On Fri, 15 May 2015 15:24:49 +0200
Valentina <[email protected]> wrote:
> 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:
Can you post the complete code reproducing the error and report FEniCS
version used?
Jan
>
> 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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