Changeset 3d919e for src/molecules.hpp

Timestamp:

Jul 7, 2009, 6:49:32 AM (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:

260b2f

Parents:

ca2587

Message:

All of Saskia Metzler's changes so far to remove bugs from Tesselation (still not working)

Principle ideas:

• allow maximum of two triangles per triple of atomic indices to also tesselate "flat" areas
• detect degeneracies by having a list of candidates and adding multiple triangles (one for each) by an angle criteria

New functions:

• existsIntersection(): Checks per distance minimiser whether two lines intersect (for intersecting triangles)
• MinIntersectDistance(): Calculates the minimal distance between two lines (function to minimize)
• sortCandidates(): Sorting function for the third point candidates
• CheckPresenceOfTriangle(): For a triple of atomic indices, checks whether a triangle between them already exists (needed for allowing max of two triangles per triple)

File:

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

src/molecules.hpp

@@ -57 +57 @@
 #define PointPair pair < int, class BoundaryPointSet * >
 #define PointTestPair pair < PointMap::iterator, bool >
-
-#define LineMap map < int, class BoundaryLineSet * >
+#define CandidateList list <class CandidateForTesselation *>
+
+#define LineMap multimap < int, class BoundaryLineSet * >
 #define LinePair pair < int, class BoundaryLineSet * >
 #define LineTestPair pair < LineMap::iterator, bool >
@@ -71 +72 @@
 #define MoleculeList list <molecule *>
 #define MoleculeListTest pair <MoleculeList::iterator, bool>
+
+#define LinkedAtoms list <atom *>
 
 /******************************** Some small functions and/or structures **********************************/