Changes in src/moleculelist.cpp [aafd77:c27778]

File:

• src/moleculelist.cpp (modified) (13 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"
@@ -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);
 
@@ -731 +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;
@@ -892 +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);
 }
@@ -1020 +1017 @@
  * \param *out output stream for debugging
  * \param *reference reference molecule with the bond structure to be copied
- * \param &FragmentCounter Counter needed to address \a **ListOfLocalAtoms
- * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
+ * \param **&ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
  * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
  * \return true - success, false - faoilure
  */
-bool MoleculeLeafClass::FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList)
+bool MoleculeLeafClass::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
 {
   atom *OtherWalker = NULL;
@@ -1034 +1030 @@
   DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
   // fill ListOfLocalAtoms if NULL was given
-  if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->getAtomCount(), FreeList)) {
+  if (!FillListOfLocalAtoms(ListOfLocalAtoms, reference->getAtomCount(), FreeList)) {
     DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     return false;
@@ -1051 +1047 @@
       AtomNo = Father->nr; // global id of the current walker
       for (BondList::const_iterator Runner = Father->ListOfBonds.begin(); Runner != Father->ListOfBonds.end(); (++Runner)) {
-        OtherWalker = ListOfLocalAtoms[FragmentCounter][(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->nr]; // local copy of current bond partner of walker
+        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->nr]; // local copy of current bond partner of walker
         if (OtherWalker != NULL) {
           if (OtherWalker->nr > (*iter)->nr)
             Leaf->AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
         } else {
-          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->nr << "] is NULL!" << endl);
+          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->nr << "] is NULL!" << endl);
           status = false;
         }
@@ -1065 +1061 @@
   if ((FreeList) && (ListOfLocalAtoms != NULL)) {
     // free the index lookup list
-    delete[](ListOfLocalAtoms[FragmentCounter]);
-    if (FragmentCounter == 0) // first fragments frees the initial pointer to list
-      delete[](ListOfLocalAtoms);
+    delete[](ListOfLocalAtoms);
   }
   DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
@@ -1113 +1107 @@
 /** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
  * \param *out output stream from debugging
- * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
- * \param FragmentCounter counts the fragments as we move along the list
+ * \param **&ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
  * \param GlobalAtomCount number of atoms in the complete molecule
  * \param &FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
- * \return true - success, false - failure
- */
-bool MoleculeLeafClass::FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList)
+ * \return true - success, false - failure (ListOfLocalAtoms != NULL)
+ */
+bool MoleculeLeafClass::FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount, bool &FreeList)
 {
   bool status = true;
 
-  if (ListOfLocalAtoms == NULL) { // allocated initial pointer
-    // allocate and set each field to NULL
-    const int Counter = Count();
-    ASSERT(FragmentCounter < Counter, "FillListOfLocalAtoms: FragmenCounter greater than present fragments.");
-    ListOfLocalAtoms = new atom**[Counter];
-    if (ListOfLocalAtoms == NULL) {
-      FreeList = FreeList && false;
-      status = false;
-    }
-    for (int i=0;i<Counter;i++)
-      ListOfLocalAtoms[i] = NULL;
-  }
-
-  if ((ListOfLocalAtoms != NULL) && (ListOfLocalAtoms[FragmentCounter] == NULL)) { // allocate and fill list of this fragment/subgraph
-    status = status && Leaf->CreateFatherLookupTable(ListOfLocalAtoms[FragmentCounter], GlobalAtomCount);
+  if (ListOfLocalAtoms == NULL) { // allocate and fill list of this fragment/subgraph
+    status = status && Leaf->CreateFatherLookupTable(ListOfLocalAtoms, GlobalAtomCount);
     FreeList = FreeList && true;
-  }
+  } else
+    return false;
 
   return status;
@@ -1161 +1142 @@
   DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
   // fill ListOfLocalAtoms if NULL was given
-  if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->getAtomCount(), FreeList)) {
+  if (!FillListOfLocalAtoms(ListOfLocalAtoms[FragmentCounter], reference->getAtomCount(), FreeList)) {
     DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     return false;
@@ -1206 +1187 @@
     // free the index lookup list
     delete[](ListOfLocalAtoms[FragmentCounter]);
-    if (FragmentCounter == 0) // first fragments frees the initial pointer to list
-      delete[](ListOfLocalAtoms);
   }
   DoLog(1) && (Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl);