#make a material
mat1 = febio.MatDef(matid=1,mname='Material 1',mtype='neo-Hookean',
elsets=['exmymzm','exmypzm','exmymzp','exmypzp','expymzm','expypzm','expymzp','expypzp'],attributes={'density': '1.0', 'E': '1000.0','v': '0.3'})
#add the material to the model
model.addMaterial(mat1)
#make the geometry section of the model
model.addGeometry(mesh=mesh,mats=[mat1])
#define a loadcurve
model.addLoadCurve(lc='1',lctype='linear',points=[0,0,1,1])
model.addLoadCurve(lc='2',lctype='linear',points=[1,0,2,1])
#initialize a boundary condition object
boundary = febio.Boundary(steps=2)
#add a fixed boundary condition to bottom z nodes
boundary.addFixed(nset=mesh.nsets['nzm'],dof='xyz')
#add a prescribed displace to top z nodes for step 1
boundary.addPrescribed(step=0,nset=mesh.nsets['nzp'],dof='z',lc='1',scale='0.1')
#add a relative prescribed displacement to top z nodes for step 2
boundary.addPrescribed(step=1,nset=mesh.nsets['nzp'],dof='z',lc='2',scale='0.2',ptype='relative')
#add boundary conditions to model
model.addBoundary(boundary=boundary)
#create a control block
ctrl = febio.Control()
#add the control block to the model step 1
model.addControl(step=0,ctrl=ctrl)
class Model():
def __init__(self, **kwargs):
self.options = FixedDict({
"Micro Model Base Name":
"cell_scale",
"Macro Model Geometry File":
"tissue.vtr",
"Macro Model Plot File":
"tissue.xplt",
"Shape Parameters":
FixedDict({
"PCM Radius": [6.976, 3.9763, 2.9175],
"Cell Radius": [6.0, 3.0, 2.0],
"PCM Squareness": [2.1, 2.1, 2.1],
"Cell Squareness": [2.1, 2.1, 2.1]
}),
"Mesh Divisions":
FixedDict({
"Cell": 4.0,
"PCM": 6.0,
"ECM": 5.0
}),
"Symmetry":
"full",
"Cell Shifts": {
"neutral": 0.0
},
"Model Centroids": [[50, 50, 490]],
"Material Properties":
FixedDict({
"PCM E ratio": 0.2,
"PCM v ratio": 1.0,
"PCM beta ratio": 1.0,
"PCM phi": 0.2,
"PCM perm ratio": 1.0,
"PCM m": 4.638,
"PCM alpha": 0.0848,
"Cell Modulus": 0.001,
"Cell Poisson": 0.01,
"Cell Permeability": 1e-3,
"Cell phi": 0.1,
"Membrane Modulus": 0.001,
"Membrane Poisson": 0.0,
"Membrane Permeability": 7e-10,
"Membrane phi": 0.1,
"Membrane Thickness": 1e-5
})
})
self.config = None
for key, value in kwargs.items():
if key == "options":
for k, v in value.items():
for k2, v2 in v.items():
self.options[k][k2] = v2
else:
setattr(self, key, value)
if self.config is not None:
self.parseConfig()
self.ecm_materials = {}
self.pcm_materials = {}
print(
"... Extracting Macro Scale Results and Geometry from \n\t {} and {}"
.format(self.options["Macro Model Plot File"],
self.options["Macro Model Geometry File"]))
self.assembleMacroData()
print("... Extraction Complete")
for case, shift in self.options["Cell Shifts"].items():
print("... Creating Mesh for {} case".format(case))
self.makeMesh(shift)
print("... Mesh Completed")
for translation in self.options["Model Centroids"]:
print(
"... ... Creating FEBio model for {} case at location: {:6.3f}, {:6.3f}, {:6.3f}"
.format(case, *translation))
self.make_febio_model(case, translation)
print("... ... Model written to {}_{}_{:d}.feb".format(
self.options["Micro Model Base Name"], case,
int(translation[2])))
def parseConfig(self):
"""
Parse configuration file in YAML format.
