applying 3D mesh in step-20

[hank...@gmail.com]

Hi

I'm studying step-20 tutorial example, watching Wolfgang's Lectures

In step20, I would like to solve that Eq in the 3D mesh that I made by myself(I attached B_coord3D.inp that is UCD format)

But, It didn't work out. 

The error message is like this....

[ 50%] Built target step-20

make[3]: Warning: File `step-20' has modification time 81 s in the future

[100%] Run step-20 with Debug configuration

Number of active cells: 36864

Total number of cells: 42048

Number of degrees of freedom: 156672 (119808+36864)

53 CG Schur complement iterations to obtain convergence.

--------------------------------------------------------

An error occurred in line <790> of file </user2/hanks318/dealii/dealii-8.3.0/source/fe/mapping_q1.cc> in function

    void dealii::MappingQ1<dim, spacedim>::fill_fe_values(const typename dealii::Triangulation<dim, spacedim>::cell_iterator&, const dealii::Quadrature<dim>&, typename dealii::Mapping<dim, spacedim>::InternalDataBase&, std::vector<dealii::Point<spacedim, double>, std::allocator<dealii::Point<spacedim, double> > >&, std::vector<double, std::allocator<double> >&, std::vector<dealii::DerivativeForm<1, spacedim, dim, double>, std::allocator<dealii::DerivativeForm<1, spacedim, dim, double> > >&, std::vector<dealii::DerivativeForm<2, dim, spacedim, double>, std::allocator<dealii::DerivativeForm<2, dim, spacedim, double> > >&, std::vector<dealii::DerivativeForm<1, spacedim, dim, double>, std::allocator<dealii::DerivativeForm<1, spacedim, dim, double> > >&, std::vector<dealii::Point<spacedim, double>, std::allocator<dealii::Point<spacedim, double> > >&, dealii::CellSimilarity::Similarity&) const [with int dim = 3, int spacedim = 3]

The violated condition was:

    det > 1e-12*Utilities::fixed_power<dim>(cell->diameter()/ std::sqrt(double(dim)))

The name and call sequence of the exception was:

    (typename Mapping<dim,spacedim>::ExcDistortedMappedCell(cell->center(), det, point))

Additional Information:

The image of the mapping applied to cell with center [-1.61075 -0.761538 0.649647] is distorted. The cell geometry or the mapping are invalid, giving a non-positive volume fraction of -1.49556e-07 in quadrature point 5.

Stacktrace:

-----------

#0  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: dealii::MappingQ1<3, 3>::fill_fe_values(dealii::TriaIterator<dealii::CellAccessor<3, 3> > const&, dealii::Quadrature<3> const&, dealii::Mapping<3, 3>::InternalDataBase&, std::vector<dealii::Point<3, double>, std::allocator<dealii::Point<3, double> > >&, std::vector<double, std::allocator<double> >&, std::vector<dealii::DerivativeForm<1, 3, 3, double>, std::allocator<dealii::DerivativeForm<1, 3, 3, double> > >&, std::vector<dealii::DerivativeForm<2, 3, 3, double>, std::allocator<dealii::DerivativeForm<2, 3, 3, double> > >&, std::vector<dealii::DerivativeForm<1, 3, 3, double>, std::allocator<dealii::DerivativeForm<1, 3, 3, double> > >&, std::vector<dealii::Point<3, double>, std::allocator<dealii::Point<3, double> > >&, dealii::CellSimilarity::Similarity&) const

#1  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: dealii::FEValues<3, 3>::do_reinit()

#2  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void dealii::FEValues<3, 3>::reinit<dealii::DoFHandler<3, 3>, false>(dealii::TriaIterator<dealii::DoFCellAccessor<dealii::DoFHandler<3, 3>, false> > const&)

#3  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void dealii::hp::FEValues<3, 3>::reinit<dealii::DoFHandler<3, 3>, false>(dealii::TriaIterator<dealii::DoFCellAccessor<dealii::DoFHandler<3, 3>, false> >, unsigned int, unsigned int, unsigned int)

#4  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void dealii::internal::DataOut::ParallelDataBase<3, 3>::reinit_all_fe_values<dealii::DoFHandler<3, 3> >(std::vector<boost::shared_ptr<dealii::internal::DataOut::DataEntryBase<dealii::DoFHandler<3, 3> > >, std::allocator<boost::shared_ptr<dealii::internal::DataOut::DataEntryBase<dealii::DoFHandler<3, 3> > > > >&, dealii::TriaIterator<dealii::CellAccessor<3, 3> > const&, unsigned int)

#5  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: dealii::DataOut<3, dealii::DoFHandler<3, 3> >::build_one_patch(std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&)

#6  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: boost::_mfi::mf5<void, dealii::DataOut<3, dealii::DoFHandler<3, 3> >, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&>::operator()(dealii::DataOut<3, dealii::DoFHandler<3, 3> >*, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&) const

