refactor: Move PVGeomechanicsAnalysis to geos-pv and GeomechanicsCalculator to geos-processing #140

RomainBaville · 2025-09-24T16:14:17Z

This pr close #139 in the context of the code refactoring.
In addition of the issue, some choses have been made:
- The filter is move to the new folder geos-processing
- The name of the paraview plugin have been updated from PVGeomechanicsAnalysis to PVGeomechanicsCalculator to be the same as the filter.
- The four workflow plugins using the filter have been updated but their refactor need to be donne in another pr.
- The filter is not tested but works on complex case. A set of meshes to test all the filter need to be donne in another pr.

alexbenedicto · 2025-09-26T23:16:40Z

Looking at #139 , I do not understand the motivation in this PR to create a new package called "geos-processing".
I agree with the original issue proposal to move the filter to geos-mesh and the PV plugin to geos-pv, not this current implementation.

paloma-martinez

The paths changed in the 4 PVGeomechanicsWorklow* have to be reverted, they don't belong to this PR and the code cannot work in this state.

Apart from that, it looks good to me, I made a few suggestions

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolume.py

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolumeSurface.py

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolumeSurfaceWell.py

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolumeWell.py

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

geos-pv/src/geos/pv/plugins/PVGeomechanicsCalculator.py

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

…latorfilterandplugin Update to the last version of the main

jafranc

Good to go ! I made a suggestion on using an embedded dataclass and limited access as you are basically setting and fetching data.

Please check there (and more largely on all deltaStress)
geomechanicsCalculatorFunctions.py:L510 deltaStress[ : , :3] shouldn't be deltaStress[ :, :]

jafranc · 2025-10-09T12:13:27Z

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolume.py

+                                         speHandler=True )
+        if not filter.logger.hasHandlers():
+            filter.setLoggerHandler( VTKHandler() )
+        filter.setGrainBulkModulus( self.getGrainBulkModulus() )


That would be nice if we had as coding style rule to use @property and @<name>.setter to control access properly

The goal of this pr was to refactor GeomechanicsCalculator only. The refactor of the 4 GeomechanicsWorkflow will be in another pr.

jafranc · 2025-10-09T12:15:58Z

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolume.py

            # 2. compute Geomechanical outputs in volume mesh
-            self.computeAdditionalOutputsVolume()
+            a = self.computeAdditionalOutputsVolume()
+            print( a )


forgotten print ?

jafranc · 2025-10-09T12:19:12Z

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolumeSurface.py

-        filter.SetLogger( self.m_logger )
-        filter.Update()
-        self.m_volumeMesh.ShallowCopy( filter.GetOutputDataObject( 0 ) )
+        filter = GeomechanicsCalculator( self.m_volumeMesh,


IIUC PVGeo..VolumeSurface is a full superset of PVGeo..Volume, please use inheritance to ease up maintainability and kinda bijection from filter to plugins

jafranc · 2025-10-09T12:23:52Z

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolumeSurfaceWell.py

-        filter.SetLogger( self.m_logger )
-        filter.Update()
-        self.m_volumeMesh.ShallowCopy( filter.GetOutputDataObject( 0 ) )
+        filter = GeomechanicsCalculator( self.m_volumeMesh,


Same remarks as in PVGeo..VolumeSurface. Next PR.

jafranc · 2025-10-09T12:27:05Z

geos-pv/src/geos/pv/plugins/PVGeomechanicsCalculator.py

+        if filter.applyFilter():
+            outputMesh.ShallowCopy( filter.getOutput() )
+            outputMesh.Modified()
+
+        return 1


Suggested change

if filter.applyFilter():

outputMesh.ShallowCopy( filter.getOutput() )

outputMesh.Modified()

return 1

if filter.applyFilter():

outputMesh.ShallowCopy( filter.getOutput() )

outputMesh.Modified()

return 1

else:

return 0

For me, if the filter return 0 does not means that the plugin failed. I have used this condition to update the outputMesh only if the filter successfully ended. That why I didn't return 0 but 1 and the plugin return the input mesh.

jafranc · 2025-10-09T12:34:09Z

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

+        self.output: Union[ vtkPointSet, vtkUnstructuredGrid ]
+        if mesh.IsA( "vtkUnstructuredGrid" ):
+            self.output = vtkUnstructuredGrid()
+        elif mesh.IsA( "vtkPointSet" ):
+            self.output = vtkPointSet()


