[deal.II] Helping collaborators write a cluster module for deal.II

[Wells, David]

Hi everyone,

I'm working with a group at another university on a deal.II-powered project 
(yay). I'd like to set things up as a module (i.e., do module load 
dealii/9.5.1) so that everyone there is using the same version of everything.

Are there any published versions of deal.II modules for various Linux 
distributions? Every cluster is different but it would be super helpful to see 
what other people have done to install deal.II and dependencies in this 
situation.

Best,
David Wells

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Re: [deal.II] how to treat the intersection point at the first and second kined bcs

[Wells, David]

Hi there,

People use many different boundary conditions with deal.II - e.g., step-22 sets 
the normal component of the normal stress to zero, whereas many other tutorial 
programs use Dirichlet or Neumann boundary conditions.

Which two boundary conditions are you referring to?

Best,
David Wells


From: dealii@googlegroups.com  on behalf of 
ztdep...@gmail.com 
Sent: Monday, November 13, 2023 12:48 AM
To: deal.II User Group 
Subject: [deal.II] how to treat the intersection point at the first and second 
kined bcs

Since the two kinds of bc has one common nodes. I want to know which one is 
impelented in idealii.

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Re: [deal.II] Re: deal.ii step-33 tests

[Wells, David]

Hi Lorenzo,

What an interesting coincidence - I saw a student show me the same error 
message last week. This is definitely a bug in deal.II!

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Lore 
Micalizzi 
Sent: Wednesday, March 8, 2023 9:42 AM
To: deal.II User Group 
Subject: [deal.II] Re: deal.ii step-33 tests

You don't often get email from lorenzomicali...@gmail.com. Learn why this is 
important

I also would like to point out that make test did not spot any problem

Test project /home/lorenzo/Desktop/GIT/dealii_source/build/tests/quick_tests
  Start  1: step.debug
  Start  2: step.release
  Start  3: affinity.debug
  Start  4: mpi.debug
  Start  5: tbb.debug
  Start  6: p4est.debug
  Start  7: step-petsc.debug
  Start  8: step-slepc.debug
 1/19 Test  #3: affinity.debug ...   Passed   27.24 sec
  Start  9: step-trilinos.debug
 2/19 Test  #5: tbb.debug    Passed   27.24 sec
  Start 10: step-metis.debug
 3/19 Test  #4: mpi.debug    Passed   27.56 sec
  Start 11: lapack.debug
 4/19 Test  #6: p4est.debug ..   Passed   37.08 sec
  Start 12: umfpack.debug
 5/19 Test  #7: step-petsc.debug .   Passed   39.04 sec
  Start 13: gsl.debug
 6/19 Test  #8: step-slepc.debug .   Passed   39.77 sec
  Start 14: hdf5.debug
 7/19 Test  #2: step.release .   Passed   44.59 sec
  Start 15: arpack.debug
 8/19 Test #11: lapack.debug .   Passed   25.24 sec
  Start 16: assimp.debug
 9/19 Test #14: hdf5.debug ...   Passed   14.94 sec
  Start 17: scalapack.debug
10/19 Test  #1: step.debug ...   Passed   54.74 sec
  Start 18: boost_zlib.debug
11/19 Test #13: gsl.debug    Passed   17.95 sec
  Start 19: gmsh.debug
12/19 Test #10: step-metis.debug .   Passed   32.16 sec
13/19 Test  #9: step-trilinos.debug ..   Passed   39.74 sec
14/19 Test #12: umfpack.debug    Passed   34.97 sec
15/19 Test #16: assimp.debug .   Passed   23.83 sec
16/19 Test #18: boost_zlib.debug .   Passed   23.89 sec
17/19 Test #15: arpack.debug .   Passed   35.10 sec
18/19 Test #19: gmsh.debug ...   Passed   22.70 sec
19/19 Test #17: scalapack.debug ..   Passed   25.61 sec

100% tests passed, 0 tests failed out of 19

Total Test time (real) =  80.35 sec
Built target test
Il giorno mercoledì 8 marzo 2023 alle 14:47:33 UTC+1 Lore Micalizzi ha scritto:
Dear deal.ii developers,

I'm Lorenzo, a PhD student in numerical analysis at Universität Zürich.

Recently, deal.ii has been recommended to me by some colleagues.
I found it interesting and I've started playing with it.

I installed it and I tried some tutorial examples which were provided.
I did not try all of them. However, they all seem to work but step-33.
The file is normally compiled but I get an error during the execution.

I'm wondering whether you experienced something similar and could help me.

NB:
-> I installed dealii-9.4.2 (but I don't think this is the problem, it's not 
too old as a version)
-> My compilation flags fulfill the dependecies of all the steps but 62, 64, 
71, 77

I attach
- what's printed in the terminal when I execute step 33, see error.txt
- a quick sketch of what I did to install the library, see installation.txt
- all what has been printed in the shell during the installation, see 
terminal.txt (I don't know if that can be useful, I did not get any error 
message)

Thanks in advance and sorry for having bothered you.

Have a nice day,

Lorenzo

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Re: [deal.II] possible to shift a support point (no vertex) of a triangulation?

[Wells, David]

Hi Simon,

Correct - we don't have a way to shift support points like that on one 
particular element.

Another possibility would be to add a constraint (i.e., with AffineConstraints) 
enforcing that the FE solution sums to zero at that point. You would have to do 
some work to find the cell on which the point is and evaluate the shape 
functions at that point but it would work for any order of element and any 
point location.

Best,
David

From: dealii@googlegroups.com  on behalf of Simon 

Sent: Tuesday, February 7, 2023 5:05 AM
To: deal.II User Group 
Subject: [deal.II] possible to shift a support point (no vertex) of a 
triangulation?

Dear all,

I am approximating a scalar function F of one single argument by discretizing 
the argument over the interval [lb;ub].
Then, I interpolate the nodal values utilizing VectorTools::interpolate.
To generate the triangulation (a line), I call
GridGenerator::hyber_cube(triangulation, lb, ub) and refine globally up to a 
desired level.
Either FE_Q(1) or FE_Q(2) elements are used.

The issue is that there is one 'point' p in [lb;ub] for which the function must 
be Zero.
In case of FE_Q(1) elements, I simply shifted the vertex which is closest to p, 
to p.
For FE_Q(2) elements, the closest point to p is a vertex *or* the support point 
in the center of the element.
I think it is not possible to 'shift' a support point as the triangulation is 
made up of vertices only, right?

Best
Simon

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Re: [deal.II] build error with AppleClang 14.0.0.14000029

[Wells, David]

Hi Rahul,

This is a bug in deal.II - we wrote "long int" where we should have written 
"types::suitesparse_index", which won't work on an ARM chip (apparently long 
long means something different there).

I wrote a patch to fix this - see

https://github.com/dealii/dealii/pull/14720

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Rahul 
Gopalan Ramachandran 
Sent: Tuesday, January 24, 2023 8:51 AM
To: deal.II User Group 
Subject: [deal.II] build error with AppleClang 14.0.0.1429

Hello All,

There seems to be a compilation error popping up after updating the Apple clang 
compilers with the new MacOs update (compiler : AppleClang 14.0.0.1429). 
Here is the error,

/softwares/dealii-9.4.1/source/lac/sparse_direct.cc:104:14: error: non-const 
lvalue reference to type 'vector>' cannot bind to a value 
of unrelated type 'vector>'
tmp.swap(Ap);

I am reaching out to know if anyone else tried recompiling dealii after 
updating to MacOs Ventura in a Apple Silicon machine? Any suggestions?

Regards,
Rahul

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Re: [deal.II] Missing libumfpack.so when compiling deal-ii

[Wells, David]

Hi there,

It sounds like gmsh (or one of gmsh's dependencies) is linked against an older 
version of umfpack - you can probably get around the issue by either 
recompiling gmsh (and its dependencies, which is a pretty large number of 
packages) or, if you don't plan on using it (its only an optional dependency 
for us) uninstalling it.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of J 

Sent: Friday, November 25, 2022 5:32 AM
To: deal.II User Group 
Subject: [deal.II] Missing libumfpack.so when compiling deal-ii

You don't often get email from americandisc...@gmail.com. Learn why this is 
important
When compiling dealii from the arch AUR I get an error during quick testing 
after complilation that libumfpack.so.5 is missing when testing gmsh. I have 
the boost libraries installed and I have libumpack.so and libumfpack.so.6 in 
/usr/lib. Does anyone know if this is an issue with the dealii wanting a 
certain version of the boost libraries or maybe the pkgbuild needs to be 
changed in the AUR? Is there a version of boost I need to downgrade to? Or 
maybe I need to recompile gmsh? Just don't want to have to attempt multiple 
compiles to find the source of the problem if someone already has an idea of 
what the problem could be.

