);
-		}
-	}
-
-	char boundc;
-	if (use_voltage_boundaries) boundc = 'v';
-	else boundc = 'c';
-
-	FILE *break_out;
-	if (include_breaking) {
-		char *break_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(break_filename, filename_len, "breaks_v_%c_%c_%u_%g.txt", boundc, boundc2, L, beta);
-		break_out = fopen(break_filename, "a");
-		free(break_filename);
-	}
-
-	uint_t voronoi_max_verts, c_dist_size, a_dist_size;
-
-	voronoi_max_verts = 4 * pow(L, 2);
-	c_dist_size = voronoi_max_verts;
-	a_dist_size = voronoi_max_verts;
-
-	if (voronoi_max_verts > CINT_MAX) {
-		exit(EXIT_FAILURE);
-	}
-
-	// define arrays for saving cluster and avalanche distributions
-	uint32_t *cluster_size_dist;
-	uint32_t *avalanche_size_dist;
-	char *c_filename;
-	char *a_filename;
-	if (save_cluster_dist) {
-		cluster_size_dist =
-				(uint32_t *)malloc(c_dist_size * sizeof(uint32_t));
-		avalanche_size_dist =
-				(uint32_t *)malloc(a_dist_size * sizeof(uint32_t));
-
-		c_filename = (char *)malloc(filename_len * sizeof(char));
-		a_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(c_filename, filename_len, "cstr_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
-		snprintf(a_filename, filename_len, "avln_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
-
-		FILE *cluster_out = fopen(c_filename, "rb");
-		FILE *avalanche_out = fopen(a_filename, "rb");
-
-		if (cluster_out != NULL) {
-			fread(cluster_size_dist, sizeof(uint32_t), c_dist_size, cluster_out);
-			fclose(cluster_out);
-		}
-		if (avalanche_out != NULL) {
-			fread(avalanche_size_dist, sizeof(uint32_t), a_dist_size, avalanche_out);
-			fclose(avalanche_out);
-		}
-	}
-
-	double *crit_stress;
-	if (save_crit_stress) {
-		crit_stress = (double *)malloc(N * sizeof(double));
-	}
-
-	double *conductivity;
-	if (save_conductivity) {
-		conductivity = (double *)malloc(N * sizeof(double));
-	}
-
-	// define arrays for saving damage distributions
-	uint32_t *damage;
-	char *d_filename;
-	if (save_damage) {
-		damage =
-				(uint32_t *)malloc(a_dist_size * sizeof(uint32_t));
-
-		d_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(d_filename, filename_len, "damg_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
-
-		FILE *damage_out = fopen(d_filename, "rb");
-
-		if (damage_out != NULL) {
-			fread(damage, sizeof(uint32_t), a_dist_size, damage_out);
-			fclose(damage_out);
-		}
-	}
-
-	double *toughness;
-	if (save_toughness) {
-		toughness = (double *)malloc(N * sizeof(double));
-	}
-
-
-	// start cholmod
-	cholmod_common c;
-	CHOL_F(start)(&c);
-
-	/* if we use voltage boundary conditions, the laplacian matrix is positive
-	 * definite and we can use a supernodal LL decomposition.  otherwise we need
-	 * to use the simplicial LDL decomposition
-	 */
-	if (use_voltage_boundaries) {
-		//(&c)->supernodal = CHOLMOD_SUPERNODAL;
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	} else {
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	}
-
-
-	printf("\n");
-	for (uint32_t i = 0; i < N; i++) {
-		printf("\033[F\033[JFRACTURE: %0*d / %d\n", (uint8_t)log10(N) + 1, i + 1, N);
-
-		graph_t *network = ini_voro_graph(L, boundary, use_dual, genfunc_hyperuniform, &c);
-		net_t *perm_instance = create_instance(network, inf, use_voltage_boundaries, true, &c);
-		double *fuse_thres = gen_fuse_thres(network->ne, network->ex, beta, beta_scaling_flat);
-		net_t *instance = copy_instance(perm_instance, &c);
-		data_t *breaking_data = fracture_network(instance, fuse_thres, &c, cutoff);
-		free_instance(instance, &c);
-		free(fuse_thres);
-
-		uint_t max_pos = 0;
-		double max_val = 0;
-
-		for (uint_t j = 0; j < breaking_data->num_broken; j++) {
-			double val = breaking_data->extern_field[j];
-
-			if (val > max_val) {
-				max_pos = j;
-				max_val = val;
-			}
-		}
-
-		if (save_crit_stress) {
-			crit_stress[i] =
-					breaking_data->extern_field[max_pos];
-		}
-
-		net_t *tmp_instance = copy_instance(perm_instance, &c);
-
-		uint_t av_size = 0;
-		double cur_val = 0;
-		for (uint_t j = 0; j < max_pos; j++) {
-			break_edge(tmp_instance, breaking_data->break_list[j], &c);
-
-			double val = breaking_data->extern_field[j];
-			if (save_cluster_dist) {
-				if (val < cur_val) {
-					av_size++;
-				}
-
-				if (val > cur_val) {
-					avalanche_size_dist[av_size]++;
-					av_size = 0;
-					cur_val = val;
-				}
-			}
-		}
-
-		if (save_conductivity) {
-			if (!use_voltage_boundaries) {
-				double *tmp_voltage = get_voltage(tmp_instance, &c);
-				conductivity[i] = 1/fabs(tmp_voltage[tmp_instance->graph->nv + 1] - tmp_voltage[tmp_instance->graph->nv]);
-				free(tmp_voltage);
-			} else {
-				conductivity[i] = breaking_data->conductivity[max_pos];
-			}
-		}
-
-		if (save_toughness) {
-			double tmp_toughness = 0;
-			if (max_pos > 0) {
-				double sigma1 = breaking_data->extern_field[0];
-				double epsilon1 = sigma1 / breaking_data->conductivity[0];
-				for (uint_t j = 0; j < max_pos - 1; j++) {
-					double sigma2 = breaking_data->extern_field[j+1];
-					double epsilon2 = sigma2 / breaking_data->conductivity[j+1];
-					if (epsilon2 > epsilon1) {
-						tmp_toughness += (sigma1 + sigma2) * (epsilon2 - epsilon1) / 2;
-						sigma1 = sigma2; epsilon1 = epsilon2;
-					}
-				}
-			}
-			toughness[i] = tmp_toughness;
-		}
-
-		if (save_damage) {
-			damage[max_pos]++;
-		}
-
-		if (save_cluster_dist) {
-			uint_t *tmp_cluster_dist = get_cluster_dist(tmp_instance, &c);
-			for (uint_t j = 0; j < tmp_instance->graph->dnv; j++) {
-				cluster_size_dist[j] += tmp_cluster_dist[j];
-			}
-			free(tmp_cluster_dist);
-		}
-
-		if (save_network) {
-			FILE *net_out = fopen("network.txt", "w");
-			for (uint_t j = 0; j < network->nv; j++) {
-				fprintf(net_out, "%f %f ", network->vx[2 * j],
-								tmp_instance->graph->vx[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < tmp_instance->graph->ne; j++) {
-				fprintf(net_out, "%u %u ", tmp_instance->graph->ev[2 * j],
-								tmp_instance->graph->ev[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < tmp_instance->graph->dnv; j++) {
-				fprintf(net_out, "%f %f ", tmp_instance->graph->dvx[2 * j],
-								tmp_instance->graph->dvx[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < tmp_instance->graph->ne; j++) {
-				fprintf(net_out, "%u %u ", tmp_instance->graph->dev[2 * j],
-								tmp_instance->graph->dev[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < tmp_instance->graph->ne; j++) {
