more refactoring

13 files changed, 114 insertions, 138 deletions

diff --git a/makefile b/makefile
index cef1573..af15cd9 100644
--- a/makefile
+++ b/makefile
@@ -3,7 +3,7 @@ CC = clang
 CFLAGS = -g -Os -O3 -Wall -fno-strict-aliasing -Wstrict-overflow -Wno-missing-field-initializers -fPIC -flto -march=native #-fopenmp 
 LDFLAGS = -lc -lcblas -llapack -ldl -lpthread -lcholmod -lamd -lcolamd -lsuitesparseconfig -lcamd -lccolamd -lm -lrt -lmetis -lgsl -lprofiler -ltcmalloc
 
-OBJ = break_data bound_set correlations randfuncs net get_dual_clusters break_edge graph_components gen_laplacian geometry net_fracture get_current update_factor gen_voltcurmat graph_create free_network fortune/edgelist fortune/geometry fortune/heap fortune/main fortune/output fortune/voronoi fortune/memory get_conductivity net_notch
+OBJ = break_data bound_set correlations graph_genfunc net_create net_copy net_free get_dual_clusters break_edge graph_components gen_laplacian geometry net_fracture get_current update_factor gen_voltcurmat graph_create graph_free fortune/edgelist fortune/geometry fortune/heap fortune/main fortune/output fortune/voronoi fortune/memory get_conductivity net_notch
 BIN = corr_test fracture
 
 all: opt ${OBJ:%=obj/%.o} ${BIN:%=obj/%.o} ${BIN:%=bin/%}
diff --git a/makefile_hal b/makefile_hal
index 78e83fe..72023fb 100644
--- a/makefile_hal
+++ b/makefile_hal
@@ -3,7 +3,7 @@ CC = clang
 CFLAGS = -g -Os -O3 -Wall -fno-strict-aliasing -Wstrict-overflow -Wno-missing-field-initializers -fPIC -flto -fopenmp
 LDFLAGS = -lc -lcblas -llapack -ldl -lpthread -lcholmod -lamd -lcolamd -lsuitesparseconfig -lcamd -lccolamd -lm -lrt -lmetis -lgsl -lprofiler -ltcmalloc
 
-OBJ = break_data bound_set correlations randfuncs net get_dual_clusters break_edge graph_components gen_laplacian geometry net_fracture get_current update_factor gen_voltcurmat graph_create free_network fortune/edgelist fortune/geometry fortune/heap fortune/main fortune/output fortune/voronoi fortune/memory get_conductivity net_notch
+OBJ = data bound_set correlations graph_genfunc net_create net_copy net_free get_dual_clusters break_edge graph_components gen_laplacian geometry net_fracture get_current update_factor gen_voltcurmat graph_create graph_free fortune/edgelist fortune/geometry fortune/heap fortune/main fortune/output fortune/voronoi fortune/memory get_conductivity net_notch
 BIN = corr_test fracture
 
