Changeset d410e25 for src/Actions/FragmentationAction

Timestamp:

May 18, 2016, 10:02:07 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, 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_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, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

70aeed

Parents:

3004d2

git-author:

Frederik Heber <heber@…> (03/07/16 16:05:37)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:07)

Message:

Interfragmenter now access singleton AtomFragmentsMap.

• i.e. we do not instantiate the map ourselves but assume that it has been filled elsewhere. We only receive a Graph ("TotalGraph") in order to add the additional fragments to it.
• FragmentationAction fills the AtomFragmentsMap already before calling interfragmenter.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -254 +254 @@
   }
 
+  // store graph internally
+  AtomFragmentsMap &atomfragments = AtomFragmentsMap::getInstance();
+  atomfragments.clear();
+  atomfragments.insert(TotalGraph);
+
   // now add interfragments
   if (params.InterOrder.get() != 0) {
@@ -262 +267 @@
         params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
     const double UpperBound = std::max(10., params.distance.get());
-    Interfragmenter fragmenter(TotalGraph);
+    Interfragmenter fragmenter;
 
     // check the largest Rcut that causes no additional inter-fragments
@@ -273 +278 @@
 
     // then add fragments
-    fragmenter(params.InterOrder.get(), params.distance.get(), treatment);
+    fragmenter(TotalGraph, params.InterOrder.get(), params.distance.get(), treatment);
 
     LOG(0, "STATUS: There are now " << TotalGraph.size() << " fragments after interfragmenting.");
   }
-
-  // store graph internally
-  AtomFragmentsMap &atomfragments = AtomFragmentsMap::getInstance();
+  // TODO: When insert only adds and replaces if already present, no clear needed
   atomfragments.clear();
   atomfragments.insert(TotalGraph);