-				fprintf(net_out, "%d ", tmp_instance->fuses[j]);
-			}
-			fclose(net_out);
-		}
-
-		free_instance(tmp_instance, &c);
-		free_instance(perm_instance, &c);
-		free_net(network, &c);
-
-		if (include_breaking) {
-			for (uint_t j = 0; j < breaking_data->num_broken; j++) {
-				fprintf(break_out, "%u %g %g ", breaking_data->break_list[j],
-								breaking_data->extern_field[j], breaking_data->conductivity[j]);
-			}
-			fprintf(break_out, "\n");
-		}
-
-		free_break_data(breaking_data);
-	}
-
-	printf("\033[F\033[JFRACTURE: COMPLETE\n");
-
-	if (save_cluster_dist) {
-		FILE *cluster_out = fopen(c_filename, "wb");
-		FILE *avalanche_out = fopen(a_filename, "wb");
-
-		fwrite(cluster_size_dist, sizeof(uint32_t), c_dist_size, cluster_out);
-		fwrite(avalanche_size_dist, sizeof(uint32_t), a_dist_size, avalanche_out);
-
-		fclose(cluster_out);
-		fclose(avalanche_out);
-
-		free(c_filename);
-		free(a_filename);
-		free(cluster_size_dist);
-		free(avalanche_size_dist);
-	}
-
-	if (save_conductivity) {
-		char *cond_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(cond_filename, filename_len, "cond_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
-		FILE *cond_file = fopen(cond_filename, "ab");
-		fwrite(conductivity, sizeof(double), N, cond_file);
-		fclose(cond_file);
-		free(cond_filename);
-		free(conductivity);
-	}
-
-	if (save_toughness) {
-		char *tough_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(tough_filename, filename_len, "tuff_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
-		FILE *tough_file = fopen(tough_filename, "ab");
-		fwrite(toughness, sizeof(double), N, tough_file);
-		fclose(tough_file);
-		free(tough_filename);
-		free(toughness);
-	}
-
-	if (save_damage) {
-		FILE *hdam_file = fopen(d_filename, "wb");
-		fwrite(damage, sizeof(uint32_t), a_dist_size, hdam_file);
-		fclose(hdam_file);
-		free(d_filename);
-		free(damage);
-	}
-
-	if (include_breaking) {
-		fclose(break_out);
-	}
-
-	if (save_crit_stress) {
-		char *str_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(str_filename, filename_len, "strs_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
-		FILE *str_file = fopen(str_filename, "ab");
-		fwrite(crit_stress, sizeof(double), N, str_file);
-		fclose(str_file);
-		free(str_filename);
-		free(crit_stress);
-	}
-
-	CHOL_F(finish)(&c);
-
-	return 0;
-}
diff --git a/src/toy_setup.c b/src/toy_setup.c
deleted file mode 100644
index 228acbc..0000000
--- a/src/toy_setup.c
+++ /dev/null
@@ -1,37 +0,0 @@
-
-#include "fracture.h"
-
-bool break_fuses(unsigned int width, double *fuse_thres, double *field,
-								 bool *fuses) {
-	assert(fuse_thres != NULL);
-	assert(field != NULL);
-	assert(fuses != NULL);
-	unsigned int size = pow(width, 2);
-
-	for (unsigned int i = 0; i < size; i++) {
-		if (fuses[i]) {
-			if (1 / fuse_thres[i] > field[i]) {
-				fuses[i] = 0;
-			}
-		}
-	}
-
-	return true;
-}
-
-bool gen_toy_field(unsigned int width, double strength, double *field) {
-	assert(field != NULL);
-	unsigned int size = pow(width, 2);
-
-	for (unsigned intint i = 0; i < size; i++) {
-		int x = i / width + 1;
-		int y = i % width + 1;
-		if (y < (width + 1) / 2.)
