Re: [deal.II] extract_surface_mesh() does not extract refined cells

2023-12-05 Thread Simon Wiesheier 
No worries :-)

Setting the boundary ids on the coarse grid did the trick (no need to do it
again on the refined grid).

A short follow-up:
After extracting the surface mesh (Triangulation<2,3>),
I want to get rid of the Z-coordinate to obtain a Triangulation<2>.
Unfortunately, GridGenerator::flatten_triangulation<2, 3, 2>(...)
does not work in the presence of hanging nodes.

Any workarounds for this issue?

Best,
Simon

Am Di., 5. Dez. 2023 um 21:48 Uhr schrieb Luca Heltai :

> By the way:
>
> Sorry if my reply was not too precise at the beginning, and if it sound
> harsh, but I cannot not run your code on my iPhone (yet), even though I’m
> working on it.
>
> :)
>
> Till then, may I suggest that you provide as much information as you can,
> if you want people to answer quickly? Asking people to download the code,
> put it somewhere where deal.II is available and then running it and
> debugging it is unlikely to produce a quick answer other than “can you tell
> us more?”.
>
> Luca
>
> Il giorno 5 dic 2023, alle ore 9:25 PM, Simon Wiesheier <
> simon.wieshe...@gmail.com> ha scritto:
>
> 
> Dear Luca,
>
> the program I provided writes the volume mesh as well as the surface mesh
> to vtk files.
> If you compare these files, for instance in paraview, you will see that
> the locally refined cells are not extracted.
>
> Best,
> Simon
>
> Am Di., 5. Dez. 2023 um 21:14 Uhr schrieb Luca Heltai <
> luca.hel...@gmail.com>:
>
>> Dear Simon,
>>
>> What do you mean by “demonstrates”? The function you refer to is supposed
>> to work with locally refined grids. What is the behavior you observe? What
>> error do you get?
>>
>> You will have to map dofs on the surface to dofs on the bulk manually.
>> The output of the function only returns a map of tria iterators to face
>> iterators, not dof to dof.
>>
>> Luca
>>
>> Il giorno 5 dic 2023, alle ore 2:23 PM, Simon 
>> ha scritto:
>>
>> Dear all,
>>
>>
>> attached is a minimal example which demonstrates that the function
>> "extract_surface_mesh()" in the GridGenerator namespace
>> does not extract refined cells.
>> That is, it seems to work only for globally refined meshes.
>> There is a comment in the implementation of this function:
>> // Create boundary mesh and mapping
>> // from only level(0) cells of the volume mesh.
>>
>> Since the documentation states nothing about the usage of this function
>> for adaptively
>> refined meshes (like it is done in flatten_triangulation, for instance),
>> I am not sure whether this is desired behavior or not.
>>
>> In my case, I probably do not need the full power of this function.
>> All I want to do is to "copy" the solution values on a surface of the
>> volume mesh
>> to a surface mesh, and to associate a DoFHandler object to the surface
>> mesh
>> that allows me to do further postprocessing.
>> So I do not care about the boundary and manifold id as well
>> as the return type, however, my volume mesh may contain hanging nodes.
>>
>>
>>
>> Best regards,
>> 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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>> "deal.II User Group" group.
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>> email to dealii+unsubscr...@googlegroups.com.
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>> https://groups.google.com/d/msgid/dealii/f3252992-4761-41b1-a691-05c5265f89bfn%40googlegroups.com
>> 
>> .
>> 
>>
>> --
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>> 
>> .
>>
>
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>

Re: [deal.II] extract_surface_mesh() does not extract refined cells

2023-12-05 Thread Luca Heltai 
By the way: Sorry if my reply was not too precise at the beginning, and if it sound harsh, but I cannot not run your code on my iPhone (yet), even though I’m working on it. :) Till then, may I suggest that you provide as much information as you can, if you want people to answer quickly? Asking people to download the code, put it somewhere where deal.II is available and then running it and debugging it is unlikely to produce a quick answer other than “can you tell us more?”.LucaIl giorno 5 dic 2023, alle ore 9:25 PM, Simon Wiesheier  ha scritto:Dear Luca,the program I provided writes the volume mesh as well as the surface mesh to vtk files.If you compare these files, for instance in paraview, you will see that the locally refined cells are not extracted.Best,SimonAm Di., 5. Dez. 2023 um 21:14 Uhr schrieb Luca Heltai :Dear Simon, What do you mean by “demonstrates”? The function you refer to is supposed to work with locally refined grids. What is the behavior you observe? What error do you get?You will have to map dofs on the surface to dofs on the bulk manually. The output of the function only returns a map of tria iterators to face iterators, not dof to dof.LucaIl giorno 5 dic 2023, alle ore 2:23 PM, Simon  ha scritto:Dear all,attached is a minimal example which demonstrates that the function "extract_surface_mesh()" in the GridGenerator namespace does not extract refined cells. That is, it seems to work only for globally refined meshes. There is a comment in the implementation of this function:// Create boundary mesh and mapping// from only level(0) cells of the volume mesh.Since the documentation states nothing about the usage of this function for adaptivelyrefined meshes (like it is done in flatten_triangulation, for instance), I am not sure whether this is desired behavior or not.In my case, I probably do not need the full power of this function. All I want to do is to "copy" the solution values on a surface of the volume mesh to a surface mesh, and to associate a DoFHandler object to the surface meshthat allows me to do further postprocessing.So I do not care about the boundary and manifold id as wellas the return type, however, my volume mesh may contain hanging nodes.Best regards,Simon



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Re: [deal.II] extract_surface_mesh() does not extract refined cells

2023-12-05 Thread Luca Heltai 
The fact that the vtk file does not contain the refined cells does not necessarily mean that they are not extracted. If you look at the source code of the function, you will see that it generates the coarse surface mesh based on the coarse boundary ids to extract, and then it loops over all cells, and if they are refined, it flags the corresponding surface cells for refinement till the refinementa are the same. You are setting boundary ids on the refined grid (not on the coarse grid), and these are not there on the coarse cells, so there is nothing to refine when the bulk cell is refined. Can you try removing the set_boundary_id, and verify if this generates a grid with refinement ?This could be the issue. The coarse ids do not match the fine ids, and therefore are not extracted. Alternatively, to keep the boundary ids, you should set the boundary ids of the parent faces  as well, for the algorithm to find them on the coarse level. LucaIl giorno 5 dic 2023, alle ore 21:25, Simon Wiesheier  ha scritto:Dear Luca,the program I provided writes the volume mesh as well as the surface mesh to vtk files.If you compare these files, for instance in paraview, you will see that the locally refined cells are not extracted.Best,SimonAm Di., 5. Dez. 2023 um 21:14 Uhr schrieb Luca Heltai :Dear Simon, What do you mean by “demonstrates”? The function you refer to is supposed to work with locally refined grids. What is the behavior you observe? What error do you get?You will have to map dofs on the surface to dofs on the bulk manually. The output of the function only returns a map of tria iterators to face iterators, not dof to dof.LucaIl giorno 5 dic 2023, alle ore 2:23 PM, Simon  ha scritto:Dear all,attached is a minimal example which demonstrates that the function "extract_surface_mesh()" in the GridGenerator namespace does not extract refined cells. That is, it seems to work only for globally refined meshes. There is a comment in the implementation of this function:// Create boundary mesh and mapping// from only level(0) cells of the volume mesh.Since the documentation states nothing about the usage of this function for adaptivelyrefined meshes (like it is done in flatten_triangulation, for instance), I am not sure whether this is desired behavior or not.In my case, I probably do not need the full power of this function. All I want to do is to "copy" the solution values on a surface of the volume mesh to a surface mesh, and to associate a DoFHandler object to the surface meshthat allows me to do further postprocessing.So I do not care about the boundary and manifold id as wellas the return type, however, my volume mesh may contain hanging nodes.Best regards,Simon



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Re: [deal.II] extract_surface_mesh() does not extract refined cells

2023-12-05 Thread Simon Wiesheier 
Dear Luca,

the program I provided writes the volume mesh as well as the surface mesh
to vtk files.
If you compare these files, for instance in paraview, you will see that the
locally refined cells are not extracted.

