Changes in src/molecule_geometry.cpp [f66195:99593f]

File:

• src/molecule_geometry.cpp (modified) (8 diffs)

src/molecule_geometry.cpp

@@ -24 +24 @@
 {
   bool status = true;
-  Vector x;
   const Vector *Center = DetermineCenterOfAll(out);
   double *M = ReturnFullMatrixforSymmetric(cell_size);
-  double *Minv = x.InverseMatrix(M);
+  double *Minv = InverseMatrix(M);
 
   // go through all atoms
@@ -46 +45 @@
 {
   bool status = true;
-  Vector x;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
-  double *Minv = x.InverseMatrix(M);
+  double *Minv = InverseMatrix(M);
 
   // go through all atoms
@@ -122 +120 @@
  * \return pointer to center of all vector
  */
-Vector * molecule::DetermineCenterOfAll(ofstream *out)
+Vector * molecule::DetermineCenterOfAll(ofstream *out) const
 {
   atom *ptr = start->next;  // start at first in list
@@ -198 +196 @@
  * \param *factor pointer to scaling factor
  */
-void molecule::Scale(double **factor)
+void molecule::Scale(const double ** const factor)
 {
   atom *ptr = start;
@@ -231 +229 @@
 void molecule::TranslatePeriodically(const Vector *trans)
 {
-  Vector x;
   double *M = ReturnFullMatrixforSymmetric(cell_size);
-  double *Minv = x.InverseMatrix(M);
+  double *Minv = InverseMatrix(M);
 
   // go through all atoms
@@ -258 +255 @@
 {
   atom *Walker = start;
-  bond *Binder = NULL;
   double *matrix = ReturnFullMatrixforSymmetric(cell_size);
   double tmp;
@@ -275 +271 @@
         Testvector.InverseMatrixMultiplication(matrix);
         Translationvector.Zero();
-        for (int i=0;i<NumberOfBondsPerAtom[Walker->nr]; i++) {
-          Binder = ListOfBondsPerAtom[Walker->nr][i];
-          if (Walker->nr < Binder->GetOtherAtom(Walker)->nr) // otherwise we shift one to, the other fro and gain nothing
+        for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
+         if (Walker->nr < (*Runner)->GetOtherAtom(Walker)->nr) // otherwise we shift one to, the other fro and gain nothing
             for (int j=0;j<NDIM;j++) {
-              tmp = Walker->x.x[j] - Binder->GetOtherAtom(Walker)->x.x[j];
+              tmp = Walker->x.x[j] - (*Runner)->GetOtherAtom(Walker)->x.x[j];
               if ((fabs(tmp)) > BondDistance) {
                 flag = false;
-                cout << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *Binder << " has to be shifted due to " << tmp << "." << endl;
+                cout << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl;
                 if (tmp > 0)
                   Translationvector.x[j] -= 1.;
@@ -298 +293 @@
 #ifdef ADDHYDROGEN
         // now also change all hydrogens
-        for (int i=0;i<NumberOfBondsPerAtom[Walker->nr]; i++) {
-          Binder = ListOfBondsPerAtom[Walker->nr][i];
-          if (Binder->GetOtherAtom(Walker)->type->Z == 1) {
-            Testvector.CopyVector(&Binder->GetOtherAtom(Walker)->x);
+        for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
+          if ((*Runner)->GetOtherAtom(Walker)->type->Z == 1) {
+            Testvector.CopyVector(&(*Runner)->GetOtherAtom(Walker)->x);
             Testvector.InverseMatrixMultiplication(matrix);
             Testvector.AddVector(&Translationvector);