def setGeometry(self, geometricField):
decomposition = iron.Decomposition()
geometricField.MeshDecompositionGet(decomposition)
geometricInterpolation = self.interpolations[0]
compNodeNumber = iron.ComputationalNodeNumberGet()
geometricMeshComponent = 1
# Set the geometric field parameters from the prolate spheroid geometry
for nodeNum, values in enumerate(self.nodeValues(), 1):
if decomposition.NodeDomainGet(
nodeNum, geometricMeshComponent) == compNodeNumber:
versionNumber = 1
for component in range(3):
componentValues = values[component]
if geometricInterpolation != 'cubic_hermite':
componentValues = componentValues[:1]
for derivativeNumber, value in componentValues:
# Note: Python uses 0-based indexing, OpenCMISS uses 1-based
geometricField.ParameterSetUpdateNode(
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, versionNumber,
derivativeNumber, nodeNum, component + 1, value)
# After modifying the geometric field, ParameterSetUpdateStart/Finish
# must be called so that the field data at ghost nodes is synchronised
# across all processes. The UpdateFinish routine could be called later
# on just before the geometric values are actually needed, to avoid
# blocking.
geometricField.ParameterSetUpdateStart(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
geometricField.ParameterSetUpdateFinish(
iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
def getDomainNodes(geometry, decomposition, component):
component_name = interpolations[component - 1]
computationalNodeNumber = iron.ComputationalNodeNumberGet()
nodes = geometry.componentNodes(component_name)
meshComponent = geometry.meshComponent(component_name)
return set(node for node in nodes
if decomposition.NodeDomainGet(node, meshComponent) == computationalNodeNumber)
def setFibres(self, fibreField):
endocardiumFibreAngle = self.endocardiumFibreAngle
epicardiumFibreAngle = self.epicardiumFibreAngle
sheetAngle = self.sheetAngle
geometricMeshComponent = 1
compNodeNumber = iron.ComputationalNodeNumberGet()
hasQuadratic = self.interpolations[0] == 'quadratic'
if hasQuadratic:
elFactor = 2
else:
elFactor = 1
# fibre, imbrication, sheet
epiAngles = np.array([epicardiumFibreAngle, 0.0, sheetAngle])
endoAngles = np.array([endocardiumFibreAngle, 0.0, sheetAngle])
lmbdaDerivs = (epiAngles - endoAngles) / self.numElements[2]
decomposition = iron.Decomposition()
fibreField.MeshDecompositionGet(decomposition)
# Set fibre angles at nodes
def setAngles(pos, angles):
nodeNumber = self.nodeAtPosition(pos)
if decomposition.NodeDomainGet(
nodeNumber, geometricMeshComponent) == compNodeNumber:
version = 1
for component, angle in enumerate(angles, 1):
derivative = 1
fibreField.ParameterSetUpdateNode(
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, version,
derivative, nodeNumber, component, angle)
# Only loop over linear component nodes
for k in range(0, self.numElements[2] * elFactor + 1, elFactor):
transmuralPos = float(k) / float(self.numElements[2] * elFactor)
fibreAngle = endocardiumFibreAngle + transmuralPos * (
epicardiumFibreAngle - endocardiumFibreAngle)
for j in range(0, self.numElements[1] * elFactor + 1, elFactor):
for i in range(0, self.numElements[0] * elFactor, elFactor):
if j == 0:
setAngles((i, j, k), [0.0, 0.0, 0.0])
else:
setAngles((i, j, k), [fibreAngle, 0.0, sheetAngle])
fibreField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
fibreField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
CellMLModelsFieldUserNumber = 4
CellMLParametersFieldUserNumber = 5
CellMLIntermediateFieldUserNumber = 6
equationsSetFieldUserNumber = 7
# Set all diganostic levels on for testing
#iron.DiagnosticsSetOn(iron.DiagnosticTypes.ALL,[1,2,3,4,5],"Diagnostics",["DOMAIN_MAPPINGS_LOCAL_FROM_GLOBAL_CALCULATE"])
if (UsePressureBasis):
numberOfMeshComponents = 2
else:
numberOfMeshComponents = 1
# 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