Refactor MatrixMap (#3176)

The 3 main items of this small patch are:

    Push elements on vectors only if they are real (means index > 0)
    Create a function that compute the index
    Remove useless plen_

src/nrniv/matrixmap.cpp

@@ -18,21 +18,13 @@ void MatrixMap::mmfree() {
 }
 
 void MatrixMap::add(double fac) {
-    for (int i = 0; i < plen_; ++i) {
+    for (int i = 0; i < pm_.size(); ++i) {
         auto [it, jt] = pm_[i];
         *ptree_[i] += fac * m_(it, jt);
     }
 }
 
-void MatrixMap::alloc(int start, int nnode, Node** nodes, int* layer) {
-    NrnThread* _nt = nrn_threads;
-    mmfree();
-
-    plen_ = 0;
-    std::vector<std::pair<int, int>> nzs = m_.nonzeros();
-    pm_.resize(nzs.size());
-    ptree_.resize(nzs.size());
-    for (const auto [i, j]: nzs) {
+int MatrixMap::compute_index(int i, int start, int nnode, Node** nodes, int* layer) const {
         int it;
         if (i < nnode) {
             it = nodes[i]->eqn_index_ + layer[i];
@@ -42,17 +34,22 @@ void MatrixMap::alloc(int start, int nnode, Node** nodes, int* layer) {
         } else {
             it = start + i - nnode;
         }
-        int jt;
-        pm_[plen_] = std::make_pair(i, j);
-        if (j < nnode) {
-            jt = nodes[j]->eqn_index_ + layer[j];
-            if (layer[j] > 0 && !nodes[j]->extnode) {
-                jt = 0;
-            }
-        } else {
-            jt = start + j - nnode;
+        return it;
+}
+
+void MatrixMap::alloc(int start, int nnode, Node** nodes, int* layer) {
+    NrnThread* _nt = nrn_threads;
+    mmfree();
+
+    std::vector<std::pair<int, int>> nzs = m_.nonzeros();
+    pm_.reserve(nzs.size());
+    ptree_.reserve(nzs.size());
+    for (const auto& [i, j]: nzs) {
+        int it = compute_index(i, start, nnode, nodes, layer);
+        int jt = compute_index(j, start, nnode, nodes, layer);
+        if (it != 0 && jt != 0) {
+            pm_.emplace_back(i, j);
+            ptree_.emplace_back(spGetElement(_nt->_sp13mat, it, jt));
         }
-        ptree_[plen_] = spGetElement(_nt->_sp13mat, it, jt);
-        ++plen_;
     }
 }

src/nrniv/matrixmap.h

@@ -115,7 +115,8 @@ class MatrixMap {
     Matrix& m_;
 
     // the map
-    int plen_ = 0;
     std::vector<std::pair<int, int>> pm_{};
     std::vector<double*> ptree_{};
+
+    int compute_index(int, int, int, Node**, int*) const;
 };