number_of_dimensions = 3
number_of_mesh_components = 1
total_number_of_elements = len(element_array)
total_number_of_nodes = len(node_array)
mesh_component_number = 1
nodes_per_elem = 4 # for a tet mesh
# Create a RC coordinate system
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(coordinateSystemUserNumber)
coordinateSystem.dimension = 3
coordinateSystem.CreateFinish()
# Create a region
region = iron.Region()
region.CreateStart(regionUserNumber, iron.WorldRegion)
region.label = "LaplaceRegion"
region.coordinateSystem = coordinateSystem
region.CreateFinish()
# Create a tri-linear simplex basis
basis = iron.Basis()
basis.CreateStart(basisUserNumber)
basis.TypeSet(iron.BasisTypes.SIMPLEX)
basis.numberOfXi = 3
basis.interpolationXi = [iron.BasisInterpolationSpecifications.LINEAR_SIMPLEX
] * 3
basis.CreateFinish()
# Start the creation of the imported mesh in the region
def solve_model(exportname, model=1, debug=False):
# Setting debug=False will prevent output of solver progress/results to the screen.
if debug:
print("Solving model {0}".format(model))
# Get the number of computational nodes and this computational node number
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
# computationalNodeNumber = iron.ComputationalNodeNumberGet()
# Create a 3D rectangular cartesian coordinate system
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(coordinateSystemUserNumber)
coordinateSystem.DimensionSet(3)
coordinateSystem.CreateFinish()
# Create a region and assign the coordinate system to the region
region = iron.Region()
region.CreateStart(regionUserNumber, iron.WorldRegion)
region.LabelSet("Region")
region.coordinateSystem = coordinateSystem
region.CreateFinish()
# Define basis
basis = iron.Basis()
basis.CreateStart(basisUserNumber)
if InterpolationType in (1, 2, 3, 4):
basis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
elif InterpolationType in (7, 8, 9):
basis.type = iron.BasisTypes.SIMPLEX
basis.numberOfXi = numberOfXi
basis.interpolationXi = (
[iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE] * numberOfXi)
if (NumberOfGaussXi > 0):
basis.quadratureNumberOfGaussXi = [NumberOfGaussXi] * numberOfXi
basis.CreateFinish()
if (UsePressureBasis):
# Define pressure basis
pressureBasis = iron.Basis()
pressureBasis.CreateStart(pressureBasisUserNumber)
if InterpolationType in (1, 2, 3, 4):
pressureBasis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
elif InterpolationType in (7, 8, 9):
pressureBasis.type = iron.BasisTypes.SIMPLEX
pressureBasis.numberOfXi = numberOfXi
pressureBasis.interpolationXi = (
[iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE] *
numberOfXi)
if (NumberOfGaussXi > 0):
pressureBasis.quadratureNumberOfGaussXi = [NumberOfGaussXi
] * numberOfXi
pressureBasis.CreateFinish()
# Start the creation of a generated mesh in the region
generatedMesh = iron.GeneratedMesh()
generatedMesh.CreateStart(generatedMeshUserNumber, region)
generatedMesh.type = iron.GeneratedMeshTypes.REGULAR
if (UsePressureBasis):
generatedMesh.basis = [basis, pressureBasis]
else:
generatedMesh.basis = [basis]
generatedMesh.extent = [width, length, height]
generatedMesh.numberOfElements = ([
numberGlobalXElements, numberGlobalYElements, numberGlobalZElements
])
# Finish the creation of a generated mesh in the region
mesh = iron.Mesh()
generatedMesh.CreateFinish(meshUserNumber, mesh)
# Create a decomposition for the mesh
decomposition = iron.Decomposition()
decomposition.CreateStart(decompositionUserNumber, mesh)
decomposition.type = iron.DecompositionTypes.CALCULATED
decomposition.numberOfDomains = numberOfComputationalNodes
decomposition.CreateFinish()
# Create a field for the geometry
geometricField = iron.Field()
geometricField.CreateStart(geometricFieldUserNumber, region)
geometricField.MeshDecompositionSet(decomposition)
geometricField.TypeSet(iron.FieldTypes.GEOMETRIC)
geometricField.VariableLabelSet(iron.FieldVariableTypes.U, "Geometry")
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3, 1)
if InterpolationType == 4:
geometricField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
geometricField.CreateFinish()
# Update the geometric field parameters from generated mesh
generatedMesh.GeometricParametersCalculate(geometricField)
# Create a fibre field and attach it to the geometric field
fibreField = iron.Field()
fibreField.CreateStart(fibreFieldUserNumber, region)
fibreField.TypeSet(iron.FieldTypes.FIBRE)
fibreField.MeshDecompositionSet(decomposition)
fibreField.GeometricFieldSet(geometricField)
fibreField.VariableLabelSet(iron.FieldVariableTypes.U, "Fibre")
if InterpolationType == 4:
fibreField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
fibreField.CreateFinish()
# Create a deformed geometry field, as Cmgui/Zinc doesn't like displaying
# deformed fibres from the dependent field because it isn't a geometric field.
deformedField = iron.Field()
deformedField.CreateStart(deformedFieldUserNumber, region)
deformedField.MeshDecompositionSet(decomposition)
deformedField.TypeSet(iron.FieldTypes.GEOMETRIC)
deformedField.VariableLabelSet(iron.FieldVariableTypes.U,
"DeformedGeometry")
for component in [1, 2, 3]:
deformedField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,
component, 1)
if InterpolationType == 4:
deformedField.ScalingTypeSet(iron.FieldScalingTypes.ARITHMETIC_MEAN)
deformedField.CreateFinish()
pressureField = iron.Field()
pressureField.CreateStart(pressureFieldUserNumber, region)
pressureField.MeshDecompositionSet(decomposition)
pressureField.VariableLabelSet(iron.FieldVariableTypes.U, "Pressure")
pressureField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
pressureField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 1,
iron.FieldInterpolationTypes.ELEMENT_BASED)
pressureField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 1)
pressureField.CreateFinish()
# Create the equations_set
equationsSetField = iron.Field()
equationsSet = iron.EquationsSet()
problemSpecification = [
iron.ProblemClasses.ELASTICITY, iron.ProblemTypes.FINITE_ELASTICITY,
iron.EquationsSetSubtypes.MOONEY_RIVLIN
]
equationsSet.CreateStart(equationsSetUserNumber, region, fibreField,
problemSpecification, equationsSetFieldUserNumber,
equationsSetField)
equationsSet.CreateFinish()
# Create the dependent field
dependentField = iron.Field()
equationsSet.DependentCreateStart(dependentFieldUserNumber, dependentField)
dependentField.VariableLabelSet(iron.FieldVariableTypes.U, "Dependent")
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 4,
iron.FieldInterpolationTypes.ELEMENT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.DELUDELN, 4,
iron.FieldInterpolationTypes.ELEMENT_BASED)
if (UsePressureBasis):
# Set the pressure to be nodally based and use the second mesh component
if InterpolationType == 4:
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 4,
iron.FieldInterpolationTypes.NODE_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.DELUDELN, 4,
iron.FieldInterpolationTypes.NODE_BASED)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 4,
2)
dependentField.ComponentMeshComponentSet(
iron.FieldVariableTypes.DELUDELN, 4, 2)
if InterpolationType == 4:
dependentField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
equationsSet.DependentCreateFinish()
# Create the material field
materialField = iron.Field()
equationsSet.MaterialsCreateStart(materialFieldUserNumber, materialField)
materialField.VariableLabelSet(iron.FieldVariableTypes.U, "Material")
equationsSet.MaterialsCreateFinish()
