Like this? This is how it looks for me. On Mon, Aug 27, 2018 at 12:21 PM, Renato Poli <rebp...@gmail.com> wrote:
> Hi Alexander, > > It did run, but the values were not assigned at the right elements. > Please find a paraview figure attached. > It was produced by the example I sent (open mesh.e in paraview). > The pressure subdomain should be a circle in the center. > > I would guess the problem lies in lines 1141-2 below (just a guess): > soln[nv*(nn++) + (var + var_num)] += > nodal_soln[n]; > (https://github.com/libMesh/libmesh/pull/1836/files/ > 126feb954ba89c5739794dd286ed8a47c2735be8) > > rgds, > Renato > > > > On Mon, Aug 27, 2018 at 12:35 PM Alexander Lindsay < > alexlindsay...@gmail.com> wrote: > >> Renato, please check to see whether https://github.com/ >> libMesh/libmesh/pull/1836 fixes your issue. It appears to work to me on >> the example you sent >> >> On Sat, Aug 25, 2018 at 3:16 PM, Renato Poli <rebp...@gmail.com> wrote: >> >>> Hi Alexander, >>> >>> Please find attached the example you asked. >>> I used introduction_ex3 as a basis... it got a little messy, I hope it >>> is enough. >>> Please let me know otherwise. >>> >>> Thanks >>> Renato >>> >>> On Sat, Aug 25, 2018 at 12:42 PM Renato Poli <rebp...@gmail.com> wrote: >>> >>>> Sure.... please give me a couple of hours. >>>> >>>> On Sat, Aug 25, 2018 at 12:04 PM Alexander Lindsay < >>>> alexlindsay...@gmail.com> wrote: >>>> >>>>> Renato, could you create a minimum example that generates the >>>>> discontinuous error, and either share it here or create a ticket on >>>>> github? >>>>> That would be useful for fixing the issue and adding a test in libmesh to >>>>> ensure we support the capability. >>>>> >>>>> On Sat, Aug 25, 2018 at 8:33 AM, Alexander Lindsay < >>>>> alexlindsay...@gmail.com> wrote: >>>>> >>>>>> Ah yes...key difference between "empty" and "zero"... >>>>>> >>>>>> On Aug 25, 2018, at 7:03 AM, Renato Poli <rebp...@gmail.com> wrote: >>>>>> >>>>>> No success. Stack trace below. >>>>>> >>>>>> Note that, if I define my variable _only_ on its domain (where there is >>>>>> fluid) it works. >>>>>> >>>>>> In this case, the problem is in >>>>>> ExodusII_IO::write_discontinuous_timestep. >>>>>> >>>>>> >>>>>> [0]PETSC ERROR: --------------------- Error Message >>>>>> -------------------------------------------------------------- >>>>>> [0]PETSC ERROR: Object is in wrong state >>>>>> [0]PETSC ERROR: Matrix is missing diagonal entry 0 >>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> for trouble shooting. >>>>>> [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017 >>>>>> [0]PETSC ERROR: obj/bin/abada_sc11 on a linux-gnu-opt named dev-vb by >>>>>> dev Sat Aug 25 09:55:36 2018 >>>>>> [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/lib/mpich >>>>>> --with-shared-libraries=1 --with-debugging=yes --download-mumps >>>>>> --download-hypre --download-scalapack --download-spai --download-parms >>>>>> [0]PETSC ERROR: #1 MatLUFactorSymbolic_SeqAIJ() line 301 in >>>>>> /opt/petsc-3.7.6/src/mat/impls/aij/seq/aijfact.c >>>>>> [0]PETSC ERROR: #2 MatLUFactorSymbolic() line 2944 in >>>>>> /opt/petsc-3.7.6/src/mat/interface/matrix.c >>>>>> [0]PETSC ERROR: #3 PCSetUp_LU() line 136 in >>>>>> /opt/petsc-3.7.6/src/ksp/pc/impls/factor/lu/lu.c >>>>>> [0]PETSC ERROR: #4 PCSetUp() line 968 in >>>>>> /opt/petsc-3.7.6/src/ksp/pc/interface/precon.c >>>>>> [0]PETSC ERROR: #5 KSPSetUp() line 390 in >>>>>> /opt/petsc-3.7.6/src/ksp/ksp/interface/itfunc.c >>>>>> [0]PETSC ERROR: #6 KSPSolve() line 599 in >>>>>> /opt/petsc-3.7.6/src/ksp/ksp/interface/itfunc.c >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Renato >>>>>> >>>>>> >>>>>> On Fri, Aug 24, 2018 at 11:49 PM Alexander Lindsay < >>>>>> alexlindsay...@gmail.com> wrote: >>>>>> >>>>>>> If you're using PETSc as your underlying solver, try the options >>>>>>> `-pc_factor_shift_type NONZERO -pc_factor_shift_amount 1e-15` >>>>>>> >>>>>>> On Thu, Aug 23, 2018 at 2:58 PM, Renato Poli <rebp...