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paloma-martinezRomainBavilleRomain Baville
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refactor: Move workflow plugins (#164)
* Move SurfaceGeomechanicsFilter and refactor functions * Move and refactor plugin * add geos-processing to install script * Add more log * Add documentation * Filter cleaning * Documentation * Refactor the basis change computation * Refactor of normal and tangential vectors computation * Replace and add tests for attribute to vector functions * Add tests and better error handling * Adding tests for SurfaceGeomechanics filter * Fix * typo * Small modifications from Romain review * Fix typing and error in getTangents function * Fix tests following previous commit modifs * SISO filter * fix docstring * fix the fix * typing * typing * . * Move the plugins and adapt the import paths * Typing and doc move * doc fix * Fix doc * Fix GeomechanicsWorkflows * fix conflict --------- Co-authored-by: Romain Baville <126683264+RomainBaville@users.noreply.github.com> Co-authored-by: Romain Baville <romain.baville@external.totalenergies.com>
1 parent 0cde8ff commit e518d95

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‎docs/geos_posp_docs/PVplugins.rst‎

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@@ -5,59 +5,9 @@ Paraview plugins were developed using Python 3.9.13 and are compatible with Para
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The plugins include:
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* A reader that parse GEOS output log file;
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* 3D mesh cleanning plugins;
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* Processing plugins to compute additional geomechanical properties;
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* Visualization plugins to plot Mohr's circles and cross plots using Paraview Python View.
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PVExtractMergeBlocksVolume plugin
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-------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolume
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PVExtractMergeBlocksVolumeSurface plugin
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--------------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurface
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PVExtractMergeBlocksVolumeSurfaceWell plugin
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------------------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurfaceWell
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PVExtractMergeBlocksVolumeWell plugin
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-----------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolumeWell
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PVGeomechanicsWorkflowVolume plugin
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---------------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolume
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PVGeomechanicsWorkflowVolumeSurface plugin
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----------------------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurface
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PVGeomechanicsWorkflowVolumeSurfaceWell plugin
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--------------------------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell
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PVGeomechanicsWorkflowVolumeWell plugin
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-------------------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeWell
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PVMohrCirclePlot plugin
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---------------------------------
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‎docs/geos_pv_docs/processing.rst‎

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Post-/Pre-processing
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=========================
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The plugins include:
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* A reader that parse GEOS output log file;
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* 3D mesh cleanning plugins;
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* Processing plugins to compute additional geomechanical properties;
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* Visualization plugins to plot Mohr's circles (currently in `geos_posp`) and cross plots using Paraview Python View.
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PVAttributeMapping
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--------------------
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.. automodule:: geos.pv.plugins.PVFillPartialArrays
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PVGeomechanicsCalculator plugin
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---------------------------------------
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.. automodule:: geos.pv.plugins.PVGeomechanicsCalculator
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PVSplitMesh
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----------------------------------
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----------------------------------
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.. automodule:: geos.pv.plugins.PVClipToMainFrame
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Geos output pre-processing
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+++++++++++++++++++++++++++++
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PVExtractMergeBlocksVolume plugin
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-------------------------------------------
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.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolume
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PVExtractMergeBlocksVolumeSurface plugin
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--------------------------------------------------
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.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolumeSurface
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PVExtractMergeBlocksVolumeSurfaceWell plugin
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------------------------------------------------------
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.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolumeSurfaceWell
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PVExtractMergeBlocksVolumeWell plugin
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-----------------------------------------------
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.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolumeWell
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Geomechanics workflows
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++++++++++++++++++++++++
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PVGeomechanicsWorkflowVolume plugin
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---------------------------------------------
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.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolume
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PVGeomechanicsWorkflowVolumeSurface plugin
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----------------------------------------------------
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.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolumeSurface
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PVGeomechanicsWorkflowVolumeSurfaceWell plugin
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--------------------------------------------------------
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.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolumeSurfaceWell
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PVGeomechanicsWorkflowVolumeWell plugin
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-------------------------------------------------
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.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolumeWell
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PVGeomechanicsCalculator plugin
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---------------------------------------
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.. automodule:: geos.pv.plugins.PVGeomechanicsCalculator

geos-posp/src/PVplugins/PVExtractMergeBlocksVolume.py renamed to geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolume.py

