source: tests/regression/Domain/RepeatBox/pre/ec.potentials@ 4b10fd

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 Candidate_v1.7.0 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 4b10fd was 9d613f, checked in by Frederik Heber <heber@…>, 14 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: 7.6 KB
RevLine 
[9d613f]1particles {
2 particle: particle_type=O, element_name=O, sigma=2.96, epsilon=0.21, sigma14=2.96, epsilon14=0.21, mass=15.9994, free=3, charge=-0.6452;
3 particle: particle_type=OS, element_name=O, sigma=3, epsilon=0.17, sigma14=3, epsilon14=0.17, mass=15.9994, free=3, charge=-0.4684;
4 particle: particle_type=C, element_name=C, sigma=3.75, epsilon=0.105, sigma14=3.75, epsilon14=0.105, mass=12.0107, free=3, charge=1.0996;
5 particle: particle_type=CT, element_name=C, sigma=3.5, epsilon=0.066, sigma14=3.5, epsilon14=0.066, mass=12.0107, free=3, charge=0.033;
6 particle: particle_type=H1, element_name=H, sigma=2.5, epsilon=0.03, sigma14=2.5, epsilon14=0.03, mass=1.00794, free=3, charge=0.1041;
7 particle: particle_type=Li, element_name=Li, sigma=1.46, epsilon=0.191, sigma14=1.46, epsilon14=0.191, mass=6.941, free=3, charge=1;
8 particle: particle_type=B, element_name=B, sigma=3.581, epsilon=0.0949, sigma14=3.581, epsilon14=0.0949, mass=10.811, free=3, charge=0.9756;
9 particle: particle_type=F, element_name=F, sigma=3, epsilon=0.068, sigma14=3, epsilon14=0.068, mass=18.9984, free=3, charge=-0.4939;
10 };
11bonds {
12 bond: particle_type1=C, particle_type2=O, bond_type=harmonic, k_b=570, r_0=1.229, k=0, e_0=0;
13 bond: particle_type1=C, particle_type2=OS, bond_type=harmonic, k_b=320, r_0=1.41, k=0, e_0=0;
14 bond: particle_type1=OS, particle_type2=CT, bond_type=harmonic, k_b=320, r_0=1.41, k=0, e_0=0;
15 bond: particle_type1=CT, particle_type2=H1, bond_type=harmonic, k_b=340, r_0=1.09, k=0, e_0=0;
16 bond: particle_type1=CT, particle_type2=CT, bond_type=harmonic, k_b=310, r_0=1.526, k=0, e_0=0;
17 bond: particle_type1=B, particle_type2=F, bond_type=harmonic, k_b=289.72, r_0=1.39, k=0, e_0=0;
18 };
19angles {
20 angle: particle_type1=O, particle_type2=C, particle_type3=OS, angle_type=harmonic, k_th=80, theta_0=126, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
21 angle: particle_type1=CT, particle_type2=OS, particle_type3=C, angle_type=harmonic, k_th=60, theta_0=109.5, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
22 angle: particle_type1=CT, particle_type2=CT, particle_type3=H1, angle_type=harmonic, k_th=50, theta_0=109.5, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
23 angle: particle_type1=H1, particle_type2=CT, particle_type3=OS, angle_type=harmonic, k_th=50, theta_0=109.5, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
24 angle: particle_type1=CT, particle_type2=CT, particle_type3=OS, angle_type=harmonic, k_th=50, theta_0=109.5, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
25 angle: particle_type1=OS, particle_type2=C, particle_type3=OS, angle_type=harmonic, k_th=80, theta_0=126, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
26 angle: particle_type1=H1, particle_type2=CT, particle_type3=H1, angle_type=harmonic, k_th=35, theta_0=109.5, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
27 angle: particle_type1=F, particle_type2=B, particle_type3=F, angle_type=harmonic, k_th=50, theta_0=109.5, k_1=39.369026, k_2=21.653705, k=0, cos_theta_0=0, k_ub=16.052141, S_0=2.561;
28 };
29torsions {
30 torsion: particle_type1=OS, particle_type2=CT, particle_type3=CT, particle_type4=OS, torsion_type=cosine, k=0, a0=0, a1=0, a2=0, a3=0, a4=0, a5=0, mult=1, k_1=1.4, n_1=3, delta_1=0;
31 torsion: particle_type1=OS, particle_type2=CT, particle_type3=CT, particle_type4=H1, torsion_type=cosine, k=0, a0=0, a1=0, a2=0, a3=0, a4=0, a5=0, mult=1, k_1=1.4, n_1=3, delta_1=0;
32 torsion: particle_type1=H1, particle_type2=CT, particle_type3=CT, particle_type4=H1, torsion_type=cosine, k=0, a0=0, a1=0, a2=0, a3=0, a4=0, a5=0, mult=1, k_1=1.4, n_1=3, delta_1=0;
33 torsion: particle_type1=CT, particle_type2=CT, particle_type3=OS, particle_type4=C, torsion_type=cosine, k=0, a0=0, a1=0, a2=0, a3=0, a4=0, a5=0, mult=1, k_1=1.15, n_1=3, delta_1=0;
34 torsion: particle_type1=H1, particle_type2=CT, particle_type3=OS, particle_type4=C, torsion_type=cosine, k=0, a0=0, a1=0, a2=0, a3=0, a4=0, a5=0, mult=1, k_1=1.15, n_1=3, delta_1=0;
35 torsion: particle_type1=O, particle_type2=C, particle_type3=OS, particle_type4=CT, torsion_type=cosine, k=0, a0=0, a1=0, a2=0, a3=0, a4=0, a5=0, mult=1, k_1=10.5, n_1=2, delta_1=180;
36 };
37nonbonded_2body_potentials {
38 lennardjones: particle_type1=O, particle_type2=O, r_cut=12.5;
39 lennardjones: particle_type1=O, particle_type2=OS, r_cut=12.5;
40 lennardjones: particle_type1=O, particle_type2=C, r_cut=12.5;
41 lennardjones: particle_type1=O, particle_type2=CT, r_cut=12.5;
42 lennardjones: particle_type1=O, particle_type2=H1, r_cut=12.5;
43 lennardjones: particle_type1=OS, particle_type2=OS, r_cut=12.5;
44 lennardjones: particle_type1=OS, particle_type2=C, r_cut=12.5;
45 lennardjones: particle_type1=OS, particle_type2=CT, r_cut=12.5;
46 lennardjones: particle_type1=OS, particle_type2=H1, r_cut=12.5;
47 lennardjones: particle_type1=C, particle_type2=C, r_cut=12.5;
48 lennardjones: particle_type1=C, particle_type2=CT, r_cut=12.5;
49 lennardjones: particle_type1=C, particle_type2=H1, r_cut=12.5;
50 lennardjones: particle_type1=CT, particle_type2=CT, r_cut=12.5;
51 lennardjones: particle_type1=CT, particle_type2=H1, r_cut=12.5;
52 lennardjones: particle_type1=H1, particle_type2=H1, r_cut=12.5;
53 ljspline: particle_type1=O, particle_type2=O, r_cut=12.5, r_l=11;
54 ljspline: particle_type1=O, particle_type2=OS, r_cut=12.5, r_l=11;
55 ljspline: particle_type1=O, particle_type2=C, r_cut=12.5, r_l=11;
56 ljspline: particle_type1=O, particle_type2=CT, r_cut=12.5, r_l=11;
57 ljspline: particle_type1=O, particle_type2=H1, r_cut=12.5, r_l=11;
58 ljspline: particle_type1=OS, particle_type2=OS, r_cut=12.5, r_l=11;
59 ljspline: particle_type1=OS, particle_type2=C, r_cut=12.5, r_l=11;
60 ljspline: particle_type1=OS, particle_type2=CT, r_cut=12.5, r_l=11;
61 ljspline: particle_type1=OS, particle_type2=H1, r_cut=12.5, r_l=11;
62 ljspline: particle_type1=C, particle_type2=C, r_cut=12.5, r_l=11;
63 ljspline: particle_type1=C, particle_type2=CT, r_cut=12.5, r_l=11;
64 ljspline: particle_type1=C, particle_type2=H1, r_cut=12.5, r_l=11;
65 ljspline: particle_type1=CT, particle_type2=CT, r_cut=12.5, r_l=11;
66 ljspline: particle_type1=CT, particle_type2=H1, r_cut=12.5, r_l=11;
67 ljspline: particle_type1=H1, particle_type2=H1, r_cut=12.5, r_l=11;
68 ljspline: particle_type1=O, particle_type2=Li, r_cut=12.5, r_l=11;
69 ljspline: particle_type1=O, particle_type2=B, r_cut=12.5, r_l=11;
70 ljspline: particle_type1=O, particle_type2=F, r_cut=12.5, r_l=11;
71 ljspline: particle_type1=OS, particle_type2=Li, r_cut=12.5, r_l=11;
72 ljspline: particle_type1=OS, particle_type2=B, r_cut=12.5, r_l=11;
73 ljspline: particle_type1=OS, particle_type2=F, r_cut=12.5, r_l=11;
74 ljspline: particle_type1=C, particle_type2=Li, r_cut=12.5, r_l=11;
75 ljspline: particle_type1=C, particle_type2=B, r_cut=12.5, r_l=11;
76 ljspline: particle_type1=C, particle_type2=F, r_cut=12.5, r_l=11;
77 ljspline: particle_type1=CT, particle_type2=Li, r_cut=12.5, r_l=11;
78 ljspline: particle_type1=CT, particle_type2=B, r_cut=12.5, r_l=11;
79 ljspline: particle_type1=CT, particle_type2=F, r_cut=12.5, r_l=11;
80 ljspline: particle_type1=H1, particle_type2=Li, r_cut=12.5, r_l=11;
81 ljspline: particle_type1=H1, particle_type2=B, r_cut=12.5, r_l=11;
82 ljspline: particle_type1=H1, particle_type2=F, r_cut=12.5, r_l=11;
83 ljspline: particle_type1=Li, particle_type2=Li, r_cut=12.5, r_l=11;
84 ljspline: particle_type1=Li, particle_type2=B, r_cut=12.5, r_l=11;
85 ljspline: particle_type1=Li, particle_type2=F, r_cut=12.5, r_l=11;
86 ljspline: particle_type1=B, particle_type2=B, r_cut=12.5, r_l=11;
87 ljspline: particle_type1=B, particle_type2=F, r_cut=12.5, r_l=11;
88 ljspline: particle_type1=F, particle_type2=F, r_cut=12.5, r_l=11;
89 };
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