Action_Thermostats
Add_AtomRandomPerturbation
Add_SelectAtomByNameAction
Adding_Graph_to_ChangeBondActions
Adding_MD_integration_tests
Adding_StructOpt_integration_tests
AutomationFragmentation_failures
Candidate_v1.6.1
Candidate_v1.7.0
ChangeBugEmailaddress
ChemicalSpaceEvaluator
EmpiricalPotential_contain_HomologyGraph_documentation
Enhance_userguide
Enhanced_StructuralOptimization
Enhanced_StructuralOptimization_continued
Example_ManyWaysToTranslateAtom
Exclude_Hydrogens_annealWithBondGraph
Fix_Verbose_Codepatterns
ForceAnnealing_oldresults
ForceAnnealing_with_BondGraph
ForceAnnealing_with_BondGraph_continued
ForceAnnealing_with_BondGraph_continued_betteresults
ForceAnnealing_with_BondGraph_contraction-expansion
GeometryObjects
Gui_displays_atomic_force_velocity
IndependentFragmentGrids_IntegrationTest
JobMarket_RobustOnKillsSegFaults
JobMarket_StableWorkerPool
PythonUI_with_named_parameters
QtGui_reactivate_TimeChanged_changes
Recreated_GuiChecks
StoppableMakroAction
TremoloParser_IncreasedPrecision
TremoloParser_MultipleTimesteps
stable
|
Last change
on this file since 2eded3e was 16c6f7, checked in by Frederik Heber <heber@…>, 9 years ago |
|
TESTFIX: Recreated fragmentation results and homology containers for all associated fragmentation and potential tests.
- TESTS: added way how to create .dat files for all fitting regression tests.
- TESTFIX: Removed again all XFAILs from tests parsing fragmentation results or
homologies.
- TESTFIX: needed to slightly modify fitted potential values and charges.
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-
Property mode
set to
100644
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|
File size:
1.4 KB
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| Line | |
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| 1 | import sys
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| 2 | import pyMoleCuilder as mol
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| 3 |
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| 4 | if len(sys.argv) < 13:
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| 5 | sys.stderr.write("Usage: "+sys.argv[0]+" <file> <order> <DoLongrange> <DoValenceOnly> <level> <near_field_cells> <server> <port> <basis> <inter-order> <distance> <steps> <bondtable>\n")
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| 6 | sys.exit(255)
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| 7 |
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| 8 | FILE=sys.argv[1]
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| 9 | ORDER=sys.argv[2]
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| 10 | LONGRANGE=sys.argv[3]
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| 11 | VALENCEONLY=sys.argv[4]
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| 12 | LEVEL=sys.argv[5]
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| 13 | NEAR_FIELD_CELLS=sys.argv[6]
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| 14 | SERVERADDRESS=sys.argv[7]
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| 15 | CONTROLLERPORT=sys.argv[8]
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| 16 | BASISNAME=sys.argv[9]
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| 17 | INTERORDER=sys.argv[10]
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| 18 | DISTANCE=sys.argv[11]
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| 19 | STEPS=int(sys.argv[12])
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| 20 | BONDTABLE=sys.argv[13]
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| 21 |
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| 22 | # load bond table file
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| 23 | mol.CommandBondLengthTable(BONDTABLE)
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| 24 | # Load molecule
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| 25 | mol.MoleculeLoad(FILE)
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| 26 | # Set parser parameter for mpqc
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| 27 | mol.ParserSetParserParameters("mpqc", "theory=CLHF;basis="+BASISNAME+";")
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| 28 | # set boundary
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| 29 | mol.WorldSetBoundaryConditions("Ignore Ignore Ignore")
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| 30 | # update molecule graph as first step setting does not change anything
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| 31 | mol.GraphUpdateMolecules()
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| 32 |
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| 33 | for i in range(0,STEPS):
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| 34 | # set current time
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| 35 | mol.WorldSetWorldTime(str(i))
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| 36 | # fragment system
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| 37 | mol.SelectionAllAtoms()
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| 38 | mol.FragmentationFragmentation("", DISTANCE, ORDER, "1", "1", "", "0.", LEVEL, INTERORDER, "0", "0")
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| 39 | mol.FragmentationFragmentationAutomation(SERVERADDRESS, CONTROLLERPORT, "mpqc", LEVEL, NEAR_FIELD_CELLS, "3", LONGRANGE, "", VALENCEONLY, "0")
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| 40 | mol.FragmentationAnalyseFragmentationResults("", "0")
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| 41 |
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| 42 | # save homologies
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| 43 | mol.PotentialSaveHomologies("homology.dat")
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| 44 |
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| 45 | # exit
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| 46 | sys.exit(0)
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|---|
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