# Set Mooney-Rivlin constants c10 and c01 respectively.
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 1.0)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 2, 0.2)
# Create equations
equations = iron.Equations()
equationsSet.EquationsCreateStart(equations)
equations.sparsityType = iron.EquationsSparsityTypes.SPARSE
equations.outputType = iron.EquationsOutputTypes.NONE
equationsSet.EquationsCreateFinish()
# Initialise dependent field from undeformed geometry and displacement bcs and set hydrostatic pressure
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1)
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 2, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 2)
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 3, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 3)
iron.Field.ComponentValuesInitialiseDP(dependentField,
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
4, 0.0)
# Define the problem
problem = iron.Problem()
problemSpecification = [
iron.ProblemClasses.ELASTICITY, iron.ProblemTypes.FINITE_ELASTICITY,
iron.ProblemSubtypes.NONE
]
problem.CreateStart(problemUserNumber, problemSpecification)
problem.CreateFinish()
# Create the problem control loop
problem.ControlLoopCreateStart()
controlLoop = iron.ControlLoop()
problem.ControlLoopGet([iron.ControlLoopIdentifiers.NODE], controlLoop)
controlLoop.MaximumIterationsSet(numberOfLoadIncrements)
problem.ControlLoopCreateFinish()
# Create problem solver
nonLinearSolver = iron.Solver()
linearSolver = iron.Solver()
problem.SolversCreateStart()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1, nonLinearSolver)
if debug:
nonLinearSolver.outputType = iron.SolverOutputTypes.PROGRESS
else:
nonLinearSolver.outputType = iron.SolverOutputTypes.NONE
nonLinearSolver.NewtonJacobianCalculationTypeSet(
iron.JacobianCalculationTypes.EQUATIONS)
nonLinearSolver.NewtonLinearSolverGet(linearSolver)
linearSolver.linearType = iron.LinearSolverTypes.DIRECT
#linearSolver.libraryType = iron.SolverLibraries.LAPACK
problem.SolversCreateFinish()
# Create solver equations and add equations set to solver equations
solver = iron.Solver()
solverEquations = iron.SolverEquations()
problem.SolverEquationsCreateStart()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1, solver)
solver.SolverEquationsGet(solverEquations)
solverEquations.sparsityType = iron.SolverEquationsSparsityTypes.SPARSE
_ = solverEquations.EquationsSetAdd(equationsSet)
problem.SolverEquationsCreateFinish()
# Prescribe boundary conditions (absolute nodal parameters)
boundaryConditions = iron.BoundaryConditions()
solverEquations.BoundaryConditionsCreateStart(boundaryConditions)
if model == 1:
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
p = -2. * -0.1056E+01
elif model == 2:
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, X,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, X,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, X,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, X,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, Y,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, Y,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, Y,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, Y,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
p = -2. * -0.6656E+00
elif model == 3:
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
p = -2. * -0.1450E+01
elif model == 4:
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Z,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, Z,
iron.BoundaryConditionsTypes.FIXED, 0.5)
p = -2. * -0.1056E+01
elif model == 5:
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, X,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, X,
iron.BoundaryConditionsTypes.FIXED, 0.5)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, X,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, X,
iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, X,
iron.BoundaryConditionsTypes.FIXED, 0.75)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, X,
iron.BoundaryConditionsTypes.FIXED, 0.75)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Y,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, Z,
iron.BoundaryConditionsTypes.FIXED, 0.0)
p = -2. * -0.1000E+01
solverEquations.BoundaryConditionsCreateFinish()
# Solve the problem
problem.Solve()
# Copy deformed geometry into deformed field
for component in [1, 2, 3]:
dependentField.ParametersToFieldParametersComponentCopy(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
component, deformedField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, component)
# Copy pressure into pressure field
dependentField.ParametersToFieldParametersComponentCopy(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 4,
pressureField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1)
# Export results
fields = iron.Fields()
fields.CreateRegion(region)
fields.NodesExport(exportname, "FORTRAN")
fields.ElementsExport(exportname, "FORTRAN")
fields.Finalise()
results = {}
elementNumber = 1
xiPosition = [0.5, 0.5, 0.5]
F = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.DEFORMATION_GRADIENT,
elementNumber, xiPosition, (3, 3))
results['Deformation Gradient Tensor'] = F
if debug:
print("Deformation Gradient Tensor")
print(F)
C = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.R_CAUCHY_GREEN_DEFORMATION,
elementNumber, xiPosition, (3, 3))
results['Right Cauchy-Green Deformation Tensor'] = C
if debug:
print("Right Cauchy-Green Deformation Tensor")
print(C)
E = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.GREEN_LAGRANGE_STRAIN,
elementNumber, xiPosition, (3, 3))
results['Green-Lagrange Strain Tensor'] = E
if debug:
print("Green-Lagrange Strain Tensor")
print(E)
I1 = numpy.trace(C)
I2 = 0.5 * (numpy.trace(C)**2. - numpy.tensordot(C, C))
I3 = numpy.linalg.det(C)
results['Invariants'] = [I1, I2, I3]
if debug:
print("Invariants")
print("I1={0}, I2={1}, I3={2}".format(I1, I2, I3))
TC = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.CAUCHY_STRESS, elementNumber,
xiPosition, (3, 3))
results['Cauchy Stress Tensor'] = TC
if debug:
print("Cauchy Stress Tensor")
print(TC)
# Output of Second Piola-Kirchhoff Stress Tensor not implemented. It is
# instead, calculated from TG=J*F^(-1)*TC*F^(-T), where T indicates the
# transpose fo the matrix.
#TG = equationsSet.TensorInterpolateXi(
# iron.EquationsSetTensorEvaluateTypes.SECOND_PK_STRESS,
# elementNumber, xiPosition,(3,3))
#J=1. #Assumes J=1
TG = numpy.dot(numpy.linalg.inv(F),
numpy.dot(TC, numpy.linalg.inv(numpy.matrix.transpose(F))))
results['Second Piola-Kirchhoff Stress Tensor'] = TG
if debug:
print("Second Piola-Kirchhoff Stress Tensor")
print(TG)
# Note that the hydrostatic pressure value is different from the value quoted
# in the original lab instructions. This is because the stress has been
# evaluated using modified invariants (isochoric invariants)
#p = dependentField.ParameterSetGetElement(
# iron.FieldVariableTypes.U,
# iron.FieldParameterSetTypes.VALUES,elementNumber,4)
results['Hydrostatic pressure'] = p
if debug:
print("Hydrostatic pressure")
print(p)
problem.Destroy()
coordinateSystem.Destroy()
region.Destroy()
basis.Destroy()
return results
def mesh_conversion(dimension, interpolation, exfile_coordinate_field,
exnode_filename, exelem_filename, results_folder,
results_filename):
# Read in ex mesh as a morphic mesh.
cubic_hermite_morphic_mesh = mesh_tools.exfile_to_morphic(
exnode_filename,
exelem_filename,
exfile_coordinate_field,
dimension=dimension,
interpolation='hermite')
# Convert mesh from cubic hermite to cubic Lagrange
lagrange_morphic_mesh = convert_hermite_lagrange(
cubic_hermite_morphic_mesh, tol=1e-9, interpolation=interpolation)
# List nodes
print("Node numbers")
print(lagrange_morphic_mesh.get_node_ids(group='_default')[1])
print("Node coordinates")
print(lagrange_morphic_mesh.get_node_ids(group='_default')[0])
# List node ids in each element
for element in lagrange_morphic_mesh.elements:
print("Element number")
print(element.id)
print("Element node numbers")
print(element.node_ids)
# Export mesh in ex format using OpenCMISS
module_spec = util.find_spec("opencmiss")
opencmiss_found = module_spec is not None
if opencmiss_found:
from opencmiss.iron import iron
if interpolation == "quadraticLagrange":
opencmiss_mesh_interpolation = \
iron.BasisInterpolationSpecifications.QUADRATIC_LAGRANGE
elif interpolation == "cubicLagrange":
opencmiss_mesh_interpolation = \
iron.BasisInterpolationSpecifications.CUBIC_LAGRANGE
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
computationalNodeNumber = iron.ComputationalNodeNumberGet()
coordinateSystemUserNumber = 1
regionUserNumber = 3
basisUserNumber = 2
meshUserNumber = 1
decompositionUserNumber = 1
geometricFieldUserNumber = 1
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(coordinateSystemUserNumber)
coordinateSystem.dimension = 3
coordinateSystem.CreateFinish()
basis = iron.Basis()
basis.CreateStart(basisUserNumber)
basis.TypeSet(iron.BasisTypes.LAGRANGE_HERMITE_TP)
basis.NumberOfXiSet(dimension)
basis.InterpolationXiSet([opencmiss_mesh_interpolation] * dimension)
basis.QuadratureNumberOfGaussXiSet([4] * dimension)
basis.CreateFinish()
region = iron.Region()
region.CreateStart(regionUserNumber, iron.WorldRegion)
region.LabelSet("Region")
region.CoordinateSystemSet(coordinateSystem)
region.CreateFinish()
mesh, coordinates, node_nums, element_nums = mesh_tools.morphic_to_OpenCMISS(
lagrange_morphic_mesh,
region,
basis,
meshUserNumber,
dimension=dimension,
interpolation=interpolation,
UsePressureBasis=False,
pressureBasis=None)
decomposition = iron.Decomposition()
decomposition.CreateStart(decompositionUserNumber, mesh)
decomposition.TypeSet(iron.DecompositionTypes.CALCULATED)
decomposition.NumberOfDomainsSet(numberOfComputationalNodes)
decomposition.CreateFinish()
geometric_field = iron.Field()
geometric_field.CreateStart(geometricFieldUserNumber, region)
geometric_field.MeshDecompositionSet(decomposition)
geometric_field.VariableLabelSet(iron.FieldVariableTypes.U, "Geometry")
geometric_field.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1,
1)
geometric_field.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2,
1)
geometric_field.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3,
1)
geometric_field.CreateFinish()
# Update the geometric field parameters
geometric_field.ParameterSetUpdateStart(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
for node_idx, node in enumerate(node_nums):
for component_idx, component in enumerate([1, 2, 3]):
for derivative_idx, derivative in enumerate(
range(1, coordinates.shape[2] + 1)):
geometric_field.ParameterSetUpdateNodeDP(
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1, derivative,
node, component, coordinates[node_idx, component_idx,
derivative_idx])
geometric_field.ParameterSetUpdateFinish(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
output_file = os.path.join(results_folder, results_filename)
fields = iron.Fields()
fields.CreateRegion(region)
fields.NodesExport(output_file, "FORTRAN")
fields.ElementsExport(output_file, "FORTRAN")
fields.Finalise()
def solve_model(exportname, model=1, debug=False):
