source: tests/Python/AllActions/options.dat@ db0833

ForceAnnealing_goodresults ForceAnnealing_tocheck
Last change on this file since db0833 was db0833, checked in by Frederik Heber <frederik.heber@…>, 8 years ago

Added RandomPerturbationAction.

  • this should be when doing structural optimization for getting given configurations out of ambivalent states, e.g. a water molecule whose three atoms define a straight line.
  • note that we need to use a sensible random number distribution, the default is not doing what's expected. Added to docu.
  • TESTS: Added regression test with undo/redo.
  • DOCU: Added documentation to userguide.
  • Property mode set to 100644
File size: 6.9 KB
Line 
1#key value
2add-atom "1"
3add-empty-boundary "5,5,5"
4Alignment-Axis "0,0,1"
5angle-x "0."
6angle-x "0"
7angle-y "0."
8angle-y "0"
9angle-z "0 "
10angle-z "0."
11angle-z "0"
12axis "0 0 1"
13axis "0 1 0"
14axis "1 2 1"
15bin-end "10"
16bin-end "20"
17bin-end "359"
18bin-end "359.5"
19bin-end "5"
20bin-output-file "bin_output-10.csv"
21bin-output-file "bin_output-20.csv"
22bin-output-file "bin_output-5.csv"
23bin-output-file "bin_output.csv"
24bin-output-file "emptybox_histogram.dat"
25bin-output-file "hydrogenbox_histogram.dat"
26bin-output-file "waterbox_histogram.dat"
27bin-output-file "waterbox-mirrored_histogram.dat"
28bin-start "0"
29bin-start "-0.5"
30bin-start "10"
31bin-start "5"
32bin-width "1."
33bond-degree "1"
34bond-file "bond.dat"
35bondside "1"
36bond-table "table.dat"
37calculate-bounding-box ""
38calculate-molar-mass ""
39center "10. 10. 10."
40center-in-box "10 0 0 10 0 10"
41change-bond-angle "100."
42change-box "10 0 0 10 0 10"
43change-element "1"
44change-molname "water"
45convex-envelope "50."
46convex-file "convexfile"
47coordinates "1,0,0"
48copy-molecule "0"
49count "12"
50create-micelle "200"
51default-molname "molname"
52deltat "0.01"
53density "1.0"
54depth-first-search "2."
55dipole-angular-correlation "H2O"
56distance "1.55"
57distances "3.1 3.1 3.1"
58distances "3.1 3.1 3.1"
59distance-to-boundary "1."
60distance-to-molecule "1.5"
61distance-to-molecule "2.1"
62distance-to-vector "named_vector"
63domain-position "0. 0. 0."
64domain-position "0 0 0"
65domain-position "10. 10. 10."
66DoCyclesFull "0"
67DoLongrange "0"
68DoOutputEveryStep "0"
69DoPrintDebug "0"
70DoRotate "0"
71DoSaturate "0"
72DoSmearElectronicCharges "0"
73DoValenceOnly "0"
74element-db "./"
75elements "1"
76elements "1 8"
77end-step "1"
78enforce-net-zero-charge "0"
79ExcludeHydrogen "1"
80fastparsing "1"
81filename "test.exttypes"
82fill-molecule "filler.xyz"
83fill-void "hydrogen.xyz"
84fill-void "water.data"
85fill-void "water.xyz"
86forces-file "test.forces"
87fragment-charges "1 1"
88fragment-executable "mpqc"
89fragment-jobs "Job00.in"
90fragment-molecule "./"
91fragment-path "test/"
92fragment-prefix "BondFragment"
93grid-level "5"
94help "help"
95id-mapping "1"
96input "test.data"
97input-to-vector "named_vector"
98inter-order "2"
99interpolation-degree "5"
100interpolation-steps "9"
101keep-bondgraph "1"
102keep-fixed-CenterOfMass "0"
103load "test.data"
104load-session "test.py"
105MaxDistance "-1"
106max-meshwidth "0.3"
107mesh-offset "0.5,0.5,0.5"
108mesh-size "10,10,10"
109min-distance "1."
110mirror-atoms "1.,1.,1."
111molecule-by-id "0"
112near-field-cells "3"
113nonconvex-envelope "25"
114nonconvex-file "NonConvexEnvelope"
115nonconvex-file "nonconvexfile"
116offset "0"
117offset "1"
118order "2"
119output-as "store.conf"
120output-as "store.data"
121output-as "store.pdb"
122output-as "store.xyz"
123output-as "test.in"
124output-every-step "1"
125output-file "emptybox_values.dat"
126output-file "hydrogenbox_values.dat"
127output-file "output-10.csv"
128output-file "output-20.csv"
129output-file "output-5.csv"
130output-file "output.csv"
131output-file "waterbox-mirrored_values.dat"
132output-file "waterbox_values.dat"
133output-types "xyz"
134output-types "xyz mpqc"
135parse-atom-fragments "atomfragments.dat"
136parse-fragment-results "results.dat"
137parse-homologies "homology.dat"
138parse-particle-parameters "water.particles"
139parse-potentials "water.potentials"
140parse-state-files "1"
141parse-tremolo-potentials "argon.potentials"
