did some refactoring

12 files changed, 165 insertions, 144 deletions

diff --git a/src/break_edge.c b/src/break_edge.c
index 7082b76..0ba1ad7 100644
--- a/src/break_edge.c
+++ b/src/break_edge.c
@@ -17,8 +17,8 @@ bool break_edge(finst *instance, unsigned int edge, cholmod_common *c) {
 		unsigned int tw1 = w1 > w2 ? w1 : w2;
 		unsigned int tw2 = w1 > w2 ? w2 : w1;
 
-		CHOL_INT *lap_p = (CHOL_INT *)instance->adjacency->p;
-		CHOL_INT *lap_i = (CHOL_INT *)instance->adjacency->i;
+		int_t *lap_p = (int_t *)instance->adjacency->p;
+		int_t *lap_i = (int_t *)instance->adjacency->i;
 		double *lap_x = (double *)instance->adjacency->x;
 
 		for (int i = 0; i < lap_p[tw1 + 1] - lap_p[tw1]; i++) {
@@ -81,8 +81,8 @@ bool break_edge(finst *instance, unsigned int edge, cholmod_common *c) {
 		unsigned int tw1 = dw1 > dw2 ? dw1 : dw2;
 		unsigned int tw2 = dw1 > dw2 ? dw2 : dw1;
 
-		CHOL_INT *lap_p = (CHOL_INT *)instance->adjacency->p;
-		CHOL_INT *lap_i = (CHOL_INT *)instance->adjacency->i;
+		int_t *lap_p = (int_t *)instance->adjacency->p;
+		int_t *lap_i = (int_t *)instance->adjacency->i;
 		double *lap_x = (double *)instance->adjacency->x;
 
 		for (int i = 0; i < lap_p[tw1 + 1] - lap_p[tw1]; i++) {
diff --git a/src/compare_voronoi_fracture.c b/src/compare_voronoi_fracture.c
index 5578987..bdb9423 100644
--- a/src/compare_voronoi_fracture.c
+++ b/src/compare_voronoi_fracture.c
@@ -8,7 +8,7 @@ int main(int argc, char *argv[]) {
 	// defining variables to be (potentially) set by command line flags
 	unsigned int N, L, filename_len;
 	double beta, inf, cutoff;
-	boundary_type boundary;
+	bound_t boundary;
 
 	filename_len = 100;
 
@@ -66,7 +66,7 @@ int main(int argc, char *argv[]) {
 	(&c)->supernodal = CHOLMOD_SIMPLICIAL;
 
 
-	fnet *network = ini_voronoi_network(L, boundary, genfunc_hyperuniform, &c);
+	fnet *network = ini_voronoi_network(L, false, boundary, genfunc_hyperuniform, &c);
 	finst *perm_voltage_instance = create_instance(network, inf, true, true, &c);
 	finst *perm_current_instance = create_instance(network, inf, false, true, &c);
 	double *fuse_thres = gen_fuse_thres(network->num_edges, network->edge_coords, beta, beta_scaling_flat);
diff --git a/src/fortune/main.c b/src/fortune/main.c
index 7571945..543f6e4 100644
--- a/src/fortune/main.c
+++ b/src/fortune/main.c
@@ -77,7 +77,7 @@ unsigned int delete_duplicates(unsigned int ne, unsigned int *etv) {
 	return newsize;
 }
 
-intptr_t *run_voronoi(unsigned int num, double *lattice, double xmin, double xmax, double ymin, double ymax)
+intptr_t *run_voronoi(unsigned int num, double *lattice, bool periodic, double xmin, double xmax, double ymin, double ymax)
 {
 	struct Site *(*next)();
 
@@ -91,45 +91,50 @@ intptr_t *run_voronoi(unsigned int num, double *lattice, double xmin, double xma
 
 	freeinit(&sfl, sizeof *sites);
 
-	unsigned int eff_num = 9 * num;
-	double *eff_lattice = (double *)malloc(2 * eff_num * sizeof(double));
+	unsigned int eff_num = num;
+	double *eff_lattice = lattice;
 
-	for (unsigned int i = 0; i < num; i++) {
-		// original sites - our baby boys
-		eff_lattice[2*i] = lattice[2*i];
-		eff_lattice[2*i+1] = lattice[2*i+1];
+	if (periodic) {
+		unsigned int eff_num = 9 * num;
+		double *eff_lattice = (double *)malloc(2 * eff_num * sizeof(double));
 
