[deal.II] MPI: Evaluating several distributed functions on each node

Dear all, I am facing a little challenge: Suppose I have several objects myFunction of a certain class MyFunction derived from a Function object on each process in my MPI universe. The number of MyFunction objects may vary from process to process. I am trying to evaluate each object at certain

[deal.II] Triangulation from lower-dimensional object

Dear all, I was recently looking for a solution to the following problem: I have a triangulation, e.g., of a unit cube. I need to solve a lower-dimensional (FEM-like) problem on all faces with BCs on edges and for each face I need to solve a problem on all edges with BCs at vertices. Can I

[deal.II] Elasticity Preconditioner

Dear all, A student and me are trying to deal with (parallel, static) linearized elasticity similar to step-8. However, the problem is slightly different since the Lame parameters are functions instead of constants. Can anyone recommend good solvers & preconditioners for the resulting

[deal.II] Re: Question about deal.II flexibility

Dear Abdo, I do think that Deal.II can help you with solving your problem. If you are just starting with Deal.II have a look at the tutorials . It is always a good idea to start with some code basis that other people have shared and

Re: [deal.II] p4est user pointer and distributed::triangulation

Thank you, Wolfgang! This is exactly what I am looking for. I don‘t need to access the pointer from outside, I am trying to extend the p4est-interface itself. Best, Konrad On Friday, May 14, 2021 at 12:42:48 AM UTC+2 Wolfgang Bangerth wrote: > On 5/13/21 3:05 PM, Konrad Simon wr

[deal.II] p4est user pointer and distributed::triangulation

Dear all, I am currently writing an interface to some p4est functions. The structure of p4est makes it often necessary to pass data around through a user pointer of whatever type (void*). When creating a new triangulation this pointer is set to „this“ (the triangulation itself), see for

Re: [deal.II] interpolate FE_Nelelec

Hi John, Maybe I can give some hints of how I would approach this problem (these are just some quick thoughts): Write this problem as a vector Laplace problem curl(nu*curl(A)) - grad(div(A)) = J which you then have to write as a system of PDEs. Note, this can only be the same as

Re: [deal.II] interpolate FE_Nelelec

> my expectations are all wrong. I would also appreciate if you will share > with me a reference to a paper or a book, so I can extend my modest library. > > Thanks! > > John > > P.S. I have sent you an e-mail as you have requested. Could you please > check your s

Re: [deal.II] Re: interpolate FE_Nelelec

Dear John, I had a look at the pdf you sent. I noticed some conceptual inconsistencies that are important for the discretization. Let me start like this: The curl-curl-problem that you are trying to solve is - according to your description of the gauge - actually a curl-curl + grad-div problem

Re: [deal.II] 2d meshes and orientation

Dear Wolfgang, On Tuesday, April 6, 2021 at 5:53:15 AM UTC+2 Wolfgang Bangerth wrote: > It's possible this is indeed a bug. In most cases, we run the 2d meshes > through the mesh orienter, so we rarely see 2d meshes that are not > correctly > oriented and it wouldn't surprise me if we have

[deal.II] 2d meshes and orientation

Dear deal.ii community, I stumbled over something in 2d meshes that confuses me a bit. Supoose I have 2 squares (a left and a right one) sharing one edge. If everything is fine all lines and faces have standard orientation, i.e., line_orientation==true and face_orientation==true for all lines

[deal.II] Re: Need help installing deal.ii with p4est and Trilinos

Dear Budhyant,, Hard, to say what should be the paths on your system. Dealing with all these large dependencies can be quite cumbersome. I would say the way you install Deal.II depends on what you want to do with it. Let me tell you how I would approach this. 1. If you just want to develop a

Re: [deal.II] Face and line orientation dependent dof permutations in FE_Q

Dear Wolfgang, > Fundamentally, the place to look is to search through the finite element > classes where they ask for face and line orientations. It is possible that > you > don't actually have to do much there: Finite element classes generally > work in > the local (cell) coordinate

[deal.II] Face and line orientation dependent dof permutations in FE_Q

Dear Deal.II community, I am currently fixing an orientation issue for some (non-primitive) vector elements with the help of two other Deal.II developers/maintainers. I have a quick question: On complicated meshes some faces can have a non-standard orientation or they can be rotated against

Re: [deal.II] Mean value of component of TrilinosWrappers::MPI::BlockVector

> > Then you need to create a vector with locally relevant entries as ghosts > and > copy your fully distributed vector to it. There is no other way if you > want to > use that function. > > But if your goal is to fix the pressure in a Stokes problem, it doesn't > have > to be the integral

Re: [deal.II] Re: Mean value of component of TrilinosWrappers::MPI::BlockVector

> That looks like an unrelated error. Can you create a small testcase for > this > issue here? > I will try to come up with an example. Thank you again and best regards, Konrad -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

Re: [deal.II] Mean value of component of TrilinosWrappers::MPI::BlockVector

> > I suspect you are passing a fully distributed vector to that function, but > it > needs to read ghost elements of the vector. Have you tried copying the > vector > into a locally_relevant vector, and passing that to the function in > question? > Thank you, Wolfgang, that was the issue.