"""
with open(self.config) as user:
user_settings = yaml.safe_load(user)
for k, v in list(user_settings.items()):
if isinstance(v, dict):
for k2, v2 in list(v.items()):
self.options[str(k)][str(k2)] = v2
else:
self.options[str(k)] = v
def assembleMacroData(self):
# read macro_model from vtk grid
reader = vtk.vtkXMLRectilinearGridReader()
reader.SetFileName(self.options["Macro Model Geometry File"])
reader.Update()
self.macro_data = reader.GetOutput()
# parse FEBio xplt
self.macro_results = febio.FebPlt(
self.options["Macro Model Plot File"])
def makeMesh(self, cell_shift):
resolution = 500 # Image resolution for image-based mesh
cell_diameter = [
r * 2 for r in self.options["Shape Parameters"]["Cell Radius"]
]
pcm_diameter = [
r * 2 for r in self.options["Shape Parameters"]["PCM Radius"]
]
ecm_diameter = [d * 10.0**(1. / 3.) for d in pcm_diameter]
cell_exponent = list(
self.options["Shape Parameters"]["Cell Squareness"])
pcm_exponent = list(self.options["Shape Parameters"]["PCM Squareness"])
ecm_exponent = pcm_exponent
symmetry = self.options["Symmetry"]
if symmetry == 'full':
position = [0.5, 0.5, 0.5]
cell_position = [0.5, 0.5, 0.5 + cell_shift / ecm_diameter[2]]
elif symmetry == 'half':
position = [0.0, 0.5, 0.5]
cell_position = [0.0, 0.5, 0.5 + cell_shift / ecm_diameter[2]]
elif symmetry == 'quarter':
position = [0.0, 0.0, 0.5]
cell_position = [0.0, 0.0, 0.5 + cell_shift / ecm_diameter[2]]
else:
raise KeyError(
"Symmetry must be set to 1 of the following: full, half, quarter"
)
dmax = np.max(ecm_diameter)
resolution = [int(d3 / dmax * resolution) for d3 in ecm_diameter]
semisizes1 = [
0.5 * d1 / d3 for d1, d3 in zip(cell_diameter, ecm_diameter)
]
semisizes2 = [
0.5 * d2 / d3 for d2, d3 in zip(pcm_diameter, ecm_diameter)
]
s1 = raster_geometry.nd_superellipsoid(resolution,
semisizes=semisizes1,
indexes=cell_exponent,
position=cell_position,
smoothing=True)
s2 = raster_geometry.nd_superellipsoid(resolution,
semisizes=semisizes2,
indexes=pcm_exponent,
position=position,
smoothing=True)
s3 = raster_geometry.nd_superellipsoid(resolution,
semisizes=[0.5, 0.5, 0.5],
indexes=ecm_exponent,
position=position,
smoothing=True)
s1 += 0.2
s2 += 0.2
s3 += 0.2
v = s1.astype(np.uint8) + s2.astype(np.uint8) + s3.astype(np.uint8)
h = [r / res for res, r in zip(resolution, ecm_diameter)]
divisions = self.options["Mesh Divisions"]
cell_sizes_map = {
1:
np.min(np.array(ecm_diameter) - np.array(pcm_diameter)) /
divisions["ECM"] / 2.0,
2:
np.min(np.array(pcm_diameter) - np.array(cell_diameter)) /
divisions["PCM"] / 2.0,
3:
np.min(np.array(cell_diameter)) / divisions["Cell"] / 2.0
}
max_facet_distance = np.min(h)
if symmetry != 'full':
max_facet_distance /= 2.0
mesh = pygalmesh.generate_from_array(
v,
h,
max_facet_distance=max_facet_distance,
max_radius_surface_delaunay_ball=cell_sizes_map[1],
max_circumradius_edge_ratio=1.3,
max_cell_circumradius=cell_sizes_map,
max_edge_size_at_feature_edges=cell_sizes_map[2],
lloyd=True,
odt=True,
verbose=False)
mesh.points = (mesh.points - np.array(ecm_diameter) / 2.0) / 1000.