-		// sites to the right
-		eff_lattice[2*(num+i)+1] = lattice[2*i+1] - xmin + xmax;
-		eff_lattice[2*(num+i)] = lattice[2*i];
+		for (unsigned int i = 0; i < num; i++) {
+			// original sites - our baby boys
+			eff_lattice[2*i] = lattice[2*i];
+			eff_lattice[2*i+1] = lattice[2*i+1];
 
-		// sites to the left
-		eff_lattice[2*(2*num+i)+1] = lattice[2*i+1] - xmax + xmin;
-		eff_lattice[2*(2*num+i)] = lattice[2*i];
+			// sites to the right
+			eff_lattice[2*(num+i)+1] = lattice[2*i+1] - xmin + xmax;
+			eff_lattice[2*(num+i)] = lattice[2*i];
 
-		// sites to the top
-		eff_lattice[2*(3*num+i)+1] = lattice[2*i+1];
-		eff_lattice[2*(3*num+i)] = lattice[2*i] - ymin + ymax;
+			// sites to the left
+			eff_lattice[2*(2*num+i)+1] = lattice[2*i+1] - xmax + xmin;
+			eff_lattice[2*(2*num+i)] = lattice[2*i];
 
-		// sites to the bottom
-		eff_lattice[2*(4*num+i)+1] = lattice[2*i+1];
-		eff_lattice[2*(4*num+i)] = lattice[2*i] - ymax + ymin;
+			// sites to the top
+			eff_lattice[2*(3*num+i)+1] = lattice[2*i+1];
+			eff_lattice[2*(3*num+i)] = lattice[2*i] - ymin + ymax;
 
-		// sites to the upper right
-		eff_lattice[2*(5*num+i)+1] = lattice[2*i+1] - xmin + xmax;
-		eff_lattice[2*(5*num+i)] = lattice[2*i] - ymin + ymax;
+			// sites to the bottom
+			eff_lattice[2*(4*num+i)+1] = lattice[2*i+1];
+			eff_lattice[2*(4*num+i)] = lattice[2*i] - ymax + ymin;
 
-		// sites to the upper left
-		eff_lattice[2*(6*num+i)+1] = lattice[2*i+1] - xmax + xmin;
-		eff_lattice[2*(6*num+i)] = lattice[2*i] - ymin + ymax;
+			// sites to the upper right
+			eff_lattice[2*(5*num+i)+1] = lattice[2*i+1] - xmin + xmax;
+			eff_lattice[2*(5*num+i)] = lattice[2*i] - ymin + ymax;
 
-		// sites to the lower left
-		eff_lattice[2*(7*num+i)+1] = lattice[2*i+1] - xmax + xmin;
-		eff_lattice[2*(7*num+i)] = lattice[2*i] + ymin - ymax;
+			// sites to the upper left
+			eff_lattice[2*(6*num+i)+1] = lattice[2*i+1] - xmax + xmin;
+			eff_lattice[2*(6*num+i)] = lattice[2*i] - ymin + ymax;
 
-		// sites to the lower right
-		eff_lattice[2*(8*num+i)+1] = lattice[2*i+1] + xmax - xmin;
-		eff_lattice[2*(8*num+i)] = lattice[2*i] + ymin - ymax;
+			// sites to the lower left
+			eff_lattice[2*(7*num+i)+1] = lattice[2*i+1] - xmax + xmin;
+			eff_lattice[2*(7*num+i)] = lattice[2*i] + ymin - ymax;
+
+			// sites to the lower right
+			eff_lattice[2*(8*num+i)+1] = lattice[2*i+1] + xmax - xmin;
+			eff_lattice[2*(8*num+i)] = lattice[2*i] + ymin - ymax;
+		}
 	}
 
 	nsites = eff_num;
@@ -160,7 +165,7 @@ intptr_t *run_voronoi(unsigned int num, double *lattice, double xmin, double xma
 	unsigned int *real_edge_list = edge_list;
 	unsigned int *real_dual_list = dual_list;
 
-	{
+	if (periodic) {
 		real_vert_count = 0;
 		real_edge_count = 0;
 		real_dual_count = 0;
diff --git a/src/fracture.h b/src/fracture.h
index fea0caf..91b2bfc 100644
--- a/src/fracture.h
+++ b/src/fracture.h
@@ -23,15 +23,18 @@
 #include <sys/types.h>
 #include <unistd.h>
 