 all: opt ${OBJ:%=obj/%.o} ${BIN:%=obj/%.o} ${BIN:%=bin/%}
diff --git a/src/break_data.c b/src/break_data.c
deleted file mode 100644
index 5c922f3..0000000
--- a/src/break_data.c
+++ /dev/null
@@ -1,34 +0,0 @@
-
-#include "fracture.h"
-
-data_t *alloc_break_data(unsigned int num_edges) {
-	data_t *data = malloc(1 * sizeof(data_t)); assert(data != NULL);
-
-	data->num_broken = 0;
-
-	data->break_list = (unsigned int *)malloc(num_edges * sizeof(unsigned int));
-	assert(data->break_list != NULL);
-
-	data->extern_field = (double *)malloc(num_edges * sizeof(double));
-	assert(data->extern_field != NULL);
-
-	data->conductivity = (double *)malloc(num_edges * sizeof(double));
-	assert(data->conductivity != NULL);
-
-	return data;
-}
-
-void free_break_data(data_t *data) {
-	free(data->break_list);
-	free(data->extern_field);
-	free(data->conductivity);
-	free(data);
-}
-
-void update_break_data(data_t *data, unsigned int last_broke, double strength, double conductivity) {
-	data->break_list[data->num_broken] = last_broke;
-	data->extern_field[data->num_broken] = strength;
-	data->conductivity[data->num_broken] = conductivity;
-	data->num_broken++;
-}
-
diff --git a/src/data.c b/src/data.c
new file mode 100644
index 0000000..b54236d
--- /dev/null
+++ b/src/data.c
@@ -0,0 +1,35 @@
+
+#include "fracture.h"
+
+data_t *data_create(uint_t ne) {
+	data_t *data = malloc(1 * sizeof(data_t));
+	assert(data != NULL);
+
+	data->num_broken = 0;
+
+	data->break_list = (uint_t *)malloc(ne * sizeof(uint_t));
+	assert(data->break_list != NULL);
+
+	data->extern_field = (double *)malloc(ne * sizeof(double));
+	assert(data->extern_field != NULL);
+
+	data->conductivity = (double *)malloc(ne * sizeof(double));
+	assert(data->conductivity != NULL);
+
+	return data;
+}
+
+void data_free(data_t *data) {
+	free(data->break_list);
+	free(data->extern_field);
+	free(data->conductivity);
+	free(data);
+}
+
+void data_update(data_t *data, uint_t last_broke, double strength, double conductivity) {
+	data->break_list[data->num_broken] = last_broke;
+	data->extern_field[data->num_broken] = strength;
+	data->conductivity[data->num_broken] = conductivity;
+	data->num_broken++;
+}
+
diff --git a/src/fracture.c b/src/fracture.c
index e7abaec..f36cfdb 100644
--- a/src/fracture.c
+++ b/src/fracture.c
@@ -412,7 +412,7 @@ int main(int argc, char *argv[]) {
 			fprintf(data_out, "\n");
 		}
 
-		free_break_data(data);
+		data_free(data);
 	}
 
 	printf("\033[F\033[JFRACTURE: COMPLETE\n");
diff --git a/src/fracture.h b/src/fracture.h
index 19b1e71..2401d25 100644
--- a/src/fracture.h
+++ b/src/fracture.h
@@ -148,8 +148,6 @@ graph_t *ini_voro_graph(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 net_t *instance, cholmod_common *c);
-
 bool break_edge(net_t *instance, unsigned int edge, cholmod_common *c);
 
 void finish_instance(net_t *instance, cholmod_common *c);
@@ -164,11 +162,7 @@ double *genfunc_uniform(unsigned int L, bound_t boundary, gsl_rng *r, unsigned i
 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);
-double beta_scaling_gaus(double beta, double x, double y);
-double beta_mag(double beta);
 
-unsigned int *dijkstra(const graph_t *network, unsigned int source);
 unsigned int **get_dists(const graph_t *network);
 double *get_corr(net_t *instance, unsigned int **dists, cholmod_common *c);
 
@@ -176,9 +170,9 @@ double *bin_values(graph_t *network, unsigned int width, double *values);
 
 cholmod_dense *bound_set(const graph_t *g, bool vb, double notch_len, cholmod_common *c);
 
-data_t *alloc_break_data(unsigned int num_edges);
-void free_break_data(data_t *data);
-void update_break_data(data_t *data, unsigned int last_broke, double strength, double conductivity);
+data_t *data_create(uint_t num_edges);
+void data_free(data_t *data);
+void data_update(data_t *data, uint_t last_broke, double strength, double conductivity);
 
 double get_conductivity(net_t *inst, double *current, cholmod_common *c);
 
