ran clang-format on all files

16 files changed, 788 insertions, 772 deletions

diff --git a/lib/bound_set.c b/lib/bound_set.c
index 65f1e6f..32d0fb7 100644
--- a/lib/bound_set.c
+++ b/lib/bound_set.c
@@ -2,101 +2,109 @@
 #include "fracture.h"
 
 double th_p(double x, double y, double th) {
-	if (x >= 0 && y >= 0) return th;
-	else if (x <  0 && y >= 0) return M_PI - th;
-	else if (x <  0 && y <  0) return th - M_PI;
-	else return -th;
-
+  if (x >= 0 && y >= 0)
+    return th;
+  else if (x < 0 && y >= 0)
+    return M_PI - th;
+  else if (x < 0 && y < 0)
+    return th - M_PI;
+  else
+    return -th;
 }
 
 double u_y(double x, double y) {
-	double r = sqrt(pow(x, 2) + pow(y, 2));
-	double th = th_p(x, y, atan(fabs(y / x)));
+  double r = sqrt(pow(x, 2) + pow(y, 2));
+  double th = th_p(x, y, atan(fabs(y / x)));
 
-	return sqrt(r) * sin(th / 2);
+  return sqrt(r) * sin(th / 2);
 }
 
 void bound_set_embedded(double *bound, const graph_t *g, double notch_len) {
-	uint_t L = g->L;
-
-	for (uint_t i = 0; i < L / 2; i++) {
-		double x1, y1, x2, y2, x3, y3, x4, y4;
-		x1 = (2. * i + 1.) / L - notch_len; y1 = 0.5 - 1.;
-		x2 = (2. * i + 1.) / L - notch_len; y2 = 0.5 - 0.;
-		y3 = (2. * i + 1.) / L - 0.5; x3 = 0.5 - 1.;
-		y4 = (2. * i + 1.) / L - 0.5; x4 = 0.5 - 0.;
-
-		bound[g->b[g->bi[0] + i]] = u_y(x1, y1);
-		bound[g->b[g->bi[1] + i]] = u_y(x2, y2);
-		bound[g->b[g->bi[2] + i]] = u_y(x3, y3);
-		bound[g->b[g->bi[3] + i]] = u_y(x4, y4);
-	}
+  uint_t L = g->L;
+
+  for (uint_t i = 0; i < L / 2; i++) {
+    double x1, y1, x2, y2, x3, y3, x4, y4;
+    x1 = (2. * i + 1.) / L - notch_len;
+    y1 = 0.5 - 1.;
+    x2 = (2. * i + 1.) / L - notch_len;
+    y2 = 0.5 - 0.;
+    y3 = (2. * i + 1.) / L - 0.5;
+    x3 = 0.5 - 1.;
+    y4 = (2. * i + 1.) / L - 0.5;
+    x4 = 0.5 - 0.;
+
+    bound[g->b[g->bi[0] + i]] = u_y(x1, y1);
+    bound[g->b[g->bi[1] + i]] = u_y(x2, y2);
+    bound[g->b[g->bi[2] + i]] = u_y(x3, y3);
+    bound[g->b[g->bi[3] + i]] = u_y(x4, y4);
+  }
 }
 
 bool is_in(uint_t len, uint_t *list, uint_t element) {
-	for (uint_t i = 0; i < len; i++) {
-		if (list[i] == element) { 
-			return true;
-		}
-	}
-	return false;
+  for (uint_t i = 0; i < len; i++) {
+    if (list[i] == element) {
+      return true;
+    }
+  }
+  return false;
 }
 
-cholmod_dense *bound_set(const graph_t *g, bool vb, double notch_len, cholmod_common *c) {
-
-	uint_t dim = g->nv;
-
-	if (vb && g->boundary != TORUS_BOUND) {
-		dim -= g->bi[g->nb];
-	} else if (!vb) {
-		dim += 2;
-	}
-
-	cholmod_dense *boundary = CHOL_F(zeros)(dim, 1, CHOLMOD_REAL, c);
-	double *bound = (double *)boundary->x;
-
-	switch (g->boundary) {
-		case TORUS_BOUND:
-			for (uint_t i = 0; i < g->bi[1]; i++) {
-				uint_t be = g->b[i];
-				uint_t v1 = g->ev[2 * be];
-				uint_t v2 = g->ev[2 * be + 1];
-				double v1y = g->vx[2 * v1 + 1];
-				double v2y = g->vx[2 * v2 + 1];
-
-				uint_t ind = v1y < v2y ? 0 : 1;
-
-				bound[g->ev[2 * be + ind]] += 1;
-				bound[g->ev[2 * be + !ind]] -= 1;
-			}
-			break;
-			/*
-		case EMBEDDED_BOUND:
-			bound_set_embedded(bound, g, notch_len);
-			break;
-			*/
-		default:
-			if (vb) {
-				for (uint_t i = 0; i < dim; i++) {
-					uint_t v = g->nbi[i];
-					for (uint_t j = 0; j < g->vei[v+1] - g->vei[v]; j++) {
-						uint_t e = g->ve[g->vei[v] + j];
-						uint_t v0 = g->ev[2 * e];
-						uint_t v1 = g->ev[2 * e + 1];
-
-						if (g->bq[v0] || g->bq[v1]) {
-							uint_t vv = v0 == v ? v1 : v0;
-							if (is_in(g->bi[1], g->b, vv)) {
-								bound[i]++;
-							}
-						}
-					}
-				}
-			} else {
-				bound[g->nv] = 1;
-				bound[g->nv + 1] = -1;
-			}
-	}
-
-	return boundary;
+cholmod_dense *bound_set(const graph_t *g, bool vb, double notch_len,
+                         cholmod_common *c) {
+
+  uint_t dim = g->nv;
+
+  if (vb && g->boundary != TORUS_BOUND) {
+    dim -= g->bi[g->nb];
+  } else if (!vb) {
+    dim += 2;
+  }
+
+  cholmod_dense *boundary = CHOL_F(zeros)(dim, 1, CHOLMOD_REAL, c);
+  double *bound = (double *)boundary->x;
+
+  switch (g->boundary) {
+  case TORUS_BOUND:
+    for (uint_t i = 0; i < g->bi[1]; i++) {
+      uint_t be = g->b[i];
+      uint_t v1 = g->ev[2 * be];
+      uint_t v2 = g->ev[2 * be + 1];
+      double v1y = g->vx[2 * v1 + 1];
+      double v2y = g->vx[2 * v2 + 1];
+
+      uint_t ind = v1y < v2y ? 0 : 1;
+
+      bound[g->ev[2 * be + ind]] += 1;
+      bound[g->ev[2 * be + !ind]] -= 1;
+    }
+    break;
+  /*
+case EMBEDDED_BOUND:
+  bound_set_embedded(bound, g, notch_len);
+  break;
+  */
+  default:
+    if (vb) {
+      for (uint_t i = 0; i < dim; i++) {
+        uint_t v = g->nbi[i];
+        for (uint_t j = 0; j < g->vei[v + 1] - g->vei[v]; j++) {
+          uint_t e = g->ve[g->vei[v] + j];
+          uint_t v0 = g->ev[2 * e];
+          uint_t v1 = g->ev[2 * e + 1];
+
+          if (g->bq[v0] || g->bq[v1]) {
+            uint_t vv = v0 == v ? v1 : v0;
+            if (is_in(g->bi[1], g->b, vv)) {
+              bound[i]++;
+            }
+          }
+        }
+      }
+    } else {
+      bound[g->nv] = 1;
+      bound[g->nv + 1] = -1;
+    }
+  }
+
+  return boundary;
 }
diff --git a/lib/break_edge.c b/lib/break_edge.c
index 2f112c2..e53f7c1 100644
--- a/lib/break_edge.c
+++ b/lib/break_edge.c
@@ -1,51 +1,50 @@
 
 #include "fracture.h"
 