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Re: [deal.II] Can I use 3D prism elements (extruded triangles) in deal.ii?

[Wells, David]

Hi Amit,

If you are interested in using symmetry then I suspect you may also want to use 
periodic boundary conditions on the "internal" faces of the octant. For an 
example of how this works (e.g., periodic boundary conditions containing a 
rotation) check out step-45:

https://dealii.org/developer/doxygen/deal.II/step_45.html

Best,
David

From: dealii@googlegroups.com  on behalf of Bruno 
Turcksin 
Sent: Friday, June 24, 2022 9:33 AM
To: deal.II User Group 
Subject: Re: [deal.II] Can I use 3D prism elements (extruded triangles) in 
deal.ii?

Amit,

I think that 
GridGenerator::quarter_hyper_shell
 is what you want.

Best,

Bruno
On Friday, June 24, 2022 at 9:02:11 AM UTC-4 Paras Kumar wrote:
HI Amit,

Focusing on the question of mesh generation, it is possible to generate an 
automated HEX mesh using Gmsh, but since that mesh is based on Delaunay based 
approaches, quality may not be very good. See discussions in this thread: 
https://groups.google.com/g/dealii/c/o_xXAur2Ao8/m/vlAjFs5ECQAJ
Alternatively, if you just want to mesh this specific geometry, you could also 
get a structured (good looking) HEX mesh using the transfinite mesh approach 
available in Gmsh.

In my limited knowledge, cf. 
[https://www.dealii.org/current/doxygen/deal.II/group__simplex.html], it seems 
that the simplex support is still experimental. As mentioned in the link, it 
might be helpful to look at the tests/simplex folder. The developers can maybe 
provide more precise answer here.

Best,
Paras




On Fri, Jun 24, 2022 at 2:19 PM Amit Singh  wrote:
Hi.
I am considering deal.ii for some nonlinear elasticity and fracture analysis.
>From what I read in the documentation, deal.ii supports hexahedral elements 
>much better than tetrahedral elements. My geometry looks as shown in the 
>attached picture. The actual geometry is a boolean difference of a big sphere 
>and a small sphere. But to exploit symmetry I am considering only one-eighth 
>of the sphere.

 I am struggling to create a mesh that has only hexahedral elements. The best I 
was able to attain was a vast majority of the elements were hexahedral but 
there were some prism elements at the poles.

Therefore, my question is can I use prism elements in deal.ii? (Or if there is 
a clever way to mesh this geometry with just hexahedral elements kindly let me 
know.)

Regards,
Amit



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Re: [deal.II] Tensor product polynomials

[Wells, David]

Hi Giselle,

What do you mean by "the hh file is not recognized in the cc file" - is there a 
specific error message this refers to?

In general, if you need to implement a new finite element, you will need to 
write some code. Can you compile any program that depends on deal.II right now?

Best,
David

From: dealii@googlegroups.com  on behalf of Giselle 
Sosa Jones 
Sent: Wednesday, June 22, 2022 10:45 AM
To: dealii@googlegroups.com 
Subject: Re: [deal.II] Tensor product polynomials

Hi David,

I've tried updating my C++ compiler and recompiling deal.II, but I have the 
same error. It is as if the hh file is not recognized in the cc file. I know 
this is a long shot, but do you happen to have any other suggestions? Maybe 
there is an easier way to create this space that I need?

Thank you!

Best,
Giselle

On Tue, May 31, 2022 at 4:28 PM Wells, David 
mailto:drwe...@email.unc.edu>> wrote:
Hi Gisselle,

This error message occurs when you use a very old (probably GCC 4.8 or 4.9) C++ 
compiler with a version of deal.II built with a newer C++ compiler (or vice 
versa). A sure fix is to make sure you use the same compilers both for your 
code and the library. In practice, though, the ABI change occurred in GCC 5 so 
combining any two newer versions is typically okay.

Best,
David

From: dealii@googlegroups.com<mailto:dealii@googlegroups.com> 
mailto:dealii@googlegroups.com>> on behalf of Giselle 
Sosa Jones mailto:giselle1...@gmail.com>>
Sent: Tuesday, May 31, 2022 11:55 AM
To: deal.II User Group mailto:dealii@googlegroups.com>>
Subject: Re: [deal.II] Tensor product polynomials

You don't often get email from 
giselle1...@gmail.com<mailto:giselle1...@gmail.com>. Learn why this is 
important<https://aka.ms/LearnAboutSenderIdentification>
Hello,

I sent this message a while ago and things became clearer for me, but I am 
still not able to create the spaces that I want. My goal is to create local 
spaces that look like this: Q_{k-1,k,k} \times Q_{k,k-1,k} \times Q_{k,k,k-1}, 
for k \geq 1.This is what I am currently doing:

- Created my own class of polynomials similar to the deal.II class 
PolynomialsRaviartThomas, but with the polynomial degrees as described above.
- Created my own class (FE_RTProj) for a finite element space similar to the 
one called FE_DGRaviartThomas. This is a derived class from FE_DGVector and the 
polynomial type is the one created in the item above.

My code does not even compile since I get error messages like: error: undefined 
reference to 'FE_RTProj::FE_RTProj<2, 2>::get_name[abi:cxx11]() const. The 
function get_name is defined in the FE_RTProj h and cc files (I basically 
copied from  FE_DGRaviartThomas). I am not sure if this is a C++ issue and/or 
if there is an easier way of doing this.

Any help is highly appreciated!

Best,
Giselle Sosa Jones

On Tuesday, August 31, 2021 at 9:59:55 a.m. UTC-5 Giselle Sosa Jones wrote:
Thank you, Dr. Bangerth, I think these extra comments clarify it for me.

Best,
Giselle

On Monday, August 30, 2021 at 8:15:16 p.m. UTC-5 Wolfgang Bangerth wrote:
On 8/28/21 4:52 PM, Giselle Sosa Jones wrote:
>
> I need to create a local space of polynomials in 3D of the form
> Q_{k-1,k,k} \times Q_{k,k-1,k} \times Q_{k,k,k-1}. This space is very
> similar to the DG Raviart-Thomas space, with the difference that the
> polynomial order of each component is one order lower in the
> corresponding direction. I was looking at the file
> polynomials_raviart_thomas.cc to get an idea of how to create them but I
> am a bit lost. Can someone offer a suggestion?

Giselle -- can you be specific about which part you have trouble with?
I've tried to improve the documentation of the key function of that
class a bit:
https://github.com/dealii/dealii/pull/12726

Best
Wolfgang

--

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

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Re: [deal.II] Tensor product polynomials

[Wells, David]

Hi Gisselle,

This error message occurs when you use a very old (probably GCC 4.8 or 4.9) C++ 
compiler with a version of deal.II built with a newer C++ compiler (or vice 
versa). A sure fix is to make sure you use the same compilers both for your 
code and the library. In practice, though, the ABI change occurred in GCC 5 so 
combining any two newer versions is typically okay.

Best,
David

From: dealii@googlegroups.com  on behalf of Giselle 
Sosa Jones 
Sent: Tuesday, May 31, 2022 11:55 AM
To: deal.II User Group 
Subject: Re: [deal.II] Tensor product polynomials

You don't often get email from giselle1...@gmail.com. Learn why this is 
important
Hello,

I sent this message a while ago and things became clearer for me, but I am 
still not able to create the spaces that I want. My goal is to create local 
spaces that look like this: Q_{k-1,k,k} \times Q_{k,k-1,k} \times Q_{k,k,k-1}, 
for k \geq 1.This is what I am currently doing:

- Created my own class of polynomials similar to the deal.II class 
PolynomialsRaviartThomas, but with the polynomial degrees as described above.
- Created my own class (FE_RTProj) for a finite element space similar to the 
one called FE_DGRaviartThomas. This is a derived class from FE_DGVector and the 
polynomial type is the one created in the item above.

My code does not even compile since I get error messages like: error: undefined 
reference to 'FE_RTProj::FE_RTProj<2, 2>::get_name[abi:cxx11]() const. The 
function get_name is defined in the FE_RTProj h and cc files (I basically 
copied from  FE_DGRaviartThomas). I am not sure if this is a C++ issue and/or 
if there is an easier way of doing this.

Any help is highly appreciated!

