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Commit 89a9ec55 authored by Lars Hubatsch's avatar Lars Hubatsch
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Updating Fenics_FloryHugg_Binary examples for Kafa.

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%% Cell type:markdown id: tags:
# Binary mixture based on Flory Huggins free energy
For $\phi_{tot}$ in a binary mixture, assuming a Flory Huggins free energy density, we obtain (Overleaf):
Reference for FEM: https://www.comsol.com/multiphysics/finite-element-method
$\partial_\mathrm{t}\phi_\mathrm{tot}=k_\mathrm{B}T\Gamma_\mathrm{0} \,\nabla\cdot\left[\left[1-2\chi\phi_\mathrm{tot}(1-\phi_\mathrm{tot})\right]\nabla \phi_\mathrm{tot}-\phi_\mathrm{tot}(1-\phi_\mathrm{tot})\kappa\nabla\nabla^2\phi_\mathrm{tot}\right]$
To solve this equation we follow the [Fenics Cahn-Hilliard example](https://bitbucket.org/fenics-project/dolfin/src/master/python/demo/documented/cahn-hilliard/demo_cahn-hilliard.py.rst#rst-header-id1) (the maths is explained [here](https://fenicsproject.org/docs/dolfinx/dev/python/demos/cahn-hilliard/demo_cahn-hilliard.py.html), for our free energy see overleaf).
$\partial_t \phi_{\mathrm{tot}} = \nabla \cdot \Gamma_{\mathrm{tot}}\nabla\mu_\mathrm{tot}$
$\mu_\mathrm{tot}=\nu\frac{\partial f}{\partial \phi_\mathrm{tot}}=\,k_\mathrm{B}T\left[\ln\phi_\mathrm{tot} - \ln\left(1-\phi_\mathrm{tot}\right)+\chi(1-2\phi_\mathrm{tot})-\kappa\nabla^2 \phi_\mathrm{tot} +1-n \right]$
The **boundary conditions** for the flux of the chemical potential and concentration read:
$\nabla\mu_\mathrm{tot}\cdot n=0 $ on $\partial \Omega\;,$
$\nabla\phi_\mathrm{tot}\cdot n = 0$ on $\partial \Omega$
Cast into the **weak form** and integrating by parts we obtain:
$\int_{\Omega} \partial_t c \;q \; dx = \int_{\partial \Omega} \Gamma_\mathrm{tot}\nabla\mu_\mathrm{tot}q \; ds - \int_\Omega \Gamma_\mathrm{tot} \nabla \mu_\mathrm{tot} \nabla q\;dx = - \int_\Omega \Gamma_\mathrm{tot} \nabla \mu_\mathrm{tot} \nabla q\;dx\;, $
$\int_\Omega \mu_\mathrm{tot} q \; dx = k_\mathrm{B} T \int_\Omega\left(\ln\left(\frac{\phi_\mathrm{tot}}{1-\phi_\mathrm{tot}}\right)+\chi(1-2\phi_\mathrm{tot})\right)q + \kappa\nabla\phi_\mathrm{tot}\nabla q \; dx$
where we dropped the boundary terms (not explicitly written in second equation) due to the boundary conditions/weak form. We also disregard 1-n, because constants don't change the flux in the absence of chemical reactions (an offset doesn't change the solution in this case, try out by adding $-6.0*v*dx$ to L1, for this check out fenics tutorial Poisson equation).
According to the review (Weber et al. 2019, eqn. 2.29) the boundary length scale is
$w = \sqrt{2\kappa/b} = \left( \frac{\kappa}{k_\mathrm{B}T\chi}\right) ^{3/5} \sqrt{ \frac{\chi}{\chi-2} }$
%% Cell type:code id: tags:
``` python
# Extended Standard Cahn-Hilliard Example to Binary Flory Huggins
# as discussed on 28/11/2019
# Example can be found at
# https://bitbucket.org/fenics-project/dolfin/src/master/python/demo/
# documented/cahn-hilliard/demo_cahn-hilliard.py.rst#rst-header-id1
# Runs with fenics 2019.01
# The resulting .pvd file can be opened using default settings in ParaView
import matplotlib.pyplot as plt
import mshr as ms
import numpy as np
from scipy.optimize import curve_fit
import time
import random
from dolfin import *
fol = '/Users/hubatsch/ownCloud/Dropbox_Lars_Christoph/frap_theory/'
fol = '/Users/hubatsch/Desktop/frap_theory/'
```
%% Cell type:code id: tags:
``` python
def create_expr(p_list):
string = ''
for p in p_list:
string = (string+'(x[0]-'+str(p[0])+')*(x[0]-'+str(p[0])+
')+(x[1]-'+str(p[1])+
')*(x[1]-'+str(p[1])+')+(x[2]-'+str(p[2])+')*(x[2]-'+
str(p[2])+')<=.05*.05 ? .76 :' )
string = string + '.268'
return string
# f = Expression((create_expr([[0.5, 0.5, 0.5]]), 1), degree=1)
file = fol+'Meshes/points_clean.txt'
points = np.loadtxt(file, delimiter=',')
f = Expression((create_expr(points), 1), degree=1)
# Class for interfacing with the Newton solver
class CahnHilliardEquation(NonlinearProblem):
def __init__(self, a, L):
NonlinearProblem.__init__(self)
self.L = L
self.a = a
def F(self, b, x):
assemble(self.L, tensor=b)
def J(self, A, x):
assemble(self.a, tensor=A)
# Model parameters
kappa = 0.25*10e-05 # surface parameter
dt = 0.5e-02 # time step
X = 2.2 # Chi Flory Huggins parameter
# time stepping family, e.g.:
# theta=1 -> backward Euler, theta=0.5 -> Crank-Nicolson
theta = 0.5
# Form compiler optionsmai
parameters["form_compiler"]["optimize"] = True