self.nodes = mesh.points
# Get face connectivity and flatten - keep only unique node ids
surface = np.sort(np.unique(mesh.get_cells_type('triangle').ravel()))
# Get Domain IDs of all nodes
node_type = mesh.point_data['medit:ref']
# Keep domain ID of only face nodes
s_node_types = node_type[surface]
# Define node set for outermost faces - domain ID = 1
self.surface_nodes = surface[s_node_types == 1]
self.elements = mesh.get_cells_type('tetra')
# get the domain ID of the solid elements
element_data = mesh.get_cell_data('medit:ref', 'tetra')
# Make sets from domain IDs
self.cell_set = np.argwhere(element_data == 3)
self.pcm_set = np.argwhere(element_data == 2)
self.ecm_set = np.argwhere(element_data == 1)
# Get Face connectivity list
triangles = mesh.get_cells_type('triangle')
# Get Domain ID of face elements
surface_data = mesh.get_cell_data('medit:ref', 'triangle')
# Define membrane elements - Domain ID = 3
self.membrane = triangles[surface_data == 3]
# Define element set for membrane
self.membrane_set = np.argwhere(surface_data == 3)
def make_vtk(self, translation):
vtk_mesh = vtk.vtkUnstructuredGrid()
translated_nodes = self.nodes + np.array(translation) / 1000.
nodearray = numpy_support.numpy_to_vtk(translated_nodes.ravel(),
deep=True,
array_type=vtk.VTK_DOUBLE)
nodearray.SetNumberOfComponents(3)
nodes = vtk.vtkPoints()
nodes.SetData(nodearray)
vtk_mesh.SetPoints(nodes)
element_array = np.hstack([
np.ones((self.elements.shape[0], 1), dtype=int) * 4, self.elements
])
size = element_array.size
element_array = numpy_support.numpy_to_vtk(element_array.ravel(),
deep=True,
array_type=vtk.VTK_ID_TYPE)
elements = vtk.vtkCellArray()
elements.SetCells(size // 5, element_array)
vtk_mesh.SetCells(10, elements)
element_set = self._interpMaterials(vtk_mesh)
element_set[self.cell_set] = 1
element_set = numpy_support.numpy_to_vtk(element_set.ravel(),
deep=True,
array_type=vtk.VTK_CHAR)
element_set.SetNumberOfComponents(1)
element_set.SetName('Material ID')
vtk_mesh.GetCellData().AddArray(element_set)
return vtk_mesh
def _interpMaterials(self, polydata):
self.ecm_materials = {}
self.pcm_materials = {}
probe = vtk.vtkProbeFilter()
probe.SetSourceData(self.macro_data)
probe.SetInputData(polydata)
probe.PassPointArraysOff()
probe.PassCellArraysOn()
probe.Update()
to_cell = vtk.vtkPointDataToCellData()
to_cell.SetInputData(probe.GetOutput())
to_cell.Update()
mapped_data = to_cell.GetOutput()
materialIDs = numpy_support.vtk_to_numpy(
mapped_data.GetCellData().GetArray('ElementSetID')).astype(int)
ksi = numpy_support.vtk_to_numpy(
mapped_data.GetCellData().GetArray('ksi'))
E = numpy_support.vtk_to_numpy(mapped_data.GetCellData().GetArray('E'))
v = numpy_support.vtk_to_numpy(mapped_data.GetCellData().GetArray('v'))
beta = numpy_support.vtk_to_numpy(
mapped_data.GetCellData().GetArray('beta'))
phi = numpy_support.vtk_to_numpy(
mapped_data.GetCellData().GetArray('phi'))
permeability = numpy_support.vtk_to_numpy(
mapped_data.GetCellData().GetArray('permeability'))
