source: tests/Python/AllActions/options.dat@ bcb593

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 bcb593 was bcb593, checked in by Frederik Heber <heber@…>, 11 years ago

FIX: VerletIntegrationAction now assumes forces have just been calculated.

  • according to Wikipedia's Velocity_Verlet info, we first integrate position, then calculate forces, then integrate velocity. This assumes that forces based on next time step's position are already known. This is possible when parsed from file but not if they are calculated dynamically via fragmentation. Hence, we now integrate velocity from last time step to current, then integrate position from current time step to next. Then we are in the position to calculate forces and do this cycle again.
  • for this, VelocityVerletUpdate was split into ..X() and ..U() for independent integration of position and velocity.
  • VelocityVerletIntegration::operator() now first corrects forces, then integrates velocites, corrects them too and finally integrates positions according to the above new scheme.
  • removed option MDSteps from VerletIntegrationAction.
  • TESTFIX: Had to change regression rest on VerletIntegration since the cycle sequence has changed. It was nonsense before to have the forces already in some file respective to future position that actually first need to come out of the time integration.
  • Property mode set to 100644
File size: 5.8 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"
104output-file "emptybox_values.dat"
105output-file "hydrogenbox_values.dat"
106output-file "output-10.csv"
107output-file "output-20.csv"
108output-file "output-5.csv"
109output-file "output.csv"
110output-file "waterbox-mirrored_values.dat"
111output-file "waterbox_values.dat"
[072f0e]112output-as "store.conf"
113output-as "store.data"
114output-as "store.pdb"
115output-as "store.xyz"
116output-as "test.in"
[5ab796]117output-types "xyz"
118output-types "xyz mpqc"
[3493da]119parse-tremolo-potentials "argon.potentials"
120parse-tremolo-potentials "tensid.potentials"
[5ab796]121parser-parameters "mpqc"
122parser-parameters "psi3"
[3493da]123periodic "0"
124position "0 0 0"
125position "0 0 1"
126position "0 0 10"
127position "10 10 10"
128position "10. 10. 10."
129position "1 2 1"
130position "5.63 5.71 5.71"
131position "7.283585982 3.275186040 3.535886037"
132position "9.78 2.64 2.64"
[48d20d]133potential-charges "1 1"
[baccf6]134potential-file "test.potentials"
[a315e8]135potential-type "morse"
[5ab796]136radius "20."
[3493da]137random-atom-displacement "0."
138random-molecule-displacement "0."
139random-number-distribution-parameters "max=20;"
140random-number-engine-parameters "seed=2;"
141repeat-box "1 1 1"
[ca331c]142reset 1
[3493da]143rotate-around-origin "180."
144rotate-around-origin "20."
145rotate-around-origin "360."
146rotate-around-origin "90."
147rotate-around-self "180."
148rotate-around-self "180"
149rotate-around-self "20."
150rotate-around-self "360."
151rotate-around-self "90."
152rotate-to-principal-axis-system ""
153save-adjacency "test.adj"
154save-bonds "test.bond"
155save-selected-atoms "testsave.xyz"
[531f27]156save-selected-atoms-as-exttypes "test.exttypes"
[3493da]157save-selected-molecules "testsave.xyz"
158save-temperature "test.ekin"
159scale-box "0.5 1. 0.9"
160select-atom-by-element "1"
161select-atom-by-element "4"
162select-atom-by-id "0"
[61c364]163select-atom-by-order "1"
[3493da]164select-atoms-inside-cuboid "10 10 10"
165select-atoms-inside-cuboid "2 2 2"
166select-atoms-inside-sphere "0.2"
167select-atoms-inside-sphere "10"
168select-atoms-inside-sphere "7."
169select-molecule-by-id "0"
170select-molecule-by-id "1"
171select-molecule-by-id "4"
172select-molecule-by-order "-1"
173select-molecule-by-order "1"
174select-molecule-by-order "-2"
175select-molecule-by-order "2"
176select-molecules-by-formula "C2H5(OH)"
177select-molecules-by-formula "C6H6"
178select-molecules-by-formula "H2O"
179select-molecules-by-name "water"
[663606]180select-shape-by-name "sphere2"
[edecba]181server-address "127.0.0.1"
182server-port "1026"
[c52e08]183set-boundary-conditions "Wrap, Wrap, Wrap"
[5ab796]184set-parser-parameters "basis = 4-31G"
185set-parser-parameters "basis = 4-31G;maxiter=499;theory=CLKS;"
186set-parser-parameters "maxiter = 499"
187set-parser-parameters "theory=CLKS"
188set-parser-parameters "wfn=scf"
189set-parser-parameters "ref=uhf"
[3493da]190set-output "tremolo"
191set-random-number-distribution "uniform_int"
192set-random-number-engine "lagged_fibonacci607"
193set-tremolo-atomdata "ATOMDATA type id x=3"
194set-world-time "10"
[6131d8]195shape-name "sphere1"
[d475a6]196shape-op "AND"
[4dc309]197shape-type "sphere"
[3493da]198skiplines "1"
199skiplines "2"
200start-step "0"
[5589e7e]201store-saturated-fragment "BondFragment"
[3a51bd]202stretch-bond "1.5"
[4dc309]203stretch "1. 1. 1."
[29ea65]204stretch-shapes "1. 2. 3."
[3493da]205suspend-in-water "1.0"
[48d20d]206take-best-of "5"
[345eda]207tesselation-radius "5."
[5ab796]208time-step-zero "0"
[a504946]209training-file "training.dat"
[3493da]210translate-atoms "1. 0. 0."
[0b5057]211translate-shapes "1. 2. 3."
[4dc309]212translation "0. 0. 0."
[3493da]213unselect-atom-by-element "1"
214unselect-atom-by-element "4"
215unselect-atom-by-id "0"
[61c364]216unselect-atom-by-order "1"
[3493da]217unselect-atoms-inside-cuboid "10 10 10"
218unselect-atoms-inside-cuboid "2 2 2"
219unselect-atoms-inside-sphere "10"
220unselect-atoms-inside-sphere "7."
221unselect-molecule-by-id "0"
222unselect-molecule-by-id "4"
223unselect-molecule-by-order "-1"
224unselect-molecule-by-order "1"
225unselect-molecule-by-order "-2"
226unselect-molecule-by-order "2"
227unselect-molecules-by-formula "C2H5(OH)"
228unselect-molecules-by-formula "C3H8"
229unselect-molecules-by-formula "C6H6"
230unselect-molecules-by-formula "H2O"
231unselect-molecules-by-name "water"
[2c004d]232unselect-shape-by-name "cube42"
[3493da]233verbose "3"
234verlet-integration "forces.dat"
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