Best,
Giselle Sosa Jones

On Tuesday, August 31, 2021 at 9:59:55 a.m. UTC-5 Giselle Sosa Jones wrote:
Thank you, Dr. Bangerth, I think these extra comments clarify it for me.

Best,
Giselle

On Monday, August 30, 2021 at 8:15:16 p.m. UTC-5 Wolfgang Bangerth wrote:
On 8/28/21 4:52 PM, Giselle Sosa Jones wrote:
>
> I need to create a local space of polynomials in 3D of the form
> Q_{k-1,k,k} \times Q_{k,k-1,k} \times Q_{k,k,k-1}. This space is very
> similar to the DG Raviart-Thomas space, with the difference that the
> polynomial order of each component is one order lower in the
> corresponding direction. I was looking at the file
> polynomials_raviart_thomas.cc to get an idea of how to create them but I
> am a bit lost. Can someone offer a suggestion?

Giselle -- can you be specific about which part you have trouble with?
I've tried to improve the documentation of the key function of that
class a bit:
https://github.com/dealii/dealii/pull/12726

Best
Wolfgang

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www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: Cannot find the header files when compiling with WSL Linux distributive in VS code

[Wells, David]

Hello there,

Sorry for the long delay in the reply. If you didn't figure this out yet: look 
under

https://launchpad.net/~ginggs/+archive/ubuntu/deal.ii-9.3.0-backports

that is linked to from the 'ubuntu' section of 
https://www.dealii.org/download.html . A PPA contains packages outside the 
normal distribution channel. You can follow the directions at the first link to 
add the new PPA and download deal.II.


@keassyguang did those instructions work for you?

Best,
Davd

From: dealii@googlegroups.com  on behalf of Jiang Hu 

Sent: Friday, January 28, 2022 8:09 PM
To: dealii@googlegroups.com 
Subject: Re: [deal.II] Re: Cannot find the header files when compiling with WSL 
Linux distributive in VS code

Hi Raghunandan,

what is PPA? I am trying to set up in vscode, would like to know.

Thanks

Martin


On Mon, 17 Jan 2022 at 00:21, Raghunandan Pratoori 
mailto:r...@iastate.edu>> wrote:
Hi,

I use VS Code with WSL. I followed the instructions on these 2 pages and was 
able to get it to work -
https://code.visualstudio.com/docs/cpp/config-wsl
https://code.visualstudio.com/docs/cpp/cmake-linux

Also, how did you install deal.ii in wsl? I used the PPA and it took care of 
all the paths to be added.

Best,
Raghunandan.



On Sunday, January 16, 2022 at 2:13:26 AM UTC-6 keassyguang wrote:

Hi, everyone. I'm interested in deal.ii, but I did have trouble configuring the 
deal.ii.

I am trying to compile the program for Linux in VS code (version 1.63.2) using 
WSL (Windows Subsystem for Linux) ubuntu 20.04.3. I successfully compile the 
"Hello, World!" program, but when I try to compile the tutorial programs shown 
in dell.ii documentation, such as the step-1, the compilation terminated with 
an error message "No such file or directory". Then, the system includePath in 
VS code has been set to "/usr/include/**" and other libs as shown in the below 
figures, however, it dosenot work.

[1.png][2.png]

Later, I manually edit some head files. For example, as shown in the below 
figure, I know the "Kokkos_MasterLock.hpp" file is in the directory of 
"/usr/include/trilinos", so I modified the 55th line of "Kokkos_Core_fwd.hpp" 
file by adding the "trilions" directory into the path "#include 
" (the original is "#include 
"). After that, the compiler can find the 
"Kokkos_MasterLock.hpp" file, however, the compilation terminated with another 
new file named "Kokkos_Macros.hpp". Truly, I can edit the path as the 
aforementioned method, it is impossible to edit all the files using this way. 
So, can someone tell me how to compile the program for Linux in VS code using 
WSL? It will be of great help to me.

[3.png][4.png][5.png]

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Re: [deal.II] Re: Mesh export, high order

[Wells, David]

Hi,

Unlike a lot of FE software deal.II does not actually store, e.g., 27 points 
for a HEX27 element. They are always implicitly defined by the FiniteElement, 
Mapping, and Triangulation put together so you have to compute their values 
explicitly.

Hence, if you want globally unique nodes, the correct things to compute are the 
support points for all locally owned degrees of freedom. The function

DoFTools::map_dofs_to_support_points()

would be what you want but that function doesn't work in parallel. Fortunately 
this function is pretty short and you can write your own version that works on 
the locally owned dofs pretty easily by starting at

https://github.com/dealii/dealii/blob/master/source/dofs/dof_tools.cc#L2102

and doing something like

  1.  Set up a quadrature with fe.get_unit_support_points()
  2.  set up FEValues with your FE, mapping, and that quadrature. Do you have a 
finite element field that describes a position or displacement? If so take a 
look at MappingFEField.
  3.  do fe_values.get_quadrature_points() on each cell, but only save the 
results if the dof corresponding to the quadrature point (i.e., its support 
point) is locally owned.

Do you see what to do?

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Joss G. 

Sent: Wednesday, November 17, 2021 7:24 AM
To: deal.II User Group 
Subject: [deal.II] Re: Mesh export, high order


Thank you for your answer.

Following the examples you mentioned, I got a vtu file where I can extract the 
points. As I am using distributed tirangulation, I am getting the (x,y) values 
of the points of each cell, meaning that the points are not unique, there are 
repeated.

DataOut data_out;
DataOutBase::VtkFlags flags;
flags.write_higher_order_cells = true;
data_out.set_flags(flags);
data_out.attach_dof_handler(dof_handler);
data_out.add_data_vector(solution, "sol");
Vector subdomain(triangulation.n_active_cells());
for (unsigned int i = 0; i < subdomain.size(); ++i)
subdomain(i) = triangulation.locally_owned_subdomain();
data_out.add_data_vector(subdomain, "subdomain");
data_out.build_patches();
data_out.write_vtu_with_pvtu_record("./", "solution", 1, mpi_communicator, 2, 
8);

I would need to get the unique points corresponding to the domain in the same 
order as the operators are assembled. Similar to what I got with 
grid_out_write.msh but including the higher order points. COuld you please 
suggest me how can I approach that?

Thank you again.



El miércoles, 27 de octubre de 2021 a las 22:06:59 UTC+2, mafe...@gmail.com 
escribió:
Hello,

yes, you can use high-order output using the `DataOut` class after setting the 
corresponding `DataOutFlags` flag 
write_higher_order_cells.

The tutorials step-11, step-44, step-65, step-67, and step-76 demonstrate that 
feature.

Best,
Marc

On Wednesday, October 27, 2021 at 5:05:22 AM UTC-6 jossg...@gmail.com wrote:
Hi all,

I am using high order methods ad I am trying to export the mesh points. I am 
using  grid_out.write_msh(triangulation, out).
Is it any other way to get the  mesh points including the ones corresponding to 
the high orders?

Thank you

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Re: [deal.II] Implementing a fiber reinforcement in a biphasic model

[Wells, David]

Hi Matt,

It is difficult to give a clear answer without some more information on how you 
want to compute with fibers and where the material model for the fibers is 
coming from.

If you have a way to compute the fourth-order tensor directly then an approach 
like the one in the linked paper works. A good alternative is to compute a 
vector field which represents the anisotropic property - a good description of 
this for cardiac simulations is given in Pasquale's paper from early this year:

https://arxiv.org/pdf/2101.10960.pdf

that process (similar to what we do at UNC) involves computing a fiber field as 
a finite element field, so you don't necessarily need to store quadrature data 
- you can just compute values that you need cell-by-cell.

Best,
David

From: dealii@googlegroups.com  on behalf of Matthew 
Rich 
Sent: Thursday, September 30, 2021 9:49 PM
To: deal.II User Group 
Subject: [deal.II] Implementing a fiber reinforcement in a biphasic model

Hi all,

I am trying to add some anisotropy to my model via fibers. These fibers would 
only be active in tension and have different orientations depending on spatial 
location in the model. My plan of attack was to simply store and extra value at 
the quadrature points that had a direction representing the fiber and update 
directions after each time step. (is this a good way to go about doing that). I 
see a lot of papers doing fiber models in ABAQUS or COMSOL, but I never see any 
details on how to do it so I am guessing it is trivial.

Then I stumbled upon https://doi.org/10.1016/j.compstruc.2020.106334 which uses 
dealii to implement a fiber model that has two grids and some sort of junction 
between the grid representing the bulk material and one presenting the fiber. 
The formulation seemed way more involved than what I was going to try.