Suggested change

self.output: Union[ vtkPointSet, vtkUnstructuredGrid ]

if mesh.IsA( "vtkUnstructuredGrid" ):

self.output = vtkUnstructuredGrid()

elif mesh.IsA( "vtkPointSet" ):

self.output = vtkPointSet()

self.output: Union[ vtkPointSet, vtkUnstructuredGrid ] = mesh.NewInstance()

should work the same

jafranc · 2025-10-09T12:40:21Z

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

+            self.logger.error( "The filter failed." )
+            return False


Suggested change

self.logger.error( "The filter failed." )

return False

return False

maybe already quite some failure messages send by the callee and it is not repeated in the other 2 conditions

jafranc · 2025-10-09T12:46:46Z

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

+        self.bulkModulus: npt.NDArray[ np.float64 ]
+        self.shearModulus: npt.NDArray[ np.float64 ]
+        self.youngModulus: npt.NDArray[ np.float64 ]
+        self.poissonRatio: npt.NDArray[ np.float64 ]
+        if self.computeYoungPoisson:


as it is basically a Compute class acting on a DataClass, I would suggest rewritting it using @dataclass and @property decorators to make it easier to get at first sight and improve access control

I have made somthing tel me if that what you thought about

…latorfilterandplugin Update to the last verion of the main

…latorfilterandplugin Update to the last version of the main

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

…latorfilterandplugin Update to the last version of the main

RomainBaville added 22 commits September 19, 2025 16:20

move GeomechnicsCalculator to geos-mesh

ab45082

move PVGeomechanicsAnalysis in geos-pv

bfd0196

move GeomechanicsCalculator in the correct folder

2836b32

Remove PVPythonAlgorithmBase

7cc21f7

refactor computeElasticModulus functions

9ef6814

refactor compute biot coefficient

a88a1e7

refactor computeCompressibilityCoefficient function

ce526f9

refactor computeRealEffectiveStressRatio

424d76d

refactor computeSpecificGravity

6a55e7f

refactor computeTotalStresses

8418261

refactor computBasicOutputs

fadec20

refactor computeAdvence

d267ad7

Add the function getOutput

8c5c28a

Clean for the ci

f366704

update the doc

c227278

Change the name to add logic

f54221b

refactor the doc

be176c9

Refactor the paraview plugin

dc1934b

clean for ci

96e8880

clean the doc

4c9c5ce

fix the ci

62e4b23

Update the workflow plugins using the filter

9d37f5c

RomainBaville requested review from alexbenedicto, jafranc and paloma-martinez September 24, 2025 16:14

RomainBaville self-assigned this Sep 24, 2025

RomainBaville added flag: ready for review type: feature labels Sep 24, 2025

RomainBaville added 2 commits September 24, 2025 18:37

fix the test

0e827b7

fix the ci

26883db

RomainBaville added 2 commits September 26, 2025 11:35

Add the new folder geos-processing

afa427f

move GeomechanicsCalculators to geos-processing

f09f60d

RomainBaville changed the title ~~refactor: Move PVGeomechanicsAnalysis to geos-pv and GeomechanicsCalculator to geos-mesh~~ refactor: Move PVGeomechanicsAnalysis to geos-pv and GeomechanicsCalculator to geos-processing Sep 26, 2025

Update to the last version of the main

af6480f

paloma-martinez requested changes Oct 7, 2025

View reviewed changes

RomainBaville and others added 9 commits October 7, 2025 11:21

Apply suggestions from Paloma's review

5188921

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

Keep the old way to load the file, this update is for another pr

2629ad2

fix the ci

45d49c8

Factorize the checkMandatoryAttributesFunction and add docs

5022f88

Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…

0858294

…latorfilterandplugin Update to the last version of the main

update import

44766fd

fix Install packages

35c3541

fix ci

7da5168

fix geos-post build

795d6d9

jafranc approved these changes Oct 9, 2025

View reviewed changes

RomainBaville added 5 commits October 14, 2025 13:08

Apply Jacques suggestion with dataclass

1902c77

update dataclass

989c5ec

fix ruff

f95b50c

Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…

b723d15

…latorfilterandplugin Update to the last verion of the main

Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…

b90dc80

…latorfilterandplugin Update to the last version of the main

paloma-martinez approved these changes Oct 15, 2025

View reviewed changes

geos-processing/src/geos/processing/post_processing/GeomechanicsCalculator.py Outdated Show resolved Hide resolved

RomainBaville and others added 4 commits October 15, 2025 15:48

update the doc

1bb88c6

Apply suggestions from Paloma's review

452d5cc

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

Fix dataclass default value

b40cb80

Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…

4beafcc

…latorfilterandplugin Update to the last version of the main

	self.logger.error( "The filter failed." )
	return False
	return False

refactor: Move PVGeomechanicsAnalysis to geos-pv and GeomechanicsCalculator to geos-processing #140

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refactor: Move PVGeomechanicsAnalysis to geos-pv and GeomechanicsCalculator to geos-processing #140

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RomainBaville commented Sep 24, 2025 •

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alexbenedicto commented Sep 26, 2025 •

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