-// these two defs allow me to switch to long int cholmod in a sitch
-#define CHOL_INT long int
-#define CHOL_F(x) cholmod_l_##x
+// these defs allow me to switch to long int cholmod in a sitch
+#define int_t int
+#define uint_t unsigned int
+#define CINT_MAX INT_MAX
+#define CHOL_F(x) cholmod_##x
 
-typedef enum boundary_type {
+typedef enum bound_t {
 	FREE_BOUND,
 	CYLINDER_BOUND,
-	TORUS_BOUND
-} boundary_type;
+	TORUS_BOUND,
+	EMBEDDED_BOUND
+} bound_t;
 
 typedef struct {
 	unsigned int num_edges;
@@ -56,7 +59,7 @@ typedef struct {
 	unsigned int num_dual_verts;
 	unsigned int break_dim;
 	cholmod_sparse *voltcurmat;
-	boundary_type boundary;
+	bound_t boundary;
 } fnet;
 
 typedef struct {
@@ -81,7 +84,7 @@ typedef struct {
 	double *extern_field;
 } break_data;
 
-intptr_t *run_voronoi(unsigned int num_coords, double *coords, double xmin, double xmax, double ymin, double ymax);
+intptr_t *run_voronoi(unsigned int num_coords, double *coords, bool periodic, double xmin, double xmax, double ymin, double ymax);
 
 int update_components(const cholmod_sparse *laplacian, unsigned int *marks,
 											int old_num_components, int v1, int v2, int exclude);
@@ -133,7 +136,7 @@ cholmod_sparse *gen_voltcurmat(unsigned int num_edges, unsigned int num_verts,
 
 finst *copy_instance(const finst *instance, cholmod_common *c);
 
-fnet *ini_square_network(unsigned int width, boundary_type boundary, bool side_bounds,
+fnet *ini_square_network(unsigned int width, bound_t boundary, bool side_bounds,
 												 cholmod_common *c);
 
 void free_fnet(fnet *network, cholmod_common *c);
@@ -142,8 +145,8 @@ void free_instance(finst *instance, cholmod_common *c);
 finst *create_instance(fnet *network, double inf, bool voltage_bound,
 											 bool startnow, cholmod_common *c);
 
-fnet *ini_voronoi_network(unsigned int L, boundary_type boundary, bool use_dual,
-													double *(*genfunc)(unsigned int, gsl_rng *, unsigned int *),
+fnet *ini_voronoi_network(unsigned int L, bound_t boundary, bool use_dual,
+													double *(*genfunc)(unsigned int, bound_t, gsl_rng *, unsigned int *),
 													cholmod_common *c);
 
 bool check_instance(const finst *instance, cholmod_common *c);
@@ -158,8 +161,8 @@ unsigned int *get_clusters(finst *instance, cholmod_common *c);
 
 unsigned int *get_cluster_dist(finst *instance, cholmod_common *c);
 
-double *genfunc_uniform(unsigned int L, gsl_rng *r, unsigned int *num);
-double *genfunc_hyperuniform(unsigned int L, gsl_rng *r, unsigned int *num);
+double *genfunc_uniform(unsigned int L, bound_t boundary, gsl_rng *r, unsigned int *num);
+double *genfunc_hyperuniform(unsigned int L, bound_t boundary, gsl_rng *r, unsigned int *num);
 void randfunc_flat(gsl_rng *r, double *x, double *y);
 void randfunc_gaus(gsl_rng *r, double *x, double *y);
 double beta_scaling_flat(double beta, double x, double y);
diff --git a/src/gen_laplacian.c b/src/gen_laplacian.c
index a282564..d8f0c6d 100644
--- a/src/gen_laplacian.c
+++ b/src/gen_laplacian.c
@@ -28,8 +28,8 @@ cholmod_sparse *gen_adjacency(const finst *instance, bool dual, bool breakv,
 
 	cholmod_triplet *t =
 			CHOL_F(allocate_triplet)(nv + pad, nv + pad, nnz, 0, CHOLMOD_REAL, c);
-	CHOL_INT *ri = (CHOL_INT *)t->i;
-	CHOL_INT *ci = (CHOL_INT *)t->j;
+	int_t *ri = (int_t *)t->i;
+	int_t *ci = (int_t *)t->j;
 	double *ai = (double *)t->x;
 
 	t->nnz = nnz;
@@ -120,8 +120,8 @@ cholmod_sparse *gen_laplacian(const finst *instance, cholmod_common *c,
 	cholmod_triplet *temp_m =
 			CHOL_F(allocate_triplet)(num_gverts, num_gverts, nnz, 0, CHOLMOD_REAL, c);
 
-	CHOL_INT *rowind = (CHOL_INT *)temp_m->i;
-	CHOL_INT *colind = (CHOL_INT *)temp_m->j;
+	int_t *rowind = (int_t *)temp_m->i;
+	int_t *colind = (int_t *)temp_m->j;
 	double *acoo = (double *)temp_m->x;
 
 	temp_m->nnz = nnz;
@@ -133,8 +133,8 @@ cholmod_sparse *gen_laplacian(const finst *instance, cholmod_common *c,
 	}
 
 	cholmod_sparse *adjacency = gen_adjacency(instance, false, true, (int)num_gverts - (int)num_verts, c);
-	CHOL_INT *ia = (CHOL_INT *)adjacency->p;
-	CHOL_INT *ja = (CHOL_INT *)adjacency->i;
+	int_t *ia = (int_t *)adjacency->p;
+	int_t *ja = (int_t *)adjacency->i;
 	double *aa = (double *)adjacency->x;
 
 	for (unsigned int i = 0; i < num_verts; i++) {
diff --git a/src/gen_voltcurmat.c b/src/gen_voltcurmat.c
index ab16150..e870140 100644
--- a/src/gen_voltcurmat.c
+++ b/src/gen_voltcurmat.c
@@ -9,8 +9,8 @@ cholmod_sparse *gen_voltcurmat(unsigned int num_edges, unsigned int num_verts,
 			num_edges, num_verts, num_edges * 2, 0, CHOLMOD_REAL, c);
 	assert(t_m != NULL);
 
-	CHOL_INT *rowind = (CHOL_INT *)t_m->i;
-	CHOL_INT *colind = (CHOL_INT *)t_m->j;
+	int_t *rowind = (int_t *)t_m->i;
+	int_t *colind = (int_t *)t_m->j;
 	double *acoo = (double *)t_m->x;
 
 	for (unsigned int i = 0; i < num_edges; i++) {
diff --git a/src/graph_components.c b/src/graph_components.c
index 036f2fe..c4e894d 100644
--- a/src/graph_components.c
+++ b/src/graph_components.c
@@ -3,10 +3,10 @@
 
 bool set_connected(const cholmod_sparse *laplacian, unsigned int *marks,
 									 int vertex, int label, int stop_at, int exclude) {
-	unsigned int num_verts = (CHOL_INT)laplacian->nrow;
+	unsigned int num_verts = (int_t)laplacian->nrow;
 
-	CHOL_INT *ia = (CHOL_INT *)laplacian->p;
-	CHOL_INT *ja = (CHOL_INT *)laplacian->i;
+	int_t *ia = (int_t *)laplacian->p;
+	int_t *ja = (int_t *)laplacian->i;
 	double *a = (double *)laplacian->x;
 
 	bool stopped = false;
diff --git a/src/homo_square_fracture.c b/src/homo_square_fracture.c
index a0dd305..9103317 100644
--- a/src/homo_square_fracture.c
+++ b/src/homo_square_fracture.c
@@ -8,7 +8,7 @@ int main(int argc, char *argv[]) {
 	// defining variables to be (potentially) set by command line flags
 	unsigned int N, L, filename_len;
 	double beta, inf, cutoff;
-	boundary_type boundary;
+	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;
diff --git a/src/homo_voronoi_fracture.c b/src/homo_voronoi_fracture.c
index 4e2d67a..65a25f8 100644
--- a/src/homo_voronoi_fracture.c
+++ b/src/homo_voronoi_fracture.c
@@ -6,12 +6,14 @@ int main(int argc, char *argv[]) {
 	int opt;
 
 	// defining variables to be (potentially) set by command line flags
-	unsigned int N, L, filename_len;
+	uint8_t filename_len;
+	uint64_t N;
+	uint_t L;
 	double beta, inf, cutoff;
-	boundary_type boundary;
 	bool include_breaking, save_cluster_dist, use_voltage_boundaries, use_dual, save_network,
-			 save_crit_stress, save_toughness, save_corr, save_conductivity,
+			 save_crit_stress, save_toughness, save_conductivity,
 			 save_damage;
+	bound_t boundary;
 
 	filename_len = 100;
 
@@ -28,11 +30,10 @@ int main(int argc, char *argv[]) {
 	save_network = false;
 	save_crit_stress = false;
 	save_damage = false;
-	save_corr = false;
 	save_conductivity = false;
 	save_toughness = false;
 
-	int boundary_int;
+	uint8_t bound_i;
 	char boundc2 = 'f';
 
 	while ((opt = getopt(argc, argv, "n:L:b:B:dVcoNsCrtD")) != -1) {
@@ -47,8 +48,8 @@ int main(int argc, char *argv[]) {
 				beta = atof(optarg);
 				break;
 			case 'B':
-				boundary_int = atoi(optarg);
-				switch (boundary_int) {
+				bound_i = atoi(optarg);
+				switch (bound_i) {
 					case 0:
 						boundary = FREE_BOUND;
 						boundc2 = 'f';
@@ -64,6 +65,7 @@ int main(int argc, char *argv[]) {
 						break;
 					default:
 						printf("boundary specifier must be 0 (FREE_BOUND), 1 (CYLINDER_BOUND), or 2 (TORUS_BOUND).\n");
+						exit(EXIT_FAILURE);
 				}
 				break;
 			case 'd':
@@ -87,9 +89,6 @@ int main(int argc, char *argv[]) {
 			case 's':
 				save_crit_stress = true;
 				break;
-			case 'C':
-				save_corr = true;
-				break;
 			case 'r':
 				save_conductivity = true;
 				//inf = 1;
@@ -114,20 +113,26 @@ int main(int argc, char *argv[]) {
 		free(break_filename);
 	}
 
-	unsigned int voronoi_max_verts = 4 * pow(L, 2);
-	unsigned int c_dist_size = voronoi_max_verts;
-	unsigned int a_dist_size = voronoi_max_verts;
+	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
-	unsigned int *cluster_size_dist;
-	unsigned int *avalanche_size_dist;
+	uint64_t *cluster_size_dist;
+	uint64_t *avalanche_size_dist;
 	char *c_filename;
 	char *a_filename;
 	if (save_cluster_dist) {
 		cluster_size_dist =
-				(unsigned int *)malloc(c_dist_size * sizeof(unsigned int));
+				(uint64_t *)malloc(c_dist_size * sizeof(uint64_t));
 		avalanche_size_dist =
-				(unsigned int *)malloc(a_dist_size * sizeof(unsigned int));
+				(uint64_t *)malloc(a_dist_size * sizeof(uint64_t));
 
 		c_filename = (char *)malloc(filename_len * sizeof(char));
 		a_filename = (char *)malloc(filename_len * sizeof(char));
@@ -138,11 +143,11 @@ int main(int argc, char *argv[]) {
 		FILE *avalanche_out = fopen(a_filename, "rb");
 
 		if (cluster_out != NULL) {
-			fread(cluster_size_dist, sizeof(unsigned int), c_dist_size, cluster_out);
+			fread(cluster_size_dist, sizeof(uint64_t), c_dist_size, cluster_out);
 			fclose(cluster_out);
 		}
 		if (avalanche_out != NULL) {
-			fread(avalanche_size_dist, sizeof(unsigned int), a_dist_size, avalanche_out);
+			fread(avalanche_size_dist, sizeof(uint64_t), a_dist_size, avalanche_out);
 			fclose(avalanche_out);
 		}
 	}
@@ -152,23 +157,17 @@ int main(int argc, char *argv[]) {
 		crit_stress = (double *)malloc(N * sizeof(double));
 	}
 
-	double *avg_corr;
-	unsigned int **dists = NULL;
-	if (save_corr) {
-		avg_corr = (double *)calloc(voronoi_max_verts, sizeof(double));
-	}
-
 	double *conductivity;
 	if (save_conductivity) {
 		conductivity = (double *)malloc(N * sizeof(double));
 	}
 
