source: tests/Python/AllActions/options.dat@ 39986b

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 39986b was 39986b, checked in by Frederik Heber <heber@…>, 11 years ago

Added new MakroAction MolecularDynamicsAction.

  • this resides within fragmentation, as we perform the four steps ...
    • verlet-integration
    • fragmentation
    • fragmentation-automation
    • analyse-fragmentation-results ... for a given number of times, using ActionSequence::loop with steps.
  • outputs after every time integration step, controlled via DoOutput option.
  • action only instantiated if HAVE_JOBMARKET.
  • Property mode set to 100644
File size: 5.9 KB
RevLine 
[3493da]1#key value
2actionname "help"
3add-atom "1"
4add-empty-boundary ""
[cb7676]5Alignment-Axis "0,0,1"
[3493da]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"
[f89b45]36calculate-bounding-box ""
[55f299]37calculate-molar-mass ""
[2db053]38center "10. 10. 10."
[3493da]39center-in-box "10 0 0 10 0 10"
[8b886f]40change-bond-angle "100."
[3493da]41change-box "10 0 0 10 0 10"
42change-element "H"
43change-molname "water"
44convex-file "convexfile"
45copy-molecule "0"
[2db053]46count "12"
[5ab796]47create-micelle "200"
[3493da]48default-molname "molname"
49deltat "0.01"
50depth-first-search "2."
[5ab796]51dipole-angular-correlation "H2O"
[3493da]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."
[69c733]61DoLongrange "0"
[b6b21a]62DoPrintDebug "0"
[3493da]63DoRotate "0"
[5ab796]64DoSaturate "0"
[6ff62c]65DoValenceOnly "0"
[3493da]66element-db "./"
67elements "1"
68elements "1 8"
69end-step "1"
[9291d04]70ExcludeHydrogen "1"
[3493da]71fastparsing "1"
[531f27]72filename "test.exttypes"
[3493da]73fill-molecule "filler.xyz"
74fill-void "hydrogen.xyz"
75fill-void "water.data"
76fill-void "water.xyz"
[4882d5]77forces-file "test.forces"
[48d20d]78fragment-charges "1 1"
[edecba]79fragment-executable "mpqc"
80fragment-jobs "Job00.in"
[3493da]81fragment-molecule "./"
[edecba]82fragment-path "test/"
[55e1bc]83fragment-resultfile "results.dat"
[065574]84grid-level "5"
[240c3e]85homology-file "homology.dat"
[3493da]86id-mapping "1"
87input "test.data"
[cd2591]88interpolation-degree "5"
[3493da]89interpolation-steps "9"
90keep-fixed-CenterOfMass "0"
91load "test.data"
92MaxDistance "-1"
[a88452]93mesh-offset "0.5,0.5,0.5"
94mesh-size "10,10,10"
95min-distance "1."
[3493da]96molecule-by-id "0"
[065574]97near-field-cells "3"
[3493da]98nonconvex-envelope "25"
99nonconvex-file "NonConvexEnvelope"
100nonconvex-file "nonconvexfile"
101offset "0"
102offset "1"
103order "2"
[39986b]104output-as "store.conf"
105output-as "store.data"
106output-as "store.pdb"
107output-as "store.xyz"
108output-as "test.in"
109output-every-step "1"
[3493da]110output-file "emptybox_values.dat"
111output-file "hydrogenbox_values.dat"
112output-file "output-10.csv"
113output-file "output-20.csv"
114output-file "output-5.csv"
115output-file "output.csv"
116output-file "waterbox-mirrored_values.dat"
117output-file "waterbox_values.dat"
[5ab796]118output-types "xyz"
119output-types "xyz mpqc"
[3493da]120parse-tremolo-potentials "argon.potentials"
121parse-tremolo-potentials "tensid.potentials"
[5ab796]122parser-parameters "mpqc"
123parser-parameters "psi3"
[3493da]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"
[48d20d]134potential-charges "1 1"
[baccf6]135potential-file "test.potentials"
[a315e8]136potential-type "morse"
[5ab796]137radius "20."
[3493da]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"
[ca331c]143reset 1
[3493da]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-selected-atoms "testsave.xyz"
[531f27]157save-selected-atoms-as-exttypes "test.exttypes"
[3493da]158save-selected-molecules "testsave.xyz"
159save-temperature "test.ekin"
160scale-box "0.5 1. 0.9"
161select-atom-by-element "1"
162select-atom-by-element "4"
163select-atom-by-id "0"
[61c364]164select-atom-by-order "1"
[3493da]165select-atoms-inside-cuboid "10 10 10"
166select-atoms-inside-cuboid "2 2 2"
167select-atoms-inside-sphere "0.2"
168select-atoms-inside-sphere "10"
169select-atoms-inside-sphere "7."
170select-molecule-by-id "0"
171select-molecule-by-id "1"
172select-molecule-by-id "4"
173select-molecule-by-order "-1"
174select-molecule-by-order "1"
175select-molecule-by-order "-2"
176select-molecule-by-order "2"
177select-molecules-by-formula "C2H5(OH)"
178select-molecules-by-formula "C6H6"
179select-molecules-by-formula "H2O"
180select-molecules-by-name "water"
[663606]181select-shape-by-name "sphere2"
[edecba]182server-address "127.0.0.1"
183server-port "1026"
[c52e08]184set-boundary-conditions "Wrap, Wrap, Wrap"
[5ab796]185set-parser-parameters "basis = 4-31G"
186set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
187set-parser-parameters "maxiter = 499"
188set-parser-parameters "theory=CLKS"
189set-parser-parameters "wfn=scf"
190set-parser-parameters "ref=uhf"
[3493da]191set-output "tremolo"
192set-random-number-distribution "uniform_int"
193set-random-number-engine "lagged_fibonacci607"
194set-tremolo-atomdata "ATOMDATA type id x=3"
195set-world-time "10"
[6131d8]196shape-name "sphere1"
[d475a6]197shape-op "AND"
[4dc309]198shape-type "sphere"
[3493da]199skiplines "1"
200skiplines "2"
201start-step "0"
[39986b]202steps "5"
[5589e7e]203store-saturated-fragment "BondFragment"
[3a51bd]204stretch-bond "1.5"
[4dc309]205stretch "1. 1. 1."
[29ea65]206stretch-shapes "1. 2. 3."
[3493da]207suspend-in-water "1.0"
[48d20d]208take-best-of "5"
[345eda]209tesselation-radius "5."
[5ab796]210time-step-zero "0"
[a504946]211training-file "training.dat"
[3493da]212translate-atoms "1. 0. 0."
[0b5057]213translate-shapes "1. 2. 3."
[4dc309]214translation "0. 0. 0."
[3493da]215unselect-atom-by-element "1"
216unselect-atom-by-element "4"
217unselect-atom-by-id "0"
[61c364]218unselect-atom-by-order "1"
[3493da]219unselect-atoms-inside-cuboid "10 10 10"
220unselect-atoms-inside-cuboid "2 2 2"
221unselect-atoms-inside-sphere "10"
222unselect-atoms-inside-sphere "7."
223unselect-molecule-by-id "0"
224unselect-molecule-by-id "4"
225unselect-molecule-by-order "-1"
226unselect-molecule-by-order "1"
227unselect-molecule-by-order "-2"
228unselect-molecule-by-order "2"
229unselect-molecules-by-formula "C2H5(OH)"
230unselect-molecules-by-formula "C3H8"
231unselect-molecules-by-formula "C6H6"
232unselect-molecules-by-formula "H2O"
233unselect-molecules-by-name "water"
[2c004d]234unselect-shape-by-name "cube42"
[3493da]235verbose "3"
236verlet-integration "forces.dat"
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