Changes in src/molecule.cpp [906822:c94eeb]

File:

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

src/molecule.cpp

@@ -27 +27 @@
 #include "tesselation.hpp"
 #include "vector.hpp"
+#include "Matrix.hpp"
 #include "World.hpp"
 #include "Plane.hpp"
@@ -79 +80 @@
 void molecule::setName(const std::string _name){
   OBSERVE;
+  cout << "Set name of molecule " << getId() << " to " << _name << endl;
   strncpy(name,_name.c_str(),MAXSTRINGSIZE);
 }
@@ -283 +285 @@
   Vector Orthovector1, Orthovector2;  // temporary vectors in coordination construction
   Vector InBondvector;    // vector in direction of *Bond
-  double *matrix = NULL;
+  Matrix matrix;
   bond *Binder = NULL;
   double * const cell_size = World::getInstance().getDomain();
@@ -306 +308 @@
       } // (signs are correct, was tested!)
     }
-    matrix = ReturnFullMatrixforSymmetric(cell_size);
+    double *matrix_double = ReturnFullMatrixforSymmetric(cell_size);
+    matrix = Matrix(matrix_double);
+    delete[](matrix_double);
     Orthovector1.MatrixMultiplication(matrix);
     InBondvector -= Orthovector1; // subtract just the additional translation
-    delete[](matrix);
     bondlength = InBondvector.Norm();
 //    Log() << Verbose(4) << "Corrected InBondvector is now: ";
@@ -540 +543 @@
       break;
   }
-  delete[](matrix);
 
 //  Log() << Verbose(3) << "End of AddHydrogenReplacementAtom." << endl;
@@ -739 +741 @@
   else
     length = strlen(molname) - strlen(endname);
+  cout << "Set name of molecule " << getId() << " to " << molname << endl;
   strncpy(name, molname, length);
   name[length]='\0';
@@ -880 +883 @@
         ElementNo[i] = current++;
     }
-    ActOnAllAtoms( &atom::OutputArrayIndexed, output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
+    ActOnAllAtoms( &atom::OutputArrayIndexed, (ostream * const) output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
     return true;
   }
@@ -1003 +1006 @@
   for(int i=MAX_ELEMENTS;i--;)
     ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
-};
-
-
-/** Counts necessary number of valence electrons and returns number and SpinType.
- * \param configuration containing everything
- */
-void molecule::CalculateOrbitals(class config &configuration)
-{
-  configuration.MaxPsiDouble = configuration.PsiMaxNoDown = configuration.PsiMaxNoUp = configuration.PsiType = 0;
-  for(int i=MAX_ELEMENTS;i--;) {
-    if (ElementsInMolecule[i] != 0) {
-      //Log() << Verbose(0) << "CalculateOrbitals: " << elemente->FindElement(i)->name << " has a valence of " << (int)elemente->FindElement(i)->Valence << " and there are " << ElementsInMolecule[i] << " of it." << endl;
-      configuration.MaxPsiDouble += ElementsInMolecule[i]*((int)elemente->FindElement(i)->Valence);
-    }
-  }
-  configuration.PsiMaxNoDown = configuration.MaxPsiDouble/2 + (configuration.MaxPsiDouble % 2);
-  configuration.PsiMaxNoUp = configuration.MaxPsiDouble/2;
-  configuration.MaxPsiDouble /= 2;
-  configuration.PsiType = (configuration.PsiMaxNoDown == configuration.PsiMaxNoUp) ? 0 : 1;
-  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2) && ((configuration.PsiMaxNoDown != 1) || (configuration.PsiMaxNoUp != 0))) {
-    configuration.ProcPEGamma /= 2;
-    configuration.ProcPEPsi *= 2;
-  } else {
-    configuration.ProcPEGamma *= configuration.ProcPEPsi;
-    configuration.ProcPEPsi = 1;
-  }
-  cout << configuration.PsiMaxNoDown << ">" << configuration.PsiMaxNoUp << endl;
-  if (configuration.PsiMaxNoDown > configuration.PsiMaxNoUp) {
-    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoDown;
-    cout << configuration.PsiMaxNoDown << " " << configuration.InitMaxMinStopStep << endl;
-  } else {
-    configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.PsiMaxNoUp;
-    cout << configuration.PsiMaxNoUp << " " << configuration.InitMaxMinStopStep << endl;
-  }
 };