Changeset 3738f0 for src/Actions/FragmentationAction

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/FragmentationAction

Files:

• CreateAdjacencyAction.cpp (modified) (1 diff)
• DepthFirstSearchAction.cpp (modified) (1 diff)
• FragmentationAction.cpp (modified) (2 diffs)
• SubgraphDissectionAction.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/CreateAdjacencyAction.cpp

@@ -58 +58 @@
   BondGraph *BG = World::getInstance().getBondGraph();
   ASSERT(BG != NULL, "FragmentationCreateAdjacencyAction: BondGraph is NULL.");
+  BG->SetMaxDistanceToMaxOfCovalentRadii(AtomSetMixin<std::vector<atom *> >(World::getInstance().getSelectedAtoms()));
   double BondDistance = BG->getMaxDistance();
   bool IsAngstroem = configuration->GetIsAngstroem();

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -52 +52 @@
   std::deque<bond *> *BackEdgeStack = NULL;
   std::deque<bond *> *LocalBackEdgeStack = NULL;
-  BondGraph *BG = World::getInstance().getBondGraph();
-  mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::getMinMaxDistance, BG);
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   if (Subgraphs != NULL) {

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -43 +43 @@
   clock_t start,end;
   molecule *mol = NULL;
-  config *configuration = World::getInstance().getConfig();
   int ExitFlag = 0;
 
@@ -55 +54 @@
     DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
     start = clock();
-    mol->CreateAdjacencyList(params.distance, configuration->GetIsAngstroem(), &BondGraph::getMinMaxDistance, World::getInstance().getBondGraph());
     DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
     if (mol->hasBondStructure()) {

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -50 +50 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
 
   // first create stuff for undo state
+  LOG(0, "STATUS: Creating undo state.");
   MolAtomList moleculelist;
   vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
@@ -66 +66 @@
 
   // 0a. remove all present molecules
+  LOG(0, "STATUS: Removing all present molecules.");
   MoleculeListClass *molecules = World::getInstance().getMolecules();
   for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
@@ -88 +89 @@
 
   // 1. create the bond structure of the single molecule
+  LOG(0, "STATUS: (Re-)constructing adjacency.");
   if (mol->getBondCount() == 0) {
     BondGraph *BG = World::getInstance().getBondGraph();
-    if (!BG->CreateAdjacencyForMolecule(mol)) {
-      World::getInstance().destroyMolecule(mol);
-      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
-      return Action::failure;
-    }
+    molecule::atomVector Set = mol->getAtomSet();
+    BG->CreateAdjacency(Set);
+//    if (mol->getBondCount() == 0) {
+//      World::getInstance().destroyMolecule(mol);
+//      ELOG(1, "There are no bonds.");
+//      return Action::failure;
+//    }
   }
 
   // 2. scan for connected subgraphs
+  LOG(0, "STATUS: Analysing adjacency graph.");
   MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
   std::deque<bond *> *BackEdgeStack = NULL;
@@ -111 +116 @@
 
   // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms
+  LOG(0, "STATUS: Creating molecules as connected subgraphs.");
   {
     {
@@ -152 +158 @@
 
   // 4. free Leafs
+  LOG(0, "STATUS: Done.");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
   while (MolecularWalker->next != NULL) {