Am I making a gross simplification in my proposed approach.

Matt




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Re: [deal.II] Deal.II programming environment

[Wells, David]

Hi Martin,

Sorry for the slow response - I have been on vacation.

If you save a source file with a new name then you will need to update your 
CMakeLists.txt file - it doesn't know what you intend to do with the new file. 
I recommend reading through

https://www.dealii.org/developer/users/cmake_user.html

to better understand how to set up your own project with CMake.

If you have the virtual machine then it is easiest to just install either 
eclipse or QT creator inside the VM itself with the "apt-get install" command.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Jiang Hu 

Sent: Wednesday, July 21, 2021 9:59 PM
To: deal.II User Group 
Subject: Re: [deal.II] Deal.II programming environment

Hi David,

Thanks for the detailed explanation.

I suppose below procedure should work:
1 Open Deal.II example, the cpp file,  with text editor
2 make changes to it, and save it as another cpp file
3 Use cMake to run this new cpp file at the command line
4 if no mistake, the new cpp file will run

am I correct?

Last, where should I install the IDE? I am using virtual box machine with 
deal.II package in a window system.
can I install Eclipse in Virtual box machine? it has Ubuntu system in the 
virtual box.

Thanks for your time

Martin

On Thursday, 22 July 2021 at 1:15:10 am UTC+10 Wells, David wrote:
Hi Martin,

No, that's a very good question - it's important to set up a good development 
environment. You CAN use plain text editors and run CMake from the command line 
(in fact, with many tools you will end up still running CMake from a window 
inside them) but its usually better to use something more sophisticated (like 
an IDE that can run a debugger).

If you look on the wiki we have instructions for both Eclipse and QT creator:

https://github.com/dealii/dealii/wiki

a lot of people use VS code - we don't have instructions for it, and I don't 
use it, but since we use CMake it shouldn't be that hard to point VS code at 
your build directory and have it extract some information. If anyone actually 
uses VS code I would appreciate if they could weigh in here!

Best,
David Wells

From: dea...@googlegroups.com  on behalf of Jiang Hu 

Sent: Wednesday, July 21, 2021 1:22 AM
To: deal.II User Group 
Subject: [deal.II] Deal.II programming environment

Hello everyone,

Quite excited to find Deal.II and its potential.

I installed virtual machine with Deal.II, and run step 7 on terminal without 
any problem.

The question is if I want to compile bigger program with Deal.II , what is the 
typical working environment?

I assume we can not with terminal for such a purpose. I saw people using Nano 
to run Deal.II, but want to ask the standard tool for such process.

Emacs or Vscode?  Do I need to connect them to Deal.II?

I am very new, and this could be a quite silly question.

Thanks

Martin

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Re: [deal.II] Deal.II programming environment

[Wells, David]

Hi Martin,

No, that's a very good question - it's important to set up a good development 
environment. You CAN use plain text editors and run CMake from the command line 
(in fact, with many tools you will end up still running CMake from a window 
inside them) but its usually better to use something more sophisticated (like 
an IDE that can run a debugger).

If you look on the wiki we have instructions for both Eclipse and QT creator:

https://github.com/dealii/dealii/wiki

a lot of people use VS code - we don't have instructions for it, and I don't 
use it, but since we use CMake it shouldn't be that hard to point VS code at 
your build directory and have it extract some information. If anyone actually 
uses VS code I would appreciate if they could weigh in here!

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Jiang Hu 

Sent: Wednesday, July 21, 2021 1:22 AM
To: deal.II User Group 
Subject: [deal.II] Deal.II programming environment

Hello everyone,

Quite excited to find Deal.II and its potential.

I installed virtual machine with Deal.II, and run step 7 on terminal without 
any problem.

The question is if I want to compile bigger program with Deal.II , what is the 
typical working environment?

I assume we can not with terminal for such a purpose. I saw people using Nano 
to run Deal.II, but want to ask the standard tool for such process.

Emacs or Vscode?  Do I need to connect them to Deal.II?

I am very new, and this could be a quite silly question.

Thanks

Martin

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Re: [deal.II] adaptive mesh refinement for Navier Stokes

[Wells, David]

Hi Andrew Jack,

This is a reasonable start but, as the error messages state, you need to 
implement some more features in your code for this to work. In particular, 
step-26 has a separate function that reinitializes all of the DoFs, sparsity 
patterns, and matrices called setup_system() - there is no equivalent ins 
tep-35 because that program does not use time-dependent AMR. The same goes for 
the solution transfer object - you will need to set up "before and after" 
vectors if you want to use prolongatation and restriction to transfer the 
solution across mesh refinements.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of andrew 
jack urombo 
Sent: Thursday, June 24, 2021 2:40 AM
To: dealii@googlegroups.com 
Subject: [deal.II] adaptive mesh refinement for Navier Stokes


I am working on a adaptive finite elements for flows. For starters I want to 
base my simulation on Step 35 and introduce the refine_mesh( )  like in Step 26 
to it:

See attached code snippet.

When I make I get the error message:

[ 50%] Building CXX object CMakeFiles/step-35a.dir/step-35a.cc.o
/home/dealii/examples/step-35a/step-35a.cc: In member function ‘void 
Step35a::NavierStokesProjection::refine_mesh(unsigned int, unsigned int)’:
/home/dealii/examples/step-35a/step-35a.cc:1057:5: error: there are no 
arguments to ‘setup_system’ that depend on a template parameter, so a 
declaration of ‘setup_system’ must be available [-fpermissive]
 1057 | setup_system();
  | ^~~~
/home/dealii/examples/step-35a/step-35a.cc:1057:5: note: (if you use 
‘-fpermissive’, G++ will accept your code, but allowing the use of an 
undeclared name is deprecated)
/home/dealii/examples/step-35a/step-35a.cc:1059:32: error: ‘previous_solution’ 
was not declared in this scope
 1059 | solution_trans.interpolate(previous_solution, output_results);
  |^
/home/dealii/examples/step-35a/step-35a.cc:1060:5: error: ‘constraints’ was not 
declared in this scope
 1060 | constraints.distribute(output_results);
  | ^~~
make[2]: *** [CMakeFiles/step-35a.dir/build.make:63: 
CMakeFiles/step-35a.dir/step-35a.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:272: CMakeFiles/step-35a.dir/all] Error 2
make: *** [Makefile:84: all] Error 2
dealii@cd3db784d9d2:~/examples/step-35a$ ^C

Anyone with any idea how to fix this, or have implemented a similar problem in 
dealii.

Thank you.



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Re: [deal.II] Higher order elements

[Wells, David]

Hi Hermes,

We typically use lower-order elements in the tutorials, but FE_Q supports 
arbitrarily high degrees - for example, step-48 uses degree 4 elements, and the 
hp tutorial programs will use up to degree 7 or 8. We don't have plots for 
these shape functions but they are implemented.

Best,
David Wells


From: dealii@googlegroups.com  on behalf of Hermes 
Sampedro 
Sent: Thursday, June 24, 2021 9:35 AM
To: deal.II User Group 
Subject: [deal.II] Higher order elements

Dear all,

I would like to ask how to handle higher-order elements. I would need to use 
4th order. Looking at the first tutorials, I found that using FE_Q, it is 
possible to use only 1st and 2nd order.

https://www.dealii.org/current/doxygen/deal.II/classFE__Q.html#ac36967b6e5de1ff1f4d54e0fa779d876

Thank you

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Re: [deal.II] 5x5 Matrix Inversion Problem

[Wells, David]

Hi Lucas,

C++ doesn't allow us to overload operator[] with multiple arguments so that 
indexing has to be with single values - so yes, it's a language thing. This 
matches the C usage of square brackets where they only accept one value at a 
time.

The state attribute is automatically set by whatever functions you call - you 
should never need to mess with it (and in debug mode the class should abort if 
you try to do something that is inconsistent with the current state of the 
matrix). Internally, LAPACK typically modifies matrices in-place so 
LAPACKFullMatrix behaves in a similar way. The only other place I would look 
for documentation is that class's own page:

https://www.dealii.org/current/doxygen/deal.II/classLAPACKFullMatrix.html

If you have to do Newton iteration by setting up a Jacobian and solving a 
matrix then what you did makes sense. No matter what, if you are doing 
iterations, you have to compute a new Jacobian and solve a new linear system. 
The reinit() call is not expensive - it just zeros the data, which is O(n^2) 
for an n x n matrix (as opposed to the LU factorization which is O(n^3)).

