date:20200923

Re: [deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

2020-09-23 Thread Jean-Paul Pelteret

Hi Animesh,

Although in that code-gallery example the system is assembled into a 
BlockSparseMatrix, the system actually has only one block. So you can 
retrieve the underlying SparseMatrix (and Vector for the RHS) 
via
tangent_matrix.block(u_dof, u_dof);
system_rhs.block(u_dof);
and use them with one of the standard eigensolvers (maybe ArpackSolver 
, since 
you want both the eigenvalues and eigenvectors).

I hope that this helps you!

Best,
Jean-Paul

> On 23 Sep 2020, at 20:53, Animesh Rastogi IIT Gandhinagar 
>  wrote:
> 
> Hi All, 
> 
> I am trying to play with the code of Quassi Static Finite Strain 
> Compressibility 
> .
>  I want to calculate the eigenvalues and eigenvectors of the System Tangent 
> Matrix (BlockSparseMatrix 
>  
> tangent_matrix) that we get at every time step after the Newton method has 
> converged. However, I could not find any function to calculate the 
> eigenvalues and eigenvectors of the BlockSparse Matrix. Could someone please 
> help me with this?
> 
> Thanks!
> 
> AR
> 
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[deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

2020-09-23 Thread Animesh Rastogi IIT Gandhinagar

Hi All, 

I am trying to play with the code of Quassi Static Finite Strain 
Compressibility 
.
 
I want to calculate the eigenvalues and eigenvectors of the System Tangent 
Matrix (BlockSparseMatrix 
 
tangent_matrix) that we get at every time step after the Newton method has 
converged. However, I could not find any function to calculate the 
eigenvalues and eigenvectors of the BlockSparse Matrix. Could someone 
please help me with this?

Thanks!

AR

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Re: [deal.II] PETSC issue while trying to run step-18

2020-09-23 Thread krishan...@gmail.com

Thanks a lot! I was able to configure it correctly. The  deal.ii 
installation following it, is able to run step-18. Adding the command that 
I used to configure it correctly, for future reference:

cmake -DCMAKE_INSTALL_PREFIX=/path/to/dealii/installation/directory 
-DPETSC_DIR=/path/to/PETSC  -DPETSC_ARCH=x86_64 -DDEAL_II_WITH_PETSC=ON 
-DDEAL_II_WITH_MPI=ON /path/to/extracted/dealii
On Wednesday, 23 September 2020 at 07:58:27 UTC-5 Timo Heister wrote:

> You will also need to set
> -D DEAL_II_WITH_MPI=ON
>
> On Tue, Sep 22, 2020 at 1:54 PM Daniel Arndt  wrote:
> >
> > https://dealii.org/developer/readme.html#configuration-options says to 
> call cmake with -DPETSC_DIR=/path/to/petsc -DPETSC_ARCH=architecture.
> > I normally just set the environment variable PETSC_DIR and configure 
> deal.II with -DDEAL_II_WITH_PETSC=ON
> >
> > Best,
> > Daniel
> >
> > Am Di., 22. Sept. 2020 um 12:29 Uhr schrieb krishan...@gmail.com <
> krishan...@gmail.com>:
> >>
> >>
> >> Hello,
> >>
> >> I tried to run step-18 and initially received the following error 
> message:
> >>
> >> Error! This tutorial requires a deal.II library that was configured with
> >> the following options:
> >>
> >> DEAL_II_WITH_MPI = ON
> >> DEAL_II_WITH_PETSC = ON
> >> DEAL_II_PETSC_WITH_COMPLEX = OFF
> >>
> >> However, the deal.II library found at
> >> /home/krishanu/Google_Drive/dealii/dealii_920/library_dealii_920 was
> >> configured with these options
> >>
> >> DEAL_II_WITH_MPI = OFF
> >> DEAL_II_WITH_PETSC = OFF
> >> DEAL_II_PETSC_WITH_COMPLEX =
> >>
> >> which conflict with the requirements.
> >>
> >> So, I used the following commands (from this link: 
> https://www.dealii.org/current/external-libs/petsc.html) to install PETSC:
> >>
> >> tar xvzf petsc-x-y-z.tar.gz cd petsc-x-y-z
> >> export PETSC_DIR=`pwd`
> >> export PETSC_ARCH=x86_64
> >> ./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1 
> --download-hypre=1
> >> make
> >> make test
> >>
> >> Then used the following commands to build, configure and install deal.ii
> >>
> >> mkdir build
> >> cd build
> >> cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II
> >>
> >> But it seems that deal.ii did not auto detect PETSC and MPI as it 
> showed the following among other configured features:
> >>
> >> Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
> DEAL_II_ALLOW_AUTODETECTION = ON):
> >>
> >> # ( DEAL_II_WITH_MPI = OFF )
> >> # ( DEAL_II_WITH_PETSC = OFF )
> >>
> >> I am wondering what I might be missing here. Could anyone please help?
> >>
> >>
> >> --
> >> 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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> .
> >
> > --
> > The deal.II project is located at http://www.dealii.org/
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> .
>
>
>
> -- 
> Timo Heister
> http://www.math.clemson.edu/~heister/
>