# Setting debug=False will prevent output of solver progress/results to the screen.
if debug:
print("Solving model {0}".format(model))
# Get the number of computational nodes and this computational node number
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
# computationalNodeNumber = iron.ComputationalNodeNumberGet()
# Create a 3D rectangular cartesian coordinate system
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(coordinateSystemUserNumber)
coordinateSystem.DimensionSet(3)
coordinateSystem.CreateFinish()
# Create a region and assign the coordinate system to the region
region = iron.Region()
region.CreateStart(regionUserNumber, iron.WorldRegion)
region.LabelSet("Region")
region.coordinateSystem = coordinateSystem
region.CreateFinish()
# Define basis
basis = iron.Basis()
basis.CreateStart(basisUserNumber)
if InterpolationType in (1, 2, 3, 4):
basis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
elif InterpolationType in (7, 8, 9):
basis.type = iron.BasisTypes.SIMPLEX
basis.numberOfXi = numberOfXi
basis.interpolationXi = (
[iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE] * numberOfXi)
if (NumberOfGaussXi > 0):
basis.quadratureNumberOfGaussXi = [NumberOfGaussXi] * numberOfXi
basis.CreateFinish()
if (UsePressureBasis):
# Define pressure basis
pressureBasis = iron.Basis()
pressureBasis.CreateStart(pressureBasisUserNumber)
if InterpolationType in (1, 2, 3, 4):
pressureBasis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
elif InterpolationType in (7, 8, 9):
pressureBasis.type = iron.BasisTypes.SIMPLEX
pressureBasis.numberOfXi = numberOfXi
pressureBasis.interpolationXi = (
[iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE] *
numberOfXi)
if (NumberOfGaussXi > 0):
pressureBasis.quadratureNumberOfGaussXi = [NumberOfGaussXi
] * numberOfXi
pressureBasis.CreateFinish()
# Start the creation of a generated mesh in the region
generatedMesh = iron.GeneratedMesh()
generatedMesh.CreateStart(generatedMeshUserNumber, region)
generatedMesh.type = iron.GeneratedMeshTypes.REGULAR
if (UsePressureBasis):
generatedMesh.basis = [basis, pressureBasis]
else:
generatedMesh.basis = [basis]
generatedMesh.extent = [width, length, height]
generatedMesh.numberOfElements = ([
numberGlobalXElements, numberGlobalYElements, numberGlobalZElements
])
# Finish the creation of a generated mesh in the region
mesh = iron.Mesh()
generatedMesh.CreateFinish(meshUserNumber, mesh)
# Create a decomposition for the mesh
decomposition = iron.Decomposition()
decomposition.CreateStart(decompositionUserNumber, mesh)
decomposition.type = iron.DecompositionTypes.CALCULATED
decomposition.numberOfDomains = numberOfComputationalNodes
decomposition.CreateFinish()
# Create a field for the geometry
geometricField = iron.Field()
geometricField.CreateStart(geometricFieldUserNumber, region)
geometricField.MeshDecompositionSet(decomposition)
geometricField.TypeSet(iron.FieldTypes.GEOMETRIC)
geometricField.VariableLabelSet(iron.FieldVariableTypes.U, "Geometry")
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3, 1)
if InterpolationType == 4:
geometricField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
geometricField.CreateFinish()
# Update the geometric field parameters from generated mesh
generatedMesh.GeometricParametersCalculate(geometricField)
# Create a fibre field and attach it to the geometric field
fibreField = iron.Field()
fibreField.CreateStart(fibreFieldUserNumber, region)
fibreField.TypeSet(iron.FieldTypes.FIBRE)
fibreField.MeshDecompositionSet(decomposition)
fibreField.GeometricFieldSet(geometricField)
fibreField.VariableLabelSet(iron.FieldVariableTypes.U, "Fibre")
if InterpolationType == 4:
fibreField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
fibreField.CreateFinish()
# Create a deformed geometry field, as Cmgui/Zinc doesn't like displaying
# deformed fibres from the dependent field because it isn't a geometric field.
deformedField = iron.Field()
deformedField.CreateStart(deformedFieldUserNumber, region)
deformedField.MeshDecompositionSet(decomposition)
deformedField.TypeSet(iron.FieldTypes.GEOMETRIC)
deformedField.VariableLabelSet(iron.FieldVariableTypes.U,
"DeformedGeometry")
for component in [1, 2, 3]:
deformedField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,
component, 1)
if InterpolationType == 4:
deformedField.ScalingTypeSet(iron.FieldScalingTypes.ARITHMETIC_MEAN)
deformedField.CreateFinish()
pressureField = iron.Field()
pressureField.CreateStart(pressureFieldUserNumber, region)
pressureField.MeshDecompositionSet(decomposition)
pressureField.VariableLabelSet(iron.FieldVariableTypes.U, "Pressure")
pressureField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
pressureField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 1,
iron.FieldInterpolationTypes.ELEMENT_BASED)
pressureField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 1)
pressureField.CreateFinish()
# Create the equations_set
equationsSetField = iron.Field()
equationsSet = iron.EquationsSet()
problemSpecification = [
iron.ProblemClasses.ELASTICITY, iron.ProblemTypes.FINITE_ELASTICITY,
iron.EquationsSetSubtypes.ORTHOTROPIC_MATERIAL_COSTA
]
equationsSet.CreateStart(equationsSetUserNumber, region, fibreField,
problemSpecification, equationsSetFieldUserNumber,
equationsSetField)
equationsSet.CreateFinish()
# Create the dependent field
dependentField = iron.Field()
equationsSet.DependentCreateStart(dependentFieldUserNumber, dependentField)
dependentField.VariableLabelSet(iron.FieldVariableTypes.U, "Dependent")
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 4,
iron.FieldInterpolationTypes.ELEMENT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.DELUDELN, 4,
iron.FieldInterpolationTypes.ELEMENT_BASED)
if (UsePressureBasis):
# Set the pressure to be nodally based and use the second mesh component
if InterpolationType == 4:
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 4,
iron.FieldInterpolationTypes.NODE_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.DELUDELN, 4,
iron.FieldInterpolationTypes.NODE_BASED)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 4,
2)
dependentField.ComponentMeshComponentSet(
iron.FieldVariableTypes.DELUDELN, 4, 2)
if InterpolationType == 4:
dependentField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
equationsSet.DependentCreateFinish()
# Create the material field
materialField = iron.Field()
equationsSet.MaterialsCreateStart(materialFieldUserNumber, materialField)
materialField.VariableLabelSet(iron.FieldVariableTypes.U, "Material")
equationsSet.MaterialsCreateFinish()
# Set Costa constitutive relation parameters.
# Q=[c_ff 2c_fs 2c_fn c_ss 2c_ns c_nn]' * [E_ff E_fs E_fn E_ss E_sn E_nn].^2;
if model in [1, 3, 4]:
c_1 = 0.0475
c_ff = 15.25
c_fs = 6.05
c_fn = c_fs
c_ss = c_ff
c_sn = c_fs
c_nn = c_ff
elif model in [2, 5, 6]:
c_1 = 0.0475
c_ff = 15.25
c_fs = 6.95
c_fn = 6.05
c_ss = 6.8
c_sn = 4.93
c_nn = 8.9
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, c_1)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 2, c_ff)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 3, c_fs)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 4, c_fn)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 5, c_ss)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 6, c_sn)
materialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 7, c_nn)
if model in [1, 2]:
angle = numpy.deg2rad(0.)
elif model == 3:
angle = numpy.deg2rad(30.)
elif model in [4, 5]:
angle = numpy.deg2rad(45.)
elif model == 6:
angle = numpy.deg2rad(90.)
fibreField.ComponentValuesInitialiseDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, angle)
# Create equations
equations = iron.Equations()
equationsSet.EquationsCreateStart(equations)
equations.sparsityType = iron.EquationsSparsityTypes.SPARSE
equations.outputType = iron.EquationsOutputTypes.NONE
equationsSet.EquationsCreateFinish()
# Initialise dependent field from undeformed geometry and displacement bcs and set hydrostatic pressure
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1)
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 2, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 2)
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 3, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 3)
iron.Field.ComponentValuesInitialiseDP(dependentField,
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
4, 0.0)
# Define the problem
problem = iron.Problem()
problemSpecification = [
iron.ProblemClasses.ELASTICITY, iron.ProblemTypes.FINITE_ELASTICITY,
iron.ProblemSubtypes.NONE
]
problem.CreateStart(problemUserNumber, problemSpecification)
problem.CreateFinish()
# Create the problem control loop
problem.ControlLoopCreateStart()
controlLoop = iron.ControlLoop()
problem.ControlLoopGet([iron.ControlLoopIdentifiers.NODE], controlLoop)
controlLoop.MaximumIterationsSet(numberOfLoadIncrements)
problem.ControlLoopCreateFinish()
# Create problem solver
nonLinearSolver = iron.Solver()
linearSolver = iron.Solver()
problem.SolversCreateStart()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1, nonLinearSolver)
if debug:
nonLinearSolver.outputType = iron.SolverOutputTypes.PROGRESS
else:
nonLinearSolver.outputType = iron.SolverOutputTypes.NONE
nonLinearSolver.NewtonJacobianCalculationTypeSet(
iron.JacobianCalculationTypes.EQUATIONS)
nonLinearSolver.NewtonLinearSolverGet(linearSolver)
linearSolver.linearType = iron.LinearSolverTypes.DIRECT
#linearSolver.libraryType = iron.SolverLibraries.LAPACK
problem.SolversCreateFinish()
# Create solver equations and add equations set to solver equations
solver = iron.Solver()
solverEquations = iron.SolverEquations()
problem.SolverEquationsCreateStart()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1, solver)
solver.SolverEquationsGet(solverEquations)
solverEquations.sparsityType = iron.SolverEquationsSparsityTypes.SPARSE
_ = solverEquations.EquationsSetAdd(equationsSet)
problem.SolverEquationsCreateFinish()
# Prescribe boundary conditions (absolute nodal parameters)
boundaryConditions = iron.BoundaryConditions()
solverEquations.BoundaryConditionsCreateStart(boundaryConditions)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
1, X, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
3, X, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
5, X, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
7, X, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
2, X, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
4, X, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
6, X, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
8, X, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
1, Y, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
2, Y, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
5, Y, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
6, Y, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
3, Y, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
4, Y, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
7, Y, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
8, Y, iron.BoundaryConditionsTypes.FIXED, 0.25)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
1, Z, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
2, Z, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
3, Z, iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U, 1, 1,
4, Z, iron.BoundaryConditionsTypes.FIXED, 0.0)
solverEquations.BoundaryConditionsCreateFinish()
# Solve the problem
problem.Solve()
# Copy deformed geometry into deformed field
for component in [1, 2, 3]:
dependentField.ParametersToFieldParametersComponentCopy(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
component, deformedField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, component)
# Copy pressure into pressure field
dependentField.ParametersToFieldParametersComponentCopy(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 4,
pressureField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1)
# Export results
fields = iron.Fields()
fields.CreateRegion(region)
fields.NodesExport(exportname, "FORTRAN")
fields.ElementsExport(exportname, "FORTRAN")
fields.Finalise()
Q = numpy.array([[numpy.cos(angle), -numpy.sin(angle), 0.],
[numpy.sin(angle), numpy.cos(angle), 0.], [0., 0., 1.]])
