Changes in src/moleculelist.cpp [389cc8:c27778]

File:

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

src/moleculelist.cpp

@@ -5 +5 @@
  */
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
 #include "Helpers/MemDebug.hpp"
 
 #include <cstring>
-
-#include <gsl/gsl_inline.h>
-#include <gsl/gsl_heapsort.h>
 
 #include "World.hpp"
@@ -26 +19 @@
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "verbose.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
+#include "memoryallocator.hpp"
 #include "periodentafel.hpp"
 #include "Helpers/Assert.hpp"
-#include "Matrix.hpp"
-#include "Box.hpp"
-#include "stackclass.hpp"
 
 #include "Helpers/Assert.hpp"
@@ -597 +587 @@
       periodentafel::const_iterator elemIter;
       for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
-        if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
+        if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
           for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
             if ((*atomIter)->type->getNumber() == (*elemIter).first) {
@@ -641 +631 @@
   int FragmentCounter = 0;
   ofstream output;
-  Matrix cell_size = World::getInstance().getDomain().getM();
-  Matrix cell_size_backup = cell_size;
-
+  double cell_size_backup[6];
+  double * const cell_size = World::getInstance().getDomain();
+
+  // backup cell_size
+  for (int i=0;i<6;i++)
+    cell_size_backup[i] = cell_size[i];
   // store the fragments as config and as xyz
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
@@ -681 +674 @@
     (*ListRunner)->CenterEdge(&BoxDimension);
     (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
+    int j = -1;
     for (int k = 0; k < NDIM; k++) {
+      j += k + 1;
       BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
-      cell_size.at(k,k) = BoxDimension[k] * 2.;
-    }
-    World::getInstance().setDomain(cell_size);
+      cell_size[j] = BoxDimension[k] * 2.;
+    }
     (*ListRunner)->Translate(&BoxDimension);
 
     // also calculate necessary orbitals
+    (*ListRunner)->CountElements(); // this is a bugfix, atoms should shoulds actually be added correctly to this fragment
     //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
 
@@ -730 +725 @@
 
   // restore cell_size
-  World::getInstance().setDomain(cell_size_backup);
+  for (int i=0;i<6;i++)
+    cell_size[i] = cell_size_backup[i];
 
   return result;
@@ -891 +887 @@
   // center at set box dimensions
   mol->CenterEdge(&center);
-  Matrix domain;
-  for(int i =0;i<NDIM;++i)
-    domain.at(i,i) = center[i];
-  World::getInstance().setDomain(domain);
+  World::getInstance().getDomain()[0] = center[0];
+  World::getInstance().getDomain()[1] = 0;
+  World::getInstance().getDomain()[2] = center[1];
+  World::getInstance().getDomain()[3] = 0;
+  World::getInstance().getDomain()[4] = 0;
+  World::getInstance().getDomain()[5] = center[2];
   insert(mol);
 }