Changeset 730d7a for src/Fragmentation/Fragmentation.cpp

Timestamp:

Oct 25, 2011, 12:08:03 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, Candidate_v1.7.0, 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:

851be8

Parents:

75363b

git-author:

Frederik Heber <heber@…> (10/20/11 10:34:17)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

New class AdaptivityMap and moved some functions from fragmentation_helpers into it.

File:

• src/Fragmentation/Fragmentation.cpp (modified) (3 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -28 +28 @@
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
+#include "Fragmentation/AdaptivityMap.hpp"
 #include "Fragmentation/fragmentation_helpers.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -464 +465 @@
       return false;
     }
-    map<int,KeySet> *IndexKeySetList = GlobalKeySetList->GraphToIndexedKeySet();
+    AdaptivityMap * IndexKeySetList = GlobalKeySetList->GraphToAdaptivityMap();
 
     // parse the EnergyPerFragment file
-    map<int, pair<double,int> > *AdaptiveCriteriaList = ScanAdaptiveFileIntoMap(path, *IndexKeySetList); // (Root No., (Value, Order)) !
+    std::map<int, std::pair<double,int> > *AdaptiveCriteriaList = IndexKeySetList->ScanAdaptiveFileIntoMap(path); // (Root No., (Value, Order)) !
     if (AdaptiveCriteriaList->empty()) {
       DoeLog(2) && (eLog()<< Verbose(2) << "Unable to parse file, incrementing all." << endl);
@@ -481 +482 @@
     }
     // then map back onto (Value, (Root Nr., Order)) (i.e. sorted by value to pick the highest ones)
-    map<double, pair<int,int> > *FinalRootCandidates = ReMapAdaptiveCriteriaListToValue(AdaptiveCriteriaList, mol);
+    std::map<double, std::pair<int,int> > *FinalRootCandidates = IndexKeySetList->ReMapAdaptiveCriteriaListToValue(AdaptiveCriteriaList, mol);
 
     // pick the ones still below threshold and mark as to be adaptively updated