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options.dat@ 6ff62c

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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 6ff62c was 6ff62c, checked in by Frederik Heber <heber@…>, 12 years ago

Added DoValenceOnly has new option to FragmentationAutomationAction.

this carries over to MPQCData, MPQCJob, MPQCFragmentController, and VMGFragmentController, that need to pass on the option.
Changes to MPQCData have been caught by increasing serialization version.
TESTFIX: Redid files for regression test AnalyseFragmentResults.

Property mode set to 100644

File size: 5.7 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"
[6ff62c]	64	DoValenceOnly "0"
[3493da]	65	element-db "./"
	66	elements "1"
	67	elements "1 8"
	68	end-step "1"
[9291d04]	69	ExcludeHydrogen "1"
[3493da]	70	fastparsing "1"
[531f27]	71	filename "test.exttypes"
[3493da]	72	fill-molecule "filler.xyz"
	73	fill-void "hydrogen.xyz"
	74	fill-void "water.data"
	75	fill-void "water.xyz"
[4882d5]	76	forces-file "test.forces"
[edecba]	77	fragment-executable "mpqc"
	78	fragment-jobs "Job00.in"
[3493da]	79	fragment-molecule "./"
[edecba]	80	fragment-path "test/"
[55e1bc]	81	fragment-resultfile "results.dat"
[065574]	82	grid-level "5"
[240c3e]	83	homology-file "homology.dat"
[3493da]	84	id-mapping "1"
	85	input "test.data"
[cd2591]	86	interpolation-degree "5"
[3493da]	87	interpolation-steps "9"
	88	keep-fixed-CenterOfMass "0"
	89	load "test.data"
	90	MaxDistance "-1"
	91	MDSteps "1"
[a88452]	92	mesh-offset "0.5,0.5,0.5"
	93	mesh-size "10,10,10"
	94	min-distance "1."
[3493da]	95	molecule-by-id "0"
[065574]	96	near-field-cells "3"
[3493da]	97	nonconvex-envelope "25"
	98	nonconvex-file "NonConvexEnvelope"
	99	nonconvex-file "nonconvexfile"
	100	offset "0"
	101	offset "1"
	102	order "2"
	103	output-file "emptybox_values.dat"
	104	output-file "hydrogenbox_values.dat"
	105	output-file "output-10.csv"
	106	output-file "output-20.csv"
	107	output-file "output-5.csv"
	108	output-file "output.csv"
	109	output-file "waterbox-mirrored_values.dat"
	110	output-file "waterbox_values.dat"
[072f0e]	111	output-as "store.conf"
	112	output-as "store.data"
	113	output-as "store.pdb"
	114	output-as "store.xyz"
	115	output-as "test.in"
[5ab796]	116	output-types "xyz"
	117	output-types "xyz mpqc"
[3493da]	118	parse-tremolo-potentials "argon.potentials"
	119	parse-tremolo-potentials "tensid.potentials"
[5ab796]	120	parser-parameters "mpqc"
	121	parser-parameters "psi3"
[3493da]	122	periodic "0"
	123	position "0 0 0"
	124	position "0 0 1"
	125	position "0 0 10"
	126	position "10 10 10"
	127	position "10. 10. 10."
	128	position "1 2 1"
	129	position "5.63 5.71 5.71"
	130	position "7.283585982 3.275186040 3.535886037"
	131	position "9.78 2.64 2.64"
[5ab796]	132	radius "20."
[3493da]	133	random-atom-displacement "0."
	134	random-molecule-displacement "0."
	135	random-number-distribution-parameters "max=20;"
	136	random-number-engine-parameters "seed=2;"
	137	repeat-box "1 1 1"
[ca331c]	138	reset 1
[3493da]	139	rotate-around-origin "180."
	140	rotate-around-origin "20."
	141	rotate-around-origin "360."
	142	rotate-around-origin "90."
	143	rotate-around-self "180."
	144	rotate-around-self "180"
