def exfile_to_OpenCMISS(nodeFilename, elementFilename, coordinateField, region, meshUserNumber,
dimension=2, interpolation='linear'):
"""Convert an exnode and exelem files to a morphic mesh.
Only Linear lagrange elements supported.
Keyword arguments:
nodeFilename -- exnode filename
elementFilename -- exelem filename
coordinateField -- the field to read in
dimension -- dimension of mesh to read in
interpolation -- the interpolation of the mesh to read in
"""
# Load exfiles
exnode = exfile.Exnode(nodeFilename)
exelem = exfile.Exelem(elementFilename, dimension)
totalNumberOfNodes = len(exnode.nodeids)
totalNumberOfElements = len(exelem.elements)
# Start the creation of a manually generated mesh in the region
mesh = iron.Mesh()
mesh.CreateStart(meshUserNumber, region, dimension)
mesh.NumberOfComponentsSet(1)
mesh.NumberOfElementsSet(totalNumberOfElements)
# Define nodes for the mesh
nodes = iron.Nodes()
nodes.CreateStart(region, totalNumberOfNodes)
nodes.UserNumbersAllSet(exnode.nodeids)
nodes.CreateFinish()
elements = iron.MeshElements()
meshComponentNumber = 1
elements.CreateStart(mesh, meshComponentNumber, basis)
elemNums = []
for elem in exelem.elements:
elemNums.append(elem.number)
elements.UserNumbersAllSet(elemNums)
for elem_idx, elem in enumerate(exelem.elements):
elements.NodesSet(elem_idx+1, elem.nodes)
elements.CreateFinish()
mesh.CreateFinish()
coordinates, node_ids = extract_exfile_coordinates(nodeFilename, coordinateField, interpolation)
return mesh, coordinates, node_ids
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
mesh = iron.Mesh()
mesh.CreateStart(meshUserNumber, region, number_of_dimensions)
mesh.NumberOfComponentsSet(number_of_mesh_components)
mesh.NumberOfElementsSet(total_number_of_elements)
# Define nodes for the mesh
nodes = iron.Nodes()
nodes.CreateStart(region, total_number_of_nodes)
# Refers to nodes by their user number as described in the original mesh
nodes.UserNumbersAllSet(node_array)
nodes.CreateFinish()
elements = iron.MeshElements()
elements.CreateStart(mesh, mesh_component_number, basis)
# Set the nodes pertaining to each element
for idx, elem_num in enumerate(element_array):
elements.NodesSet(idx + 1, element_nodes_array[idx])
# Refers to elements by their user number as described in the original mesh
elements.UserNumbersAllSet(element_array)
def exfile_to_OpenCMISS(nodeFilename,
elementFilename,
coordinateField,
basis,
region,
meshUserNumber,
dimension=2,
interpolation='linear',
pressure_basis=None,
use_pressure_basis=False,
elements=[]):
"""Convert an exnode and exelem files to a morphic mesh.
Only Linear lagrange elements supported.
Keyword arguments:
nodeFilename -- exnode filename
elementFilename -- exelem filename
coordinateField -- the field to read in
dimension -- dimension of mesh to read in
interpolation -- the interpolation of the mesh to read in
"""
from opencmiss.iron import iron
# Load exfiles
exnode = mesh_tools.Exnode(nodeFilename)
exelem = mesh_tools.Exelem(elementFilename, dimension)
if elements == []:
ex_elems = exelem.elements
else:
ex_elems = []
elements = exelem.elements
for elem in exelem.elements:
if elem.number in elements:
ex_elems.append(elem)
totalNumberOfNodes = len(exnode.nodeids)
totalNumberOfElements = len(ex_elems)
# Start the creation of a manually generated mesh in the region
mesh = iron.Mesh()
mesh.CreateStart(meshUserNumber, region, dimension)
mesh.NumberOfComponentsSet(1)
mesh.NumberOfElementsSet(totalNumberOfElements)
# Define nodes for the mesh
nodes = iron.Nodes()
nodes.CreateStart(region, totalNumberOfNodes)
nodes.UserNumbersAllSet(exnode.nodeids)
nodes.CreateFinish()
MESH_COMPONENT1 = 1