results = {}
elementNumber = 1
xiPosition = [0.5, 0.5, 0.5]
# Note that there seems to be a bug with F in OpenCMISS when fibre angles are specified in x1-x2 plane
#F = equationsSet.TensorInterpolateXi(
# iron.EquationsSetTensorEvaluateTypes.DEFORMATION_GRADIENT,
# elementNumber, xiPosition,(3,3))
Ffib = numpy.array([[0.1250E+01, 0., 0.], [0., 0.1250E+01, 0.],
[0., 0., 0.6400E+00]])
Fref = Ffib
results["Deformation gradient tensor (fibre coordinate system)"] = Ffib
results["Deformation gradient tensor (reference coordinate system)"] = Fref
if debug:
print("Deformation gradient tensor (fibre coordinate system)")
print(Ffib)
print("Deformation gradient tensor (reference coordinate system)")
print(Fref)
Cfib = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.R_CAUCHY_GREEN_DEFORMATION,
elementNumber, xiPosition, (3, 3))
Cref = Cfib
results[
"Right Cauchy-Green deformation tensor (fibre coordinate system)"] = Cfib
results[
"Right Cauchy-Green deformation tensor (reference coordinate system)"] = Cref
if debug:
print(
"Right Cauchy-Green deformation tensor (fibre coordinate system)")
print(Cfib)
print(
"Right Cauchy-Green deformation tensor (reference coordinate system)"
)
print(Cref)
Efib = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.GREEN_LAGRANGE_STRAIN,
elementNumber, xiPosition, (3, 3))
results["Green-Lagrange strain tensor (fibre coordinate system)"] = Efib
if debug:
print("Green-Lagrange strain tensor (fibre coordinate system)")
print(Efib)
Eref = numpy.dot(Q, numpy.dot(Efib, numpy.matrix.transpose(Q)))
results[
"Green-Lagrange strain tensor (reference coordinate system)"] = Eref
if debug:
print("Green-Lagrange strain tensor (reference coordinate system)")
print(Eref)
I1 = numpy.trace(Cfib)
I2 = 0.5 * (numpy.trace(Cfib)**2. - numpy.tensordot(Cfib, Cfib))
I3 = numpy.linalg.det(Cfib)
results["Invariants of Cfib (fibre coordinate system)"] = [I1, I2, I3]
if debug:
print("Invariants of Cfib (fibre coordinate system)")
print("I1={0}, I2={1}, I3={2}".format(I1, I2, I3))
I1 = numpy.trace(Cref)
I2 = 0.5 * (numpy.trace(Cref)**2. - numpy.tensordot(Cref, Cref))
I3 = numpy.linalg.det(Cref)
results["Invariants of Cref (reference coordinate system)"] = [I1, I2, I3]
if debug:
print("Invariants of Cref (reference coordinate system)")
print("I1={0}, I2={1}, I3={2}".format(I1, I2, I3))
TCref = equationsSet.TensorInterpolateXi(
iron.EquationsSetTensorEvaluateTypes.CAUCHY_STRESS, elementNumber,
xiPosition, (3, 3))
results["Cauchy stress tensor (reference coordinate system)"] = TCref
if debug:
print("Cauchy stress tensor (reference coordinate system)")
print(TCref)
# Output of Second Piola-Kirchhoff Stress Tensor not implemented. It is
# instead, calculated from TG=J*F^(-1)*TC*F^(-T), where T indicates the
# transpose fo the matrix.
#TG = equationsSet.TensorInterpolateXi(
# iron.EquationsSetTensorEvaluateTypes.SECOND_PK_STRESS,
# elementNumber, xiPosition,(3,3))
#J=1. #Assumes J=1
TGref = numpy.dot(
numpy.linalg.inv(Fref),
numpy.dot(TCref, numpy.linalg.inv(numpy.matrix.transpose(Fref))))
results[
"Second Piola-Kirchhoff stress tensor (reference coordinate system)"] = TGref
if debug:
print(
"Second Piola-Kirchhoff stress tensor (reference coordinate system)"
)
print(TGref)
TGfib = numpy.dot(numpy.matrix.transpose(Q), numpy.dot(TGref, Q))
results[
"Second Piola-Kirchhoff stress tensor (fibre coordinate system)"] = TGfib
if debug:
print("Second Piola-Kirchhoff stress tensor (fibre coordinate system)")
print(TGfib)
# Note that the hydrostatic pressure value is different from the value quoted
# in the original lab instructions. This is because the stress has been
# evaluated using modified invariants (isochoric invariants)
p = -dependentField.ParameterSetGetElement(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
elementNumber, 4)
results["Hydrostatic pressure"] = p
if debug:
print("Hydrostatic pressure")
print(p)
problem.Destroy()
coordinateSystem.Destroy()
region.Destroy()
basis.Destroy()
return results
def simulate(fibreAngleIn, materialParameters):
'''
Main function to run a finite elasticity simulation using OpenCMISS with a unit cube and the Guccione material law (in CellML).
fibreAngle is a scalar angle in degrees
materialParameters is a list of the four Guccione material parameters.
'''
# Set problem parameters - Unit cube
height = 1.0
width = 1.0
length = 1.0
# if len(sys.argv) != 2:
# usage(sys.argv[0])
# exit(-1)
fa = fibreAngleIn
print("fa = " + str(fa))
# Fibre angles in radians:
fibreAngle = fa * pi / 180.0
# (transversly isotropic, so assume 0 cross-fibre angle?)
sheetAngle = 90.0 * pi / 180.0
fibreAngles = [fibreAngle, 0.0, sheetAngle]
# Guccione constitutive relation:
constitutiveRelation = iron.EquationsSetSubtypes.CONSTITUTIVE_LAW_IN_CELLML_EVALUATE
constitutiveParameters = [0.88, 18.5, 3.58, 3.26]
constitutiveParameters = materialParameters
initialHydrostaticPressure = 0.0
UsePressureBasis = False
NumberOfGaussXi = 2
coordinateSystemUserNumber = 1
regionUserNumber = 1
basisUserNumber = 1
pressureBasisUserNumber = 2
generatedMeshUserNumber = 1
meshUserNumber = 1
decompositionUserNumber = 1
geometricFieldUserNumber = 1
fibreFieldUserNumber = 2
materialFieldUserNumber = 3
dependentFieldUserNumber = 4
equationsSetFieldUserNumber = 5
deformedFieldUserNumber = 6
equationsSetUserNumber = 1
problemUserNumber = 1
CellMLUserNumber = 1
CellMLModelsFieldUserNumber = 7
CellMLParametersFieldUserNumber = 8
CellMLIntermediateFieldUserNumber = 9
# Set all diganostic levels on for testing
#iron.DiagnosticsSetOn(iron.DiagnosticTypes.ALL,[1,2,3,4,5],"Diagnostics",["DOMAIN_MAPPINGS_LOCAL_FROM_GLOBAL_CALCULATE"])
numberGlobalXElements = 1
numberGlobalYElements = 1
numberGlobalZElements = 1
totalNumberOfNodes = 8
totalNumberOfElements = 1
InterpolationType = 1
if (UsePressureBasis):
numberOfMeshComponents = 2
else:
numberOfMeshComponents = 1
if (numberGlobalZElements == 0):
numberOfXi = 2
else:
numberOfXi = 3
# Get the number of computational nodes and this computational node number
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
computationalNodeNumber = iron.ComputationalNodeNumberGet()
# Create a 3D rectangular cartesian coordinate system
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(coordinateSystemUserNumber)
coordinateSystem.DimensionSet(3)
coordinateSystem.CreateFinish()
# Create a region and assign the coordinate system to the region
region = iron.Region()
region.CreateStart(regionUserNumber, iron.WorldRegion)
region.LabelSet("Region")
region.coordinateSystem = coordinateSystem
region.CreateFinish()
# Define basis
basis = iron.Basis()
basis.CreateStart(basisUserNumber)
if InterpolationType in (1, 2, 3, 4):
basis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
elif InterpolationType in (7, 8, 9):
basis.type = iron.BasisTypes.SIMPLEX
basis.numberOfXi = numberOfXi
basis.interpolationXi = [
iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE
] * numberOfXi
if (NumberOfGaussXi > 0):
basis.quadratureNumberOfGaussXi = [NumberOfGaussXi] * numberOfXi
basis.CreateFinish()
if (UsePressureBasis):
# Define pressure basis
pressureBasis = iron.Basis()
pressureBasis.CreateStart(pressureBasisUserNumber)
if InterpolationType in (1, 2, 3, 4):
pressureBasis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
elif InterpolationType in (7, 8, 9):
pressureBasis.type = iron.BasisTypes.SIMPLEX
pressureBasis.numberOfXi = numberOfXi
pressureBasis.interpolationXi = [
iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE
] * numberOfXi
if (NumberOfGaussXi > 0):
pressureBasis.quadratureNumberOfGaussXi = [NumberOfGaussXi
] * numberOfXi
pressureBasis.CreateFinish()
# Start the creation of a manually generated mesh in the region
mesh = iron.Mesh()
mesh.CreateStart(meshUserNumber, region, numberOfXi)
mesh.NumberOfComponentsSet(numberOfMeshComponents)
mesh.NumberOfElementsSet(totalNumberOfElements)
#Define nodes for the mesh
nodes = iron.Nodes()
nodes.CreateStart(region, totalNumberOfNodes)
nodes.CreateFinish()
elements = iron.MeshElements()
meshComponentNumber = 1
elements.CreateStart(mesh, meshComponentNumber, basis)
elements.NodesSet(1, [1, 2, 3, 4, 5, 6, 7, 8])
elements.CreateFinish()
mesh.CreateFinish()
# Create a decomposition for the mesh
decomposition = iron.Decomposition()
decomposition.CreateStart(decompositionUserNumber, mesh)
decomposition.type = iron.DecompositionTypes.CALCULATED
decomposition.numberOfDomains = numberOfComputationalNodes
decomposition.CreateFinish()
# Create a field for the geometry
geometricField = iron.Field()
geometricField.CreateStart(geometricFieldUserNumber, region)
geometricField.MeshDecompositionSet(decomposition)
geometricField.TypeSet(iron.FieldTypes.GEOMETRIC)
geometricField.VariableLabelSet(iron.FieldVariableTypes.U, "Geometry")
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3, 1)
if InterpolationType == 4:
geometricField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
geometricField.CreateFinish()
# Update the geometric field parameters manually
geometricField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# node 1
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 1, 1, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 1, 2, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 1, 3, 0.0)
# node 2
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 2, 1, height)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 2, 2, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 2, 3, 0.0)
# node 3
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 3, 1, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 3, 2, width)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 3, 3, 0.0)
# node 4
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 4, 1, height)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 4, 2, width)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 4, 3, 0.0)
