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authorJaron Kent-Dobias <jaron@kent-dobias.com>2017-02-10 12:19:46 -0500
committerJaron Kent-Dobias <jaron@kent-dobias.com>2017-02-10 12:19:46 -0500
commit0ef0c0ce1d904be2b4e1f4da62dc029d8572c983 (patch)
tree12978013d870186240c08d1fdd6a7ce8781bca93 /lib
parent9a93a3b88a604672f557950e6c7f3fe815bcf163 (diff)
parent901b9f16494f37890be17ef4bb66e6efc6873340 (diff)
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Merge branch 'tmp'
Diffstat (limited to 'lib')
-rw-r--r--lib/bound_set.c102
-rw-r--r--lib/break_edge.c51
-rw-r--r--lib/correlations.c47
-rw-r--r--lib/data.c35
-rw-r--r--lib/factor_update.c68
-rw-r--r--lib/fracture.h123
-rw-r--r--lib/gen_laplacian.c137
-rw-r--r--lib/gen_voltcurmat.c36
-rw-r--r--lib/geometry.c55
-rw-r--r--lib/get_dual_clusters.c30
-rw-r--r--lib/net.c144
-rw-r--r--lib/net_conductivity.c35
-rw-r--r--lib/net_currents.c51
-rw-r--r--lib/net_fracture.c67
-rw-r--r--lib/net_voltages.c40
-rw-r--r--lib/rand.c15
16 files changed, 1036 insertions, 0 deletions
diff --git a/lib/bound_set.c b/lib/bound_set.c
new file mode 100644
index 0000000..65f1e6f
--- /dev/null
+++ b/lib/bound_set.c
@@ -0,0 +1,102 @@
+
+#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;
+
+}
+
+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)));
+
+ 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);
+ }
+}
+
+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;
+}
+
+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
new file mode 100644
index 0000000..2f112c2
--- /dev/null
+++ b/lib/break_edge.c
@@ -0,0 +1,51 @@
+
+#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;
+}
diff --git a/lib/correlations.c b/lib/correlations.c
new file mode 100644
index 0000000..63532ec
--- /dev/null
+++ b/lib/correlations.c
@@ -0,0 +1,47 @@
+
+#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));
+
+ 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];
+ }
+ }
+
+ if (nulldists) {
+ for (int i = 0; i < nv; i++) {
+ free(dists[i]);
+ }
+ free(dists);
+ }
+
+ return corr;
+}
+
diff --git a/lib/data.c b/lib/data.c
new file mode 100644
index 0000000..2047c44
--- /dev/null
+++ b/lib/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 = (long double *)malloc(ne * sizeof(long 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, 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
new file mode 100644
index 0000000..a51705a
--- /dev/null
+++ b/lib/factor_update.c
@@ -0,0 +1,68 @@
+
+#include "fracture.h"
+
+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);
+
+ 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;
+
+ for (uint_t i = 0; i <= s1; i++) {
+ pp[i] = 0;
+ }
+
+ for (uint_t i = s1 + 1; i <= n; i++) {
+ pp[i] = 2;
+ }
+
+ 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);
+
+ CHOL_F(updown)(false, perm_update_mat, factor, 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;
+
+ 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;
+
+ for (uint_t i = 0; i <= v; i++) {
+ pp[i] = 0;
+ }
+
+ for (uint_t i = v + 1; i <= n; i++) {
+ pp[i] = 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);
+
+ CHOL_F(updown)(false, perm_update_mat, factor, 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
new file mode 100644
index 0000000..b1114fb
--- /dev/null
+++ b/lib/fracture.h
@@ -0,0 +1,123 @@
+
+#pragma once
+
+#include <assert.h>
+#include <cholmod.h>
+#include <float.h>
+#include <getopt.h>
+#include <gsl/gsl_math.h>
+#include <gsl/gsl_randist.h>
+#include <gsl/gsl_rng.h>
+#include <gsl/gsl_sf_erf.h>
+#include <gsl/gsl_sf_exp.h>
+#include <gsl/gsl_sf_log.h>
+#include <inttypes.h>
+#include <math.h>
+#include <omp.h>
+#include <stdbool.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <unistd.h>
+
+#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
+#define CINT_MAX INT_MAX
+#define CHOL_F(x) cholmod_##x
+
+#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;
+} net_t;
+
+typedef struct {
+ 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);
+
+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 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);
+
+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_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);
+
+double update_beta(double beta, uint_t width, const double *stress,
+ 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);
+
+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);
+
+bool break_edge(net_t *instance, uint_t edge, cholmod_common *c);
