Changeset df5b8c

Timestamp:

Feb 11, 2016, 8:07:11 AM (9 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:

2affd1

Parents:

2bfc5b

git-author:

Frederik Heber <heber@…> (12/30/15 10:16:33)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:07:11)

Message:

Replaced MoleculeListClass in ExportGraph by vector of molecules.

• AddHydrogenCorrection did never really worked and is dropped (was commented out in .._ToFiles anyway).

Location:

src/Fragmentation

Files:

• Exporters/ExportGraph.cpp (modified) (2 diffs)
• Exporters/ExportGraph.hpp (modified) (3 diffs)
• Exporters/ExportGraph_ToFiles.cpp (modified) (2 diffs)
• Exporters/ExportGraph_ToFiles.hpp (modified) (1 diff)
• Fragmentation.cpp (modified) (1 diff)

src/Fragmentation/Exporters/ExportGraph.cpp ¶

@@ -61 +61 @@
   const SaturatedFragment::GlobalSaturationPositions_t &_globalsaturationpositions) :
   TotalGraph(_graph),
-  BondFragments(World::getPointer()),
   treatment(_treatment),
   saturation(_saturation),
@@ -75 +74 @@
 {
   // remove all create molecules again from the World including their atoms
-  for (MoleculeList::iterator iter = BondFragments.ListOfMolecules.begin();
-      !BondFragments.ListOfMolecules.empty();
-      iter = BondFragments.ListOfMolecules.begin()) {
+  for (std::vector<molecule *>::iterator iter = BondFragments.begin();
+      !BondFragments.empty();
+      iter = BondFragments.begin()) {
     // remove copied atoms and molecule again
     molecule *mol = *iter;
-    BondFragments.ListOfMolecules.erase(iter);
+    BondFragments.erase(iter);
     removeAtomsinMolecule(mol);
   }

src/Fragmentation/Exporters/ExportGraph.hpp ¶

@@ -14 +14 @@
 #endif
 
+#include <vector>
+
 #include <boost/shared_ptr.hpp>
 
@@ -20 +22 @@
 #include "Fragmentation/Exporters/HydrogenPool.hpp"
 #include "Fragmentation/Exporters/SaturatedFragment.hpp"
-#include "MoleculeListClass.hpp"
 
 #include "Fragmentation/Graph.hpp"
@@ -97 +98 @@
   const Graph &TotalGraph;
   //!> internal list of created molecules
-  MoleculeListClass BondFragments;
+  std::vector<molecule *> BondFragments;
   //!> whether to always add already present hydrogens or not
   const enum HydrogenTreatment treatment;

src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp ¶

@@ -45 +45 @@
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
-#include "Fragmentation/SortIndex.hpp"
 #include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
@@ -149 +148 @@
   // store keysets file
   TotalGraph.StoreKeySetFile(prefix);
-
-  // store Hydrogen saturation correction file
-//  BondFragments.AddHydrogenCorrection(prefix);
 
   // restore orbital and Stop values

src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp ¶

@@ -19 +19 @@
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Exporters/ExportGraph.hpp"
-#include "MoleculeListClass.hpp"
+#include "Fragmentation/SortIndex.hpp"
 
 class ListOfLocalAtoms_t;

src/Fragmentation/Fragmentation.cpp ¶

@@ -261 +261 @@
   int RootNr = 0;
 
-  // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
+  // FragmentLowerOrdersList is a 2D-array of pointer to vector of molecule objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
   // with all needed lower orders that are subtracted, the other dimension is the BondOrder (i.e. from 1 to 5)
   NumMoleculesOfOrder = new int[UpgradeCount];