Ignore:
Timestamp:
Feb 17, 2012, 3:24:18 PM (13 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:
cdaae6
Parents:
ac5c36
git-author:
Frederik Heber <heber@…> (01/06/12 16:49:11)
git-committer:
Frederik Heber <heber@…> (02/17/12 15:24:18)
Message:

AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own IdPool.

  • molecule now also has an internal IdPool to be able to hand out unique ids, according to uniqueId policy.
  • new functions: molecule::changeAtomNr(), molecule::setAtomName()
  • molecule::erase() and ::insert() release and set the id (and the name).
  • molecule::setAtomName() uses getNr() with id increased by one.
  • AtomicInfo stores and sets ParticleInfo::Nr.
  • atom::changeNr() is similar to changeId() only for the molecule.
  • molecule::AddAtom() does not set the name anymore, is done by ::insert().
  • simplified molecule::doCountAtoms() a lot, no more naming of atoms.
  • SPEEDUP: This speeds up the GUI already a lot.
  • TESTFIX: changed regression test Tesselation/BigNonConvex due to different ordering of node ids (due to above), surface is still the same (checked).
File:
1 edited

Legend:

Unmodified
Added
Removed

  • tests/regression/Tesselation/BigNonConvex/post/NonConvexEnvelope.r3d

    rac5c36 r560bbe  
    33# All atoms as spheres
    442
     5  0.777562 -3.65286 1.28459     0.1     1. 1. 1.
     62
     7  0.904762 -3.62316 -0.490507   0.1     1. 1. 1.
     82
     9  1.91486 -2.53606 0.492393     0.1     1. 1. 1.
     102
     11  -0.587138 -0.162455 -0.830407         0.1     1. 1. 1.
     122
     13  -1.53704 -3.60006 0.497793    0.1     1. 1. 1.
     142
     15  -0.771938 -0.223855 1.47919   0.1     1. 1. 1.
     162
     17  -0.300138 -1.62946 2.47449    0.1     1. 1. 1.
     182
     19  2.17906 -1.47276 -0.873307    0.1     1. 1. 1.
     202
     21  -0.586638 -1.38326 -2.92321   0.1     1. 1. 1.
     222
     23  0.438062 -2.68776 -2.23921    0.1     1. 1. 1.
     242
     25  -2.47214 -1.59546 1.71589     0.1     1. 1. 1.
     262
     27  -1.64154 -3.70136 -1.80061    0.1     1. 1. 1.
     282
     29  -2.50954 -2.13946 -1.80561    0.1     1. 1. 1.
     302
     31  1.45166 0.153645 2.50359      0.1     1. 1. 1.
     322
     33  2.04886 -1.35716 1.79219      0.1     1. 1. 1.
     342
     35  1.14346 1.15214 0.320993      0.1     1. 1. 1.
     362
     37  1.75376 -0.319055 -2.99941    0.1     1. 1. 1.
     382
     39  1.01996 1.06104 -2.15101      0.1     1. 1. 1.
     402
     41  -1.71014 0.133845 0.126293    0.1     1. 1. 1.
     422
     43  -2.78704 -0.528955 -1.12651   0.1     1. 1. 1.
     442
     45  -4.76454 -1.89276 0.930293    0.1     1. 1. 1.
     462
     47  -4.18614 -2.49696 -0.640907   0.1     1. 1. 1.
     482
     49  -3.92214 -3.45776 0.834093    0.1     1. 1. 1.
     502
     51  3.60736 1.29684 -2.87381      0.1     1. 1. 1.
     522
     53  -4.75094 -0.0564554 0.311693  0.1     1. 1. 1.
     542
     55  -3.67414 0.606345 1.56439     0.1     1. 1. 1.
     562
     57  3.22946 1.45274 2.47189       0.1     1. 1. 1.
     582
     59  4.33006 2.26874 1.33549       0.1     1. 1. 1.
     602
     61  2.57536 2.54894 1.23139       0.1     1. 1. 1.
     622
     63  4.07696 -0.484155 2.10119     0.1     1. 1. 1.
     642
     65  3.61706 -1.46676 0.692693     0.1     1. 1. 1.
     662
     67  -2.88384 2.33404 -0.0290068   0.1     1. 1. 1.
     682
     69  -3.96064 1.67134 -1.28171     0.1     1. 1. 1.
     702
     71  5.67566 1.42984 -1.78291      0.1     1. 1. 1.
     722
     73  5.10266 2.74254 -0.715907     0.1     1. 1. 1.
     742
     75  6.16236 -0.927955 1.16559     0.1     1. 1. 1.
     762
     77  5.53756 -0.911555 -0.496607   0.1     1. 1. 1.
     782
     79  -4.84774 2.80654 1.40919      0.1     1. 1. 1.
     802
