Fixing temporary vector size on massic to atomic conversion

It fixes the erroneous temporary vectors used to copy the converted stoichiometry between the compounds and elements objects.
By other had the Compound constructor algorithm was simplified.

src/ReactionYield.cpp

@@ -794,37 +794,13 @@ double ElementExtra::GetMassFraction(int ElementID)
 }
 
 
-// Main constructor for Compound, that in this case, a single Element are sent to the designed group
+// Main constructor for Compound.
 Compound::Compound(Element ThisElement)
 {
  CompoundGroupNumber = ThisElement.GetCompoundGroup();
  ChemicalFormula.Add(ThisElement);
 }
 
-// Merge two compounds to the original, if it shares the same group. Also return a boolean value if a merge actually occurs
-bool Compound::MergeCompound(Compound Additional)
-{
- if (Additional.GetGroupNumber() == 0 || CompoundGroupNumber == 0)
-  {
-  return false;
-  }
-  else
-  {
-   if (CompoundGroupNumber == Additional.GetGroupNumber())
-   {
-    for (int i=0; i<Additional.ChemicalFormula.GetCount(); i++)  // Copy the additional Elements
-    {
-     ChemicalFormula.Add(Additional.ChemicalFormula.Item(i));
-    }
-    return true;
-   }
-   else
-   {
-    return false;
-   }
-  }
-}
-
 // Get the number of fitting elements from the selected compound
 int Compound::GetNumberFitElements()
 {
@@ -837,27 +813,49 @@ int Compound::GetNumberFitElements()
  return NFE;
 }
 
+// Add a candidate Element if belongs to the same compound ID
+bool Compound::AddElement(Element ThisElement)
+{
+ if(CompoundGroupNumber == ThisElement.GetCompoundGroup())
+ {
+   ChemicalFormula.Add(ThisElement);
+   return true;
+ }
+ else
+ {
+   return false;
+ }
+}
+
 // Generate the compounds from the main spreadsheet itself
 CompoundExtra::CompoundExtra(ElementExtra CurrentSelectedElements)
 {
- // Create a temporary Compound array, where use the alternative Compound constructor
- for (int i=0; i<CurrentSelectedElements.GetCount(); i++)  // Create the first list of compounds
-   {
-     Compound SingleElement = Compound(CurrentSelectedElements.Item(i));
-     this->Add(SingleElement);
-   }
- // Merging main cycle
-  for (int j=0; j<this->GetCount(); j++)
-   {
-     for (int k=j+1; k<this->GetCount(); k++)
-     {
-       if(this->Item(j).MergeCompound(this->Item(k)))
-        {
-          this->RemoveAt(k);
-          k--;
-        }
-     }
-   }
+ // Copy each element from the original elements array to the array of compounds
+ for(int k=0; k<CurrentSelectedElements.GetCount(); k++)
+ {
+  if(CurrentSelectedElements.Item(k).GetCompoundGroup() == 0) // Independent Elements are always isolated
+  {
+    Compound SingleElement = Compound(CurrentSelectedElements.Item(k));
+    this->Add(SingleElement);
+  }
+  else // Otherwise they should merge with the compounds
+  {
+    bool ElementMerged = false;
+    for(int i=0; i < this->GetCount(); i++)
+    {
+      if(this->Item(i).AddElement(CurrentSelectedElements.Item(k)))
+      {
+        ElementMerged = true;
+        break;
+      }
+    }
+    if(!ElementMerged)
+    {
+      Compound SingleElement = Compound(CurrentSelectedElements.Item(k));
+      this->Add(SingleElement);
+    }
+  }
+ }
   // Set flag for sucefulness
    Sucess = true;
 }
@@ -990,12 +988,12 @@ bool CompoundExtra::CheckMassAtomicStoichiometry()
  // Treat first the trivial cases
  if(this->GetCount() == 0)
   return false;
- 
+
  // Create the counters and make a single run-check.
  double SumMass = 0;
  double ProductMass = 0;
  int TotalElements = 0;
- 
+
  for(int i=0; i<this->GetCount(); i++)
  {
   for(int j=0; j<this->Item(i).GetNumberElements(); j++)
@@ -1014,7 +1012,7 @@ bool CompoundExtra::CheckMassAtomicStoichiometry()
     MassAtomicStoichiometryMode = 0; // Empty Mass Fraction column means the default mode, which is the sample was already defined by the atomic fraction column
     return true;
  }
- else 
+ else
  {
     MassAtomicStoichiometryMode = 1; // Requires further control
     return true;
@@ -1033,6 +1031,15 @@ bool CompoundExtra::ConvertMassAtomicToStoichiometry()
  else if(MassAtomicStoichiometryMode == 1) // A mixture of compounds with fixed atomic ratios but with their mass known, along independent elements with their mass known
  {
    // For each independent element or compound find the absolute mass value, and convert the relative atomic ratios to mass ratios
+   double TotalSampleMass = 0;
+   for(int i=0; i<this->GetCount(); i++)
+   {
+    for(int j=0; j<this->Item(i).GetNumberElements(); j++)
+    {
+     TotalSampleMass = TotalSampleMass+ this->Item(i).GetMassQuantityAt(j);
+    }
+   }
+   // Convert for each compound the absolute mass to the respective mass fraction.
    for(int i=0; i<this->GetCount(); i++)
    {
     double CompoundMass = 0; // To retrieve the compound or independent element mass
@@ -1062,7 +1069,7 @@ bool CompoundExtra::ConvertMassAtomicToStoichiometry()
     for(int j=0; j<this->Item(i).GetNumberElements(); j++)
     {
      double temp = this->Item(i).GetStoichiometryAt(j) * this->Item(i).GetAtomicMassAt(j);
-     double x = this->Item(i).SetMassQuantityAt(j,temp*CompoundMass/CompoundStoichiometry);
+     double x = this->Item(i).SetMassQuantityAt(j,(temp*CompoundMass)/(CompoundStoichiometry*TotalSampleMass));
     }
    }
   // With the whole sample mass fraction evaluated, it is straighforward to convert back to atomic fraction
@@ -1093,13 +1100,18 @@ bool CompoundExtra::ConvertMassAtomicToStoichiometry()
 
