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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

Last change on this file since a275b3 was 9d613f, checked in by Frederik Heber <heber@…>, 13 years ago

FIX: RepeatBoxAction did not use CopyMolecule() but copied by hand. Kudos: Gregor Bollerhey.

this causes trouble with FormatParsers such as Tremolo... who have internally additional information stored.
extended regression tests Domain/RepeatBox with a test of a repeated .data file with "special" element names.

Kudos to Gregor Bollerhey for finding this bug.

Property mode set to 100644

File size: 3.4 KB

Line
1	# ATOMDATA Id type x=3 u=3 neighbors=4
2	1 O 7.36404 5 5.01 0 0 0 4 0 0 0
3	2 OS 5.50419 6.07129 5 0 0 0 4 5 0 0
4	3 OS 5.50419 3.92871 5.01 0 0 0 4 6 0 0
5	4 C 6.13037 5 5 0 0 0 1 2 3 0
6	5 CT 4.12159 5.74744 5.01 0 0 0 2 6 7 8
7	6 CT 4.12159 4.25256 5 0 0 0 3 5 9 10
8	7 H1 3.52075 6.15873 5.8045 0 0 0 5 0 0 0
9	8 H1 3.52075 6.15873 4.1955 0 0 0 5 0 0 0
10	9 H1 3.52075 3.84127 5.8045 0 0 0 6 0 0 0
11	10 H1 3.52075 3.84127 4.1955 0 0 0 6 0 0 0
12	11 O 7.36404 5 25.01 0 0 0 14 0 0 0
13	12 OS 5.50419 6.07129 25 0 0 0 14 15 0 0
14	13 OS 5.50419 3.92871 25.01 0 0 0 14 16 0 0
15	14 C 6.13037 5 25 0 0 0 11 12 13 0
16	15 CT 4.12159 5.74744 25.01 0 0 0 12 16 17 18
17	16 CT 4.12159 4.25256 25 0 0 0 13 15 19 20
18	17 H1 3.52075 6.15873 25.8045 0 0 0 15 0 0 0
19	18 H1 3.52075 6.15873 24.1955 0 0 0 15 0 0 0
20	19 H1 3.52075 3.84127 25.8045 0 0 0 16 0 0 0
21	20 H1 3.52075 3.84127 24.1955 0 0 0 16 0 0 0
22	21 O 7.36404 25 5.01 0 0 0 24 0 0 0
23	22 OS 5.50419 26.0713 5 0 0 0 24 25 0 0
24	23 OS 5.50419 23.9287 5.01 0 0 0 24 26 0 0
25	24 C 6.13037 25 5 0 0 0 21 22 23 0
26	25 CT 4.12159 25.7474 5.01 0 0 0 22 26 27 28
27	26 CT 4.12159 24.2526 5 0 0 0 23 25 29 30
28	27 H1 3.52075 26.1587 5.8045 0 0 0 25 0 0 0
29	28 H1 3.52075 26.1587 4.1955 0 0 0 25 0 0 0
30	29 H1 3.52075 23.8413 5.8045 0 0 0 26 0 0 0
31	30 H1 3.52075 23.8413 4.1955 0 0 0 26 0 0 0
32	31 O 7.36404 25 25.01 0 0 0 34 0 0 0
33	32 OS 5.50419 26.0713 25 0 0 0 34 35 0 0
34	33 OS 5.50419 23.9287 25.01 0 0 0 34 36 0 0
35	34 C 6.13037 25 25 0 0 0 31 32 33 0
36	35 CT 4.12159 25.7474 25.01 0 0 0 32 36 37 38
37	36 CT 4.12159 24.2526 25 0 0 0 33 35 39 40
38	37 H1 3.52075 26.1587 25.8045 0 0 0 35 0 0 0
39	38 H1 3.52075 26.1587 24.1955 0 0 0 35 0 0 0
40	39 H1 3.52075 23.8413 25.8045 0 0 0 36 0 0 0
41	40 H1 3.52075 23.8413 24.1955 0 0 0 36 0 0 0
42	41 O 27.364 5 5.01 0 0 0 44 0 0 0
43	42 OS 25.5042 6.07129 5 0 0 0 44 45 0 0
44	43 OS 25.5042 3.92871 5.01 0 0 0 44 46 0 0
45	44 C 26.1304 5 5 0 0 0 41 42 43 0
46	45 CT 24.1216 5.74744 5.01 0 0 0 42 46 47 48
47	46 CT 24.1216 4.25256 5 0 0 0 43 45 49 50
48	47 H1 23.5207 6.15873 5.8045 0 0 0 45 0 0 0
49	48 H1 23.5207 6.15873 4.1955 0 0 0 45 0 0 0
50	49 H1 23.5207 3.84127 5.8045 0 0 0 46 0 0 0
51	50 H1 23.5207 3.84127 4.1955 0 0 0 46 0 0 0
52	51 O 27.364 5 25.01 0 0 0 54 0 0 0
53	52 OS 25.5042 6.07129 25 0 0 0 54 55 0 0
54	53 OS 25.5042 3.92871 25.01 0 0 0 54 56 0 0
55	54 C 26.1304 5 25 0 0 0 51 52 53 0
56	55 CT 24.1216 5.74744 25.01 0 0 0 52 56 57 58
57	56 CT 24.1216 4.25256 25 0 0 0 53 55 59 60
58	57 H1 23.5207 6.15873 25.8045 0 0 0 55 0 0 0
59	58 H1 23.5207 6.15873 24.1955 0 0 0 55 0 0 0
60	59 H1 23.5207 3.84127 25.8045 0 0 0 56 0 0 0
61	60 H1 23.5207 3.84127 24.1955 0 0 0 56 0 0 0
62	61 O 27.364 25 5.01 0 0 0 64 0 0 0
63	62 OS 25.5042 26.0713 5 0 0 0 64 65 0 0
64	63 OS 25.5042 23.9287 5.01 0 0 0 64 66 0 0
65	64 C 26.1304 25 5 0 0 0 61 62 63 0
66	65 CT 24.1216 25.7474 5.01 0 0 0 62 66 67 68
67	66 CT 24.1216 24.2526 5 0 0 0 63 65 69 70
68	67 H1 23.5207 26.1587 5.8045 0 0 0 65 0 0 0
69	68 H1 23.5207 26.1587 4.1955 0 0 0 65 0 0 0
70	69 H1 23.5207 23.8413 5.8045 0 0 0 66 0 0 0
71	70 H1 23.5207 23.8413 4.1955 0 0 0 66 0 0 0
72	71 O 27.364 25 25.01 0 0 0 74 0 0 0
73	72 OS 25.5042 26.0713 25 0 0 0 74 75 0 0
74	73 OS 25.5042 23.9287 25.01 0 0 0 74 76 0 0
75	74 C 26.1304 25 25 0 0 0 71 72 73 0
76	75 CT 24.1216 25.7474 25.01 0 0 0 72 76 77 78
77	76 CT 24.1216 24.2526 25 0 0 0 73 75 79 80
78	77 H1 23.5207 26.1587 25.8045 0 0 0 75 0 0 0
79	78 H1 23.5207 26.1587 24.1955 0 0 0 75 0 0 0
80	79 H1 23.5207 23.8413 25.8045 0 0 0 76 0 0 0
81	80 H1 23.5207 23.8413 24.1955 0 0 0 76 0 0 0

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