-
 bool break_edge(net_t *net, uint_t edge, cholmod_common *c) {
-	net->fuses[edge] = true;
-	net->num_broken++;
-
-	double *x = (double *)net->boundary_cond->x;
-	const graph_t *g = net->graph;
-
-	uint_t v1 = net->graph->ev[2 * edge];
-	uint_t v2 = net->graph->ev[2 * edge + 1];
-
-	uint_t s1 = v1 < v2 ? v1 : v2;
-	uint_t s2 = v1 < v2 ? v2 : v1;
-
-	if (net->graph->boundary == TORUS_BOUND) {
-		if (net->graph->bq[edge]) {
-			double v1y = g->vx[2 * v1 + 1];
-			double v2y = g->vx[2 * v2 + 1];
-			uint_t ind = v1y < v2y ? 0 : 1;
-			x[g->ev[2 * edge + ind]] -= 1;
-			x[g->ev[2 * edge + !ind]] += 1;
-		}
-		if (net->factor != NULL) {
-			factor_update(net->factor, s1, s2, c);
-		}
-	} else if (net->voltage_bound) {
-		if (g->bq[v1] || g->bq[v2]) {
-			uint_t vv = g->bq[v1] ? v2 : v1;
-			uint_t uu = v1 == vv ? v2 : v1;
-			if (is_in(g->bi[1], g->b, uu)) {
-				x[g->bni[vv]] -= 1;
-			}
-			if (net->factor != NULL) {
-				factor_update2(net->factor, g->bni[vv], c);
-			}
-		} else {
-			if (net->factor != NULL) {
-				factor_update(net->factor, g->bni[s1], g->bni[s2], c);
-			}
-		}
-	} else {
-		if (net->factor != NULL) {
-			factor_update(net->factor, s1, s2, c);
-		}
-	}
-
-	return true;
+  net->fuses[edge] = true;
+  net->num_broken++;
+
+  double *x = (double *)net->boundary_cond->x;
+  const graph_t *g = net->graph;
+
+  uint_t v1 = net->graph->ev[2 * edge];
+  uint_t v2 = net->graph->ev[2 * edge + 1];
+
+  uint_t s1 = v1 < v2 ? v1 : v2;
+  uint_t s2 = v1 < v2 ? v2 : v1;
+
+  if (net->graph->boundary == TORUS_BOUND) {
+    if (net->graph->bq[edge]) {
+      double v1y = g->vx[2 * v1 + 1];
+      double v2y = g->vx[2 * v2 + 1];
+      uint_t ind = v1y < v2y ? 0 : 1;
+      x[g->ev[2 * edge + ind]] -= 1;
+      x[g->ev[2 * edge + !ind]] += 1;
+    }
+    if (net->factor != NULL) {
+      factor_update(net->factor, s1, s2, c);
+    }
+  } else if (net->voltage_bound) {
+    if (g->bq[v1] || g->bq[v2]) {
+      uint_t vv = g->bq[v1] ? v2 : v1;
+      uint_t uu = v1 == vv ? v2 : v1;
+      if (is_in(g->bi[1], g->b, uu)) {
+        x[g->bni[vv]] -= 1;
+      }
+      if (net->factor != NULL) {
+        factor_update2(net->factor, g->bni[vv], c);
+      }
+    } else {
+      if (net->factor != NULL) {
+        factor_update(net->factor, g->bni[s1], g->bni[s2], c);
+      }
+    }
+  } else {
+    if (net->factor != NULL) {
+      factor_update(net->factor, s1, s2, c);
+    }
+  }
+
+  return true;
 }
diff --git a/lib/correlations.c b/lib/correlations.c
index 63532ec..98c5767 100644
--- a/lib/correlations.c
+++ b/lib/correlations.c
@@ -2,46 +2,45 @@
 #include "fracture.h"
 
 double *get_corr(net_t *instance, uint_t **dists, cholmod_common *c) {
-	uint_t nv = instance->graph->dnv;
-	uint_t ne = instance->graph->ne;
-	uint_t *ev = instance->graph->dev;
-	bool nulldists = false;
-	if (dists == NULL) {
-		dists = graph_dists(instance->graph, false);
-		nulldists = true;
-	}
-	double *corr = calloc(nv, sizeof(double));
-	uint_t *numat = calloc(nv, sizeof(uint_t));
+  uint_t nv = instance->graph->dnv;
+  uint_t ne = instance->graph->ne;
+  uint_t *ev = instance->graph->dev;
+  bool nulldists = false;
+  if (dists == NULL) {
+    dists = graph_dists(instance->graph, false);
+    nulldists = true;
+  }
+  double *corr = calloc(nv, sizeof(double));
+  uint_t *numat = calloc(nv, sizeof(uint_t));
 
-	for (uint_t i = 0; i < ne; i++) {
-		uint_t v1 = ev[2 * i];
-		uint_t v2 = ev[2 * i + 1];
-		for (uint_t j = 0; j < ne; j++) {
-			uint_t v3 = ev[2 * j];
-			uint_t v4 = ev[2 * j + 1];
-			uint_t dist1 = dists[v1][v3];
-			uint_t dist2 = dists[v1][v4];
-			uint_t dist3 = dists[v2][v3];
-			uint_t dist4 = dists[v2][v4];
-			uint_t dist = (dist1 + dist2 + dist3 + dist4) / 4;
-			corr[dist] += instance->fuses[i] && instance->fuses[j];
-			numat[dist]++;
-		}
-	}
+  for (uint_t i = 0; i < ne; i++) {
+    uint_t v1 = ev[2 * i];
+    uint_t v2 = ev[2 * i + 1];
+    for (uint_t j = 0; j < ne; j++) {
+      uint_t v3 = ev[2 * j];
+      uint_t v4 = ev[2 * j + 1];
+      uint_t dist1 = dists[v1][v3];
+      uint_t dist2 = dists[v1][v4];
+      uint_t dist3 = dists[v2][v3];
+      uint_t dist4 = dists[v2][v4];
+      uint_t dist = (dist1 + dist2 + dist3 + dist4) / 4;
+      corr[dist] += instance->fuses[i] && instance->fuses[j];
+      numat[dist]++;
+    }
+  }
 
-	for (uint_t i = 0; i < nv; i++) {
-		if (numat[i] > 0) {
-			corr[i] /= numat[i];
-		}
-	}
+  for (uint_t i = 0; i < nv; i++) {
+    if (numat[i] > 0) {
+      corr[i] /= numat[i];
+    }
+  }
 
-	if (nulldists) {
-		for (int i = 0; i < nv; i++) {
-			free(dists[i]);
-		}
-		free(dists);
-	}
+  if (nulldists) {
+    for (int i = 0; i < nv; i++) {
+      free(dists[i]);
+    }
+    free(dists);
+  }
 
-	return corr;
+  return corr;
 }
-
diff --git a/lib/data.c b/lib/data.c
index 2047c44..e39c450 100644
--- a/lib/data.c
+++ b/lib/data.c
@@ -2,34 +2,34 @@
 #include "fracture.h"
 
 data_t *data_create(uint_t ne) {
-	data_t *data = malloc(1 * sizeof(data_t));
-	assert(data != NULL);
+  data_t *data = malloc(1 * sizeof(data_t));
+  assert(data != NULL);
 
-	data->num_broken = 0;
+  data->num_broken = 0;
 
-	data->break_list = (uint_t *)malloc(ne * sizeof(uint_t));
-	assert(data->break_list != NULL);
+  data->break_list = (uint_t *)malloc(ne * sizeof(uint_t));
+  assert(data->break_list != NULL);
 
-	data->extern_field = (long double *)malloc(ne * sizeof(long double));
-	assert(data->extern_field != NULL);
+  data->extern_field = (long double *)malloc(ne * sizeof(long double));
+  assert(data->extern_field != NULL);
 
-	data->conductivity = (double *)malloc(ne * sizeof(double));
-	assert(data->conductivity != NULL);
+  data->conductivity = (double *)malloc(ne * sizeof(double));
+  assert(data->conductivity != NULL);
 
-	return data;
+  return data;
 }
 
 void data_free(data_t *data) {
-	free(data->break_list);
-	free(data->extern_field);
-	free(data->conductivity);
-	free(data);
+  free(data->break_list);
+  free(data->extern_field);
+  free(data->conductivity);
+  free(data);
 }
 
-void data_update(data_t *data, uint_t last_broke, long 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++;
+void data_update(data_t *data, uint_t last_broke, long 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/lib/factor_update.c b/lib/factor_update.c
index a51705a..ceaa01a 100644
--- a/lib/factor_update.c
+++ b/lib/factor_update.c
@@ -1,68 +1,69 @@
 
 #include "fracture.h"
 
-void factor_update(cholmod_factor *factor, uint_t v1, uint_t v2, cholmod_common *c) {
-	uint_t n = factor->n;
+void factor_update(cholmod_factor *factor, uint_t v1, uint_t v2,
+                   cholmod_common *c) {
+  uint_t n = factor->n;
 
-	cholmod_sparse *update_mat =
-			CHOL_F(allocate_sparse)(n, n, 2, true, true, 0, CHOLMOD_REAL, c);
+  cholmod_sparse *update_mat =
+      CHOL_F(allocate_sparse)(n, n, 2, true, true, 0, CHOLMOD_REAL, c);
 