[deal.II] Re: Mean value of component of TrilinosWrappers::MPI::BlockVector

I am pretty sure that this is related to the following problem: When I try to run AMR with this FESystem (Nedelec-RaviartThomas-DGQ) with more than one MPI rank I get this error "An error occurred in line <1626> of file in function void

[deal.II] Mean value of component of TrilinosWrappers::MPI::BlockVector

Dear all, I am trying to compute the mean value of the pressure component of a Trilinos block vector with three blocks and 7 components (vorticity-velocity-pressure). Using one MPI rank is fine but if I use more I get the error "An error occurred in line <666> of file in function

Re: [deal.II] Div-conforming elements in 3D

Dear Jean-Paul, Many thanks for your reply. On Tuesday, December 29, 2020 at 9:31:49 PM UTC+1 Jean-Paul Pelteret wrote: > Hi Konrad, > > I'm sorry for taking some time to reply. To be honest, the inner working > of the FE classes is not something that I've ever had the time or > opportunity

[deal.II] Re: Mean Value Constraints

scaling+90 degree rotation and two independent shifts) and dimension 6 in 3D. Once you project the rhs a Krylov solver can deal with your singular problem. Cheers, Konrad On Saturday, December 26, 2020 at 11:06:36 AM UTC+1 Konrad Simon wrote: > Hi, > > On Saturday, December 26, 2020 at 6

[deal.II] Re: Mean Value Constraints

Hi, On Saturday, December 26, 2020 at 6:43:21 AM UTC+1 smetca...@gmail.com wrote: > Hi all, > > Does anyone here have any experience applying mean value constraints > (specifically with periodic boundary conditions)? I'm having some trouble. > As far as I can tell, there are two approaches

Re: [deal.II] Div-conforming elements in 3D

lement it in the current structures without interfering with them (too much). Best, Konrad On Wednesday, December 16, 2020 at 9:33:57 PM UTC+1 Konrad Simon wrote: > Dear Jean-Paul, dear Deal.II community, > > I partially solved the problem of sign flipping and permuting the degrees > of freedom and

Re: [deal.II] Div-conforming elements in 3D

ent such a table then. This is a lot of work and more complicated for Nedelec elements. Best, Konrad On Saturday, December 12, 2020 at 8:07:19 PM UTC+1 Konrad Simon wrote: > Hi Jean-Paul, > > On Thursday, December 10, 2020 at 11:39:08 PM UTC+1 Jean-Paul Pelteret > wrote: > >

Re: [deal.II] Div-conforming elements in 3D

Hi Jean-Paul, On Thursday, December 10, 2020 at 11:39:08 PM UTC+1 Jean-Paul Pelteret wrote: > HI Konrad, > > I have no familiarity with the H-div elements, so I could be wrong with > this suggestion... > > The Fe_Nedelec element suffered from a similar issue, where adjacent cells > had to

Re: [deal.II] Div-conforming elements in 3D

hasing the bug and hopefully come up with a merge request soon. Best, Konrad On Wednesday, December 9, 2020 at 3:44:58 PM UTC+1 Konrad Simon wrote: > Hi David, > > Many thanks for the hint. After some research I believe I stumbled over this > issue#7970 <https://github.com/deal

Re: [deal.II] Div-conforming elements in 3D

ss but for > FE_RaviartThomas this is just a comment in the source file. Would you be > willing to write a patch explaining things better for the other Hdiv > classes? > > Best, > David > -- > *From:* dea...@googlegroups.com on behalf of >

Re: [deal.II] Boundary conditions on components in with FESystem

Dear Wolfgang, I may have stumbled over something. I created a 3D hyper_shell with 6 coarse cells which is nothing but a cube with a cubical void in the center. I then asked for the face orientations of each face in each cell. In each of the 6 cells all faces have standard orientation

[deal.II] Boundary conditions on components in with FESystem

Dear all, I have a code version in which I am using a FESystem (3d) composed of three elements: FE_Nedelec (w), FE_RaviartThomas (u) and DGQ (p). The code compiles fine but gives unreasonable results and I do not see what I am doing wrong or what I forgot. I need to impose (essential)

