def test_project_over_subspace(self):
from glimslib import fenics_local as fenics
nx = ny = nz = 10
mesh = fenics.RectangleMesh(fenics.Point(-2, -2), fenics.Point(2, 2),
nx, ny)
E1 = fenics.FiniteElement("Lagrange", mesh.ufl_cell(), 1)
V1 = fenics.FunctionSpace(mesh, E1)
E2 = fenics.VectorElement("Lagrange", mesh.ufl_cell(), 1)
V2 = fenics.FunctionSpace(mesh, E2)
expr_1 = fenics.Expression(
('exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))'),
degree=1,
a=1,
x0=0.0,
y0=0.0)
expr_2 = fenics.Expression(('x[0]', 'x[1]'), degree=1)
self.subspaces.set_functionspaces([V1, V2])
f_1 = self.subspaces.project_over_subspace(expr_1, 0)
if fenics.is_version("<2018.1.x"):
self.assertEqual(type(f_1), fenics.functions.Function)
else:
self.assertEqual(type(f_1), fenics.function.function.Function)
f_2 = self.subspaces.project_over_subspace(expr_2, 0)
self.assertEqual(f_2, None)
f_1 = self.subspaces.project_over_subspace(expr_1, 1)
self.assertEqual(f_1, None)
f_2 = self.subspaces.project_over_subspace(expr_2, 1)
if fenics.is_version("<2018.1.x"):
self.assertEqual(type(f_2), fenics.functions.Function)
else:
self.assertEqual(type(f_2), fenics.function.function.Function)
def setUp(self):
self.nx = 40
self.ny = 20
mesh = fenics.RectangleMesh(fenics.Point(-2, -2), fenics.Point(2, 2), self.nx, self.ny)
# function spaces
U = fenics.VectorFunctionSpace(mesh, "Lagrange", 1)
V = fenics.FunctionSpace(mesh, "Lagrange", 1)
u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 1 ? (1.0) : (0.0)', degree=1,
x0=1,
y0=1)
u_0_disp_expr = fenics.Constant((1.0, 1.0))
self.conc = fenics.project(u_0_conc_expr, V)
self.disp = fenics.project(u_0_disp_expr, U)
# 3D
mesh3d = fenics.BoxMesh(fenics.Point(-2, -2, -2), fenics.Point(2, 2, 2), 10, 20, 30)
# function spaces
U3 = fenics.VectorFunctionSpace(mesh3d, "Lagrange", 1)
V3 = fenics.FunctionSpace(mesh3d, "Lagrange", 1)
u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)+pow(x[2]-z0,2)) < 1 ? (1.0) : (0.0)', degree=1,
x0=1, y0=1, z0=1 )
u_0_disp_expr = fenics.Constant((1.0, 1.0, 1.0))
self.conc3 = fenics.project(u_0_conc_expr, V3)
self.disp3 = fenics.project(u_0_disp_expr, U3)
self.test_path = os.path.join(config.output_dir_testing, 'test_data_io')
fu.ensure_dir_exists(self.test_path)
def setUp(self):
# Domain
nx = ny = nz = 10
self.mesh = fenics.RectangleMesh(fenics.Point(-2, -2),
fenics.Point(2, 2), nx, ny)
self.sim = TumorGrowth(self.mesh)
label_funspace = fenics.FunctionSpace(self.mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0.5) ? (1.0) : (2.0)', degree=1)
self.labels = fenics.project(label_expr, label_funspace)
self.tissue_map = {0: 'outside', 1: 'tissue', 2: 'tumor'}
boundary = Boundary()
self.boundary_dict = {'boundary_1': boundary, 'boundary_2': boundary}
self.dirichlet_bcs = {
'clamped_0': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary': Boundary(),
'subspace_id': 0
},
'clamped_1': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary_id': 0,
'subspace_id': 0
},
'clamped_2': {
'bc_value': fenics.Constant((0.0, 0.0)),
'boundary_name': 'boundary_1',
'subspace_id': 0
}
}
self.von_neuman_bcs = {
'no_flux': {
'bc_value': fenics.Constant(0.0),
'boundary_id': 0,
'subspace_id': 1
},
'no_flux_2': {
'bc_value': fenics.Constant(0.0),
'boundary_name': 'boundary_1',
'subspace_id': 1
},
}
self.u_0_conc_expr = fenics.Expression(
'sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
degree=1,
x0=0.25,
y0=0.5)
self.u_0_disp_expr = fenics.Constant((0.0, 0.0))
self.youngmod = {'outside': 10E6, 'tissue': 1, 'tumor': 1000}
self.poisson = {'outside': 0.4, 'tissue': 0.4, 'tumor': 0.49}
self.diffusion = {'outside': 0.0, 'tissue': 1.0, 'tumor': 0.1}
self.prolif = {'outside': 0.0, 'tissue': 0.1, 'tumor': 1.0}
self.coupling = {'outside': 0.0, 'tissue': 0.0, 'tumor': 0.5}
def setUp(self):
# Domain
nx = ny = nz = 10
mesh = fenics.RectangleMesh(fenics.Point(-2, -2), fenics.Point(2, 2),
nx, ny)
# function spaces
displacement_element = fenics.VectorElement("Lagrange",
mesh.ufl_cell(), 1)
concentration_element = fenics.FiniteElement("Lagrange",
mesh.ufl_cell(), 1)
element = fenics.MixedElement(
[displacement_element, concentration_element])
subspace_names = {0: 'displacement', 1: 'concentration'}
functionspace = FunctionSpace(mesh)
functionspace.init_function_space(element, subspace_names)
# build a 'solution' function
u_0_conc_expr = fenics.Expression(
'sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
degree=1,
x0=0.25,
y0=0.5)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
self.U = functionspace.project_over_space(function_expr={
0: u_0_disp_expr,
1: u_0_conc_expr
})
self.tsd = TimeSeriesData(functionspace=functionspace, name='solution')
def setUp(self):
# Domain
nx = ny = nz = 10
self.mesh = fenics.RectangleMesh(fenics.Point(-2, -2),
fenics.Point(2, 2), nx, ny)
# function spaces
self.displacement_element = fenics.VectorElement(
"Lagrange", self.mesh.ufl_cell(), 1)
self.concentration_element = fenics.FiniteElement(
"Lagrange", self.mesh.ufl_cell(), 1)
self.element = fenics.MixedElement(
[self.displacement_element, self.concentration_element])
subspace_names = {0: 'displacement', 1: 'concentration'}
self.functionspace = FunctionSpace(self.mesh)
self.functionspace.init_function_space(self.element, subspace_names)
# subdomains
label_funspace = fenics.FunctionSpace(self.mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0) ? (1.0) : (2.0)', degree=1)
labels = fenics.project(label_expr, label_funspace)
self.labels = labels
self.tissue_id_name_map = {0: 'outside', 1: 'tissue', 2: 'tumor'}
self.parameter = {'outside': 0.0, 'tissue': 1.0, 'tumor': 0.1}
self.boundary = Boundary()
boundary_dict = {
'boundary_1': self.boundary,
'boundary_2': self.boundary
}
self.boundary_dict = boundary_dict
self.subdomains = SubDomains(self.mesh)
self.subdomains.setup_subdomains(label_function=self.labels)
self.subdomains.setup_boundaries(tissue_map=self.tissue_id_name_map,
boundary_fct_dict=self.boundary_dict)
self.subdomains.setup_measures()
# parameter instance
self.params = Parameters(self.functionspace, self.subdomains)
def test_set_initial_value_expressions(self):
u_0_conc_expr = fenics.Expression(
'sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
degree=1,
x0=0.25,
y0=0.5)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
ivs = {1: u_0_conc_expr, 0: u_0_disp_expr}
self.params.set_initial_value_expressions(ivs)
self.assertEqual(self.params.get_iv(1), u_0_conc_expr)
self.assertEqual(self.params.get_iv(0), u_0_disp_expr)
def test_create_initial_value_function(self):
self.params = Parameters(self.functionspace,
self.subdomains,
time_dependent=False)
u_0_conc_expr = fenics.Expression(
'sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)',
degree=1,
x0=0.25,
y0=0.5)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
ivs = {1: u_0_conc_expr, 0: u_0_disp_expr}
self.params.set_initial_value_expressions(ivs)
u = self.params.create_initial_value_function()
def test_split_function(self):
subspace_names = {0: 'displacement', 1: 'concentration'}
functionspace = FunctionSpace(self.mesh)
functionspace.init_function_space(self.element, subspace_names)
u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)) < 0.1 ? (1.0) : (0.0)', degree=1,
x0=0.25,
y0=0.5)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
U_orig = functionspace.project_over_space(function_expr={0: u_0_disp_expr, 1: u_0_conc_expr})
U = functionspace.split_function(U_orig)
self.assertEqual(U_orig, U)
U_1 = functionspace.split_function(U_orig, subspace_id=1)
U_0 = functionspace.split_function(U_orig, subspace_id=0)
def setUp(self):
nx = ny = nz = 5
self.ny = ny
self.nx = nx
mesh = fenics.RectangleMesh(fenics.Point(-2, -2), fenics.Point(2, 2),
nx, ny)
self.subdomains = SubDomains(mesh)
# 'LabelMap'
label_funspace = fenics.FunctionSpace(mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0) ? (1.0) : (2.0)', degree=1)
labels = fenics.project(label_expr, label_funspace)
self.labels = labels
# tissue_id_name_map
self.tissue_id_name_map = {0: 'outside', 1: 'tissue', 2: 'tumor'}
self.parameter = {'outside': 0.0, 'tissue': 1.0, 'tumor': 0.1}
class Boundary(fenics.SubDomain):
def inside(self, x, on_boundary):
return on_boundary
self.boundary = Boundary()
boundary_dict = {'boundary_1': self.boundary}
self.boundary_dict = boundary_dict
dirichlet_bcs = {
'clamped_0': {
'bc_value': fenics.Constant((0.0, 0.0)),
'named_boundary': 'boundary_all',
'subspace_id': 0
}
}
von_neuman_bcs = {}
von_neuman_bcs = {}
# Initial Values
u_0_conc_expr = fenics.Expression(
'exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))',
degree=1,
a=0.5,
x0=148,
y0=-67)
u_0_disp_expr = fenics.Constant((0.0, 0.0))
ivs = {0: u_0_disp_expr, 1: u_0_conc_expr}
# ==============================================================================
# Parameters
# ==============================================================================
sim_time = 50
sim_time_step = 1
E_GM = 3000E-6
E_WM = 3000E-6
E_CSF = 1000E-6
E_VENT = 1000E-6
nu_GM = 0.4
# Problem Settings
# ==============================================================================
class Boundary(fenics.SubDomain):
def inside(self, x, on_boundary):
return on_boundary
# Mesh
nx = ny = 50
mesh = fenics.RectangleMesh(fenics.Point(-5, -5), fenics.Point(5, 5), nx, ny)
# LabelMap
label_funspace = fenics.FunctionSpace(mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0.0) ? (1.0) : (2.0)', degree=1)
labels = fenics.project(label_expr, label_funspace)
tissue_map = {0: 'outside', 1: 'A', 2: 'B'}
# Boundaries & BCs
boundary = Boundary()
boundary_dict = {'boundary_all': boundary}
dirichlet_bcs = {
'clamped_outside': {
'bc_value': fenics.Constant((0.0, 0.0)),
'named_boundary': 'boundary_all',
'subspace_id': 0
},
# Test to show that Dirichlet BCs can be applied to subdomain interfaces
# 'clamped_A_B' : {'bc_value': fenics.Constant((0.0, 0.0)),
# 'subdomain_boundary': 'A_B',
mesh = fenics.RectangleMesh(fenics.Point(-5, -5), fenics.Point(5, 5), nx, ny)
boundary = Boundary()
boundary_dict = {'boundary_all': boundary}
dirichlet_bcs = {
'clamped_0': {
'bc_value': fenics.Constant((0.0, 0.0)),
'named_boundary': 'boundary_all',
'subspace_id': 0
}
}
von_neuman_bcs = {}
u_0_conc_expr = fenics.Expression(
('exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2))'),
degree=1,
a=1,
x0=0.0,
y0=0.0)
u_0_disp_expr = fenics.Expression(('0', '0'), degree=1)
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 10
sim_time_step = 1
sim = TumorGrowth(mesh)