MESH_COMPONENT2 = 2
if (use_pressure_basis):
mesh.NumberOfComponentsSet(2)
else:
mesh.NumberOfComponentsSet(1)
elements = iron.MeshElements()
elements.CreateStart(mesh, MESH_COMPONENT1, basis)
elemNums = []
for elem in ex_elems:
elemNums.append(elem.number)
elements.UserNumbersAllSet(elemNums)
for elem_idx, elem in enumerate(ex_elems):
elements.NodesSet(elem_idx + 1, elem.nodes)
elements.CreateFinish()
if (use_pressure_basis):
linear_elem_node_idxs = [0, 3, 12, 15, 48, 51, 60, 63]
pressure_elements = iron.MeshElements()
pressure_elements.CreateStart(mesh, MESH_COMPONENT2, pressure_basis)
pressure_elements.UserNumbersAllSet(elemNums)
for elem_idx, elem in enumerate(ex_elems):
pressure_elements.NodesSet(
elem_idx + 1,
np.array(elem.nodes, dtype=np.int32)[linear_elem_node_idxs])
pressure_elements.CreateFinish()
mesh.CreateFinish()
coordinates, node_ids = mesh_tools.extract_exfile_coordinates(
nodeFilename, coordinateField, interpolation)
return mesh, coordinates, node_ids
def morphic_to_OpenCMISS(morphicMesh,
region,
basis,
meshUserNumber,
dimension=2,
interpolation='linear',
UsePressureBasis=False,
pressureBasis=None,
include_derivatives=True):
"""Convert an exnode and exelem files to a morphic mesh.
Only Linear lagrange elements supported.
Keyword arguments:
morphicMesh -- morphic mesh
dimension -- dimension of mesh to read in
include_derivatives -- whether to include derivatives when returning mesh
coordinates.
"""
from opencmiss.iron import iron
# Create mesh topology
mesh = iron.Mesh()
mesh.CreateStart(meshUserNumber, region, 3)
if (UsePressureBasis):
mesh.NumberOfComponentsSet(2)
else:
mesh.NumberOfComponentsSet(1)
node_list = morphicMesh.get_node_ids()[1]
if len(node_list) == 0:
node_list = morphicMesh.get_node_ids(group='_default')[1]
element_list = morphicMesh.get_element_ids()
mesh.NumberOfElementsSet(len(element_list))
nodes = iron.Nodes()
nodes.CreateStart(region, len(node_list))
nodes.UserNumbersAllSet((np.array(node_list)).astype('int32'))
nodes.CreateFinish()
MESH_COMPONENT1 = 1
MESH_COMPONENT2 = 2
elements = iron.MeshElements()
elements.CreateStart(mesh, MESH_COMPONENT1, basis)
elements.UserNumbersAllSet((np.array(element_list).astype('int32')))
global_element_idx = 0
for element_idx, element in enumerate(morphicMesh.elements):
global_element_idx += 1
elements.NodesSet(global_element_idx,
np.array(element.node_ids, dtype='int32'))
elements.CreateFinish()
if (UsePressureBasis):
pressure_elements = iron.MeshElements()
pressure_elements.CreateStart(mesh, MESH_COMPONENT2, pressureBasis)
pressure_elements.AllUserNumbersSet(
(np.array(element_list).astype('int32')))
for element_idx, element in enumerate(morphicMesh.elements):
pressure_elements.NodesSet(
element.id, np.array(element.node_ids, dtype='int32'))
pressure_elements.CreateFinish()
mesh.CreateFinish()
# Add nodes
if interpolation == 'linear' or interpolation == 'cubicLagrange':
derivatives = [1]
elif interpolation == 'hermite':
derivatives = range(1, 9)
if include_derivatives:
coordinates = np.zeros((len(node_list), 3, len(derivatives)))
else:
derivatives = [1]
coordinates = np.zeros((len(node_list), 3))
for node_idx, morphic_node in enumerate(morphicMesh.nodes):
for component_idx in range(3):
for derivative_idx, derivative in enumerate(derivatives):
if include_derivatives:
coordinates[node_idx,component_idx, derivative_idx] = \
morphic_node.values[component_idx]
else:
coordinates[node_idx,component_idx] = \
morphic_node.values[component_idx]
return mesh, coordinates, node_list, element_list
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 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
