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options.dat@ f89b45

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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 f89b45 was f89b45, checked in by Frederik Heber <heber@…>, 13 years ago

Added Reaction CalculateBoundingBoxAction.

calculate bounding box via Box::getBoundingPlanes() of the current domain.
also added regression test Analysis/CalculateBoundingBox.

exporting std::vector<double> as return value.

had to add trick with exporting std::vector<double> to python with help from stackoverflow("does boost python support a function returning a vector, by ref or value?") answer. We construct a vec_item template class which exports getter/setter, append, ... functionality to python.
This ends in typedef doubleVec in namespace MoleCuilder::PythonTypes, while within the Reaction its just a typedef defined in the .def file.
this type had to be prefix with PythonType_ to make it distinguishable from the functions in dir(mol) for Python/AllActions regression test.
TESTFIX: Also we modified Python/AllActions regression test to go in a loop over each command, thus stdout and stderr can be uniquely associated to the very command that caused them. This makes debugging a lot easier ... for this purpose the dir(mol) and filtering was placed into new listcmds.py.

Property mode set to 100644

File size: 4.5 KB

Line
1	#key value
2	actionname "help"
3	add-atom "1"
4	add-empty-boundary ""
5	angle-x "0."
6	angle-x "0"
7	angle-y "0."
8	angle-y "0"
9	angle-z "0 "
10	angle-z "0."
11	angle-z "0"
12	axis "0 0 1"
13	axis "0 1 0"
14	axis "1 2 1"
15	bin-end "10"
16	bin-end "20"
17	bin-end "359"
18	bin-end "359.5"
19	bin-end "5"
20	bin-output-file "bin_output-10.csv"
21	bin-output-file "bin_output-20.csv"
22	bin-output-file "bin_output-5.csv"
23	bin-output-file "bin_output.csv"
24	bin-output-file "emptybox_histogram.dat"
25	bin-output-file "hydrogenbox_histogram.dat"
26	bin-output-file "waterbox_histogram.dat"
27	bin-output-file "waterbox-mirrored_histogram.dat"
28	bin-start "0"
29	bin-start "-0.5"
30	bin-start "10"
31	bin-start "5"
32	bin-width "1."
33	bond-file "bond.dat"
34	bond-table "table.dat"
35	calculate-bounding-box ""
36	calculate-molar-mass ""
37	center-in-box "10 0 0 10 0 10"
38	change-box "10 0 0 10 0 10"
39	change-element "H"
40	change-molname "water"
41	convex-file "convexfile"
42	copy-molecule "0"
43	default-molname "molname"
44	deltat "0.01"
45	depth-first-search "2."
46	distance "1.55"
47	distances "3.1 3.1 3.1"
48	distances "3.1 3.1 3.1"
49	distance-to-boundary "1."
50	distance-to-molecule "1.5"
51	distance-to-molecule "2.1"
52	domain-position "0. 0. 0."
53	domain-position "0 0 0"
54	domain-position "10. 10. 10."
55	DoRotate "0"
56	element-db "./"
57	elements "1"
58	elements "1 8"
59	end-step "1"
60	fastparsing "1"
61	fill-molecule "filler.xyz"
62	fill-void "hydrogen.xyz"
63	fill-void "water.data"
64	fill-void "water.xyz"
65	fragment-molecule "./"
66	id-mapping "1"
67	input "test.data"
68	interpolation-steps "9"
69	keep-fixed-CenterOfMass "0"
70	load "test.data"
71	MaxDistance "-1"
72	MDSteps "1"
73	molecule-by-id "0"
74	nonconvex-envelope "25"
75	nonconvex-file "NonConvexEnvelope"
76	nonconvex-file "nonconvexfile"
77	offset "0"
78	offset "1"
79	order "2"
80	output-file "emptybox_values.dat"
