date:20230117

Re: [deal.II] Interpolate H1 shape function to H1curl shape function

2023-01-17 Thread Wolfgang Bangerth




I'm solving a 3-d vector Maxwell's wave equation problem with nodal basis 
functions. To overcome spurious solution and singularity, the "regularized 
Maxwell equation 
" is applied. The question is, I cannot judge if my solution is same as the one solved with Nedelec elements (shown in the figure, FE_Q(3) on the left with "Nonlinear subdivision Level" and Nedelec(0) on the right) from visualization. Even if the results are identical, FE_Q has dof on nodes and FE_Nedelec has dof on edge, so FE_Q's visualization results always  have a asymptotic effect around singularity on the central edge. Is there a away to display nodal-based result as edge-based? FETools::interpolate does not support this because Nedelec is non-primitive.


I think it took all of us a month to get back to your question because it's 
not quite clear what it is you want to do. If I understand correctly, you want 
to *compare* the two solutions somehow, and for that you tried (i) to 
interpolate the Nedelec solution to the FE_Q space and (ii) to interpolate the 
FE_Q solution onto the Nedelec space.


The first of these does not immediately work because the Nedelec solution is, 
in general, discontinuous at nodes and so the interpolation operator is not 
easily defined. The second of these does not immediately work because 
FETools::interpolate() does not work for Nedelec target elements.


But in the end, what that points out is that it isn't quite clear to me what 
you are trying to do. The two solutions live in different function spaces that 
are not nested, and so interpolation in either direction can not preserve the 
solution: Even if FETools::interpolate() would work, the FE_Q solution would 
not be equal to the interpolated function.


As a consequence, I don't quite know what you would learn from comparing the 
interpolated FE_Q solution and the Nedelec solution. My suggestion would be to 
treat both the FE_Q solution and the Nedelec solution as L2 functions (namely, 
piecewise polynomials, possibly discontinuous). Then compare them as such. In 
fact, that would be easy enough if you just output both in a graphical format 
via DataOut and show both solutions at the same time; typical visualization 
programs also allow you to define derived variables that can, for example, be 
the difference between the two solutions which will help you understand how 
the two differ.


Best
 W.

--

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


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Re: [deal.II] Wave equation in temporal domain

2023-01-17 Thread Wolfgang Bangerth


On 1/16/23 06:29, Alexander Kiselyov wrote:

I'm trying to solve inhomogeneous Maxwellian equations in 4-potential
form in 3D space. In terms of math it is equivalent to solving a system
of 4 independent scalar wave equations. I'm using "free space" b/c of
Neumann type, calculated via solving an integral boundary problem. The
initial state is stationary (i.e. no external wave sources), so the
"input data" are RHS functions. The EM spectrum is assumed to be quite
wide, so, in contrast to the usual approach to Maxwellian equations,
the problem is solved in the temporal domain.

This approach produces artifacts of wave reflection from the
computational domain borders. It seems that to combat the issue some
kind of PML or ABC has to be introduced, which are commonly formulated
in frequency domain.

What literature would you suggest that deals with PML-like boundaries
specifically in the temporal domain?


I don't actually have much experience with PML-type boundary conditions 
myself, but there are quite a number of papers on the topic:

https://scholar.google.com/scholar?hl=en_sdt=0%2C6=perfectly+matched+layer+time+domain=

There are of course also absorbing boundary conditions for time-domain 
problems. These range for relatively simple "impedance" conditions that relate 
Dirichlet to Neumann values (i.e., they are of Robin type) to much more 
complex ones like those you can find in the works of Marcus Grote, Joe Keller, 
and Tom Hagstrom.


Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/


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Re: [deal.II] Extracting elements of a SparseMatrix

2023-01-17 Thread Wolfgang Bangerth


On 1/17/23 06:42, Wasim Niyaz Munshi ce21d400 wrote:
Hello everyone. I am trying to plot load displacement curves for an elasticity 
problem.
For this I need to extract the non-zero elements of my sparse stiffness 
matrix. I tried something like system_matrix[I][j] to extract the ij-th entry 
but it seems this doesn't work for the SparseMatrix.

  Can anyone help me with this?


Wasim -- yes, this is the wrong syntax to extract elements from a sparse 
matrix. Fortunately, the documentation of the class offers a number of ways to 
access matrix elements:

  https://dealii.org/developer/doxygen/deal.II/classSparseMatrix.html

Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/


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Re: [deal.II] INSTALLING DEALII ON MAC OSX VENTURA

2023-01-17 Thread Timo Heister

Erkin,
Please take a look at the conversation at
https://github.com/dealii/candi/issues/309#issuecomment-1295958250
that discusses the issue. You might be able to compile by going back
to the older version as mentioned in the comment.

Alternatively, you could disable Trilinos explicit instantiations:
https://github.com/dealii/candi/blob/beef9258162adcdc80ed0d8166600d5009640332/deal.II-toolchain/packages/trilinos.package#L211

Please let us know your results by posting in that issue!

On Tue, Jan 17, 2023 at 1:38 PM erkin yildiz  wrote:
>
> Dear community I have been trying to install deal. ii on my new MacBookPRO M2 
> OSX 13. 1 (22C65) following the instructions at the webpage https: //github. 
> com/dealii/dealii/wiki/Apple-ARM-M1-OSX After brewing brew install cmake 
> open-mpi gcc@ 11 ‍
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> Use caution when opening links or attachments if you do not recognize the 
> sender.
>
> ZjQcmQRYFpfptBannerEnd
> Dear community
>
> I have been trying to install deal.ii on my new MacBookPRO M2 OSX 13.1 (22C65)
> following the instructions at the webpage 
> https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX
>
> After brewing
>
> brew install cmake open-mpi gcc@11
>
> (I tried also gcc@12, BTW) deal.ii has been installed according to
>
> git clone https://github.com/dealii/candi
> cd candi
> ./candi.sh -j 8 --packages="hdf5 p4est trilinos dealii"
>
> An error occurs in installing Trilinos, namely
>
> [ … ]
>
> [ 69%] Linking CXX shared library libstratimikosamesos2.dylib
>
> [ 69%] Linking CXX shared library libstratimikosbelos.dylib
>
> Undefined symbols for architecture arm64:
>
>   "Amesos2::TachoSolver Kokkos::Compat::KokkosDeviceWrapperNode >, 
> Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::TachoSolver(Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> >, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>)", referenced from:
>
>   Amesos2::create_solver_with_supported_type Tpetra::CrsMatrix Kokkos::Compat::KokkosDeviceWrapperNode >, 
> Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::apply(Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> >, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>) in Thyra_Amesos2LinearOpWithSolveFactory.cpp.o
>
>   "Amesos2::KLU2 Kokkos::Compat::KokkosDeviceWrapperNode >, 
> Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::KLU2(Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> >, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>)", referenced from:
>
>   Amesos2::create_solver_with_supported_type Tpetra::CrsMatrix Kokkos::Compat::KokkosDeviceWrapperNode >, 
> Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::apply(Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> >, Teuchos::RCP Kokkos::Compat::KokkosDeviceWrapperNode > 
> const>) in Thyra_Amesos2LinearOpWithSolveFactory.cpp.o
>
> ld: symbol(s) not found for architecture arm64
>
> clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
>
> make[2]: *** 
> [packages/stratimikos/adapters/amesos2/src/libstratimikosamesos2.13.2.dylib] 
> Error 1
>
> make[1]: *** 
> [packages/stratimikos/adapters/amesos2/src/CMakeFiles/stratimikosamesos2.dir/all]
>  Error 2
>
> make[1]: *** Waiting for unfinished jobs
>
> Undefined symbols for architecture arm64:
>
>   "Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode 
> >::getNumVectors() const", referenced from:
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDense(std::__1::basic_ostream >&, 
> Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, std::__1::basic_string, 
> std::__1::allocator > const&, std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, 
> Teuchos::RCP > 
> > const&, Teuchos::RCP std::__1::char_traits > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDenseHeader(std::__1::basic_ostream 
> >&, Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, std::__1::basic_string, 
> std::__1::allocator > const&, std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, 
> Teuchos::RCP > 
> > const&, Teuchos::RCP std::__1::char_traits > > const&) in Thyra_BelosLinearOpWithSolve.cpp.o
>
>   Tpetra::MatrixMarket::Writer Kokkos::Compat::KokkosDeviceWrapperNode > 
> >::writeDenseColumn(std::__1::basic_ostream 
> >&, Tpetra::MultiVector Kokkos::Compat::KokkosDeviceWrapperNode > 
> const&, Teuchos::RCP std::__1::char_traits > > const&, 
> Teuchos::RCP >

[deal.II] INSTALLING DEALII ON MAC OSX VENTURA

2023-01-17 Thread erkin yildiz

Dear community

I have been trying to install deal.ii on my new MacBookPRO M2 OSX 13.1 
(22C65)
following the instructions at the 
webpage https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX

After brewing 

brew install cmake open-mpi gcc@11

(I tried also gcc@12, BTW) deal.ii has been installed according to 

git clone https://github.com/dealii/candi 
cd candi 
./candi.sh -j 8 --packages="hdf5 p4est trilinos dealii"

An error occurs in installing Trilinos, namely

[ … ]

[ 69%] Linking CXX shared library libstratimikosamesos2.dylib

[ 69%] Linking CXX shared library libstratimikosbelos.dylib

Undefined symbols for architecture arm64:

  "Amesos2::TachoSolver 
>, Tpetra::MultiVector 
> >::TachoSolver(Teuchos::RCP 
> const>, Teuchos::RCP 
> >, Teuchos::RCP 
> const>)", referenced from:

  Amesos2::create_solver_with_supported_type 
>, Tpetra::MultiVector 
> >::apply(Teuchos::RCP 
> const>, Teuchos::RCP 
> >, Teuchos::RCP 
> const>) in Thyra_Amesos2LinearOpWithSolveFactory.cpp.o

  "Amesos2::KLU2 
>, Tpetra::MultiVector 
> >::KLU2(Teuchos::RCP 
> const>, Teuchos::RCP 
> >, Teuchos::RCP 
> const>)", referenced from:

  Amesos2::create_solver_with_supported_type 
>, Tpetra::MultiVector 
> >::apply(Teuchos::RCP 
> const>, Teuchos::RCP 
> >, Teuchos::RCP 
> const>) in Thyra_Amesos2LinearOpWithSolveFactory.cpp.o

ld: symbol(s) not found for architecture arm64

clang: error: linker command failed with exit code 1 (use -v to see 
invocation)

make[2]: *** 
[packages/stratimikos/adapters/amesos2/src/libstratimikosamesos2.13.2.dylib] 
Error 1

make[1]: *** 
[packages/stratimikos/adapters/amesos2/src/CMakeFiles/stratimikosamesos2.dir/all]
 
Error 2

make[1]: *** Waiting for unfinished jobs

Undefined symbols for architecture arm64:

  "Tpetra::MultiVector 
>::getNumVectors() const", referenced from:

  Tpetra::MatrixMarket::Writer 
> >::writeDense(std::__1::basic_ostream 
>&, Tpetra::MultiVector 
> const&, std::__1::basic_string, 
std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, 
Teuchos::RCP 
> > const&, Teuchos::RCP > > const&) in 
Thyra_BelosLinearOpWithSolve.cpp.o

  Tpetra::MatrixMarket::Writer 
> >::writeDenseHeader(std::__1::basic_ostream >&, Tpetra::MultiVector 
> const&, std::__1::basic_string, 
std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, 
Teuchos::RCP 
> > const&, Teuchos::RCP > > const&) in 
Thyra_BelosLinearOpWithSolve.cpp.o

  Tpetra::MatrixMarket::Writer 
> >::writeDenseColumn(std::__1::basic_ostream >&, Tpetra::MultiVector 
> const&, Teuchos::RCP > > const&, 
Teuchos::RCP 
> > const&) in Thyra_BelosLinearOpWithSolve.cpp.o

  "Tpetra::MultiVector 
>::getLocalLength() const", referenced from:

  Tpetra::MatrixMarket::Writer 
> >::writeDenseColumn(std::__1::basic_ostream >&, Tpetra::MultiVector 
> const&, Teuchos::RCP > > const&, 
Teuchos::RCP 
> > const&) in Thyra_BelosLinearOpWithSolve.cpp.o

  "Tpetra::MultiVector 
>::getGlobalLength() const", referenced from:

  Tpetra::MatrixMarket::Writer 
> >::writeDenseHeader(std::__1::basic_ostream >&, Tpetra::MultiVector 
> const&, std::__1::basic_string, 
std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, 
Teuchos::RCP 
> > const&, Teuchos::RCP > > const&) in 
Thyra_BelosLinearOpWithSolve.cpp.o

  "Tpetra::MultiVector 
>::get1dCopy(Teuchos::ArrayView const&, unsigned long) const", 
referenced from:

  Tpetra::MatrixMarket::Writer 
> >::writeDenseColumn(std::__1::basic_ostream >&, Tpetra::MultiVector 
> const&, Teuchos::RCP > > const&, 
Teuchos::RCP 
> > const&) in Thyra_BelosLinearOpWithSolve.cpp.o

  "Tpetra::MultiVector 
>::getVector(unsigned long) const", referenced from:

  Tpetra::MatrixMarket::Writer 
> >::writeDense(std::__1::basic_ostream 
>&, Tpetra::MultiVector 
> const&, std::__1::basic_string, 
std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, 
Teuchos::RCP 
> > const&, Teuchos::RCP > > const&) in 
Thyra_BelosLinearOpWithSolve.cpp.o

ld: symbol(s) not found for architecture arm64

clang: error: linker command failed with exit code 1 (use -v to see 
invocation)

make[2]: *** 
[packages/stratimikos/adapters/belos/src/libstratimikosbelos.13.2.dylib] 
Error 1

make[1]: *** 
[packages/stratimikos/adapters/belos/src/CMakeFiles/stratimikosbelos.dir/all] 
Error 2

make: *** [all] Error 2

*Failure with exit status: 2*

*Exit message: There was a problem building trilinos 13-2-0.*



Can anyone provide me some way to address the issue? Is it perhaps related 
to the version of Trilinos? Can I install a former version (and in case, 
how to?)?

Many thanks

Erkin




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[deal.II] deal.II Newsletter #238

2023-01-17 Thread 'Rene Gassmoeller' via deal.II User Group

Hello everyone!

This is deal.II newsletter #238.
It automatically reports recently merged features and discussions about the 
deal.II finite element library.


## Below you find a list of recently proposed or merged features:

#14692: Fix two small things in FiniteElement. (proposed by drwells) 
https://github.com/dealii/dealii/pull/14692

#14691: Fix vertex numbering from deal to UCD (proposed by nlsmrg) 
https://github.com/dealii/dealii/pull/14691

#14690: Testsuite: run quick tests during build test (proposed by tamiko) 
https://github.com/dealii/dealii/pull/14690

#14689: CMake: Promote "tester-ng" to official regression tester (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/14689

#14688: step-59, step-64, step85 keywords added (proposed by vyushut) 
https://github.com/dealii/dealii/pull/14688

#14687: Re-implement a compiler warning workaround (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/14687

#14686: PETScWrappers: add a couple of missing reinits (proposed by 
stefanozampini) https://github.com/dealii/dealii/pull/14686

#14685: PETScWrappers: improve preconditioner class (proposed by 
stefanozampini) https://github.com/dealii/dealii/pull/14685

#14684: PETScWrappers::MatrixBase implement clear_rows_columns (proposed by 
stefanozampini) https://github.com/dealii/dealii/pull/14684

#14683: PETScWrappers::MPI::SparseMatrix: use SEQAIJ with one process (proposed 
by stefanozampini) https://github.com/dealii/dealii/pull/14683

#14682: PETScWrappers::MPI::Vector use VectorBase contructor from Vec (proposed 
by stefanozampini; merged) https://github.com/dealii/dealii/pull/14682

#14681: Replace ucd to deal with local vertex numbering (proposed by nlsmrg; 
merged) https://github.com/dealii/dealii/pull/14681

#14680: Use switch statements in ReferenceCell (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/14680

#14679: Minor cleanup in the VTU writer. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/14679

#14678: do not finalize PETSc/SLEPc if not initalized from deal.II (proposed by 
stefanozampini; merged) https://github.com/dealii/dealii/pull/14678

#14677: Configure: support KOKKOS when found with PETSc (proposed by 
stefanozampini; merged) https://github.com/dealii/dealii/pull/14677

#14676: Minor changes to examples comments (proposed by stefanozampini; merged) 
https://github.com/dealii/dealii/pull/14676

#14675: Avoid a deprecated function in the last context where it is used. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/14675

#14674: Centralize translation between deal.II and VTK numbering for pyramids. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/14674

#14673: Replace ucd_to_deal with a local vertex numbering in GridGenerator 
(proposed by nlsmrg; merged) https://github.com/dealii/dealii/pull/14673

#14672: Augment documentation of the PETSc block sparse matrix. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/14672

#14671: Fix OpenMP flag for Kokkos >= 4.0.00 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/14671

#14670: Implement ReferenceCell::contains_points() for the remaining reference 
cells. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/14670

#14669: Clean up BarycentricPolynomials a bit. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/14669

#14668: Fix the name of a variable: 'ratio' instead of 'ration'. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/14668

#14666: Minor updates to bounding box documentation. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/14666

#14665: Remove comments that are no longer useful. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/14665

#14664: Deprecate functions in ReferenceCell and introduce replacements. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/14664

#14663: Make special casing in VTU output more explicit. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/14663

#14662: Use TriaObjectsOrientations in connectivity.h. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/14662

#14661: Test output of a simplex cell with n_subdivisions=2. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/14661

#14660: Use std::array instead of a C-style array. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/14660

#14659: Do not write gratuitous output files into test directories. (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/14659

#14658: Augment documentation of DataOutBase::Patch. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/14658

#14657: Hermite polynomials (proposed by ivweber) 
https://github.com/dealii/dealii/pull/14657

#14655: Improve grammar in error messages. (proposed by bangerth; merged)

[deal.II] Extracting elements of a SparseMatrix

2023-01-17 Thread Wasim Niyaz Munshi ce21d400

Hello everyone. I am trying to plot load displacement curves for an 
elasticity problem.
For this I need to extract the non-zero elements of my sparse stiffness 
matrix. I tried something like system_matrix[I][j] to extract the ij-th 
entry but it seems this doesn't work for the SparseMatrix.
 Can anyone help me with this?

Thanks and regards
Wasim

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Re: [deal.II] Interpolate H1 shape function to H1curl shape function

Re: [deal.II] Wave equation in temporal domain

Re: [deal.II] Extracting elements of a SparseMatrix

Re: [deal.II] INSTALLING DEALII ON MAC OSX VENTURA

[deal.II] INSTALLING DEALII ON MAC OSX VENTURA

[deal.II] deal.II Newsletter #238

[deal.II] Extracting elements of a SparseMatrix

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