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@@ -2,20 +2,20 @@
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# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
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# SPDX-FileContributor: Martin Lemay
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# ruff: noqa: E402 # disable Module level import not at top of file
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import os
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import sys
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from pathlib import Path
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import numpy as np
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import numpy.typing as npt
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from typing_extensions import Self
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from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
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from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
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dir_path = os.path.dirname( os.path.realpath( __file__ ) )
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parent_dir_path = os.path.dirname( dir_path )
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if parent_dir_path not in sys.path:
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sys.path.append( parent_dir_path )
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# update sys.path to load all GEOS Python Package dependencies
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geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
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sys.path.insert( 0, str( geos_pv_path / "src" ) )
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from geos.pv.utils.config import update_paths
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import PVplugins # noqa: F401
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update_paths()
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from geos.utils.GeosOutputsConstants import (
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GeosMeshOutputsEnum,
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copyAttribute,
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createCellCenterAttribute,
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)
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from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
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from geos.pv.utils.paraviewTreatments import getTimeStepIndex
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from paraview.util.vtkAlgorithm import ( # type: ignore[import-not-found]
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VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
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)

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeSurface.py renamed to geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolumeSurface.py

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# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
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# SPDX-FileContributor: Martin Lemay
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# ruff: noqa: E402 # disable Module level import not at top of file
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import os
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import sys
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from pathlib import Path
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import numpy as np
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import numpy.typing as npt
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from typing_extensions import Self
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from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
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from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
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dir_path = os.path.dirname( os.path.realpath( __file__ ) )
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parent_dir_path = os.path.dirname( dir_path )
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if parent_dir_path not in sys.path:
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sys.path.append( parent_dir_path )
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# update sys.path to load all GEOS Python Package dependencies
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geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
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sys.path.insert( 0, str( geos_pv_path / "src" ) )
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from geos.pv.utils.config import update_paths
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import PVplugins # noqa: F401
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update_paths()
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from geos.utils.GeosOutputsConstants import (
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GeosMeshOutputsEnum,
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copyAttribute,
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createCellCenterAttribute,
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)
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from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
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from geos.pv.utils.paraviewTreatments import getTimeStepIndex
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from paraview.util.vtkAlgorithm import ( # type: ignore[import-not-found]
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VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
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)

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeSurfaceWell.py renamed to geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolumeSurfaceWell.py

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# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
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# SPDX-FileContributor: Martin Lemay
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# ruff: noqa: E402 # disable Module level import not at top of file
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import os
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import sys
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from pathlib import Path
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import numpy as np
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import numpy.typing as npt
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from typing_extensions import Self
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from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
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from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
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dir_path = os.path.dirname( os.path.realpath( __file__ ) )
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parent_dir_path = os.path.dirname( dir_path )
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if parent_dir_path not in sys.path:
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sys.path.append( parent_dir_path )
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# update sys.path to load all GEOS Python Package dependencies
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geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
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sys.path.insert( 0, str( geos_pv_path / "src" ) )
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from geos.pv.utils.config import update_paths
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import PVplugins # noqa: F401
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update_paths()
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from geos.utils.GeosOutputsConstants import (
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GeosMeshOutputsEnum,
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copyAttribute,
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createCellCenterAttribute,
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)
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from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
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from geos.pv.utils.paraviewTreatments import getTimeStepIndex
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from paraview.util.vtkAlgorithm import ( # type: ignore[import-not-found]
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VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
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)

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeWell.py renamed to geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolumeWell.py

