[deal.II] Convective Heat Flux Boundary Conditions in deall ii?

[Morris Jowas]

Hello everyone,

 

I am trying to solve a simple thermal problem  but finding the 
documentation helpfully detailed yet overwhelming. My problem is on heat 
conduction within a cubic domain with internal heat generation. 

 I have studied the transient heat transfer problem in step 26, in addition 
to the laplace problem solved on a 3D domain in step 4, as well as the 
problem in Step 7 where Neumann boundary conditions are applied. These have 
gotten me up and running.

However, *I am stuck on how to apply a convective heat flux boundary 
condition of the form: q = h(T-T_ext) programmatically*, whereby I must 
choose the external temperature (T_ext) and the heat transfer coefficient 
*(h)* to define the boundary condition. Is this possible to do in deal ii? 
If so, how might one go about it? I would appreciate any existing 
implementation of convective heat flux BCs that I can build up on. 

 

Thank you everyone,

 

Morris

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[deal.II] What I learned from 20 years of leading open source projects

[Wolfgang Bangerth]

All:
in case you wonder what is going on in the heads of the principal 
developers of deal.II: I will be giving a webinar tomorrow on this topic:


https://bssw.io/events/webinar-what-i-learned-from-20-years-of-leading-open-source-projects
I believe that you have to register (it's free!) but also think that the 
talk will be recorded for later viewing if you can't attend at the time.


In general, I would like to also give a shout-out to the organization 
that puts on this webinar (the Better Scientific Software, or BSSw: 
https://bssw.io/). They have a lot of really good resources for all of 
us who are working on and with scientific software and have really been 
a force for good in making us all better programmers and software 
maintainers. Go check out their website!


Best
 Wolfgang

--

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

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[deal.II] deal.II Newsletter #182

['Rene Gassmoeller' via deal.II User Group]

Hello everyone!

This is deal.II newsletter #182.
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:

#12758: Rename VECTOR to VectorType (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/12758

#12757: Add a CutFEM tutorial as step-85 (proposed by simonsticko) 
https://github.com/dealii/dealii/pull/12757

#12756: Add class NonMatching::FEValues (proposed by simonsticko) 
https://github.com/dealii/dealii/pull/12756

#12755: Allow TrilinosPayload to use another TrilinosPayload as an exemplar 
operator (proposed by jppelteret) https://github.com/dealii/dealii/pull/12755

#12753: Reduce run time of FEEvaluation tests with Hessians (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/12753

#12751: Bugfix: Invalid dofs on lines with similar FEs not correctly merged. 
(proposed by marcfehling; merged) https://github.com/dealii/dealii/pull/12751

#12750: Avoid warning about unused variable (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/12750

#12749: Consistently declare size_type in preconditioners derived from 
PreconditionRelaxation. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/12749

#12747: Fix unused-but-set-variable warnings (proposed by Rombur; merged) 
https://github.com/dealii/dealii/pull/12747

#12744: Hessians on general cells and faces (proposed by bergbauer; merged) 
https://github.com/dealii/dealii/pull/12744

#12692: Make Tensor::unroll() work with iterators. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/12692

#12651: Extend ScratchData to return jumps and averages of FE functions on an 
interface (proposed by jppelteret; merged) 
https://github.com/dealii/dealii/pull/12651


## And this is a list of recently opened or closed discussions:

#12754: Using TrilinosWrappers::SolverCG in inverse_operator() (opened) 
https://github.com/dealii/dealii/issues/12754

#12752: Bug: Triangulation::load()/save() with large output files (opened) 
https://github.com/dealii/dealii/issues/12752

#10401: Implement FEEvaluation::submit_hessian() (closed) 
https://github.com/dealii/dealii/issues/10401


A list of all major changes since the last release can be found at 
https://www.dealii.org/developer/doxygen/deal.II/recent_changes.html.


Thanks for being part of the community!


Let us know about questions, problems, bugs or just share your experience by 
writing to dealii@googlegroups.com, or by opening issues or pull requests at 
https://www.github.com/dealii/dealii.
Additional information can be found at https://www.dealii.org/.

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Re: [deal.II] Re: step-29 & step-40

[Hermes Sampedro]

Thank you very much.

