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options.dat@ 240c3e

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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 240c3e was 240c3e, checked in by Frederik Heber <heber@…>, 12 years ago

FragmentationAutomationAction now uses a file containing a serialized HomologyContainer.

the idea is that we append the calculated keysets als HomologyGraphs to the instance that is afterwards again serialized to file.
so far, we do not yet create the graphs, we only parse the file and write again the instance.
new parameter "homology-file".

Property mode set to 100644

File size: 5.5 KB

Rev	Line
[3493da]	1	#key value
	2	actionname "help"
	3	add-atom "1"
	4	add-empty-boundary ""
[cb7676]	5	Alignment-Axis "0,0,1"
[3493da]	6	angle-x "0."
	7	angle-x "0"
	8	angle-y "0."
	9	angle-y "0"
	10	angle-z "0 "
	11	angle-z "0."
	12	angle-z "0"
	13	axis "0 0 1"
	14	axis "0 1 0"
	15	axis "1 2 1"
	16	bin-end "10"
	17	bin-end "20"
	18	bin-end "359"
	19	bin-end "359.5"
	20	bin-end "5"
	21	bin-output-file "bin_output-10.csv"
	22	bin-output-file "bin_output-20.csv"
	23	bin-output-file "bin_output-5.csv"
	24	bin-output-file "bin_output.csv"
	25	bin-output-file "emptybox_histogram.dat"
	26	bin-output-file "hydrogenbox_histogram.dat"
	27	bin-output-file "waterbox_histogram.dat"
	28	bin-output-file "waterbox-mirrored_histogram.dat"
	29	bin-start "0"
	30	bin-start "-0.5"
	31	bin-start "10"
	32	bin-start "5"
	33	bin-width "1."
	34	bond-file "bond.dat"
	35	bond-table "table.dat"
[f89b45]	36	calculate-bounding-box ""
[55f299]	37	calculate-molar-mass ""
[2db053]	38	center "10. 10. 10."
[3493da]	39	center-in-box "10 0 0 10 0 10"
[8b886f]	40	change-bond-angle "100."
[3493da]	41	change-box "10 0 0 10 0 10"
	42	change-element "H"
	43	change-molname "water"
	44	convex-file "convexfile"
	45	copy-molecule "0"
[2db053]	46	count "12"
[5ab796]	47	create-micelle "200"
[3493da]	48	default-molname "molname"
	49	deltat "0.01"
	50	depth-first-search "2."
[5ab796]	51	dipole-angular-correlation "H2O"
[3493da]	52	distance "1.55"
	53	distances "3.1 3.1 3.1"
	54	distances "3.1 3.1 3.1"
	55	distance-to-boundary "1."
	56	distance-to-molecule "1.5"
	57	distance-to-molecule "2.1"
	58	domain-position "0. 0. 0."
	59	domain-position "0 0 0"
	60	domain-position "10. 10. 10."
[69c733]	61	DoLongrange "0"
[3493da]	62	DoRotate "0"
[5ab796]	63	DoSaturate "0"
[3493da]	64	element-db "./"
	65	elements "1"
	66	elements "1 8"
	67	end-step "1"
	68	fastparsing "1"
[531f27]	69	filename "test.exttypes"
[3493da]	70	fill-molecule "filler.xyz"
	71	fill-void "hydrogen.xyz"
	72	fill-void "water.data"
	73	fill-void "water.xyz"
[4882d5]	74	forces-file "test.forces"
[edecba]	75	fragment-executable "mpqc"
	76	fragment-jobs "Job00.in"
[3493da]	77	fragment-molecule "./"
[edecba]	78	fragment-path "test/"
[065574]	79	grid-level "5"
[240c3e]	80	homology-file "homology.dat"
[3493da]	81	id-mapping "1"
	82	input "test.data"
[cd2591]	83	interpolation-degree "5"
[3493da]	84	interpolation-steps "9"
	85	keep-fixed-CenterOfMass "0"
	86	load "test.data"
	87	MaxDistance "-1"
	88	MDSteps "1"
[a88452]	89	mesh-offset "0.5,0.5,0.5"
	90	mesh-size "10,10,10"
	91	min-distance "1."
[3493da]	92	molecule-by-id "0"
[065574]	93	near-field-cells "3"
[3493da]	94	nonconvex-envelope "25"
	95	nonconvex-file "NonConvexEnvelope"
	96	nonconvex-file "nonconvexfile"
	97	offset "0"
	98	offset "1"
	99	order "2"
	100	output-file "emptybox_values.dat"
	101	output-file "hydrogenbox_values.dat"
	102	output-file "output-10.csv"
	103	output-file "output-20.csv"
	104	output-file "output-5.csv"
	105	output-file "output.csv"
	106	output-file "waterbox-mirrored_values.dat"
	107	output-file "waterbox_values.dat"
[072f0e]	108	output-as "store.conf"
	109	output-as "store.data"
	110	output-as "store.pdb"
	111	output-as "store.xyz"
	112	output-as "test.in"
[5ab796]	113	output-types "xyz"
	114	output-types "xyz mpqc"
[3493da]	115	parse-tremolo-potentials "argon.potentials"
	116	parse-tremolo-potentials "tensid.potentials"
[5ab796]	117	parser-parameters "mpqc"
	118	parser-parameters "psi3"
[3493da]	119	periodic "0"
	120	position "0 0 0"
	121	position "0 0 1"
	122	position "0 0 10"
	123	position "10 10 10"
	124	position "10. 10. 10."
	125	position "1 2 1"
	126	position "5.63 5.71 5.71"
	127	position "7.283585982 3.275186040 3.535886037"
	128	position "9.78 2.64 2.64"
[5ab796]	129	radius "20."
[3493da]	130	random-atom-displacement "0."
	131	random-molecule-displacement "0."
	132	random-number-distribution-parameters "max=20;"
	133	random-number-engine-parameters "seed=2;"
	134	repeat-box "1 1 1"
[ca331c]	135	reset 1
[3493da]	136	rotate-around-origin "180."
	137	rotate-around-origin "20."
	138	rotate-around-origin "360."
	139	rotate-around-origin "90."
	140	rotate-around-self "180."
	141	rotate-around-self "180"
	142	rotate-around-self "20."
	143	rotate-around-self "360."
	144	rotate-around-self "90."
	145	rotate-to-principal-axis-system ""
	146	save-adjacency "test.adj"
	147	save-bonds "test.bond"
	148	save-selected-atoms "testsave.xyz"
[531f27]	149	save-selected-atoms-as-exttypes "test.exttypes"
[3493da]	150	save-selected-molecules "testsave.xyz"
	151	save-temperature "test.ekin"
	152	scale-box "0.5 1. 0.9"
	153	select-atom-by-element "1"
	154	select-atom-by-element "4"
	155	select-atom-by-id "0"
[61c364]	156	select-atom-by-order "1"
[3493da]	157	select-atoms-inside-cuboid "10 10 10"
	158	select-atoms-inside-cuboid "2 2 2"
	159	select-atoms-inside-sphere "0.2"
	160	select-atoms-inside-sphere "10"
	161	select-atoms-inside-sphere "7."
	162	select-molecule-by-id "0"
	163	select-molecule-by-id "1"
	164	select-molecule-by-id "4"
	165	select-molecule-by-order "-1"
	166	select-molecule-by-order "1"
	167	select-molecule-by-order "-2"
	168	select-molecule-by-order "2"
	169	select-molecules-by-formula "C2H5(OH)"
	170	select-molecules-by-formula "C6H6"
	171	select-molecules-by-formula "H2O"
	172	select-molecules-by-name "water"
[663606]	173	select-shape-by-name "sphere2"
[edecba]	174	server-address "127.0.0.1"
	175	server-port "1026"
[c52e08]	176	set-boundary-conditions "Wrap, Wrap, Wrap"
[5ab796]	177	set-parser-parameters "basis = 4-31G"
	178	set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
	179	set-parser-parameters "maxiter = 499"
	180	set-parser-parameters "theory=CLKS"
	181	set-parser-parameters "wfn=scf"
	182	set-parser-parameters "ref=uhf"
[3493da]	183	set-output "tremolo"
	184	set-random-number-distribution "uniform_int"
	185	set-random-number-engine "lagged_fibonacci607"
	186	set-tremolo-atomdata "ATOMDATA type id x=3"
	187	set-world-time "10"
[6131d8]	188	shape-name "sphere1"
[d475a6]	189	shape-op "AND"
[4dc309]	190	shape-type "sphere"
[3493da]	191	skiplines "1"
	192	skiplines "2"
	193	start-step "0"
[3a51bd]	194	stretch-bond "1.5"
[4dc309]	195	stretch "1. 1. 1."
[3493da]	196	suspend-in-water "1.0"
[345eda]	197	tesselation-radius "5."
[5ab796]	198	time-step-zero "0"
[3493da]	199	translate-atoms "1. 0. 0."
[4dc309]	200	translation "0. 0. 0."
[3493da]	201	unselect-atom-by-element "1"
	202	unselect-atom-by-element "4"
	203	unselect-atom-by-id "0"
[61c364]	204	unselect-atom-by-order "1"
[3493da]	205	unselect-atoms-inside-cuboid "10 10 10"
	206	unselect-atoms-inside-cuboid "2 2 2"
	207	unselect-atoms-inside-sphere "10"
	208	unselect-atoms-inside-sphere "7."
	209	unselect-molecule-by-id "0"
	210	unselect-molecule-by-id "4"
	211	unselect-molecule-by-order "-1"
	212	unselect-molecule-by-order "1"
	213	unselect-molecule-by-order "-2"
	214	unselect-molecule-by-order "2"
	215	unselect-molecules-by-formula "C2H5(OH)"
	216	unselect-molecules-by-formula "C3H8"
	217	unselect-molecules-by-formula "C6H6"
	218	unselect-molecules-by-formula "H2O"
	219	unselect-molecules-by-name "water"
[2c004d]	220	unselect-shape-by-name "cube42"
[3493da]	221	verbose "3"
	222	verlet-integration "forces.dat"

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