Changeset 3738f0 for src/Actions/MoleculeAction

Timestamp:

Mar 1, 2011, 12:49:28 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:

0cbad2

Parents:

ce5f05

git-author:

Frederik Heber <heber@…> (02/26/11 00:10:05)

git-committer:

Frederik Heber <heber@…> (03/01/11 12:49:28)

Message:

Moved molecule::CreateAdjacencyList over to class BondGraph.

to make this possible we had to:

• enhance AtomSet such that individual const_ and iterator are templated.
• FIX: FragmentationCreateAdjacencyAction needs to call BondGraph::SetMaxDistanceToMaxOfCovalentRadii() before getMaxDistance() is valid.
• new function molecule::getAtomSet() which copies the internal atomSet to a vector AtomSetMixin and delivers. This is needed as PointCloudAdaptor needs a reference to a AtomSetMixin and we don't want to expose the internal set.

other changes:

• the following Actions do not create adjacency beforehand anymore:
  • DepthFirstSearchAction
  • MoleculeSaveAdjacencyAction
  • MoleculeSaveBondsAction
• changes to BondGraph:
  • removed CreateAdjacencyForMolecule()
  • removed SetMaxDistanceToMaxOfCovalentRadii()
  • new function CreateAdjacency on LinkedCell reference
• new BondGraph functions that work on AtomSetMixin reference: CreateAdjacency(), cleanAdjacencyList(), CorrectBondDegree(), resetBondDegree(), calculateBondDegree()

TESTFIXES:

• the regression test for all Actions mentioned above that don't create adjacency themselves anymore needed to be prepended with --select-all-atoms --create-adjacency.

Location:

src/Actions/MoleculeAction

Files:

• FillVoidWithMoleculeAction.cpp (modified) (1 diff)
• FillWithMoleculeAction.cpp (modified) (1 diff)
• SaveAdjacencyAction.cpp (modified) (1 diff)
• SaveBondsAction.cpp (modified) (1 diff)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -73 +73 @@
   molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
   filler->SetNameFromFilename(params.fillername.string().c_str());
-  World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(filler);
+  molecule::atomVector Set = filler->getAtomSet();
+  World::getInstance().getBondGraph()->CreateAdjacency(Set);
 
   // call routine

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -84 +84 @@
 //    filler->AddBond(first, third, 1);
 //    filler->AddBond(second, third, 1);
-  World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(filler);
+  molecule::atomVector Set = filler->getAtomSet();
+  World::getInstance().getBondGraph()->CreateAdjacency(Set);
 //    filler->SetNameFromFilename("water");
   // TODO: Remove the erasure of molecule when saving does not depend on them anymore.

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -49 +49 @@
     mol = iter->second;
     DoLog(0) && (Log() << Verbose(0) << "Storing adjacency to path " << params.adjacencyfile << "." << endl);
-    World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(mol);
     // TODO: sollte stream nicht filename benutzen, besser fuer unit test
     mol->StoreAdjacencyToFile(params.adjacencyfile.leaf(), params.adjacencyfile.branch_path().string());

src/Actions/MoleculeAction/SaveBondsAction.cpp

@@ -49 +49 @@
     mol = iter->second;
     DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << params.bondsfile << "." << endl);
-    World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(mol);
     // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
     mol->StoreBondsToFile(params.bondsfile.leaf(), params.bondsfile.branch_path().string());