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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 eee966 was eee966, checked in by Frederik Heber <heber@…>, 14 years ago

New Action FillVoidWithMoleculeAction.

in contrast to FillWithMoleculeAction we fill all empty space, not just outside of surfaces.
TEST: new tests in Filling/3 that fill with butane and a tenside micelle.
new function FillVoidWithMolecule().

Property mode set to 100644

File size: 3.3 KB

Rev	Line
[eee966]	1	# ATOMDATA Id name resName chainID x=3 Type neighbors=4 charge
	2	1 NA SLES 1 17.397 20.231 11.737 Na 0 0 0 0 1.000000e+00
	3	2 S SLES 1 16.282 18.88 14.208 S 3 4 5 6 1.330000e+00
	4	3 OS1 SLES 1 15.788 18.072 13.08 O 2 7 0 0 -2.800000e-01
	5	4 OS2 SLES 1 15.674 20.071 13.658 O 2 0 0 0 -6.500000e-01
	6	5 OS3 SLES 1 17.652 18.652 13.81 O 2 0 0 0 -6.500000e-01
	7	6 OS4 SLES 1 15.761 18.284 15.406 O 2 0 0 0 -6.500000e-01
	8	7 C2 SLES 1 15.018 16.938 13.128 C 3 8 9 10 -1.100000e-01
	9	8 H2A SLES 1 14.033 17.147 13.623 H 7 0 0 0 9.000000e-02
	10	9 H2B SLES 1 15.55 16.115 13.675 H 7 0 0 0 9.000000e-02
	11	10 C1 SLES 1 14.84 16.605 11.631 C 7 11 12 13 -1.000000e-02
	12	11 H1B SLES 1 14.337 17.448 11.09 H 10 0 0 0 9.000000e-02
	13	12 H1A SLES 1 15.828 16.408 11.147 H 10 0 0 0 9.000000e-02
	14	13 O1 SLES 1 14.087 15.49 11.279 O 10 14 0 0 -3.400000e-01
	15	14 C2 SLES 1 13.503 14.727 12.319 C 13 15 16 17 -1.000000e-02
	16	15 H2A SLES 1 12.804 15.366 12.931 H 14 0 0 0 9.000000e-02
	17	16 H2B SLES 1 14.281 14.306 12.998 H 14 0 0 0 9.000000e-02
	18	17 C1 SLES 1 12.786 13.897 11.193 C 14 18 19 20 -1.000000e-02
	19	18 H1B SLES 1 11.806 14.197 11.587 H 17 0 0 0 9.000000e-02
	20	19 H1A SLES 1 13.461 13.076 11.632 H 17 0 0 0 9.000000e-02
	21	20 O1 SLES 1 12.309 12.793 10.468 O 17 21 0 0 -3.400000e-01
	22	21 C1 SLES 1 11.479 11.857 11.141 C 20 22 23 24 -1.800000e-01
	23	22 H11 SLES 1 10.639 12.291 11.752 H 21 0 0 0 9.000000e-02
	24	23 H12 SLES 1 12.089 11.219 11.829 H 21 0 0 0 9.000000e-02
	25	24 C2 SLES 1 10.959 11.079 9.933 C 21 25 26 27 -1.800000e-01
	26	25 H21 SLES 1 10.299 11.683 9.265 H 24 0 0 0 9.000000e-02
	27	26 H22 SLES 1 11.775 10.623 9.321 H 24 0 0 0 9.000000e-02
	28	27 C3 SLES 1 10.166 10 10.552 C 24 28 29 30 -1.800000e-01
	29	28 H31 SLES 1 9.374 10.53 11.148 H 27 0 0 0 9.000000e-02
	30	29 H32 SLES 1 10.893 9.446 11.208 H 27 0 0 0 9.000000e-02
	31	30 C4 SLES 1 9.47 8.973 9.719 C 27 31 32 33 -1.800000e-01
	32	31 H41 SLES 1 8.721 9.443 9.035 H 30 0 0 0 9.000000e-02
	33	32 H42 SLES 1 10.193 8.397 9.095 H 30 0 0 0 9.000000e-02
	34	33 C5 SLES 1 8.845 8.159 10.86 C 30 34 35 36 -1.800000e-01
	35	34 H51 SLES 1 8.187 8.811 11.494 H 33 0 0 0 9.000000e-02
	36	35 H52 SLES 1 9.641 7.777 11.552 H 33 0 0 0 9.000000e-02
	37	36 C6 SLES 1 8.033 6.996 10.484 C 33 37 38 39 -1.800000e-01
	38	37 H61 SLES 1 7.025 7.151 10.956 H 36 0 0 0 9.000000e-02
	39	38 H62 SLES 1 8.483 6.114 11.014 H 36 0 0 0 9.000000e-02
	40	39 C7 SLES 1 7.888 6.707 8.985 C 36 40 41 42 -1.800000e-01
	41	40 H71 SLES 1 7.373 7.516 8.415 H 39 0 0 0 9.000000e-02
	42	41 H72 SLES 1 8.849 6.466 8.474 H 39 0 0 0 9.000000e-02
	43	42 C8 SLES 1 7.025 5.5 9.062 C 39 43 44 45 -1.800000e-01
	44	43 H81 SLES 1 6.09 5.813 9.606 H 42 0 0 0 9.000000e-02
	45	44 H82 SLES 1 7.598 4.741 9.667 H 42 0 0 0 9.000000e-02
	46	45 C9 SLES 1 6.583 4.808 7.82 C 42 46 47 48 -1.800000e-01
	47	46 H91 SLES 1 5.987 5.501 7.185 H 45 0 0 0 9.000000e-02
	48	47 H92 SLES 1 7.466 4.449 7.245 H 45 0 0 0 9.000000e-02
	49	48 C10 SLES 1 5.753 3.675 8.42 C 45 49 50 51 -1.800000e-01
	50	49 H10 SLES 1 4.924 4.1 9.048 H 48 0 0 0 9.000000e-02
	51	50 H10 SLES 1 6.392 3.056 9.107 H 48 0 0 0 9.000000e-02
	52	51 C11 SLES 1 5.134 2.748 7.425 C 48 52 53 54 -1.800000e-01
	53	52 H11 SLES 1 4.484 3.362 6.759 H 51 0 0 0 9.000000e-02
	54	53 H11 SLES 1 5.961 2.312 6.818 H 51 0 0 0 9.000000e-02
	55	54 C12 SLES 1 4.337 1.67 8.165 C 51 55 56 57 -2.700000e-01
	56	55 H12 SLES 1 3.268 1.727 7.882 H 54 0 0 0 9.000000e-02
	57	56 H12 SLES 1 4.755 0.669 7.942 H 54 0 0 0 9.000000e-02
	58	57 H12 SLES 1 4.381 1.794 9.275 H 54 0 0 0 9.000000e-02

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