Python Tools
Python Tools Setup
The preferred method to setup the GEOS python tools is to run the following command in the build directory:
make geosx_python_tools
The ats setup command also sets up the python tools:
make ats_environment
These will attempt to install the required packages into the python distribution indicated via the Python3_EXECUTABLE cmake variable (also used by pygeosx). If any package dependencies are missing, then the install script will attempt to fetch them from the internet using pip. After installation, these packages will be available for import within the associated python distribution, and a set of console scripts will be available within the GEOS build bin directory.
Note
To re-install or update an installed version of geosPythonTools, you can run the make geosx_python_tools_clean and make geosx_python_tools commands.
Manual Installation
In some cases, you may need to manually install or update geosPythonPackages. To do this, you can clone a copy of the geosPythonPackages repository and install them using pip:
cd /path/to/store/python/tools
git clone https://github.com/GEOS-DEV/geosPythonPackages.git
# Install/upgrade geos-ats
cd geosPythonPackages/
python -m pip install --upgrade geos-ats
Note
To upgrade an existing installation, the python executable in the above command should correspond to the version you indicated in your host config. If you have previously built the tools, this version will be linked in the build directory: build_dir/bin/python.
Development & Debugging
Be default, the python environment setup commands target the “main” branch of geosPythonTools. To target another version of the tools, you can set the GEOS_PYTHON_PACKAGES_BRANCH cmake variable to the name of another valid branch (or git tag) in the host config file. In this case, the code will pull the most recent commit of the desired branch when building geosPythonTools.
Note
If you are working on significant updates to geosPythonTools, you should open a testing branch in the main GEOS repository that defines the GEOS_PYTHON_PACKAGES_BRANCH variable. This will ensure that your changes are tested as part of the GEOS CI.
If you need to debug one of the packages in geosPythonTools, we recommend using VSCode with the Python extension installed. Some of the packages contain specific entry point scripts that can be used to assist in this process.
Packages
- HDF5 Wrapper
- GEOS ATS
- run_geos_ats
- Debugging
- API
- Restart Check
FileComparison
FileComparison.compareAttributes()
FileComparison.compareCharArrays()
FileComparison.compareData()
FileComparison.compareDatasets()
FileComparison.compareFloatArrays()
FileComparison.compareFloatScalars()
FileComparison.compareGroups()
FileComparison.compareIntArrays()
FileComparison.compareIntScalars()
FileComparison.compareStringArrays()
FileComparison.compareStringScalars()
FileComparison.errorMsg()
FileComparison.isExcluded()
FileComparison.warningMsg()
findMaxMatchingFile()
main()
write()
writeHeader()
- Curve Check
- Restart Check
- GEOS Mesh Tools
- GEOS Post-Processing tools
- Home
- Processing
- vtk Filters
- geos_posp.filters.AttributeMappingFromCellCoords module