81	output-file "hydrogenbox_values.dat"
82	output-file "output-10.csv"
83	output-file "output-20.csv"
84	output-file "output-5.csv"
85	output-file "output.csv"
86	output-file "waterbox-mirrored_values.dat"
87	output-file "waterbox_values.dat"
88	output "store.conf"
89	output "store.data"
90	output "store.pdb"
91	output "store.xyz"
92	output "test.in"
93	parse-tremolo-potentials "argon.potentials"
94	parse-tremolo-potentials "tensid.potentials"
95	periodic "0"
96	position "0 0 0"
97	position "0 0 1"
98	position "0 0 10"
99	position "10 10 10"
100	position "10. 10. 10."
101	position "1 2 1"
102	position "5.63 5.71 5.71"
103	position "7.283585982 3.275186040 3.535886037"
104	position "9.78 2.64 2.64"
105	random-atom-displacement "0."
106	random-molecule-displacement "0."
107	random-number-distribution-parameters "max=20;"
108	random-number-engine-parameters "seed=2;"
109	repeat-box "1 1 1"
110	rotate-around-origin "180."
111	rotate-around-origin "20."
112	rotate-around-origin "360."
113	rotate-around-origin "90."
114	rotate-around-self "180."
115	rotate-around-self "180"
116	rotate-around-self "20."
117	rotate-around-self "360."
118	rotate-around-self "90."
119	rotate-to-principal-axis-system ""
120	save-adjacency "test.adj"
121	save-bonds "test.bond"
122	save-selected-atoms "testsave.xyz"
123	save-selected-molecules "testsave.xyz"
124	save-temperature "test.ekin"
125	scale-box "0.5 1. 0.9"
126	select-atom-by-element "1"
127	select-atom-by-element "4"
128	select-atom-by-id "0"
129	select-atoms-inside-cuboid "10 10 10"
130	select-atoms-inside-cuboid "2 2 2"
131	select-atoms-inside-sphere "0.2"
132	select-atoms-inside-sphere "10"
133	select-atoms-inside-sphere "7."
134	select-molecule-by-id "0"
135	select-molecule-by-id "1"
136	select-molecule-by-id "4"
137	select-molecule-by-order "-1"
138	select-molecule-by-order "1"
139	select-molecule-by-order "-2"
140	select-molecule-by-order "2"
141	select-molecules-by-formula "C2H5(OH)"
142	select-molecules-by-formula "C6H6"
143	select-molecules-by-formula "H2O"
144	select-molecules-by-name "water"
145	set-mpqc-parameters "basis = 4-31G"
146	set-mpqc-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
147	set-mpqc-parameters "maxiter = 499"
148	set-mpqc-parameters "theory=CLKS"
149	set-output "tremolo"
150	set-random-number-distribution "uniform_int"
151	set-random-number-engine "lagged_fibonacci607"
152	set-tremolo-atomdata "ATOMDATA type id x=3"
153	set-world-time "10"
154	skiplines "1"
155	skiplines "2"
156	start-step "0"
157	suspend-in-water "1.0"
158	translate-atoms "1. 0. 0."
159	unselect-atom-by-element "1"
160	unselect-atom-by-element "4"
161	unselect-atom-by-id "0"
162	unselect-atoms-inside-cuboid "10 10 10"
163	unselect-atoms-inside-cuboid "2 2 2"
164	unselect-atoms-inside-sphere "10"
165	unselect-atoms-inside-sphere "7."
166	unselect-molecule-by-id "0"
167	unselect-molecule-by-id "4"
168	unselect-molecule-by-order "-1"
169	unselect-molecule-by-order "1"
170	unselect-molecule-by-order "-2"
171	unselect-molecule-by-order "2"
172	unselect-molecules-by-formula "C2H5(OH)"
173	unselect-molecules-by-formula "C3H8"
174	unselect-molecules-by-formula "C6H6"
175	unselect-molecules-by-formula "H2O"
176	unselect-molecules-by-name "water"
177	verbose "3"
178	verlet-integration "forces.dat"

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