-			field[i] = fabs((width) / 2. - x) / strength;
-		else
-			field[i] =
-					sqrt(pow((width) / 2. - x, 2) + pow((width) / 2. - y, 2)) / strength;
-	}
-
-	return true;
-}
diff --git a/src/update_beta.c b/src/update_beta.c
deleted file mode 100644
index 4c1bf65..0000000
--- a/src/update_beta.c
+++ /dev/null
@@ -1,34 +0,0 @@
-
-#include "fracture.h"
-
-double f(double damage) {
-	assert(damage <= 1 && damage >= 0);
-	return sqrt(1 - sqrt(1 - damage));
-	//	return 0.5 - 0.68182 * (0.5 - damage);
-}
-
-double update_beta(double beta, unsigned int width, const double *stress,
-									 const double *damage, double bound_total) {
-
-	double total = 0;
-	unsigned int num_totaled = 0;
-
-	for (unsigned int i = 0; i < pow(width, 2); i++) {
-		unsigned int stress_index =
-				width / 4 + (width / 4 + (i / width) / 2) * width + (i % width) / 2;
-		double outer_damage = f(pow(fabs(stress[i]), beta));
-		double inner_stress = fabs(2 * stress[stress_index] / bound_total);
-
-		if (outer_damage > 0 && inner_stress > 0 && inner_stress != 1) {
-			total += log(outer_damage) / log(inner_stress);
-			num_totaled++;
-		}
-	}
-
-	assert(num_totaled > 0);
-	assert(total == total);
-
-	double new_beta = total / num_totaled;
-
-	return new_beta;
-}
diff --git a/src/update_boundary.c b/src/update_boundary.c
deleted file mode 100644
index 6bc4fca..0000000
--- a/src/update_boundary.c
+++ /dev/null
@@ -1,86 +0,0 @@
-
-#include "fracture.h"
-
-void update_boundary(net_t *instance, const double *avg_field) {
-	int size = instance->graph->ne;
-	int width = sqrt(size);
-	int num_verts = instance->graph->nv;
-	double *boundary = (double *)instance->boundary_cond->x;
-
-	boundary[num_verts] = 0;
-	boundary[num_verts + 1] = 0;
-
-	if (instance->voltage_bound) {
-		for (int i = 0; i < width / 4; i++) {
-			int t_ind = (width + 1) * (width / 8) + width / 4 - 1 + i;
-			double t_val = avg_field[t_ind];
-			boundary[2 * i] = t_val;
-			boundary[2 * i + 1] = t_val;
-
-			int b_ind = num_verts - (width + 1) * (width / 8) - width / 4 - i;
-			double b_val = avg_field[b_ind];
-			boundary[num_verts - 1 - 2 * i] = b_val;
-			boundary[num_verts - 2 - 2 * i] = b_val;
-
-			int l_ind = (width + 1) * (width / 8) + width / 2 + width / 4 - 1 +
-									i * (width + 1);
-			double l_val = avg_field[l_ind];
-			boundary[width / 2 + 2 * i * (width + 1)] = l_val;
-			boundary[width / 2 + (2 * i + 1) * (width + 1)] = l_val;
-
-			int r_ind = (width + 1) * (width / 8) + width - 1 + i * (width + 1);
-			double r_val = avg_field[r_ind];
-			boundary[width + 2 * i * (width + 1)] = r_val;
-			boundary[width + (2 * i + 1) * (width + 1)] = r_val;
-		}
-	} else {
-		const double *stress = avg_field;
-
-		for (int i = 0; i < width / 4; i++) {
-			boundary[2 * i] = stress[(width / 4 - 1) * width + width / 4 + 2 * i] +
-												stress[(width / 4 - 1) * width + width / 4 + 1 + 2 * i];
-			boundary[2 * i + 1] =
-					stress[(width / 4 - 1) * width + width / 4 + 2 * i] +
-					stress[(width / 4 - 1) * width + width / 4 + 1 + 2 * i];
-
-			boundary[num_verts - 2 * i - 1] =
-					-stress[size - 1 - ((width / 4 - 1) * width + width / 4 + 2 * i)] -
-					stress[size - 1 - ((width / 4 - 1) * width + width / 4 + 1 + 2 * i)];
-			boundary[num_verts - 2 * i - 2] =
-					-stress[size - 1 - ((width / 4 - 1) * width + width / 4 + 2 * i)] -
-					stress[size - 1 - ((width / 4 - 1) * width + width / 4 + 1 + 2 * i)];
-
-			boundary[(width + 1) / 2 + 2 * i * (width + 1)] =
-					stress[((width / 4) + 2 * i) * width + width / 4 - 1] -
-					stress[((width / 4) + 2 * i + 1) * width + width / 4 - 1];