#7  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void boost::_bi::list6<boost::_bi::value<dealii::DataOut<3, dealii::DoFHandler<3, 3> >*>, boost::arg<1>, boost::arg<2>, boost::arg<3>, boost::_bi::value<dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion>, boost::reference_wrapper<std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > > > >::operator()<boost::_mfi::mf5<void, dealii::DataOut<3, dealii::DoFHandler<3, 3> >, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&>, boost::_bi::list3<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&> >(boost::_bi::type<void>, boost::_mfi::mf5<void, dealii::DataOut<3, dealii::DoFHandler<3, 3> >, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&>&, boost::_bi::list3<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&>&, int)

#8  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void boost::_bi::bind_t<void, boost::_mfi::mf5<void, dealii::DataOut<3, dealii::DoFHandler<3, 3> >, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&>, boost::_bi::list6<boost::_bi::value<dealii::DataOut<3, dealii::DoFHandler<3, 3> >*>, boost::arg<1>, boost::arg<2>, boost::arg<3>, boost::_bi::value<dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion>, boost::reference_wrapper<std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > > > > >::operator()<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >(std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&)

#9  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: boost::detail::function::void_function_obj_invoker3<boost::_bi::bind_t<void, boost::_mfi::mf5<void, dealii::DataOut<3, dealii::DoFHandler<3, 3> >, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int> const*, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&, dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion, std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > >&>, boost::_bi::list6<boost::_bi::value<dealii::DataOut<3, dealii::DoFHandler<3, 3> >*>, boost::arg<1>, boost::arg<2>, boost::arg<3>, boost::_bi::value<dealii::DataOut<3, dealii::DoFHandler<3, 3> >::CurvedCellRegion>, boost::reference_wrapper<std::vector<dealii::DataOutBase::Patch<3, 3>, std::allocator<dealii::DataOutBase::Patch<3, 3> > > > > >, void, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&>::invoke(boost::detail::function::function_buffer&, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&)

#10  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: boost::function3<void, std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&>::operator()(std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const&, dealii::internal::DataOut::ParallelData<3, 3>&, dealii::DataOutBase::Patch<3, 3>&) const

#11  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >::operator()(tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&)

#12  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>::operator()(dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >&, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&) const

#13  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void boost::_bi::list2<boost::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> > >, boost::arg<1> >::operator()<boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>, boost::_bi::list1<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >&> >(boost::_bi::type<void>, boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&> const&, boost::_bi::list1<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >&>&, int) const

#14  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void boost::_bi::bind_t<void, boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>, boost::_bi::list2<boost::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> > >, boost::arg<1> > >::operator()<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > >(tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >&) const

#15  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >, boost::_bi::bind_t<void, boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>, boost::_bi::list2<boost::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> > >, boost::arg<1> > >, tbb::auto_partitioner const>::run_body(tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >&)

#16  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: void tbb::interface6::internal::partition_type_base<tbb::interface6::internal::auto_partition_type>::execute<tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >, boost::_bi::bind_t<void, boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>, boost::_bi::list2<boost::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> > >, boost::arg<1> > >, tbb::auto_partitioner const>, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > >(tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >, boost::_bi::bind_t<void, boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>, boost::_bi::list2<boost::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> > >, boost::arg<1> > >, tbb::auto_partitioner const>&, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >&)

#17  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > >, boost::_bi::bind_t<void, boost::_mfi::mf1<void, dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> >, tbb::blocked_range<__gnu_cxx::__normal_iterator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>* const*, std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*> > > > const&>, boost::_bi::list2<boost::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<std::pair<dealii::TriaIterator<dealii::CellAccessor<3, 3> >, unsigned int>*, dealii::internal::DataOut::ParallelData<3, 3>, dealii::DataOutBase::Patch<3, 3> > >, boost::arg<1> > >, tbb::auto_partitioner const>::execute()

#18  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::internal::custom_scheduler<tbb::internal::IntelSchedulerTraits>::local_wait_for_all(tbb::task&, tbb::task*)

#19  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::internal::arena::process(tbb::internal::generic_scheduler&)

#20  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::internal::market::process(rml::job&)

#21  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::internal::rml::private_worker::run()

#22  /user2/hanks318/dealii/dealii_pre/lib/libdeal_II.g.so.8.3.0: tbb::internal::rml::private_worker::thread_routine(void*)

--------------------------------------------------------

I can't understand the meaning of distorted image of mapping, non positive volume etc...

The below picture is the 3D mesh I used for the calculation(it is refined twice by triangulation.refine_global(2);)

From this picture, It seems that The Mesh is fine. I don't know what the problem is.

