Changeset fcc9b0 for src/molecules.cpp

Timestamp:

Jul 27, 2009, 2:53:57 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:

a567c3

Parents:

3c4f04

Message:

FIX: DetermineCenterOfAll() did point in wrong direction, convex envelope working again, but algorithm is not stable

• molecule::DetermineCenterOfAll() center was the sum of all scaled by -1/Number instead of 1/Number. This was corrected for in the code elsewhere. Now, it returns the correct center and where it's elsewhere called we subtract instead of add
• Tesselation::TesselateOnBoundary() does now something meaningful. The NormalVector for the starting triangle could not be constructed, as we lacked the initial normal vector. It is however easy to construct from the center of all and the center of the starting triangle. However, the algorithm is faulty for 1_2_dimethylethane.
• GetBoundaryPoints() - as we do not translate to center of gravity anymore, we have to subtract the center of all. Otherwise the radial method for determining boundary points does not work.

Is not yet working.

File:

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

src/molecules.cpp

@@ -739 +739 @@
 };
 
-/** Returns vector pointing to center of gravity.
+/** Returns vector pointing to center of all atoms.
  * \param *out output stream for debugging
- * \return pointer to center of gravity vector
+ * \return pointer to center of all vector
  */
 Vector * molecule::DetermineCenterOfAll(ofstream *out)
@@ -759 +759 @@
       a->AddVector(&tmp);
     }
-    a->Scale(-1./Num); // divide through total mass (and sign for direction)
+    a->Scale(1./Num); // divide through total mass (and sign for direction)
   }
   //cout << Verbose(1) << "Resulting center of gravity: ";