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[deal.II] install problems with clang@12.0.0 and Xcode12.0 from spack

2020-09-23 Thread 'Alexander Greiner' via deal.II User Group

Hi,

I'm new here (and also relatively new to deal.II). I'm trying to install 
dealii@9.2.0 from spack, running into errors. These errors are not directly 
linked to deal.II and therefore I'm not sure if this is the right place to 
post my problem. Unfortunately, clang@12.0.0 and Xcode12.0 seem to be quite 
new and there is not a lot to find in the www... Furthermore, I'm using 
gcc@10.2.0.

spack install dealii

1) Thereby, installing OpenBlas leads to the error:
Error: ProcessError: Command exited with status 2: 'make' '-j12'
Then, I tried to install the most recent develop version of OpenBlas -- 
with success. And continue with:

spack install dealii ^openblas@develop

2) Thereby, installing arpack-ng leads again to:
Error: ProcessError: Command exited with status 2: 'make' '-j12'
Then, I tried to install the most recent develop version of arpack-ng -- 
with success. And continue with:

spack install dealii ^openblas@develop ^arpack-ng@develop

3) Thereby, installing netlib-scalapack leads again to:
Error: ProcessError: Command exited with status 2: 'make' '-j12'
Unfortunately, there is no newer version of this package.

Now my question, has anyone else tried to install dealii 9.2.0 and macOS 
Catalina with clang@12.0.0 and Xcode12.0? Or has anyone suggestions how to 
overcome these issues? I'm looking forward to any help and ideas! Let me 
know if you need more detailed information.

Kind regards 
Alex

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Re: [deal.II] PETSC issue while trying to run step-18

2020-09-23 Thread Timo Heister

You will also need to set
-D DEAL_II_WITH_MPI=ON

On Tue, Sep 22, 2020 at 1:54 PM Daniel Arndt  wrote:
>
> https://dealii.org/developer/readme.html#configuration-options says to call 
> cmake with -DPETSC_DIR=/path/to/petsc -DPETSC_ARCH=architecture.
> I normally just set the environment variable PETSC_DIR and configure deal.II 
> with -DDEAL_II_WITH_PETSC=ON
>
> Best,
> Daniel
>
> Am Di., 22. Sept. 2020 um 12:29 Uhr schrieb krishan...@gmail.com 
> :
>>
>>
>> Hello,
>>
>> I tried to run step-18 and initially received the following error message:
>>
>>  Error! This tutorial requires a deal.II library that was configured with
>>   the following options:
>>
>>   DEAL_II_WITH_MPI = ON
>>   DEAL_II_WITH_PETSC = ON
>>   DEAL_II_PETSC_WITH_COMPLEX = OFF
>>
>>   However, the deal.II library found at
>>   /home/krishanu/Google_Drive/dealii/dealii_920/library_dealii_920 was
>>   configured with these options
>>
>>   DEAL_II_WITH_MPI = OFF
>>   DEAL_II_WITH_PETSC = OFF
>>   DEAL_II_PETSC_WITH_COMPLEX =
>>
>>   which conflict with the requirements.
>>
>> So, I used the following commands (from this link: 
>> https://www.dealii.org/current/external-libs/petsc.html) to install PETSC:
>>
>> tar xvzf petsc-x-y-z.tar.gz cd petsc-x-y-z
>> export PETSC_DIR=`pwd`
>> export PETSC_ARCH=x86_64
>> ./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1 
>> --download-hypre=1
>> make
>> make test
>>
>> Then used the following commands to build, configure and install deal.ii
>>
>> mkdir build
>> cd build
>> cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II
>>
>> But it seems that deal.ii did not auto detect PETSC and MPI as it showed the 
>> following among other configured features:
>>
>> Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
>> = ON):
>>
>> #  ( DEAL_II_WITH_MPI = OFF )
>> #  ( DEAL_II_WITH_PETSC = OFF )
>>
>> I am wondering what I might be missing here. Could anyone please help?
>>
>>
>> --
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>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
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>
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-- 
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http://www.math.clemson.edu/~heister/

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Re: [deal.II] Issue with unstructured hex mesh

2020-09-23 Thread Timo Heister

I am coming late to the conversation (and I only looked at it quickly,
sorry), but I have two additional suggestions:
1. Depending on the deformation of cells and the PDE in question, it
might be important to check if the quadrature degree is high enough to
not contribute to the overall error. This is easy to check by
increasing the quadrature degree in all places but you can of course
go back to your PDE and check what you need.
2. Did you play with linear solver tolerances to see if this matters?

On Tue, Sep 22, 2020 at 6:31 PM Wolfgang Bangerth
 wrote:
>
> On 9/22/20 4:27 PM, Wolfgang Bangerth wrote:
> > I wished every student project were as comprehensively explored! :-)
>
> I tacitly assumed that Maurice Rohracker is your student. I didn't mean to
> imply that the work you're doing is at the "student level" -- quite the
> contrary: What your reports show is just really impressive!
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
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-- 
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Re: [deal.II] Multi-physics implementation

2020-09-23 Thread Ray Mclaren

Mr. Pelteret 

Sir, thank you for your guidance. 

I am new to using dealii and I am very thankful for your support

Thanks 

On Wednesday, September 23, 2020 at 4:55:04 AM UTC+9 Jean-Paul Pelteret 
wrote:

> Hi Ray,
>
> I’m happy to see that Simon has already given a great explanation as to 
> how to solve your problem. It’s probably more on point than the code that 
> mentioned that I would direct you towards. So it really was worthwhile 
> asking the question again here :-)
>
> Best,
> Jean-Paul
>
> On 22 Sep 2020, at 16:03, Ray Mclaren  wrote:
>
> Mr. Simon
>
> thank you for your response, It was exactly what I was looking for. 
>
> On Tuesday, September 22, 2020 at 5:01:42 PM UTC+9 simon...@gmail.com 
> wrote:
>
>> Hi,
>> I would do it like this:
>>
>>   // Setup two DoFHandlers, one for the heat and one for Allen-Cahn
>>   DoFHandler heat_dof_handler(triangulation);
>>   DoFHandler allen_cahn_dof_handler(triangulation);
>>
>>// Solve for this first
>>   Vector heat_solution;
>>
>>   // Lots of things in between here...
>>
>>   // When assembling for allen_cahn, create two FEValues objects.
>>   FEValues fe_values(allen_cahn_element, quadrature, update_flags);
>>   FEValues heat_fe_values(heat_element, quadrature, update_values);
>>
>>   for (auto cell : allen_cahn_dof_handler.active_cell_iterators())
>> {
>>   // Cast to an iterator on the heat_dof_handler
>>   typename DoFHandler::active_cell_iterator heat_cell(
>> , cell->level(), cell->index(), _dof_handler);
>>
>>   // Call reinit with the corresponding cells.
>>   fe_values.reinit(cell);
>>   heat_fe_values.reinit(heat_cell);
>>
>>   // Get the heat values at the quadrature points using 
>> heat_fe_values
>>   std::vector heat_values(heat_element.dofs_per_cell);
>>   heat_fe_values.get_function_values(heat_solution, heat_values);
>>
>>   // Assemble the system using fe_values here ...
>> }
>>
>> Best,
>> Simon
>> On Tuesday, September 22, 2020 at 2:31:01 AM UTC+2 mclaren...@gmail.com 
>> wrote:
>>
>>> Hi,
>>> I have a question regrading multi-physics problem implementation.
>>>
>>> I am developing a program that will solve the steady-state thermal 
>>> conduction (laplace) first and then the allen-Cahn equation.
>>>
>>> both of the problems are solved on the same mesh, however due to the 
>>> nature of my specific implementation they solved separately. To solve the 
>>> allen-Cahn equation, I need to evaluate temperature dependent functions at 
>>> each node in the domain.
>>>
>>> Hence, they only share the same triangulation, but everything else is 
>>> separate.
>>>
>>> My question is, how to use the solution vector from the thermal 
>>> conduction (the temperature) in the assembly of the allen-cahn equation ?
>>>
>>>  how to access the temperature at these nodes and make sure that they 
>>> are synchronized ? 
>>>
>>> thank you
>>>
>>>
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>  
> 
> .
>
>
>

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Re: [deal.II] Using DataOut when dim != spacedim

2020-09-23 Thread Malhar Tidke

Hello Daniel,
It worked, Thank you. I had somehow missed step-38, I will look into it.
Again, thank you for your help.

Best Regards,
Malhar

On Tue, Sep 22, 2020 at 7:17 PM Daniel Arndt  wrote:

> Malhar,
>
> the template arguments for DataOut are dim and DoFHandlerType where
> DoFHandlerType defaults to DoFHandler
> since you are using a DoFHandler<2, 3> object you need to specify the
> second template argument explicitly, i.e.
>
> DataOut<2, DoFHandler<2,3>> data_out;
>
> You could have a look at step-38.
>
> Best,
> Daniel
>
> Am Di., 22. Sept. 2020 um 01:37 Uhr schrieb Malhar T. <
> malhar.ti...@gmail.com>:
>
>> Hello All,
>> I hope you are doing well !
>>
>> I am working on a surface patch in 3D (dim=2 & spacedim=3 and developed
>> using ChartManifold<2,3> by following code similar to step-53
>> ) and I
>> would like to output the results into a vtk file. I am mostly following
>> tutorials, as I am not really great with C++. So, initially I used the
>> class DataOut and tried to specify the geometry using attach_dof_handler.
>>
>> This is how its defined,
>>
>> Triangulation<2, 3> triangulation;
>> DoFHandler<2, 3>dof_handler;
>>
>> And output_results function was written as
>>
>> {
>> DataOut data_out;
>> data_out.attach_dof_handler(dof_handler);
>> }
>>
>> But I got the error
>>
>>
>> error: cannot convert ‘const dealii::DoFHandler<2, 3>’ to ‘const 
>> dealii::DoFHandler<2, 2>&’
>> note:   initializing argument 1 of ‘void 
>> dealii::DataOut_DoFData> patch_space_dim>::attach_dof_handler(const DoFHandlerType&) [with 
>> DoFHandlerType = dealii::DoFHandler<2, 2>; int patch_dim = 2; int 
>> patch_space_dim = 2]’
>>
>> I tried searching in the forum and came to know about DataOutFaces
>> (through this post
>> ), and
>> I also looked at the step-61
>> 
>> tutorial on its implementation, but I got the same error again. I have a
>> feeling that I am not understanding something very trivial, thus, any
>> pointers would be really helpful.
>>
>> Thank You.
>>
>>
>> I tried searching in the forum and came to know about DataOutFaces
>> (through this post)
>> , and I
>> also looked at the step-61
>> 
>> tutorial on its implementation, but I got the same error again. I have a
>> feeling that I am not understanding something very trivial, any pointers
>> would be helpful. Thank You.
>>
>> --
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>> 
>> .
>>
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Re: [deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

[deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

Re: [deal.II] PETSC issue while trying to run step-18

[deal.II] install problems with clang@12.0.0 and Xcode12.0 from spack

Re: [deal.II] PETSC issue while trying to run step-18

Re: [deal.II] Issue with unstructured hex mesh

Re: [deal.II] Multi-physics implementation

Re: [deal.II] Using DataOut when dim != spacedim

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