[deal.II] Re: Moving vertices of parallel triangulation breaks periodic face pair match

The approach which i discussed in the last post worked on 2 processors but didn't work for 16 processors- periodic face pair match failed, but I am no longer getting segfaults. I think the ghost values are still not being set correctly. The parallel distributed diplacement vector constructor

[deal.II] Re: Crack propagation

Timo, If I use your user element, I have to use OPEN MPI? now I have some issues with Open MPI in Deal.ii Regards, Yaakov On Thursday, March 30, 2017 at 3:13:16 PM UTC+2, Seyed Ali Mohseni wrote: > > Dear Timo Heister and Thomas Wick, > > I am trying to run your phase-field crack propagation

Re: [deal.II] Re: Cmake-MPI

On 12/04/2017 06:13 PM, feap...@gmail.com wrote: /usr/include/petsc/petscsys.h:165:6: error: #error "PETSc was configured with OpenMPI but now appears to be compiling using a non-OpenMPI mpi.h"  #    error "PETSc was configured with OpenMPI but now appears to be compiling using a non-OpenMPI

[deal.II] Re: Cmake-MPI

Bruno, Many thanks for your help. Now I reinstall used packets, and I got another Bug: [ 16%] Building CXX object source/numerics/CMakeFiles/obj_numerics_release.dir/data_out.cc.o In file included from /usr/include/petsc/petscbag.h:4:0, from /usr/include/petsc/petsc.h:5,

[deal.II] Re: Moving vertices of parallel triangulation breaks periodic face pair match

Hello, I wanted to update that I have resolved the issue by using a custom parallel partitioned displacement vector initialized with all the ghost indices I would need for moving the ghost elements of the triangulation. parallel::distributed::Vector

[deal.II] Re: Moving vertices of parallel triangulation breaks periodic face pair match

Hello Rajat, Thanks for the suggestion. It worked for the simple case of moving all nodes of the triangulation by a constant displacement. In the actual application, I want to move the mesh using the values from a parallel:distributed displacement field which also has periodic boundary

Re: [deal.II] step-22 partial boundary conditions

Jane, I get that the stress boundary can be put into the weak form, but only really when you have Neumann conditions. Correct, but prescribing the stress in an elasticity problem is exactly a Neumann boundary condition. And why would I have to use a compute_nonzero_normal_flux for a

Re: [deal.II] New Assert class (Discussion)

> Thanks for your reply. I was thinking of something like that but was not > sure how to do it in cmake. > I mean something like "make moderate". > > Can you please tell me where should I edit so that code compilation follows > from the mode given to "make". Doing this as a cmake target is

Re: [deal.II] sparse matrix multiplication

On 12/04/2017 12:43 PM, Wolfgang Bangerth wrote: Can I figure out the pattern of B*B or BA^{-1}B ? In general, A^{-1} is going to be a dense matrix even if A is a sparse matrix. So building this matrix is not efficient. Of course, you say that A is diagonal, in which case this doesn't

Re: [deal.II] sparse matrix multiplication

On 12/04/2017 12:04 PM, Peimeng Yin wrote: I want to solve a linear system, which has the following form (A+B A^{-1} B) u = f Here A is a diagonal black matrix, B is a block matrix that I can figure out the pattern. Are there any solver that I can use to solve the linear system? Yes. Have

Re: [deal.II] New Assert class (Discussion)

One solution could be having a new mode : like *debug* and *release*, "*Moderate*" mode, where only user-defined myAsserts + AsserThrow will be checked. *So when build in moderate mode*:  myAssert (+ Asserthrow) would work like "Assert". This is just to avoid huge overhead that debug mode

Re: [deal.II] Re: Periodic boundary conditions

Hello, I came across this old thread, and successfully used the provided code in my own code (https://github.com/l-korous/mhdeal) - thank you Andreas - and I want to share how I used it: - here are the (slightly changed) files provided by Andreas:

[deal.II] Re: Moving vertices of parallel triangulation breaks periodic face pair match

Hello Sambit, Can you try doing this? Also move the vertices of the ghost cell and avoid calling dftPtr->triangulation.communicate_locally_moved_vertices(locally_owned_vertices); When I tried to use triangulation.communicate_locally_moved_vertices(locally_owned_vertices) last time,

[deal.II] sparse matrix multiplication

I want to solve a linear system, which has the following form (A+B A^{-1} B) u = f Here A is a diagonal black matrix, B is a block matrix that I can figure out the pattern. Are there any solver that I can use to solve the linear system? or Can I figure out the pattern of B*B or BA^{-1}B ?

