refactored much of the fracture library and fixed some percolation measurements

1 files changed, 217 insertions, 0 deletions

diff --git a/lib/src/problem.cpp b/lib/src/problem.cpp
new file mode 100644
index 0000000..f66a35c
--- /dev/null
+++ b/lib/src/problem.cpp
@@ -0,0 +1,217 @@
+
+#include "problem.hpp"
+
+class nanException: public std::exception
+{
+  virtual const char* what() const throw()
+  {
+    return "The linear problem returned NaN.";
+  }
+} nanex;
+
+problem::problem(const graph& G, unsigned axis, cholmod_sparse *vcmat, cholmod_common *c) : G(G), axis(axis), voltcurmat(vcmat), c(c) {
+  b = CHOL_F(zeros)(G.vertices.size(), 1, CHOLMOD_REAL, c);
+  for (unsigned i = 0; i < G.edges.size(); i++) {
+    graph::coordinate v0 = G.vertices[G.edges[i].v[0]].r;
+    graph::coordinate v1 = G.vertices[G.edges[i].v[1]].r;
+
+    if (G.edges[i].crossings[axis]) {
+      bool ind;
+      if (axis == 1) {
+        ind = v0.y < v1.y ? 0 : 1;
+      } else {
+        ind = v0.x < v1.x ? 0 : 1;
+      }
+
+      ((double *)b->x)[G.edges[i].v[ind]]  += 1.0;
+      ((double *)b->x)[G.edges[i].v[!ind]] -= 1.0;
+    }
+  }
+
+  unsigned nnz = G.vertices.size() + G.edges.size();
+
+  cholmod_triplet *t = CHOL_F(allocate_triplet)(G.vertices.size(), G.vertices.size(), nnz,  1, CHOLMOD_REAL, c);
+
+  for (unsigned i = 0; i < G.vertices.size(); i++) {
+    ((CHOL_INT *)t->i)[i] = i;
+    ((CHOL_INT *)t->j)[i] = i;
+    ((double *)t->x)[i] = 0.0;
+  }
+
+  unsigned terms = G.vertices.size();
+
+  std::unordered_map<std::array<unsigned, 2>, unsigned> known_edges;
+
+  for (unsigned i = 0; i < G.edges.size(); i++) {
+    unsigned v0 = G.edges[i].v[0];
+    unsigned v1 = G.edges[i].v[1];
+
+    ((double *)t->x)[v0]++;
+    ((double *)t->x)[v1]++;
+
+    unsigned s0 = v0 < v1 ? v0 : v1;
+    unsigned s1 = v0 < v1 ? v1 : v0;
+
+    auto it = known_edges.find({s0, s1});
+
+    if (it == known_edges.end()) {
+      ((CHOL_INT *)t->i)[terms] = s1;
+      ((CHOL_INT *)t->j)[terms] = s0;
+      ((double *)t->x)[terms] = -1.0;
+
+      known_edges[{s0, s1}] = terms;
+      terms++;
+    } else {
+      ((double *)t->x)[it->second] -= 1.0;
+    }
+  }
+
+  ((double *)t->x)[0]++;
+
+  t->nnz = terms;
+
+  cholmod_sparse *laplacian = CHOL_F(triplet_to_sparse)(t, terms, c);
+  CHOL_F(free_triplet)(&t, c);
+  factor = CHOL_F(analyze)(laplacian, c);
+  CHOL_F(factorize)(laplacian, factor, c);
+  CHOL_F(free_sparse)(&laplacian, c);
+}
+
+problem::problem(const graph& G, unsigned axis, cholmod_common *c) : problem(G, axis, NULL, c) {
+  cholmod_triplet *t = CHOL_F(allocate_triplet)(G.edges.size(), G.vertices.size(), 2 * G.edges.size(), 0, CHOLMOD_REAL, c);
+
+  t->nnz = 2 * G.edges.size();
+
+  for (unsigned i = 0; i < G.edges.size(); i++) {
+    ((CHOL_INT *)t->i)[2 * i] = i;
+    ((CHOL_INT *)t->j)[2 * i] = G.edges[i].v[0];
+    ((double *)t->x)[2 * i] = 1.0;
+
+    ((CHOL_INT *)t->i)[2 * i + 1] = i;
+    ((CHOL_INT *)t->j)[2 * i + 1] = G.edges[i].v[1];
+    ((double *)t->x)[2 * i + 1] = -1.0;