-			boundary[(width + 1) / 2 + (2 * i + 1) * (width + 1)] =
-					stress[((width / 4) + 2 * i) * width + width / 4 - 1] -
-					stress[((width / 4) + 2 * i + 1) * width + width / 4 - 1];
-
-			boundary[(width + 1) / 2 + 2 * i * (width + 1) + width / 2] =
-					stress[((width / 4) + 2 * i) * width + width / 4 + width / 2] -
-					stress[((width / 4) + 2 * i + 1) * width + width / 4 + width / 2];
-			boundary[(width + 1) / 2 + (2 * i + 1) * (width + 1) + width / 2] =
-					stress[((width / 4) + 2 * i) * width + width / 4 + width / 2] -
-					stress[((width / 4) + 2 * i + 1) * width + width / 4 + width / 2];
-		}
-
-		double s_total = 0;
-		double total = 0;
-		for (int i = 0; i < num_verts; i++) {
-			if (boundary[i] != boundary[i]) {
-				boundary[i] = 0;
-			} else {
-				total += fabs(boundary[i]);
-				s_total += boundary[i];
-			}
-		}
-
-		// assert(fabs(s_total) < inf);
-		boundary[num_verts] -= s_total;
-
-		for (int i = 0; i < num_verts + 1; i++) {
-			boundary[i] /= total;
-		}
-	}
-}
diff --git a/src/voro_fracture.c b/src/voro_fracture.c
deleted file mode 100644
index 237192a..0000000
--- a/src/voro_fracture.c
+++ /dev/null
@@ -1,492 +0,0 @@
-
-
-#include "fracture.h"
-
-int main(int argc, char *argv[]) {
-	int opt;
-
-	// defining variables to be (potentially) set by command line flags
-	uint8_t filename_len;
-	uint32_t N;
-	uint_t L;
-	double beta, inf, cutoff, crack_len;
-	bool save_data, save_cluster_dist, use_voltage_boundaries, use_dual, save_network,
-			 save_crit_stress, save_stress_field, save_voltage_field, save_toughness, save_conductivity,
-			 save_damage, save_damage_field;
-	bound_t boundary;
-
-
-	// assume filenames will be less than 100 characters
-
-	filename_len = 100;
-
-
-	// set default values
-
-	N = 100;
-	L = 16;
-	crack_len = 0.;
-	beta = .3;
-	inf = 1e10;
-	cutoff = 1e-9;
-	boundary = FREE_BOUND;
-	save_data = false;
-	save_cluster_dist = false;
-	use_voltage_boundaries = false;
-	use_dual = false;
-	save_network = false;
-	save_crit_stress = false;
-	save_stress_field = false;
-	save_voltage_field = false;
-	save_damage = false;
-	save_damage_field = false;
-	save_conductivity = false;
-	save_toughness = false;
-
-
-	uint8_t bound_i;
-	char boundc2 = 'f';
-
-
-	// get commandline options
-
-	while ((opt = getopt(argc, argv, "n:L:b:B:dVcoNsCrtDSvel:")) != -1) {
-		switch (opt) {
-			case 'n':
-				N = atoi(optarg);
-				break;
-			case 'L':
-				L = atoi(optarg);
-				break;
-			case 'b':
-				beta = atof(optarg);
-				break;
-			case 'l':
-				crack_len = atof(optarg);
-				break;
-			case 'B':
-				bound_i = atoi(optarg);
-				switch (bound_i) {
-					case 0:
-						boundary = FREE_BOUND;
-						boundc2 = 'f';
-						break;
-					case 1:
-						boundary = CYLINDER_BOUND;
-						boundc2 = 'c';
-						break;
-					case 2:
-						boundary = TORUS_BOUND;
-						use_voltage_boundaries = true;
-						boundc2 = 't';
-						break;
-					case 3:
-						boundary = EMBEDDED_BOUND;
-						boundc2 = 'e';
-						use_dual = true;
-						use_voltage_boundaries = true;
-						break;
-					default:
-						printf("boundary specifier must be 0 (FREE_BOUND), 1 (CYLINDER_BOUND), or 2 (TORUS_BOUND).\n");
-						exit(EXIT_FAILURE);
-				}
-				break;
-			case 'd':
-				save_damage = true;
-				break;
-			case 'e':
-				save_damage_field = true;
-				break;
-			case 'V':
-				use_voltage_boundaries = true;
-				break;
-			case 'D':
-				use_dual = true;
-				break;
-			case 'c':
-				save_cluster_dist = true;
-				break;
-			case 'o':
-				save_data = true;
-				break;
-			case 'N':
-				save_network = true;
-				break;
-			case 's':
-				save_crit_stress = true;
-				break;
-			case 'S':
-				save_stress_field = true;
-				break;
-			case 'v':
-				save_voltage_field = true;
-				break;
-			case 'r':
-				save_conductivity = true;
-				//inf = 1;
-				break;
-			case 't':
-				save_toughness = true;
-				break;
-			default: /* '?' */
-				exit(EXIT_FAILURE);
-		}
-	}
-
-
-	char boundc;
-	if (use_voltage_boundaries) boundc = 'v';
-	else boundc = 'c';
-
-	FILE *data_out;
-	if (save_data) {
-		char *data_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(data_filename, filename_len, "data_v_%c_%c_%u_%g_%g.txt", boundc, boundc2, L, beta, crack_len);
-		data_out = fopen(data_filename, "a");
-		free(data_filename);
-	}
-
-	uint_t voronoi_max_verts, c_dist_size, a_dist_size;
-
-	voronoi_max_verts = 4 * pow(L, 2);
-	c_dist_size = voronoi_max_verts;
-	a_dist_size = voronoi_max_verts;
-
-	if (voronoi_max_verts > CINT_MAX) {
-		exit(EXIT_FAILURE);
-	}
-
-	// define arrays for saving cluster and avalanche distributions
-	uint32_t *cluster_size_dist;
-	uint32_t *avalanche_size_dist;
-	char *c_filename;
-	char *a_filename;
-	if (save_cluster_dist) {
-		cluster_size_dist =
-				(uint32_t *)malloc(c_dist_size * sizeof(uint32_t));
-		avalanche_size_dist =
-				(uint32_t *)malloc(a_dist_size * sizeof(uint32_t));
-
-		c_filename = (char *)malloc(filename_len * sizeof(char));
-		a_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(c_filename, filename_len, "cstr_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		snprintf(a_filename, filename_len, "avln_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-
-		FILE *cluster_out = fopen(c_filename, "rb");
-		FILE *avalanche_out = fopen(a_filename, "rb");
-
-		if (cluster_out != NULL) {
-			fread(cluster_size_dist, sizeof(uint32_t), c_dist_size, cluster_out);
-			fclose(cluster_out);
-		}
-		if (avalanche_out != NULL) {
-			fread(avalanche_size_dist, sizeof(uint32_t), a_dist_size, avalanche_out);
-			fclose(avalanche_out);
-		}
-	}
-
-	double *crit_stress;
-	if (save_crit_stress) {
-		crit_stress = (double *)malloc(N * sizeof(double));
-	}
-
-	double *stress_field;
-	unsigned int stress_pos = 0;
-	if (save_stress_field) {
-		stress_field = (double *)malloc(3 * N * voronoi_max_verts * sizeof(double));
-	}
-
-	double *voltage_field;
-	unsigned int voltage_pos = 0;
-	if (save_voltage_field) {
-		voltage_field = (double *)malloc(3 * N * voronoi_max_verts * sizeof(double));
-	}
-
-	double *damage_field;
-	unsigned int damage_pos = 0;
-	if (save_damage_field) {
-		damage_field = (double *)malloc(2 * N * voronoi_max_verts * sizeof(double));
-	}
-
-	double *conductivity;
-	if (save_conductivity) {
-		conductivity = (double *)malloc(N * sizeof(double));
-	}
-
-	// define arrays for saving damage distributions
-	uint32_t *damage;
-	char *d_filename;
-	if (save_damage) {
-		damage =
-				(uint32_t *)malloc(a_dist_size * sizeof(uint32_t));
-
-		d_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(d_filename, filename_len, "damg_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-
-		FILE *damage_out = fopen(d_filename, "rb");
-
-		if (damage_out != NULL) {
-			fread(damage, sizeof(uint32_t), a_dist_size, damage_out);
-			fclose(damage_out);
-		}
-	}
-
-	double *toughness;
-	if (save_toughness) {
-		toughness = (double *)malloc(N * sizeof(double));
-	}
-
-
-	// start cholmod
-	cholmod_common c;
-	CHOL_F(start)(&c);
-
-	/* if we use voltage boundary conditions, the laplacian matrix is positive
-	 * definite and we can use a supernodal LL decomposition.  otherwise we need
-	 * to use the simplicial LDL decomposition
-	 */
-	if (use_voltage_boundaries) {
-		//(&c)->supernodal = CHOLMOD_SUPERNODAL;
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	} else {
-		(&c)->supernodal = CHOLMOD_SIMPLICIAL;
-	}
-
-
-	printf("\n");
-	for (uint32_t i = 0; i < N; i++) {
-		printf("\033[F\033[JFRACTURE: %0*d / %d\n", (uint8_t)log10(N) + 1, i + 1, N);
-
-		graph_t *g = ini_voro_graph(L, boundary, use_dual, genfunc_hyperuniform, &c);
-		net_t *net = net_create(g, inf, beta, crack_len, use_voltage_boundaries, &c);
-		net_t *tmp_net = net_copy(net, &c);
-		data_t *data = net_fracture(tmp_net, &c, cutoff);
-		net_free(tmp_net, &c);
-
-		uint_t max_pos = 0;
-		double max_val = 0;
-
-		for (uint_t j = 0; j < data->num_broken; j++) {
-			double val = data->extern_field[j];
-
-			if (val > max_val) {
-				max_pos = j;
-				max_val = val;
-			}
-		}
-
-		if (save_crit_stress) crit_stress[i] = data->extern_field[max_pos];
-
-		if (save_conductivity) conductivity[i] = data->conductivity[max_pos];
-
-		if (save_damage) damage[max_pos]++;
-
-		uint_t av_size = 0;
-		double cur_val = 0;
-		for (uint_t j = 0; j < max_pos; j++) {
-			break_edge(net, data->break_list[j], &c);
-
-			double val = data->extern_field[j];
-			if (save_cluster_dist) {
-				if (val < cur_val) {
-					av_size++;
-				}
-
-				if (val > cur_val) {
-					avalanche_size_dist[av_size]++;
-					av_size = 0;
-					cur_val = val;
-				}
-			}
-		}
-
-		if (save_stress_field || save_voltage_field) {
-			double *tmp_voltages = get_voltage(net, &c);
-			if (save_voltage_field) {
-				for (uint_t j = 0; j < g->nv; j++) {
-					voltage_field[3 * voltage_pos] = g->vx[2 * j];
-					voltage_field[3 * voltage_pos + 1] = g->vx[2 * j + 1];
-					voltage_field[3 * voltage_pos + 2] = tmp_voltages[j];
-					voltage_pos++;
-				}
-			}
-			if (save_stress_field) {
-				double *tmp_currents = get_current_v(net, tmp_voltages, &c);
-				for (uint_t j = 0; j < g->ne; j++) {
-					stress_field[3 * stress_pos] = g->ex[2 * j];
-					stress_field[3 * stress_pos + 1] = g->ex[2 * j + 1];
-					stress_field[3 * stress_pos + 2] = tmp_currents[j];
-					stress_pos++;
-				}
-				free(tmp_currents);
-			}
-			free(tmp_voltages);
-		}
-
-		if (save_damage_field) {
-			for (uint_t j = 0; j < max_pos; j++) {
-				damage_field[2 * damage_pos] = g->ex[2 * data->break_list[j]];
-				damage_field[2 * damage_pos + 1] = g->ex[2 * data->break_list[j] + 1];
-				damage_pos++;
-			}
-		}
-
-		if (save_toughness) {
-			double tmp_toughness = 0;
-			if (max_pos > 0) {
-				double sigma1 = data->extern_field[0];
-				double epsilon1 = sigma1 / data->conductivity[0];
-				for (uint_t j = 0; j < max_pos - 1; j++) {
-					double sigma2 = data->extern_field[j+1];
-					double epsilon2 = sigma2 / data->conductivity[j+1];
-					if (epsilon2 > epsilon1) {
-						tmp_toughness += (sigma1 + sigma2) * (epsilon2 - epsilon1) / 2;
-						sigma1 = sigma2; epsilon1 = epsilon2;
-					}
-				}
-			}
-			toughness[i] = tmp_toughness;
-		}
-
-		if (save_cluster_dist) {
-			uint_t *tmp_cluster_dist = get_cluster_dist(net, &c);
-			for (uint_t j = 0; j < g->dnv; j++) {
-				cluster_size_dist[j] += tmp_cluster_dist[j];
-			}
-			free(tmp_cluster_dist);
-		}
-
-		if (save_network) {
-			FILE *net_out = fopen("network.txt", "w");
-			for (uint_t j = 0; j < g->nv; j++) {
-				fprintf(net_out, "%f %f ", g->vx[2 * j],
-						g->vx[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < g->ne; j++) {
-				fprintf(net_out, "%u %u ", g->ev[2 * j], g->ev[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < g->dnv; j++) {
-				fprintf(net_out, "%f %f ", g->dvx[2 * j],
-						g->dvx[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < g->ne; j++) {
-				fprintf(net_out, "%u %u ", g->dev[2 * j], g->dev[2 * j + 1]);
-			}
-			fprintf(net_out, "\n");
-			for (uint_t j = 0; j < g->ne; j++) {
-				fprintf(net_out, "%d ", net->fuses[j]);
-			}
-			fclose(net_out);
-		}
-
-		net_free(net, &c);
-		graph_free(g, &c);
-
-		if (save_data) {
-			for (uint_t j = 0; j < data->num_broken; j++) {
-				fprintf(data_out, "%u %g %g ", data->break_list[j],
-								data->extern_field[j], data->conductivity[j]);
-			}
-			fprintf(data_out, "\n");
-		}
-
-		free_break_data(data);
-	}
-
-	printf("\033[F\033[JFRACTURE: COMPLETE\n");
-
-	if (save_cluster_dist) {
-		FILE *cluster_out = fopen(c_filename, "wb");
-		FILE *avalanche_out = fopen(a_filename, "wb");
-
-		fwrite(cluster_size_dist, sizeof(uint32_t), c_dist_size, cluster_out);
-		fwrite(avalanche_size_dist, sizeof(uint32_t), a_dist_size, avalanche_out);
-
-		fclose(cluster_out);
-		fclose(avalanche_out);
-
-		free(c_filename);
-		free(a_filename);
-		free(cluster_size_dist);
-		free(avalanche_size_dist);
-	}
-
-	if (save_voltage_field) {
-		char *vfld_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(vfld_filename, filename_len, "vfld_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		FILE *vfld_file = fopen(vfld_filename, "ab");
-		fwrite(voltage_field, sizeof(double), 3 * voltage_pos, vfld_file);
-		fclose(vfld_file);
-		free(vfld_filename);
-		free(voltage_field);
-	}
-
-	if (save_stress_field) {
-		char *cfld_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(cfld_filename, filename_len, "cfld_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		FILE *cfld_file = fopen(cfld_filename, "ab");
-		fwrite(stress_field, sizeof(double), 3 * stress_pos, cfld_file);
-		fclose(cfld_file);
-		free(cfld_filename);
-		free(stress_field);
-	}
-
-	if (save_damage_field) {
-		char *dfld_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(dfld_filename, filename_len, "dfld_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		FILE *dfld_file = fopen(dfld_filename, "ab");
-		fwrite(damage_field, sizeof(double), 2 * damage_pos, dfld_file);
-		fclose(dfld_file);
-		free(dfld_filename);
-		free(damage_field);
-	}
-
-	if (save_conductivity) {
-		char *cond_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(cond_filename, filename_len, "cond_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		FILE *cond_file = fopen(cond_filename, "ab");
-		fwrite(conductivity, sizeof(double), N, cond_file);
-		fclose(cond_file);
-		free(cond_filename);
-		free(conductivity);
-	}
-
-	if (save_toughness) {
-		char *tough_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(tough_filename, filename_len, "tuff_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		FILE *tough_file = fopen(tough_filename, "ab");
-		fwrite(toughness, sizeof(double), N, tough_file);
-		fclose(tough_file);
-		free(tough_filename);
-		free(toughness);
-	}
-
-	if (save_damage) {
-		FILE *hdam_file = fopen(d_filename, "wb");
-		fwrite(damage, sizeof(uint32_t), a_dist_size, hdam_file);
-		fclose(hdam_file);
-		free(d_filename);
-		free(damage);
-	}
-
-	if (save_data) {
-		fclose(data_out);
-	}
-
-	if (save_crit_stress) {
-		char *str_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(str_filename, filename_len, "strs_v_%c_%c_%d_%g_%g.dat", boundc, boundc2, L, beta, crack_len);
-		FILE *str_file = fopen(str_filename, "ab");
-		fwrite(crit_stress, sizeof(double), N, str_file);
-		fclose(str_file);
-		free(str_filename);
-		free(crit_stress);
-	}
-
-	CHOL_F(finish)(&c);
-
-	return 0;
-}