Changeset 04dcc0 for molecuilder/src/molecules.cpp

Timestamp:

Aug 4, 2009, 1:47:05 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

eeefb3

Parents:

f4a346

Message:

Smaller FIXES to molecule class

• new pointer TesselStruct was not initialzied to NULL
• corrected molecule::CenterInBox(), it now really centers in the given cell_size box (no idea what it did before that)
• as TesselStruct is now a part of the molecule, we remove it on deleting the molecule if it's not NULL

File:

• molecuilder/src/molecules.cpp (modified) (3 diffs)

molecuilder/src/molecules.cpp

@@ -67 +67 @@
   IndexNr  = -1;
   ActiveFlag = false;
+  TesselStruct = NULL;
 };
 
@@ -79 +80 @@
   Free((void **)&ListOfBondsPerAtom, "molecule::~molecule: ListOfBondsPerAtom");
   Free((void **)&NumberOfBondsPerAtom, "molecule::~molecule: NumberOfBondsPerAtom");
+  if (TesselStruct != NULL)
+    delete(TesselStruct);
   CleanupMolecule();
   delete(first);
@@ -710 +713 @@
 {
   bool status = true;
-  atom *ptr = NULL;
   Vector x;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
   double *Minv = x.InverseMatrix(M);
-  double value;
-
-//  cout << "The box matrix is :" << endl;
-//  for (int i=0;i<NDIM;++i) {
-//    for (int j=0;j<NDIM;++j)
-//      cout << M[i*NDIM+j] << "\t";
-//    cout << endl;
-//  }
-//  cout << "And its inverse is :" << endl;
-//  for (int i=0;i<NDIM;++i) {
-//    for (int j=0;j<NDIM;++j)
-//      cout << Minv[i*NDIM+j] << "\t";
-//    cout << endl;
-//  }
+  Vector *Center = DetermineCenterOfAll(out);
+
   // go through all atoms
-  ptr = start->next;  // start at first in list
-  if (ptr != end) {  //list not empty?
-    while (ptr->next != end) {  // continue with second if present
-      ptr = ptr->next;
-      //ptr->Output(1,1,out);
-      // multiply its vector with matrix inverse
-      x.CopyVector(&ptr->x);
-      x.MatrixMultiplication(Minv);
-      // truncate to [0,1] for each axis
-      for (int i=0;i<NDIM;i++) {
-        value = floor(x.x[i]);  // next lower integer
-        if (x.x[i] >=0) {
-          x.x[i] -= value;
-        } else {
-          x.x[i] += value+1;
-        }
-      }
-    }
+  atom *ptr = start;  // start at first in list
+  while (ptr->next != end) {  // continue with second if present
+    ptr = ptr->next;
+    //ptr->Output(1,1,out);
+    // multiply its vector with matrix inverse
+    x.CopyVector(&ptr->x);
+    x.SubtractVector(Center); // now, it's centered at origin
+    x.MatrixMultiplication(Minv);
+    // truncate to [0,1] for each axis
+    for (int i=0;i<NDIM;i++) {
+      x.x[i] += 0.5;  // set to center of box
+      while (x.x[i] >= 1.)
+        x.x[i] -= 1.;
+      while (x.x[i] < 0.)
+        x.x[i] += 1.;
+    }
+    x.MatrixMultiplication(M);
+    ptr->x.CopyVector(&x);
   }
   delete(M);
   delete(Minv);
+  delete(Center);
   return status;
 };