diff --git a/src/free_network.c b/src/free_network.c
deleted file mode 100644
index 2001479..0000000
--- a/src/free_network.c
+++ /dev/null
@@ -1,22 +0,0 @@
-
-#include "fracture.h"
-
-void graph_free(graph_t *network, cholmod_common *c) {
-	free(network->ev);
-	if (network->ev_break != network->ev) {
-		free(network->ev_break);
-	}
-	free(network->vei);
-	free(network->ve);
-	free(network->bound_inds);
-	free(network->bound_verts);
-	free(network->vx);
-	free(network->ex);
-	free(network->dev);
-	free(network->dvx);
-	free(network->dvei);
-	free(network->dve);
-	free(network->spanning_edges);
-	CHOL_F(free_sparse)(&(network->voltcurmat), c);
-	free(network);
-}
diff --git a/src/graph_free.c b/src/graph_free.c
new file mode 100644
index 0000000..e9c55d7
--- /dev/null
+++ b/src/graph_free.c
@@ -0,0 +1,22 @@
+
+#include "fracture.h"
+
+void graph_free(graph_t *g, cholmod_common *c) {
+	free(g->ev);
+	if (g->ev_break != g->ev) {
+		free(g->ev_break);
+	}
+	free(g->vei);
+	free(g->ve);
+	free(g->bound_inds);
+	free(g->bound_verts);
+	free(g->vx);
+	free(g->ex);
+	free(g->dev);
+	free(g->dvx);
+	free(g->dvei);
+	free(g->dve);
+	free(g->spanning_edges);
+	CHOL_F(free_sparse)(&(g->voltcurmat), c);
+	free(g);
+}
diff --git a/src/randfuncs.c b/src/graph_genfunc.c
index 137c7ff..991e127 100644
--- a/src/randfuncs.c
+++ b/src/graph_genfunc.c
@@ -76,18 +76,3 @@ double *genfunc_hyperuniform(unsigned int L, bound_t boundary, gsl_rng *r, unsig
 	return lattice;
 }
 
-void randfunc_flat(gsl_rng *r, double *x, double *y) {
-	*x = gsl_ran_flat(r, 0, 1);
-	*y = gsl_ran_flat(r, 0, 1);
-}
-
-void randfunc_gaus(gsl_rng *r, double *x, double *y) {
-	*x = 100;
-	*y = 100;
-	double sigma = 0.25;
-	while (fabs(*x) > 0.5 || fabs(*y) > 0.5) {
-		gsl_ran_bivariate_gaussian(r, sigma, sigma, 0, x, y);
-	}
-	*x += 0.5;
-	*y += 0.5;
-}
diff --git a/src/net_copy.c b/src/net_copy.c
new file mode 100644
index 0000000..dcb4080
--- /dev/null
+++ b/src/net_copy.c
@@ -0,0 +1,35 @@
+
+#include "fracture.h"
+
+net_t *net_copy(const net_t *net, cholmod_common *c) {
+	net_t *net_copy = (net_t *)calloc(1, sizeof(net_t));
+	assert(net_copy != NULL);
+	memcpy(net_copy, net, sizeof(net_t));
+
+	size_t fuses_size = (net->graph)->ne * sizeof(bool);
+	net_copy->fuses = (bool *)malloc(fuses_size);
+	assert(net_copy->fuses != NULL);
+	memcpy(net_copy->fuses, net->fuses, fuses_size);
+
+	size_t thres_size = (net->graph)->ne * sizeof(double);
+	net_copy->thres = (double *)malloc(thres_size);
+	assert(net_copy->thres != NULL);
+	memcpy(net_copy->thres, net->thres, thres_size);
+
+	size_t marks_size = (net->graph->break_dim) * sizeof(uint_t);
+	net_copy->marks = (uint_t *)malloc(marks_size);
+	assert(net_copy->marks != NULL);
+	memcpy(net_copy->marks, net->marks, marks_size);
+
+	size_t dual_marks_size = (net->graph->dnv) * sizeof(uint_t);
+	net_copy->dual_marks = (uint_t *)malloc(dual_marks_size);
+	assert(net_copy->dual_marks != NULL);
+	memcpy(net_copy->dual_marks, net->dual_marks, dual_marks_size);
+
+	net_copy->adjacency = CHOL_F(copy_sparse)(net->adjacency, c);
+	net_copy->boundary_cond = CHOL_F(copy_dense)(net->boundary_cond, c);
+	net_copy->factor = CHOL_F(copy_factor)(net->factor, c);
+
+	return net_copy;
+}
+
diff --git a/src/net.c b/src/net_create.c
index d090a9a..fedcb3a 100644
--- a/src/net.c
+++ b/src/net_create.c
@@ -27,7 +27,6 @@ double *get_thres(uint_t ne, double beta) {
 	return thres;
 }
 
-
 net_t *net_create(const graph_t *g, double inf, double beta, double notch_len, bool vb, cholmod_common *c) {
 	net_t *net = (net_t *)calloc(1, sizeof(net_t));
 	assert(net != NULL);
@@ -68,54 +67,3 @@ net_t *net_create(const graph_t *g, double inf, double beta, double notch_len, b
 	return net;
 }
 