+
+components_t *get_clusters(net_t *instance);
+
+uint_t *get_cluster_dist(net_t *instance);
+
+void randfunc_flat(gsl_rng *r, double *x, double *y);
+void randfunc_gaus(gsl_rng *r, double *x, double *y);
+
+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);
+
+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);
+
+long double rand_dist_pow(const gsl_rng *r, double beta);
+
+bool is_in(uint_t len, uint_t *list, uint_t element);
diff --git a/lib/gen_laplacian.c b/lib/gen_laplacian.c
new file mode 100644
index 0000000..1cc93a4
--- /dev/null
+++ b/lib/gen_laplacian.c
@@ -0,0 +1,137 @@
+
+#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_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;
+}
diff --git a/lib/gen_voltcurmat.c b/lib/gen_voltcurmat.c
new file mode 100644
index 0000000..e870140
--- /dev/null
+++ b/lib/gen_voltcurmat.c
@@ -0,0 +1,36 @@
+
+#include "fracture.h"
+
+cholmod_sparse *gen_voltcurmat(unsigned int num_edges, unsigned int num_verts,
+ 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);
+
+ 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;
+ }
+
+ t_m->nnz = num_edges * 2;
+
+ assert(CHOL_F(check_triplet)(t_m, c));
+
+ cholmod_sparse *m = CHOL_F(triplet_to_sparse)(t_m, num_edges * 2, c);
+
+ CHOL_F(free_triplet)(&t_m, c);
+
+ return m;
+}
diff --git a/lib/geometry.c b/lib/geometry.c
new file mode 100644
index 0000000..ec788f1
--- /dev/null
+++ b/lib/geometry.c
@@ -0,0 +1,55 @@
+
+#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;
+ }
+}
+
+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;
+ }
+}
+
+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);
+ }
+}
diff --git a/lib/get_dual_clusters.c b/lib/get_dual_clusters.c
new file mode 100644
index 0000000..eaf7562
--- /dev/null
+++ b/lib/get_dual_clusters.c
@@ -0,0 +1,30 @@
+
+#include "fracture.h"
+
+components_t *get_clusters(net_t *instance) {
+ 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));
+
+ 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;
+
+ cluster_dist[num_in_cluster - 1]++;
+ }
+
+ graph_components_free(c);
+
+ return cluster_dist;
+}
diff --git a/lib/net.c b/lib/net.c
new file mode 100644
index 0000000..eb44721
--- /dev/null
+++ b/lib/net.c
@@ -0,0 +1,144 @@
+
+#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);
+
+ 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);
+ }
+
+ gsl_rng_free(r);
+
+ 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);
+ }
+ }
+}
+
+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);
+
+ 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);
+}
diff --git a/lib/net_conductivity.c b/lib/net_conductivity.c
new file mode 100644
index 0000000..e9325bb
--- /dev/null
+++ b/lib/net_conductivity.c
@@ -0,0 +1,35 @@
+
+#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]);
+ }
+}
diff --git a/lib/net_currents.c b/lib/net_currents.c
new file mode 100644
index 0000000..a078336
--- /dev/null
+++ b/lib/net_currents.c
@@ -0,0 +1,51 @@
+
+#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;
+}
diff --git a/lib/net_fracture.c b/lib/net_fracture.c
new file mode 100644
index 0000000..e7f18fc
--- /dev/null
+++ b/lib/net_fracture.c
@@ -0,0 +1,67 @@
+
+#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;
+
+ 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 (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);
+ }
+
+ return max_pos;
+}
+
+data_t *net_fracture(net_t *net, cholmod_common *c, double cutoff) {
+ 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);
+
+ double conductivity = net_conductivity(net, voltages);
+
+ if (conductivity < cutoff) {
+ free(voltages);
+ free(currents);
+ break;
+ }
+
+ uint_t last_broke = get_next_broken(net, currents, cutoff);
+
+ long double sim_current;
+
+ 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);
+
+ free(voltages);
+ free(currents);
+
+ break_edge(net, last_broke, c);
+ }
+
+ return data;
+}
+
diff --git a/lib/net_voltages.c b/lib/net_voltages.c
new file mode 100644
index 0000000..7b07201
--- /dev/null
+++ b/lib/net_voltages.c
@@ -0,0 +1,40 @@
+
+#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;
+ }
+}
+
diff --git a/lib/rand.c b/lib/rand.c
new file mode 100644
index 0000000..16aeba4
--- /dev/null
+++ b/lib/rand.c
@@ -0,0 +1,15 @@
+
+#include "fracture.h"
+
+long double rand_dist_pow(const gsl_rng *r, double beta) {
+ 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);
+ }
+
+ return x;
+}