+  }
+
+  voltcurmat = CHOL_F(triplet_to_sparse)(t, 2 * G.edges.size(), c);
+
+  CHOL_F(free_triplet)(&t, c);
+}
+
+problem::problem(const problem& other) : G(other.G), axis(other.axis), c(other.c) {
+  b = CHOL_F(copy_dense)(other.b, c);
+  factor = CHOL_F(copy_factor)(other.factor, c);
+  voltcurmat = CHOL_F(copy_sparse)(other.voltcurmat, c);
+} 
+
+problem::~problem() {
+  CHOL_F(free_dense)(&b, c);
+  CHOL_F(free_factor)(&factor, c);
+  CHOL_F(free_sparse)(&voltcurmat, c);
+}
+
+current_info problem::solve(std::vector<bool>& fuses) {
+  cholmod_dense *x = CHOL_F(solve)(CHOLMOD_A, factor, b, c);
+
+  if (((double *)x->x)[0] != ((double *)x->x)[0]) {
+    throw nanex;
+  }
+
+  cholmod_dense *y = CHOL_F(allocate_dense)(G.edges.size(), 1, G.edges.size(), CHOLMOD_REAL, c);
+
+  double alpha[2] = {1, 0};
+  double beta[2] = {0, 0};
+  CHOL_F(sdmult)(voltcurmat, 0, alpha, beta, x, y, c);
+
+  std::vector<double> currents(G.edges.size());
+
+  std::array<double, 2> total_current = {0, 0};
+
+  for (int i = 0; i < G.edges.size(); i++) {
+    if (fuses[i]) {
+      currents[i] = 0;
+    } else {
+      currents[i] = ((double *)y->x)[i];
+
+      graph::coordinate v0 = G.vertices[G.edges[i].v[0]].r;
+      graph::coordinate v1 = G.vertices[G.edges[i].v[1]].r;
+
+      if (G.edges[i].crossings[axis]) {
+        bool comp;
+        if (axis == 1) {
+          comp = v0.y > v1.y;
+        } else {
+          comp = v0.x > v1.x;
+        }
+
+        if (comp) {
+          currents[i] += 1.0;
+          total_current[axis] += currents[i];
+        } else {
+          currents[i] -= 1.0;
+          total_current[axis] -= currents[i];
+        }
+      }
+    }
+  }
+
+  total_current[!axis] = 0.0;
+
+  CHOL_F(free_dense)(&x, c);
+  CHOL_F(free_dense)(&y, c);
+
+  return {total_current, currents};
+}
+
+void problem::break_edge(unsigned e, bool unbreak) {
+  unsigned v0 = G.edges[e].v[0];
+  unsigned v1 = G.edges[e].v[1];
+
+  unsigned n = factor->n;
+
+  cholmod_sparse *update_mat = CHOL_F(allocate_sparse)(n, n, 2, true, true, 0, CHOLMOD_REAL, c);
+
+  unsigned s1, s2;
+  s1 = v0 < v1 ? v0 : v1;
+  s2 = v0 < v1 ? v1 : v0;
+
+  CHOL_INT *pp = (CHOL_INT *)update_mat->p;
+  CHOL_INT *ii = (CHOL_INT *)update_mat->i;
+  double *xx = (double *)update_mat->x;
+
+  for (unsigned i = 0; i <= s1; i++) {
+    pp[i] = 0;
+  }
+
+  for (unsigned 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, (CHOL_INT *)factor->Perm, factor->n, NULL, -1, true, true, c);
+
+  CHOL_F(updown)(unbreak, perm_update_mat, factor, c);
+
+  CHOL_F(free_sparse)(&perm_update_mat, c);
+  CHOL_F(free_sparse)(&update_mat, c);
+
+  graph::coordinate r0 = G.vertices[v0].r;
+  graph::coordinate r1 = G.vertices[v1].r;
+
+  if (G.edges[e].crossings[axis]) {
+    bool ind;
+    if (axis == 1) {
+      ind = r0.y < r1.y ? unbreak : !unbreak;
+    } else {
+      ind = r0.x < r1.x ? unbreak : !unbreak;
+    }
+
+    ((double *)b->x)[G.edges[e].v[ind]]  -= 1.0;
+    ((double *)b->x)[G.edges[e].v[!ind]] += 1.0;
+  }
+}
+