If you want to save some time you can reuse Jacobians (and therefore their 
factorizations) in Newton's method but that will cause things to converge more 
slowly, but it can be tricky to determine how often to recompute the Jacobian.

Is it bad programming practice to not reinitialize it? It isn't the worst thing 
you can do, but reinitializing it to guarantee that there aren't any irrelevant 
values stored is the right choice. In this case I think you have to reinitalize 
the matrix in order to keep the state of the matrix consistent (it doesn't make 
sense to modify a matrix containing an LU factorization computed by LAPACK 
unless you have some knowledge of how LAPACK internally stores the 
factorization), so you need to do it no matter what.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Lucas 
Myers 
Sent: Tuesday, June 22, 2021 4:04 PM
To: deal.II User Group 
Subject: Re: [deal.II] 5x5 Matrix Inversion Problem

Hi David,

Thanks so much, this is exactly what I was looking for! For some reason I was 
trying to use the square bracket notation. Is there any reason why the (i, j) 
syntax is used rather than [i, j]? Is it just a restriction of c++?

A few follow-up questions about the LAPACKFullMatrix class: is there anywhere 
that I can find more information about the class besides the reference 
documentation 
here<https://www.dealii.org/current/doxygen/deal.II/namespaceLAPACKSupport.html>?
 In particular, I'm wondering how to deal with the state attribute. It looks 
like the compute_lu_factorization() method sets the state to lu (reasonable), 
but I'd like to repopulate the same matrix (meaning it has to be in the matrix 
state, I think). For now I'm using reinit() because that seems to change the 
state back to matrix, but I worry that it's expensive to keep reinitializing 
the matrix every Newton's method iteration. Is there a way to avoid 
reinitializing it? And is it bad programming practice to not reinitialize it?

Again, thanks so much for the help.

Kind regards,
Lucas



On Monday, June 21, 2021 at 1:08:50 PM UTC-5 Wells, David wrote:
Hi Lucas,

You should be able to use syntax like

A(i, j) = 5;

to assign values to a FullMatrix - it's what we do in most of the tutorial 
programs. TableIndices are somewhat hard to use (you are right) - they are 
intended to be used as a generic interface to Table where N is not known 
until compile time. Once you populate the matrix, you should be able to do what 
you mentioned before with the Gauss-Jordan algorithm to get the inverse.

That being said - do you need the inverse itself, or the action of the inverse? 
If you only ever need the action of the inverse a much better approach would be 
to use LAPACKFullMatrix and factorize it (via 
LAPACKFullMatrix::compute_lu_factorization() and LAPACKFullMatrix::solve()) 
since there is a significant amount of roundoff error accumulation in computing 
inverses.

The Solver classes are more than you need here - they are optimized for large 
sparse problems, not small dense ones.

Best,
David Wells



From: dea...@googlegroups.com  on behalf of Lucas 
Myers 
Sent: Monday, June 21, 2021 1:50 PM
To: deal.II User Group 
Subject: [deal.II] 5x5 Matrix Inversion Problem

Hi Everyone,

I have a problem wherein one of the terms in my PDE is a 5-component vector 
function \Lambda of the 5-component solution vector Q. However, I only have an 
explicit formula for Q as a function of \Lambda and so I am trying to write a 
numerical inversion class (as a `dealii::Function`) to get \Lambda as a 
function of Q.

I am using Newton's method, and so I need to solve a 5x5 matrix equation. I was 
planning on just inverting the Jacobian which I have implemented as a 
`dealii::Tensor`, but it looks like the `invert` function is only implement

Re: [deal.II] 5x5 Matrix Inversion Problem

[Wells, David]

Hi Lucas,

You should be able to use syntax like

A(i, j) = 5;

to assign values to a FullMatrix - it's what we do in most of the tutorial 
programs. TableIndices are somewhat hard to use (you are right) - they are 
intended to be used as a generic interface to Table where N is not known 
until compile time. Once you populate the matrix, you should be able to do what 
you mentioned before with the Gauss-Jordan algorithm to get the inverse.

That being said - do you need the inverse itself, or the action of the inverse? 
If you only ever need the action of the inverse a much better approach would be 
to use LAPACKFullMatrix and factorize it (via 
LAPACKFullMatrix::compute_lu_factorization() and LAPACKFullMatrix::solve()) 
since there is a significant amount of roundoff error accumulation in computing 
inverses.

The Solver classes are more than you need here - they are optimized for large 
sparse problems, not small dense ones.

Best,
David Wells



From: dealii@googlegroups.com  on behalf of Lucas 
Myers 
Sent: Monday, June 21, 2021 1:50 PM
To: deal.II User Group 
Subject: [deal.II] 5x5 Matrix Inversion Problem

Hi Everyone,

I have a problem wherein one of the terms in my PDE is a 5-component vector 
function \Lambda of the 5-component solution vector Q. However, I only have an 
explicit formula for Q as a function of \Lambda and so I am trying to write a 
numerical inversion class (as a `dealii::Function`) to get \Lambda as a 
function of Q.

I am using Newton's method, and so I need to solve a 5x5 matrix equation. I was 
planning on just inverting the Jacobian which I have implemented as a 
`dealii::Tensor`, but it looks like the `invert` function is only implemented 
up to dimension 3 (?). It looks like the `dealii::FullMatrix` class can do this 
via a Gauss Jordan method, but I was having some trouble using the `FullMatrix` 
class directly. In particular, to read and write individual elements I need to 
create a `dealii::TableIndices` object, which seems tedious and makes me think 
it's meant to be used internally.

Given all this, I am looking for advice at any level: is this a reasonable way 
to numerically get \Lambda as a function of Q? Is it recommended to use a 
`dealii::Tensor` object as opposed to a `dealii::FullMatrix` object? And if I 
am supposed to use the latter, is there a nicer way to index it than with the 
`dealii::TableIndices` object? Lastly is it a good idea to be using an `invert` 
operation to solve the Newton's method linear equation? I know that the `Eigen` 
package recommends against that 
here, and 
instead recommends one of its solution methods. I haven't seen any of those 
here besides one of the `Solver` classes, but those seem like a lot of overhead 
for a 5x5 matrix (I'm going to have to do this operation for every degree of 
freedom, so I want too minimize overhead). I also don't really want to use the 
Eigen package, just because (1) I want to avoid unnecessary value-copying and 
(2) I'd like to not have to try to interface multiple packages.

Any help is appreciated, and let me know if you need more information about the 
problem.

Kind regards,
Lucas

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Re: [deal.II] initial velocity

[Wells, David]

Hi there,

It looks like you have a simple copy-paste error: you define lambda2 but call 
lambda in line 1058. lambda2 is unused.

Best,
David

From: dealii@googlegroups.com  on behalf of Nikki 
Holtzer 
Sent: Monday, May 17, 2021 2:31 PM
To: deal.II User Group 
Subject: [deal.II] initial velocity

Hello all,

This code just solves the wave equation. Despite the fact that I have provided 
an initial velocity in line 106, it does not appear to be reading it in lines 
1024-1062. My solution looks like the wave equation with 0 initial velocity, 
i.e. one hump turns into two moving away from each other. How can I ensure it 
is properly reading in the initial velocity I have provided?

Thank you

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Re: [deal.II] Outputting DataOut Object into Personal Object Rather Than Outputing to File

[Wells, David]

Hi Chen,

The internal data structures are designed so that we have a consistent 
intermediate representation that works for all supported output formats. It's 
generally not what you want to use since it works with the lowest common 
denominator (DG elements) representation of the solution. The 'right' answer is 
that you should use normal-looking deal.II code to compute whatever output 
quantities you care about.

What kind of results do you want to get out of this class?

Best,
David

From: dealii@googlegroups.com  on behalf of Chen R 

Sent: Wednesday, May 26, 2021 7:58 AM
To: deal.II User Group 
Subject: [deal.II] Outputting DataOut Object into Personal Object Rather Than 
Outputing to File

Hi all,

I am trying to run a basic elasticity calculation based on the tutorial 
(tutorial 8). I want to output the results and thought of using DataOut class 
similar to the tutorial so that the results are in a predefined order. But I 
don't want to output the data into a file but instead return some object that 
contains the data.\

The data structures in the DataOut class are all protected/private. Is there no 
API of this class to just get the result itself without writing into a file 
format of some kind?

Is there such a way or am I going about this wrong?

Thank you,
Chen R.

