source: tests/Python/AllActions/options.dat@ 69c733

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 69c733 was 69c733, checked in by Frederik Heber <heber@…>, 12 years ago

Added second part to FragmentationAutomationAction that calculates long-range part.

  • we create VMGJobs, as of now with a lot of 0 as sampled_grid.
  • added HAVE_VMG to compile on VMGJob only if vmg is available.
  • new option DoLongrange to FragmentationAutomationAction to deactivate long-range calculations by default.
  • Property mode set to 100644
File size: 5.2 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-box "10 0 0 10 0 10"
41change-element "H"
42change-molname "water"
43convex-file "convexfile"
44copy-molecule "0"
45count "12"
46create-micelle "200"
47default-molname "molname"
48deltat "0.01"
49depth-first-search "2."
50dipole-angular-correlation "H2O"
51distance "1.55"
52distances "3.1 3.1 3.1"
53distances "3.1 3.1 3.1"
54distance-to-boundary "1."
55distance-to-molecule "1.5"
56distance-to-molecule "2.1"
57domain-position "0. 0. 0."
58domain-position "0 0 0"
59domain-position "10. 10. 10."
60DoLongrange "0"
61DoRotate "0"
62DoSaturate "0"
63element-db "./"
64elements "1"
65elements "1 8"
66end-step "1"
67fastparsing "1"
68filename "test.exttypes"
69fill-molecule "filler.xyz"
70fill-void "hydrogen.xyz"
71fill-void "water.data"
72fill-void "water.xyz"
73fragment-executable "mpqc"
74fragment-jobs "Job00.in"
75fragment-molecule "./"
76fragment-path "test/"
77id-mapping "1"
78input "test.data"
79interpolation-steps "9"
80keep-fixed-CenterOfMass "0"
81load "test.data"
82MaxDistance "-1"
83MDSteps "1"
84mesh-offset "0.5,0.5,0.5"
85mesh-size "10,10,10"
86min-distance "1."
87molecule-by-id "0"
88nonconvex-envelope "25"
89nonconvex-file "NonConvexEnvelope"
90nonconvex-file "nonconvexfile"
91offset "0"
92offset "1"
93order "2"
94output-file "emptybox_values.dat"
95output-file "hydrogenbox_values.dat"
96output-file "output-10.csv"
97output-file "output-20.csv"
98output-file "output-5.csv"
99output-file "output.csv"
100output-file "waterbox-mirrored_values.dat"
101output-file "waterbox_values.dat"
102output-as "store.conf"
103output-as "store.data"
104output-as "store.pdb"
105output-as "store.xyz"
106output-as "test.in"
107output-types "xyz"
108output-types "xyz mpqc"
109parse-tremolo-potentials "argon.potentials"
110parse-tremolo-potentials "tensid.potentials"
111parser-parameters "mpqc"
112parser-parameters "psi3"
113periodic "0"
114position "0 0 0"
115position "0 0 1"
116position "0 0 10"
117position "10 10 10"
118position "10. 10. 10."
119position "1 2 1"
120position "5.63 5.71 5.71"
121position "7.283585982 3.275186040 3.535886037"
122position "9.78 2.64 2.64"
123radius "20."
124random-atom-displacement "0."
125random-molecule-displacement "0."
126random-number-distribution-parameters "max=20;"
127random-number-engine-parameters "seed=2;"
128repeat-box "1 1 1"
129reset 1
130rotate-around-origin "180."
131rotate-around-origin "20."
132rotate-around-origin "360."
133rotate-around-origin "90."
134rotate-around-self "180."
135rotate-around-self "180"
136rotate-around-self "20."
137rotate-around-self "360."
138rotate-around-self "90."
139rotate-to-principal-axis-system ""
140save-adjacency "test.adj"
141save-bonds "test.bond"
142save-selected-atoms "testsave.xyz"
143save-selected-atoms-as-exttypes "test.exttypes"
144save-selected-molecules "testsave.xyz"
145save-temperature "test.ekin"
146scale-box "0.5 1. 0.9"
147select-atom-by-element "1"
148select-atom-by-element "4"
149select-atom-by-id "0"
150select-atom-by-order "1"
151select-atoms-inside-cuboid "10 10 10"
152select-atoms-inside-cuboid "2 2 2"
153select-atoms-inside-sphere "0.2"
154select-atoms-inside-sphere "10"
155select-atoms-inside-sphere "7."
156select-molecule-by-id "0"
157select-molecule-by-id "1"
158select-molecule-by-id "4"
159select-molecule-by-order "-1"
160select-molecule-by-order "1"
161select-molecule-by-order "-2"
162select-molecule-by-order "2"
163select-molecules-by-formula "C2H5(OH)"
164select-molecules-by-formula "C6H6"
165select-molecules-by-formula "H2O"
166select-molecules-by-name "water"
167server-address "127.0.0.1"
168server-port "1026"
169set-boundary-conditions "Wrap, Wrap, Wrap"
170set-parser-parameters "basis = 4-31G"
171set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
172set-parser-parameters "maxiter = 499"
173set-parser-parameters "theory=CLKS"
174set-parser-parameters "wfn=scf"
175set-parser-parameters "ref=uhf"
176set-output "tremolo"
177set-random-number-distribution "uniform_int"
178set-random-number-engine "lagged_fibonacci607"
179set-tremolo-atomdata "ATOMDATA type id x=3"
180set-world-time "10"
181skiplines "1"
182skiplines "2"
183start-step "0"
184stretch-bond "1.5"
185suspend-in-water "1.0"
186tesselation-radius "5."
187time-step-zero "0"
188translate-atoms "1. 0. 0."
189unselect-atom-by-element "1"
190unselect-atom-by-element "4"
191unselect-atom-by-id "0"
192unselect-atom-by-order "1"
193unselect-atoms-inside-cuboid "10 10 10"
194unselect-atoms-inside-cuboid "2 2 2"
195unselect-atoms-inside-sphere "10"
196unselect-atoms-inside-sphere "7."
197unselect-molecule-by-id "0"
198unselect-molecule-by-id "4"
199unselect-molecule-by-order "-1"
200unselect-molecule-by-order "1"
201unselect-molecule-by-order "-2"
202unselect-molecule-by-order "2"
203unselect-molecules-by-formula "C2H5(OH)"
204unselect-molecules-by-formula "C3H8"
205unselect-molecules-by-formula "C6H6"
206unselect-molecules-by-formula "H2O"
207unselect-molecules-by-name "water"
208verbose "3"
209verlet-integration "forces.dat"
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