m = numpy_support.vtk_to_numpy(mapped_data.GetCellData().GetArray('m'))
alpha = numpy_support.vtk_to_numpy(
mapped_data.GetCellData().GetArray('alpha'))
unique_materialIDs = np.sort(np.unique(materialIDs))
pcm_counter = 0
pcm_offset = unique_materialIDs.size
for i, matid in enumerate(unique_materialIDs):
idx = np.argwhere(materialIDs == matid)
ecm_ids = np.intersect1d(idx.ravel(), self.ecm_set)
pcm_ids = np.intersect1d(idx.ravel(), self.pcm_set)
E_ratio = self.options['Material Properties']['PCM E ratio']
v_ratio = self.options['Material Properties']['PCM v ratio']
beta_ratio = self.options['Material Properties']['PCM beta ratio']
perm_ratio = self.options['Material Properties']['PCM perm ratio']
self.ecm_materials[i + 3] = {
'E': E[idx[0]][0],
'v': v[idx[0]][0],
'beta': beta[idx[0]][0],
'phi': phi[idx[0]][0],
'permeability': permeability[idx[0]][0],
'm': m[idx[0]][0],
'alpha': alpha[idx[0]][0],
'ksi': ksi[idx[0], :][0],
'element_ids': ecm_ids
}
materialIDs[ecm_ids] = i + 3
if pcm_ids.any():
self.pcm_materials[pcm_counter + 3 + pcm_offset] = {
'E': E[idx[0]][0] * E_ratio,
'v': v[idx[0]][0] * v_ratio,
'beta': beta[idx[0]][0] * beta_ratio,
'phi': phi[idx[0]][0],
'permeability': permeability[idx[0]][0] * perm_ratio,
'm': m[idx[0]][0],
'alpha': alpha[idx[0]][0],
'element_ids': pcm_ids
}
materialIDs[pcm_ids] = pcm_counter + 3 + pcm_offset
pcm_counter += 1
return materialIDs
def make_febio_model(self, case, translation):
model_name = "{}_{}_{:d}".format(self.options["Micro Model Base Name"],
case, int(translation[2]))
fe_mesh = febio.MeshDef()
for i in range(self.nodes.shape[0]):
fe_mesh.nodes.append([i + 1] + list(self.nodes[i, :] +
np.array(translation) / 1000.))
for i in range(self.elements.shape[0]):
fe_mesh.elements.append(['tet4', i + 1] +
list(self.elements[i, :] + 1))
membrane_set = np.zeros(self.membrane.shape[0], dtype=int)
for i in range(self.membrane.shape[0]):
fe_mesh.elements.append(['tri3', i + 1 + self.elements.shape[0]] +
list(self.membrane[i] + 1))
membrane_set[i] = i + 1 + self.elements.shape[0]
vtkmesh = self.make_vtk(translation)
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetFileName(model_name + '.vtu')
writer.SetInputData(vtkmesh)
writer.Write()
# Cell Element Set
fe_mesh.addElementSet(setname='Cell', eids=self.cell_set + 1)
# Membrane Element Set
fe_mesh.addElementSet(setname='Membrane', eids=membrane_set)
# PCM Element Set
for k, v in self.pcm_materials.items():
fe_mesh.addElementSet(setname='PCM {:d}'.format(k),
eids=v['element_ids'] + 1)
# ECM Element Set
for k, v in self.ecm_materials.items():
fe_mesh.addElementSet(setname='ECM {:d}'.format(k),
eids=v['element_ids'] + 1)
fe_model = febio.Model(modelfile='.'.join([model_name, 'feb']),
steps=[{
'Displace': 'biphasic'
}])
mat_props = self.options["Material Properties"]
# Cell Material
cell_mat = febio.MatDef(
matid=1,
mname='Cell',
mtype='biphasic',
elsets='Cell',
attributes={'phi0': '{:.6E}'.format(mat_props["Cell phi"])})
cell_mat.addBlock(branch=1,
btype='solid',
mtype='neo-Hookean',
attributes={
"E": "{:.6E}".format(mat_props["Cell Modulus"]),
"v": "{:.6E}".format(mat_props["Cell Poisson"])
})
cell_mat.addBlock(branch=1,
btype='permeability',
mtype='perm-const-iso',
attributes={
"perm":
"{:.6E}".format(mat_props["Cell Permeability"])
})
fe_model.addMaterial(cell_mat)
# Membrane Material
mem_mat = febio.MatDef(
matid=2,
mname='Membrane',
mtype='biphasic',
elsets='Membrane',
attributes={"phi0": "{:.6E}".format(mat_props["Membrane phi"])})
mem_mat.addBlock(branch=1,
btype='solid',
mtype='neo-Hookean',
attributes={
"E":
"{:.6E}".format(mat_props["Membrane Modulus"]),
"v":
"{:.6E}".format(mat_props["Membrane Poisson"])
})
mem_mat.addBlock(branch=1,
btype='permeability',
mtype='perm-const-iso',
attributes={
"perm":
"{:.6E}".format(
mat_props["Membrane Permeability"])
})
fe_mesh.addElementData(elset='Membrane',
attributes={
"thickness":
"{:.6E}".format(
mat_props["Membrane Thickness"])
})
fe_model.addMaterial(mem_mat)
# ECM Materials
ecm_mats = []
for k, v in self.ecm_materials.items():
mname = 'ECM {:d}'.format(k)
ecm_mats.append(
febio.MatDef(matid=k,
mname=mname,
mtype='biphasic',
elsets=mname,
attributes={'phi0': '{:6E}'.format(v['phi'])}))
ecm_mats[-1].addBlock(
branch=1,
btype='solid',
mtype='solid mixture',
attributes={'mat_axis': ['vector', "1,0,0", "0,1,0"]})
ecm_mats[-1].addBlock(branch=2,
btype='solid',
mtype='Holmes-Mow',
attributes={
"E": "{:.6E}".format(v["E"]),
"v": "{:.6E}".format(v["v"]),
"beta": "{:.6E}".format(v["beta"])
})
ecm_mats[-1].addBlock(
branch=2,
btype='solid',
mtype='ellipsoidal fiber distribution',
attributes={
"ksi":
"{:.6E}, {:.6E}, {:.6E}".format(v["ksi"][0], v["ksi"][1],
v["ksi"][2]),
"beta":
"{:.6E}, {:.6E}, {:.6E}".format(2.0, 2.0, 2.0)
})
ecm_mats[-1].addBlock(branch=1,
btype='permeability',
mtype='perm-Holmes-Mow',
attributes={
"perm":
"{:.6E}".format(v["permeability"]),
"M": "{:.6E}".format(v["m"]),
"alpha": "{:.6E}".format(v["alpha"])
})
fe_model.addMaterial(ecm_mats[-1])
# PCM Material
pcm_mats = []
for k, v in self.pcm_materials.items():
mname = 'PCM {:d}'.format(k)
pcm_mats.append(
febio.MatDef(matid=k,
mname=mname,
mtype='biphasic',
elsets=mname,
attributes={'phi0': '{:6E}'.format(v['phi'])}))
pcm_mats[-1].addBlock(branch=1,
btype='solid',
mtype='Holmes-Mow',
attributes={
"E": "{:.6E}".format(v["E"]),
"v": "{:.6E}".format(v["v"]),
"beta": "{:.6E}".format(v["beta"])
})
pcm_mats[-1].addBlock(branch=1,
btype='permeability',
mtype='perm-Holmes-Mow',
attributes={
"perm":
"{:.6E}".format(v["permeability"]),
"M": "{:.6E}".format(v["m"]),
"alpha": "{:.6E}".format(v["alpha"])
})
fe_model.addMaterial(pcm_mats[-1])
fe_model.addGeometry(mesh=fe_mesh,
mats=[cell_mat, mem_mat] + ecm_mats + pcm_mats)
# Boundary Conditions
fe_model.addLoadCurve(lc='1',
lctype='linear',
points=np.ravel(
list(
zip(self.macro_results.TIME,
self.macro_results.TIME))))
boundary = febio.Boundary()
nids = self.surface_nodes
dx, dy, dz, p = self._interpBCs(vtkmesh)
cnt = 2
