Context Navigation

options.dat@ bf1d1b

Visit:

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 bf1d1b was bf1d1b, checked in by Frederik Heber <heber@…>, 11 years ago

HomologyContainer now stores full struct as value to HomologyGraph key.

this structure does not only contain fragment and energy but also the sampled charge and potential distribution.
added version handling to HomologyContainer::value_t serialization.
added option "store-grids" to AnalyseFragmentationResultsAction.
TESTFIX: adapted HomologyContainerUnitTest such that new values are correctly constructed.

Property mode set to 100644

File size: 5.9 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"
[b6b21a]	62	DoPrintDebug "0"
[3493da]	63	DoRotate "0"
[5ab796]	64	DoSaturate "0"
[6ff62c]	65	DoValenceOnly "0"
[3493da]	66	element-db "./"
	67	elements "1"
	68	elements "1 8"
	69	end-step "1"
[9291d04]	70	ExcludeHydrogen "1"
[3493da]	71	fastparsing "1"
[531f27]	72	filename "test.exttypes"
[3493da]	73	fill-molecule "filler.xyz"
	74	fill-void "hydrogen.xyz"
	75	fill-void "water.data"
	76	fill-void "water.xyz"
[4882d5]	77	forces-file "test.forces"
[48d20d]	78	fragment-charges "1 1"
[edecba]	79	fragment-executable "mpqc"
	80	fragment-jobs "Job00.in"
[3493da]	81	fragment-molecule "./"
[edecba]	82	fragment-path "test/"
[55e1bc]	83	fragment-resultfile "results.dat"
[065574]	84	grid-level "5"
[3493da]	85	id-mapping "1"
	86	input "test.data"
[cd2591]	87	interpolation-degree "5"
[3493da]	88	interpolation-steps "9"
	89	keep-fixed-CenterOfMass "0"
	90	load "test.data"
	91	MaxDistance "-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"
[39986b]	103	output-as "store.conf"
	104	output-as "store.data"
	105	output-as "store.pdb"
	106	output-as "store.xyz"
	107	output-as "test.in"
	108	output-every-step "1"
[3493da]	109	output-file "emptybox_values.dat"
	110	output-file "hydrogenbox_values.dat"
	111	output-file "output-10.csv"
	112	output-file "output-20.csv"
	113	output-file "output-5.csv"
	114	output-file "output.csv"
	115	output-file "waterbox-mirrored_values.dat"
	116	output-file "waterbox_values.dat"
[5ab796]	117	output-types "xyz"
	118	output-types "xyz mpqc"
[d449a9]	119	parse-homologies "homology.dat"
[3493da]	120	parse-tremolo-potentials "argon.potentials"
	121	parse-tremolo-potentials "tensid.potentials"
[5ab796]	122	parser-parameters "mpqc"
	123	parser-parameters "psi3"
[3493da]	124	periodic "0"
	125	position "0 0 0"
	126	position "0 0 1"
	127	position "0 0 10"
	128	position "10 10 10"
	129	position "10. 10. 10."
	130	position "1 2 1"
	131	position "5.63 5.71 5.71"
	132	position "7.283585982 3.275186040 3.535886037"
	133	position "9.78 2.64 2.64"
[48d20d]	134	potential-charges "1 1"
[baccf6]	135	potential-file "test.potentials"
[a315e8]	136	potential-type "morse"
[5ab796]	137	radius "20."
[3493da]	138	random-atom-displacement "0."
	139	random-molecule-displacement "0."
	140	random-number-distribution-parameters "max=20;"
	141	random-number-engine-parameters "seed=2;"
	142	repeat-box "1 1 1"
[ca331c]	143	reset 1
[3493da]	144	rotate-around-origin "180."
	145	rotate-around-origin "20."
	146	rotate-around-origin "360."
	147	rotate-around-origin "90."
	148	rotate-around-self "180."
	149	rotate-around-self "180"
	150	rotate-around-self "20."
	151	rotate-around-self "360."
	152	rotate-around-self "90."
	153	rotate-to-principal-axis-system ""
	154	save-adjacency "test.adj"
	155	save-bonds "test.bond"
[d449a9]	156	save-homologies "homology.dat"
[3493da]	157	save-selected-atoms "testsave.xyz"
[531f27]	158	save-selected-atoms-as-exttypes "test.exttypes"
[3493da]	159	save-selected-molecules "testsave.xyz"
	160	save-temperature "test.ekin"
	161	scale-box "0.5 1. 0.9"
	162	select-atom-by-element "1"
	163	select-atom-by-element "4"
	164	select-atom-by-id "0"
[61c364]	165	select-atom-by-order "1"
[3493da]	166	select-atoms-inside-cuboid "10 10 10"
	167	select-atoms-inside-cuboid "2 2 2"
	168	select-atoms-inside-sphere "0.2"
	169	select-atoms-inside-sphere "10"
	170	select-atoms-inside-sphere "7."
	171	select-molecule-by-id "0"
	172	select-molecule-by-id "1"
	173	select-molecule-by-id "4"
	174	select-molecule-by-order "-1"
	175	select-molecule-by-order "1"
	176	select-molecule-by-order "-2"
	177	select-molecule-by-order "2"
	178	select-molecules-by-formula "C2H5(OH)"
	179	select-molecules-by-formula "C6H6"
	180	select-molecules-by-formula "H2O"
	181	select-molecules-by-name "water"
[663606]	182	select-shape-by-name "sphere2"
[edecba]	183	server-address "127.0.0.1"
	184	server-port "1026"
[c52e08]	185	set-boundary-conditions "Wrap, Wrap, Wrap"
[5ab796]	186	set-parser-parameters "basis = 4-31G"
	187	set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
	188	set-parser-parameters "maxiter = 499"
	189	set-parser-parameters "theory=CLKS"
	190	set-parser-parameters "wfn=scf"
	191	set-parser-parameters "ref=uhf"
[3493da]	192	set-output "tremolo"
	193	set-random-number-distribution "uniform_int"
	194	set-random-number-engine "lagged_fibonacci607"
	195	set-tremolo-atomdata "ATOMDATA type id x=3"
	196	set-world-time "10"
[6131d8]	197	shape-name "sphere1"
[d475a6]	198	shape-op "AND"
[4dc309]	199	shape-type "sphere"
[3493da]	200	skiplines "1"
	201	skiplines "2"
	202	start-step "0"
[39986b]	203	steps "5"
[bf1d1b]	204	store-grids "0"
[5589e7e]	205	store-saturated-fragment "BondFragment"
[3a51bd]	206	stretch-bond "1.5"
[4dc309]	207	stretch "1. 1. 1."
[29ea65]	208	stretch-shapes "1. 2. 3."
[3493da]	209	suspend-in-water "1.0"
[48d20d]	210	take-best-of "5"
[345eda]	211	tesselation-radius "5."
[5ab796]	212	time-step-zero "0"
[a504946]	213	training-file "training.dat"
[3493da]	214	translate-atoms "1. 0. 0."
[0b5057]	215	translate-shapes "1. 2. 3."
[4dc309]	216	translation "0. 0. 0."
[3493da]	217	unselect-atom-by-element "1"
	218	unselect-atom-by-element "4"
	219	unselect-atom-by-id "0"
[61c364]	220	unselect-atom-by-order "1"
[3493da]	221	unselect-atoms-inside-cuboid "10 10 10"
	222	unselect-atoms-inside-cuboid "2 2 2"
	223	unselect-atoms-inside-sphere "10"
	224	unselect-atoms-inside-sphere "7."
	225	unselect-molecule-by-id "0"
	226	unselect-molecule-by-id "4"
	227	unselect-molecule-by-order "-1"
	228	unselect-molecule-by-order "1"
	229	unselect-molecule-by-order "-2"
	230	unselect-molecule-by-order "2"
	231	unselect-molecules-by-formula "C2H5(OH)"
	232	unselect-molecules-by-formula "C3H8"
	233	unselect-molecules-by-formula "C6H6"
	234	unselect-molecules-by-formula "H2O"
	235	unselect-molecules-by-name "water"
[2c004d]	236	unselect-shape-by-name "cube42"
[3493da]	237	verbose "3"
	238	verlet-integration "forces.dat"

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

Original Format