Re: [deal.II] shape function gradient at arbitrary points in the element

2022-07-06 Thread Wolfgang Bangerth 

On 7/5/22 09:28, Simon Wiesheier wrote:


What is the approach to achieve this?
My only idea is to create a new FEValues object for each quadrature point and 
pass an appropriate Quadrature object. But seems to be very inefficient.


This is basically what the VectorTools::point_value() and 
VectorTools::point_gradient() functions do. You might want to read through 
their implementations to see how this is done.


The only other approach is with classes like FEPointEvaluation. If you read 
through their implementation, you might be able to understand how they can 
also be used to evaluate just a single shape function. In the end, the values 
and gradients of a single shape function correspond to the values and 
gradients of a finite element field that corresponds to a solution vector with 
one 1.0 and the rest of the elements set to zero.


Best
 W.


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Re: [deal.II] discretization of a analytical function on a second triangulation

2022-07-06 Thread Wolfgang Bangerth 

On 7/6/22 01:02, Simon Wiesheier wrote:


Basically, my motivation to call VectorTools::interpolate is to compute the 
nodal values (scalar field --> DOFs) in the triangulation based on the formula 
implemented in the just derived class.
During the assembly routine, I access some interpolated values at quadrature 
points,...


With this in mind, is this an appropriate way?


Why query the values at quadrature points from the interpolated field when you 
could query them from the original function object?


Best
 W.

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Re: [deal.II] error: installation of dealii using spack

2022-07-06 Thread Jean-Paul Pelteret 
Hi Simon,

Daniel is right — only Sundials versions 5 through 5.8 are compatible with 
deal.II 9.3.2, while Sundials 6 is compatible with 9.3.4 onwards. This is in 
fact what is stated in the Spack package, so I don’t quite know how it is that 
you’re able to get this mixed configuration:
https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py#L212-L213
 

The spack package has now been updated for deal.II 9.4, so you should be able 
to update the repo and install the latest version of deal.II without having to 
worry about the Sundials version.

Best,
Jean-Paul


> On 6. Jul 2022, at 16:01, Daniel Arndt  wrote:
> 
> Simon,
> 
> It looks like all the errors are related to the Sundials dependency (release 
> 6.0.0). Looking at https://github.com/dealii/dealii/pull/13918 
> , it seems that you need the 
> latest deal.II release (9.4.0) to support that Sundials version.
> If you don't anticipate needing it I would just turn the dependency off if I 
> were you.
> 
> Best,
> Daniel
> 
> On Wed, Jul 6, 2022 at 9:38 AM Simon  > wrote:
> Dear all:
> 
> I already have an older version of dealii installed and wanted to install now 
> a newer version of dealii including all the dependencies using the command
> 'spack install dealii'.
> 
> Many dependencies are installed successfully (see "spack_error.png"), 
> however, the installation of dealii itself failes at some point. 
> The error message states that I should have a look in the file 
> "spack-build-out.txt", which I attached as well.
> In there, there are indeed a bunch of error messages, which refer to a 
> similar message that too few arguments are passed to certain functions.
> 
> How can I fix this?
> 
> Thanks you,
> Simon
> 
> -- 
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> .
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Re: [deal.II] discretization of a analytical function on a second triangulation

2022-07-06 Thread Daniel Arndt 
Simon,

if you get all information you need using VectorTools::interpolate then
this sounds good.
Note that there also is FEFieldFunction(
https://www.dealii.org/current/doxygen/deal.II/classFunctions_1_1FEFieldFunction.html
)
that implements the interpolation for you.

Best,
Daniel



On Wed, Jul 6, 2022 at 3:03 AM Simon Wiesheier 
wrote:

