Re: [deal.II] extrude triangulation with n_slices = 1

2023-04-04 Thread Wolfgang Bangerth 



Greg:

We want to construct a 3D triangulation by extruding a 2D triangulation 
(one that potentially contains hanging nodes) and we only want one 
slice/layer of mesh on the extrusion direction.


Looking around in the GridGenerator namespace led me to the 
extrude_triangulation function. It’s doing everything we desire except 
for that (a) the slices/layers on the extrusion direction has to be at 
least two


I think this is poorly described in the documentation. The number of 
slices = the number of cell layers plus one. Two slices => one layer of 
cells. I've fixed this here:

  https://github.com/dealii/dealii/pull/15028

and (b) the 2D mesh must be a coarse mesh. I’m wondering if 
there are tips on getting around these two restrictions.


This you can't get around.


Originally I was using GridGenerator::hyper_rectangle teamed with 
anisotropic refinement cut_xy. But this ceases to work after the code 
was re-implemented with parallel::distributed::Triangulation because 
“this class does not support anisotropic refinement, because it relies 
on the p4est library that does not support this” [1].


Yes, and this is true regardless of how you generate the mesh. You can't 
create an anisotropically refined mesh for p::d::T. This also means that 
you cannot extrude a refined 2d mesh into 3d that has only one layer of 
cells. You can extrude a coarse mesh, though, and then refine the 
resulting mesh -- it will then have more than one layer in z-direction 
in some locations, however.


Best
 W.

--

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

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Re: [deal.II] Understanding MeshWorker::mesh_loop order with adaptive refinement

2023-04-04 Thread Timo Heister 
Corbin,

Do you know if this problem is only present in 1d?



-- https://www.math.clemson.edu/~heister/

On Mon, Apr 3, 2023, 18:36 Corbin Foucart  wrote:

> Hello everyone,  I'm solving a 1D explicit DG-FEM problem and I've
> encountered behavior that I don't understand using MeshWorker: : mesh_loop.
> I'm using the MeshWorker: : assemble_own_interior_faces_both flag since I
> want to do work on each face
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> Use caution when opening links or attachments if you do not recognize the
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> Hello everyone,
>
> I'm solving a 1D explicit DG-FEM problem and I've encountered behavior
> that I don't understand using MeshWorker::mesh_loop.
>
>- I'm using the MeshWorker::assemble_own_interior_faces_both flag
>since I want to do work on each face corresponding to the same cell 
> interior
>- If the grid is created using typical GridGenerator calls, the order
>is exactly as I'd expect: first, work is done on the cell, then the faces
>(boundary or interior), followed by the next cell (further, all mass
>matrices are the same)
>- However, if I manually adapt the mesh by refining some cells, the
>order seems to change; the face work is done without respect to the cell
>interior last worked on
>
> I've attached a stripped-down program that illustrates this behavior on a
> toy mesh in 1D, as well as the output.
>
>- Ultimately, my goal is to assemble an inverse mass matrix on each
>cell, and apply it to a residual vector containing interior and face
>contributions (which can be done element-wise since the elements are
>FE_DGQ)
>- I was attempting to store the inverse via CopyData and then apply it
>in the copy worker.
>- However, I'm finding that due to the order of execution, I can't
>rely on the face work being done immediately after the cell work, and the
>inverse mass matrix stored to CopyData is often from another cell than the
>faces being worked on.
>- I could do the assembly and application of the inverse mass matrices
>separately, or store the inverse mass matrices in a map to the cell
>iterators, but I'm curious why this ordering occurs.
>
> Am I misunderstanding how mesh_loop is supposed to work? Any guidance
> would be appreciated!
>
> Corbin
>
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> .
>

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Re: [deal.II] Installation of Deal II hangs

2023-04-04 Thread Marc Fehling 
Hello Claudia,

have you considered using the prebuilt virtual machine image? A current 
deal.II release will be readily available for you without compilation.
https://www.dealii.org/download.html
https://www.math.clemson.edu/~heister/dealvm/

Of course, that doesn't solve the compilation problem. But if you are only 
interested in using deal.II and not changing its source, you should be fine!

Best,
Marc

On Tuesday, April 4, 2023 at 4:14:50 AM UTC-6 mallimac...@gmail.com wrote:

> When it hangs both the virtual machine and the computer hang, and it does 
> not finish the job. I set the maximum Ram I can set (about 5GB) and at 28% 
> of the make install the RAM reaches 99% occupied and the installation 
> hangs. Once the virtual machine gives me the error in the attached photo, 
> other times it gives me error and asks me to close the virtual machine. 
> If I call make -j1 it hangs at about the same point as the make install. 
>
> On Mon, Apr 3, 2023, 2:11 AM Wolfgang Bangerth  
> wrote:
>
>> On 4/2/23 06:48, Claudia mallimaci wrote:
>> > **
>> > 
>> > I tried many times to install the deal II library, but the installation 
>> hangs 
>> > always at the same point, and I don't understand the error. I followed 
>> the 
>> > read me indications, but it did not work. I attach the photos showing 
>> where 
>> > the installation hangs.
>>
>> Claudia: What happens when it hangs? Does it *eventually* finish after a 
>> long 
>> time? If you look at a memory monitor on your system, can you see whether 
>> it 
>> takes more memory than you have? Does it work if you call 'make -j1'?
>>
>> Best
>>   W.
>>
>> -- 
>> 
>> Wolfgang Bangerth  email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>
>> -- 
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>>
>

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[deal.II] deal.II Newsletter #248

2023-04-04 Thread 'Rene Gassmoeller' via deal.II User Group 
Hello everyone!

This is deal.II newsletter #248.
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:

#15024: Make FEPointEval expose same types as FEEval (proposed by jh66637; 
merged) https://github.com/dealii/dealii/pull/15024

#15023: instantiate mapped quadrature for dim=1 and spacedim=2 (proposed by 
jh66637; merged) https://github.com/dealii/dealii/pull/15023

#15022: Address some compile time issues. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/15022

#15019: Increment the majorest version number. (proposed by drwells) 
https://github.com/dealii/dealii/pull/15019

#15015: FEPointEvaluation: disconnect from MappingInfo (proposed by peterrum; 
merged) https://github.com/dealii/dealii/pull/15015

#15014: Clean up notions of CUDA in the codebase (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/15014

#15013: Enable vectorization over quadrature points in whole FEPointEvaluation 
(proposed by bergbauer) https://github.com/dealii/dealii/pull/15013

#15012: FEPointEvaluation::integrate: Choose better loop layout (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/15012

#15011: Work around nvcc compiler bug in 
mg_transfer_global_coarsening.templates.h (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/15011

#15010: Introduce helper Utilities::callable_member (proposed by sebproell) 
https://github.com/dealii/dealii/pull/15010

#15009: Check whether construct_multigrid_hierarchy is set ealier. (proposed by 
adamqc) https://github.com/dealii/dealii/pull/15009

#15008: Add Functions::SignedDistance::Rectangle (proposed by mschreter) 
https://github.com/dealii/dealii/pull/15008

#15007: Fix copy constructor of MappingQ (proposed by peterrum) 
https://github.com/dealii/dealii/pull/15007

#15006: CMake: fix variable name (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/15006

#15005: Add a test for GridTools::Cache::get_covering_rtree(). (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/15005

#15004: Minor doc updates in GridTools. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/15004

#15003: Use Kokkos for data structures in CUDA matrix-free framework (proposed 
by Rombur) https://github.com/dealii/dealii/pull/15003

#15002: Fix a unused variable compiler warning in tria.cc (proposed by 
masterleinad; merged) https://github.com/dealii/dealii/pull/15002

#15001: OSX tester does not pick up /rebuild (proposed by marcfehling; merged) 
https://github.com/dealii/dealii/pull/15001

#15000: Update SUNDIALS link in doc/readme.html (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/15000

#14999: Fix nodal and Gauss-type quadratures for dim = 0. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/14999

#14998: CMake: refactor repetitive option handling into two macros (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/14998

#14997: Explain the purpose of some computations in CellIDTranslator. (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/14997

#14995: MatrixFreeTools: fix some refs and const (proposed by sebproell; 
merged) https://github.com/dealii/dealii/pull/14995

#14993: CMake: Rename DEAL_II_NAMESPACE to DEAL_II_TARGET_NAME (proposed by 
tamiko; merged) https://github.com/dealii/dealii/pull/14993

#14992: CMake: prefer CMAKE_CXX_STANDARD and export cxx_std_?? COMPILE_FEATURES 
target property (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/14992

#14991: CMake: use POSITION_INDEPENDENT_CODE target property instead of setting 
-fPIC by hand (proposed by tamiko; merged) 
https://github.com/dealii/dealii/pull/14991

#14990: CMake: separate warning flags into DEAL_II_WARNING_FLAGS variable 
(proposed by tamiko; merged) https://github.com/dealii/dealii/pull/14990

#14989: Fix FEPointEvaluation for different n_q_points with same MappingInfo 
for different evaluators (proposed by bergbauer; merged) 
https://github.com/dealii/dealii/pull/14989

#14988: Rework the introduction to step-7. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/14988

#14987: Leave a hint in step-7. (proposed by bangerth) 
https://github.com/dealii/dealii/pull/14987

#14986: Step-70: remove unused variable (proposed by mschreter; merged) 
https://github.com/dealii/dealii/pull/14986

#14983: Change default `compression_level` of vtu output (proposed by 
c-p-schmidt) https://github.com/dealii/dealii/pull/14983

#14982: Compute values_of_array only once and optimize instructions (proposed 
by bergbauer; merged) https://github.com/dealii/dealii/pull/14982

#14981: Add benchmark for multgrid with global coarsening (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/14981

#14971: Create dealii::dealii target and add compile options (proposed by