Changeset df793a for src/molecules.hpp

Timestamp:

Oct 9, 2008, 6:27:56 PM (17 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:

ad85c2

Parents:

ba4432

Message:

BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected subgraphs, AssignKeySetsToFragment() and FillBondStructureFromReference() memory cleanup corrected

+ molecule::DepthFirstSearchAnalysis() now just returns BackEdgeStack, not MinimumRingSize. CyclicStructureAnalysis() is called during FragmentMolecule(), after subgraphs bonds list have been filled by FillBondStructureFromReference().
+ new function molecule::PickLocalBackEdges(), as the BackEdgeStack returned by DepthFirstSearchAnalysis() co
ntains only global bonds, not the local ones for the subgraph, we have to step through it and pick the right
ones out.
+ molecule::FragmentMolecule() now calls molecule::CyclicStructureAnalysis() separately for each subgraph, along with a BackEdgeStack filled by PickLocalBackEdges(), and allocates&initialises MinimumRingSize array. Als
o AssignKeySetsToFragment() frees the LocalListOfAtoms now (FreeList=true), now longer after the following wh
ile
+ molecule::CyclicStructureAnalysis() takes a local BackEdgeStack and analysis the subgraphs cycles, returnin
g minimum ring size
+ MoleculeLeafClass::AssignKeySetsToFragment() now frees memory for ListOfLocalAtoms when FreeList is set. BUGFIX: test of first key was testing against ..->nr != -1. However, LocalListOfAtoms was not even initialised correctly to NULL, hence ...->nr pointed in some cases to nowhere. Now it test atom* against NULL.
+ MoleculeLeafClass::FillBondStructureFromReference() now frees memory for ListOfLocalAtoms when FreeList is set correctly (only free initial pointer when FragmentCounter == 0, also it was decreased not before but after freeing, hence we free'd the wrong list). Also, father replaced by GetTrueFather() (makes the function moregenerally useable, was not a bug).
+ ParseCommandLineOptions() option 'D': adapted to changes in DepthFirstSearchAnalysis() in a similar manner
to FragmentMolecule()
+ molecule::CountCyclicBonds() adapted but does not perform CyclicStructureAnalysis()
+ molecule::CreateAdjacencyList() counts the bonds that could not be brought to covalently corrected degree (i.e. the remaining ionic atoms)
+ molecule::CreateListOfBondsPerAtom() prints atom names and number, which is helpful as name contains global

and number contains local number (helped in finding above bugs)

+ CreateFatherLookupTable(): BUGFIX: LookupTable was not initialised to NULL (see above)

File:

• src/molecules.hpp (modified) (2 diffs)

src/molecules.hpp

@@ -284 +284 @@
   
   // Graph analysis
-  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, int *&MinimumRingSize);
+  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
   void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
+  bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
   bond * FindNextUnused(atom *vertex);
   void SetNextComponentNumber(atom *vertex, int nr);
@@ -378 +379 @@
   bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
   bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
-  bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, int &FragmentCounter, int GlobalAtomCount, bool &FreeList);
+  bool FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
   void TranslateIndicesToGlobalIDs(ofstream *out, Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
   int Count() const;