-	uint_t s1, s2;
-	s1 = v1 < v2 ? v1 : v2;
-	s2 = v1 > v2 ? v1 : v2;
+  uint_t s1, s2;
+  s1 = v1 < v2 ? v1 : v2;
+  s2 = v1 > v2 ? v1 : v2;
 
-	int_t *pp = (int_t *)update_mat->p;
-	int_t *ii = (int_t *)update_mat->i;
-	double *xx = (double *)update_mat->x;
+  int_t *pp = (int_t *)update_mat->p;
+  int_t *ii = (int_t *)update_mat->i;
+  double *xx = (double *)update_mat->x;
 
-	for (uint_t i = 0; i <= s1; i++) {
-		pp[i] = 0;
-	}
+  for (uint_t i = 0; i <= s1; i++) {
+    pp[i] = 0;
+  }
 
-	for (uint_t i = s1 + 1; i <= n; i++) {
-		pp[i] = 2;
-	}
+  for (uint_t i = s1 + 1; i <= n; i++) {
+    pp[i] = 2;
+  }
 
-	ii[0] = s1;
-	ii[1] = s2;
-	xx[0] = 1;
-	xx[1] = -1;
+  ii[0] = s1;
+  ii[1] = s2;
+  xx[0] = 1;
+  xx[1] = -1;
 
-	cholmod_sparse *perm_update_mat = CHOL_F(submatrix)(
-			update_mat, factor->Perm, factor->n, NULL, -1, true, true, c);
+  cholmod_sparse *perm_update_mat = CHOL_F(submatrix)(
+      update_mat, factor->Perm, factor->n, NULL, -1, true, true, c);
 
-	CHOL_F(updown)(false, perm_update_mat, factor, c);
+  CHOL_F(updown)(false, perm_update_mat, factor, c);
 
-	CHOL_F(free_sparse)(&perm_update_mat, c);
-	CHOL_F(free_sparse)(&update_mat, c);
+  CHOL_F(free_sparse)(&perm_update_mat, c);
+  CHOL_F(free_sparse)(&update_mat, c);
 }
 
 void factor_update2(cholmod_factor *factor, uint_t v, cholmod_common *c) {
-	uint_t n = factor->n;
+  uint_t n = factor->n;
 
-	cholmod_sparse *update_mat =
-			CHOL_F(allocate_sparse)(n, n, 1, true, true, 0, CHOLMOD_REAL, c);
+  cholmod_sparse *update_mat =
+      CHOL_F(allocate_sparse)(n, n, 1, true, true, 0, CHOLMOD_REAL, c);
 
-	int_t *pp = (int_t *)update_mat->p;
-	int_t *ii = (int_t *)update_mat->i;
-	double *xx = (double *)update_mat->x;
+  int_t *pp = (int_t *)update_mat->p;
+  int_t *ii = (int_t *)update_mat->i;
+  double *xx = (double *)update_mat->x;
 
-	for (uint_t i = 0; i <= v; i++) {
-		pp[i] = 0;
-	}
+  for (uint_t i = 0; i <= v; i++) {
+    pp[i] = 0;
+  }
 
-	for (uint_t i = v + 1; i <= n; i++) {
-		pp[i] = 1;
-	}
+  for (uint_t i = v + 1; i <= n; i++) {
+    pp[i] = 1;
+  }
 
-	ii[0] = v;
-	xx[0] = 1;
+  ii[0] = v;
+  xx[0] = 1;
 
-	cholmod_sparse *perm_update_mat = CHOL_F(submatrix)(
-			update_mat, factor->Perm, factor->n, NULL, -1, true, true, c);
+  cholmod_sparse *perm_update_mat = CHOL_F(submatrix)(
+      update_mat, factor->Perm, factor->n, NULL, -1, true, true, c);
 
-	CHOL_F(updown)(false, perm_update_mat, factor, c);
+  CHOL_F(updown)(false, perm_update_mat, factor, c);
 
-	CHOL_F(free_sparse)(&perm_update_mat, c);
-	CHOL_F(free_sparse)(&update_mat, c);
+  CHOL_F(free_sparse)(&perm_update_mat, c);
+  CHOL_F(free_sparse)(&update_mat, c);
 }
diff --git a/lib/fracture.h b/lib/fracture.h
index b1114fb..7b4f146 100644
--- a/lib/fracture.h
+++ b/lib/fracture.h
@@ -17,7 +17,6 @@
 #include <stdbool.h>
 #include <stdint.h>
 #include <stdio.h>
-#include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <sys/types.h>
@@ -26,7 +25,6 @@
 #include <jst/graph.h>
 #include <jst/rand.h>
 
-
 // these defs allow me to switch to long int cholmod in a sitch
 #define int_t int
 #define uint_t unsigned int
@@ -36,68 +34,69 @@
 #define GSL_RAND_GEN gsl_rng_mt19937
 
 typedef struct {
-	const graph_t *graph;
-	bool *fuses;
-	long double *thres;
-	double inf;
-	cholmod_dense *boundary_cond;
-	cholmod_factor *factor;
-	bool voltage_bound;
-	uint_t num_broken;
-	uint_t dim;
-	uint_t nep;
-	uint_t *evp;
-	cholmod_sparse *voltcurmat;
+  const graph_t *graph;
+  bool *fuses;
+  long double *thres;
+  double inf;
+  cholmod_dense *boundary_cond;
+  cholmod_factor *factor;
+  bool voltage_bound;
+  uint_t num_broken;
+  uint_t dim;
+  uint_t nep;
+  uint_t *evp;
+  cholmod_sparse *voltcurmat;
 } net_t;
 
 typedef struct {
-	uint_t num_broken;
-	uint_t *break_list;
-	double *conductivity;
-	long double *extern_field;
+  uint_t num_broken;
+  uint_t *break_list;
+  double *conductivity;
+  long double *extern_field;
 } data_t;
 
-intptr_t *run_voronoi(uint_t num_coords, double *coords, bool periodic, double xmin, double xmax, double ymin, double ymax);
+intptr_t *run_voronoi(uint_t num_coords, double *coords, bool periodic,
+                      double xmin, double xmax, double ymin, double ymax);
 
-cholmod_sparse *gen_adjacency(const net_t *net, bool dual, bool use_gp, bool symmetric, cholmod_common *c);
+cholmod_sparse *gen_adjacency(const net_t *net, bool dual, bool use_gp,
+                              bool symmetric, cholmod_common *c);
 
 cholmod_sparse *gen_laplacian(const net_t *net, cholmod_common *c);
 
-int edge_to_verts(uint_t width, bool periodic, uint_t edge,
-									bool index);
+int edge_to_verts(uint_t width, bool periodic, uint_t edge, bool index);
 
-int dual_edge_to_verts(uint_t width, bool periodic, uint_t edge,
-											 bool index);
+int dual_edge_to_verts(uint_t width, bool periodic, uint_t edge, bool index);
 
-double dual_vert_to_coord(uint_t width, bool periodic, uint_t vert,
-													bool index);
+double dual_vert_to_coord(uint_t width, bool periodic, uint_t vert, bool index);
 
-void factor_update(cholmod_factor *factor, uint_t v1, uint_t v2, cholmod_common *c);
+void factor_update(cholmod_factor *factor, uint_t v1, uint_t v2,
+                   cholmod_common *c);
 void factor_update2(cholmod_factor *factor, uint_t v1, cholmod_common *c);
 
 void net_notch(net_t *net, double notch_len, cholmod_common *c);
 data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff);
 double *net_voltages(const net_t *net, cholmod_common *c);
-double *net_currents(const net_t *net, const double *voltages, cholmod_common *c);
+double *net_currents(const net_t *net, const double *voltages,
+                     cholmod_common *c);
 double net_conductivity(const net_t *net, const double *voltages);
 
 void update_boundary(net_t *instance, const double *avg_field);
 
-FILE *get_file(const char *prefix, uint_t width, uint_t crack,
-							 double beta, uint_t iter, uint_t num_iter,
-							 uint_t num, bool read);
+FILE *get_file(const char *prefix, uint_t width, uint_t crack, double beta,
+               uint_t iter, uint_t num_iter, uint_t num, bool read);
 
 double update_beta(double beta, uint_t width, const double *stress,
-									 const double *damage, double bound_total);
+                   const double *damage, double bound_total);
 
 cholmod_sparse *gen_voltcurmat(uint_t num_edges, uint_t num_verts,
-															 uint_t *edges_to_verts, cholmod_common *c);
+                               uint_t *edges_to_verts, cholmod_common *c);
 
 net_t *net_copy(const net_t *net, cholmod_common *c);
 
 void net_free(net_t *instance, cholmod_common *c);
 
