Changeset c6123b

Timestamp:

Mar 2, 2011, 9:53:07 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

99752a

Parents:

341f22

git-author:

Frederik Heber <heber@…> (02/25/11 15:22:51)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:07)

Message:

Moved FillListOfLocalAtoms() from MoleculeLeafClass to molecule.

Location:

src

Files:

• molecule.hpp (modified) (2 diffs)
• molecule_graph.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (3 diffs)

src/molecule.hpp

@@ -228 +228 @@
   // Recognize doubly appearing molecules in a list of them
   int * GetFatherSonAtomicMap(molecule *OtherMolecule);
+  bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount);
 
   // Output routines.
@@ -302 +303 @@
   bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
   bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
-  bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount, bool &FreeList);
   void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
   int Count() const;

src/molecule_graph.cpp

@@ -1379 +1379 @@
   return true;
 }
+
+/** 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 GlobalAtomCount number of atoms in the complete molecule
+ * \return true - success, false - failure (ListOfLocalAtoms != NULL)
+ */
+bool molecule::FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount)
+{
+  bool status = true;
+
+  if (ListOfLocalAtoms == NULL) { // allocate and fill list of this fragment/subgraph
+    status = status && CreateFatherLookupTable(ListOfLocalAtoms, GlobalAtomCount);
+  } else
+    return false;
+
+  return status;
+}
+

src/moleculelist.cpp

@@ -794 +794 @@
   DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
   // fill ListOfLocalAtoms if NULL was given
-  if (!FillListOfLocalAtoms(ListOfLocalAtoms, reference->getAtomCount(), FreeList)) {
+  if (!Leaf->FillListOfLocalAtoms(ListOfLocalAtoms, reference->getAtomCount())) {
     DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     return false;
@@ -871 +871 @@
 };
 
-/** 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 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 (ListOfLocalAtoms != NULL)
- */
-bool MoleculeLeafClass::FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount, bool &FreeList)
-{
-  bool status = true;
-
-  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;
-};
-
 /** The indices per keyset are compared to the respective father's Atom::Nr in each subgraph and thus put into \a **&FragmentList.
  * \param *out output stream fro debugging
@@ -908 +888 @@
   DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
   // fill ListOfLocalAtoms if NULL was given
-  if (!FillListOfLocalAtoms(ListOfLocalAtoms[FragmentCounter], reference->getAtomCount(), FreeList)) {
+  if (!Leaf->FillListOfLocalAtoms(ListOfLocalAtoms[FragmentCounter], reference->getAtomCount())) {
     DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     return false;