Thank you for pointing those out. I made a simpler MWE as in posted https://fenicsproject.discourse.group/t/missing-diagonal-entry-when-solving-mixed-domain-pde/17469/3?u=caglar and made the following changes as you suggested,
du, dphi = ufl.TestFunctions(V)
eps = ufl.variable(ufl.sym(ufl.grad(u)))
H = ufl.variable(-ufl.grad(phi))
and got rid of “eps_var” and “H_var”,
u_, phi_ = ufl.TrialFunctions(V)
jac = ufl.derivative(F, u, u_) + ufl.derivative(F, phi, phi_)However, I still get the following error,
File "petsc4py/PETSc/KSP.pyx", line 1782, in petsc4py.PETSc.KSP.solve
petsc4py.PETSc.Error: error code 73
[0] KSPSolve() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/ksp/ksp/interface/itfunc.c:1094
[0] KSPSolve_Private() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/ksp/ksp/interface/itfunc.c:843
[0] KSPSetUp() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/ksp/ksp/interface/itfunc.c:427
[0] PCSetUp() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/ksp/pc/interface/precon.c:1086
[0] PCSetUp_ILU() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/ksp/pc/impls/factor/ilu/ilu.c:135
[0] MatILUFactorSymbolic() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/mat/interface/matrix.c:7094
[0] MatILUFactorSymbolic_SeqAIJ() at /Users/runner/miniforge3/conda-bld/bld/rattler-build_petsc_1738766455/work/src/mat/impls/aij/seq/aijfact.c:1738
[0] Object is in wrong state
[0] Matrix is missing diagonal entry 0
Exception ignored in: <function _DeleteDummyThreadOnDel.__del__ at 0x104c06b60>
Traceback (most recent call last):
File "/Applications/PyCharm.app/Contents/plugins/python-ce/helpers/pydev/_pydevd_bundle/pydevd_pep_669_tracing.py", line 561, in py_raise_callback
File "/opt/homebrew/anaconda3/envs/fenicsx-env/lib/python3.13/threading.py", line 1435, in current_thread
TypeError: 'NoneType' object is not subscriptable