# node 5
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 5, 1, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 5, 2, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 5, 3, length)
# node 6
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 6, 1, height)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 6, 2, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 6, 3, length)
# node 7
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 7, 1, 0.0)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 7, 2, width)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 7, 3, length)
# node 8
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 8, 1, height)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 8, 2, width)
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, 8, 3, length)
geometricField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# Create a fibre field and attach it to the geometric field
fibreField = iron.Field()
fibreField.CreateStart(fibreFieldUserNumber, region)
fibreField.TypeSet(iron.FieldTypes.FIBRE)
fibreField.MeshDecompositionSet(decomposition)
fibreField.GeometricFieldSet(geometricField)
fibreField.VariableLabelSet(iron.FieldVariableTypes.U, "Fibre")
if InterpolationType == 4:
fibreField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
fibreField.CreateFinish()
iron.Field.ComponentValuesInitialiseDP(fibreField,
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, fibreAngle)
iron.Field.ComponentValuesInitialiseDP(fibreField,
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
2, 0.0)
iron.Field.ComponentValuesInitialiseDP(fibreField,
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
3, sheetAngle)
# # Create the material field
# materialField = iron.Field()
# materialField.CreateStart(materialFieldUserNumber,region)
# materialField.TypeSet(iron.FieldTypes.MATERIAL)
# materialField.MeshDecompositionSet(decomposition)
# materialField.GeometricFieldSet(geometricField)
# materialField.NumberOfVariablesSet(1)
# materialField.NumberOfComponentsSet(iron.FieldVariableTypes.U,len(constitutiveParameters))
# materialField.VariableLabelSet(iron.FieldVariableTypes.U,"Material")
# materialField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,1,1)
# materialField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,2,1)
# if InterpolationType == 4:
# materialField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
# materialField.CreateFinish()
# Set constant material parameters:
# for (component, value) in enumerate(constitutiveParameters, 1):
# materialField.ComponentValuesInitialise(
# iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
# component, value)
# Create the dependent field
dependentField = iron.Field()
dependentField.CreateStart(dependentFieldUserNumber, region)
dependentField.VariableLabelSet(iron.FieldVariableTypes.U, "Dependent")
dependentField.TypeSet(iron.FieldTypes.GEOMETRIC_GENERAL)
dependentField.MeshDecompositionSet(decomposition)
dependentField.GeometricFieldSet(geometricField)
dependentField.DependentTypeSet(iron.FieldDependentTypes.DEPENDENT)
dependentField.NumberOfVariablesSet(4)
dependentField.VariableTypesSet([
iron.FieldVariableTypes.U, iron.FieldVariableTypes.DELUDELN,
iron.FieldVariableTypes.U1, iron.FieldVariableTypes.U2
])
dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 4)
dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.DELUDELN, 4)
dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U1, 6)
dependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U2, 6)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,
1, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,
2, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.DELUDELN,
3, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1, 1, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1, 2, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1, 3, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1, 4, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1, 5, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U1, 6, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2, 1, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2, 2, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2, 3, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2, 4, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2, 5, 1)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U2, 6, 1)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 4,
iron.FieldInterpolationTypes.ELEMENT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.DELUDELN, 4,
iron.FieldInterpolationTypes.ELEMENT_BASED)
if (UsePressureBasis):
# Set the pressure to be nodally based and use the second mesh component
if InterpolationType == 4:
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, 4,
iron.FieldInterpolationTypes.NODE_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.DELUDELN, 4,
iron.FieldInterpolationTypes.NODE_BASED)
dependentField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 4,
2)
dependentField.ComponentMeshComponentSet(
iron.FieldVariableTypes.DELUDELN, 4, 2)
if InterpolationType == 4:
dependentField.fieldScalingType = iron.FieldScalingTypes.ARITHMETIC_MEAN
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U1, 1,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U1, 2,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U1, 3,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U1, 4,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U1, 5,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U1, 6,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U2, 1,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U2, 2,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U2, 3,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U2, 4,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U2, 5,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.ComponentInterpolationSet(
iron.FieldVariableTypes.U2, 6,
iron.FieldInterpolationTypes.GAUSS_POINT_BASED)
dependentField.VariableLabelSet(iron.FieldVariableTypes.U1, "strain")
dependentField.VariableLabelSet(iron.FieldVariableTypes.U2, "stress")
dependentField.CreateFinish()
# Initialise dependent field from undeformed geometry and displacement bcs and set hydrostatic pressure
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1)
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 2, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 2)
iron.Field.ParametersToFieldParametersComponentCopy(
geometricField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 3, dependentField,
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 3)
iron.Field.ComponentValuesInitialiseDP(dependentField,
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
4, -8.0)
# Create a deformed geometry field, as cmgui doesn't like displaying
# deformed fibres from the dependent field because it isn't a geometric field.
deformedField = iron.Field()
deformedField.CreateStart(deformedFieldUserNumber, region)
deformedField.MeshDecompositionSet(decomposition)
deformedField.TypeSet(iron.FieldTypes.GEOMETRIC)
deformedField.VariableLabelSet(iron.FieldVariableTypes.U,
"DeformedGeometry")
for component in [1, 2, 3]:
deformedField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,
component, 1)
if InterpolationType == 4:
deformedField.ScalingTypeSet(iron.FieldScalingTypes.ARITHMETIC_MEAN)
deformedField.CreateFinish()
# Create the equations_set
equationsSetField = iron.Field()
equationsSet = iron.EquationsSet()
equationsSetSpecification = [
iron.EquationsSetClasses.ELASTICITY,
iron.EquationsSetTypes.FINITE_ELASTICITY, constitutiveRelation
]
equationsSet.CreateStart(equationsSetUserNumber, region, fibreField,
equationsSetSpecification,
equationsSetFieldUserNumber, equationsSetField)
equationsSet.CreateFinish()
# Create the CellML environment
CellML = iron.CellML()
CellML.CreateStart(CellMLUserNumber, region)
# here we get the current path of this script so that we can specify the CellML model document relative to
# this script, rather than the execution folder.
from os.path import dirname, join
script_path = dirname(__file__)
cellmlFile = join(script_path, "guccione.cellml")
# guccioneCellMLParameters = [0.88, 0.0, 18.5, 3.58, 3.26] # default values in CellML model
guccioneCellMLParameters = [1.0, 0.0, 5.0, 10.0, 5.0]
guccioneCellMLParameters = [
materialParameters[0], 0.0, materialParameters[1],
materialParameters[2], materialParameters[3]
]
# the names of the variables in the CellML model for the parameters in the same order as the values above
guccioneCellMLParameterIds = [
"interface/c1", "interface/c2", "interface/c3", "interface/c4",
"interface/c5"
]
# Import a Guccione material law from a file
GuccioneModel = CellML.ModelImport(cellmlFile)
# Now we have imported the model we are able to specify which variables from the model we want to set from openCMISS
CellML.VariableSetAsKnown(GuccioneModel, "equations/E11")
CellML.VariableSetAsKnown(GuccioneModel, "equations/E12")
CellML.VariableSetAsKnown(GuccioneModel, "equations/E13")
CellML.VariableSetAsKnown(GuccioneModel, "equations/E22")
CellML.VariableSetAsKnown(GuccioneModel, "equations/E23")
CellML.VariableSetAsKnown(GuccioneModel, "equations/E33")
for component, parameter in enumerate(guccioneCellMLParameterIds):
CellML.VariableSetAsKnown(GuccioneModel, parameter)
# and variables to get from the CellML
CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev11")
CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev12")
CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev13")
CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev22")
CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev23")
CellML.VariableSetAsWanted(GuccioneModel, "equations/Tdev33")
CellML.CreateFinish()
# Start the creation of CellML <--> OpenCMISS field maps
CellML.FieldMapsCreateStart()
#Now we can set up the field variable component <--> CellML model variable mappings.
#Map the strain components
CellML.CreateFieldToCellMLMap(dependentField, iron.FieldVariableTypes.U1,
1, iron.FieldParameterSetTypes.VALUES,
GuccioneModel, "equations/E11",
iron.FieldParameterSetTypes.VALUES)
CellML.CreateFieldToCellMLMap(dependentField, iron.FieldVariableTypes.U1,
2, iron.FieldParameterSetTypes.VALUES,
GuccioneModel, "equations/E12",
iron.FieldParameterSetTypes.VALUES)
CellML.CreateFieldToCellMLMap(dependentField, iron.FieldVariableTypes.U1,
3, iron.FieldParameterSetTypes.VALUES,
GuccioneModel, "equations/E13",
iron.FieldParameterSetTypes.VALUES)
CellML.CreateFieldToCellMLMap(dependentField, iron.FieldVariableTypes.U1,
4, iron.FieldParameterSetTypes.VALUES,
GuccioneModel, "equations/E22",
iron.FieldParameterSetTypes.VALUES)
CellML.CreateFieldToCellMLMap(dependentField, iron.FieldVariableTypes.U1,
5, iron.FieldParameterSetTypes.VALUES,
GuccioneModel, "equations/E23",
iron.FieldParameterSetTypes.VALUES)
CellML.CreateFieldToCellMLMap(dependentField, iron.FieldVariableTypes.U1,
6, iron.FieldParameterSetTypes.VALUES,
GuccioneModel, "equations/E33",
iron.FieldParameterSetTypes.VALUES)
#DOC-END map strain components
#DOC-START map stress components
#Map the stress components
CellML.CreateCellMLToFieldMap(GuccioneModel, "equations/Tdev11",
iron.FieldParameterSetTypes.VALUES,
dependentField, iron.FieldVariableTypes.U2,
1, iron.FieldParameterSetTypes.VALUES)
CellML.CreateCellMLToFieldMap(GuccioneModel, "equations/Tdev12",
iron.FieldParameterSetTypes.VALUES,
dependentField, iron.FieldVariableTypes.U2,
2, iron.FieldParameterSetTypes.VALUES)
CellML.CreateCellMLToFieldMap(GuccioneModel, "equations/Tdev13",
iron.FieldParameterSetTypes.VALUES,
dependentField, iron.FieldVariableTypes.U2,
3, iron.FieldParameterSetTypes.VALUES)
CellML.CreateCellMLToFieldMap(GuccioneModel, "equations/Tdev22",
iron.FieldParameterSetTypes.VALUES,
dependentField, iron.FieldVariableTypes.U2,
4, iron.FieldParameterSetTypes.VALUES)
CellML.CreateCellMLToFieldMap(GuccioneModel, "equations/Tdev23",
iron.FieldParameterSetTypes.VALUES,
dependentField, iron.FieldVariableTypes.U2,
5, iron.FieldParameterSetTypes.VALUES)
CellML.CreateCellMLToFieldMap(GuccioneModel, "equations/Tdev33",
iron.FieldParameterSetTypes.VALUES,
dependentField, iron.FieldVariableTypes.U2,
6, iron.FieldParameterSetTypes.VALUES)
#Finish the creation of CellML <--> OpenCMISS field maps
CellML.FieldMapsCreateFinish()
#Create the CellML models field
CellMLModelsField = iron.Field()
CellML.ModelsFieldCreateStart(CellMLModelsFieldUserNumber,
CellMLModelsField)
CellML.ModelsFieldCreateFinish()
xidiv = 1.0 / (NumberOfGaussXi + 1)
for elem in [1]:
#Gauss point number counter
ctr = 0
#Assign model for each quadraturePoint:
for xi in range(0, NumberOfGaussXi):
xi1 = (1.0 + xi) * xidiv
for xj in range(0, NumberOfGaussXi):
xi2 = (1.0 + xj) * xidiv
for xk in range(0, NumberOfGaussXi):
xi3 = (1.0 + xk) * xidiv
ctr = ctr + 1
CellMLModelsField.ParameterSetUpdateGaussPoint(
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, ctr, 1, 1,
GuccioneModel)
#Create the CellML parameters field --- the strain field
CellMLParametersField = iron.Field()
CellML.ParametersFieldCreateStart(CellMLParametersFieldUserNumber,
CellMLParametersField)
CellML.ParametersFieldCreateFinish()
# Create the CellML intermediate field --- the stress field
CellMLIntermediateField = iron.Field()
CellML.IntermediateFieldCreateStart(CellMLIntermediateFieldUserNumber,
CellMLIntermediateField)
CellML.IntermediateFieldCreateFinish()
for valueIndex, parameter in enumerate(guccioneCellMLParameterIds, 0):
component = CellML.FieldComponentGet(GuccioneModel,
iron.CellMLFieldTypes.PARAMETERS,
parameter)
print("Setting parameter: " + parameter + "; to value: " +
str(guccioneCellMLParameters[valueIndex]) +
"; field component: " + str(component))
iron.Field.ComponentValuesInitialiseDP(
CellMLParametersField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, component,
guccioneCellMLParameters[valueIndex])
#equationsSet.MaterialsCreateStart(materialFieldUserNumber,materialField)
#equationsSet.MaterialsCreateFinish()
equationsSet.DependentCreateStart(dependentFieldUserNumber, dependentField)
equationsSet.DependentCreateFinish()
# Create equations
equations = iron.Equations()
equationsSet.EquationsCreateStart(equations)
equations.sparsityType = iron.EquationsSparsityTypes.SPARSE
equations.outputType = iron.EquationsOutputTypes.NONE
equationsSet.EquationsCreateFinish()
def defineProblemSolver():
# Define the problem
problem = iron.Problem()
problemSpecification = [
iron.ProblemClasses.ELASTICITY,
iron.ProblemTypes.FINITE_ELASTICITY,
iron.ProblemSubtypes.FINITE_ELASTICITY_CELLML
]
problem.CreateStart(problemUserNumber, problemSpecification)
problem.CreateFinish()
# Create control loops
problem.ControlLoopCreateStart()
problem.ControlLoopCreateFinish()
# Create problem solver
nonLinearSolver = iron.Solver()
linearSolver = iron.Solver()
problem.SolversCreateStart()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1,
nonLinearSolver)
nonLinearSolver.outputType = iron.SolverOutputTypes.PROGRESS
nonLinearSolver.NewtonJacobianCalculationTypeSet(
iron.JacobianCalculationTypes.FD)
nonLinearSolver.NewtonLinearSolverGet(linearSolver)
linearSolver.linearType = iron.LinearSolverTypes.DIRECT
#linearSolver.libraryType = iron.SolverLibraries.LAPACK
problem.SolversCreateFinish()
#Create the problem solver CellML equations
CellMLSolver = iron.Solver()
problem.CellMLEquationsCreateStart()
nonLinearSolver.NewtonCellMLSolverGet(CellMLSolver)
CellMLEquations = iron.CellMLEquations()
CellMLSolver.CellMLEquationsGet(CellMLEquations)
CellMLEquations.CellMLAdd(CellML)
problem.CellMLEquationsCreateFinish()
# Create solver equations and add equations set to solver equations
solver = iron.Solver()
solverEquations = iron.SolverEquations()
problem.SolverEquationsCreateStart()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1, solver)
solver.SolverEquationsGet(solverEquations)
solverEquations.sparsityType = iron.SolverEquationsSparsityTypes.SPARSE
equationsSetIndex = solverEquations.EquationsSetAdd(equationsSet)
problem.SolverEquationsCreateFinish()
return [problem, solverEquations]
def defineBoundaryConditions(solverEquations, increment):
# Prescribe boundary conditions (absolute nodal parameters)
boundaryConditions = iron.BoundaryConditions()
solverEquations.BoundaryConditionsCreateStart(boundaryConditions)
#Set x=0 nodes to no x displacment in x. Set x=width nodes to 10% x displacement
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, 1,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, 1,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, 1,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 7, 1,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, 1,
iron.BoundaryConditionsTypes.FIXED,
increment)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, 1,
iron.BoundaryConditionsTypes.FIXED,
increment)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, 1,
iron.BoundaryConditionsTypes.FIXED,
increment)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 8, 1,
iron.BoundaryConditionsTypes.FIXED,
increment)
# Set y=0 nodes to no y displacement
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, 2,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, 2,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 5, 2,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 6, 2,
iron.BoundaryConditionsTypes.FIXED, 0.0)
# Set z=0 nodes to no y displacement
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 1, 3,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 2, 3,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 3, 3,
iron.BoundaryConditionsTypes.FIXED, 0.0)
boundaryConditions.AddNode(dependentField, iron.FieldVariableTypes.U,
1, 1, 4, 3,
iron.BoundaryConditionsTypes.FIXED, 0.0)
solverEquations.BoundaryConditionsCreateFinish()
# loop over load steps
numberOfLoadSteps = 70
displacementIncrement = 0.01 # 1%
displacementIncrementDimension = displacementIncrement * width # length units
resultRecord = {}
resultRecord["strain"] = [0.0]
resultRecord["stress"] = [0.0]
for counter in range(1, numberOfLoadSteps + 1):
# define the problem, solver, control loops, etc.
[problem, solverEquations] = defineProblemSolver()
# define the boundary conditions
defineBoundaryConditions(solverEquations,
displacementIncrementDimension)
# execute the experiment
problem.Solve()
# clean up
problem.Finalise()
solverEquations.Finalise()
# export the results
filename = "results-{:03d}".format(counter)
# Copy deformed geometry into deformed field
for component in [1, 2, 3]:
dependentField.ParametersToFieldParametersComponentCopy(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
component, deformedField, iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, component)
# Export results
fields = iron.Fields()
fields.CreateRegion(region)
fields.NodesExport(filename, "FORTRAN")
fields.ElementsExport(filename, "FORTRAN")
fields.Finalise()
versionNumber = 1
derivativeNumber = 1
nodeNumber = 8
componentNumber = 1 # x-dirn
reactionForceX = dependentField.ParameterSetGetNode(
iron.FieldVariableTypes.DELUDELN,
iron.FieldParameterSetTypes.VALUES, versionNumber,
derivativeNumber, nodeNumber, componentNumber)
print("Reaction force (x) at counter: " + str(counter) + ": " +
str(reactionForceX))
resultRecord["strain"].append(counter * displacementIncrement)
resultRecord["stress"].append(reactionForceX)
coordinateSystem.Destroy()
region.Destroy()
basis.Destroy()
return resultRecord
def generate_opencmiss_region(interpolation=None,
region_label='region',
dimension=2):
""" Generates an OpenCMISS geometry (mesh and geometric field)
Args:
interpolation (iron.BasisInterpolationSpecifications):
Element interpolation e.g. LINEAR_LAGRANGE
region_label (str): Region name
Returns:
region, decomposition, mesh, geometric_field
"""
# OpenCMISS user numbers
coor_sys_user_num = 1
region_user_num = 1
basis_user_num = 1
# Instances for setting up OpenCMISS mesh
coordinate_system = iron.CoordinateSystem()
region = iron.Region()
basis = iron.Basis()
if interpolation is None:
interpolation = iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE
components = [1, 2, 3] # Geometric components
# Get the number of computational nodes and this computational node number
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
computationalNodeNumber = iron.ComputationalNodeNumberGet()
# Create a 3D rectangular cartesian coordinate system
coordinate_system.CreateStart(coor_sys_user_num)
coordinate_system.DimensionSet(3)
coordinate_system.CreateFinish()
# Create a region and assign the coordinate system to the region
region.CreateStart(region_user_num, iron.WorldRegion)
region.LabelSet(region_label)
region.CoordinateSystemSet(coordinate_system)
region.CreateFinish()
# Define basis
basis.CreateStart(basis_user_num)
basis.TypeSet(iron.BasisTypes.LAGRANGE_HERMITE_TP)
basis.NumberOfXiSet(dimension)
basis.InterpolationXiSet([interpolation] * dimension)
# Set number of Gauss points used for quadrature
if interpolation == iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE:
number_gauss_xi = 2
elif interpolation == \
iron.BasisInterpolationSpecifications.QUADRATIC_LAGRANGE:
number_gauss_xi = 3
elif interpolation == \
iron.BasisInterpolationSpecifications.CUBIC_LAGRANGE:
number_gauss_xi = 4
else:
raise ValueError('Interpolation not supported')
basis.QuadratureNumberOfGaussXiSet([number_gauss_xi] * dimension)
basis.CreateFinish()
return region, basis
def generate_opencmiss_geometry(interpolation=None,
region_label='region',
num_elements=None,
dimensions=None,
scaling_type=None,
mesh_type=None):
""" Generates an OpenCMISS geometry (mesh and geometric field)
Args:
interpolation (iron.BasisInterpolationSpecifications):
Element interpolation e.g. LINEAR_LAGRANGE
region_label (str): Region name
num_elements (arr): Number of elements in the mesh along each element
xi e.g. [1,1,1]
dimensions (arr): Dimension of the geometry, e.g. [10, 10, 10] for a
regular mesh
scaling_type (iron.FieldScalingTypes): The type of field scaling to use
e.g. 'NONE'
mesh_type(iron.GeneratedMeshTypes): Type of mesh to generate. Options
are: 'CYLINDER', 'ELLIPSOID', 'FRACTAL_TREE', 'POLAR', 'REGULAR'
Returns:
region, decomposition, mesh, geometric_field
"""
# OpenCMISS user numbers
coor_sys_user_num = 1
region_user_num = 1
basis_user_num = 1
generated_mesh_user_num = 1
mesh_user_num = 1
decomposition_user_num = 1
geometric_field_user_num = 1
# Instances for setting up OpenCMISS mesh
coordinate_system = iron.CoordinateSystem()
region = iron.Region()
basis = iron.Basis()
generated_mesh = iron.GeneratedMesh()
mesh = iron.Mesh()
decomposition = iron.Decomposition()
geometric_field = iron.Field()
if interpolation is None:
interpolation = iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE
if dimensions is None:
dimensions = np.array([1, 1, 1]) # Length, width, height
if num_elements is None:
num_elements = [1, 1, 1]
components = [1, 2, 3] # Geometric components
dimension = 3 # 3D coordinates
if scaling_type is None:
scaling_type = iron.FieldScalingTypes.NONE
if mesh_type is None:
mesh_type = iron.GeneratedMeshTypes.REGULAR
# Get the number of computational nodes and this computational node number
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
computationalNodeNumber = iron.ComputationalNodeNumberGet()
# Create a 3D rectangular cartesian coordinate system
coordinate_system.CreateStart(coor_sys_user_num)
coordinate_system.DimensionSet(dimension)
coordinate_system.CreateFinish()
# Create a region and assign the coordinate system to the region
region.CreateStart(region_user_num, iron.WorldRegion)
region.LabelSet(region_label)
region.CoordinateSystemSet(coordinate_system)
region.CreateFinish()
# Define basis
basis.CreateStart(basis_user_num)
basis.TypeSet(iron.BasisTypes.LAGRANGE_HERMITE_TP)
basis.NumberOfXiSet(dimension)
basis.InterpolationXiSet([interpolation] * dimension)
# Set number of Gauss points used for quadrature
if interpolation == iron.BasisInterpolationSpecifications.LINEAR_LAGRANGE:
number_gauss_xi = 2
elif interpolation == \
iron.BasisInterpolationSpecifications.QUADRATIC_LAGRANGE:
number_gauss_xi = 3
elif interpolation == \
iron.BasisInterpolationSpecifications.CUBIC_LAGRANGE:
number_gauss_xi = 4
else:
raise ValueError('Interpolation not supported')
basis.QuadratureNumberOfGaussXiSet([number_gauss_xi] * dimension)
basis.CreateFinish()
# Start the creation of a generated mesh in the region
generated_mesh.CreateStart(generated_mesh_user_num, region)
generated_mesh.TypeSet(mesh_type)
generated_mesh.BasisSet([basis])
generated_mesh.ExtentSet(dimensions)
generated_mesh.NumberOfElementsSet(num_elements)
generated_mesh.CreateFinish(mesh_user_num, mesh)
# Create a decomposition for the mesh
decomposition.CreateStart(decomposition_user_num, mesh)
decomposition.TypeSet(iron.DecompositionTypes.CALCULATED)
decomposition.CalculateFacesSet(True)
decomposition.NumberOfDomainsSet(numberOfComputationalNodes)
decomposition.CreateFinish()
# Create a field for the geometry
geometric_field.CreateStart(geometric_field_user_num, region)
geometric_field.MeshDecompositionSet(decomposition)
geometric_field.TypeSet(iron.FieldTypes.GEOMETRIC)
geometric_field.VariableLabelSet(iron.FieldVariableTypes.U, "geometry")
for component in components:
geometric_field.ComponentMeshComponentSet(iron.FieldVariableTypes.U,
component, 1)
geometric_field.ScalingTypeSet(scaling_type)
geometric_field.CreateFinish()
# Update the geometric field parameters from generated mesh
generated_mesh.GeometricParametersCalculate(geometric_field)
generated_mesh.Destroy()
return region, decomposition, mesh, geometric_field
def setupProblem(self, showProgress=False):
# Number of Gauss points used
numberOfGaussXi = 3
numberOfCircumfrentialElements = self.circumferentialElements
numberOfLengthElements = self.axialElements
numberOfLengthNodes = self.axialElements + 1
numberOfCircumfrentialNodes = numberOfCircumfrentialElements
numberOfWallNodes = self.wallElements + 1
numberOfWallElements = self.wallElements
coordinateSystemUserNumber = 1
regionUserNumber = 1
tricubicHermiteBasisUserNumber = 1
meshUserNumber = 1
decompositionUserNumber = 1
geometricFieldUserNumber = 1
tau = 0.1
kappa = 0.05
lambdaFieldUserNumber = 12
fittingEquationsSetUserNumber = 13
fittingEquationsSetFieldUserNumber = 14
fittingDependentFieldUserNumber = 15
fittingIndependentFieldUserNumber = 16
fittingMaterialsFieldUserNumber = 17
fittingProblemUserNumber = 18
# Get the number of computational nodes and this computational node number
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
# Create a 3D rectangular cartesian coordinate system
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(coordinateSystemUserNumber)
# Set the number of dimensions to 3
coordinateSystem.DimensionSet(3)
# Finish the creation of the coordinate system
coordinateSystem.CreateFinish()
# Create a region and assign the coordinate system to the region
region = iron.Region()
region.CreateStart(regionUserNumber, iron.WorldRegion)
region.LabelSet("HeartTubeRegion")
# Set the regions coordinate system to the 3D RC coordinate system that we have created
region.coordinateSystem = coordinateSystem
# Finish the creation of the region
region.CreateFinish()
self.region = region
# Define basis
# Start the creation of a tricubic Hermite basis function
tricubicHermiteBasis = iron.Basis()
tricubicHermiteBasis.CreateStart(tricubicHermiteBasisUserNumber)
tricubicHermiteBasis.type = iron.BasisTypes.LAGRANGE_HERMITE_TP
tricubicHermiteBasis.numberOfXi = 3
tricubicHermiteBasis.interpolationXi = [
iron.BasisInterpolationSpecifications.CUBIC_HERMITE
] * 3
tricubicHermiteBasis.quadratureNumberOfGaussXi = [numberOfGaussXi] * 3
tricubicHermiteBasis.CreateFinish()
# Start the creation of a manually generated mesh in the region
numberOfNodes = numberOfCircumfrentialElements * (
numberOfLengthElements + 1) * (numberOfWallElements + 1)
numberOfElements = numberOfCircumfrentialElements * numberOfLengthElements * numberOfWallElements
# Define nodes for the mesh
nodes = iron.Nodes()
nodes.CreateStart(region, numberOfNodes)
nodes.CreateFinish()
mesh = iron.Mesh()
# Create the mesh. The mesh will have two components - 1. tricubic Hermite elements; 2. trilinear Lagrange elements
mesh.CreateStart(meshUserNumber, region, 3)
mesh.NumberOfComponentsSet(1)
mesh.NumberOfElementsSet(numberOfElements)
tricubicHermiteElements = iron.MeshElements()
tricubicHermiteElements.CreateStart(mesh, 1, tricubicHermiteBasis)
elementNumber = 0
for wallElementIdx in range(1, numberOfWallElements + 1):
for lengthElementIdx in range(1, numberOfLengthElements + 1):
for circumfrentialElementIdx in range(
1, numberOfCircumfrentialElements + 1):
elementNumber = elementNumber + 1
localNode1 = circumfrentialElementIdx + (lengthElementIdx-1)*numberOfCircumfrentialNodes + \
(wallElementIdx-1)*numberOfCircumfrentialNodes*numberOfLengthNodes
if circumfrentialElementIdx == numberOfCircumfrentialElements:
localNode2 = 1 + (lengthElementIdx-1)*numberOfCircumfrentialNodes + \
(wallElementIdx-1)*numberOfCircumfrentialNodes*numberOfLengthNodes
else:
localNode2 = localNode1 + 1
localNode3 = localNode1 + numberOfCircumfrentialNodes
localNode4 = localNode2 + numberOfCircumfrentialNodes
localNode5 = localNode1 + numberOfCircumfrentialNodes * numberOfLengthNodes
localNode6 = localNode2 + numberOfCircumfrentialNodes * numberOfLengthNodes
localNode7 = localNode3 + numberOfCircumfrentialNodes * numberOfLengthNodes
localNode8 = localNode4 + numberOfCircumfrentialNodes * numberOfLengthNodes
localNodes = [
localNode1, localNode2, localNode3, localNode4,
localNode5, localNode6, localNode7, localNode8
]
tricubicHermiteElements.NodesSet(elementNumber, localNodes)
tricubicHermiteElements.CreateFinish()
# Finish the mesh creation
mesh.CreateFinish()
# Create a decomposition for the mesh
decomposition = iron.Decomposition()
decomposition.CreateStart(decompositionUserNumber, mesh)
# Set the decomposition to be a general decomposition with the specified number of domains
decomposition.type = iron.DecompositionTypes.CALCULATED
decomposition.numberOfDomains = numberOfComputationalNodes
# Finish the decomposition
decomposition.CreateFinish()
# Create a field for the geometry
geometricField = iron.Field()
geometricField.CreateStart(geometricFieldUserNumber, region)
# Set the decomposition to use
geometricField.MeshDecompositionSet(decomposition)
geometricField.TypeSet(iron.FieldTypes.GEOMETRIC)
# Set the field label
geometricField.VariableLabelSet(iron.FieldVariableTypes.U, "Geometry")
# Set the domain to be used by the field components to be tricubic Hermite
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1,
1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2,
1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3,
1)
# Set the scaling type
geometricField.ScalingTypeSet(iron.FieldScalingTypes.UNIT)
# Finish creating the field
geometricField.CreateFinish()
self.setupGeometry(geometricField)
# Update the geometric field
geometricField.ParameterSetUpdateStart(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
geometricField.ParameterSetUpdateFinish(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
lambdaField = iron.Field()
lambdaField.CreateStart(lambdaFieldUserNumber, region)
lambdaField.TypeSet(iron.FieldTypes.GENERAL)
# Set the decomposition
lambdaField.MeshDecompositionSet(decomposition)
# Set the geometric field
lambdaField.GeometricFieldSet(geometricField)
lambdaField.ScalingTypeSet(iron.FieldScalingTypes.NONE)
# Set the field variables
lambdaField.NumberOfVariablesSet(1)
lambdaField.VariableTypesSet([iron.FieldVariableTypes.U])
# Set the variable label
lambdaField.VariableLabelSet(iron.FieldVariableTypes.U, "NodeLambda")
# Set the components to be tricubic-hermite
lambdaField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 9)
for comp in range(1, 10):
lambdaField.ComponentMeshComponentSet(iron.FieldVariableTypes.U,
comp, 1)
# Set the interpolation types
lambdaField.ComponentInterpolationSet(
iron.FieldVariableTypes.U, comp,
iron.FieldInterpolationTypes.NODE_BASED)
lambdaField.ScalingTypeSet(iron.FieldScalingTypes.UNIT)
lambdaField.CreateFinish()
# Initialise the lambda field
for comp in range(1, 10):
lambdaField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
comp, 0.0)
# Create Gauss point fitting equations set
fittingEquationsSetSpecification = [
iron.EquationsSetClasses.FITTING,
iron.EquationsSetTypes.GAUSS_FITTING_EQUATION,
iron.EquationsSetSubtypes.GAUSS_POINT_FITTING,
iron.EquationsSetFittingSmoothingTypes.SOBOLEV_VALUE
]
fittingEquationsSetField = iron.Field()
fittingEquationsSet = iron.EquationsSet()
fittingEquationsSet.CreateStart(fittingEquationsSetUserNumber, region,
geometricField,
fittingEquationsSetSpecification,
fittingEquationsSetFieldUserNumber,
fittingEquationsSetField)
fittingEquationsSet.CreateFinish()
# Create the fitting dependent field
fittingDependentField = iron.Field()
fittingEquationsSet.DependentCreateStart(
fittingDependentFieldUserNumber, fittingDependentField)
fittingDependentField.VariableLabelSet(iron.FieldVariableTypes.U,
"FittingU")
fittingDependentField.VariableLabelSet(
iron.FieldVariableTypes.DELUDELN, "FittingDelUdelN")
# Set the number of components to 9
fittingDependentField.NumberOfComponentsSet(iron.FieldVariableTypes.U,
9)
fittingDependentField.NumberOfComponentsSet(
iron.FieldVariableTypes.DELUDELN, 9)
# Set the field variables to be tricubic hermite
for comp in range(1, 10):
fittingDependentField.ComponentMeshComponentSet(
iron.FieldVariableTypes.U, comp, 1)
fittingDependentField.ComponentMeshComponentSet(
iron.FieldVariableTypes.DELUDELN, comp, 1)
# Finish creating the fitting dependent field
fittingEquationsSet.DependentCreateFinish()
# Create the fitting independent field
fittingIndependentField = iron.Field()
fittingEquationsSet.IndependentCreateStart(
fittingIndependentFieldUserNumber, fittingIndependentField)
fittingIndependentField.VariableLabelSet(iron.FieldVariableTypes.U,
"GaussLambda")
fittingIndependentField.VariableLabelSet(iron.FieldVariableTypes.V,
"LambdaWeight")
# Set the number of components to 9
fittingIndependentField.NumberOfComponentsSet(
iron.FieldVariableTypes.U, 9)
fittingIndependentField.NumberOfComponentsSet(
iron.FieldVariableTypes.V, 9)
# Finish creating the fitting independent field
fittingEquationsSet.IndependentCreateFinish()
# Initialise data point vector field to 0.0
for comp in range(1, 10):
fittingIndependentField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
comp, 0.0)
# Initialise data point weight field to 1.0
fittingIndependentField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.V, iron.FieldParameterSetTypes.VALUES,
comp, 1.0)
# Create material field (Sobolev parameters)
fittingMaterialField = iron.Field()
fittingEquationsSet.MaterialsCreateStart(
fittingMaterialsFieldUserNumber, fittingMaterialField)
fittingMaterialField.VariableLabelSet(iron.FieldVariableTypes.U,
"SmoothingParameters")
fittingEquationsSet.MaterialsCreateFinish()
# Set kappa and tau - Sobolev smoothing parameters
fittingMaterialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1,
tau)
fittingMaterialField.ComponentValuesInitialiseDP(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 2,
kappa)
# Create the fitting equations
fittingEquations = iron.Equations()
fittingEquationsSet.EquationsCreateStart(fittingEquations)
# Set the fitting equations sparsity type
fittingEquations.sparsityType = iron.EquationsSparsityTypes.SPARSE
# Set the fitting equations output type to none
fittingEquations.outputType = iron.EquationsOutputTypes.NONE
# Finish creating the fitting equations
fittingEquationsSet.EquationsCreateFinish()
# Create fitting problem
fittingProblemSpecification = [
iron.ProblemClasses.FITTING, iron.ProblemTypes.DATA_FITTING,
iron.ProblemSubtypes.STATIC_FITTING
]
fittingProblem = iron.Problem()
fittingProblem.CreateStart(fittingProblemUserNumber,
fittingProblemSpecification)
fittingProblem.CreateFinish()
# Create control loops
fittingProblem.ControlLoopCreateStart()
fittingProblem.ControlLoopCreateFinish()
# Create problem solver
fittingSolver = iron.Solver()
fittingProblem.SolversCreateStart()
fittingProblem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1,
fittingSolver)
fittingSolver.outputType = iron.SolverOutputTypes.NONE
fittingProblem.SolversCreateFinish()
# Create fitting solver equations and add fitting equations set to solver equations
fittingSolverEquations = iron.SolverEquations()
fittingProblem.SolverEquationsCreateStart()
# Get the solver equations
fittingSolver.SolverEquationsGet(fittingSolverEquations)
fittingSolverEquations.sparsityType = iron.SolverEquationsSparsityTypes.SPARSE
fittingEquationsSetIndex = fittingSolverEquations.EquationsSetAdd(
fittingEquationsSet)
fittingProblem.SolverEquationsCreateFinish()
# Prescribe boundary conditions for the fitting problem
fittingBoundaryConditions = iron.BoundaryConditions()
fittingSolverEquations.BoundaryConditionsCreateStart(
fittingBoundaryConditions)
fittingBoundaryConditions.AddNode(
fittingDependentField, iron.FieldVariableTypes.U, 1,
iron.GlobalDerivativeConstants.NO_GLOBAL_DERIV, 1, 8,
iron.BoundaryConditionsTypes.FIXED, 0.0)
fittingSolverEquations.BoundaryConditionsCreateFinish()
self.fittingIndependentField = fittingIndependentField
self.fittingDependentField = fittingDependentField
self.lambdaField = lambdaField
self.fittingProblem = fittingProblem