Re: [deal.II] Tools for parallel debugging

Thank you, Wolfgang and Daniel. Seems like I will go with the command line then. I was just wondering if people here use Eclipse's PTP which sounded like a good graphical tool. In my case it frequently crashes or simply gets stuck. Best, Konrad On Sunday, October 11, 2020 at 11:35:34 PM UTC+2

Re: [deal.II] Tools for parallel debugging

Oh, seems like I missed that. Thanks you! Konrad On Sunday, October 11, 2020 at 11:35:34 PM UTC+2 Wolfgang Bangerth wrote: > On 10/11/20 3:26 PM, Daniel Arndt wrote: > > > > have a look at > > > https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#how-do-i-debug-mpi-programs >

[deal.II] Tools for parallel debugging

Hi deal.ii community, I have a short question about tools (which probably also concerns many other people). I am using eclipse for C++ development and I frequently use the debugger. So far everything fine. Now I need to use parallel debugging tools for MPI but my eclipse crashes many times

Re: [deal.II] Re: Evaluating FE-solution on distributed mesh, semi-Lagrangian method

(but not always) p will be in a ghost layer. ) Any way to get the actual MPI rank of the owner? Any help would be much appreciated. Best, Konrad On Thursday, May 14, 2020 at 4:10:33 PM UTC+2 Konrad Simon wrote: > Thank you, Bruno. :-) > > > On Tuesday, May 12, 2020 at 2:50:35 PM UTC+2, Bruno Tu

Re: [deal.II] Re: Evaluating FE-solution on distributed mesh, semi-Lagrangian method

to change the code. If that's the way you > want to go, I am sure that someone will be able to provide you with > some guidance. > > Best, > > Bruno > > Le mar. 12 mai 2020 à 06:04, Konrad Simon > a écrit : > > > > Thank you, Bruno. What is sometime

[deal.II] Evaluating FE-solution on distributed mesh, semi-Lagrangian method

Dear all, I am currently working on a semi-Lagrangian method for an advection-diffusion equation. During runtime I must evaluate the (known) FE-solution at a previous time step but the mesh is distributed. Problem: It can well be that I must evaluate the solution at a point that is in a cell

Re: [deal.II] Installation with spack - no access to adol-c

Jean-Paul, thanks a lot. Works! :-) Cheers, Konrad -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group"

[deal.II] Installation with spack - no access to adol-c

Hi all, A colleague and myself had problems to install dealii 9.1.1 via spack. Quick question: Did anyone have problems to install deal.ii via spack lately? I see that it depends on the development version of adol-c but this one requires a gitlab account and access to adol-c. Does deal.ii

[deal.II] Re: Interpolating to globally refined distributed mesh

Dear deal.ii community, I solved it, sorry for bugging you with it but simple mistakes can bug you for long... I simply forgot to re-distribute the dofs for the finite element after refining the mesh. Ooofff :-/ Best, Konrad -- The deal.II project is located at http://www.dealii.org/ For

[deal.II] Re: Interpolating to globally refined distributed mesh

Add-on: The problem is in the function RefineInterpolate::refine_and_interpolate_on_distributed_mesh() -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are

[deal.II] Re: Interpolating to globally refined distributed mesh

Add-on: The problem is in the function RefineInterpolate::refine_and_interpolate_on_distributed_mesh() -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are

[deal.II] Interpolating to globally refined distributed mesh

Dear deal.ii community, I am trying to interpolate a distributed solution vector onto a globally refined distributed mesh. Actually I need to globally refine more than once but I believe I can iterate this procedure (is there a more efficient way? The finite element can be vector or scalar

Re: [deal.II] Re: cmake with library and executables

Many thanks, Matthias! Works! Best, Konrad On Wednesday, December 25, 2019 at 2:07:41 PM UTC+1, Matthias Maier wrote: > > > On Fri, Dec 20, 2019, at 13:07 CST, Konrad Simon

Re: [deal.II] Re: cmake with library and executables

Hi Wolfgang, On Tuesday, December 24, 2019 at 5:59:31 PM UTC+1, Wolfgang Bangerth wrote: > > > Konrad, > your email has no question :-) Is your problem that you can't call 'make > -j8' > and your question how to make that possible? If so, what happens if you > try? > What is the error

[deal.II] Re: cmake with library and executables

Hello deal.ii community, I am posting again (sorry) with a bit more info since I did not find the mistake in my cmake setup. I have essentially the following project structure: project/source project/include project/doc project/test. In project/ I have this CMakeLists.txt:

[deal.II] projecting function onto TrilinosWrappers::MPI::BlockVector

Hi all, I am having a little problem with projecting a function onto (parts of) FE spaces. I am getting the error The violated condition was: (dynamic_cast *>( &(dof.get_triangulation())) == nullptr) Additional information: You are trying to use functionality in deal.II that is

[deal.II] Question about postprocessing

Hi deal.ii community, I also have a little question about postprocessing in different spaces. I am post processing two solutions of the same problem but solved in two different (pairs of) spaces. One quantity, for example, is called u and is either in H(curl) or in H(div) depending on the form

[deal.II] cmake with library and executables

Hi deal.ii community, Little cmake question: I set up a user project with include, test, doc and source directory. I am collecting some code in a library and then I link a few application files to the library. I followed the guidelines of the documentation and everything is fine. Now one

Re: [deal.II] Evaluate shape functions for an element on a given cell in a triangulation

Many thanks, Wolfgang. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from

[deal.II] Re: How to use CellId class

Hi Zhidong, On Monday, October 21, 2019 at 1:42:30 AM UTC+2, Zhidong Brian Zhang wrote: > > Thank you very much for your prompt reply, Konrad! > > My confusion is the output of cell->id(), for example, > 0_3:000 > 0_3:200 > 0_3:003 > 0_3:006 > 0_3:406 > 0_3:606 > 0_3:206 > 0_3:007 > 0_3:407 >

[deal.II] Evaluate shape functions for an element on a given cell in a triangulation

Hi deal.ii community, I have a little implementation problem to bug you with... Is there a way to evaluate a given shape function on a given cell like a normal Function or TensorFunction? I need to do many computations on a coarse cell that itself is meshed. I have an implementation but it

[deal.II] Re: How to use CellId class

Hi Zhidong, I don't know what exactly you want to do but I found it quite useful that the CellId class has an order relation. That makes it usable in a std::map. Use the CellId (you can retrieve it through cell-->id() if cell is a cell accessor like the one you use to loop over all your

[deal.II] Re: Issue with boost serialization and spack?

Hi Denis, I don't have the build folders any more so I can not post the error log. But the error (using spack) occurred with both boost versions. I will post something once I will find a solution. At any rate, thank you for your help. Best, Konrad -- The deal.II project is located at

[deal.II] Re: Issue with boost serialization and spack?

> > >> I guess I have a clue why I get the error. My backend nodes run on a >> different architecture. The openmpi version (i.e. mpirun) is the correct >> one. This is made sure in the slurm script. >> > That's always a pain to deal with. If you can, I would get an interactive > session on a

[deal.II] Re: Issue with boost serialization and spack?

> > Thank you, Denis. I use a pretty stupid (but simple) workaround: I setup >> and compile deal.ii myself since all dependencies are compiled and use the >> cmake command used by spack. That works. And I do not get the serialization >> error. >> > > > now that is strange. Are you sure you

[deal.II] Re: Issue with boost serialization and spack?

Thank you, Denis. I use a pretty stupid (but simple) workaround: I setup and compile deal.ii myself since all dependencies are compiled and use the cmake command used by spack. That works. And I do not get the serialization error. However, now my code runs on the machine I installed it on. But

[deal.II] Issue with boost serialization and spack?

Dear deal.ii community, I am having a little problem and I was wondering if this issue is known. I installed deal.ii on our cluster and all dependencies build nicely with my chosen compiler (gcc v7.3). BLAS and LAPACK are being built as well as openmpi (the versions on the cluster are not

[deal.II] Re: Configuration of PETSc

Hi Toni, Seems like I missed that little note in the documentation. Thank you :-) Best, Konrad -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are

[deal.II] Re: deal.II for Inverse problems in non-linear elasticity

Hi Prashant, > I am trying to solve an Inverse Cauchy problem in 3D nonlinear elasticity. > I have observed displacement data at partial boundary as well in partial > regions inside the body, and want to reconstruct the traction field. From > documentation of deal.II, I understood how

[deal.II] Configuration of PETSc

Dear deal.ii community, I am using deali.ii with PETSc and Trilinos. However, when I am using the PETSc PreconditionILU I get an error that suggests that a solver package is missing (with Trilinos it works). Petsc's PreconditionAMG works fine (although not very efficiently for my problem). Do

Re: [deal.II] Initialization of iterative solver

> > Yes, you just set the solution vector to your best guess before you pass > it to the solver. But you'll find that in practice, this rarely reduced > the number of iterations by any significant amount :-( > Many thanks, Wolfgang. Now, I also saw that in the source code of solver_cg.h. I

[deal.II] Initialization of iterative solver

Dear deal.ii community, I have a quick question: Suppose I know a vector that is close to the solution of my linear system. Is there a method to initialize an iterative solver with this vector? Best, Konrad -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum