Changes in src/moleculelist.cpp [952f38:d74077]

File:

• src/moleculelist.cpp (modified) (6 diffs)

src/moleculelist.cpp

@@ -23 +23 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "Helpers/helpers.hpp"
+#include "helpers.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "Helpers/Verbose.hpp"
-#include "Helpers/Log.hpp"
+#include "verbose.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "Helpers/Assert.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "Matrix.hpp"
 #include "Box.hpp"
 #include "stackclass.hpp"
@@ -182 +182 @@
       size=0.;
       for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
-        counts[(*iter)->type->getNumber()]++;
-        if ((*iter)->x.DistanceSquared(Origin) > size)
-          size = (*iter)->x.DistanceSquared(Origin);
+        counts[(*iter)->getType()->getNumber()]++;
+        if ((*iter)->DistanceSquared(Origin) > size)
+          size = (*iter)->DistanceSquared(Origin);
       }
       // output Index, Name, number of atoms, chemical formula
@@ -354 +354 @@
   for (molecule::const_iterator iter = srcmol->begin(); iter != srcmol->end(); ++iter) {
     DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << **iter << "." << endl);
-    if (!TesselStruct->IsInnerPoint((*iter)->x, LCList)) {
+    if (!TesselStruct->IsInnerPoint((*iter)->getPosition(), LCList)) {
       CopyAtoms[(*iter)->nr] = (*iter)->clone();
       mol->AddAtom(CopyAtoms[(*iter)->nr]);
@@ -501 +501 @@
     for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
       //Log() << Verbose(1) << "(*iter): " << *(*iter) << " with first bond " << *((*iter)->ListOfBonds.begin()) << "." << endl;
-      if (((*iter)->type->Z == 1) && (((*iter)->father == NULL)
-          || ((*iter)->father->type->Z != 1))) { // if it's a hydrogen
+      if (((*iter)->getType()->Z == 1) && (((*iter)->father == NULL)
+          || ((*iter)->father->getType()->Z != 1))) { // if it's a hydrogen
         for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
           //Log() << Verbose(2) << "Runner: " << *(*runner) << " with first bond " << *((*iter)->ListOfBonds.begin()) << "." << endl;
           // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
           Binder = *((*runner)->ListOfBonds.begin());
-          if (((*runner)->type->Z == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
+          if (((*runner)->getType()->Z == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
             // 4. evaluate the morse potential for each matrix component and add up
-            distance = (*runner)->x.distance((*iter)->x);
+            distance = (*runner)->distance(*(*iter));
             //Log() << Verbose(0) << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":" << endl;
             for (int k = 0; k < a; k++) {
@@ -599 +599 @@
         if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
           for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
-            if ((*atomIter)->type->getNumber() == (*elemIter).first) {
+            if ((*atomIter)->getType()->getNumber() == (*elemIter).first) {
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
                 //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
@@ -1089 +1089 @@
         if (AtomMask[Father->nr]) // apply mask
 #ifdef ADDHYDROGEN
-          if ((*iter)->type->Z != 1) // skip hydrogen
+          if ((*iter)->getType()->Z != 1) // skip hydrogen
 #endif
           RootStack[FragmentCounter].push_front((*iter)->nr);