Changeset 4b8630 for src/World.cpp

Timestamp:

Oct 25, 2011, 3:31:54 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:

be0c61

Parents:

4fc828

git-author:

Frederik Heber <heber@…> (02/19/11 00:09:43)

git-committer:

Frederik Heber <heber@…> (10/25/11 15:31:54)

Message:

World::setTime() now updates bond structure of system and related changes to DipoleAngularCorrelation.

• extended regression test Analysis/DipoleAngularCorrelation with xyz example whose bond structure is updated per time step.
• FIX: DepthFirstSearchAnalysis::operator() did not reset bonds to unused.
• FIX: DipoleAngularCorrelationAction has to work on atoms not molecules as the latter are subject to changes due to changing bond structure.
• FIX: DipoleAngularCorrelation() re-calculates current set of molecules from the select atoms and stores first atom in values file, not molecule name.

File:

• src/World.cpp (modified) (3 diffs)

src/World.cpp

@@ -25 +25 @@
 
 #include "Actions/ActionTraits.hpp"
-//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "Actions/ManipulateAtomsProcess.hpp"
 #include "atom.hpp"
@@ -37 +36 @@
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
 #include "Descriptors/SelectiveIterator_impl.hpp"
+#include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "Helpers/defs.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
@@ -137 +137 @@
     // set new time
     WorldTime::setTime(_step);
-    // re-instantiate bond structure
-    //FragmentationSubgraphDissection();
+    // TODO: removed when BondGraph creates the adjacency
+    // 1. remove all of World's molecules
+    for (MoleculeIterator iter = getMoleculeIter();
+        getMoleculeIter() != moleculeEnd();
+        iter = getMoleculeIter()) {
+      getMolecules()->erase(*iter);
+      destroyMolecule(*iter);
+    }
+    // 2. (re-)create bondgraph
+    AtomComposite Set = getAllAtoms();
+    BG->CreateAdjacency(Set);
+
+    // 3. scan for connected subgraphs => molecules
+    DepthFirstSearchAnalysis DFS;
+    DFS();
+    DFS.UpdateMoleculeStructure();
   }
 }