Is that "p"? On Mon, Aug 27, 2018 at 5:51 PM Alexander Lindsay <alexlindsay...@gmail.com> wrote:
> 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
