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Error in NewtonSolver(). TypeError: in method 'NewtonSolver_solve', argument 3 of type 'dolfin::GenericVector &'

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Hi am solving a nonlinear time dependent system of pde and am following the cahnHilliard demo. I got this error in the newton solver which I dont quiet understand. Below is my complete code

from dolfin import *


# Class representing initial conditions
class InitialConditions(Expression):
def eval(self, values, x):
    values[0] = x[1]
    values[1] = x[1]
    values[2] = x[1]
    values[3] = x[1]
    values[4] = 0.01
    values[5] = 0
def value_shape(self):
    return (6,)

#constants
c = Constant(2/3)
xi0= Constant(1)
n = Constant(2)
alpha = Constant(25)

# Class interfacing with newton solver
class MyEquations(NonlinearProblem):
def __init__(self, a, L, bcs):
    NonlinearProblem.__init__(self)
    self.L = L
    self.a = a
self.bcs = bcs
    self.reset_sparsity = True
def F(self, b, x):
    assemble(self.L, tensor=b, bcs = self.bcs)
def J(self, A, x):
    assemble(self.a, tensor=A, reset_sparsity=self.reset_sparsity, bcs=self.bcs)
    self.reset_sparsity = False

class PeriodicBoundary(SubDomain):

# left boundary is "target domain"
def inside(self, x, on_boundary):
    return bool(x[0]< DOLFIN_EPS and x[0]> - DOLFIN_EPS and on_boundary)

# Map right boundary to left boundary
def map(self, x, y):
    y[0] = x[0] - 1.0
    y[1] = x[1]


 pbc = PeriodicBoundary()

 mesh = RectangleMesh(Point(-1,-1),Point(1,1),20,20) #Domain[-1,1]*[-1,1]

V1= VectorFunctionSpace(mesh, 'Lagrange',degree=2, constrained_domain = pbc)
V2=VectorFunctionSpace(mesh, 'Lagrange', degree=2, constrained_domain= pbc)
Q1 = FunctionSpace(mesh, 'Lagrange', degree=1, constrained_domain = pbc )
Q2 = FunctionSpace(mesh, 'Lagrange', degree=1, constrained_domain = pbc)
VQ = MixedFunctionSpace([V1,V2, Q1, Q2])

# Define trial and test functions
m,h,q,r = TestFunctions(VQ)
duu = TrialFunction(VQ)

H= Function(VQ)  # Current solution
H0 = Function(VQ)   # solution from previous converged steps


#dUU, du, dphi, dp = split(duu)
U, u, phi, p = split(H)
U0, u0, phi0, p0 = split(H0)

#Create initial conditions and interpolate
u_init = InitialConditions()
H.interpolate(u_init)
H0.interpolate(u_init)

# Sub domain for Dirichlet boundary condition
class Top(SubDomain):
def inside(self, x, on_boundary):
    return (x[1]>1 - DOLFIN_EPS and on_boundary)

class Bottom(SubDomain):
def inside(self, x, on_boundary):
    return (x[1]< -1 + DOLFIN_EPS and on_boundary)

 UB= Constant((-1,0))
UT= Constant((1,0))
ub= Constant((-1,0))
ut= Constant((1,0))

 top= Top()
bott = Bottom()

bcUB= DirichletBC(VQ.sub(0), UB  ,bott)
bcUT= DirichletBC(VQ.sub(0), UB  ,top)
bcub= DirichletBC(VQ.sub(1), ub  ,bott )
bcut= DirichletBC(VQ.sub(1), ub  ,top )

bcs = [bcUB,bcUT, bcub,bcut]

k_phi = (phi/phi0)**n
eta = exp(-alpha*(phi-phi0))
 xi = xi0* eta
 dt=0.0001


f1 = phi*q*dx - phi0*q*dx - dt*div((1-phi)*U)*q*dx

f2 = inner(phi*(u-U), m)*dx  + k_phi * p*div(m)*dx   

f3 = p*div(h)*dx + eta*inner(grad(U) + grad(U).T, grad(h))*dx - (xi*div(U)) *div(h)*dx  + c*(eta*div(U))*div(h)*dx 

f4 = div(phi*u + (1-phi)*U)*r*dx     

L = f1 + f2 + f3 + f4    

 a = derivative(L, H, duu )
 problem = MyEquations(a, L, bcs)
 solver = NewtonSolver()
 solver.parameters['linear_solver']='lu'
solver.parameters['convergence_criterion'] = 'incremental'
solver.parameters['relative_tolerance'] = 1e-6

T_total = 50*dt
t=0.0
while (t<T_total):
  t+=dt
  H0 = H
  solver.solve(problem, H)

The error is below as

solver.solve(problem, H)
TypeError: in method 'NewtonSolver_solve', argument 3 of type 'dolfin::GenericVector &'

I dont quiet understand this error. Could anyone help please. Thanks.

asked Nov 26, 2015 by Vivian FEniCS Novice (550 points)

1 Answer

0 votes

You need to pass a vector to the solver. Try the following for the time loop.

while (t < T_total):
    t += dt
    H0.vector()[:] = H.vector()
    solver.solve(problem, H.vector())
answered Dec 1, 2015 by Magne Nordaas FEniCS Expert (13,820 points)

Thank you Magne. I tried as you suggested but now it says got an unexpected keyword argument. Below is my error

Traceback (most recent call last):
File "copy_math8112.py", line 144, in <module>
solver.solve(problem, H.vector())
File "copy_math8112.py", line 31, in F
assemble(self.L, tensor=b, bcs = self.bcs)
TypeError: assemble() got an unexpected keyword argument 'bcs'

Is that not where tthe boundary condition should be applied

commented Dec 2, 2015 by Vivian FEniCS Novice (550 points)
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