Changes in src/Parser/PcpParser.cpp [e97a44:d74077]

File:

• src/Parser/PcpParser.cpp (modified) (5 diffs)

src/Parser/PcpParser.cpp

@@ -14 +14 @@
 #include "element.hpp"
 #include "Helpers/Assert.hpp"
-#include "Helpers/Log.hpp"
-#include "Helpers/Verbose.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
 #include "PcpParser.hpp"
 #include "periodentafel.hpp"
 #include "ThermoStatContainer.hpp"
+#include "verbose.hpp"
 #include "World.hpp"
+#include "Matrix.hpp"
 #include "Box.hpp"
 
@@ -332 +332 @@
 void PcpParser::save(std::ostream* file)
 {
-  DoLog(0) && (Log() << Verbose(0) << "Saving changes to pcp." << std::endl);
-
   const Matrix &domain = World::getInstance().getDomain().getM();
   class ThermoStatContainer *Thermostats = World::getInstance().getThermostats();
@@ -462 +460 @@
   PlaneWaveSpecifics.MaxPsiDouble = PlaneWaveSpecifics.PsiMaxNoDown = PlaneWaveSpecifics.PsiMaxNoUp = PlaneWaveSpecifics.PsiType = 0;
   for (vector<atom *>::iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
-    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->type->NoValenceOrbitals;
+    PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->NoValenceOrbitals;
   }
   cout << PlaneWaveSpecifics.MaxPsiDouble << endl;
@@ -497 +495 @@
   // insert all found elements into the map
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->type->Z, 1));
+    Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->Z, 1));
     if (!Inserter.second) // increase if present
       Inserter.first->second += 1;
@@ -528 +526 @@
   int nr = 0;
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
-    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->type->Z, 1) );
+    Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->Z, 1) );
     if (!Inserter.second)
       Inserter.first->second += 1;
-    const int Z = (*AtomRunner)->type->Z;
+    const int Z = (*AtomRunner)->getType()->Z;
     *file << "Ion_Type" << ZtoIndexMap[Z] << "_" << ZtoCountMap[Z] << "\t"  << fixed << setprecision(9) << showpoint;
-    *file << (*AtomRunner)->x[0] << "\t" << (*AtomRunner)->x[1] << "\t" << (*AtomRunner)->x[2];
+    *file << (*AtomRunner)->at(0) << "\t" << (*AtomRunner)->at(1) << "\t" << (*AtomRunner)->at(2);
     *file << "\t" << (*AtomRunner)->FixedIon;
-    if ((*AtomRunner)->v.Norm() > MYEPSILON)
-      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->v[0] << "\t" << (*AtomRunner)->v[1] << "\t" << (*AtomRunner)->v[2] << "\t";
+    if ((*AtomRunner)->AtomicVelocity.Norm() > MYEPSILON)
+      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->AtomicVelocity[0] << "\t" << (*AtomRunner)->AtomicVelocity[1] << "\t" << (*AtomRunner)->AtomicVelocity[2] << "\t";
     *file << " # molecule nr " << nr++ << endl;
   }