Changeset 66fd49 for tests/regression/Filling

Timestamp:

Feb 3, 2011, 9:51:18 AM (14 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:

d6f886

Parents:

0b15bb

git-author:

Frederik Heber <heber@…> (12/30/10 20:52:17)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

Rewrite of FillVoidWithMoleculeAction.

FillVoidWithMoleculeAction:

• new parameter MinDistance and default value of 0.
• BUGFIX: filler is already created when parsing file, removed useless creation of it initially (also caused lots of confusion due to an "extra" molecule).
• Undo implemented, regression test inserted.
• Redo is somewhat hard to implement, as one would use performCall() if it only it would not retrieve its values from ValueStorage ...

FillVoidWithMolecule():

• filler is now the zeroth not the last molecule, marked by firstInsertion and firstInserter. Filler is removed if no molecules are filled.
• outsourced stuff into smaller functions
  • RandomizeMoleculePositions()
  • RemoveAtomsOutsideDomain()
  • isSpaceAroundPointVoid()
• removed FillIt to through every atom despite only CurrentPosition, indepedent of atom position, is checked.

TESTFIXES:

• Analysis/3: test.xyz changed because boundary is now 1.5 instead of 2.1 as 2.1 is not enough of molecules get filled in (and the filler already is).
• Analysis/3: tensid.data was actually lacking water at (0,0,0) which is after the rewrite present.

Location:

tests/regression/Filling/3/post

Files:

• empty.xyz (added)
• tensid.data (modified) (2 diffs)
• test.xyz (modified) (9 diffs)

tests/regression/Filling/3/post/tensid.data

@@ -57 +57 @@
 56      H12     SLES    1       4.755   0.669   7.942   H       54      0       0       0       9.000000e-02    
 57      H12     SLES    1       4.381   1.794   9.275   H       54      0       0       0       9.000000e-02    
-58      -       -       0       27      27      27.5043 O       59      60      0       0       0       
-59      -       -       0       27.7586 27      28.0086 H       58      0       0       0       0       
-60      -       -       0       27.7586 27      27      H       58      0       0       0       0       
+58      -       -       0       0       0       0.504284        O       59      60      0       0       0       
+59      -       -       0       0.758602        0       1.00857 H       58      0       0       0       0       
+60      -       -       0       0.758602        0       0       H       58      0       0       0       0       
 61      -       -       0       0       0       3.50428 O       62      63      0       0       0       
 62      -       -       0       0.758602        0       4.00857 H       61      0       0       0       0       
@@ -2964 +2964 @@
 2963    -       -       0       27.7586 27      25.0086 H       2962    0       0       0       0       
 2964    -       -       0       27.7586 27      24      H       2962    0       0       0       0       
+2965    -       -       0       27      27      27.5043 O       2966    2967    0       0       0       
+2966    -       -       0       27.7586 27      28.0086 H       2965    0       0       0       0       
+2967    -       -       0       27.7586 27      27      H       2965    0       0       0       0       

tests/regression/Filling/3/post/test.xyz

@@ -1 @@
-1004
-        Created by molecuilder on Sat Aug 28 07:59:41 2010
+1028
+        Created by molecuilder on Thu Dec 30 21:46:40 2010
 H       9.78209 2.64589 2.64589
 H       9.78209 2.64589 4.42589
@@ -12 +12 @@
 C       8.53279 4.15859 3.53589
 C       7.28359 3.27519 3.53589
-O       17.1429 17.1429 17.6471
-H       17.9015 17.1429 18.1514
-H       17.9015 17.1429 17.1429
+O       0       0       0.504284
+H       0.758602        0       1.00857
+H       0.758602        0       0
+O       0       0       3.36143
+H       0.758602        0       3.86571
+H       0.758602        0       2.85714
 O       0       0       6.21857
 H       0.758602        0       6.72285
@@ -156 +159 @@
 H       0.758602        17.1429 18.1514
 H       0.758602        17.1429 17.1429
+O       2.85714 0       0.504284
+H       3.61574 0       1.00857
+H       3.61574 0       0
 O       2.85714 0       3.36143
 H       3.61574 0       3.86571
@@ -324 +330 @@
 H       6.47289 2.85714 1.00857
 H       6.47289 2.85714 0
+O       5.71429 2.85714 6.21857
+H       6.47289 2.85714 6.72285
+H       6.47289 2.85714 5.71429
 O       5.71429 2.85714 9.07571
 H       6.47289 2.85714 9.58
@@ -339 +348 @@
 H       6.47289 5.71429 1.00857
 H       6.47289 5.71429 0
+O       5.71429 5.71429 3.36143
+H       6.47289 5.71429 3.86571
+H       6.47289 5.71429 2.85714
 O       5.71429 5.71429 6.21857
 H       6.47289 5.71429 6.72285
@@ -462 +474 @@
 H       9.33003 2.85714 1.00857
 H       9.33003 2.85714 0
+O       8.57143 2.85714 6.21857
+H       9.33003 2.85714 6.72285
+H       9.33003 2.85714 5.71429
 O       8.57143 2.85714 9.07571
 H       9.33003 2.85714 9.58
@@ -477 +492 @@
 H       9.33003 5.71429 1.00857
 H       9.33003 5.71429 0
+O       8.57143 5.71429 6.21857
+H       9.33003 5.71429 6.72285
+H       9.33003 5.71429 5.71429
 O       8.57143 5.71429 9.07571
 H       9.33003 5.71429 9.58
@@ -615 +633 @@
 H       12.1872 5.71429 1.00857
 H       12.1872 5.71429 0
+O       11.4286 5.71429 3.36143
+H       12.1872 5.71429 3.86571
+H       12.1872 5.71429 2.85714
 O       11.4286 5.71429 6.21857
 H       12.1872 5.71429 6.72285
@@ -1005 +1026 @@
 H       17.9015 17.1429 15.2943
 H       17.9015 17.1429 14.2857
+O       17.1429 17.1429 17.6471
+H       17.9015 17.1429 18.1514
+H       17.9015 17.1429 17.1429