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

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"
@@ -19 +26 @@
 #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"
@@ -587 +597 @@
       periodentafel::const_iterator elemIter;
       for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
-        if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
+        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) {
@@ -631 +641 @@
   int FragmentCounter = 0;
   ofstream output;
-  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];
+  Matrix cell_size = World::getInstance().getDomain().getM();
+  Matrix cell_size_backup = cell_size;
+
   // store the fragments as config and as xyz
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
@@ -674 +681 @@
     (*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[j] = BoxDimension[k] * 2.;
-    }
+      cell_size.at(k,k) = BoxDimension[k] * 2.;
+    }
+    World::getInstance().setDomain(cell_size);
     (*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);
 
@@ -725 +730 @@
 
   // restore cell_size
-  for (int i=0;i<6;i++)
-    cell_size[i] = cell_size_backup[i];
+  World::getInstance().setDomain(cell_size_backup);
 
   return result;
@@ -887 +891 @@
   // center at set box dimensions
   mol->CenterEdge(&center);
-  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];
+  Matrix domain;
+  for(int i =0;i<NDIM;++i)
+    domain.at(i,i) = center[i];
+  World::getInstance().setDomain(domain);
   insert(mol);
 }