equationsSetSpecification = [
iron.EquationsSetClasses.ELASTICITY,
iron.EquationsSetTypes.FINITE_ELASTICITY,
iron.EquationsSetSubtypes.CONSTITUTIVE_LAW_IN_CELLML_EVALUATE
]
equationsSet.CreateStart(equationsSetUserNumber, region, fibreField,
equationsSetSpecification,
equationsSetFieldUserNumber, equationsSetField)
equationsSet.CreateFinish()
equationsSet.DependentCreateStart(dependentFieldUserNumber, dependentField)
equationsSet.DependentCreateFinish()
#DOC-START create cellml environment
# Create the CellML environment
CellML = iron.CellML()
CellML.CreateStart(CellMLUserNumber, region)
# Import a Mooney-Rivlin material law from a file
MooneyRivlinModel = CellML.ModelImport("mooney_rivlin.xml")
#DOC-END create cellml environment
#DOC-START flag variables
# Now we have imported the model we are able to specify which variables from the model we want to set from openCMISS
CellML.VariableSetAsKnown(MooneyRivlinModel, "equations/E11")
CellML.VariableSetAsKnown(MooneyRivlinModel, "equations/E12")
CellML.VariableSetAsKnown(MooneyRivlinModel, "equations/E13")
CellML.VariableSetAsKnown(MooneyRivlinModel, "equations/E22")
CellML.VariableSetAsKnown(MooneyRivlinModel, "equations/E23")
CellML.VariableSetAsKnown(MooneyRivlinModel, "equations/E33")
# and variables to get from the CellML
CellML.VariableSetAsWanted(MooneyRivlinModel, "equations/Tdev11")
# Create the equations_set
equationsSetField = iron.Field()
equationsSet = iron.EquationsSet()
equationsSetSpecification = [iron.EquationsSetClasses.ELASTICITY,
iron.EquationsSetTypes.FINITE_ELASTICITY,
iron.EquationsSetSubtypes.CONSTIT_AND_GROWTH_LAW_IN_CELLML]
equationsSet.CreateStart(equationsSetUserNumber,region,fibreField,
equationsSetSpecification,equationsSetFieldUserNumber,equationsSetField)
equationsSet.CreateFinish()
equationsSet.DependentCreateStart(dependentFieldUserNumber,dependentField)
equationsSet.DependentCreateFinish()
# Create the CellML environment for the growth law. Set the rates as known so that we can spatially vary them.
growthCellML = iron.CellML()
growthCellML.CreateStart(growthCellMLUserNumber,region)
growthCellMLIdx = growthCellML.ModelImport("simplegrowth.cellml")
growthCellML.VariableSetAsKnown(growthCellMLIdx,"Main/fibrerate")
growthCellML.VariableSetAsKnown(growthCellMLIdx,"Main/sheetrate")
growthCellML.VariableSetAsKnown(growthCellMLIdx,"Main/normalrate")
growthCellML.CreateFinish()
# Create CellML <--> OpenCMISS field maps. Map the lambda's to the U3/growth dependent field variable
growthCellML.FieldMapsCreateStart()
growthCellML.CreateCellMLToFieldMap(growthCellMLIdx,"Main/lambda1",iron.FieldParameterSetTypes.VALUES,
dependentField,iron.FieldVariableTypes.U3,1,iron.FieldParameterSetTypes.VALUES)
growthCellML.CreateCellMLToFieldMap(growthCellMLIdx,"Main/lambda2",iron.FieldParameterSetTypes.VALUES,
dependentField,iron.FieldVariableTypes.U3,2,iron.FieldParameterSetTypes.VALUES)
growthCellML.CreateCellMLToFieldMap(growthCellMLIdx,"Main/lambda3",iron.FieldParameterSetTypes.VALUES,
dependentField,iron.FieldVariableTypes.U3,3,iron.FieldParameterSetTypes.VALUES)