source: tests/Python/AllActions/options.dat@ ff09f3

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 ff09f3 was d449a9, checked in by Frederik Heber <heber@…>, 11 years ago

Split off parsing and saving of homologies into new Actions.

  • Property mode set to 100644
File size: 5.9 KB
Line 
1#key value
2actionname "help"
3add-atom "1"
4add-empty-boundary ""
5Alignment-Axis "0,0,1"
6angle-x "0."
7angle-x "0"
8angle-y "0."
9angle-y "0"
10angle-z "0 "
11angle-z "0."
12angle-z "0"
13axis "0 0 1"
14axis "0 1 0"
15axis "1 2 1"
16bin-end "10"
17bin-end "20"
18bin-end "359"
19bin-end "359.5"
20bin-end "5"
21bin-output-file "bin_output-10.csv"
22bin-output-file "bin_output-20.csv"
23bin-output-file "bin_output-5.csv"
24bin-output-file "bin_output.csv"
25bin-output-file "emptybox_histogram.dat"
26bin-output-file "hydrogenbox_histogram.dat"
27bin-output-file "waterbox_histogram.dat"
28bin-output-file "waterbox-mirrored_histogram.dat"
29bin-start "0"
30bin-start "-0.5"
31bin-start "10"
32bin-start "5"
33bin-width "1."
34bond-file "bond.dat"
35bond-table "table.dat"
36calculate-bounding-box ""
37calculate-molar-mass ""
38center "10. 10. 10."
39center-in-box "10 0 0 10 0 10"
40change-bond-angle "100."
41change-box "10 0 0 10 0 10"
42change-element "H"
43change-molname "water"
44convex-file "convexfile"
45copy-molecule "0"
46count "12"
47create-micelle "200"
48default-molname "molname"
49deltat "0.01"
50depth-first-search "2."
51dipole-angular-correlation "H2O"
52distance "1.55"
53distances "3.1 3.1 3.1"
54distances "3.1 3.1 3.1"
55distance-to-boundary "1."
56distance-to-molecule "1.5"
57distance-to-molecule "2.1"
58domain-position "0. 0. 0."
59domain-position "0 0 0"
60domain-position "10. 10. 10."
61DoLongrange "0"
62DoPrintDebug "0"
63DoRotate "0"
64DoSaturate "0"
65DoValenceOnly "0"
66element-db "./"
67elements "1"
68elements "1 8"
69end-step "1"
70ExcludeHydrogen "1"
71fastparsing "1"
72filename "test.exttypes"
73fill-molecule "filler.xyz"
74fill-void "hydrogen.xyz"
75fill-void "water.data"
76fill-void "water.xyz"
77forces-file "test.forces"
78fragment-charges "1 1"
79fragment-executable "mpqc"
80fragment-jobs "Job00.in"
81fragment-molecule "./"
82fragment-path "test/"
83fragment-resultfile "results.dat"
84grid-level "5"
85id-mapping "1"
86input "test.data"
87interpolation-degree "5"
88interpolation-steps "9"
89keep-fixed-CenterOfMass "0"
90load "test.data"
91MaxDistance "-1"
92mesh-offset "0.5,0.5,0.5"
93mesh-size "10,10,10"
94min-distance "1."
95molecule-by-id "0"
96near-field-cells "3"
97nonconvex-envelope "25"
98nonconvex-file "NonConvexEnvelope"
99nonconvex-file "nonconvexfile"
100offset "0"
101offset "1"
102order "2"
103output-as "store.conf"
104output-as "store.data"
105output-as "store.pdb"
106output-as "store.xyz"
107output-as "test.in"
108output-every-step "1"
109output-file "emptybox_values.dat"
110output-file "hydrogenbox_values.dat"
111output-file "output-10.csv"
112output-file "output-20.csv"
113output-file "output-5.csv"
114output-file "output.csv"
115output-file "waterbox-mirrored_values.dat"
116output-file "waterbox_values.dat"
117output-types "xyz"
118output-types "xyz mpqc"
119parse-homologies "homology.dat"
120parse-tremolo-potentials "argon.potentials"
121parse-tremolo-potentials "tensid.potentials"
122parser-parameters "mpqc"
123parser-parameters "psi3"
124periodic "0"
125position "0 0 0"
126position "0 0 1"
127position "0 0 10"
128position "10 10 10"
129position "10. 10. 10."
130position "1 2 1"
131position "5.63 5.71 5.71"
