Right, thanks.
>> B*g_0*(1-((g_0+m_0)/Tm))*v1*dx+
>> C*g_0*inner(nabla_grad(g_0),nabla_grad(v1))*v1*dx)
I remove that error, but I receive a new kind of error:
Traceback (most recent call last):
File "gbm_sys.py", line 56, in <module>
problem = NonlinearVariationalProblem(F, U)
File
"/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/fem/solving.py",
line 117, in __init__
F = Form(F, form_compiler_parameters=form_compiler_parameters)
File
"/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/fem/form.py",
line 58, in __init__
sd = form.subdomain_data()
File
"/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/form.py",
line 169, in subdomain_data
self._analyze_subdomain_data()
File
"/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/form.py",
line 327, in _analyze_subdomain_data
data = subdomain_data[domain].get(it)
KeyError: Domain(Cell('tetrahedron', 3), label=None, data=None)
Valentina
> Il giorno 15/mag/2015, alle ore 15:17, Jan Blechta
> <[email protected]> ha scritto:
>
> On Fri, 15 May 2015 15:07:32 +0200
> Valentina <[email protected] <mailto:[email protected]>> wrote:
>
>> Hi,
>>
>> I need to solve a system of 3 PDE and neumann boundary conditions
>> with FEniCS but i have some problem. This is a piece of my code:
>>
>> “V = FunctionSpace (mesh, 'CG',1)
>> W = MixedFunctionSpace ([V,V,V])
>> # Trial function and test function
>> U = Function(W)
>> u0 = Function (W)
>> dU = TrialFunction(W)
>> v1, v2, v3 = TestFunctions (W)
>> # Split mixed function
>> (dg,dm,dw) = split(dU)
>> (g,m,w) = split(U)
>> (g_0,m_0,w_0) = split(u0)
>>
>> g_0 = Expression('c', c=Constant(0.0), cell = tetrahedron)
>> m_0 = Expression('c', c=Constant(0.0), cell = tetrahedron)
>> w_0 = Expression('c', c=Constant(0.0), cell = tetrahedron)
>>
>> F1 = g*v1*dx +
>> A*inner(nabla_grad(g),nabla_grad(v1))*dx-B*g*(1-(g+m)/Tm)*v1*dx-C*g*inner(nabla_grad(w),nabla_grad(v1))*v1*dx
>> + \
>> - (g_0*v1*dx - A*inner(nabla_grad(g_0),nabla_grad(v1))*dx +
>> B*g_0*(1-((g_0+m_0)/Tm))*v1*dx+
>> C*g_0*inner(nabla_grad(g_0),nabla_grad(v1))*v1*dx)
> ^^ ^^
> This term is quadratic in test function. It must be linear form, i.e.
> linear in test function.
>
> Jan
>
>>
>> F2 = m*v2*dx + Am * inner(nabla_grad(m),nabla_grad(v2))*dx +
>> C*g*inner(nabla_grad(w),nabla_grad(v2))*dx + \
>> - (m_0*v2*dx -Am*inner(nabla_grad(m_0),nabla_grad(v2))*dx -
>> C*g_0*inner(nabla_grad(w_0),nabla_grad(v2))*dx)
>>
>> F3 = w*v3*dx + D*w*((g+w)/(theta + g+ w))*v3*dx + \
>> - (w_0*v3*dx - D*w_0*((g_0+w_0)/(theta + g_0 + w_0))*v3*dx)
>>
>> F = F1 + F2 + F3
>>
>> dF = derivative(F,U,dU)
>>
>> problem = NonlinearVariationalProblem(F, U, J=dF)
>> pdesys_newton = NonlinearVariationalSolver(problem) “
>>
>>
>> When I run it, I receive this message error:
>>
>> "Traceback (most recent call last):
>> File "gbm_sys.py", line 56, in <module>
>> problem = NonlinearVariationalProblem(F, U)
>> File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/fem/solving.py",
>> line 117, in __init__ F = Form(F,
>> form_compiler_parameters=form_compiler_parameters) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/fem/form.py",
>> line 70, in __init__ mpi_comm=mesh.mpi_comm()) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/jit.py",
>> line 64, in mpi_jit return local_jit(*args, **kwargs) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/jit.py",
>> line 128, in jit return form_compiler.jit(form, parameters=p) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ffc/jitcompiler.py",
>> line 74, in jit return jit_form(ufl_object, parameters) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ffc/jitcompiler.py",
>> line 130, in jit_form parameters=parameters) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ffc/compiler.py",
>> line 151, in compile_form analysis = analyze_forms(forms, parameters)
>> File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ffc/analysis.py",
>> line 59, in analyze_forms parameters) for form in forms) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ffc/analysis.py",
>> line 59, in <genexpr> parameters) for form in forms) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ffc/analysis.py",
>> line 132, in _analyze_form form_data = compute_form_data(form) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/algorithms/compute_form_data.py",
>> line 304, in compute_form_data check_form_arity(preprocessed_form,
>> form.arguments()) # Currently testing how fast this is File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/algorithms/check_arities.py",
>> line 123, in check_form_arity check_integrand_arity(itg.integrand(),
>> arguments) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/algorithms/check_arities.py",
>> line 117, in check_integrand_arity args = map_expr_dag(rules, expr,
>> compress=False) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/corealg/map_dag.py",
>> line 67, in map_expr_dag r = function(v, *rops) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/corealg/multifunction.py",
>> line 72, in __call__ return self._handlers[o._ufl_typecode_](o,
>> *args) File
>> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/ufl/algorithms/check_arities.py",
>> line 54, in product raise ArityMismatch("Multiplying expressions with
>> overlapping form argument number {0}, argument is
>> {1}.".format(x.number(), x))
>> ufl.algorithms.check_arities.ArityMismatch: Multiplying expressions
>> with overlapping form argument number 0, argument is v_0.”
>>
>> I don’t know very well the function NonlinearVariationalProblem and
>> NonlinearVariationalSolver, and I think there’s a syntax error. How
>> can I resolve my problem or where can I see the instruction to solve
>> a system of PDE in FEniCS? Thanks.
>>
>> King regards,
>> Valentina S.
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