-net_t *net_copy(const net_t *net, cholmod_common *c) {
-	net_t *net_copy = (net_t *)calloc(1, sizeof(net_t));
-	assert(net_copy != NULL);
-	memcpy(net_copy, net, sizeof(net_t));
-
-	size_t fuses_size = (net->graph)->ne * sizeof(bool);
-	net_copy->fuses = (bool *)malloc(fuses_size);
-	assert(net_copy->fuses != NULL);
-	memcpy(net_copy->fuses, net->fuses, fuses_size);
-
-	size_t thres_size = (net->graph)->ne * sizeof(double);
-	net_copy->thres = (double *)malloc(thres_size);
-	assert(net_copy->thres != NULL);
-	memcpy(net_copy->thres, net->thres, thres_size);
-
-	size_t marks_size = (net->graph->break_dim) * sizeof(uint_t);
-	net_copy->marks = (uint_t *)malloc(marks_size);
-	assert(net_copy->marks != NULL);
-	memcpy(net_copy->marks, net->marks, marks_size);
-
-	size_t dual_marks_size = (net->graph->dnv) * sizeof(uint_t);
-	net_copy->dual_marks = (uint_t *)malloc(dual_marks_size);
-	assert(net_copy->dual_marks != NULL);
-	memcpy(net_copy->dual_marks, net->dual_marks, dual_marks_size);
-
-	net_copy->adjacency = CHOL_F(copy_sparse)(net->adjacency, c);
-	net_copy->boundary_cond = CHOL_F(copy_dense)(net->boundary_cond, c);
-	net_copy->factor = CHOL_F(copy_factor)(net->factor, c);
-
-	return net_copy;
-}
-
-void net_free(net_t *net, cholmod_common *c) {
-	free(net->fuses);
-	free(net->thres);
-	CHOL_F(free_dense)(&(net->boundary_cond), c);
-	CHOL_F(free_sparse)(&(net->adjacency), c);
-	CHOL_F(free_factor)(&(net->factor), c);
-	free(net->marks);
-	free(net->dual_marks);
-	free(net);
-}
-
-bool check_instance(const net_t *instance, cholmod_common *c) {
-	assert(instance != NULL);
-	assert(instance->fuses != NULL);
-	assert(CHOL_F(check_dense)(instance->boundary_cond, c));
-	assert(CHOL_F(check_factor)(instance->factor, c));
-
-	return true;
-}
diff --git a/src/net_fracture.c b/src/net_fracture.c
index b7fa61d..48e81f9 100644
--- a/src/net_fracture.c
+++ b/src/net_fracture.c
@@ -27,9 +27,8 @@ uint_t get_next_broken(net_t *net, double *currents, double cutoff) {
 	return max_pos;
 }
 
-
 data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff) {
-	data_t *data = alloc_break_data(net->graph->ne);
+	data_t *data = data_create(net->graph->ne);
 
 	while (true) {
 		double *voltages = get_voltage(net, c);
@@ -45,7 +44,7 @@ data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff) {
 
 		uint_t last_broke = get_next_broken(net, currents, cutoff);
 
-		update_break_data(data, last_broke, fabs(conductivity * (net->thres)[last_broke] / currents[last_broke]), conductivity);
+		data_update(data, last_broke, fabs(conductivity * (net->thres)[last_broke] / currents[last_broke]), conductivity);
 
 		free(voltages);
 		free(currents);
diff --git a/src/net_free.c b/src/net_free.c
new file mode 100644
index 0000000..8b5af50
--- /dev/null
+++ b/src/net_free.c
@@ -0,0 +1,14 @@
+
+#include "fracture.h"
+
+void net_free(net_t *net, cholmod_common *c) {
+	free(net->fuses);
+	free(net->thres);
+	CHOL_F(free_dense)(&(net->boundary_cond), c);
+	CHOL_F(free_sparse)(&(net->adjacency), c);
+	CHOL_F(free_factor)(&(net->factor), c);
+	free(net->marks);
+	free(net->dual_marks);
+	free(net);
+}
+