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feat: Implement EDFM loading from VTK #3510

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feat: Implement EDFM loading from VTK #3510

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d77d082
initial embedded surface block abc
ouassimkh Sep 6, 2023
35196c8
minor change
ouassimkh Sep 7, 2023
2135a21
start concrete implementation
ouassimkh Sep 13, 2023
7eb79a5
add the cpp
ouassimkh Sep 13, 2023
b20dd27
add embedded surfaces to CellBlockManager
ouassimkh Sep 15, 2023
738c14a
this should not be commited
Sep 29, 2023
2fcdeed
upate cellBlock Manger and embedded Ruface block
ouassimkh Sep 27, 2023
186a222
Correct edfm to cell type
ouassimkh Oct 26, 2023
2401cc7
corrections
ouassimkh Apr 16, 2024
e2346e7
create edfm patches in bulk
ouassimkh Apr 9, 2024
c42b37f
small changes
ouassimkh Apr 17, 2024
55239bd
add flag to enable experimentation
ouassimkh Apr 18, 2024
4b2363e
missed files
ouassimkh Apr 18, 2024
0fde8c6
add bulk edfm fracs
ouassimkh Apr 26, 2024
dd8d49e
All is running
ouassimkh Apr 29, 2024
2e43180
uncrustify pass
ouassimkh Apr 29, 2024
cd555e0
start VTK edfm support
ouassimkh Jun 4, 2024
041d290
Finish EDFM loading from VTK (no parallel)
ouassimkh Jun 24, 2024
3bda862
builds after master rebase issues
ouassimkh Oct 31, 2024
256efee
working serial run
ouassimkh Nov 5, 2024
2d6583d
clearning
ouassimkh Nov 7, 2024
8d52abc
cleraning
ouassimkh Nov 8, 2024
c718d96
bug
ouassimkh Nov 8, 2024
ba87177
uncrustify pass
ouassimkh Nov 8, 2024
6d70f05
remove comments
ouassimkh Nov 11, 2024
c4a913b
use faceBlockName + some fixes for build (#3436)
paveltomin Nov 11, 2024
584a601
add edfm vtk example
ouassimkh Nov 13, 2024
29a20e8
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Nov 20, 2024
7b9014e
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
rrsettgast Nov 22, 2024
31118bb
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Dec 2, 2024
5caf9aa
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Dec 9, 2024
c84e27a
build fix
Dec 9, 2024
b4a5df4
remove
Dec 10, 2024
cec6ed2
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Dec 12, 2024
b079426
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Dec 16, 2024
3e0357e
doxygen fix
Dec 16, 2024
1388970
fix one crash and introduce another
Dec 16, 2024
ef54e9c
just to see if test fail because of this
paveltomin Dec 16, 2024
12e1747
fix old edfm cases
Dec 17, 2024
9716f90
Merge branch 'Feature/ouassim/edfm_loader_new' of https://github.com/…
Dec 17, 2024
a742215
chansing the paralllel issue
Dec 17, 2024
b3cee3b
fix global to local mapping
Dec 19, 2024
b7cd2b8
Update edfm_vtk_fractures.vtu
paveltomin Dec 19, 2024
71ec173
code style
Dec 19, 2024
4fb1ac9
Merge branch 'Feature/ouassim/edfm_loader_new' of https://github.com/…
Dec 19, 2024
7784585
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Dec 23, 2024
4150280
doxygen fix
Dec 23, 2024
c3d501a
Update VTKUtilities.hpp
paveltomin Dec 26, 2024
8fc88c1
Update EmbeddedSurfaceBlock.hpp
paveltomin Dec 26, 2024
8384539
Merge branch 'develop' into Feature/ouassim/edfm_loader_new
paveltomin Jan 8, 2025
1bf96de
Merge remote-tracking branch 'origin/develop' into ouassim/edfm_loader
CusiniM Jan 13, 2025
b1fa4c4
move creation of EmbeddedFractures upon input.
CusiniM Jan 15, 2025
21f2e06
wip: move things around add useful comments.
