Changeset 99593f for src/molecule_graph.cpp

Timestamp:

Nov 4, 2009, 5:34:05 PM (16 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:

7ea9e6

Parents:

c9bce3e

Message:

Extension to the periodic boundary case for analysis_correlation.cpp

• Distance() -> PeriodicDistance(): PairCorrelation(), CorrelationToPoint(), CorrelationToSurface()
• CorrelationToSurface() - goes through periodic cells given by a ranges variable and puts into map as well.
• const: ReturnFullMatrixforSymmetric() and InverseMatrix() now have const * const parameter
• InverseMatrix() shifted from class Vector into helpers.cpp
• adapted due to InverseMatrix(): molecule::CenterInBox(), molecule::BoundInBox(), molecule::TranslatePeriodically()
• new function: RDET3(), RDET2() (former #define's)
• FIX: molecule::CorrectBondDegree() would loop eternally, if bonds cannot be fully corrected.
• FIX for NULL return: Tesselation::FindClosestTrianglesToPoint(), Tesselation::GetCircleOfConnectedPoints()
• FIX: Vector::DistanceToPlane() - did not give correct sign before according to PlaneNormal orientation

other stuff:

• less output: BondedParticle::CorrectBondDegree(), molecule::CyclicStructureAnalysis()

File:

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

src/molecule_graph.cpp

@@ -221 +221 @@
 int molecule::CorrectBondDegree(ofstream *out) const
 {
-  int No = 0;
+  int No = 0, OldNo = -1;
 
   if (BondCount != 0) {
     *out << Verbose(1) << "Correcting Bond degree of each bond ... " << endl;
     do {
+      OldNo = No;
       No = SumPerAtom(&atom::CorrectBondDegree, out);
-    } while (No);
+    } while (OldNo != No);
     *out << " done." << endl;
   } else {
@@ -418 +419 @@
   if (!DFS.BackStepping) { // coming from (8) want to go to (3)
     // (9) remove all from stack till Walker (including), these and Root form a component
-    DFS.AtomStack->Output(out);
+    //DFS.AtomStack->Output(out);
     mol->SetNextComponentNumber(DFS.Root, DFS.ComponentNumber);
     *out << Verbose(3) << "(9) Root[" << DFS.Root->Name << "]'s Component is " << DFS.ComponentNumber << "." << endl;
@@ -881 +882 @@
   InitializeBFSAccounting(out, BFS, AtomCount);
 
-  *out << Verbose(1) << "Back edge list - ";
-  BackEdgeStack->Output(out);
+  //*out << Verbose(1) << "Back edge list - ";
+  //BackEdgeStack->Output(out);
 
   *out << Verbose(1) << "Analysing cycles ... " << endl;