- geos_posp.filters.AttributeMappingFromCellId module
- geos_posp.filters.GeomechanicsCalculator module
- geos_posp.filters.GeosBlockExtractor module
- geos_posp.filters.GeosBlockMerge module
- geos_posp.filters.SurfaceGeomechanics module
- geos_posp.filters.TransferAttributesVolumeSurface module
- geos_posp.filters.VolumeSurfaceMeshMapper module
- vtk Readers
- Processing functions
- geos_posp.processing.geomechanicsCalculatorFunctions module
biotCoefficient()
bulkModulus()
compressibility()
compressibilityOed()
compressibilityReal()
computeNormalShearStress()
computeStressPrincipalComponents()
computeStressPrincipalComponentsFromStressVector()
criticalPorePressure()
criticalPorePressureThreshold()
criticalTotalStressRatio()
deviatoricStressPathOed()
elasticStrainFromBulkShear()
elasticStrainFromYoungPoisson()
lambdaCoefficient()
lithostaticStress()
oedometricModulus()
poissonRatio()
reservoirStressPathOed()
reservoirStressPathReal()
shearCapacityUtilization()
shearModulus()
specificGravity()
stressRatio()
totalStress()
totalStressRatioThreshold()
youngModulus()
- geos_posp.processing.geosLogReaderFunctions module
buildPropertiesNameForComponents()
buildPropertiesNameForPhases()
buildPropertiesNameFromGeosProperties()
buildPropertiesNameNoPhases()
convertValues()
correctZeroValuesInListOfValues()
countNumberLines()
elementsAreInLog()
extractAquifer()
extractFirstIntFromString()
extractFloatsFromString()
extractLinearIter()
extractListIntsFromString()
extractNewtonIter()
extractPhaseId()
extractPhaseModel()
extractPropertiesFlow()
extractPropertiesWell()
extractRegion()
extractStatsName()
extractTimeAndDt()
extractValueAndNameAquifer()
extractValuesFlow()
extractValuesWell()
extractWell()
extractWellTags()
findNumberPhasesSimulation()
formatPropertyName()
identifyCurrentWell()
identifyProperties()
isFloat()
phaseNamesBuilder()
replaceSpecialCharactersWithWhitespace()
timeInSecond()
transformUserChoiceToListPhases()
- geos_posp.processing.MohrCircle module
- geos_posp.processing.MohrCoulomb module
- geos_posp.processing.multiblockInpectorTreeFunctions module
- geos_posp.processing.vtkUtils module
computeCellCenterCoordinates()
copyAttribute()
copyAttributeDataSet()
createAttribute()
createCellCenterAttribute()
createConstantAttribute()
createConstantAttributeDataSet()
createConstantAttributeMultiBlock()
createEmptyAttribute()
doCreateCellCenterAttribute()
extractBlock()
extractSurfaceFromElevation()
fillAllPartialAttributes()
fillPartialAttributes()
getArrayInObject()
getAttributeSet()
getAttributeValuesAsDF()
getAttributesFromDataSet()
getAttributesFromMultiBlockDataSet()
getAttributesWithNumberOfComponents()
getBounds()
getComponentNames()
getComponentNamesDataSet()
getComponentNamesMultiBlock()
getMonoBlockBounds()
getMultiBlockBounds()
getNumberOfComponents()
getNumberOfComponentsDataSet()
getNumberOfComponentsMultiBlock()
getVtkArrayInObject()
isAttributeInObject()
isAttributeInObjectDataSet()
isAttributeInObjectMultiBlockDataSet()
mergeBlocks()
renameAttribute()
transferPointDataToCellData()
- geos_posp.processing.geomechanicsCalculatorFunctions module
- pyvistaTools
- vtk Filters
- Visualization