 	// define arrays for saving damage distributions
-	unsigned int *damage;
+	uint64_t *damage;
 	char *d_filename;
 	if (save_damage) {
 		damage =
-				(unsigned int *)malloc(a_dist_size * sizeof(unsigned int));
+				(uint64_t *)malloc(a_dist_size * sizeof(uint64_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);
@@ -176,7 +175,7 @@ int main(int argc, char *argv[]) {
 		FILE *damage_out = fopen(d_filename, "rb");
 
 		if (damage_out != NULL) {
-			fread(damage, sizeof(unsigned int), a_dist_size, damage_out);
+			fread(damage, sizeof(uint64_t), a_dist_size, damage_out);
 			fclose(damage_out);
 		}
 	}
@@ -204,22 +203,21 @@ int main(int argc, char *argv[]) {
 
 
 	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);
+	for (uint64_t i = 0; i < N; i++) {
+		printf("\033[F\033[JFRACTURE: %0*d / %d\n", (uint8_t)log10(N) + 1, i + 1, N);
 
 		fnet *network = ini_voronoi_network(L, boundary, use_dual, genfunc_hyperuniform, &c);
 		finst *perm_instance = create_instance(network, inf, use_voltage_boundaries, true, &c);
 		double *fuse_thres = gen_fuse_thres(network->num_edges, network->edge_coords, beta, beta_scaling_flat);
 		finst *instance = copy_instance(perm_instance, &c);
 		break_data *breaking_data = fracture_network(instance, fuse_thres, &c, cutoff);
-		bool debug_stop = instance->debug_stop;
 		free_instance(instance, &c);
 		free(fuse_thres);
 
-		unsigned int max_pos = 0;
+		uint_t max_pos = 0;
 		double max_val = 0;
 
-		for (unsigned int j = 0; j < breaking_data->num_broken; j++) {
+		for (uint_t j = 0; j < breaking_data->num_broken; j++) {
 			double val = breaking_data->extern_field[j];
 
 			if (val > max_val) {
@@ -235,9 +233,9 @@ int main(int argc, char *argv[]) {
 
 		finst *tmp_instance = copy_instance(perm_instance, &c);
 
-		unsigned int av_size = 0;
+		uint_t av_size = 0;
 		double cur_val = 0;
-		for (unsigned int j = 0; j < max_pos; j++) {
+		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];
@@ -269,7 +267,7 @@ int main(int argc, char *argv[]) {
 			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++) {
+				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) {
@@ -286,44 +284,36 @@ int main(int argc, char *argv[]) {
 		}
 
 		if (save_cluster_dist) {
-			unsigned int *tmp_cluster_dist = get_cluster_dist(tmp_instance, &c);
-			for (unsigned int j = 0; j < tmp_instance->network->num_dual_verts; j++) {
+			uint_t *tmp_cluster_dist = get_cluster_dist(tmp_instance, &c);
+			for (uint_t j = 0; j < tmp_instance->network->num_dual_verts; 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->network->num_dual_verts; 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->num_verts; j++) {
+			for (uint_t j = 0; j < network->num_verts; j++) {
 				fprintf(net_out, "%f %f ", network->vert_coords[2 * j],
 								tmp_instance->network->vert_coords[2 * j + 1]);
 			}
 			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->network->num_edges; j++) {
+			for (uint_t j = 0; j < tmp_instance->network->num_edges; j++) {
 				fprintf(net_out, "%u %u ", tmp_instance->network->edges_to_verts[2 * j],
 								tmp_instance->network->edges_to_verts[2 * j + 1]);
 			}
 			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->network->num_dual_verts; j++) {
+			for (uint_t j = 0; j < tmp_instance->network->num_dual_verts; j++) {
 				fprintf(net_out, "%f %f ", tmp_instance->network->dual_vert_coords[2 * j],
 								tmp_instance->network->dual_vert_coords[2 * j + 1]);
 			}
 			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->network->num_edges; j++) {
+			for (uint_t j = 0; j < tmp_instance->network->num_edges; j++) {
 				fprintf(net_out, "%u %u ", tmp_instance->network->dual_edges_to_verts[2 * j],
 								tmp_instance->network->dual_edges_to_verts[2 * j + 1]);
 			}
 			fprintf(net_out, "\n");
-			for (unsigned int j = 0; j < tmp_instance->network->num_edges; j++) {
+			for (uint_t j = 0; j < tmp_instance->network->num_edges; j++) {
 				fprintf(net_out, "%d ", tmp_instance->fuses[j]);
 			}
 			fclose(net_out);
@@ -334,7 +324,7 @@ int main(int argc, char *argv[]) {
 		free_fnet(network, &c);
 
 		if (include_breaking) {
-			for (unsigned int j = 0; j < breaking_data->num_broken; j++) {
+			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]);
 			}
@@ -350,8 +340,8 @@ int main(int argc, char *argv[]) {
 		FILE *cluster_out = fopen(c_filename, "wb");
 		FILE *avalanche_out = fopen(a_filename, "wb");
 