-net_t *net_create(const graph_t *g, double inf, double beta, double notch_len, bool vb, cholmod_common *c);
+net_t *net_create(const graph_t *g, double inf, double beta, double notch_len,
+                  bool vb, cholmod_common *c);
 
 bool break_edge(net_t *instance, uint_t edge, cholmod_common *c);
 
@@ -112,11 +111,13 @@ double *get_corr(net_t *instance, uint_t **dists, cholmod_common *c);
 
 double *bin_values(graph_t *network, uint_t width, double *values);
 
-cholmod_dense *bound_set(const graph_t *g, bool vb, double notch_len, cholmod_common *c);
+cholmod_dense *bound_set(const graph_t *g, bool vb, double notch_len,
+                         cholmod_common *c);
 
 data_t *data_create(uint_t num_edges);
 void data_free(data_t *data);
-void data_update(data_t *data, uint_t last_broke, long double strength, double conductivity);
+void data_update(data_t *data, uint_t last_broke, long double strength,
+                 double conductivity);
 
 long double rand_dist_pow(const gsl_rng *r, double beta);
 
diff --git a/lib/gen_laplacian.c b/lib/gen_laplacian.c
index 1cc93a4..75dccce 100644
--- a/lib/gen_laplacian.c
+++ b/lib/gen_laplacian.c
@@ -1,137 +1,142 @@
 
 #include "fracture.h"
 
-cholmod_sparse *gen_adjacency(const net_t *net, bool dual, bool use_gp, bool symmetric, cholmod_common *c) {
-	const graph_t *g = net->graph;
-	uint_t nv;
-	uint_t ne;
-	uint_t nre;
-	uint_t *ev;
-
-	if (use_gp) {
-		nv = net->dim;
-		ne = net->nep;
-		nre = (int_t)net->nep - (int_t)net->num_broken;
-		ev = net->evp;
-	} else if (dual) {
-		nv = g->dnv;
-		ne = g->ne;
-		nre = net->num_broken;
-		ev = g->dev;
-	} else {
-		nv = g->nv;
-		ne = g->ne;
-		nre = (int_t)g->ne - (int_t)net->num_broken;
-		ev = g->ev;
-	}
-
-	uint_t nnz = nre;
-
-	cholmod_triplet *t = CHOL_F(allocate_triplet)(nv, nv, nnz, 1, CHOLMOD_REAL, c);
-
-	int_t *ri = (int_t *)t->i;
-	int_t *ci = (int_t *)t->j;
-	double *ai = (double *)t->x;
-
-	t->nnz = nnz;
-
-	uint_t a = 0;
-
-	for (uint_t i = 0; i < ne; i++) {
-		if ((net->fuses[i] && dual) || (!net->fuses[i] && !dual)) {
-			uint_t v1 = ev[2 * i];
-			uint_t v2 = ev[2 * i + 1];
-
-			uint_t s1 = v1 < v2 ? v1 : v2;
-			uint_t s2 = v1 < v2 ? v2 : v1;
-
-			ri[a] = s2;
-			ci[a] = s1;
-			ai[a] = 1;
-
-			a++;
-		}
-	}
-
-	cholmod_sparse *s = CHOL_F(triplet_to_sparse)(t, nnz, c);
-	CHOL_F(free_triplet)(&t, c);
-
-	if (!symmetric) {
-		cholmod_sparse *tmp_s = CHOL_F(copy)(s, 0, 1, c);
-		CHOL_F(free_sparse)(&s, c);
-		s = tmp_s;
-	}
-
-	return s;
+cholmod_sparse *gen_adjacency(const net_t *net, bool dual, bool use_gp,
+                              bool symmetric, cholmod_common *c) {
+  const graph_t *g = net->graph;
+  uint_t nv;
+  uint_t ne;
+  uint_t nre;
+  uint_t *ev;
+
+  if (use_gp) {
+    nv = net->dim;
+    ne = net->nep;
+    nre = (int_t)net->nep - (int_t)net->num_broken;
+    ev = net->evp;
+  } else if (dual) {
+    nv = g->dnv;
+    ne = g->ne;
+    nre = net->num_broken;
+    ev = g->dev;
+  } else {
+    nv = g->nv;
+    ne = g->ne;
+    nre = (int_t)g->ne - (int_t)net->num_broken;
+    ev = g->ev;
+  }
+
+  uint_t nnz = nre;
+
+  cholmod_triplet *t =
+      CHOL_F(allocate_triplet)(nv, nv, nnz, 1, CHOLMOD_REAL, c);
+
+  int_t *ri = (int_t *)t->i;
+  int_t *ci = (int_t *)t->j;
+  double *ai = (double *)t->x;
+
+  t->nnz = nnz;
+
+  uint_t a = 0;
+
+  for (uint_t i = 0; i < ne; i++) {
+    if ((net->fuses[i] && dual) || (!net->fuses[i] && !dual)) {
+      uint_t v1 = ev[2 * i];
+      uint_t v2 = ev[2 * i + 1];
+
+      uint_t s1 = v1 < v2 ? v1 : v2;
+      uint_t s2 = v1 < v2 ? v2 : v1;
+
+      ri[a] = s2;
+      ci[a] = s1;
+      ai[a] = 1;
+
+      a++;
+    }
+  }
+
+  cholmod_sparse *s = CHOL_F(triplet_to_sparse)(t, nnz, c);
+  CHOL_F(free_triplet)(&t, c);
+
+  if (!symmetric) {
+    cholmod_sparse *tmp_s = CHOL_F(copy)(s, 0, 1, c);
+    CHOL_F(free_sparse)(&s, c);
+    s = tmp_s;
+  }
+
+  return s;
 }
 
 cholmod_sparse *gen_laplacian(const net_t *net, cholmod_common *c) {
-	const graph_t *g = net->graph;
-	uint_t nv = net->dim;
-	uint_t ne = net->nep;
-	uint_t *ev = net->evp;
-
-	uint_t nnz = nv;
-
-	cholmod_triplet *temp_m = CHOL_F(allocate_triplet)(nv, nv, nnz, 1, CHOLMOD_REAL, c);
-
-	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;
-
-	for (uint_t i = 0; i < nv; i++) {
-		rowind[i] = i;
-		colind[i] = i;
-		acoo[i] = 0;
-	}
-
-	cholmod_sparse *adjacency = gen_adjacency(net, false, true, true, c);
-
-	for (uint_t i = 0; i < ne; i++) {
-		if (!net->fuses[i]){
-			uint_t v1 = ev[2 * i];
-			uint_t v2 = ev[2 * i + 1];
-
-			acoo[v1]++;
-			acoo[v2]++;
-		}
-	}
-
-	if (net->voltage_bound && g->boundary != TORUS_BOUND) {
-		for (uint_t i = 0; i < net->dim; i++) {
-			uint_t v = g->nbi[i];
-			for (uint_t j = 0; j < g->vei[v+1] - g->vei[v]; j++) {
-				uint_t e = g->ve[g->vei[v] + j];
-				uint_t v0 = g->ev[2 * e];
-				uint_t v1 = g->ev[2 * e + 1];
-
-				if (g->bq[v0] || g->bq[v1]) {
-					acoo[i]++;
-				}
-			}
-		}
-	} else {
-		acoo[0]++;
-	}
-
-	for (uint_t i = 0; i < nv; i++) {
-		if (acoo[i] == 0) acoo[i]++;
-	}
-
-	//assert(CHOL_F(check_triplet)(temp_m, c));
-
-	cholmod_sparse *t_out = CHOL_F(triplet_to_sparse)(temp_m, nnz, c);
-	//assert(CHOL_F(check_sparse)(t_out, c));
-
-	double alpha[2] = {1, 0};
-	double beta[2] = {-1, 0};
-	cholmod_sparse *laplacian = CHOL_F(add)(t_out, adjacency, alpha, beta, 1, 1, c);
-
-	CHOL_F(free_sparse)(&t_out, c);
-	CHOL_F(free_sparse)(&adjacency, c);
-	CHOL_F(free_triplet)(&temp_m, c);
-
-	return laplacian;
+  const graph_t *g = net->graph;
+  uint_t nv = net->dim;
+  uint_t ne = net->nep;
+  uint_t *ev = net->evp;
+
+  uint_t nnz = nv;
+
+  cholmod_triplet *temp_m =
+      CHOL_F(allocate_triplet)(nv, nv, nnz, 1, CHOLMOD_REAL, c);
+
+  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;
+
+  for (uint_t i = 0; i < nv; i++) {
+    rowind[i] = i;
+    colind[i] = i;
+    acoo[i] = 0;
+  }
+
+  cholmod_sparse *adjacency = gen_adjacency(net, false, true, true, c);
+
+  for (uint_t i = 0; i < ne; i++) {
+    if (!net->fuses[i]) {
+      uint_t v1 = ev[2 * i];
+      uint_t v2 = ev[2 * i + 1];
+
+      acoo[v1]++;
+      acoo[v2]++;
+    }
+  }
+
+  if (net->voltage_bound && g->boundary != TORUS_BOUND) {
+    for (uint_t i = 0; i < net->dim; i++) {
+      uint_t v = g->nbi[i];
+      for (uint_t j = 0; j < g->vei[v + 1] - g->vei[v]; j++) {
+        uint_t e = g->ve[g->vei[v] + j];
+        uint_t v0 = g->ev[2 * e];
+        uint_t v1 = g->ev[2 * e + 1];
+
+        if (g->bq[v0] || g->bq[v1]) {
+          acoo[i]++;
+        }
+      }
+    }
+  } else {
+    acoo[0]++;
+  }
+
+  for (uint_t i = 0; i < nv; i++) {
+    if (acoo[i] == 0)
+      acoo[i]++;
+  }
+
+  // assert(CHOL_F(check_triplet)(temp_m, c));
+
+  cholmod_sparse *t_out = CHOL_F(triplet_to_sparse)(temp_m, nnz, c);
+  // assert(CHOL_F(check_sparse)(t_out, c));
+
+  double alpha[2] = {1, 0};
+  double beta[2] = {-1, 0};
+  cholmod_sparse *laplacian =
+      CHOL_F(add)(t_out, adjacency, alpha, beta, 1, 1, c);
+
+  CHOL_F(free_sparse)(&t_out, c);
+  CHOL_F(free_sparse)(&adjacency, c);
+  CHOL_F(free_triplet)(&temp_m, c);
+
+  return laplacian;
 }
diff --git a/lib/gen_voltcurmat.c b/lib/gen_voltcurmat.c
index e870140..fede836 100644
--- a/lib/gen_voltcurmat.c
+++ b/lib/gen_voltcurmat.c
@@ -2,35 +2,35 @@
 #include "fracture.h"
 
