Skip to content

Commit

Permalink
Changing GEOSX to GEOS in external mesh import
Browse files Browse the repository at this point in the history
  • Loading branch information
@ryar9534
ryar9534 committed Aug 12, 2024
1 parent b4b1a3a commit f7f9add
Show file tree
Hide file tree
Showing 17 changed files with 37 additions and 37 deletions.
2 changes: 1 addition & 1 deletion inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
logLevel="5"
file="../../../../../GEOSDATA/DataSets/Class09_p3/Johansen_faces.vtu"
fieldsToImport="{ perm, poro }"
fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
<InternalWell
name="wellInjector1"
wellRegionName="wellRegion"
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark_mc.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
logLevel="5"
file="../../../../../GEOSXDATA/DataSets/Class09_p3/Johansen_faces.vtu"
fieldsToImport="{ perm, poro }"
fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
<InternalWell
name="wellInjector1"
wellRegionName="wellRegion"
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark_mct.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
logLevel="5"
file="../../../../../GEOSXDATA/DataSets/Class09_p3/Johansen_faces.vtu"
fieldsToImport="{ perm, poro }"
fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
<InternalWell
name="wellInjector1"
wellRegionName="wellRegion"
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEggVTK_benchmark.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
name="mesh"
file="../../../../../GEOSDATA/DataSets/Egg/egg.vtu"
fieldsToImport="{ PERM }"
fieldNamesInGEOSX="{ rockPerm_permeability }">
fieldNamesInGEOS="{ rockPerm_permeability }">

<VTKWell
name="wellProducer1"
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEgg_benchmark.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
name="mesh"
file="../../../../../GEOSDATA/DataSets/Egg/egg.vtu"
fieldsToImport="{ PERM }"
fieldNamesInGEOSX="{ rockPerm_permeability }">
fieldNamesInGEOS="{ rockPerm_permeability }">

<InternalWell
name="wellProducer1"
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/compositionalMultiphaseWell/staircase_co2_wells_hybrid_3d.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@
name="mesh1"
file="staircase3d_tet_with_properties.vtu"
fieldsToImport="{ FluidComposition, PERM, PORO }"
fieldNamesInGEOSX="{ globalCompFraction, rockPerm_permeability, rockPorosity_referencePorosity }"
fieldNamesInGEOS="{ globalCompFraction, rockPerm_permeability, rockPorosity_referencePorosity }"
partitionRefinement="1"
logLevel="2">

Expand Down
2 changes: 1 addition & 1 deletion inputFiles/poromechanics/PoroElastic_hybridHexPrism_co2_base.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
partitionMethod="ptscotch"
scale="{ 50, 50, 50 }"
fieldsToImport="{ PORO, NTG, DENSITY, BULKMOD }"
fieldNamesInGEOSX="{ rockPorosity_referencePorosity, netToGross, skeleton_density, skeleton_bulkModulus }"
fieldNamesInGEOS="{ rockPorosity_referencePorosity, netToGross, skeleton_density, skeleton_bulkModulus }"
file="../singlePhaseFlow/pebi3d_with_properties.vtu"/>

</Mesh>
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/poromechanics/nonlinearAcceleration/smallEggModel/smallEggModel.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@
file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_small.vts"
regionAttribute="elementRegionMarker"
fieldsToImport="{ PERM }"
fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
fieldNamesInGEOS="{ rockPermeability_permeability }"/>
</Mesh>

<Geometry>
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/poromechanicsFractures/PoroElastic_efem-edfm_eggModel_large.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@
file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_large.vts"
regionAttribute="regionAttribute"
fieldsToImport="{ PERM }"
fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
fieldNamesInGEOS="{ rockPermeability_permeability }"/>
</Mesh>

<Geometry>
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/poromechanicsFractures/PoroElastic_efem-edfm_eggModel_small.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@
file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_small.vts"
regionAttribute="elementRegionMarker"
fieldsToImport="{ PERM }"
fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
fieldNamesInGEOS="{ rockPermeability_permeability }"/>
</Mesh>

<Geometry>
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/poromechanicsFractures/verticalFault_ExternalMesh.vtm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
name="main"
file="Domain_Mesh_FaultModel.vtu"
fieldsToImport="{ YoungModulus, PoissonRatio }"
fieldNamesInGEOSX="{ rock_youngModulus, rock_poissonRatio }"
fieldNamesInGEOS="{ rock_youngModulus, rock_poissonRatio }"
/>
<DataSet
name="fracture"
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/singlePhaseFlow/incompressible_pebi3d.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
partitionRefinement="3"
useGlobalIds="1"
fieldsToImport="{ PERM, PORO, NTG }"
fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity, netToGross }"
fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity, netToGross }"

file="pebi3d_with_properties.vtu"/>
</Mesh>
Expand Down
2 changes: 1 addition & 1 deletion inputFiles/thermoPoromechanicsFractures/ThermoPoroElastic_efem-edfm_eggModel_small.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@
file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_small.vts"
regionAttribute="elementRegionMarker"
fieldsToImport="{ PERM }"
fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
fieldNamesInGEOS="{ rockPermeability_permeability }"/>
</Mesh>