[deal.II] Re: Moving vertices of parallel triangulation breaks periodic face pair match

Hello Dr. Arndt, Thank you for your reply. My apologies for not being clear on the " breaks the periodic face pairs match". Following is the error message I get when I run on parallel. *An error occurred in line <3699> of file in function* *void

Re: [deal.II] Re: mapping_collection and step-27

On 12/01/2017 08:36 PM, Juan Carlos Araujo Cabarcas wrote: path/petsc_eigs/pFEM.cc:370: error: undefined reference to 'void dealii::VectorTools::interpolate_boundary_values<2, 2, std::complex >(dealii::hp::MappingCollection<2, 2> const&, dealii::hp::DoFHandler<2, 2> const&,

[deal.II] Re: Using FunctionMap for nonzero normal flux (eg in step-22)

Jane, I'm wondering whether I've misunderstood how to use the FunctionMap > declaration. I'm needing it to use for > VectorTools::compute_nonzero_normal_flux_constraints > > At the moment I am trying to apply nonzero normal component of the normal > stress in step-22 on a boundary id that is

[deal.II] Using FunctionMap for nonzero normal flux (eg in step-22)

I'm wondering whether I've misunderstood how to use the FunctionMap declaration. I'm needing it to use for VectorTools::compute_nonzero_normal_flux_constraints At the moment I am trying to apply nonzero normal component of the normal stress in step-22 on a boundary id that is 2 I have tried

Re: [deal.II] Assemble the rhs of time-dependent linear elasticity

On 11/29/2017 09:39 PM, Jie Cheng wrote: Here is what I suspect: Method 1 uses the stiffness_matrix that has been modified during the assembly, while method 2 is using the original stiffness. Although method 2 will eventually distribute the rhs vector as well as the matrix, it is distributed

Re: [deal.II] New Assert class (Discussion)

I have seen other libraries with a release+asserts mode. I don't think having a third variant of the deal.II internals makes a lot of sense, but one could talk about having a compile option for it. If you want something like Assert() in release mode inside your programs, you could easily do

[deal.II] Re: Moving vertices of parallel triangulation breaks periodic face pair match

Sambit, I am trying to move all parallel triangulation nodes by a constant > displacement, but that breaks the periodic face pairs match when I > call GridTools::collect_periodic_faces(...). I use the following code for > the mesh movement. The dftPtr->triangulation has periodicity constraints

[deal.II] Moving vertices of parallel triangulation breaks periodic face pair match

I forgot to add that this works on serial but fails for multiple processors -- 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

[deal.II] Re: Cmake-MPI

Yaakov, On Monday, December 4, 2017 at 2:47:00 AM UTC-5, feap...@gmail.com wrote: > [ 77%] Linking CXX executable ../bin/step-8.release > ../lib/libdeal_II.so.9.0.0-pre: error: undefined reference to > 'Epetra_MpiComm::Epetra_MpiComm(int)' > There is a problem with Trilinos. deal.II can't link

[deal.II] Moving vertices of parallel triangulation breaks periodic face pair match

Hi All, I am trying to move all parallel triangulation nodes by a constant displacement, but that breaks the periodic face pairs match when I call GridTools::collect_periodic_faces(...). I use the following code for the mesh movement. The dftPtr->triangulation has periodicity constraints

[deal.II] Re: time dependent problem with time dependent dirichlet boundary conditions

Thanks Daniel. I will try the first approach. My time dependent Function class returns an update and not a new value. Actually, I am trying to solve a free surface flow problem with moving mesh(for very small displacements). I am implementing the flow and mesh movement in a decoupled way. So

Re: [deal.II] step-22 partial boundary conditions

Hi Wolfgang, Apologies but could you just clarify? I get that the stress boundary can be put into the weak form, but only really when you have Neumann conditions. And why would I have to use a compute_nonzero_normal_flux for a zero one? I believe it my have been my fault not being clearer.

[deal.II] Re: how to refine only the outer cells of a mesh?

Alex, have a look at step-1 . The relevant piece of code there looks like Triangulation<2>::active_cell_iterator cell = triangulation.begin_active

[deal.II] Re: time dependent problem with time dependent dirichlet boundary conditions

Bhanu, [...] > VectorTools::interpolate_boundary_values(move_dof_handler, 106, > move_boundary_values_function, move_boundary_values); > MatrixTools::apply_boundary_values(move_boundary_values, > move_system_matrix, move_solution, move_system_rhs); > > instead of 'constraints'. >

[deal.II] how to refine only the outer cells of a mesh?

Hello! I have hyper_ball triangulation refined couple of times globally. Now I want to refine only the cells which lay on the surface. In tutorial I've found the function refine_and_coarsen_fixed_number but I have not arrived at formulating the proper criteria. In examples you use a solution

[deal.II] time dependent problem with time dependent dirichlet boundary conditions

Dear deal.II developers/users, I am solving a time dependent problem (parabolic) with time dependent dirichlet boundary conditions(at a particular boundary). So I apply dirichlet boundary values at the beginning of each time step to the system matrix(assembled only once outside the time loop)