Regards,
Hermes

El mar, 14 sept 2021 a las 16:28, Bruno Turcksin ()
escribió:

> Hermes,
>
> You probably don't need to use reinit() in your case. You want to use
> reinit() if the structure of the matrix changes with frequency. For
> example, if you change the degree of finite elements you need to call
> reinit(). If you want to change the values but the structure matrix is
> unchanged then you don't need to call reinit(). Instead, you can simply do
> matrix = 0; to clean the matrix.
>
> Best,
>
> Bruno
>
> On Tuesday, September 14, 2021 at 10:18:19 AM UTC-4 hermes...@gmail.com
> wrote:
>
>> Dear Bruno thank you very much for pointing step-17, I could solve the
>> problem.
>>
>> I would like to ask the last question. I am computing step-29 in parallel
>> for different frequencies. I have a loop for each of the frequencies as
>> follows:
>>
>>
>> make_grid();
>>
>> setup_system();
>>
>> assemble_system(sI[0]);
>>
>>
>>
>>
>>*for* ( *int* i = 0; i < Ns; ++i)
>>
>> {
>>
>> update_system(sI[i]);
>>
>> solve();
>>
>> output_results();
>>
>> }
>>
>> In orther to not setup the system and assemble in each iteration I
>> created update_system() to update the system matrix  as it change due to
>> the frequency. I need to do system_matrix .reinit before the update to
>> clean the matrix which I realize is time comsuming. I would like to ask if
>> there is another efficient way to update the matrix.
>>
>> Thank you
>> Regards,
>> H
>>
>>
>>
>> El mar, 14 sept 2021 a las 14:11, Bruno Turcksin ()
>> escribió:
>>
>>> Hermes,
>>>
>>> Le mar. 14 sept. 2021 à 05:19, Hermes Sampedro
>>>  a écrit :
>>> >
>>> > Should I use dealii::PETScWrappers::MPI::SparseMatrix system_matrix
>>> instead? If so could ou please help me to with the reinit() function? I do
>>> not fully understand how to call it.
>>>
>>> That's right, you need the matrix to be distributed too. Take a look
>>> at step-17 to see how to use PETScWrappers.
>>>
>>> Best,
>>>
>>> Bruno
>>>
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>>> .
>>>
>> --
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>

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Re: [deal.II] MatrixTools::apply_boundary_values for BlockSparseMatrix> and BlockVector> entries

[Daniel Arndt]

Mariia,

You need to make sure that the std::map also uses values of type
std::complex. The compile error you shared shows that you use
doubles.

Best,
Daniel

Am Di., 14. Sept. 2021 um 07:30 Uhr schrieb Мария Бронзова <
masianic...@gmail.com>:

> Hi everyone,
>
> I ran into the following difficulty: I have a vector-valued problem with
> complex numbers as entries for my BlockSparseMatrix system_matrix and
> BlockVector system_rhs and solution vectors and I am trying to apply
> Dirichlet boundary conditions, using the
> MatrixTools::apply_boundary_values(boundary_values, system_matrix,
> solution, system_rhs) function.
>
> The compiler is complaining, indicating the error: no matching function
> for call to ‘apply_boundary_values(std::map&,
> dealii::BlockSparseMatrix >&,
> dealii::BlockVector >&,
> dealii::BlockVector >&)’.
>
> Is it not possible to use the function for complex-values systems?
>
> Thank you!
>
> Kind regards,
> Mariia
>
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> 
> .
>

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Re: [deal.II] Re: step-29 & step-40

[Bruno Turcksin]

Hermes,

You probably don't need to use reinit() in your case. You want to use 
reinit() if the structure of the matrix changes with frequency. For 
example, if you change the degree of finite elements you need to call 
reinit(). If you want to change the values but the structure matrix is 
unchanged then you don't need to call reinit(). Instead, you can simply do 
matrix = 0; to clean the matrix.

Best,

Bruno

On Tuesday, September 14, 2021 at 10:18:19 AM UTC-4 hermes...@gmail.com 
wrote:

> Dear Bruno thank you very much for pointing step-17, I could solve the 
> problem.
>
> I would like to ask the last question. I am computing step-29 in parallel 
> for different frequencies. I have a loop for each of the frequencies as 
> follows:
>
>
> make_grid();
>
> setup_system();
>
> assemble_system(sI[0]);
>
>  
>
>
>*for* ( *int* i = 0; i < Ns; ++i)
>
> {
>
> update_system(sI[i]);
>
> solve();
>
> output_results();
>
> }
>
> In orther to not setup the system and assemble in each iteration I created 
> update_system() to update the system matrix  as it change due to the 
> frequency. I need to do system_matrix .reinit before the update to clean 
> the matrix which I realize is time comsuming. I would like to ask if there 
> is another efficient way to update the matrix.
>
> Thank you
> Regards, 
> H
>
>
>
> El mar, 14 sept 2021 a las 14:11, Bruno Turcksin () 
> escribió:
>
>> Hermes,
>>
>> Le mar. 14 sept. 2021 à 05:19, Hermes Sampedro
>>  a écrit :
>> >
>> > Should I use dealii::PETScWrappers::MPI::SparseMatrix system_matrix 
>> instead? If so could ou please help me to with the reinit() function? I do 
>> not fully understand how to call it.
>>
>> That's right, you need the matrix to be distributed too. Take a look
>> at step-17 to see how to use PETScWrappers.
>>
>> Best,
>>
>> Bruno
>>
>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
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>>
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>> https://groups.google.com/d/msgid/dealii/CAGVt9eNeuUqiA8-c0Zd%3DNn%2BTNx%2BVT3-xao0io8QT_D0rk0WjgQ%40mail.gmail.com
>> .
>>
>

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Re: [deal.II] Re: step-29 & step-40

[Hermes Sampedro]

Dear Bruno thank you very much for pointing step-17, I could solve the
problem.

I would like to ask the last question. I am computing step-29 in parallel
for different frequencies. I have a loop for each of the frequencies as
follows:


make_grid();

setup_system();

assemble_system(sI[0]);




   *for* ( *int* i = 0; i < Ns; ++i)

{

update_system(sI[i]);

solve();

output_results();

}

In orther to not setup the system and assemble in each iteration I created
update_system() to update the system matrix  as it change due to the
frequency. I need to do system_matrix .reinit before the update to clean
the matrix which I realize is time comsuming. I would like to ask if there
is another efficient way to update the matrix.

Thank you
Regards,
H



El mar, 14 sept 2021 a las 14:11, Bruno Turcksin ()
escribió:

> Hermes,
>
> Le mar. 14 sept. 2021 à 05:19, Hermes Sampedro
>  a écrit :
> >
> > Should I use dealii::PETScWrappers::MPI::SparseMatrix system_matrix
> instead? If so could ou please help me to with the reinit() function? I do
> not fully understand how to call it.
>
> That's right, you need the matrix to be distributed too. Take a look
> at step-17 to see how to use PETScWrappers.
>
> Best,
>
> Bruno
>
> --
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> .
>

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Re: [deal.II] Re: step-29 & step-40

[Bruno Turcksin]

Hermes,

Le mar. 14 sept. 2021 à 05:19, Hermes Sampedro
 a écrit :
>
> Should I use dealii::PETScWrappers::MPI::SparseMatrix system_matrix instead? 
> If so could ou please help me to with the reinit() function? I do not fully 
> understand how to call it.

That's right, you need the matrix to be distributed too. Take a look
at step-17 to see how to use PETScWrappers.

Best,

Bruno

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[deal.II] MatrixTools::apply_boundary_values for BlockSparseMatrix> and BlockVector> entries

[Мария Бронзова]

Hi everyone,

I ran into the following difficulty: I have a vector-valued problem with 
complex numbers as entries for my BlockSparseMatrix system_matrix and 
BlockVector system_rhs and solution vectors and I am trying to apply 
Dirichlet boundary conditions, using the 
MatrixTools::apply_boundary_values(boundary_values, system_matrix, 
solution, system_rhs) function. 

The compiler is complaining, indicating the error: no matching function for 
call to ‘apply_boundary_values(std::map&, 
dealii::BlockSparseMatrix >&, 
dealii::BlockVector >&, 
dealii::BlockVector >&)’.

Is it not possible to use the function for complex-values systems?

Thank you!

Kind regards,
Mariia

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Re: [deal.II] Re: step-29 & step-40

[Hermes Sampedro]

Dear Bruno, thank you for your answer it helped me to solve the problem.

