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Commit 0a761893 by Jigyasa Watwani
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fixed vform -- no imex for v

parent cb568e30
Inline Side-by-side
Showing with 20 additions and 30 deletions
no_c_fixed_bdry_fenics.py
...@@ -13,8 +13,8 @@ class Growth(object): ...@@ -13,8 +13,8 @@ class Growth(object):
# create mesh, mixed element and function space # create mesh, mixed element and function space
self.mesh = df.IntervalMesh(self.resolution, 0.0, 2.0*np.pi*self.system_size_by_2PI) self.mesh = df.IntervalMesh(self.resolution, 0.0, 2.0*np.pi*self.system_size_by_2PI)
conc_element = df.FiniteElement('P', self.mesh.ufl_cell(), 1) scalar_element = df.FiniteElement('P', self.mesh.ufl_cell(), 1)
mixed_element = df.MixedElement([conc_element, conc_element, conc_element]) # u, v, rho mixed_element = df.MixedElement([scalar_element, scalar_element, scalar_element]) # u, v, rho
# define function space with this mixed element # define function space with this mixed element
self.function_space = df.FunctionSpace(self.mesh, mixed_element) self.function_space = df.FunctionSpace(self.mesh, mixed_element)
...@@ -32,8 +32,14 @@ class Growth(object): ...@@ -32,8 +32,14 @@ class Growth(object):
def advection(self, conc, vel, tconc): def advection(self, conc, vel, tconc):
return (df.inner((vel * conc).dx(0), tconc)) return (df.inner((vel * conc).dx(0), tconc))
def active_stress(self, rho, tv): def active_stress(self, rho):
return self.lamda * df.inner((rho/(rho + self.saturation_rho)).dx(0), tv) return self.lamda * rho/(rho + self.saturation_rho)
def passive_stress(self, u, v):
return (self.elasticity * u.dx(0) + self.viscosity * v.dx(0))
def stress(self, u, v, rho):
return (self.passive_stress(u, v) + self.active_stress(rho))
def reaction_rho(self, rho, trho): def reaction_rho(self, rho, trho):
return self.turnover_rho * df.inner(rho - self.average_rho, trho) return self.turnover_rho * df.inner(rho - self.average_rho, trho)
...@@ -46,16 +52,15 @@ class Growth(object): ...@@ -46,16 +52,15 @@ class Growth(object):
u0 = df.interpolate(u0, self.function_space.sub(0).collapse()) u0 = df.interpolate(u0, self.function_space.sub(0).collapse())
rho0 = df.interpolate(rho0, self.function_space.sub(2).collapse()) rho0 = df.interpolate(rho0, self.function_space.sub(2).collapse())
v0_function_space = df.FunctionSpace(self.mesh, 'P', 1) v0_function_space = self.function_space.sub(1).collapse()
v0 = df.Function(v0_function_space) v0 = df.Function(v0_function_space)
tv0 = df.TestFunction(v0_function_space) tv0 = df.TestFunction(v0_function_space)
v0form = (df.inner(v0,tv0) v0form = (self.friction * df.inner(v0, tv0)
+ self.elasticity * df.inner(u0.dx(0),tv0.dx(0)) + df.inner(self.stress(u0, v0, rho0), tv0.dx(0))
+ self.viscosity * df.inner(v0.dx(0), tv0.dx(0))
- self.lamda * df.inner((rho0/(rho0 + self.saturation_rho)).dx(0),tv0)
) * df.dx ) * df.dx
bcv0 = df.DirichletBC(v0_function_space, df.Constant(0.0), 'on_boundary')
bcv0 = df.DirichletBC(v0_function_space, df.Constant(0.0), 'on_boundary')
df.solve(v0form == 0, v0, bcv0) df.solve(v0form == 0, v0, bcv0)
df.assign(self.f0, [u0, v0, rho0]) df.assign(self.f0, [u0, v0, rho0])
self.fminus1.assign(self.f0) self.fminus1.assign(self.f0)
...@@ -71,19 +76,9 @@ class Growth(object): ...@@ -71,19 +76,9 @@ class Growth(object):
- 3/8 * df.inner(v0, tu) - 3/8 * df.inner(v0, tu)
- 1/16 * df.inner(vminus1, tu) - 1/16 * df.inner(vminus1, tu)
) )
vform = ( df.inner(v, tv) vform = (self.friction * df.inner(v, tv)
+ 9/16 * self.elasticity * df.inner(u.dx(0), tv.dx(0)) + df.inner(self.stress(u, v, rho), tv.dx(0))
+ 3/8 * self.elasticity * df.inner(u0.dx(0), tv.dx(0)) )
+ 1/16 * self.elasticity * df.inner(uminus1.dx(0), tv.dx(0))
- 9/16 * self.active_stress(rho0, tv)
- 3/8 * self.active_stress(rhominus1, tv)
- 1/16 * self.active_stress(rhominus1, tv)
+ 9/16 * self.viscosity * df.inner(v.dx(0),tv.dx(0))
+ 3/8 * self.viscosity * df.inner(v0.dx(0),tv.dx(0))
+ 1/16 * self.viscosity * df.inner(vminus1.dx(0),tv.dx(0))
)
rhoform = (df.inner((rho - rho0)/self.timestep, trho) rhoform = (df.inner((rho - rho0)/self.timestep, trho)
+ 3/2 * self.advection(rho0, v, trho) + 3/2 * self.advection(rho0, v, trho)
...@@ -104,7 +99,7 @@ class Growth(object): ...@@ -104,7 +99,7 @@ class Growth(object):
self.setup_initial_conditions(u0, rho0) self.setup_initial_conditions(u0, rho0)
self.setup_weak_forms() self.setup_weak_forms()
u,v,rho = self.f0.split(deepcopy=True) u, v, rho = self.f0.split(deepcopy=True)
u_array[0] = u.compute_vertex_values(self.mesh) u_array[0] = u.compute_vertex_values(self.mesh)
v_array[0] = v.compute_vertex_values(self.mesh) v_array[0] = v.compute_vertex_values(self.mesh)
rho_array[0] = rho.compute_vertex_values(self.mesh) rho_array[0] = rho.compute_vertex_values(self.mesh)
...@@ -120,23 +115,18 @@ class Growth(object): ...@@ -120,23 +115,18 @@ class Growth(object):
return (u_array, v_array, rho_array) return (u_array, v_array, rho_array)
if __name__ == '__main__': if __name__ == '__main__':
import dolfin as df
import json import json
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from matplotlib.widgets import Slider from matplotlib.widgets import Slider
with open('growth_parameters.json') as jsonFile: with open('growth_parameters.json') as jsonFile:
params = json.load(jsonFile) params = json.load(jsonFile)
assert(params['dimension']==1)
g = Growth(params) g = Growth(params)
u0 = df.Expression('sin(x[0])', degree=1) u0 = df.Expression('sin(x[0])', degree=1)
u0 = df.interpolate(u0, g.function_space.sub(0).collapse())
rho0 = df.Expression('cos(x[0])+cos(x[0]/2)', degree=1) rho0 = df.Expression('rho0 + 0.1 * (cos(x[0])+cos(x[0]/2))', rho0 =g.average_rho, degree=1)
rho0 = df.interpolate(rho0, g.function_space.sub(2).collapse())
(u, v, rho) = g.solve(u0, rho0) (u, v, rho) = g.solve(u0, rho0)
......
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