for i in range(dx.shape[0]):
fe_model.addLoadCurve(
lc='{:d}'.format(cnt),
lctype='smooth',
points=np.ravel(list(zip(self.macro_results.TIME, dx[i, :]))))
boundary.addPrescribed(nodeid=nids[i] + 1,
scale=1.0,
dof='x',
lc='{:d}'.format(cnt))
cnt += 1
fe_model.addLoadCurve(
lc='{:d}'.format(cnt),
lctype='smooth',
points=np.ravel(list(zip(self.macro_results.TIME, dy[i, :]))))
boundary.addPrescribed(nodeid=nids[i] + 1,
scale=1.0,
dof='y',
lc='{:d}'.format(cnt))
cnt += 1
fe_model.addLoadCurve(
lc='{:d}'.format(cnt),
lctype='smooth',
points=np.ravel(list(zip(self.macro_results.TIME, dz[i, :]))))
boundary.addPrescribed(nodeid=nids[i] + 1,
scale=1.0,
dof='z',
lc='{:d}'.format(cnt))
cnt += 1
fe_model.addLoadCurve(
lc='{:d}'.format(cnt),
lctype='smooth',
points=np.ravel(list(zip(self.macro_results.TIME, p[i, :]))))
boundary.addPrescribed(nodeid=nids[i] + 1,
scale=1.0,
dof='p',
lc='{:d}'.format(cnt))
cnt += 1
fe_model.addBoundary(boundary)
ctrl = febio.Control()
ctrl.setAttributes({
'title':
model_name,
'time_steps':
'{:d}'.format(
np.ceil(self.macro_results.TIME[-1] /
self.macro_results.TIME[1]).astype(int)),
'step_size':
'{:12.6f}'.format(self.macro_results.TIME[1]),
'time_stepper': {
'aggressiveness': '0',
'dtmin': '0.01',
'dtmax': 'lc=1',
'max_retries': '10',
'opt_iter': '10'
},
'max_ups':
'0',
'max_refs':
'10',
'dtol':
'0.001',
'ptol':
'0.01',
'lstol':
'0.9',
'plot_level':
'PLOT_MUST_POINTS'
})
fe_model.addControl(ctrl, step=0)
fe_model.addOutput(output=[
"shell strain", "Lagrange strain",
"effective shell fluid pressure", "relative volume"
])
fe_model.writeModel()
def performFEA(self):
for filename in self.pickles:
fid = open(filename, 'rb')
self.data[filename] = pickle.load(fid)
fid.close()
mesh = febio.MeshDef()
# would be good to vectorize these
for i, e in enumerate(self.data[filename]['elements']):
mesh.elements.append(['tet4', i + 1] + e)
for i, n in enumerate(self.data[filename]['nodes']):
mesh.nodes.append([i + 1] + n)
mesh.addElementSet(setname='cell',
eids=list(range(1,
len(mesh.elements) + 1)))
modelname = filename.replace('.pkl', '.feb')
model = febio.Model(modelfile=modelname,
steps=[{
'Displace': 'solid'
}])
#lookup table for proper FEBio keyword vs GUI text
keywords = {
"neoHookean": "neo-Hookean",
"Young's Modulus": "E",
"Poisson's Ratio": "v",
"Mooney-Rivlin": "Mooney-Rivlin",
"C_1": "c1",
"C_2": "c2",
"Bulk Modulus": "k",
"Transversely Isotropic": "orthotropic elastic",
"Young's Modulus (radial)": "E1",
"Young's Modulus (tangential)": ["E2", "E3"],
"Poisson's Ratio (radial:tangential)": "v12",
"Poisson's Ratio (tangential:radial)": ["v23", "v31"],
"Shear Modulus (radial planes)": ["G12", "G23", "G31"],
"Continuous Fibre Distribution":
"ellipsoidal fiber distribution"
}
#Ground Substance
gtype = keywords[self.groundSubstances[self.groundSubstance.get() -
1]]
gattributes = {}
for (k,
v) in list(self.groundParameters[self.groundSubstance.get() -
1].items()):
# transversely isotropic case
if isinstance(keywords[k], list):