> Dear Daniel,
>
>
> yes, I defined a class derived from deal::Function and it seems to work
> for me.
>
> Basically, my motivation to call VectorTools::interpolate is to compute
> the nodal values (scalar field --> DOFs) in the triangulation based on the
> formula implemented in the just derived class.
> During the assembly routine, I access some interpolated values at
> quadrature points,...
>
> With this in mind, is this an appropriate way?
>
>
> Best
> Simon
>
> Am Di., 5. Juli 2022 um 09:16 Uhr schrieb Daniel Arndt <
> d.arndt.m...@gmail.com>:
>
>> Simon,
>>
>> defining a class derived from dealii::Function sounds sensible.
>> Whether calling VectorTools::interpolate makes sense, depends on what you
>> want to do with the interpolated function. In may cases, it's enough to
>> just evaluate it locally during assembly using functionality like
>> FEValues::get_function_values.
>>
>> Best,
>> Daniel
>>
>> On Mon, Jul 4, 2022 at 10:26 AM Simon  wrote:
>>
>>> Dear all:
>>>
>>>
>>> I am solving a nonlinear PDE on a Triangulation T_1.
>>>
>>> I know the analytical representation of a scalar function of two
>>> variables (no space co-ordinates, but two invariants of a quantity)
>>> and my goal is to find a discretized version of the analytical function
>>> (on a second, two-dimensional triangulation T_2).
>>> The nodal values of T_2 should be the exact values corresponding to the
>>> analytical solution.
>>> As for the values between the nodes, I want to start with a bilinear
>>> interpolation.
>>>
>>> The coupling to my original PDE works as follows:
>>> For each quadrature point defined on T_1, I compute the two input
>>> variables of the above function based on my solution vector, find the
>>> corresponding cell of T_2 and want to retrieve the interpolated nodal
>>> values.
>>>
>>> My idea is to use the function
>>> VectorTools::interpolate ,
>>> but I do not know a suitable Function object to hand over.
>>>
>>> Is this an appropriate approach at all?
>>>
>>>
>>> Thank you,
>>> Simon
>>>
>>> --
>>> 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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>> 
>> .
>>
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[deal.II] deal.II Newsletter #218

2022-07-06 Thread 'Rene Gassmoeller' via deal.II User Group 
Hello everyone!

This is deal.II newsletter #218.
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:

#14101: Vector tools project 1 (proposed by gfcas) 
https://github.com/dealii/dealii/pull/14101

#14099: [WIP] RPE: allow to evaluate cell-data vector (proposed by peterrum) 
https://github.com/dealii/dealii/pull/14099

#14097: Clean cgal utilities (proposed by fdrmrc) 
https://github.com/dealii/dealii/pull/14097

#14096: Function to restrict matrices (proposed by peterrum) 
https://github.com/dealii/dealii/pull/14096

#14094: [CI] limit parallelism in docker master build (proposed by tjhei) 
https://github.com/dealii/dealii/pull/14094

#14093: Fix formatting (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/14093

#14092: Bugfix: Use correct relative tolerance in MappingCartesian assert. 
(proposed by gassmoeller; merged) https://github.com/dealii/dealii/pull/14092

#14091: DoFTools::make_periodicity_constraints move asserts (proposed by 
peterrum; merged) https://github.com/dealii/dealii/pull/14091

#14090: FEEvaluationBase::read_write_operation_contiguous enable masking 
(proposed by bergbauer; merged) https://github.com/dealii/dealii/pull/14090

#14089: Added explicit instantiations of 
DoFTools::distribute_cell_to_dof_vector (proposed by a-shahba) 
https://github.com/dealii/dealii/pull/14089

#14088: [9.4] Take over multiple PRs (proposed by peterrum) 
https://github.com/dealii/dealii/pull/14088

#14087: doxygen: fix errors in formulas (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/14087

#14086: doxygen: fix SymmetricTensor friends (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/14086

#14085: FEEvaluationBase::read_write_operation case 3: enable masking (proposed 
by peterrum; merged) https://github.com/dealii/dealii/pull/14085

#14084: Be explicit regarding zero tolerance in merge_triangulations (proposed 
by peterrum; merged) https://github.com/dealii/dealii/pull/14084

#14083: Fix bug when we have no line dofs in assignment/renumbering of face mg 
dofs (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/14083

#14082: Restructure execute_refinement(Triangulation<3, spacedim>&) (proposed 
by kronbichler; merged) https://github.com/dealii/dealii/pull/14082

#14081: Add function to extract raw coarsen flags (proposed by kronbichler; 
merged) https://github.com/dealii/dealii/pull/14081

#14080: Use get_line_indices_of_cell in DoFHandlerPolicy (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/14080

#14076: Use faster data structure to compute matrix-free renumbering (proposed 
by kronbichler; merged) https://github.com/dealii/dealii/pull/14076

#14059: find_active_cell_around_point should only find cells with marked 
vertices (proposed by jh66637; merged) 
https://github.com/dealii/dealii/pull/14059

