Changeset bd6bfa for tests/regression/Molecules

Timestamp:

Jun 1, 2010, 7:28:15 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:

acf800

Parents:

1b9321

Message:

Fixes after first,last removal.

• BUGFIX: molecule::OutputGraphInfoPerBond() - had removal loop, not go-through-each-loop.
• BUGFIX: MoleculeListClass::~MoleculeListClass() - did falsely destroy molecules too although this is done by World.
• new function MoleculeListClass::erase() - handles signing off molecule as observer and removes from list.
• FIX: MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs()
  • all molecules are removed from MoleculeListClass and also from World.
  • all bonds are removed, by going through all atoms of World.
  • molecule::getAtomCount() - calls doCountAtoms() which re-numbers and -labels atoms. This confused stuff.
• TESTFIX: Molecules/6 and Molecules/7 had wrong (old) ordering in their test.conf

Location:

tests/regression/Molecules

Files:

• 6/post/test.conf (modified) (1 diff)
• 7/post/test.conf (modified) (1 diff)

tests/regression/Molecules/6/post/test.conf

@@ -71 +71 @@
 Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type2_1     10.782085945    4.275186040     4.535886037     0 # molecule nr 0
-Ion_Type2_2     9.532785963     5.158586027     4.535886037     0 # molecule nr 1
-Ion_Type2_3     8.283585982     4.275186040     4.535886037     0 # molecule nr 2
-Ion_Type1_1     10.782085945    3.645886050     3.645886050     0 # molecule nr 3
-Ion_Type1_2     10.782085945    3.645886050     5.425886024     0 # molecule nr 4
-Ion_Type1_3     11.672039608    4.904536878     4.535886037     0 # molecule nr 5
-Ion_Type1_4     9.532785963     5.787886018     3.645886050     0 # molecule nr 6
-Ion_Type1_5     9.532785963     5.787886018     5.425886024     0 # molecule nr 7
-Ion_Type1_6     7.393632318     4.904536877     4.535886037     0 # molecule nr 8
-Ion_Type1_7     8.283585982     3.645886050     3.645886050     0 # molecule nr 9
-Ion_Type1_8     8.283585982     3.645886050     5.425886024     0 # molecule nr 10
+Ion_Type1_1     10.782085945    3.645886050     3.645886050     0 # molecule nr 0
+Ion_Type1_2     10.782085945    3.645886050     5.425886024     0 # molecule nr 1
+Ion_Type1_3     11.672039608    4.904536878     4.535886037     0 # molecule nr 2
+Ion_Type1_4     9.532785963     5.787886018     3.645886050     0 # molecule nr 3
+Ion_Type1_5     9.532785963     5.787886018     5.425886024     0 # molecule nr 4
+Ion_Type1_6     7.393632318     4.904536877     4.535886037     0 # molecule nr 5
+Ion_Type1_7     8.283585982     3.645886050     3.645886050     0 # molecule nr 6
+Ion_Type1_8     8.283585982     3.645886050     5.425886024     0 # molecule nr 7
+Ion_Type2_1     10.782085945    4.275186040     4.535886037     0 # molecule nr 8
+Ion_Type2_2     9.532785963     5.158586027     4.535886037     0 # molecule nr 9
+Ion_Type2_3     8.283585982     4.275186040     4.535886037     0 # molecule nr 10

tests/regression/Molecules/7/post/test.conf

@@ -71 +71 @@
 Ion_Type2       3       6       1.0     3       3       12.01100000000  Carbon  C
 #Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)
-Ion_Type2_1     1.782085945     15.275186040    15.535886037    0 # molecule nr 0
-Ion_Type2_2     0.532785963     16.158586027    15.535886037    0 # molecule nr 1
-Ion_Type2_3     19.283585982    15.275186040    15.535886037    0 # molecule nr 2
-Ion_Type1_1     1.782085945     14.645886050    14.645886050    0 # molecule nr 3
-Ion_Type1_2     1.782085945     14.645886050    16.425886024    0 # molecule nr 4
-Ion_Type1_3     2.672039608     15.904536878    15.535886037    0 # molecule nr 5
-Ion_Type1_4     0.532785963     16.787886018    14.645886050    0 # molecule nr 6
-Ion_Type1_5     0.532785963     16.787886018    16.425886024    0 # molecule nr 7
-Ion_Type1_6     18.393632318    15.904536877    15.535886037    0 # molecule nr 8
-Ion_Type1_7     19.283585982    14.645886050    14.645886050    0 # molecule nr 9
-Ion_Type1_8     19.283585982    14.645886050    16.425886024    0 # molecule nr 10
+Ion_Type1_1     1.782085945     14.645886050    14.645886050    0 # molecule nr 0
+Ion_Type1_2     1.782085945     14.645886050    16.425886024    0 # molecule nr 1
+Ion_Type1_3     2.672039608     15.904536878    15.535886037    0 # molecule nr 2
+Ion_Type1_4     0.532785963     16.787886018    14.645886050    0 # molecule nr 3
+Ion_Type1_5     0.532785963     16.787886018    16.425886024    0 # molecule nr 4
+Ion_Type1_6     18.393632318    15.904536877    15.535886037    0 # molecule nr 5
+Ion_Type1_7     19.283585982    14.645886050    14.645886050    0 # molecule nr 6
+Ion_Type1_8     19.283585982    14.645886050    16.425886024    0 # molecule nr 7
+Ion_Type2_1     1.782085945     15.275186040    15.535886037    0 # molecule nr 8
+Ion_Type2_2     0.532785963     16.158586027    15.535886037    0 # molecule nr 9
+Ion_Type2_3     19.283585982    15.275186040    15.535886037    0 # molecule nr 10