And FYI, I used "SphericalManifold<dim> boundary" in this code, even though the boundary is not sphere. I used this to make the boundary smoother after every refinement.

But, When I didn't use this, The problem is not solved. So, I thought it is not related to this problem

I also attach the step-20.cc that I revised a little bit.(I commented what I change in step-20.cc)  

please help me to solve this problem....

Thank you

Regards,
Kyusik

[Jean-Paul Pelteret]

Dear Kyusik,

If you open your original mesh file in Paraview (version 5.1 detects it as an AVS UCD file) and you clip the mesh to view its section, then I think you'll see the problem. Although the mesh looks fine from the outside, all of the inner vertices of your torus converge on an annulus (so the hexahedra degenerate into prisms). This is not allowed. You'll need to generate a new mesh with higher quality elements before proceeding.

Regards,

J-P 

[Jean-Paul Pelteret]

Image attached to clarify of what I've indicated.

[hank...@gmail.com]

First of all, Thank you very much for your answering my Question.

Could I have one more question...?

Then, Is it okay If I use Prism cell instead of the Hexahedron cell in UCD format?? Can the deal.II treat the Prism cell??

And, Do you also agree with that "SphericalManifold<dim> boundary" is not related to this problem??

Thank you.

Regard

Kyusik 

2016년 8월 31일 수요일 오후 10시 36분 4초 UTC+9, Jean-Paul Pelteret 님의 말:

[Jean-Paul Pelteret]

Hi Kyusik,

You welcome :-) No, deal.II only supports quads/hexes so you cannot use prisms. However, since meshing an object with a circular cross section with a structured mesh is not particularly difficult, I don't think that this should be particularly challenging for you to fix. 

I must admit that I haven't looked at your application of the SphericalManifold - you should probably deal with one problem at a time, especially since your mesh quality issue is such a fundamental one and might have a significant role to play here. If you fix your mesh and continue to run into issues that you cannot resolve yourself, then perhaps you could post again (with the updated mesh) and I'll (or someone else) take another look at it.

Regards,

J-P

[Bruno Turcksin]

Kyusik,

On Wednesday, August 31, 2016 at 10:45:08 AM UTC-4, Jean-Paul Pelteret wrote:

You welcome :-) No, deal.II only supports quads/hexes so you cannot use prisms. However, since meshing an object with a circular cross section with a structured mesh is not particularly difficult, I don't think that this should be particularly challenging for you to fix. 

You can use GridGenerator::torus (http://dealii.org/8.4.1/doxygen/deal.II/namespaceGridGenerator.html#a71cf8f32c898246be99b1130bf05704b) Note that if you are using the development version of deal.II there is a Torus manifold (http://dealii.org/developer/doxygen/deal.II/namespaceGridGenerator.html#a706244fbc35b96c34ef6065cd047dc32)

Best,

Bruno

[hank...@gmail.com]

Oh, Thank you very much!!!!!

The problem is solved!!!

you are right. My mesh was the problem. I was stupid!!!

But, Could I have the last question....?

I have to show my result to my boss(variable p). And, To show the inside of torus, It seems that I have to use contour plot using Visit.(In the Wolfgang lecture, he used contour plot to see the inside of the calculated result in 3D problem)

 But, When I used  Contour plot in Visit for variable p, It is said that " The Contour plot of variable "p" yielded no data."

Is there anyway for me to show the inside of the calculated result to my boss?

Please help me....

2016년 8월 31일 수요일 오후 11시 45분 8초 UTC+9, Jean-Paul Pelteret 님의 말:

[hank...@gmail.com]

Thanks for your Answer Bruno.

But, It seems that I am using the old version.

When I try to use Torus manifold, The Error message occurs.

And, the problem is solved by making new mesh.

Anyway, Thank you very much for your Answering my Question.

Best.

Kyusik

2016년 8월 31일 수요일 오후 11시 55분 34초 UTC+9, Bruno Turcksin 님의 말:

[Wolfgang Bangerth]

On 09/04/2016 05:38 AM, hank...@gmail.com wrote:
>
> I have to show my result to my boss(variable p). And, To show the inside of
> torus, It seems that I have to use contour plot using Visit.(In the Wolfgang
> lecture, he used contour plot to see the inside of the calculated result in 3D
> problem)
>
> But, When I used Contour plot in Visit for variable p, It is said that " The
> Contour plot of variable "p" yielded no data."

That's because you use piecewise constant pressures. Any given isosurface
values does not typically equal the value the pressure has on any of the cells.

> Is there anyway for me to show the inside of the calculated result to my boss?

Use cutplanes, cutspheres, thresholds, etc., to cut away some cells while
showing the others.

Best
Wolfgang

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[hank...@gmail.com]

Thank you very much!!

2016년 9월 5일 월요일 오전 4시 38분 52초 UTC+9, Wolfgang Bangerth 님의 말: