# Create a generated mesh
generatedMesh = iron.GeneratedMesh()
generatedMesh.CreateStart(generatedMeshUserNumber, region)
generatedMesh.type = iron.GeneratedMeshTypes.REGULAR
generatedMesh.basis = [basis]
generatedMesh.extent = [width, height, length]
generatedMesh.numberOfElements = [
numberGlobalXElements, numberGlobalYElements, numberGlobalZElements
]
mesh1 = iron.Mesh()
generatedMesh.CreateFinish(mesh1UserNumber, mesh1)
# Find the total number of nodes and elements from the generated mesh
meshNodes = iron.MeshNodes()
mesh1.NodesGet(mesh_component_number, meshNodes)
total_number_of_nodes = meshNodes.NumberOfNodesGet()
total_number_of_elements = mesh1.NumberOfElementsGet()
# Start the creation of a second manually generated mesh
mesh2 = iron.Mesh()
mesh2.CreateStart(mesh2UserNumber, region, number_of_dimensions)
mesh2.NumberOfComponentsSet(1)
# Define which elements are included in the new mesh, and the total number of elements
original_elements_list = range(1, total_number_of_elements + 1)
removed_elements = (numpy.array([1, 750]) -
1).tolist() # list of elements to be removed from mesh
new_elements_list = numpy.delete(original_elements_list,
def OpenCMISS_to_morphic(c_mesh,
geometric_field,
element_nums,
node_nums,
dimension=2,
interpolation='linear'):
"""Convert an OpenCMISS mesh to a morphic mesh.
Only Linear lagrange elements supported.
Keyword arguments:
morphicMesh -- morphic mesh
dimension -- dimension of mesh to read in
"""
from opencmiss.iron import iron
mesh_nodes = iron.MeshNodes()
mesh_elements = iron.MeshElements()
c_mesh.NodesGet(1, mesh_nodes)
c_mesh.ElementsGet(1, mesh_elements)
# Create morphic mesh
mesh = morphic.Mesh()
# Add nodes
if interpolation in ['linear', 'quadratic', 'cubic']:
derivatives = [1]
elif interpolation == 'hermite':
derivatives = range(1, 9)
for node_num in node_nums:
coordinates = []
for c_idx, c in enumerate([1, 2, 3]): # Component
componentValues = []
for derivative_idx, derivative in enumerate(derivatives):
componentValues.append(
geometric_field.ParameterSetGetNodeDP(
iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES, 1, derivative,
int(node_num), c))
coordinates.append(componentValues)
mesh.add_stdnode(node_num, coordinates, group='_default')
#print('Morphic node added', node_num, coordinates)
if dimension == 2:
if interpolation == 'linear':
element_interpolation = ['L1', 'L1']
num_elem_nodes = 4
if interpolation == 'quadratic':
element_interpolation = ['L2', 'L2']
num_elem_nodes = 16
elif dimension == 3:
if interpolation == 'linear':
element_interpolation = ['L1', 'L1', 'L1']
num_elem_nodes = 8
if interpolation == 'quadratic':
element_interpolation = ['L2', 'L2', 'L2']
num_elem_nodes = 27
if interpolation == 'cubic':
element_interpolation = ['L3', 'L3', 'L3']
num_elem_nodes = 64
if interpolation == 'hermite':
element_interpolation = ['H3', 'H3', 'H3']
num_elem_nodes = 8
# Add elements
for elem in element_nums:
elem_nodes = mesh_elements.NodesGet(int(elem), num_elem_nodes)
mesh.add_element(elem, element_interpolation, elem_nodes)
#print('Morphic element added', elem.number)
# Generate the mesh
mesh.generate(True)
return mesh
def num_nodes_get(mesh, mesh_component=1):
nodes = iron.MeshNodes()
mesh.NodesGet(mesh_component, nodes)
return nodes.NumberOfNodesGet()