Changes in src/linkedcell.cpp [0f4538:042f82]

File:

• src/linkedcell.cpp (modified) (6 diffs)

src/linkedcell.cpp

@@ -6 +6 @@
 LinkedCell::LinkedCell()
 {
-        LC = NULL;
-        for(int i=0;i<NDIM;i++)
-                N[i] = 0;
-        index = -1;
-        RADIUS = 0.;
-        max.Zero();
-        min.Zero();
+  LC = NULL;
+  for(int i=0;i<NDIM;i++)
+    N[i] = 0;
+  index = -1;
+  RADIUS = 0.;
+  max.Zero();
+  min.Zero();
 };
 
@@ -21 +21 @@
 LinkedCell::LinkedCell(molecule *mol, double radius)
 {
-        atom *Walker = NULL;
+  atom *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 (mol->start->next == mol->end) {
-                cerr << "ERROR: molecule contains no atoms!" << endl;
-                return;
-        }
-        // 1. find max and min per axis of atoms
-        Walker = mol->start->next;
-        for (int i=0;i<NDIM;i++) {
-                max.x[i] = Walker->x.x[i];
-                min.x[i] = Walker->x.x[i];
-        }
-        while (Walker != mol->end) {
-                for (int i=0;i<NDIM;i++) {
-                        if (max.x[i] < Walker->x.x[i])
-                                max.x[i] = Walker->x.x[i];
-                        if (min.x[i] > Walker->x.x[i])
-                                min.x[i] = Walker->x.x[i];
-                }
-                Walker = Walker->next;
-        }
-        cout << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl;
+  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 (mol->start->next == mol->end) {
+    cerr << "ERROR: molecule contains no atoms!" << endl;
+    return;
+  }
+  // 1. find max and min per axis of atoms
+  Walker = mol->start->next;
+  for (int i=0;i<NDIM;i++) {
+    max.x[i] = Walker->x.x[i];
+    min.x[i] = Walker->x.x[i];
+  }
+  while (Walker != mol->end) {
+    for (int i=0;i<NDIM;i++) {
+      if (max.x[i] < Walker->x.x[i])
+        max.x[i] = Walker->x.x[i];
+      if (min.x[i] > Walker->x.x[i])
+        min.x[i] = Walker->x.x[i];
+    }
+    Walker = Walker->next;
+  }
+  cout << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl;
 
-        // 2. find then umber 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;
+  // 2. find then umber 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 LinkedAtoms[N[0]*N[1]*N[2]];
-        for (index=0;index<N[0]*N[1]*N[2];index++) {
-                LC [index].clear();
-        }
-        cout << "done."  << 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 LinkedAtoms[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
+  // 4. put each atom into its respective cell
   cout << Verbose(2) << "Filling cells ... ";
-        Walker = mol->start;
-        while (Walker->next != mol->end) {
-                Walker = Walker->next;
-                for (int i=0;i<NDIM;i++) {
-                        n[i] = (int)floor((Walker->x.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;
-        }
+  Walker = mol->start;
+  while (Walker->next != mol->end) {
+    Walker = Walker->next;
+    for (int i=0;i<NDIM;i++) {
+      n[i] = (int)floor((Walker->x.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;
-        cout << Verbose(1) << "End of LinkedCell" << endl;
+  cout << Verbose(1) << "End of LinkedCell" << endl;
 };
 
@@ -90 +90 @@
 LinkedCell::~LinkedCell()
 {
-        if (LC != NULL)
-        for (index=0;index<N[0]*N[1]*N[2];index++)
-                LC[index].clear();
-        delete[](LC);
-        for(int i=0;i<NDIM;i++)
-                N[i] = 0;
-        index = -1;
-        max.Zero();
-        min.Zero();
+  if (LC != NULL)
+  for (index=0;index<N[0]*N[1]*N[2];index++)
+    LC[index].clear();
+  delete[](LC);
+  for(int i=0;i<NDIM;i++)
+    N[i] = 0;
+  index = -1;
+  max.Zero();
+  min.Zero();
 };
 