 cholmod_sparse *gen_voltcurmat(unsigned int num_edges, unsigned int num_verts,
-															 unsigned int *edges_to_verts,
-															 cholmod_common *c) {
+                               unsigned int *edges_to_verts,
+                               cholmod_common *c) {
 
-	cholmod_triplet *t_m = CHOL_F(allocate_triplet)(
-			num_edges, num_verts, num_edges * 2, 0, CHOLMOD_REAL, c);
-	assert(t_m != NULL);
+  cholmod_triplet *t_m = CHOL_F(allocate_triplet)(
+      num_edges, num_verts, num_edges * 2, 0, CHOLMOD_REAL, c);
+  assert(t_m != NULL);
 
-	int_t *rowind = (int_t *)t_m->i;
-	int_t *colind = (int_t *)t_m->j;
-	double *acoo = (double *)t_m->x;
+  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++) {
-		unsigned int v1 = edges_to_verts[2 * i];
-		unsigned int v2 = edges_to_verts[2 * i + 1];
-		rowind[2 * i] = i;
-		rowind[2 * i + 1] = i;
-		colind[2 * i] = v1;
-		colind[2 * i + 1] = v2;
-		acoo[2 * i] = 1;
-		acoo[2 * i + 1] = -1;
-	}
+  for (unsigned int i = 0; i < num_edges; i++) {
+    unsigned int v1 = edges_to_verts[2 * i];
+    unsigned int v2 = edges_to_verts[2 * i + 1];
+    rowind[2 * i] = i;
+    rowind[2 * i + 1] = i;
+    colind[2 * i] = v1;
+    colind[2 * i + 1] = v2;
+    acoo[2 * i] = 1;
+    acoo[2 * i + 1] = -1;
+  }
 
-	t_m->nnz = num_edges * 2;
+  t_m->nnz = num_edges * 2;
 
-	assert(CHOL_F(check_triplet)(t_m, c));
+  assert(CHOL_F(check_triplet)(t_m, c));
 
-	cholmod_sparse *m = CHOL_F(triplet_to_sparse)(t_m, num_edges * 2, c);
+  cholmod_sparse *m = CHOL_F(triplet_to_sparse)(t_m, num_edges * 2, c);
 
-	CHOL_F(free_triplet)(&t_m, c);
+  CHOL_F(free_triplet)(&t_m, c);
 
-	return m;
+  return m;
 }
diff --git a/lib/geometry.c b/lib/geometry.c
index ec788f1..2c1987b 100644
--- a/lib/geometry.c
+++ b/lib/geometry.c
@@ -2,54 +2,54 @@
 #include "fracture.h"
 
 int edge_to_verts(unsigned int width, bool periodic, unsigned int edge,
-									bool index) {
-	assert(edge < pow(width, 2));
-
-	int x = edge / width + 1;
-	int y = edge % width + 1;
-
-	if (periodic) {
-		return (((index ^ (x % 2)) + 2 * ((y + (index ^ (!(x % 2)))) / 2) - 1) %
-								width +
-						(x - index) * width) /
-					 2;
-	} else {
-		return ((index ^ (x % 2)) + 2 * ((y + (index ^ (!(x % 2)))) / 2) +
-						(x - index) * (width + 1) - 1) /
-					 2;
-	}
+                  bool index) {
+  assert(edge < pow(width, 2));
+
+  int x = edge / width + 1;
+  int y = edge % width + 1;
+
+  if (periodic) {
+    return (((index ^ (x % 2)) + 2 * ((y + (index ^ (!(x % 2)))) / 2) - 1) %
+                width +
+            (x - index) * width) /
+           2;
+  } else {
+    return ((index ^ (x % 2)) + 2 * ((y + (index ^ (!(x % 2)))) / 2) +
+            (x - index) * (width + 1) - 1) /
+           2;
+  }
 }
 
 int dual_edge_to_verts(unsigned int width, bool periodic, unsigned int edge,
-											 bool index) {
-	assert(edge < pow(width, 2));
-
-	int x = edge / width + 1;
-	int y = edge % width + 1;
-
-	if (periodic) {
-		return (((index ^ (!(x % 2))) + 2 * ((y + (index ^ (x % 2))) / 2) - 1) %
-								width +
-						(x - index) * width) /
-					 2;
-	} else {
-		return ((index ^ (!(x % 2))) + 2 * ((y + (index ^ (x % 2))) / 2) +
-						(x - index) * (width + 1) - 1) /
-					 2;
-	}
+                       bool index) {
+  assert(edge < pow(width, 2));
+
+  int x = edge / width + 1;
+  int y = edge % width + 1;
+
+  if (periodic) {
+    return (((index ^ (!(x % 2))) + 2 * ((y + (index ^ (x % 2))) / 2) - 1) %
+                width +
+            (x - index) * width) /
+           2;
+  } else {
+    return ((index ^ (!(x % 2))) + 2 * ((y + (index ^ (x % 2))) / 2) +
+            (x - index) * (width + 1) - 1) /
+           2;
+  }
 }
 
 double dual_vert_to_coord(unsigned int width, bool periodic, unsigned int vert,
-													bool index) {
-	if (periodic) {
-		if (index)
-			return (2 * vert) % width + (2 * vert / width) % 2;
-		else
-			return 2 * vert / width;
-	} else {
-		if (index)
-			return (2 * vert) % (width + 1);
-		else
-			return (2 * vert) / (width + 1);
-	}
+                          bool index) {
+  if (periodic) {
+    if (index)
+      return (2 * vert) % width + (2 * vert / width) % 2;
+    else
+      return 2 * vert / width;
+  } else {
+    if (index)
+      return (2 * vert) % (width + 1);
+    else
+      return (2 * vert) / (width + 1);
+  }
 }
diff --git a/lib/get_dual_clusters.c b/lib/get_dual_clusters.c
index eaf7562..9336106 100644
--- a/lib/get_dual_clusters.c
+++ b/lib/get_dual_clusters.c
@@ -2,29 +2,30 @@
 #include "fracture.h"
 
 components_t *get_clusters(net_t *instance) {
-	components_t *c = graph_components_get(instance->graph, instance->fuses, true);
-	return c;
+  components_t *c =
+      graph_components_get(instance->graph, instance->fuses, true);
+  return c;
 }
 
 unsigned int *get_cluster_dist(net_t *instance) {
-	components_t *c = get_clusters(instance);
-	unsigned int *cluster_dist = (unsigned int *)calloc(
-			instance->graph->dnv, sizeof(unsigned int));
+  components_t *c = get_clusters(instance);
+  unsigned int *cluster_dist =
+      (unsigned int *)calloc(instance->graph->dnv, sizeof(unsigned int));
 