142parse-tremolo-potentials "tensid.potentials"
143parser-parameters "mpqc"
144parser-parameters "psi3"
145periodic "0"
146plane-offset "5."
147plane-to-vector "named_vector"
148position "0 0 0"
149position "0 0 1"
150position "0 0 10"
151position "10 10 10"
152position "10. 10. 10."
153position "1 2 1"
154position "5.63 5.71 5.71"
155position "7.283585982 3.275186040 3.535886037"
156position "9.78 2.64 2.64"
157position-to-vector "named_vector"
158potential-charges "1 1"
159potential-type "morse"
160radius "20."
161random-atom-displacement "0."
162random-molecule-displacement "0."
163random-number-distribution-parameters "max=20;"
164random-number-engine-parameters "seed=2;"
165random-perturbation "0.1"
166remove-geometry "named_vector"
167repeat-box "1 1 1"
168reset 1
169reverse "0"
170rotate-around-bond "90."
171rotate-around-origin "180."
172rotate-around-origin "20."
173rotate-around-origin "360."
174rotate-around-origin "90."
175rotate-around-self "180."
176rotate-around-self "180"
177rotate-around-self "20."
178rotate-around-self "360."
179rotate-around-self "90."
180rotate-to-principal-axis-system "0,0,1"
181save-adjacency "test.adj"
182save-bonds "test.bond"
183save-atom-fragments "atomfragments.dat"
184save-fragment-results "results.dat"
185save-homologies "homology.dat"
186save-particle-parameters "water.particles"
187save-potentials "water.potentials"
188save-selected-atoms "testsave.xyz"
189save-selected-atoms-as-exttypes "test.exttypes"
190save-selected-molecules "testsave.xyz"
191save-temperature "test.ekin"
192scale-box "0.5 1. 0.9"
193select-atom-by-element "1"
194select-atom-by-element "4"
195select-atom-by-id "0"
196select-atom-by-order "1"
197select-atoms-inside-cuboid "10 10 10"
198select-atoms-inside-cuboid "2 2 2"
199select-atoms-inside-sphere "0.2"
200select-atoms-inside-sphere "10"
201select-atoms-inside-sphere "7."
202select-molecule-by-id "0"
203select-molecule-by-id "1"
204select-molecule-by-id "4"
205select-molecule-by-order "-1"
206select-molecule-by-order "1"
207select-molecule-by-order "-2"
208select-molecule-by-order "2"
209select-molecules-by-formula "C2H5(OH)"
210select-molecules-by-formula "C6H6"
211select-molecules-by-formula "H2O"
212select-molecules-by-name "water"
213select-shape-by-name "sphere2"
214server-address "127.0.0.1"
215server-port "1026"
216session-type "cli"
217set-bond-degree "1"
218set-boundary-conditions "Wrap, Wrap, Wrap"
219set-max-iterations "10"
220set-parser-parameters "basis = 4-31G"
221set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
222set-parser-parameters "maxiter = 499"
223set-parser-parameters "theory=CLKS"
224set-parser-parameters "wfn=scf"
225set-parser-parameters "ref=uhf"
226set-output "tremolo"
227set-random-number-distribution "uniform_int"
228set-random-number-engine "lagged_fibonacci607"
229set-threshold "1e-6"
230set-tremolo-atomdata "ATOMDATA type id x=3"
231set-world-time "10"
232shape-name "sphere1"
233shape-op "AND"
234shape-type "sphere"
235skiplines "1"
236skiplines "2"
237start-step "0"
238steps "5"
239step-world-time "1"
240store-grids "0"
241store-saturated-fragment "BondFragment"
242store-session "test.sh"
243stretch-bond "1.5"
244stretch "1. 1. 1."
245stretch-shapes "1. 2. 3."
246take-best-of "5"
247tesselation-radius "5."
248time-step-zero "0"
249training-file "training.dat"
250translate-atoms "1. 0. 0."
251translate-shapes "1. 2. 3."
252translation "0. 0. 0."
253unselect-atom-by-element "1"
254unselect-atom-by-element "4"
255unselect-atom-by-id "0"
256unselect-atom-by-order "1"
257unselect-atoms-inside-cuboid "10 10 10"
258unselect-atoms-inside-cuboid "2 2 2"
259unselect-atoms-inside-sphere "10"
260unselect-atoms-inside-sphere "7."
261unselect-molecule-by-id "0"
262unselect-molecule-by-id "4"
263unselect-molecule-by-order "-1"
264unselect-molecule-by-order "1"
265unselect-molecule-by-order "-2"
266unselect-molecule-by-order "2"
267unselect-molecules-by-formula "C2H5(OH)"
268unselect-molecules-by-formula "C3H8"
269unselect-molecules-by-formula "C6H6"
270unselect-molecules-by-formula "H2O"
271unselect-molecules-by-name "water"
272unselect-shape-by-name "cube42"
273UseImplicitCharges "1"
274verbose "3"
275verlet-integration "forces.dat"
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