-		fwrite(cluster_size_dist, sizeof(unsigned int), c_dist_size, cluster_out);
-		fwrite(avalanche_size_dist, sizeof(unsigned int), a_dist_size, avalanche_out);
+		fwrite(cluster_size_dist, sizeof(uint64_t), c_dist_size, cluster_out);
+		fwrite(avalanche_size_dist, sizeof(uint64_t), a_dist_size, avalanche_out);
 
 		fclose(cluster_out);
 		fclose(avalanche_out);
@@ -362,19 +352,6 @@ int main(int argc, char *argv[]) {
 		free(avalanche_size_dist);
 	}
 
-	if (save_corr) {
-		char *corr_filename = (char *)malloc(filename_len * sizeof(char));
-		snprintf(corr_filename, filename_len, "corr_v_%c_%c_%d_%g.txt", boundc, boundc2, L,
-						 beta);
-		FILE *corr_file = fopen(corr_filename, "w");
-		for (unsigned int i = 0; i < voronoi_max_verts; 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_v_%c_%c_%d_%g.dat", boundc, boundc2, L, beta);
@@ -397,7 +374,7 @@ int main(int argc, char *argv[]) {
 
 	if (save_damage) {
 		FILE *hdam_file = fopen(d_filename, "wb");
-		fwrite(damage, sizeof(unsigned int), a_dist_size, hdam_file);
+		fwrite(damage, sizeof(uint64_t), a_dist_size, hdam_file);
 		fclose(hdam_file);
 		free(d_filename);
 		free(damage);
diff --git a/src/ini_network.c b/src/ini_network.c
index f1dbe70..edf1539 100644
--- a/src/ini_network.c
+++ b/src/ini_network.c
@@ -96,7 +96,7 @@ unsigned int *get_verts_to_edges(unsigned int num_verts, unsigned int num_edges,
 	return output;
 }
 
-fnet *ini_square_network(unsigned int width, boundary_type boundary, bool side_bounds,
+fnet *ini_square_network(unsigned int width, bound_t boundary, bool side_bounds,
 												 cholmod_common *c) {
 	fnet *network = (fnet *)calloc(1, sizeof(fnet));
 
@@ -300,8 +300,8 @@ unsigned int *get_voro_dual_edges(unsigned int num_edges,
 	return dual_edges;
 }
 
-fnet *ini_voronoi_network(unsigned int L, boundary_type boundary, bool use_dual,
-													double *(*genfunc)(unsigned int, gsl_rng *, unsigned int *),
+fnet *ini_voronoi_network(unsigned int L, bound_t boundary, bool use_dual,
+													double *(*genfunc)(unsigned int, bound_t, gsl_rng *, unsigned int *),
 													cholmod_common *c) {
 	fnet *network = (fnet *)calloc(1, sizeof(fnet));
 
@@ -315,12 +315,15 @@ fnet *ini_voronoi_network(unsigned int L, boundary_type boundary, bool use_dual,
 		fread(&seed, sizeof(unsigned long int), 1, rf);
 		fclose(rf);
 		gsl_rng_set(r, seed);
-		lattice = genfunc(L, r, &num);
+		lattice = genfunc(L, boundary, r, &num);
 		gsl_rng_free(r);
 	}
 
 	// retrieve a periodic voronoi tesselation of the lattice
-	intptr_t *vout = run_voronoi(num, lattice, 0, 1, 0, 1);
+	bool run_periodic;
+	if (boundary == EMBEDDED_BOUND) run_periodic = false;
+	else run_periodic = true;
+	intptr_t *vout = run_voronoi(num, lattice, run_periodic, 0, 1, 0, 1);
 