I had some issues with Trilinos library so I decided to implement step-29
in parallel (similar to step-40) using dealii::PETSxWrappers. I get an
error on the solve() function on the red line:

*template* <*int* dim>

*void* UltrasoundProblem::solve()

{

PETScWrappers::MPI::Vector
completely_distributed_solution(locally_owned_dofs,mpi_communicator);

SolverControl cn;

PETScWrappers::SparseDirectMUMPS solver(cn, mpi_communicator);

solver.solve(system_matrix, completely_distributed_solution, system_rhs);

constraints.distribute(completely_distributed_solution);

locally_relevant_solution = completely_distributed_solution;

}

where it was declared:

  dealii::PETScWrappers::SparseMatrix system_matrix;

  dealii::PETScWrappers::MPI::Vector   locally_relevant_solution;

  dealii::PETScWrappers::MPI::Vector   system_rhs;

[0]PETSC ERROR: - Error Message
--

[0]PETSC ERROR: Nonconforming object sizes

[0]PETSC ERROR: Preconditioner number of local rows 51842 does not equal
resulting vector number of rows 26114

[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
for trouble shooting.

[0]PETSC ERROR: Petsc Release Version 3.13.1, May 02, 2020

[0]PETSC ERROR: ./step-29 on a  named gbarlogin1 by hsllo Tue Sep 14
11:11:04 2021

[0]PETSC ERROR: Configure options
--prefix=/zhome/32/9/115503/dealii-candi/petsc-3.13.1 --with-debugging=0
--with-shared-libraries=1 --with-mpi=1 --with-x=0 --with-64-bit-indices=0
--download-hypre=1 CC=mpicc CXX=mpicxx FC=mpif90
--with-blaslapack-dir=/appl/OpenBLAS/0.3.17/XeonE5-2660v3/gcc-11.2.0/lib
--with-parmetis-dir=/zhome/32/9/115503/dealii-candi/parmetis-4.0.3
--with-metis-dir=/zhome/32/9/115503/dealii-candi/parmetis-4.0.3
--download-scalapack=1 --download-mumps=1

[0]PETSC ERROR: #1 PCApply() line 436 in
/zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/pc/interface/precon.c

[0]PETSC ERROR: #2 KSP_PCApply() line 281 in
/zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/include/petsc/private/kspimpl.h

[0]PETSC ERROR: #3 KSPSolve_PREONLY() line 22 in
/zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/ksp/impls/preonly/preonly.c

[0]PETSC ERROR: #4 KSPSolve_Private() line 694 in
/zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/ksp/interface/itfunc.c

[0]PETSC ERROR: #5 KSPSolve() line 853 in
/zhome/32/9/115503/dealii-candi/tmp/build/petsc-lite-3.13.1/src/ksp/ksp/interface/itfunc.c





Exception on processing:




An error occurred in line <807> of file

in function

void dealii::PETScWrappers::SparseDirectMUMPS::solve(const
dealii::PETScWrappers::MatrixBase&, dealii::PETScWrappers::VectorBase&,
const dealii::PETScWrappers::VectorBase&)

The violated condition was:

ierr == 0

Additional information:

deal.II encountered an error while calling a PETSc function.

The description of the error provided by PETSc is "Nonconforming

object sizes".

The numerical value of the original error code is 60.




Aborting!

-




Should I use dealii::PETScWrappers::MPI::SparseMatrix system_matrix
instead? If so could ou please help me to with the reinit() function? I do
not fully understand how to call it.


Thank you

Regards,

H

El vie, 10 sept 2021 a las 14:56, Bruno Turcksin ()
escribió:

> Hermes,
>
> There is no recommended way to write a plain .txt file, it's left to the
> user to write their own function. The reason deal.II provides a function to
> write a .vtu file is that you need to use a very specific format. There is
> no format that you need to follow when writing a .txt file.
>
> Best,
>
> Bruno
>
> On Friday, September 10, 2021 at 5:58:45 AM UTC-4 hermes...@gmail.com
> wrote:
>
>> Dear Bruno,
>>
>> Thank you very much for your help.
>>
>> I would kindly like to ask what is the recommended way in Dealii to write
>> on a plain .txt file the results of a single point when using MPI. I solve
>> for different frequencies and would like to write the solution after each
>> iteration. In the non-parallel version it works as follows:
>>
>> *ofstream myfile;*
>>
>> * myfile.open ("solution.txt");*
>>
>>
>>
>> *   for ( int freq = 0; freí< 10; ++i)*
>>
>> *{*
>>
>> *setup_system();*
>>
>> *assemble_system(freq);*
>>
>> *solve();*
>>
>> * output_results(myfile);*
>>
>> *}*
>>
>> *myfile.close();*
>>
>>
>>
>>The function  *output_results(myfile) *takes care of writing the
>> solution of a single point in a plain .txt file for each frequency.
>>
>>
>> Step-40 shows a way to write .vtu files format when using MPI, but I did
>> not find any function to write the plain