parameters["form_compiler"]["cpp_optimize"] = True
# mesh = Mesh('/Users/hubatsch/Desktop/test_par/Meshes/spheres.xml')
# domain = ms.Sphere(Point(0, 0, 0), 1.0)
# mesh = ms.generate_mesh(domain, 100)
mesh = Mesh()
with XDMFFile("Meshes/mesh1.xdmf") as infile:
infile.read(mesh)
P1 = FiniteElement("Lagrange", mesh.ufl_cell(), 1)
ME = FunctionSpace(mesh, P1*P1)
P1 = FiniteElement("Lagrange", mesh.ufl_cell(), 1)
ME = FunctionSpace(mesh, P1*P1)
# Define trial and test functions
du = TrialFunction(ME)
q, v = TestFunctions(ME)
# Define functions
u = Function(ME) # current solution
u0 = Function(ME) # solution from previous converged step
tis = time.time()
# Split mixed functions
dc, dmu = split(du)
c, mu = split(u)
c0, mu0 = split(u0)
# Create intial conditions and interpolate
# u_init = InitialConditions(degree=1)
# u.interpolate(u_init)
# u0.interpolate(u_init)
u.interpolate(f)
u0.interpolate(f)
print(time.time()-tis)
# Compute the chemical potential df/dc
c = variable(c)
# mu_(n+theta)
mu_mid = (1.0-theta)*mu0 + theta*mu
# Weak statement of the equations
L0 = c*q*dx - c0*q*dx + dt*c*(1-c)*dot(grad(mu_mid), grad(q))*dx
L1 = mu*v*dx - (ln(c/(1-c))+X*(1-2*c))*v*dx - kappa*dot(grad(c), grad(v))*dx
L = L0 + L1
# Compute directional derivative about u in the direction of du (Jacobian)
a = derivative(L, u, du)
# Create nonlinear problem and Newton solver
problem = CahnHilliardEquation(a, L)
solver = NewtonSolver()
# solver.parameters["linear_solver"] = "lu"
solver.parameters["linear_solver"] = 'gmres'
solver.parameters["preconditioner"] = 'ilu'
# solver.parameters["convergence_criterion"] = "incremental"
solver.parameters["relative_tolerance"] = 1e-6
```
%% Cell type:code id: tags:
``` python
mesh.num_cells()
```
%% Cell type:code id: tags:
``` python
# Output file
# file = File("output.pvd", "compressed")
file_c = XDMFFile('c_long.xdmf')
# Step in time
t = 0.0
T = 70*dt
T = 5*dt
ti = time.time()
while (t < T):
# file << (u.split()[0], t)
file_c.write(u.split()[0], t)
t += dt
u0.vector()[:] = u.vector()
solver.solve(problem, u.vector())
print(time.time() - ti)
file_c.close()
```
%% Cell type:code id: tags:
``` python
def tanh_fit(x, a, b, c, d):
return np.tanh((x-a)/b)*c+d
# xdata = np.linspace(0, x_mesh, x_mesh+1)
# ydata = u.compute_vertex_values()[0:x_mesh+1]
xdata = np.linspace(0.1, 0.5, 100)
ydata = np.array([u0([x, 0.5, 0.5])[0] for x in xdata])
popt, pcov = curve_fit(tanh_fit, xdata, ydata)
plt.plot(xdata[65:], ydata[65:], lw=1)
a, b, c, d = popt
plt.plot(xdata[65:], tanh_fit(xdata[65:], a, b, c, d), lw=1)
```
%% Cell type:markdown id: tags:
## Thoughts on stability of algorithm
### Thoughts on stability of algorithm
- relatively robust to grid size changes
- initial conditions seem to have strong influence
- time step also plays a role for Newton solver
- best results with small time step and initial conditions close to final concentrations
%% Cell type:markdown id: tags:
**Example for how to use Spheres class to create n positions of non-overlapping spheres inside a box of dimensions ls.**
### Example for use of 'Spheres' class
...to create n positions of non-overlapping spheres inside a box of dimensions ls.
%% Cell type:code id: tags:
``` python
from fem_utils import Spheres
a = Spheres(n=17, ls = [2, 2, 2])
a.create_list()
a.point_list
a.write_to_txt()
```
%% Cell type:markdown id: tags:
**Example on how to use convert_msh_to_xdmf to convert a mesh created in gmsh via 'gmsh -3 file -format msh2' to xdmf, which can be parallelised, in contrast to .xml meshes.**
The resulting points in points.txt can now be used in a .geo file, e.g. box_with_spheres. Simply copy them in, then create the mesh (see below).
%% Cell type:code id: tags:
%% Cell type:markdown id: tags:
``` python
from fem_utils import convert_msh_to_xdmf
path_to_msh = "/Users/hubatsch/ownCloud/Dropbox_Lars_Christoph/frap_theory/Meshes/box_with_spheres.msh"
path_to_xdmf = "mesh1.xdmf"
convert_msh_to_xdmf(path_to_msh, path_to_xdmf)
```
### Example on how to use convert_msh_to_xdmf
...to convert a mesh created in gmsh via 'gmsh -3 file -format msh2' to xdmf, which can be parallelised, in contrast to .xml meshes.
%% Cell type:code id: tags:
``` python
from fem_utils import convert_msh_to_xdmf
path_to_msh = "/Users/hubatsch/Desktop/frap_theory/Meshes/box_with_spheres.msh"
path_to_xdmf = "Meshes/mesh1.xdmf"
convert_msh_to_xdmf(path_to_msh, path_to_xdmf)
```
......
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