Best,
Simon

Am Di., 5. Dez. 2023 um 21:14 Uhr schrieb Luca Heltai :

> Dear Simon,
>
> What do you mean by “demonstrates”? The function you refer to is supposed
> to work with locally refined grids. What is the behavior you observe? What
> error do you get?
>
> You will have to map dofs on the surface to dofs on the bulk manually. The
> output of the function only returns a map of tria iterators to face
> iterators, not dof to dof.
>
> Luca
>
> Il giorno 5 dic 2023, alle ore 2:23 PM, Simon 
> ha scritto:
>
> Dear all,
>
>
> attached is a minimal example which demonstrates that the function
> "extract_surface_mesh()" in the GridGenerator namespace
> does not extract refined cells.
> That is, it seems to work only for globally refined meshes.
> There is a comment in the implementation of this function:
> // Create boundary mesh and mapping
> // from only level(0) cells of the volume mesh.
>
> Since the documentation states nothing about the usage of this function
> for adaptively
> refined meshes (like it is done in flatten_triangulation, for instance),
> I am not sure whether this is desired behavior or not.
>
> In my case, I probably do not need the full power of this function.
> All I want to do is to "copy" the solution values on a surface of the
> volume mesh
> to a surface mesh, and to associate a DoFHandler object to the surface mesh
> that allows me to do further postprocessing.
> So I do not care about the boundary and manifold id as well
> as the return type, however, my volume mesh may contain hanging nodes.
>
>
>
> Best regards,
> 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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Re: [deal.II] extract_surface_mesh() does not extract refined cells

2023-12-05 Thread Luca Heltai 
Dear Simon, What do you mean by “demonstrates”? The function you refer to is supposed to work with locally refined grids. What is the behavior you observe? What error do you get?You will have to map dofs on the surface to dofs on the bulk manually. The output of the function only returns a map of tria iterators to face iterators, not dof to dof.LucaIl giorno 5 dic 2023, alle ore 2:23 PM, Simon  ha scritto:Dear all,attached is a minimal example which demonstrates that the function "extract_surface_mesh()" in the GridGenerator namespace does not extract refined cells. That is, it seems to work only for globally refined meshes. There is a comment in the implementation of this function:// Create boundary mesh and mapping// from only level(0) cells of the volume mesh.Since the documentation states nothing about the usage of this function for adaptivelyrefined meshes (like it is done in flatten_triangulation, for instance), I am not sure whether this is desired behavior or not.In my case, I probably do not need the full power of this function. All I want to do is to "copy" the solution values on a surface of the volume mesh to a surface mesh, and to associate a DoFHandler object to the surface meshthat allows me to do further postprocessing.So I do not care about the boundary and manifold id as wellas the return type, however, my volume mesh may contain hanging nodes.Best regards,Simon



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The Storynory podcast offers short weekly audiobooks based on folklore and 
fairy tales from around the world. Popular retold tales include stories by 
The Brothers Grimm, Hans Christian Andersen, and Aesop.

Try this Library Finder to find the library nearest to you that uses 
OverDrive. If your local library does not use Overdrive, ask them if they 
offer a similar audiobook platform. Most libraries do, and they will be 
happy to get you set up!

Reading can be an expensive hobby. Sure, libraries still exist, but fewer 
people seem to use them. Instead, many opt for buying ebooks straight to 
their Kindles and iPads or, as has become increasingly popular in recent 
years, tuning in to an audiobook on Audible.