 IntegerVector CompoundExtra::GetElementsID()
 {
- IntegerVector InitialID = IntegerVector(this->GetCount());
+ int TotalNumberElements = 0;
+ for(int z=0; z<this->GetCount(); z++)
+ {
+   TotalNumberElements = TotalNumberElements + this->Item(z).GetNumberElements();
+ }
+ IntegerVector InitialID = IntegerVector(TotalNumberElements);
  int k = 0;
  for(int i=0; i<this->GetCount(); i++)
  {
   for(int j=0; j<this->Item(i).GetNumberElements(); j++)
   {
-    double temp = this->Item(i).GetElementIDAt(j);
+    int temp = this->Item(i).GetElementIDAt(j);
     InitialID.SetValue(k,temp);
     k = k + 1;
   }
@@ -1109,7 +1121,12 @@ IntegerVector CompoundExtra::GetElementsID()
 
 Vector CompoundExtra::GetAllStoichiometry()
 {
- Vector InitialID = Vector(this->GetCount());
+ int TotalNumberElements = 0;
+ for(int z=0; z<this->GetCount(); z++)
+ {
+   TotalNumberElements = TotalNumberElements + this->Item(z).GetNumberElements();
+ }
+ Vector InitialID = Vector(TotalNumberElements);
  int k = 0;
  for(int i=0; i<this->GetCount(); i++)
  {

src/ReactionYield.h

@@ -130,7 +130,7 @@ bool Sucess;
 ElementArray ChemicalFormula;
 public:
 Compound(Element ThisElement);
-bool MergeCompound(Compound Additional);
+bool AddElement(Element ThisElement);
 int GetNumberElements() {return ChemicalFormula.GetCount();};
 int GetNumberFitElements();
 int GetElementIDAt(int position) {return ChemicalFormula.Item(position).GetElementID();};