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>>> Hi >>>>>>>> >>>>>>>> I am getting trouble here again ... really need some help. >>>>>>>> >>>>>>>> I have part of the domain without flow (and thus without the >>>>>>>> pressure >>>>>>>> variable defined). >>>>>>>> As I could not export that (could not get >>>>>>>> write_discontinuous_exodusII to >>>>>>>> work) I just left the matrix empty, without major impact so far. >>>>>>>> However, now I am using LU preconditioning, which does not accept >>>>>>>> empty >>>>>>>> entries in the diagonal. >>>>>>>> >>>>>>>> How can I get through? >>>>>>>> Any suggestion? >>>>>>>> >>>>>>>> Thanks upfront. >>>>>>>> Renato >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Aug 16, 2018 at 6:47 PM Renato Poli <rebp...@gmail.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>> > Hi >>>>>>>> > >>>>>>>> > I see the stack trace below when writing a discontinuous timestep >>>>>>>> > (exo.write_discontinuous_timestep). >>>>>>>> > It happens when my variable is set only in part of the domain. >>>>>>>> > No problem arises if I use, instead: >>>>>>>> > exo.write_equation_systems(fname, >>>>>>>> es) >>>>>>>> > >>>>>>>> > Any hint/workaround/idea? >>>>>>>> > >>>>>>>> > Thanks, >>>>>>>> > Renato >>>>>>>> > >>>>>>>> > This is how the variable is set. >>>>>>>> > | std::set<subdomain_id_type> active_subdomains; >>>>>>>> > | active_subdomains.clear(); >>>>>>>> > | active_subdomains.insert(SUBDOMAIN_A); >>>>>>>> > | press_sys.add_variable ("p", SECOND, LAGRANGE, & >>>>>>>> active_subdomains); >>>>>>>> > >>>>>>>> > 0: libMesh::print_trace(std::ostream&) >>>>>>>> > 1: libMesh::MacroFunctions::report_error(char const*, int, char >>>>>>>> const*, >>>>>>>> > char const*) >>>>>>>> > 2: >>>>>>>> > libMesh::EquationSystems::build_discontinuous_solution_ >>>>>>>> vector(std::__debug::vector<double, >>>>>>>> > std::allocator<double> >&, >>>>>>>> > std::__debug::set<std::__cxx11::basic_string<char, >>>>>>>> std::char_traits<char>, >>>>>>>> > std::allocator<char> >, std::less<std::__cxx11::basic_ >>>>>>>> string<char, >>>>>>>> > std::char_traits<char>, std::allocator<char> > >, >>>>>>>> > std::allocator<std::__cxx11::basic_string<char, >>>>>>>> std::char_traits<char>, >>>>>>>> > std::allocator<char> > > > const*) const >>>>>>>> > 3: >>>>>>>> > libMesh::ExodusII_IO::write_discontinuous_exodusII(std::__ >>>>>>>> cxx11::basic_string<char, >>>>>>>> > std::char_traits<char>, std::allocator<char> > const&, >>>>>>>> > libMesh::EquationSystems const&, >>>>>>>> > std::__debug::set<std::__cxx11::basic_string<char, >>>>>>>> std::char_traits<char>, >>>>>>>> > std::allocator<char> >, std::less<std::__cxx11::basic_ >>>>>>>> string<char, >>>>>>>> > std::char_traits<char>, std::allocator<char> > >, >>>>>>>> > std::allocator<std::__cxx11::basic_string<char, >>>>>>>> std::char_traits<char>, >>>>>>>> > std::allocator<char> > > > const*) >>>>>>>> > 4: >>>>>>>> > libMesh::ExodusII_IO::write_timestep_discontinuous(std::__ >>>>>>>> cxx11::basic_string<char, >>>>>>>> > std::char_traits<char>, std::allocator<char> > const&, >>>>>>>> > libMesh::EquationSystems const&, int, double, >>>>>>>> > std::__debug::set<std::__cxx11::basic_string<char, >>>>>>>> std::char_traits<char>, >>>>>>>> > std::allocator<char> >, std::less<std::__cxx11::basic_ >>>>>>>> string<char, >>>>>>>> > std::char_traits<char>, std::allocator<char> > >, >>>>>>>> > std::allocator<std::__cxx11::basic_string<char, >>>>>>>> std::char_traits<char>, >>>>>>>> > std::allocator<char> > > > const*) >>>>>>>> > >>>>>>>> > >>>>>>>> ------------------------------------------------------------ >>>>>>>> ------------------ >>>>>>>> Check out the vibrant tech community on one of the world's most >>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>>>> _______________________________________________ >>>>>>>> Libmesh-users mailing list >>>>>>>> Libmesh-users@lists.sourceforge.net >>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users >>>>>>>> >>>>>>> >>>>>>> >>>>> >> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
