Changes in src/linkedcell.cpp [1999d8:f66195]

File:

• src/linkedcell.cpp (modified) (2 diffs)

src/linkedcell.cpp

@@ -6 +6 @@
 
 
+#include "atom.hpp"
+#include "helpers.hpp"
 #include "linkedcell.hpp"
-#include "molecules.hpp"
+#include "molecule.hpp"
 #include "tesselation.hpp"
+#include "vector.hpp"
 
 // ========================================================= class LinkedCell ===========================================
@@ -96 +99 @@
     //cout << Verbose(2) << *Walker << " goes into cell " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
     set->GoToNext();
+  }
+  cout << "done."  << endl;
+  cout << Verbose(1) << "End of LinkedCell" << endl;
+};
+
+
+/** Puts all atoms in \a *mol into a linked cell list with cell's lengths of \a RADIUS
+ * \param *set LCNodeSet class with all LCNode's
+ * \param RADIUS edge length of cells
+ */
+LinkedCell::LinkedCell(LinkedNodes *set, double radius)
+{
+  class TesselPoint *Walker = NULL;
+  RADIUS = radius;
+  LC = NULL;
+  for(int i=0;i<NDIM;i++)
+    N[i] = 0;
+  index = -1;
+  max.Zero();
+  min.Zero();
+  cout << Verbose(1) << "Begin of LinkedCell" << endl;
+  if (set->empty()) {
+    cerr << "ERROR: set contains no linked cell nodes!" << endl;
+    return;
+  }
+  // 1. find max and min per axis of atoms
+  LinkedNodes::iterator Runner = set->begin();
+  for (int i=0;i<NDIM;i++) {
+    max.x[i] = (*Runner)->node->x[i];
+    min.x[i] = (*Runner)->node->x[i];
+  }
+  for (LinkedNodes::iterator Runner = set->begin(); Runner != set->end(); Runner++) {
+    Walker = *Runner;
+    for (int i=0;i<NDIM;i++) {
+      if (max.x[i] < Walker->node->x[i])
+        max.x[i] = Walker->node->x[i];
+      if (min.x[i] > Walker->node->x[i])
+        min.x[i] = Walker->node->x[i];
+    }
+  }
+  cout << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl;
+
+  // 2. find then number of cells per axis
+  for (int i=0;i<NDIM;i++) {
+    N[i] = (int)floor((max.x[i] - min.x[i])/RADIUS)+1;
+  }
+  cout << Verbose(2) << "Number of cells per axis are " << N[0] << ", " << N[1] << " and " << N[2] << "." << endl;
+
+  // 3. allocate the lists
+  cout << Verbose(2) << "Allocating cells ... ";
+  if (LC != NULL) {
+    cout << Verbose(1) << "ERROR: Linked Cell list is already allocated, I do nothing." << endl;
+    return;
+  }
+  LC = new LinkedNodes[N[0]*N[1]*N[2]];
+  for (index=0;index<N[0]*N[1]*N[2];index++) {
+    LC [index].clear();
+  }
+  cout << "done."  << endl;
+
+  // 4. put each atom into its respective cell
+  cout << Verbose(2) << "Filling cells ... ";
+  for (LinkedNodes::iterator Runner = set->begin(); Runner != set->end(); Runner++) {
+    Walker = *Runner;
+    for (int i=0;i<NDIM;i++) {
+      n[i] = (int)floor((Walker->node->x[i] - min.x[i])/RADIUS);
+    }
+    index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
+    LC[index].push_back(Walker);
+    //cout << Verbose(2) << *Walker << " goes into cell " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
   }
   cout << "done."  << endl;