-	for (uint32_t i = 1; i <= c->n; i++) {
-		unsigned int num_in_cluster = 0;
-		for (unsigned int j = 0; j < instance->graph->dnv; j++) {
-			if (c->labels[j] == i)
-				num_in_cluster++;
-		}
+  for (uint32_t i = 1; i <= c->n; i++) {
+    unsigned int num_in_cluster = 0;
+    for (unsigned int j = 0; j < instance->graph->dnv; j++) {
+      if (c->labels[j] == i)
+        num_in_cluster++;
+    }
 
-		if (num_in_cluster == 0)
-			break;
+    if (num_in_cluster == 0)
+      break;
 
-		cluster_dist[num_in_cluster - 1]++;
-	}
+    cluster_dist[num_in_cluster - 1]++;
+  }
 
-	graph_components_free(c);
+  graph_components_free(c);
 
-	return cluster_dist;
+  return cluster_dist;
 }
diff --git a/lib/net.c b/lib/net.c
index d26b22c..ac89415 100644
--- a/lib/net.c
+++ b/lib/net.c
@@ -2,144 +2,145 @@
 #include "fracture.h"
 
 long double *get_thres(uint_t ne, double beta) {
-	long double *thres = (long double *)malloc(ne * sizeof(long double));
-	assert(thres != NULL);
+  long double *thres = (long double *)malloc(ne * sizeof(long double));
+  assert(thres != NULL);
 
-	gsl_rng *r = gsl_rng_alloc(GSL_RAND_GEN);
-	gsl_rng_set(r, jst_rand_seed());
+  gsl_rng *r = gsl_rng_alloc(GSL_RAND_GEN);
+  gsl_rng_set(r, jst_rand_seed());
 
-	for (uint_t i = 0; i < ne; i++) {
-		thres[i] = rand_dist_pow(r, beta);
-	}
+  for (uint_t i = 0; i < ne; i++) {
+    thres[i] = rand_dist_pow(r, beta);
+  }
 
-	gsl_rng_free(r);
+  gsl_rng_free(r);
 
-	return thres;
+  return thres;
 }
 
 void net_notch(net_t *net, double notch_len, cholmod_common *c) {
-	for (uint_t i = 0; i < net->graph->ne; i++) {
-		uint_t v1, v2;
-		double v1x, v1y, v2x, v2y, dy;
-		bool crosses_center, not_wrapping, correct_length;
-
-		v1 = net->graph->ev[2 * i];
-		v2 = net->graph->ev[2 * i + 1];
-
-		v1x = net->graph->vx[2 * v1];
-		v1y = net->graph->vx[2 * v1 + 1];
-		v2x = net->graph->vx[2 * v2];
-		v2y = net->graph->vx[2 * v2 + 1];
-
-		dy = v1y - v2y;
-
-		crosses_center = (v1y >= 0.5 && v2y <= 0.5) || (v1y <= 0.5 && v2y >= 0.5);
-		not_wrapping = fabs(dy) < 0.5;
-		//correct_length = v1x + dx / dy * (v1y - 0.5) <= notch_len;
-		correct_length = v1x < notch_len && v2x < notch_len;
-
-		if (crosses_center && not_wrapping && correct_length) {
-			break_edge(net, i, c);
-		}
-	}
+  for (uint_t i = 0; i < net->graph->ne; i++) {
+    uint_t v1, v2;
+    double v1x, v1y, v2x, v2y, dy;
+    bool crosses_center, not_wrapping, correct_length;
+
+    v1 = net->graph->ev[2 * i];
+    v2 = net->graph->ev[2 * i + 1];
+
+    v1x = net->graph->vx[2 * v1];
+    v1y = net->graph->vx[2 * v1 + 1];
+    v2x = net->graph->vx[2 * v2];
+    v2y = net->graph->vx[2 * v2 + 1];
+
+    dy = v1y - v2y;
+
+    crosses_center = (v1y >= 0.5 && v2y <= 0.5) || (v1y <= 0.5 && v2y >= 0.5);
+    not_wrapping = fabs(dy) < 0.5;
+    // correct_length = v1x + dx / dy * (v1y - 0.5) <= notch_len;
+    correct_length = v1x < notch_len && v2x < notch_len;
+
+    if (crosses_center && not_wrapping && correct_length) {
+      break_edge(net, i, c);
+    }
+  }
 }
 
-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);
-
-	net->graph = g;
-	net->num_broken = 0;
-
-	net->fuses = (bool *)calloc(g->ne, sizeof(bool));
-	assert(net->fuses != NULL);
-
-	net->thres = get_thres(g->ne, beta);
-	net->inf = inf;
-
-	net->dim = g->nv;
-
-	if (g->boundary == TORUS_BOUND) {
-		net->nep = g->ne;
-		net->evp = (uint_t *)malloc(2 * g->ne * sizeof(uint_t));
-		memcpy(net->evp, g->ev, 2 * g->ne * sizeof(uint_t));
-	} else {
-		if (vb) {
-			net->dim -= g->bi[g->nb];
-			net->evp = (uint_t *)malloc(2 * g->ne * sizeof(uint_t));
-			net->nep = 0;
-			for (uint_t i = 0; i < g->ne; i++) {
-				if (!(g->bq[g->ev[2*i]] || g->bq[g->ev[2*i+1]])) {
-					net->evp[2*net->nep] = g->bni[g->ev[2*i]];
-					net->evp[2*net->nep + 1] = g->bni[g->ev[2*i + 1]];
-					net->nep++;
-				}
-			}
-		} else {
-			net->dim += 2;
-			net->evp = (uint_t *)malloc(2 * (g->ne + g->bi[2]) * sizeof(uint_t));
-			memcpy(net->evp, g->ev, 2 * g->ne * sizeof(uint_t));
-			net->nep = g->ne + g->bi[2];
-
-			for (uint_t i = 0; i < 2; i++) {
-				for (uint_t j = 0; j < g->bi[i+1] - g->bi[i]; j++){ 
-					net->evp[2 * (g->ne + g->bi[i] + j)] = g->b[g->bi[i] + j];
-					net->evp[2 * (g->ne + g->bi[i] + j) + 1] = g->nv + i;
-				}
-			}
-		}
-	}
-
-	net->voltage_bound = vb;
-	net->boundary_cond = bound_set(g, vb, notch_len, c);
-
-	net_notch(net, notch_len, c);
-
-	{
-		cholmod_sparse *laplacian = gen_laplacian(net, c);
-		net->factor = CHOL_F(analyze)(laplacian, c);
-		CHOL_F(factorize)(laplacian, net->factor, c);
-		CHOL_F(free_sparse)(&laplacian, c);
-	}
-
-	net->voltcurmat = gen_voltcurmat(g->ne, g->nv, g->ev, c);
-
-	return net;
+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);
+
+  net->graph = g;
+  net->num_broken = 0;
+
+  net->fuses = (bool *)calloc(g->ne, sizeof(bool));
+  assert(net->fuses != NULL);
+
+  net->thres = get_thres(g->ne, beta);
+  net->inf = inf;
+
+  net->dim = g->nv;
+
+  if (g->boundary == TORUS_BOUND) {
+    net->nep = g->ne;
+    net->evp = (uint_t *)malloc(2 * g->ne * sizeof(uint_t));
+    memcpy(net->evp, g->ev, 2 * g->ne * sizeof(uint_t));
+  } else {
+    if (vb) {
+      net->dim -= g->bi[g->nb];
+      net->evp = (uint_t *)malloc(2 * g->ne * sizeof(uint_t));
+      net->nep = 0;
+      for (uint_t i = 0; i < g->ne; i++) {
+        if (!(g->bq[g->ev[2 * i]] || g->bq[g->ev[2 * i + 1]])) {
+          net->evp[2 * net->nep] = g->bni[g->ev[2 * i]];
+          net->evp[2 * net->nep + 1] = g->bni[g->ev[2 * i + 1]];
+          net->nep++;
+        }
+      }
+    } else {
+      net->dim += 2;
+      net->evp = (uint_t *)malloc(2 * (g->ne + g->bi[2]) * sizeof(uint_t));
+      memcpy(net->evp, g->ev, 2 * g->ne * sizeof(uint_t));
+      net->nep = g->ne + g->bi[2];
+
+      for (uint_t i = 0; i < 2; i++) {
+        for (uint_t j = 0; j < g->bi[i + 1] - g->bi[i]; j++) {
+          net->evp[2 * (g->ne + g->bi[i] + j)] = g->b[g->bi[i] + j];
+          net->evp[2 * (g->ne + g->bi[i] + j) + 1] = g->nv + i;
+        }
+      }
+    }
+  }
+
+  net->voltage_bound = vb;
+  net->boundary_cond = bound_set(g, vb, notch_len, c);
+
+  net_notch(net, notch_len, c);
+
+  {
+    cholmod_sparse *laplacian = gen_laplacian(net, c);
+    net->factor = CHOL_F(analyze)(laplacian, c);
+    CHOL_F(factorize)(laplacian, net->factor, c);
+    CHOL_F(free_sparse)(&laplacian, c);
+  }
+
+  net->voltcurmat = gen_voltcurmat(g->ne, g->nv, g->ev, c);
+
+  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(long double);
-	net_copy->thres = (long double *)malloc(thres_size);
-	assert(net_copy->thres != NULL);
-	memcpy(net_copy->thres, net->thres, thres_size);
-
-	size_t evp_size = 2 * net->nep * sizeof(uint_t);
-	net_copy->evp = (uint_t *)malloc(thres_size);
-	assert(net_copy->evp != NULL);
-	memcpy(net_copy->evp, net->evp, evp_size);
-
-	net_copy->boundary_cond = CHOL_F(copy_dense)(net->boundary_cond, c);
-	net_copy->factor = CHOL_F(copy_factor)(net->factor, c);
-	net_copy->voltcurmat = CHOL_F(copy_sparse)(net->voltcurmat, c);
-
-	return net_copy;
+  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(long double);
+  net_copy->thres = (long double *)malloc(thres_size);
+  assert(net_copy->thres != NULL);
+  memcpy(net_copy->thres, net->thres, thres_size);
+
+  size_t evp_size = 2 * net->nep * sizeof(uint_t);
+  net_copy->evp = (uint_t *)malloc(thres_size);
+  assert(net_copy->evp != NULL);
+  memcpy(net_copy->evp, net->evp, evp_size);
+
+  net_copy->boundary_cond = CHOL_F(copy_dense)(net->boundary_cond, c);
+  net_copy->factor = CHOL_F(copy_factor)(net->factor, c);
+  net_copy->voltcurmat = CHOL_F(copy_sparse)(net->voltcurmat, 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_factor)(&(net->factor), c);
-	CHOL_F(free_sparse)(&(net->voltcurmat), c);
-	free(net->evp);
-	free(net);
+  free(net->fuses);
+  free(net->thres);
+  CHOL_F(free_dense)(&(net->boundary_cond), c);
+  CHOL_F(free_factor)(&(net->factor), c);
+  CHOL_F(free_sparse)(&(net->voltcurmat), c);
+  free(net->evp);
+  free(net);
 }
diff --git a/lib/net_conductivity.c b/lib/net_conductivity.c
index e9325bb..61148da 100644
--- a/lib/net_conductivity.c
+++ b/lib/net_conductivity.c
@@ -2,34 +2,34 @@
 #include "fracture.h"
 
 double net_conductivity(const net_t *net, const double *voltages) {
-	if (net->voltage_bound) {
-		// the voltage drop across the network is fixed to one with voltage
-		// boundary conditions, so the conductivity is the total current flowing
-		double tot_cur = 0;
-		for (uint_t i = 0; i < net->graph->num_spanning_edges; i++) {
-			uint_t e = net->graph->spanning_edges[i];
-
-			if (!net->fuses[e]) {
-				uint_t v1, v2, s1, s2;
-				double v1y, v2y;
-
-				v1 = net->graph->ev[2 * e];
-				v2 = net->graph->ev[2 * e + 1];
-
-				v1y = net->graph->vx[2 * v1 + 1];
-				v2y = net->graph->vx[2 * v2 + 1];
-
-				s1 = v1y < v2y ? v1 : v2;
-				s2 = v1y < v2y ? v2 : v1;
-
-				tot_cur += voltages[s1] - voltages[s2];
-			}
-		}
-
-		return fabs(tot_cur);
-	} else {
-		// the current across the network is fixed to one with current boundary
-		// conditions, so the conductivity is the inverse of the total voltage drop
-		return 1 / fabs(voltages[net->graph->nv] - voltages[net->graph->nv + 1]);
-	}
+  if (net->voltage_bound) {
+    // the voltage drop across the network is fixed to one with voltage
+    // boundary conditions, so the conductivity is the total current flowing
+    double tot_cur = 0;
+    for (uint_t i = 0; i < net->graph->num_spanning_edges; i++) {
+      uint_t e = net->graph->spanning_edges[i];
+
+      if (!net->fuses[e]) {
+        uint_t v1, v2, s1, s2;
+        double v1y, v2y;
+
+        v1 = net->graph->ev[2 * e];
+        v2 = net->graph->ev[2 * e + 1];
+
+        v1y = net->graph->vx[2 * v1 + 1];
+        v2y = net->graph->vx[2 * v2 + 1];
+
+        s1 = v1y < v2y ? v1 : v2;
+        s2 = v1y < v2y ? v2 : v1;
+
+        tot_cur += voltages[s1] - voltages[s2];
+      }
+    }
+
+    return fabs(tot_cur);
+  } else {
+    // the current across the network is fixed to one with current boundary
+    // conditions, so the conductivity is the inverse of the total voltage drop
+    return 1 / fabs(voltages[net->graph->nv] - voltages[net->graph->nv + 1]);
+  }
 }
diff --git a/lib/net_currents.c b/lib/net_currents.c
index a078336..32dba04 100644
--- a/lib/net_currents.c
+++ b/lib/net_currents.c
@@ -1,51 +1,52 @@
 
 #include "fracture.h"
 
-double *net_currents(const net_t *net, const double *voltages, cholmod_common *c) {
-	uint_t ne = net->graph->ne;
-	uint_t dim = net->graph->nv;
-	cholmod_sparse *voltcurmat = net->voltcurmat;
-
-	cholmod_dense *x = CHOL_F(allocate_dense)(dim, 1, dim, CHOLMOD_REAL, c);
-
-	double *tmp_x = x->x;
-	x->x = (void *)voltages;
-
-	cholmod_dense *y = CHOL_F(allocate_dense)(ne, 1, ne, CHOLMOD_REAL, c);
-
-	double alpha[2] = {1, 0};
-	double beta[2] = {0, 0};
-	CHOL_F(sdmult)(voltcurmat, 0, alpha, beta, x, y, c);
-
-	double *currents = (double *)malloc(ne * sizeof(double));
-
-	for (int i = 0; i < ne; i++) {
-		if (net->fuses[i]) {
-			currents[i] = 0;
-		} else {
-			currents[i] = ((double *)y->x)[i];
-		}
-	}
-
-	if (net->graph->boundary == TORUS_BOUND) {
-		for (uint_t i = 0; i < net->graph->bi[1]; i++) {
-			uint_t e = net->graph->b[i];
-			uint_t v1 = net->graph->ev[2 * e];
-			uint_t v2 = net->graph->ev[2 * e + 1];
-			double v1y = net->graph->vx[2 * v1 + 1];
-			double v2y = net->graph->vx[2 * v2 + 1];
-
-			if (v1y > v2y) {
-				currents[e] += 1;
-			} else {
-				currents[e] -= 1;
-			}
-		}
-	}
-
-	x->x = tmp_x;
-	CHOL_F(free_dense)(&x, c);
-	CHOL_F(free_dense)(&y, c);
-
-	return currents;
+double *net_currents(const net_t *net, const double *voltages,
+                     cholmod_common *c) {
+  uint_t ne = net->graph->ne;
+  uint_t dim = net->graph->nv;
+  cholmod_sparse *voltcurmat = net->voltcurmat;
+
+  cholmod_dense *x = CHOL_F(allocate_dense)(dim, 1, dim, CHOLMOD_REAL, c);
+
+  double *tmp_x = x->x;
+  x->x = (void *)voltages;
+
+  cholmod_dense *y = CHOL_F(allocate_dense)(ne, 1, ne, CHOLMOD_REAL, c);
+
+  double alpha[2] = {1, 0};
+  double beta[2] = {0, 0};
+  CHOL_F(sdmult)(voltcurmat, 0, alpha, beta, x, y, c);
+
+  double *currents = (double *)malloc(ne * sizeof(double));
+
+  for (int i = 0; i < ne; i++) {
+    if (net->fuses[i]) {
+      currents[i] = 0;
+    } else {
+      currents[i] = ((double *)y->x)[i];
+    }
+  }
+
+  if (net->graph->boundary == TORUS_BOUND) {
+    for (uint_t i = 0; i < net->graph->bi[1]; i++) {
+      uint_t e = net->graph->b[i];
+      uint_t v1 = net->graph->ev[2 * e];
+      uint_t v2 = net->graph->ev[2 * e + 1];
+      double v1y = net->graph->vx[2 * v1 + 1];
+      double v2y = net->graph->vx[2 * v2 + 1];
+
+      if (v1y > v2y) {
+        currents[e] += 1;
+      } else {
+        currents[e] -= 1;
+      }
+    }
+  }
+
+  x->x = tmp_x;
+  CHOL_F(free_dense)(&x, c);
+  CHOL_F(free_dense)(&y, c);
+
+  return currents;
 }
diff --git a/lib/net_fracture.c b/lib/net_fracture.c
index e7f18fc..65ede9b 100644
--- a/lib/net_fracture.c
+++ b/lib/net_fracture.c
@@ -2,66 +2,67 @@
 #include "fracture.h"
 