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Re: [deal.II] order of dofs within a cell in a FESystem

[Wells, David]

Hi Praveen,

I don't think its possible to change the internal numbering used by FESystem 
itself since it must support the case where not all finite elements have the 
same number of degrees of freedom. If you really need to accomplish this you 
will have to write a new finite element class. Another possibility (if all the 
base elements are the same) would be to only have one finite element and do the 
block-based numbering manually since each component will have the same number 
of dofs.

Best,
David

From: dealii@googlegroups.com  on behalf of Praveen C 

Sent: Tuesday, June 1, 2021 5:34 AM
To: Deal. II Googlegroup 
Subject: [deal.II] order of dofs within a cell in a FESystem

Is it possible to change the order of dofs within a cell in a FESystem ?

I have situation like this:

FESystem fe;

degree = 1
nvar   = 4 // number of unknowns at each support point

fe(FE_DGQArbitrarynodes(QGauss<1>(degree+1), nvar)

I print

for i = 0; ihttp://www.dealii.org/
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Re: [deal.II] make install fails with ld signal 9

[Wells, David]

Hi Vachan,

The debug version of the library on my mac requires about 3.8 GB of memory to 
link: if you are patient and willing to use all your swap space then you should 
be able to compile the library. I recommend trying:

1) close all other applications on your machine (if possible, try to boot 
directly to the command line)
2) if you can, compile deal.II with the bare minimum number of dependencies 
that you might want to use. Every dependency you can skip will save some memory.
3) make sure you are only compiling with a single processor (i.e., make -j1)

Best,
David Wells

From: dealii@googlegroups.com  on behalf of 
vachanpo...@gmail.com 
Sent: Tuesday, May 4, 2021 2:45 AM
To: deal.II User Group 
Subject: [deal.II] make install fails with ld signal 9

Dear all,

I am trying to do a new installation of dealii. `make install` exits while 
compiling libdeal_II.g.so with ld signal 9. I had a look at this 
question and 
noted that this might be due to RAM shortage, but my device has >2 gb RAM. The 
output of `free -h` is:
  totalusedfree  shared  buff/cache   available
Mem:  3.7Gi   652Mi   2.4Gi   116Mi   733Mi   2.7Gi
Swap: 2.0Gi   838Mi   1.2Gi

What can I do to solve this issue? Are there any fixes or is higher RAM is 
required?

Thanking in anticipation
Vachan

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Re: [deal.II] Problem related to make_hanging_nodes_constraints in the hp cases

[Wells, David]

Hi Chong,

There is not an easy way to do this in the library. Fundamentally, hanging node 
constraints are like continuity constraints across varying levels of 
h-refinement and setting up these continuity constraints will take both into 
account.

If you really want to disable those continuity constraints for the other FE 
type, I think the best approach would be to
1) determine the DoFs associated with those elements
2) create a new AffineConstraints object which does not have any lines 
corresponding to the DoFs listed in the previous step

You can do 2 with AffineConstraints::get_lines().

Best,
David Wells

From: dealii@googlegroups.com  on behalf of chong liu 

Sent: Tuesday, May 4, 2021 12:06 PM
To: dealii@googlegroups.com 
Subject: [deal.II] Problem related to make_hanging_nodes_constraints in the hp 
cases


Dear all


I am trying to use the function of 
"make_hanging_node_constraints(hp::dofhandler, constraints)" to constraint 
hanging nodes when a local domain is refined. However, I came across a problem. 
I guess the problem is related to hp finite elements.


Background

The domain includes two different finite elements (hp_FE(fe_type_1, 
fe_type_2)), and one local region is refined (as shown in the figure).


I want to use the "make_hanging_node_constraints()" function to constrain the 
hanging nodes for fe_type_1 (shown as circles in the figure). However, I found 
that this function also constrains fe_type_2's degrees of freedom (dofs) 
adjacent to fe_type_1 cells (shown as triangles in the figure).


Question:

How can I only constrain the hanging nodes for fe_type_1?


I guess one possible solution is to remove the constrained fe_type_2's dofs 
from the AffineConstraints container. However, I did not find a function to do 
this.


I will be grateful for any help you can provide.


Sincerely,

Chong Liu

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Re: [deal.II] Problem with Debugging step-26 program

[Wells, David]

Hi Pushkar,

That error is usually a result of having a sparse matrix with no sparsity 
pattern attached to it. Could you please verify that you attach sparsity 
patterns to all the matrices you use in assembly?

Best,
David Wells

From: dealii@googlegroups.com  on behalf of 
pushkar...@gmail.com 
Sent: Wednesday, May 5, 2021 12:16 AM
To: deal.II User Group 
Subject: [deal.II] Problem with Debugging step-26 program

Deal deal.II community

In my attempt to simulate the additive manufacturing process, I modified the 
step-26 program to reproduce the results in which I ran into an error which 
produces the output as :

$ make run
Consolidate compiler generated dependencies of target step-26
[ 66%] Built target step-26
[100%] Run step-26 with Debug configuration
***Time step 0 at t=0

===
Number of active cells: 1024
Number of degrees of freedom: 99



An error occurred in line <367> of file 
 in function
T* dealii::SmartPointer::operator->() const [with T = const 
dealii::SparsityPattern; P = dealii::SparseMatrix]
The violated condition was:
t != nullptr
Additional information:
(none)

Stacktrace:
---
#0  ./step-26: Step26::HeatEquation<2>::assemble_system()
#1  ./step-26: Step26::HeatEquation<2>::run()
#2  ./step-26: main


make[3]: *** [CMakeFiles/run.dir/build.make:71: CMakeFiles/run] Aborted (core 
dumped)
make[2]: *** [CMakeFiles/Makefile2:116: CMakeFiles/run.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2
make: *** [Makefile:137: run] Error 2
I tried to debug with gdb but coudnt make track the error. So any help in this 
regard to debug the code  will prove beneficialMoreover,I have attached 
step-26.cc file which was modified.

Sincerely
Pushkar




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Re: [deal.II]Change from dealii-9.0.0 to deal.ii-9.2.0

[Wells, David]

Hi Chen,

No and yes - the same functionality has been moved into the Manifold classes, 
which are much more general than the old Boundary classes. For example, 
GridGenerator::hyper_ball automatically attaches a SphericalManifold to the 
boundary of the input Triangulation, which achieves the same result as 
attaching a HyperBallBoundary.

More information is available at the module page:

https://www.dealii.org/current/doxygen/deal.II/group__manifold.html

Do you need to do anything more complex than generate a spherical geometry? If 
not, using SphericalManifold in place of HyperBallBoundary should do most of 
what you need to do (though, again, this is now done automatically by the grid 
generator functions).

Best,
David Wells

From: dealii@googlegroups.com  on behalf of 陈敏 

Sent: Thursday, April 8, 2021 12:14 PM
To: dealii@googlegroups.com 
Subject: [deal.II]Change from dealii-9.0.0 to deal.ii-9.2.0

Dear all,
>From the website[The deal.II Library: Changes between Version 9.1.1 and 
>9.2.0],
> I knew that  have been removed:

Removed: The deprecated headers deal.II/grid/tria_boundary.h and 
deal.II/grid/tria_boundary_lib.h have been removed.

In dealii-9.2.0, is there anyway to use some functions to realize the same 
function like the following codes which must include 
 and will work in dealii-9.0.0?

static const HyperBallBoundary boundary(p,radius);
  triangulation.set_boundary (80, boundary);

Best,
Chen

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Re: [deal.II] PETSc Vector set deprecated

[Wells, David]

Hi everyone,

Oh my - I never got around to finishing this - we need to actually implement 
the function otherwise there is no sense in deprecating this. I'll open an 
issue and get it done before the release.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Wolfgang 
Bangerth 
Sent: Monday, March 29, 2021 12:25 AM
To: dealii@googlegroups.com 
Subject: Re: [deal.II] PETSc Vector set deprecated


> I am building PETSc vectors with the set operation and I see it’s deprecated. 
>  The documentation suggests to use “import( )” but I don’t see how to use it.
>
> How can I use import( ) as a replacement for set( ) as the documentation 
> suggests?  Please provide an example.

I don't know the answer, but maybe David Wells does given that the deprecation
was added in
   https://github.com/dealii/dealii/pull/10398

For sure, you could simply write into the vector elements one by one. That
doesn't require 'import()' at all.

Best
  W.


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Re: [deal.II] Tags and Communicators

[Wells, David]

Hi Wolfgang,

Thanks for writing this up. I think that, in my circumstance, I will be able to 
get away with duplicating communicators since the objects should exist for the 
entire program run (i.e,. I might make a few dozen instances at most) - e.g., 
each object can duplicate a communicator and then set up vectors and whatnot 
with it. I should be able to do all of this in my own code and not in deal.II 
so I don't think I'll have to dig up any old patches to the library.