132position "7.283585982 3.275186040 3.535886037"
133position "9.78 2.64 2.64"
134potential-charges "1 1"
135potential-file "test.potentials"
136potential-type "morse"
137radius "20."
138random-atom-displacement "0."
139random-molecule-displacement "0."
140random-number-distribution-parameters "max=20;"
141random-number-engine-parameters "seed=2;"
142repeat-box "1 1 1"
143reset 1
144rotate-around-origin "180."
145rotate-around-origin "20."
146rotate-around-origin "360."
147rotate-around-origin "90."
148rotate-around-self "180."
149rotate-around-self "180"
150rotate-around-self "20."
151rotate-around-self "360."
152rotate-around-self "90."
153rotate-to-principal-axis-system ""
154save-adjacency "test.adj"
155save-bonds "test.bond"
156save-homologies "homology.dat"
157save-selected-atoms "testsave.xyz"
158save-selected-atoms-as-exttypes "test.exttypes"
159save-selected-molecules "testsave.xyz"
160save-temperature "test.ekin"
161scale-box "0.5 1. 0.9"
162select-atom-by-element "1"
163select-atom-by-element "4"
164select-atom-by-id "0"
165select-atom-by-order "1"
166select-atoms-inside-cuboid "10 10 10"
167select-atoms-inside-cuboid "2 2 2"
168select-atoms-inside-sphere "0.2"
169select-atoms-inside-sphere "10"
170select-atoms-inside-sphere "7."
171select-molecule-by-id "0"
172select-molecule-by-id "1"
173select-molecule-by-id "4"
174select-molecule-by-order "-1"
175select-molecule-by-order "1"
176select-molecule-by-order "-2"
177select-molecule-by-order "2"
178select-molecules-by-formula "C2H5(OH)"
179select-molecules-by-formula "C6H6"
180select-molecules-by-formula "H2O"
181select-molecules-by-name "water"
182select-shape-by-name "sphere2"
183server-address "127.0.0.1"
184server-port "1026"
185set-boundary-conditions "Wrap, Wrap, Wrap"
186set-parser-parameters "basis = 4-31G"
187set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
188set-parser-parameters "maxiter = 499"
189set-parser-parameters "theory=CLKS"
190set-parser-parameters "wfn=scf"
191set-parser-parameters "ref=uhf"
192set-output "tremolo"
193set-random-number-distribution "uniform_int"
194set-random-number-engine "lagged_fibonacci607"
195set-tremolo-atomdata "ATOMDATA type id x=3"
196set-world-time "10"
197shape-name "sphere1"
198shape-op "AND"
199shape-type "sphere"
200skiplines "1"
201skiplines "2"
202start-step "0"
203steps "5"
204store-saturated-fragment "BondFragment"
205stretch-bond "1.5"
206stretch "1. 1. 1."
207stretch-shapes "1. 2. 3."
208suspend-in-water "1.0"
209take-best-of "5"
210tesselation-radius "5."
211time-step-zero "0"
212training-file "training.dat"
213translate-atoms "1. 0. 0."
214translate-shapes "1. 2. 3."
215translation "0. 0. 0."
216unselect-atom-by-element "1"
217unselect-atom-by-element "4"
218unselect-atom-by-id "0"
219unselect-atom-by-order "1"
220unselect-atoms-inside-cuboid "10 10 10"
221unselect-atoms-inside-cuboid "2 2 2"
222unselect-atoms-inside-sphere "10"
223unselect-atoms-inside-sphere "7."
224unselect-molecule-by-id "0"
225unselect-molecule-by-id "4"
226unselect-molecule-by-order "-1"
227unselect-molecule-by-order "1"
228unselect-molecule-by-order "-2"
229unselect-molecule-by-order "2"
230unselect-molecules-by-formula "C2H5(OH)"
231unselect-molecules-by-formula "C3H8"
232unselect-molecules-by-formula "C6H6"
233unselect-molecules-by-formula "H2O"
234unselect-molecules-by-name "water"
235unselect-shape-by-name "cube42"
236verbose "3"
237verlet-integration "forces.dat"
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