     81  5.68906 1.58194 1.24439       0.1     1. 1. 1.
     822
     83  -5.82304 4.61784 0.0247932    0.1     1. 1. 1.
     842
     85  -4.05744 4.53424 -0.184207    0.1     1. 1. 1.
     862
     87  -5.13424 3.87154 -1.43691     0.1     1. 1. 1.
     882
     89  -6.29174 0.967445 0.583993    0.1     1. 1. 1.
     902
     91  -7.12784 2.53484 0.473393     0.1     1. 1. 1.
     922
     93  -6.43904 1.78854 -0.988307    0.1     1. 1. 1.
     942
     95  7.55546 2.01984 -0.0120068    0.1     1. 1. 1.
     962
    597  0.939662 -3.01666 0.414493    0.1     1. 1. 1.
    6982
    … …  
    581502
    59151  7.32406 1.08574 0.0829932     0.1     1. 1. 1.
    60 2
    61   0.777562 -3.65286 1.28459     0.1     1. 1. 1.
    62 2
    63   0.904762 -3.62316 -0.490507   0.1     1. 1. 1.
    64 2
    65   1.91486 -2.53606 0.492393     0.1     1. 1. 1.
    66 2
    67   -0.587138 -0.162455 -0.830407         0.1     1. 1. 1.
    68 2
    69   -1.53704 -3.60006 0.497793    0.1     1. 1. 1.
    70 2
    71   -0.771938 -0.223855 1.47919   0.1     1. 1. 1.
    72 2
    73   -0.300138 -1.62946 2.47449    0.1     1. 1. 1.
    74 2
    75   2.17906 -1.47276 -0.873307    0.1     1. 1. 1.
    76 2
    77   -0.586638 -1.38326 -2.92321   0.1     1. 1. 1.
    78 2
    79   0.438062 -2.68776 -2.23921    0.1     1. 1. 1.
    80 2
    81   -2.47214 -1.59546 1.71589     0.1     1. 1. 1.
    82 2
    83   -1.64154 -3.70136 -1.80061    0.1     1. 1. 1.
    84 2
    85   -2.50954 -2.13946 -1.80561    0.1     1. 1. 1.
    86 2
    87   1.45166 0.153645 2.50359      0.1     1. 1. 1.
    88 2
    89   2.04886 -1.35716 1.79219      0.1     1. 1. 1.
    90 2
    91   1.14346 1.15214 0.320993      0.1     1. 1. 1.
    92 2
    93   1.75376 -0.319055 -2.99941    0.1     1. 1. 1.
    94 2
    95   1.01996 1.06104 -2.15101      0.1     1. 1. 1.
    96 2
    97   -1.71014 0.133845 0.126293    0.1     1. 1. 1.
    98 2
    99   -2.78704 -0.528955 -1.12651   0.1     1. 1. 1.
    100 2
    101   -4.76454 -1.89276 0.930293    0.1     1. 1. 1.
    102 2
    103   -4.18614 -2.49696 -0.640907   0.1     1. 1. 1.
    104 2
    105   -3.92214 -3.45776 0.834093    0.1     1. 1. 1.
    106 2
    107   3.60736 1.29684 -2.87381      0.1     1. 1. 1.
    108 2
    109   -4.75094 -0.0564554 0.311693  0.1     1. 1. 1.
    110 2
    111   -3.67414 0.606345 1.56439     0.1     1. 1. 1.
    112 2
    113   3.22946 1.45274 2.47189       0.1     1. 1. 1.
    114 2
    115   4.33006 2.26874 1.33549       0.1     1. 1. 1.
    116 2
    117   2.57536 2.54894 1.23139       0.1     1. 1. 1.
    118 2
    119   4.07696 -0.484155 2.10119     0.1     1. 1. 1.
    120 2
    121   3.61706 -1.46676 0.692693     0.1     1. 1. 1.
    122 2
    123   -2.88384 2.33404 -0.0290068   0.1     1. 1. 1.
    124 2
    125   -3.96064 1.67134 -1.28171     0.1     1. 1. 1.
    126 2
    127   5.67566 1.42984 -1.78291      0.1     1. 1. 1.
    128 2
    129   5.10266 2.74254 -0.715907     0.1     1. 1. 1.
    130 2
    131   6.16236 -0.927955 1.16559     0.1     1. 1. 1.
    132 2
    133   5.53756 -0.911555 -0.496607   0.1     1. 1. 1.
    134 2
    135   -4.84774 2.80654 1.40919      0.1     1. 1. 1.
    136 2
    137   5.68906 1.58194 1.24439       0.1     1. 1. 1.
    138 2
    139   -5.82304 4.61784 0.0247932    0.1     1. 1. 1.
    140 2
    141   -4.05744 4.53424 -0.184207    0.1     1. 1. 1.
    142 2
    143   -5.13424 3.87154 -1.43691     0.1     1. 1. 1.
    144 2
    145   -6.29174 0.967445 0.583993    0.1     1. 1. 1.
    146 2
    147   -7.12784 2.53484 0.473393     0.1     1. 1. 1.
    148 2
    149   -6.43904 1.78854 -0.988307    0.1     1. 1. 1.
    150 2
    151   7.55546 2.01984 -0.0120068    0.1     1. 1. 1.
    152152# All tesselation triangles
    1531538
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