CusiniM Jan 15, 2025
da7b7fa
moved all needed functions.
CusiniM Jan 16, 2025
f1555ab
Fixed CI computation.
CusiniM Jan 16, 2025
1ecec46
fixed compilation issues.
CusiniM Jan 16, 2025
e49b685
Merge branch 'develop' into ouassim/edfm_loader
paveltomin Jan 28, 2025
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78 changes: 78 additions & 0 deletions inputFiles/singlePhaseFlowFractures/edfm_vtk_fractures.vtu
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Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
<?xml version="1.0"?>
<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<UnstructuredGrid>
<Piece NumberOfPoints="6" NumberOfCells="2">
<PointData>
<DataArray type="Int32" Name="fracture_ids_points" NumberOfComponents="1" format="ascii">
0
1
2
3
4
5
</DataArray>
</PointData>
<CellData GlobalIds="GLOBAL_IDS_CELLS">
<DataArray type="Int64" IdType="1" Name="GLOBAL_IDS_CELLS" format="ascii" RangeMin="18" RangeMax="19">
18 19
</DataArray>
<DataArray type="Int32" Name="fracture_to_parent_matrix_cell_mapping" NumberOfComponents="2" format="ascii">
18 4
19 13
</DataArray>
<DataArray type="Float32" Name="permeability" NumberOfComponents="1" format="ascii" RangeMin="0.1" RangeMax="0.1">
0.1
0.1
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<DataArray type="Float32" Name="aperture" NumberOfComponents="1" format="ascii" RangeMin="0.0001" RangeMax="0.0001">
0.0001
0.0001
</DataArray>
<DataArray type="Float32" Name="tangential_width_vectors" NumberOfComponents="3" format="ascii">
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0 0 1
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<DataArray type="Float32" Name="tangential_length_vectors" NumberOfComponents="3" format="ascii">
0 1 0
0 1 0
</DataArray>
<DataArray type="Float32" Name="normal_vectors" NumberOfComponents="3" format="ascii">
1 0 0
1 0 0
</DataArray>
</CellData>
<Points>
<DataArray type="Float32" Name="Points" NumberOfComponents="3" format="ascii" RangeMin="0" RangeMax="1">
0.5 0.3333 0
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<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
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<Cells>
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<DataArray type="Int64" Name="offsets" format="ascii" RangeMin="4" RangeMax="8">
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<DataArray type="UInt8" Name="types" format="ascii" RangeMin="9" RangeMax="9">
9
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</DataArray>
</Cells>
</Piece>
</UnstructuredGrid>
</VTKFile>
122 changes: 122 additions & 0 deletions inputFiles/singlePhaseFlowFractures/edfm_vtk_matrix.vtu
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<VTKFile type="UnstructuredGrid" version="1.0" byte_order="LittleEndian" header_type="UInt64">
<UnstructuredGrid>
<Piece NumberOfPoints="48" NumberOfCells="18">
<PointData GlobalIds="GLOBAL_IDS_POINTS">
<DataArray type="Int64" IdType="1" Name="GLOBAL_IDS_POINTS" format="ascii" RangeMin="0" RangeMax="47">
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Comment on lines +89 to +108
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@CusiniM CusiniM Jan 15, 2025 •
edited
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is this ever used? I don't think we use this field. Or is it needed by vtk?

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@ouassimkh ouassimkh Jan 15, 2025 •
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I think it is used internally by VTK to map fracture patches to their nodes. I use it here VtkEmbeddedSurfaceBlockUtilities.cpp

ArrayOfArrays< localIndex > elem2dToNodes( numEdfmFracs );
  for( vtkIdType i = 0; i < numEdfmFracs; ++i )
  {
    auto const val = grid->GetCell( i )->GetPointIds();
    elem2dToNodes.emplaceBack( i, val->GetId( 0 ));
    elem2dToNodes.emplaceBack( i, val->GetId( 1 ));
    elem2dToNodes.emplaceBack( i, val->GetId( 2 ));
    elem2dToNodes.emplaceBack( i, val->GetId( 3 ));
  }

<DataArray type="Int64" Name="offsets" format="ascii" RangeMin="8" RangeMax="144">
8 16 24 32 40 48
56 64 72 80 88 96
104 112 120 128 136 144
</DataArray>
<DataArray type="UInt8" Name="types" format="ascii" RangeMin="12" RangeMax="12">
12 12 12 12 12 12
12 12 12 12 12 12
12 12 12 12 12 12
</DataArray>
</Cells>
</Piece>
</UnstructuredGrid>
</VTKFile>
137 changes: 137 additions & 0 deletions inputFiles/singlePhaseFlowFractures/fractureMatrixFlow_edfm_vtk.xml
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Original file line number Diff line number Diff line change
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<?xml version="1.0" ?>

<Problem>
<Solvers
gravityVector="{ 0.0, 0.0, -9.81 }">
<SinglePhaseFVM
name="SinglePhaseFlow"
logLevel="1"
discretization="singlePhaseTPFA"
targetRegions="{ RockMatrix, Fracture }">
<NonlinearSolverParameters
newtonTol="1.0e-6"
newtonMaxIter="8"/>
<LinearSolverParameters
directParallel="0"/>
</SinglePhaseFVM>

<EmbeddedSurfaceGenerator
name="SurfaceGenerator"
logLevel="1"
discretization="FE1"
targetRegions="{ RockMatrix, Fracture }"
fractureRegion="Fracture"
mpiCommOrder="1"/>
</Solvers>

<NumericalMethods>
<FiniteVolume>
<TwoPointFluxApproximation
name="singlePhaseTPFA"/>
</FiniteVolume>
<FiniteElements>
<FiniteElementSpace
name="FE1"
order="1"/>
</FiniteElements>
</NumericalMethods>

<ElementRegions>
<CellElementRegion
name="RockMatrix"
cellBlocks="{ hexahedra }"
materialList="{ water, rock }"/>

<SurfaceElementRegion
name="Fracture"
faceBlock = "edfm_vtk_fractures"
defaultAperture="1e-3"
materialList="{ water, fractureFilling }"
subRegionType="embeddedElement"/>
</ElementRegions>

<Constitutive>
<CompressibleSinglePhaseFluid
name="water"
defaultDensity="1000"
defaultViscosity="0.001"
referencePressure="0.0"
compressibility="0.0"
viscosibility="0.0"/>

<CompressibleSolidParallelPlatesPermeability
name="fractureFilling"
solidModelName="nullSolid"
porosityModelName="fracturePorosity"
permeabilityModelName="fracturePerm"/>

<CompressibleSolidConstantPermeability
name="rock"
solidModelName="nullSolid"
porosityModelName="rockPorosity"
permeabilityModelName="rockPerm"/>

<NullModel
name="nullSolid"/>

<PressurePorosity
name="rockPorosity"
defaultReferencePorosity="0.1"
referencePressure="0.0"
compressibility="0.0"/>

<ConstantPermeability
name="rockPerm"
permeabilityComponents="{ 2.0e-15, 2.0e-15, 2.0e-15 }"/>

<PressurePorosity
name="fracturePorosity"
defaultReferencePorosity="1.00"
referencePressure="0.0"
compressibility="0.0"/>

<ParallelPlatesPermeability
name="fracturePerm"/>
</Constitutive>

<FieldSpecifications>

<FieldSpecification
name="Porosity"
initialCondition="1"
setNames="{ all }"
objectPath="ElementRegions/RockMatrix/hexahedra"
fieldName="rockPorosity_referencePorosity"
scale="0.1"/>

<FieldSpecification
name="fracPorosity"
initialCondition="1"
setNames="{ all }"
objectPath="ElementRegions/Fracture"
fieldName="fracturePorosity_porosity"
scale="1.00"/>

<FieldSpecification
name="initialPressure"
initialCondition="1"
setNames="{ all }"
objectPath="ElementRegions/RockMatrix/hexahedra"
fieldName="pressure"
scale="0.0"/>

<FieldSpecification
name="sourceTerm"
objectPath="ElementRegions/RockMatrix/hexahedra"
fieldName="pressure"
scale="1e7"
setNames="{ source }"/>

<FieldSpecification
name="sinkTerm"
objectPath="ElementRegions/RockMatrix/hexahedra"
fieldName="pressure"
scale="0.0"
setNames="{ sink }"/>
</FieldSpecifications>
</Problem>
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