	145	rotate-around-self "20."
	146	rotate-around-self "360."
	147	rotate-around-self "90."
	148	rotate-to-principal-axis-system ""
	149	save-adjacency "test.adj"
	150	save-bonds "test.bond"
	151	save-selected-atoms "testsave.xyz"
[531f27]	152	save-selected-atoms-as-exttypes "test.exttypes"
[3493da]	153	save-selected-molecules "testsave.xyz"
	154	save-temperature "test.ekin"
	155	scale-box "0.5 1. 0.9"
	156	select-atom-by-element "1"
	157	select-atom-by-element "4"
	158	select-atom-by-id "0"
[61c364]	159	select-atom-by-order "1"
[3493da]	160	select-atoms-inside-cuboid "10 10 10"
	161	select-atoms-inside-cuboid "2 2 2"
	162	select-atoms-inside-sphere "0.2"
	163	select-atoms-inside-sphere "10"
	164	select-atoms-inside-sphere "7."
	165	select-molecule-by-id "0"
	166	select-molecule-by-id "1"
	167	select-molecule-by-id "4"
	168	select-molecule-by-order "-1"
	169	select-molecule-by-order "1"
	170	select-molecule-by-order "-2"
	171	select-molecule-by-order "2"
	172	select-molecules-by-formula "C2H5(OH)"
	173	select-molecules-by-formula "C6H6"
	174	select-molecules-by-formula "H2O"
	175	select-molecules-by-name "water"
[663606]	176	select-shape-by-name "sphere2"
[edecba]	177	server-address "127.0.0.1"
	178	server-port "1026"
[c52e08]	179	set-boundary-conditions "Wrap, Wrap, Wrap"
[5ab796]	180	set-parser-parameters "basis = 4-31G"
	181	set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
	182	set-parser-parameters "maxiter = 499"
	183	set-parser-parameters "theory=CLKS"
	184	set-parser-parameters "wfn=scf"
	185	set-parser-parameters "ref=uhf"
[3493da]	186	set-output "tremolo"
	187	set-random-number-distribution "uniform_int"
	188	set-random-number-engine "lagged_fibonacci607"
	189	set-tremolo-atomdata "ATOMDATA type id x=3"
	190	set-world-time "10"
[6131d8]	191	shape-name "sphere1"
[d475a6]	192	shape-op "AND"
[4dc309]	193	shape-type "sphere"
[3493da]	194	skiplines "1"
	195	skiplines "2"
	196	start-step "0"
[5589e7e]	197	store-saturated-fragment "BondFragment"
[3a51bd]	198	stretch-bond "1.5"
[4dc309]	199	stretch "1. 1. 1."
[29ea65]	200	stretch-shapes "1. 2. 3."
[3493da]	201	suspend-in-water "1.0"
[345eda]	202	tesselation-radius "5."
[5ab796]	203	time-step-zero "0"
[3493da]	204	translate-atoms "1. 0. 0."
[0b5057]	205	translate-shapes "1. 2. 3."
[4dc309]	206	translation "0. 0. 0."
[3493da]	207	unselect-atom-by-element "1"
	208	unselect-atom-by-element "4"
	209	unselect-atom-by-id "0"
[61c364]	210	unselect-atom-by-order "1"
[3493da]	211	unselect-atoms-inside-cuboid "10 10 10"
	212	unselect-atoms-inside-cuboid "2 2 2"
	213	unselect-atoms-inside-sphere "10"
	214	unselect-atoms-inside-sphere "7."
	215	unselect-molecule-by-id "0"
	216	unselect-molecule-by-id "4"
	217	unselect-molecule-by-order "-1"
	218	unselect-molecule-by-order "1"
	219	unselect-molecule-by-order "-2"
	220	unselect-molecule-by-order "2"
	221	unselect-molecules-by-formula "C2H5(OH)"
	222	unselect-molecules-by-formula "C3H8"
	223	unselect-molecules-by-formula "C6H6"
	224	unselect-molecules-by-formula "H2O"
	225	unselect-molecules-by-name "water"
[2c004d]	226	unselect-shape-by-name "cube42"
[3493da]	227	verbose "3"
	228	verlet-integration "forces.dat"

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