for a in keywords[k]:
# G12 = E2 / (2 * (1 + v12))
if a == "G12":
gattributes[a] = str(
old_div(float(gattributes["E2"]),
(2.0 *
(1 + float(gattributes["v12"])))))
else:
gattributes[a] = str(v.get())
# any other case
else:
gattributes[keywords[k]] = str(v.get())
if self.tensileNetwork.get() == 1:
mat = febio.MatDef(matid=1,
mname='cell',
mtype=gtype,
elsets='cell',
attributes=gattributes)
model.addMaterial(mat)
model.addGeometry(mesh=mesh, mats=[mat])
#With a tensile network
else:
self.makeVTK(filename)
self.findLocalCsys(filename)
ind = self.tensileNetwork.get() - 1
ttype = keywords[self.tensileNetworks[ind]]
ksi = [
self.tensileParameters[ind][k].get()
for k in ("ksi1", "ksi2=ksi3", "ksi2=ksi3")
]
beta = [
self.tensileParameters[ind][k].get()
for k in ("beta1", "beta2=beta3", "beta2=beta3")
]
mats = []
I1n2 = np.eye(3)[0:2, :]
distances = numpy_support.vtk_to_numpy(
self.vtkMeshes[filename].GetCellData().GetArray(
"Signed Distances"))
maxd = np.max(np.abs(distances))
for i, e in enumerate(self.data[filename]['elements']):
normal = self.vtkMeshes[filename].GetCellData().GetArray(
"LevelSet Normals").GetTuple3(i)
# cross with both e1 and e2 to ensure linearly independent
crossed = np.cross(normal, I1n2)
norms = np.linalg.norm(crossed, axis=1)
# get the index of the maximum norm; so never zero
ind2 = np.argmax(norms)
b = old_div(crossed[ind, :], norms[ind2])
normal = list(map(str, list(normal)))
b = list(map(str, list(b)))
d = self.tensileParameters[ind][
"Distance Cutoff [0, 1]"].get()
k = self.tensileParameters[ind]["Cutoff Grade (0, 1]"].get(
)
x = old_div(np.abs(distances[i]), maxd)
w = 0.5 * (1 - np.tanh(old_div((x - d), k)))
if w < 0.05:
w = 0.05
tmp_ksi = [w * v for v in ksi]
tattributes = {
"ksi": ",".join(map(str, tmp_ksi)),
"beta": ",".join(map(str, beta))
}
mesh.addElementSet(setname='e{:d}'.format(i + 1),
eids=[i + 1])
mats.append(
febio.MatDef(
matid=i + 1,
mname='cell',
mtype="solid mixture",
elsets='e{:d}'.format(i + 1),
attributes={
'mat_axis':
['vector', ','.join(normal), ','.join(b)]
}))
mats[-1].addBlock(branch=1,
btype='solid',
mtype=gtype,
attributes=gattributes)
mats[-1].addBlock(branch=1,
btype='solid',
mtype=ttype,
attributes=tattributes)
model.addMaterial(mats[-1])
model.addGeometry(mesh=mesh, mats=mats)
ctrl = febio.Control()
ctrl.setAttributes({'title': 'cell', 'max_ups': '0'})
model.addControl(ctrl, step=0)
boundary = febio.Boundary(steps=1)
for i, bc in enumerate(self.data[filename]['boundary conditions']):
boundary.addPrescribed(
step=0,
nodeid=self.data[filename]['surfaces'][i],
dof='x',
lc='1',
scale=str(bc[0]))
boundary.addPrescribed(
step=0,
nodeid=self.data[filename]['surfaces'][i],
dof='y',
lc='1',
scale=str(bc[1]))
boundary.addPrescribed(
step=0,
nodeid=self.data[filename]['surfaces'][i],
dof='z',
lc='1',
scale=str(bc[2]))
model.addBoundary(boundary=boundary)
model.addLoadCurve(lc='1', lctype='linear', points=[0, 0, 1, 1])
model.writeModel()
subprocess.call(self._FEBIO_BIN + " -i " + modelname, shell=True)