#14055: Add cross-references for global indices (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/14055

#13962: Support HDF5 output with one rank having no cells (proposed by tjhei; 
merged) https://github.com/dealii/dealii/pull/13962


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

#14100: GridTools::compute_active_cell_halo_layer() not working for PBC 
(opened) https://github.com/dealii/dealii/issues/14100

#14098: Performance of FEEvaluation::read_dof_values with masks (opened) 
https://github.com/dealii/dealii/issues/14098

#14095: doxygen errors (opened) https://github.com/dealii/dealii/issues/14095

#14053: Sundials test fail. (closed) 
https://github.com/dealii/dealii/issues/14053


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] error: installation of dealii using spack

2022-07-06 Thread Daniel Arndt 
Simon,

It looks like all the errors are related to the Sundials dependency
(release 6.0.0). Looking at https://github.com/dealii/dealii/pull/13918, it
seems that you need the latest deal.II release (9.4.0) to support that
Sundials version.
If you don't anticipate needing it I would just turn the dependency off if
I were you.

Best,
Daniel

On Wed, Jul 6, 2022 at 9:38 AM Simon  wrote:

> Dear all:
>
> I already have an older version of dealii installed and wanted to install
> now a newer version of dealii including all the dependencies using the
> command
> 'spack install dealii'.
>
> Many dependencies are installed successfully (see "spack_error.png"),
> however, the installation of dealii itself failes at some point.
> The error message states that I should have a look in the file
> "spack-build-out.txt", which I attached as well.
> In there, there are indeed a bunch of error messages, which refer to a
> similar message that too few arguments are passed to certain functions.
>
> How can I fix this?
>
> Thanks you,
> Simon
>
> --
> 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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[deal.II] Re: error while installing dealii using candi

2022-07-06 Thread Bruno Turcksin 
Hello,

This error often happens when you don't have enough memory to compile the 
program. Try using only one or two cores.

Best,

Bruno

On Wednesday, July 6, 2022 at 4:01:45 AM UTC-4 me20...@iittp.ac.in wrote:

> Dear all,
> please find the error attached.
>
> thank you in advance.[image: PHOTO-2022-07-06-00-19-11.jpg]
>

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Re: [deal.II] discretization of a analytical function on a second triangulation

2022-07-06 Thread Simon Wiesheier 
Dear Daniel,


yes, I defined a class derived from deal::Function and it seems to work for
me.

Basically, my motivation to call VectorTools::interpolate is to compute the
nodal values (scalar field --> DOFs) in the triangulation based on the
formula implemented in the just derived class.
During the assembly routine, I access some interpolated values at
quadrature points,...

With this in mind, is this an appropriate way?


Best
Simon

Am Di., 5. Juli 2022 um 09:16 Uhr schrieb Daniel Arndt <
d.arndt.m...@gmail.com>:

> Simon,
>
> defining a class derived from dealii::Function sounds sensible.
> Whether calling VectorTools::interpolate makes sense, depends on what you
> want to do with the interpolated function. In may cases, it's enough to
> just evaluate it locally during assembly using functionality like
> FEValues::get_function_values.
>
> Best,
> Daniel
>
> On Mon, Jul 4, 2022 at 10:26 AM Simon  wrote:
>
>> Dear all:
>>
>>
>> I am solving a nonlinear PDE on a Triangulation T_1.
>>
>> I know the analytical representation of a scalar function of two
>> variables (no space co-ordinates, but two invariants of a quantity)
>> and my goal is to find a discretized version of the analytical function
>> (on a second, two-dimensional triangulation T_2).
>> The nodal values of T_2 should be the exact values corresponding to the
>> analytical solution.
>> As for the values between the nodes, I want to start with a bilinear
>> interpolation.
>>
>> The coupling to my original PDE works as follows:
>> For each quadrature point defined on T_1, I compute the two input
>> variables of the above function based on my solution vector, find the
>> corresponding cell of T_2 and want to retrieve the interpolated nodal
>> values.
>>
>> My idea is to use the function
>> VectorTools::interpolate ,
>> but I do not know a suitable Function object to hand over.
>>
>> Is this an appropriate approach at all?
>>
>>
>> Thank you,
>> Simon
>>
>> --
>> 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
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "deal.II User Group" group.
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>> 
>> .
>>
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> 
> .
>

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