The thing is, Audible isn't cheap. While $15 a month for an otherwise $20+ 
audiobook might seem like a steal, there are plenty of other audiobook apps 
out there that are either completely free or at least much

[deal.II] Adadaniki Astulu Ante Pasupu Kun

2023-12-05 Thread Perry Dearmas 
Adadaniki Astulu Ante Pasupu Kun

*Download* https://t.co/Ll091buEyr


eebf2c3492

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Re: [deal.II] Reporting issue with repo

2023-12-05 Thread Daniel Arndt 
Alex,

grid_reordering,h was removed in
https://github.com/dealii/dealii/commit/fd0c356263d7115ebf58fcea15d0412a32da199e
(which isn't part of any release yet).

Best,
Daniel

On Tue, Dec 5, 2023 at 7:47 AM Alex Quinlan 
wrote:

> Dear deal.ii devs,
>
> I cloned the deal.ii repo yesterday and found that the header file
> grid_reorder.h has been removed from include/deal.II/grid/.
>
> I searched the logs and the documentation and it appeared that the file
> *should* still be there, though I'm not 100% sure of that.
>
> I am not very savvy with git, so I thought I would just post here.  Is
> this the correct place to make this kind of report, or is there a preferred
> process that I should take in the future?
>
> Thanks,
> Alex
>
> --
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> 
> .
>

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[deal.II] extract_surface_mesh() does not extract refined cells

2023-12-05 Thread Simon 
Dear all,


attached is a minimal example which demonstrates that the function 
"extract_surface_mesh()" in the GridGenerator namespace 
does not extract refined cells. 
That is, it seems to work only for globally refined meshes. 
There is a comment in the implementation of this function:
// Create boundary mesh and mapping
// from only level(0) cells of the volume mesh.

Since the documentation states nothing about the usage of this function for 
adaptively
refined meshes (like it is done in flatten_triangulation, for instance), 
I am not sure whether this is desired behavior or not.

In my case, I probably do not need the full power of this function. 
All I want to do is to "copy" the solution values on a surface of the 
volume mesh 
to a surface mesh, and to associate a DoFHandler object to the surface mesh
that allows me to do further postprocessing.
So I do not care about the boundary and manifold id as well
as the return type, however, my volume mesh may contain hanging nodes.



Best regards,
Simon

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#include 
#include 
#include 
#include 

#include 

#include 

using namespace dealii;

int main()
{

  Triangulation<3> tria, triaTmp;
  
  dealii::Point<3> center;
  double radius = 2.5;
  unsigned int boundaryID = 2;

  GridGenerator::hyper_cube_with_cylindrical_hole(triaTmp,
radius,
7.5,
2.0,
1,
false);
  triaTmp.refine_global(2);

  // symmetry in global Z
  std::set::active_cell_iterator> cellsToRemove;
  for (const auto  : triaTmp.active_cell_iterators())
if ( cell->center()[2] > 1.0)
  cellsToRemove.insert(cell);
  dealii::GridGenerator::create_triangulation_with_removed_cells(triaTmp,
  cellsToRemove,
  tria);
  // one local refinement along hole
  for (const auto  : tria.active_cell_iterators())
for (unsigned int f = 0; f < dealii::GeometryInfo<3>::faces_per_cell; ++f)
  {
dealii::Point<3> faceCenter(cell->face(f)->center());
faceCenter[2] = 0.0;
if ((std::abs(center.distance(faceCenter)) < radius))
  cell->set_refine_flag();
  }
  tria.execute_coarsening_and_refinement();

  // set boundary ID for surface mesh
  for (const auto  : tria.active_cell_iterators())
for (unsigned int f = 0; f < dealii::GeometryInfo<3>::faces_per_cell; ++f)
  if(std::abs(cell->face(f)->center()[2]) < 1e-5 && cell->face(f)->at_boundary())
cell->face(f)->set_boundary_id(boundaryID);

  // extract surface mesh
  dealii::Triangulation<2, 3> tria2d;
  dealii::GridGenerator::extract_boundary_mesh(
tria,
tria2d,
std::set{boundaryID});

  // output the volume mesh
  std::ofstream file("tria.vtk");
  dealii::GridOut   gridOut;
  dealii::GridOutFlags::Vtk vtkFlags(true, true, true, false);
  gridOut.set_flags(vtkFlags);
  gridOut.write_vtk(tria, file);

  // and the surface mesh
  std::ofstream file2d("tria2d.vtk");
  gridOut.write_vtk(tria2d, file2d);

  return 0;
}

[deal.II] Reporting issue with repo

2023-12-05 Thread Alex Quinlan 
Dear deal.ii devs,

I cloned the deal.ii repo yesterday and found that the header file 
grid_reorder.h has been removed from include/deal.II/grid/.

I searched the logs and the documentation and it appeared that the file 
*should* still be there, though I'm not 100% sure of that.

I am not very savvy with git, so I thought I would just post here.  Is this 
the correct place to make this kind of report, or is there a preferred 
process that I should take in the future?

Thanks,
Alex

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[deal.II] Re: Issue with intersection of two meshes with curved boundaries

2023-12-05 Thread Marco Feder 
After debugging this particular instance, it turns out the issue is related 
to the CGAL kernels used by deal.II. In particular, with CGAL it's possible 
to rely on the so-called "exact computation paradigm" (a brief explanation 
is available here: https://www.cgal.org/exact.html). In the 
dealii::CGALWrappers namespace this kernel is **not** used for the 
quad-quad intersections, which is the one relevant for this example. 
Switching to exact kernels allows to keep the error around 1e-13 for most 
of the refinement cycles with this particular configuration. 

Maybe it could be nice to provide a policy that allows the used to simply 
tweak the CGAL kernels that are employed.


Best,
Marco

Il giorno domenica 26 novembre 2023 alle 09:58:51 UTC+1 najwaa...@gmail.com 
ha scritto:

> Dear team,
>
> I am adding the two domain meshes (cycle 0) in .vtk format for a better 
> understanding of what type of grid I am working with
>
>
> [image: mesh_intersection.png]
>
>
> On Saturday, November 25, 2023 at 10:50:25 AM UTC+3 Najwa Alshehri wrote:
>
>> Dear developers and users,
>>
>>  
>>
>> I have two meshes one is immersed in the other. I wanted to find the 
>> intersection between the two meshes, so I used the following function.
>>
>>  
>>
>> NonMatching::compute_intersection(omega_grid_tools_cache,
>>
>>   omega2_grid_tools_cache,
>>
>>   4,  // degree
>>
>>   1e-20); // to
>>
>>
>> include header 
>> 
>>
>> source code 
>> 
>>
>>
>> This function uses CGAL to find a quadrature formula to integrate exactly 
>> on the intersection of two meshes which neglecte intersections of areas 
>> with tolerance smaller than “tol“ that one chooses and gives a quadrature 
>> formula on the triangulation of the intersection area that integrates 
>> exactly polynomials of a specific degree ( which allows maximum degree of 
>> 4).
>>
>>
>> Say that I want to integrate, on the intersection area, a polynomial of 
>> order 4.
>>
>>  
>>
>> I noticed that If I am considering a circular immersed domain (unlike 
>> square or L-shaped domains), after a few cycles, the quadrature formula is 
>> not accurate enough. To be precise, I find that the sum of the weights of 
>> the quadrature formula defined on the triangulation of the exact 
>> intersection of the two meshes does not sum up (up to a tolerance) to the 
>> measure of the domain. When this occurs, the solution that is solved by 
>> evaluating the integral considering the quadrature formula on the exact 
>> intersection is no longer correct and the error starts to diverge in the 
>> later cycles after this point.
>>
>>  
>>
>> Moreover, the difference gets large suddenly, in one cycle, the 
>> difference was relatively smaller (1e-13), and in the next, it is much 
>> larger (1e-8) as can be seen in the attached plot (Plot shows the 
>> difference between the sum of the weights on the whole domain defined on 
>> the triangulation of the exact intersection of the two meshes and the 
>> measure of the domain under uniform refinement of the mesh). 
>>
>>  
>>
>> Any suggestion on what could be the issue and what should I do to fix it?
>>
>>  
>>
>> Thanks
>>
>> Najwa
>>
>

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