> It only manifested in a crash after a program had been running for
many hours, and small changes to the program made the bug move to unrelated
pieces of the code but not make it appear any earlier in the run time of the
program.

That's frightening and now I'm not sure how PETSc avoids this problem, and I am 
somewhat afraid to even look.

Best,
David

From: dealii@googlegroups.com  on behalf of Wolfgang 
Bangerth 
Sent: Thursday, February 18, 2021 12:19 PM
To: dealii@googlegroups.com 
Subject: Re: [deal.II] Tags and Communicators


> One fix that I have found (PETSc does this) is to assign every object its
> own duplicated communicator which can then keep track of its own tags with
> MPI's own get and set attributes functions.

Sometime back in the day (in the 2005-2010 range) I spent an inordinate amount
of time going through every class that receives a communicator in some way or
other in the constructor or a reinit() call, and had that class duplicate the
communicator in the way you mention (Utilities::MPI::duplicate_communicator()
does that). You can probably still find those patches if you look long enough.

The reason I did this was primarily because I wanted to have one added layer
of security. If for some reason one process does not participate in a
collective communication, you should get a deadlock, whereas you would either
get funny errors or just completely unreliable results if that process
proceeds to the next communication on the same communicator. Right now, in
practice, all communication happens on MPI_COMM_WORLD.

But, after spending a good amount of time to duplicate all of these
communicators (probably several days of work), I spent *an even larger amount
of time* to track down what was quite likely the worst-to-find bug I have ever
worked on. It only manifested in a crash after a program had been running for
many hours, and small changes to the program made the bug move to unrelated
pieces of the code but not make it appear any earlier in the run time of the
program.

In the end, what it boiled down is that the MPI implementation I was using was
only able to provide 64k different communicators and if you asked for the
64k+1'st communicator, it just crashed. In programs that do thousands of time
steps and allocate a few vectors for temp operations in each time step, you'd
get there in a matter of hours.

I had sort of expected that MPI implementations recycle released
communicators, and I would expect that that's what they do today, but they
didn't back then. So after all of this time spent, I ripped out the
duplication of communicators again. You can probably also find that patch in
the repository and, with some luck, you might even be able to revert it if you
allow some fuzz in indentation etc. It would certainly be interesting to try
this again.

I'm still in favor of this approach. It's conceptually the right thing, it
would help uncover bugs, and it is *necessary* if you want to do things
multithreaded. (All of the MPI implementations have reentrant public
interfaces these days, but we can't use them unless you also duplicate
communicators somewhere.) But I would first want to try with a small test
program whether that is scalable to very large numbers of communicators -- I
think we would quite easily run into millions of communicators with this
approach if programs run long enough, though of course only a rather small
number would be live at any given time.

Best
  W.

--

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www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Tags and Communicators

[Wells, David]

Dear everyone,

I have a question on tagged messages and the best way to generate tags. A while 
back we went through the whole library and consistently tagged all of our MPI 
point-to-point messages - there was a long discussion about how to do this in

https://github.com/dealii/dealii/issues/8958

and some cited follow-up pull requests. This strategy is nice because it scales 
and we can reuse the same communicator for everything. A drawback is that there 
are some hard limits on the number of times we can call a particular _start() 
function before calling its corresponding _finish() function (e.g., with the 
same communicator, we can only do 10 ghost updates inside LA::d::Vector 
concurrently).

I'm working on a problem where I want to do this communication inside some 
library code that will potentially be called many, many times (about 20 at once 
for one situation my code's predecessor deals with). Hence I want to work 
around these hard-coded limits in some way that does not require the caller to 
set tags, batch things, etc.

One fix that I have found (PETSc does this) is to assign every object its own 
duplicated communicator which can then keep track of its own tags with MPI's 
own get and set attributes functions.

Hence, the question: has anyone else here encountered a similar problem where 
they want to post potentially dozens of ghost updates or other communications 
at once? If so - are there better solutions than duplicating communicators? Do 
you happen to know if there are any downsides to making lots of MPI 
communicators? I'd appreciate hearing back from anyone with experience with 
this sort of MPI problem.

Best,
David Wells

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Re: [deal.II] More than one instance of _axpy

[Wells, David]

Hi Victor,

I don't know exactly what is causing this but I would bet that it's related to 
the fix we applied in

https://github.com/dealii/dealii/pull/10287

namely, some other package (I'm working from memory here, but I think it's 
Trilinos) defines its own LAPACK wrappers in a slightly different way (they put 
const in different places or something like that).

I don't use ASPECT but I suspect commenting out the inclusion of 
full_matrix.templates.h might resolve the issue. Someone who uses ASPECT should 
take a look.

Best,
David Wells

From: dealii@googlegroups.com  on behalf of Victor 
Eijkhout 
Sent: Wednesday, January 20, 2021 8:07 PM
To: deal.II User Group 
Subject: [deal.II] More than one instance of _axpy

```
[ 43%] Building CXX object 
CMakeFiles/aspect.dir/source/particle/interpolator/bilinear_least_squares.cc.o
In file included from 
/opt/apps/intel18/cray_mpich_7_7/dealii/9.2.0/include/deal.II/lac/full_matrix.templates.h(33),
 from 
/work/00434/eijkhout/lonestar/aspect/aspect-2.2.0/source/particle/interpolator/bilinear_least_squares.cc(27):
/opt/apps/intel18/cray_mpich_7_7/dealii/9.2.0/include/deal.II/lac/lapack_templates.h(31):
 error: more than one instance of overloaded function "saxpy_" has "C" linkage
saxpy_(const dealii::types::blas_int *n,
^

In file included from 
/opt/apps/intel18/cray_mpich_7_7/dealii/9.2.0/include/deal.II/lac/full_matrix.templates.h(33),
 from 
/work/00434/eijkhout/lonestar/aspect/aspect-2.2.0/source/particle/interpolator/bilinear_least_squares.cc(27):
/opt/apps/intel18/cray_mpich_7_7/dealii/9.2.0/include/deal.II/lac/lapack_templates.h(39):
 error: more than one instance of overloaded function "daxpy_" has "C" linkage
daxpy_(const dealii::types::blas_int *n,
^
```

I get this when installing Aspect on our Cray. On the Dell/intel cluster it 
works fine.

And as hard as I look at that file, I can not see how it sees more than one 
instance of those functions.


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Re: [deal.II] Build error | resizing a vector of FunctionParsers

[Wells, David]

Hi Vachan,

We explicitly disabled copying and moving instances of FunctionParser because 
it depends (for threaded parallelism) on several objects that cannot be copied 
or moved - that's why your code works as long as you don't try to resize the 
vector. The best workaround is to use

std::vector, 4>>

(or switch the order of unique pointer and the array - what matters is that we 
move pointers instead of FunctionParser instances) so that no copies or moves 
are required.

Best,
David

From: dealii@googlegroups.com  on behalf of 
vachanpo...@gmail.com 
Sent: Wednesday, January 13, 2021 1:23 AM
To: deal.II User Group 
Subject: [deal.II] Build error | resizing a vector of FunctionParsers


Dear all,

I require to use a vector of an array of FunctionParsers in my code

std::vector< std::array, 4> > fps_vec;

At a later point when I know its size, I call

fps_vec.resize(size);

This line produces a long build error message (attached) starting with

invalid application of ‘sizeof’ to incomplete type ‘mu::Parser’
  static_assert(sizeof(_Tp)>0,

If I comment out the resize line, then the remaining program compiles 
successfully. I noted that such an error occurs when the compiler is not able 
to see the object's declaration. But I already included the header file 
deal.II/base/function_parser.h. Wouldn't that point to relevant muparser's 
header file?

In a different file, I had used an std array of FunctionParsers and that worked 
fine. Doesn't that mean that the definition of mu::Parser is visible to 
compiler? I am unable to understand what is causing this error.

Is there any workaround for this? Thanks in advance!

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Re: [deal.II] Surface / volume interactions for a 3D extruded mesh

[Wells, David]

Hi Corbin,

> Is there a better way I could go about mapping the 3D volume data and 
> depth-averaged data to the surface mesh?

This is a tough question - other deal.II developers are trying to figure out 
how to do this in parallel here:

https://github.com/dealii/dealii/issues/10037

for now I'll assume you are doing things in serial. Collecting columns by 
material id sounds reasonable to me: GridGenerator::extrude_triangulation 
extrudes material ids so this should be pretty easy to do.