 	unsigned int tmp_num_verts = ((unsigned int *)vout[0])[0];
 	unsigned int tmp_num_edges = ((unsigned int *)vout[0])[1];
@@ -595,6 +598,19 @@ fnet *ini_voronoi_network(unsigned int L, boundary_type boundary, bool use_dual,
 			network->break_dim = num_verts;
 			break;
 											}
+		case EMBEDDED_BOUND: {
+			num_bounds = 4;
+			bound_inds = (unsigned int *)malloc(5 * sizeof(unsigned int));
+			bound_verts = (unsigned int *)malloc(2 * L * sizeof(unsigned int));
+			for (unsigned int i = 0; i < 5; i++) bound_inds[i] = i * L / 2;
+			for (unsigned int i = 0; i < 2 * L; i++) bound_verts[i] = i;
+			num_edges = tmp_num_edges;
+			num_verts = tmp_num_verts;
+			edges = tmp_edges;
+			dual_edges = tmp_dual_edges;
+			num_edges = tmp_num_edges;
+			vert_coords = tmp_vert_coords;
+		}
 	}
 
 	network->boundary = boundary;
diff --git a/src/randfuncs.c b/src/randfuncs.c
index 260c047..35b9f56 100644
--- a/src/randfuncs.c
+++ b/src/randfuncs.c
@@ -1,7 +1,7 @@
 
 #include "fracture.h"
 
-double *genfunc_uniform(unsigned int L, gsl_rng *r, unsigned int *num) {
+double *genfunc_uniform(unsigned int L, bound_t boundary, gsl_rng *r, unsigned int *num) {
 	*num = pow(L / 2 + 1, 2) + pow((L + 1) / 2, 2);
 
 	double *lattice = (double *)malloc(2 * (*num) * sizeof(double));
@@ -13,7 +13,7 @@ double *genfunc_uniform(unsigned int L, gsl_rng *r, unsigned int *num) {
 	return lattice;
 }
 
-double *genfunc_hyperuniform(unsigned int L, gsl_rng *r, unsigned int *num) {
+double *genfunc_hyperuniform(unsigned int L, bound_t boundary, gsl_rng *r, unsigned int *num) {
 	*num = pow(L / 2 + 1, 2) + pow((L + 1) / 2, 2);
 
 	// necessary to prevent crashing when underflow occurs
@@ -21,7 +21,27 @@ double *genfunc_hyperuniform(unsigned int L, gsl_rng *r, unsigned int *num) {
 
 	double *lattice = (double *)malloc(2 * (*num) * sizeof(double));
 	double rho = *num;
-	for (unsigned int i = 0; i < (*num); i++) {
+	unsigned int to_gen = *num;
+
+	if (boundary == EMBEDDED_BOUND) {
+		for (unsigned int i = 0; i < L / 2; i++) {
+			lattice[2 * i] = 0;
+			lattice[2 * i + 1] = (2. * i + 1.) / L;
+
+			lattice[L / 2 + 2 * i] = 1;
+			lattice[L / 2 + 2 * i + 1] = (2. * i + 1.) / L;
+
+			lattice[L + 2 * i] = (2. * i + 1.) / L;
+			lattice[L + 2 * i + 1] = 0;
+
+			lattice[3 * L / 2 + 2 * i] = (2. * i + 1.) / L;
+			lattice[3 * L / 2 + 2 * i + 1] = 1;
+		}
+
+		to_gen -= 2 * L;
+	}
+
+	for (unsigned int i = 0; i < to_gen; i++) {
 		bool reject = true;
 		double x, y;
 		while(reject) {
diff --git a/src/update_factor.c b/src/update_factor.c
index 6b8e05e..debfe7b 100644
--- a/src/update_factor.c
+++ b/src/update_factor.c
@@ -16,13 +16,13 @@ bool update_factor(cholmod_factor *factor, unsigned int v1, unsigned int v2,
 
 	for (int i = 0; i < n; i++) {
 		if (i <= v3)
-			((CHOL_INT *)update_mat->p)[i] = 0;
+			((int_t *)update_mat->p)[i] = 0;
 		else
-			((CHOL_INT *)update_mat->p)[i] = 2;
+			((int_t *)update_mat->p)[i] = 2;
 	}
-	((CHOL_INT *)update_mat->p)[n] = 2;
-	((CHOL_INT *)update_mat->i)[0] = v3;
-	((CHOL_INT *)update_mat->i)[1] = v4;
+	((int_t *)update_mat->p)[n] = 2;
+	((int_t *)update_mat->i)[0] = v3;
+	((int_t *)update_mat->i)[1] = v4;
 	((double *)update_mat->x)[0] = 1;
 	((double *)update_mat->x)[1] = -1;