@@ -106 +106 @@
 bool LinkedCell::CheckBounds()
 {
-        bool status = true;
-        for(int i=0;i<NDIM;i++)
-                status = status && ((n[i] >=0) && (n[i] < N[i]));
-        if (!status)
-        cerr << "ERROR: indices are out of bounds!" << endl;
-        return status;
+  bool status = true;
+  for(int i=0;i<NDIM;i++)
+    status = status && ((n[i] >=0) && (n[i] < N[i]));
+  if (!status)
+  cerr << "ERROR: indices are out of bounds!" << endl;
+  return status;
 };
 
@@ -120 +120 @@
 LinkedAtoms* LinkedCell::GetCurrentCell()
 {
-        if (CheckBounds()) {
-                index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
-                return (&(LC[index]));
-        } else {
-                return NULL;
-        }
+  if (CheckBounds()) {
+    index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
+    return (&(LC[index]));
+  } else {
+    return NULL;
+  }
 };
 
 /** Calculates the index for a given atom *Walker.
- * \param Walker atom to set index to
+ * \param *Walker atom to set index to
  * \return if the atom is also found in this cell - true, else - false
  */
-bool LinkedCell::SetIndexToAtom(const atom &Walker)
+bool LinkedCell::SetIndexToAtom(atom *Walker)
 {
-        bool status = false;
-        for (int i=0;i<NDIM;i++) {
-                n[i] = (int)floor((Walker.x.x[i] - min.x[i])/RADIUS);
-        }
-
-        index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
-        if (CheckBounds()) {
-                for (LinkedAtoms::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
-                        status = status || ((*Runner) == &Walker);
-                return status;
-        } else {
-                cerr << Verbose(1) << "WARN: Atom "<< Walker << " at " << Walker.x << " is out of bounds." << endl;
-                return false;
-        }
-};
-
-/** Calculates the interval bounds of the linked cell grid.
- * \param *lower lower bounds
- * \param *upper upper bounds
- */
-void LinkedCell::GetNeighbourBounds(int lower[NDIM], int upper[NDIM])
-{
+  bool status = false;
   for (int i=0;i<NDIM;i++) {
-    lower[i] = ((n[i]-1) >= 0) ? n[i]-1 : 0;
-    upper[i] = ((n[i]+1) < N[i]) ? n[i]+1 : N[i]-1;
-    //cout << " [" << Nlower[i] << "," << Nupper[i] << "] ";
-    // check for this axis whether the point is outside of our grid
-    if (n[i] < 0)
-      upper[i] = lower[i];
-    if (n[i] > N[i])
-      lower[i] = upper[i];
-
-    //cout << "axis " << i << " has bounds [" << lower[i] << "," << upper[i] << "]" << endl;
+    n[i] = (int)floor((Walker->x.x[i] - min.x[i])/RADIUS);
+  }
+  index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
+  if (CheckBounds()) {
+    for (LinkedAtoms::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
+      status = status || ((*Runner) == Walker);
+    return status;
+  } else {
+    cerr << Verbose(1) << "ERROR: Atom "<< *Walker << " at " << Walker->x << " is out of bounds." << endl;
+    return false;
   }
 };
@@ -174 +153 @@
  * \return Vector is inside bounding box - true, else - false
  */
-bool LinkedCell::SetIndexToVector(const Vector *x)
+bool LinkedCell::SetIndexToVector(Vector *x)
 {
-        bool status = true;
-        for (int i=0;i<NDIM;i++) {
-                n[i] = (int)floor((x->x[i] - min.x[i])/RADIUS);
-                if (max.x[i] < x->x[i])
-                        status = false;
-                if (min.x[i] > x->x[i])
-                        status = false;
-        }
-        return status;
+  bool status = true;
+  for (int i=0;i<NDIM;i++) {
+    n[i] = (int)floor((x->x[i] - min.x[i])/RADIUS);
+    if (max.x[i] < x->x[i])
+      status = false;
+    if (min.x[i] > x->x[i])
+      status = false;
+  }
+  return status;
 };