- Paraview plugins
- PVplugins.PVAttributeMapping module
- PVplugins.PVCreateConstantAttributePerRegion module
- PVplugins.PVExtractMergeBlocksVolume module
- PVplugins.PVExtractMergeBlocksVolumeSurface module
- PVplugins.PVExtractMergeBlocksVolumeSurfaceWell module
- PVplugins.PVExtractMergeBlocksVolumeWell module
- PVplugins.PVGeomechanicsAnalysis module
- PVplugins.PVGeomechanicsWorkflowVolume module
- PVplugins.PVGeomechanicsWorkflowVolumeSurface module
- PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell module
- PVplugins.PVGeomechanicsWorkflowVolumeWell module
- PVplugins.PVGeosLogReader module
- PVplugins.PVMergeBlocksEnhanced module
- PVplugins.PVMohrCirclePlot module
- PVplugins.PVPythonViewConfigurator module
- PVplugins.PVSurfaceGeomechanics module
- PVplugins.PVTransferAttributesVolumeSurface module
- Utilities
- Paraview plugins
- Time History Tools
- GEOS Utilities
- API
- geos.utils.ConnectionSet module
ConnectionSet
ConnectionSetCollection
ConnectionSetCollection.add()
ConnectionSetCollection.addMultiple()
ConnectionSetCollection.containsCellIdRef()
ConnectionSetCollection.containsEqual()
ConnectionSetCollection.discard()
ConnectionSetCollection.discardCellIdRef()
ConnectionSetCollection.get()
ConnectionSetCollection.getReversedConnectionSetCollection()
ConnectionSetCollection.replace()
ConnectionSetCollection.update()
- geos.utils.enumUnits module
- geos.utils.geometryFunctions module
- geos.utils.GeosOutputsConstants module
AttributeEnum
ComponentNameEnum
FluidPrefixEnum
GeosDomainNameEnum
GeosLogOutputsEnum
GeosMeshOutputsEnum
GeosMeshOutputsEnum.BULK_MODULUS
GeosMeshOutputsEnum.CELL_ID
GeosMeshOutputsEnum.DELTA_PRESSURE
GeosMeshOutputsEnum.DISPLACEMENT_JUMP
GeosMeshOutputsEnum.ELEMENT_CENTER
GeosMeshOutputsEnum.GRAIN_BULK_MODULUS
GeosMeshOutputsEnum.MASS
GeosMeshOutputsEnum.PERMEABILITY
GeosMeshOutputsEnum.POINT
GeosMeshOutputsEnum.POINTS_ID
GeosMeshOutputsEnum.POROSITY
GeosMeshOutputsEnum.POROSITY_INI
GeosMeshOutputsEnum.PRESSURE
GeosMeshOutputsEnum.ROCK_DENSITY
GeosMeshOutputsEnum.SHEAR_MODULUS
GeosMeshOutputsEnum.STRESS_EFFECTIVE
GeosMeshOutputsEnum.TOTAL_DISPLACEMENT
GeosMeshOutputsEnum.TRACTION
GeosMeshOutputsEnum.VTK_ORIGINAL_CELL_ID
GeosMeshOutputsEnum.WATER_DENSITY
GeosMeshSuffixEnum
GeosMeshSuffixEnum.BIOT_COEFFICIENT_SUFFIX
GeosMeshSuffixEnum.BULK_MODULUS_SUFFIX
GeosMeshSuffixEnum.DENSITY_SUFFIX
GeosMeshSuffixEnum.GRAIN_BULK_MODULUS_SUFFIX
GeosMeshSuffixEnum.PERMEABILITY_SUFFIX
GeosMeshSuffixEnum.PHASE_DENSITY_SUFFIX
GeosMeshSuffixEnum.PHASE_FRACTION_SUFFIX
GeosMeshSuffixEnum.PHASE_MASS_DENSITY_SUFFIX
GeosMeshSuffixEnum.PHASE_VISCOSITY_SUFFIX
GeosMeshSuffixEnum.POROSITY_REF_SUFFIX
GeosMeshSuffixEnum.POROSITY_SUFFIX
GeosMeshSuffixEnum.SHEAR_MODULUS_SUFFIX
GeosMeshSuffixEnum.STRAIN_SUFFIX
GeosMeshSuffixEnum.STRESS_SUFFIX
GeosMeshSuffixEnum.SURFACE_MINUS_SUFFIX
GeosMeshSuffixEnum.SURFACE_PLUS_SUFFIX
OutputObjectEnum
PHASE_SEP
PhaseTypeEnum
PostProcessingOutputsEnum
PostProcessingOutputsEnum.ADJACENT_CELL_SIDE
PostProcessingOutputsEnum.BIOT_COEFFICIENT
PostProcessingOutputsEnum.BIOT_COEFFICIENT_INITIAL
PostProcessingOutputsEnum.BLOCK_INDEX
PostProcessingOutputsEnum.BULK_MODULUS_INITIAL
