Changes in src/molecule.cpp [e4afb4:76ff55]

File:

• src/molecule.cpp (modified) (7 diffs)

src/molecule.cpp

@@ -640 +640 @@
  * \return copy of molecule
  */
-molecule *molecule::CopyMolecule() const
+molecule *molecule::CopyMolecule()
 {
   molecule *copy = World::getInstance().createMolecule();
@@ -648 +648 @@
 
   // copy all bonds
-  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
-    for(BondList::const_iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
+  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
+    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); BondRunner != (*AtomRunner)->ListOfBonds.end(); ++BondRunner)
       if ((*BondRunner)->leftatom == *AtomRunner) {
         bond *Binder = (*BondRunner);
@@ -874 +874 @@
  * \param *out output stream
  */
-bool molecule::Output(ostream * const output) const
+bool molecule::Output(ostream * const output)
 {
   if (output == NULL) {
@@ -882 +882 @@
     memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
     enumeration<const element*> elementLookup = formula.enumerateElements();
+    for(map<const element*,unsigned int>::iterator iter=elementLookup.there.begin();
+        iter!=elementLookup.there.end();++iter){
+      cout << "Enumerated element " << *iter->first << " with number " << iter->second << endl;
+    }
     *output << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
     for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
@@ -891 +895 @@
  * \param *out output stream
  */
-bool molecule::OutputTrajectories(ofstream * const output) const
-{
+bool molecule::OutputTrajectories(ofstream * const output)
+{
+  int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
+
   if (output == NULL) {
     return false;
@@ -902 +908 @@
         *output << "# ====== MD step " << step << " =========" << endl;
       }
-      int AtomNo[MAX_ELEMENTS];
-      memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
-      enumeration<const element*> elementLookup = formula.enumerateElements();
-      for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputTrajectory,_1,output,elementLookup, AtomNo, (const int)step));
+      for (int i=0;i<MAX_ELEMENTS;++i) {
+        AtomNo[i] = 0;
+        ElementNo[i] = 0;
+      }
+      for(molecule::iterator iter = begin(); iter != end(); ++iter) {
+        ElementNo[(*iter)->getType()->getAtomicNumber()] = 1;
+      }
+      int current=1;
+      for (int i=0;i<MAX_ELEMENTS;++i) {
+        if (ElementNo[i] == 1)
+          ElementNo[i] = current++;
+      }
+      ActOnAllAtoms( &atom::OutputTrajectory, output, (const int *)ElementNo, AtomNo, (const int)step );
     }
     return true;
@@ -1040 +1055 @@
     *output << "# Step Temperature [K] Temperature [a.u.]" << endl;
   for (int step=startstep;step < endstep; step++) { // loop over all time steps
-    temperature = atoms.totalTemperatureAtStep(step);
+    temperature = 0.;
+    ActOnAllAtoms( &TrajectoryParticle::AddKineticToTemperature, &temperature, step);
     *output << step << "\t" << temperature*AtomicEnergyToKelvin << "\t" << temperature << endl;
   }
   return true;
+};
+
+void molecule::SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::*index) const
+{
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    array[((*iter)->*index)] = (*iter);
+  }
 };