<Geometry>
Expand Down
20 changes: 10 additions & 10 deletions src/coreComponents/mesh/generators/ExternalMeshGeneratorBase.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,20 +46,20 @@ ExternalMeshGeneratorBase::ExternalMeshGeneratorBase( string const & name,
setInputFlag( InputFlags::OPTIONAL ).
setDescription( "Volumic fields to be imported from the external mesh file" );

registerWrapper( viewKeyStruct::volumicFieldsInGEOSXString(), &m_volumicFieldsInGEOSX ).
registerWrapper( viewKeyStruct::volumicFieldsInGEOSString(), &m_volumicFieldsInGEOS ).
setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
setInputFlag( InputFlags::OPTIONAL ).
setDescription( "Names of the volumic fields in GEOSX to import into" );
setDescription( "Names of the volumic fields in GEOS to import into" );

registerWrapper( viewKeyStruct::surfacicFieldsToImportString(), &m_surfacicFieldsToImport ).
setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
setInputFlag( InputFlags::OPTIONAL ).
setDescription( "Surfacic fields to be imported from the external mesh file" );

registerWrapper( viewKeyStruct::surfacicFieldsInGEOSXString(), &m_surfacicFieldsInGEOSX ).
registerWrapper( viewKeyStruct::surfacicFieldsInGEOSString(), &m_surfacicFieldsInGEOS ).
setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
setInputFlag( InputFlags::OPTIONAL ).
setDescription( "Names of the surfacic fields in GEOSX to import into" );
setDescription( "Names of the surfacic fields in GEOS to import into" );
}

void ExternalMeshGeneratorBase::postInputInitialization()
Expand All @@ -73,8 +73,8 @@ void ExternalMeshGeneratorBase::postInputInitialization()
" must contain the same number of values.",
InputError );
};
checkSizes( m_volumicFieldsToImport, m_volumicFieldsInGEOSX, viewKeyStruct::volumicFieldsToImportString(), viewKeyStruct::volumicFieldsInGEOSXString() );
checkSizes( m_surfacicFieldsToImport, m_surfacicFieldsInGEOSX, viewKeyStruct::surfacicFieldsToImportString(), viewKeyStruct::surfacicFieldsInGEOSXString() );
checkSizes( m_volumicFieldsToImport, m_volumicFieldsInGEOS, viewKeyStruct::volumicFieldsToImportString(), viewKeyStruct::volumicFieldsInGEOSString() );
checkSizes( m_surfacicFieldsToImport, m_surfacicFieldsInGEOS, viewKeyStruct::surfacicFieldsToImportString(), viewKeyStruct::surfacicFieldsInGEOSString() );

auto const checkDuplicates = [this]( arrayView1d< string const > v, string const & key )
{
Expand All @@ -86,8 +86,8 @@ void ExternalMeshGeneratorBase::postInputInitialization()
"' already present in list of fields to import.",
InputError );
};
checkDuplicates( m_volumicFieldsInGEOSX, viewKeyStruct::volumicFieldsInGEOSXString() );
checkDuplicates( m_surfacicFieldsInGEOSX, viewKeyStruct::surfacicFieldsInGEOSXString() );
checkDuplicates( m_volumicFieldsInGEOS, viewKeyStruct::volumicFieldsInGEOSString() );
checkDuplicates( m_surfacicFieldsInGEOS, viewKeyStruct::surfacicFieldsInGEOSString() );

// Building the fields mapping from the two separated input/output vectors.
auto const buildMapping = [&]( arrayView1d< string const > from,
Expand All @@ -101,8 +101,8 @@ void ExternalMeshGeneratorBase::postInputInitialization()
return mapping;
};

MeshGeneratorBase::m_volumicFields = buildMapping( m_volumicFieldsToImport.toViewConst(), m_volumicFieldsInGEOSX.toViewConst() );
MeshGeneratorBase::m_surfacicFields = buildMapping( m_surfacicFieldsToImport.toViewConst(), m_surfacicFieldsInGEOSX.toViewConst() );
MeshGeneratorBase::m_volumicFields = buildMapping( m_volumicFieldsToImport.toViewConst(), m_volumicFieldsInGEOS.toViewConst() );
MeshGeneratorBase::m_surfacicFields = buildMapping( m_surfacicFieldsToImport.toViewConst(), m_surfacicFieldsInGEOS.toViewConst() );
}

} // namespace geos
16 changes: 8 additions & 8 deletions src/coreComponents/mesh/generators/ExternalMeshGeneratorBase.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,9 @@ class ExternalMeshGeneratorBase : public MeshGeneratorBase
constexpr static char const * scaleString() { return "scale"; }
constexpr static char const * translateString() { return "translate"; }
constexpr static char const * volumicFieldsToImportString() { return "fieldsToImport"; }
constexpr static char const * volumicFieldsInGEOSXString() { return "fieldNamesInGEOSX"; }
constexpr static char const * volumicFieldsInGEOSString() { return "fieldNamesInGEOS"; }
constexpr static char const * surfacicFieldsToImportString() { return "surfacicFieldsToImport"; }
constexpr static char const * surfacicFieldsInGEOSXString() { return "surfacicFieldsInGEOSX"; }
constexpr static char const * surfacicFieldsInGEOSString() { return "surfacicFieldsInGEOS"; }
};
/// @endcond

Expand All @@ -66,17 +66,17 @@ class ExternalMeshGeneratorBase : public MeshGeneratorBase
/// Scale factor that will be applied to the point coordinates (after translation)
R1Tensor m_scale;

/// Names of the fields to be copied from an external reader into GEOSX data structure
/// Names of the fields to be copied from an external reader into GEOS data structure
array1d< string > m_volumicFieldsToImport;

/// String array of the GEOSX user declared volumic fields
array1d< string > m_volumicFieldsInGEOSX;
/// String array of the GEOS user declared volumic fields
array1d< string > m_volumicFieldsInGEOS;

/// Names of the surfacic fields to be copied from an external reader into GEOSX data structure
/// Names of the surfacic fields to be copied from an external reader into GEOS data structure
array1d< string > m_surfacicFieldsToImport;

/// String array of the GEOSX user declared surfacic fields
array1d< string > m_surfacicFieldsInGEOSX;
/// String array of the GEOS user declared surfacic fields
array1d< string > m_surfacicFieldsInGEOS;
};

} // namespace geos
Expand Down
8 changes: 4 additions & 4 deletions src/coreComponents/mesh/generators/MeshGeneratorBase.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -114,22 +114,22 @@ class MeshGeneratorBase : public dataRepository::Group
virtual void freeResources() {}

/**
* @brief Get the name mapping between mesh volumic field names and internal GEOSX volumic field names.
* @brief Get the name mapping between mesh volumic field names and internal GEOS volumic field names.
* @return The string to string mapping of field names.
*/
std::map< string, string > const & getVolumicFieldsMapping() const { return m_volumicFields; }

/**
* @brief Get the name mapping between mesh surfacic field names and internal GEOSX surfacic field names.
* @brief Get the name mapping between mesh surfacic field names and internal GEOS surfacic field names.
* @return The string to string mapping of field names.
*/
std::map< string, string > const & getSurfacicFieldsMapping() const { return m_surfacicFields; }

protected:
/// Mapping from volumic field source to GEOSX field.
/// Mapping from volumic field source to GEOS field.
std::map< string, string > m_volumicFields;

/// Mapping from surfacic field source to GEOSX field.
/// Mapping from surfacic field source to GEOS field.
std::map< string, string > m_surfacicFields;

private:
Expand Down
4 changes: 2 additions & 2 deletions src/coreComponents/schema/docs/VTKMesh.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
Name Type Default Description
====================== ======================== ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================
faceBlocks groupNameRef_array {} For multi-block files, names of the face mesh block.
fieldNamesInGEOSX groupNameRef_array {} Names of the volumic fields in GEOSX to import into
fieldNamesInGEOS groupNameRef_array {} Names of the volumic fields in GEOS to import into
fieldsToImport groupNameRef_array {} Volumic fields to be imported from the external mesh file
file path required Path to the mesh file
logLevel integer 0 Log level
Expand All @@ -15,7 +15,7 @@ partitionMethod geos_vtk_PartitionMethod parmetis Method (library) used
partitionRefinement integer 1 Number of partitioning refinement iterations (defaults to 1, recommended value).A value of 0 disables graph partitioning and keeps simple kd-tree partitions (not recommended). Values higher than 1 may lead to slightly improved partitioning, but yield diminishing returns.
regionAttribute groupNameRef attribute Name of the VTK cell attribute to use as region marker
scale R1Tensor {1,1,1} Scale the coordinates of the vertices by given scale factors (after translation)
surfacicFieldsInGEOSX groupNameRef_array {} Names of the surfacic fields in GEOSX to import into
surfacicFieldsInGEOS groupNameRef_array {} Names of the surfacic fields in GEOS to import into
surfacicFieldsToImport groupNameRef_array {} Surfacic fields to be imported from the external mesh file
translate R1Tensor {0,0,0} Translate the coordinates of the vertices by a given vector (prior to scaling)
useGlobalIds integer 0 Controls the use of global IDs in the input file for cells and points. If set to 0 (default value), the GlobalId arrays in the input mesh are used if available, and generated otherwise. If set to a negative value, the GlobalId arrays in the input mesh are not used, and generated global Ids are automatically generated. If set to a positive value, the GlobalId arrays in the input mesh are used and required, and the simulation aborts if they are not available
Expand Down

0 comments on commit f7f9add

Please sign in to comment.