> I could probably do this with FEFaceValues, but it's unclear to me how to 
> "request" values on a top or bottom face (since element orientation is 
> general). Is there an ordering I could rely on if I know it for a single 
> element?

The simplest way to do this would be to loop across the faces find the one with 
a downward-facing normal vector and the one with an upward-facing normal 
vector. If things really are extruded in the normal way then these should be 
the second to last and last faces, respectively, but checking the normal 
vectors should always work.

In particular, if you want to use FEFaceValues, you could try looping over the 
faces of the cell and only reinitialize FEFaceValues when a face has the right 
normal vector.

Best,
David

From: dealii@googlegroups.com  on behalf of Corbin 
Foucart 
Sent: Friday, January 1, 2021 12:53 PM
To: deal.II User Group 
Subject: [deal.II] Surface / volume interactions for a 3D extruded mesh

Hello deal.ii community,

I've really enjoyed using deal.ii over the past few weeks -- it's very 
impressive how complete the software is. I'm in the process of implementing an 
ocean equations solver which has a few unusual features:

  1.  The problem is to be solved over a 3D mesh extruded downwards in depth 
from a 2D surface mesh
  2.  There is a free surface equation which makes use of the original 2D mesh
  3.  3D data is communicated to the 2D surface by integrating finite element 
fields vertically over the entire domain in depth (depth-averaged fields)
  4.  From a 3D scalar field, I will need to compute another 3D scalar field 
representing the original field integrated to depth z (like a hydrostatic 
pressure at every point in the domain)

How I was thinking of doing this:

  *   (1) Mesh the 2D region with gmsh and extrude it using the approach in 
step-49; this seems clear
  *   (2,3) I was considering holding the original 2D mesh in memory and 
creating some type of map between the top-level volume elements and the 
surface. Is there a better way I could go about mapping the 3D volume data and 
depth-averaged data to the surface mesh?
  *   (4) I can re-write the hydrostatic integrals as an ode in depth and march 
element-by-element from surface to bottom along each vertical column using a DG 
scheme.
 *   To isolate each vertical column, I could assign a material ID to each 
one
 *   However, I need to extract the value on the bottom of each element 
above as a boundary condition to the element below
 *   I could probably do this with FEFaceValues, but it's unclear to me how 
to "request" values on a top or bottom face (since element orientation is 
general). Is there an ordering I could rely on if I know it for a single 
element?

Any tips would be appreciated!

Best,
Corbin

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Re: [deal.II] Unable to run 'make test'

[Wells, David]

Hi Romin,

That error means that the quicktest for gmsh failed - in particular, deal.II 
was not able to successfully run your gmsh executable. This usually means that 
there is something wrong with your gmsh installation.

Unless you plan on using gmsh from inside deal.II (i.e., calling gmsh to 
generate a mesh, not reading a mesh that already exists) you can ignore this 
error.

Do you want to use gmsh in this way? If so, can you try running gmsh outside of 
deal.II to try and isolate the problem?

Best,
David

From: dealii@googlegroups.com  on behalf of Romin 
Chittettu 
Sent: Tuesday, December 29, 2020 7:55 AM
To: deal.II User Group 
Subject: [deal.II] Unable to run 'make test'

Hi all,
I am new to deal.ii and have tried my best to get a solution to this error. 
Couldnt find any. Hope someone could help me out. The installation was done 
following the steps mentioned on the website. on an Ubuntu environment
the previous steps of installation work perfectly fine. I get an error in 'make 
test' which is as follows:



[100%] Running quicktests...
Test project /home/romin/dealii-9.2.0/build/tests/quick_tests
Start 6: gmsh.debug
Start 1: step.debug
Start 2: step.release
Start 3: affinity.debug
1/6 Test #3: affinity.debug ...   Passed1.06 sec
Start 4: tbb.debug
2/6 Test #2: step.release .   Passed1.21 sec
Start 5: boost_zlib.debug
3/6 Test #6: gmsh.debug ...***Failed1.34 sec
make[7]: *** [tests/quick_tests/CMakeFiles/gmsh.debug.run.dir/build.make:76: 
tests/quick_tests/CMakeFiles/gmsh.debug.run] Error 1
make[6]: *** [CMakeFiles/Makefile2:5883: 
tests/quick_tests/CMakeFiles/gmsh.debug.run.dir/all] Error 2
make[5]: *** [CMakeFiles/Makefile2:5890: 
tests/quick_tests/CMakeFiles/gmsh.debug.run.dir/rule] Error 2
make[4]: *** [Makefile:2393: gmsh.debug.run] Error 2
Test gmsh.debug: RUN
===   OUTPUT BEGIN  ===
[  0%] Built target kill-gmsh.debug-OK
[  0%] Built target obj_sundials_inst
[  0%] Built target obj_sundials_debug
[  5%] Built target obj_tbb_debug
[  7%] Built target obj_muparser_debug
[ 13%] Built target expand_instantiations_exe
[ 21%] Built target obj_numerics_inst
[ 28%] Built target obj_numerics_debug
[ 36%] Built target obj_fe_inst
[ 55%] Built target obj_fe_debug
[ 57%] Built target obj_dofs_inst
[ 69%] Built target obj_dofs_debug
[ 71%] Built target obj_lac_inst
[ 78%] Built target obj_lac_debug
[ 82%] Built target obj_base_inst
[103%] Built target obj_base_debug
[103%] Built target obj_gmsh_inst
[103%] Built target obj_gmsh_debug
[107%] Built target obj_grid_inst
[123%] Built target obj_grid_debug
[125%] Built target obj_hp_inst
[125%] Built target obj_hp_debug
[125%] Built target obj_multigrid_inst
[130%] Built target obj_multigrid_debug
[132%] Built target obj_distributed_inst
[136%] Built target obj_distributed_debug
[136%] Built target obj_algorithms_inst
[138%] Built target obj_algorithms_debug
[138%] Built target obj_matrix_free_inst
[140%] Built target obj_matrix_free_debug
[142%] Built target obj_meshworker_inst
[142%] Built target obj_meshworker_debug
[142%] Built target obj_opencascade_inst
[142%] Built target obj_opencascade_debug
[144%] Built target obj_particle_inst
[146%] Built target obj_particle_debug
[148%] Built target obj_differentiation_ad_inst
[150%] Built target obj_differentiation_ad_debug
[153%] Built target obj_differentiation_sd_inst
[153%] Built target obj_differentiation_sd_debug
[153%] Built target obj_physics_inst
[155%] Built target obj_physics_debug
[155%] Built target obj_physics_elasticity_inst
[157%] Built target obj_physics_elasticity_debug
[157%] Built target obj_non_matching_inst
[157%] Built target obj_non_matching_debug
[159%] Built target deal_II.g
[161%] Built target gmsh.debug
gmsh.debug: RUN failed. Output:


An error occurred in line <54> of file 
 in function
int main()
The violated condition was:
ierr == 0
Additional information:
This exception -- which is used in many places in the library -- usually 
indicates that some condition which the author of the code thought must be 
satisfied at a certain point in an algorithm, is not fulfilled. An example 
would be that the first part of an algorithm sorts elements of an array in 
ascending order, and a second part of the algorithm later encounters an element 
that is not larger than the previous one.

There is usually not very much you can do if you encounter such an exception 
since it indicates an error in deal.II, not in your own program. Try to come up 
with the smallest possible program that still demonstrates the error and 
contact the deal.II mailing lists with it to obtain help.

Stacktrace:
---
#0  /home/romin/dealii-9.2.0/build/tests/quick_tests/gmsh.debug: main


Aborted (core dumped)

Re: [deal.II] Running new tests with argument

[Wells, David]

Hi Zachary,

Are you adding a test to deal.II itself? If so all tests are compiled with the 
macro SOURCE_DIR defined as the absolute path to the test's source directory. 
This is how we load grids in, e.g., tests/grid/grid_in.cc.

If you are adding tests using our test framework but not deal.II: I am pretty 
sure that this macro is defined in the same way.

Best,
David

From: dealii@googlegroups.com  on behalf of Zachary 
42! 
Sent: Wednesday, November 4, 2020 6:38 PM
To: dealii@googlegroups.com 
Subject: [deal.II] Running new tests with argument

Hi folks,

I am trying to add a new test that requires reading in a file so I’m passing it 
in as an argument.  I am not sure how to use CTest and the other test setup in 
deal.II to pass in a file as an argument.

Cheers,

Zachary

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