sim.setup_global_parameters(boundaries=boundary_dict,
dirichlet_bcs=dirichlet_bcs,
von_neumann_bcs=von_neuman_bcs)
def setUp(self):
# Domain
nx = ny = nz = 10
self.nx, self.ny = nx, ny
self.mesh = fenics.RectangleMesh(fenics.Point(-2, -2), fenics.Point(2, 2), nx, ny)
# function spaces
self.displacement_element = fenics.VectorElement("Lagrange", self.mesh.ufl_cell(), 1)
self.concentration_element = fenics.FiniteElement("Lagrange", self.mesh.ufl_cell(), 1)
self.element = fenics.MixedElement([self.displacement_element, self.concentration_element])
subspace_names = {0: 'displacement', 1: 'concentration'}
self.functionspace = FunctionSpace(self.mesh)
self.functionspace.init_function_space(self.element, subspace_names)
# define 'solution' with concentration=1 everywhere
self.conc_expr = fenics.Constant(1.0)
self.conc = self.functionspace.project_over_space(self.conc_expr, subspace_name='concentration')
# subdomains
label_funspace = fenics.FunctionSpace(self.mesh, "DG", 1)
label_expr = fenics.Expression('(x[0]>=0) ? (1.0) : (2.0)', degree=1)
labels = fenics.project(label_expr, label_funspace)
self.labels = labels
self.tissue_id_name_map = {0: 'outside',
1: 'tissue',
2: 'tumor'}
self.parameter = {'outside': 0.0,
'tissue': 1.0,
'tumor': 0.1}
self.boundary_pos = BoundaryPos()
self.boundary_neg = BoundaryNeg()
boundary_dict = {'boundary_pos': self.boundary_pos,
'boundary_neg': self.boundary_neg}
self.boundary_dict = boundary_dict
self.subdomains = SubDomains(self.mesh)
self.subdomains.setup_subdomains(label_function=self.labels)
self.subdomains.setup_boundaries(tissue_map=self.tissue_id_name_map,
boundary_fct_dict=self.boundary_dict)
self.subdomains.setup_measures()
# BCs
self.bcs = BoundaryConditions(self.functionspace, self.subdomains)
self.dirichlet_bcs = {'clamped_0': {'bc_value': fenics.Constant((0.0, 0.0)),
'boundary': BoundaryPos(),
'subspace_id': 0},
'clamped_1': {'bc_value': fenics.Constant((0.0, 0.0)),
'subdomain_boundary': 'tissue_tumor',
'subspace_id': 0},
'clamped_pos': {'bc_value': fenics.Constant((0.0, 0.0)),
'named_boundary': 'boundary_pos',
'subspace_id': 0},
'clamped_neg': {'bc_value': fenics.Constant((0.0, 0.0)),
'named_boundary': 'boundary_neg',
'subspace_id': 0}
}
self.von_neuman_bcs = {
'flux_boundary_pos': {'bc_value': fenics.Constant(1.0),
'named_boundary': 'boundary_pos',
'subspace_id': 1},
'flux_boundary_neg': {'bc_value': fenics.Constant(-5.0),
'named_boundary': 'boundary_neg',
'subspace_id': 1}
# 'no_flux_domain_boundary': {'bc_value': fenics.Constant(1.0),
# 'subdomain_boundary': 'tissue_tumor',
# 'subspace_id': 1},
}
boundaries_no_flux = ['WM_Ventricles', 'GM_Ventricles', 'CSF_WM', 'CSF_GM']
von_neuman_bcs = {}
for boundary in boundaries_no_flux:
bc_name = "no_flux_%s" % boundary
bc_dict = {
'bc_value': fenics.Constant(0.0),
'boundary_name': boundary,
'subspace_id': 1
}
von_neuman_bcs[bc_name] = bc_dict
# Initial Values
u_0_conc_expr = fenics.Expression(
'exp(-a*pow(x[0]-x0, 2) - a*pow(x[1]-y0, 2) - a*pow(x[2]-z0,2))',
degree=1,
a=0.5,
x0=118,
y0=-109,
z0=72)
# u_0_conc_expr = fenics.Expression('sqrt(pow(x[0]-x0,2)+pow(x[1]-y0,2)+pow(x[2]-z0,2)) < 15 ? (1.0) : (0.0)',
# degree=1, x0=118, y0=-109, z0=72)
u_0_disp_expr = fenics.Expression(('0.0', '0.0', '0.0'), degree=1)
# ==============================================================================
# Class instantiation & Setup
# ==============================================================================
sim_time = 5
sim_time_step = 1
sim = TumorGrowth(mesh)
