Changeset b32dbb for src/unittests

Timestamp:

May 29, 2010, 12:59:31 PM (15 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:

a7c344

Parents:

bfd839

git-author:

Frederik Heber <heber@…> (05/27/10 11:04:42)

git-committer:

Frederik Heber <heber@…> (05/29/10 12:59:31)

Message:

Fixes and changes to tesselation and concavity measurements.

Here, we implement two attempts for a concavity measure:

1. Measure concavity per point by looking at neighbouring triangles
   • BoundaryLineSet::CheckConvexityCriterion() split up (calculation of angle outsourced to CalculateConvexity())
   • CHANGE: CalculateConcavityPerBoundaryPoint() uses new concavity measure per BoundaryPointSet containing:
     • concavity per line uses angle instead of +/-1 for line, averaged by number of lines
     • also concavity over all attached triangles uses area of triangle and only in case of concavity, averaged by total area
   • new functions
     • BoundaryLineSet::CalculateConvexity() - calculates the angle between two triangles.
     • BoundaryLineSet::GetOtherTriangle() - for a closed line returns the other triangle for a given one
     • BoundaryTriangleSet::GetThirdLine() - for a given boundary point returns the line of the three which does not contain it (opposite line to a point)
     • CalculateAreaofGeneralTriangle() - calculates area of arbitrary triangle

2. Measure concavity by the distance to a more convex envelope (i.e. created with bigger sphere radius)
   • ParseCommandLineOptions(): case 'N' - two envelopes are created and the distance used as concavity measure via CalculateConstrictionPerBoundaryPoint()
   • FIX: CandidateForTesselation::CheckValidity() - checked against OptCenter instead of (*VRunner), animate_sphere line is printed as error, hence always visible
   • FIX: Tesselation::FindThirdPointForTesselation() - error if circumcenter is not the equidistant from each triangle node is now an error mesage
   • BUGFIX: Tesselation::RemoveDegeneratedTriangles() - would fail for more than two degenerate triangles to remove due to faulty loop construction and break instead of continue
   • BUGFIX: GetCenterofCircumcircle() - is numerically unstable (>1e-10) for big sphere radii, there are two other variants, not using angles.
   • FindNonConvexBorder() - RemoveDegeneratedTriangles() commented-out as runs into infinite loop for small radii (<5) for L-shaped cluster

Other unrelated stuff:

• DOCUFIX: CalculateVolumeofGeneralTetraeder() - four times "first vector"
• FIX: Tesselation::FindAllDegeneratedTriangles() - iterator integrated into for-loop statement

Signed-off-by: Frederik Heber <heber@…>

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