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# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
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# SPDX-FileContributor: Martin Lemay
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# ruff: noqa: E402 # disable Module level import not at top of file
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import os
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import sys
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from pathlib import Path
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import numpy as np
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import numpy.typing as npt
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from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
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from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
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dir_path = os.path.dirname( os.path.realpath( __file__ ) )
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parent_dir_path = os.path.dirname( dir_path )
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if parent_dir_path not in sys.path:
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sys.path.append( parent_dir_path )
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# update sys.path to load all GEOS Python Package dependencies
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geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
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sys.path.insert( 0, str( geos_pv_path / "src" ) )
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from geos.pv.utils.config import update_paths
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import PVplugins # noqa: F401
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update_paths()
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from geos.utils.GeosOutputsConstants import (
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GeosMeshOutputsEnum,
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copyAttribute,
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createCellCenterAttribute,
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)
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from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
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from geos.pv.utils.paraviewTreatments import getTimeStepIndex
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__doc__ = """
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PVExtractMergeBlocksVolumeWell is a Paraview plugin that allows to merge

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolume.py renamed to geos-pv/src/geos/pv/plugins/PVGeomechanicsWorkflowVolume.py

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# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
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# SPDX-FileContributor: Martin Lemay
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# ruff: noqa: E402 # disable Module level import not at top of file
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import os
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import sys
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from pathlib import Path
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import numpy as np
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from typing_extensions import Self
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from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
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from vtkmodules.vtkCommonDataModel import (
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vtkMultiBlockDataSet, )
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dir_path = os.path.dirname( os.path.realpath( __file__ ) )
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parent_dir_path = os.path.dirname( dir_path )
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if parent_dir_path not in sys.path:
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sys.path.append( parent_dir_path )
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# update sys.path to load all GEOS Python Package dependencies
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geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
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sys.path.insert( 0, str( geos_pv_path / "src" ) )
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from geos.pv.utils.config import update_paths
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import PVplugins # noqa: F401
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update_paths()
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from geos.utils.Logger import Logger, getLogger
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from geos.utils.PhysicalConstants import (
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from paraview.util.vtkAlgorithm import ( # type: ignore[import-not-found]
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VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
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)
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from paraview.detail.loghandler import ( # type: ignore[import-not-found]
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VTKHandler,
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) # source: https://github.com/Kitware/ParaView/blob/master/Wrapping/Python/paraview/detail/loghandler.py
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from PVplugins.PVExtractMergeBlocksVolume import PVExtractMergeBlocksVolume
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from geos.processing.post_processing.GeomechanicsCalculator import GeomechanicsCalculator
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from geos.pv.plugins.PVExtractMergeBlocksVolume import PVExtractMergeBlocksVolume
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from geos.pv.plugins.PVGeomechanicsCalculator import PVGeomechanicsCalculator
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3936
__doc__ = """
4037
PVGeomechanicsWorkflowVolume is a Paraview plugin that execute multiple filters
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Returns:
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bool: True if calculation successfully eneded, False otherwise.
374371
"""
375-
filter = GeomechanicsCalculator( self.m_volumeMesh,
376-
computeAdvancedOutputs=self.getComputeAdvancedOutputs(),
377-
speHandler=True )
378-
if not filter.logger.hasHandlers():
379-
filter.setLoggerHandler( VTKHandler() )
380-
filter.physicalConstants.grainBulkModulus = self.grainBulkModulus
381-
filter.physicalConstants.specificDensity = self.specificDensity
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filter.physicalConstants.rockCohesion = self.rockCohesion
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filter.physicalConstants.frictionAngle = self.frictionAngle
384-
filter.applyFilter()
385-
self.m_volumeMesh.ShallowCopy( filter.getOutput() )
372+
filter = PVGeomechanicsCalculator()
373+
filter.SetInputDataObject( self.m_volumeMesh ),
374+
filter.setComputeAdvancedProperties( self.getComputeAdvancedOutputs() )
375+
filter.setGrainBulkModulus( self.m_grainBulkModulus )
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filter.setSpecificDensity = ( self.m_specificDensity )
377+
filter.setRockCohesion = ( self.m_rockCohesion )
378+
filter.setFrictionAngle = ( self.m_frictionAngle )
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filter.Update()
380+
self.m_volumeMesh.ShallowCopy( filter.GetOutputDataObject( 0 ) )
386381
self.m_volumeMesh.Modified()
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return True

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