 uint_t get_next_broken(net_t *net, double *currents, double cutoff) {
-	uint_t max_pos = UINT_MAX;
-	long double max_val = 0;
+  uint_t max_pos = UINT_MAX;
+  long double max_val = 0;
 
-	for (uint_t i = 0; i < net->graph->ne; i++) {
-		long double current = fabs(currents[i]);
-		bool broken = net->fuses[i];
+  for (uint_t i = 0; i < net->graph->ne; i++) {
+    long double current = fabs(currents[i]);
+    bool broken = net->fuses[i];
 
-		if (!broken && current > cutoff) {
-			long double val = current / net->thres[i];
+    if (!broken && current > cutoff) {
+      long double val = current / net->thres[i];
 
-			if (val > max_val) {
-				max_val = val;
-				max_pos = i;
-			}
-		}
-	}
+      if (val > max_val) {
+        max_val = val;
+        max_pos = i;
+      }
+    }
+  }
 
-	if (max_pos == UINT_MAX) {
-		printf("GET_NEXT_BROKEN: currents is zero or NaN, no max_val found\n");
-		exit(EXIT_FAILURE);
-	}
+  if (max_pos == UINT_MAX) {
+    printf("GET_NEXT_BROKEN: currents is zero or NaN, no max_val found\n");
+    exit(EXIT_FAILURE);
+  }
 
-	return max_pos;
+  return max_pos;
 }
 
 data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff) {
-	data_t *data = data_create(net->graph->ne);
+  data_t *data = data_create(net->graph->ne);
 
-	uint_t n = 0;
-	while (true) {
-		n++;
-		double *voltages = net_voltages(net, c);
-		double *currents = net_currents(net, voltages, c);
+  uint_t n = 0;
+  while (true) {
+    n++;
+    double *voltages = net_voltages(net, c);
+    double *currents = net_currents(net, voltages, c);
 
-		double conductivity = net_conductivity(net, voltages);
+    double conductivity = net_conductivity(net, voltages);
 
-		if (conductivity < cutoff) {
-			free(voltages);
-			free(currents);
-			break;
-		}
+    if (conductivity < cutoff) {
+      free(voltages);
+      free(currents);
+      break;
+    }
 
-		uint_t last_broke = get_next_broken(net, currents, cutoff);
+    uint_t last_broke = get_next_broken(net, currents, cutoff);
 
-		long double sim_current;
+    long double sim_current;
 
-		if (net->voltage_bound) {
-			sim_current = conductivity;
-		} else {
-			sim_current = 1;
-		}
+    if (net->voltage_bound) {
+      sim_current = conductivity;
+    } else {
+      sim_current = 1;
+    }
 
-		data_update(data, last_broke, fabsl(sim_current * (net->thres)[last_broke] / ((long double)currents[last_broke])), conductivity);
+    data_update(data, last_broke, fabsl(sim_current * (net->thres)[last_broke] /
+                                        ((long double)currents[last_broke])),
+                conductivity);
 
-		free(voltages);
-		free(currents);
+    free(voltages);
+    free(currents);
 
-		break_edge(net, last_broke, c);
-	}
+    break_edge(net, last_broke, c);
+  }
 
-	return data;
+  return data;
 }
-
diff --git a/lib/net_voltages.c b/lib/net_voltages.c
index 7b07201..d456a65 100644
--- a/lib/net_voltages.c
+++ b/lib/net_voltages.c
@@ -2,39 +2,38 @@
 #include "fracture.h"
 
 double *net_voltages(const net_t *net, cholmod_common *c) {
-	cholmod_dense *b = net->boundary_cond;
-	cholmod_factor *factor = net->factor;
-
-	cholmod_dense *x = CHOL_F(solve)(CHOLMOD_A, factor, b, c);
-
-	if (((double *)x->x)[0] != ((double *)x->x)[0]) {
-		printf("GET_VOLTAGE: value is NaN\n");
-		exit(EXIT_FAILURE);
-	}
-
-	double *t_voltages = (double *)x->x;
-	x->x = NULL;
-	CHOL_F(free_dense)(&x, c);
-
-	const graph_t *g = net->graph;
-
-	if (g->boundary == TORUS_BOUND) {
-		return t_voltages;
-	} else if (net->voltage_bound) {
-		double *voltages = (double *)malloc(g->nv * sizeof(double));
-		for (uint_t i = 0; i < g->nv - g->bi[g->nb]; i++) {
-			voltages[g->nbi[i]] = t_voltages[i];
-		}
-		for (uint_t i = 0; i < 2; i++) {
-			for (uint_t j = 0; j < g->bi[i + 1] - g->bi[i]; j++) {
-				voltages[g->b[g->bi[i] + j]] = 1 - i;
-			}
-		}
-
-		free(t_voltages);
-		return voltages;
-	} else {
-		return t_voltages;
-	}
+  cholmod_dense *b = net->boundary_cond;
+  cholmod_factor *factor = net->factor;
+
+  cholmod_dense *x = CHOL_F(solve)(CHOLMOD_A, factor, b, c);
+
+  if (((double *)x->x)[0] != ((double *)x->x)[0]) {
+    printf("GET_VOLTAGE: value is NaN\n");
+    exit(EXIT_FAILURE);
+  }
+
+  double *t_voltages = (double *)x->x;
+  x->x = NULL;
+  CHOL_F(free_dense)(&x, c);
+
+  const graph_t *g = net->graph;
+
+  if (g->boundary == TORUS_BOUND) {
+    return t_voltages;
+  } else if (net->voltage_bound) {
+    double *voltages = (double *)malloc(g->nv * sizeof(double));
+    for (uint_t i = 0; i < g->nv - g->bi[g->nb]; i++) {
+      voltages[g->nbi[i]] = t_voltages[i];
+    }
+    for (uint_t i = 0; i < 2; i++) {
+      for (uint_t j = 0; j < g->bi[i + 1] - g->bi[i]; j++) {
+        voltages[g->b[g->bi[i] + j]] = 1 - i;
+      }
+    }
+
+    free(t_voltages);
+    return voltages;
+  } else {
+    return t_voltages;
+  }
 }
-
diff --git a/lib/rand.c b/lib/rand.c
index 16aeba4..8ba2b2b 100644
--- a/lib/rand.c
+++ b/lib/rand.c
@@ -2,14 +2,14 @@
 #include "fracture.h"
 
 long double rand_dist_pow(const gsl_rng *r, double beta) {
-	long double x = 0;
+  long double x = 0;
 
-	// underflow means that for very small beta x is sometimes identically zero,
-	// which causes problems
-	while (x == 0.0) {
-		long double y = logl(gsl_rng_uniform_pos(r)) / beta;
-		x = expl(y);
-	}
+  // underflow means that for very small beta x is sometimes identically zero,
+  // which causes problems
+  while (x == 0.0) {
+    long double y = logl(gsl_rng_uniform_pos(r)) / beta;
+    x = expl(y);
+  }
 
-	return x;
+  return x;
 }