PostProcessingOutputsEnum.COMPRESSIBILITY
PostProcessingOutputsEnum.COMPRESSIBILITY_OED
PostProcessingOutputsEnum.COMPRESSIBILITY_REAL
PostProcessingOutputsEnum.CRITICAL_PORE_PRESSURE
PostProcessingOutputsEnum.CRITICAL_PORE_PRESSURE_THRESHOLD
PostProcessingOutputsEnum.CRITICAL_TOTAL_STRESS_RATIO
PostProcessingOutputsEnum.LITHOSTATIC_STRESS
PostProcessingOutputsEnum.OEDOMETRIC_MODULUS
PostProcessingOutputsEnum.POISSON_RATIO
PostProcessingOutputsEnum.POISSON_RATIO_INITIAL
PostProcessingOutputsEnum.RSP_OED
PostProcessingOutputsEnum.RSP_REAL
PostProcessingOutputsEnum.SCU
PostProcessingOutputsEnum.SHEAR_MODULUS_INITIAL
PostProcessingOutputsEnum.SPECIFIC_GRAVITY
PostProcessingOutputsEnum.STRAIN_ELASTIC
PostProcessingOutputsEnum.STRESS_EFFECTIVE_INITIAL
PostProcessingOutputsEnum.STRESS_EFFECTIVE_RATIO_OED
PostProcessingOutputsEnum.STRESS_EFFECTIVE_RATIO_REAL
PostProcessingOutputsEnum.STRESS_TOTAL
PostProcessingOutputsEnum.STRESS_TOTAL_DELTA
PostProcessingOutputsEnum.STRESS_TOTAL_INITIAL
PostProcessingOutputsEnum.STRESS_TOTAL_RATIO_REAL
PostProcessingOutputsEnum.TOTAL_STRESS_RATIO_THRESHOLD
PostProcessingOutputsEnum.YOUNG_MODULUS
PostProcessingOutputsEnum.YOUNG_MODULUS_INITIAL
getAttributeToConvertFromLocalToXYZ()
getAttributeToTransferFromInitialTime()
getRockSuffixRenaming()
- geos.utils.algebraFunctions module
- geos.utils.Logger module
CustomLoggerFormatter
Logger
Logger.addHandler()
Logger.callHandlers()
Logger.critical()
Logger.debug()
Logger.error()
Logger.exception()
Logger.fatal()
Logger.findCaller()
Logger.getChild()
Logger.getEffectiveLevel()
Logger.handle()
Logger.hasHandlers()
Logger.info()
Logger.isEnabledFor()
Logger.log()
Logger.makeRecord()
Logger.manager
Logger.removeHandler()
Logger.root
Logger.setLevel()
Logger.warn()
Logger.warning()
getLogger()
- geos.utils.PhysicalConstants module
- geos.utils.UnitRepository module
- geos.utils.ConnectionSet module
- API
- GEOS XML Tools
- convert_abaqus
- format_xml
- check_xml_attribute_coverage
- check_xml_redundancy
- API
check_mpi_rank()
format_geosx_arguments()
preprocess_parallel()
preprocess_serial()
wait_for_file_write_rank_0()
apply_regex_to_node()
generate_random_name()
merge_included_xml_files()
merge_xml_nodes()
process()
validate_xml()
format_attribute()
format_file()
format_xml_level()
main()
UnitManager
DictRegexHandler
SymbolicMathRegexHandler()
check_redundancy_level()
check_xml_redundancy()
main()
process_xml_files()
collect_xml_attributes()
collect_xml_attributes_level()
main()
parse_schema()
parse_schema_element()
process_xml_files()
write_attribute_usage_xml()
write_attribute_usage_xml_level()
read_GEOS_table()
write_GEOS_table()
write_read_GEOS_table_example()
- PyGEOS Tools
- API
allgather_wrapper()
gather_wrapper()
get_global_value_range()
get_matching_wrapper_path()
get_wrapper()
get_wrapper_par()
plot_history()
print_global_value_range()
run_queries()
search_datastructure_wrappers_recursive()
set_wrapper_to_value()
set_wrapper_with_function()
load_tables()
save_tables()
apply_to_bins()
extrapolate_nan_values()
get_random_realization()
get_realizations()
convert_E_nu_to_K_G()
estimate_shmin()
parse_las()
- API