[deal.II] Re: Thermoelastic Problem

g/8.4.1/doxygen/deal.II/classFEValuesViews_1_1Vector.html> > [2] > https://dealii.org/8.4.1/doxygen/deal.II/classFEValuesViews_1_1Vector.html#ad7b4df64147989229f566eff541ddebc > > <https://dealii.org/8.4.1/doxygen/deal.II/classFEValuesViews_1_1Vector.html> > > &

[deal.II] External point forces on elastic bodies

Dear Friends, I want to solve a very simple elastic problem to obtain stress and displacement field, applying a point force on one of the external surfaces of a rectangular 2D domain. Although I found some sort of external forces only in step 8, it is not a point force. I was wondering how to

[deal.II] Re: How to output a single scalar in a parallel code

Dear Rajat, > ... which I then write in a file on a master process. > I was wondering how to write in a file on a master process so that there would be just one output file not as many as processor exist. I use the following commands to write in my file in serial code : std::ofstream

Re: [deal.II] How to addapt MappingQEulerian class for Parallel codes using the PETSc wrapper classes

Dear Timo and Wolfgang, Thank you very much for your guidance. I should have passed the ghosted solution vector itself as the third parameter in MappingQEulerian instead of a non-ghosted copy of it. Best, Regards, Hamed On Monday, October 24, 2016 at 3:37:48 PM UTC-5, Timo Heister wrote: > >

[deal.II] Re: what do SolverControl do for Direct Solvers?

I want to add that for running on Cluster I used up to 64 processors (4 nodes, each with 16 processor). -- 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

[deal.II] what do SolverControl do for Direct Solvers?

Hi all, I have two question which may be somehow related: First: I have parallelized a code in which I use TrilinosWrappers::SolverDirect . The problem is that with around 2 DOFs the code is run on my own machine and on the cluster as well but when I increase DOF even to 15 it get

[deal.II] Re: what do SolverControl do for Direct Solvers?

Thursday, October 27, 2016 at 5:40:04 PM UTC-4, Hamed Babaei wrote: > >> First: I have parallelized a code in which I use >> TrilinosWrappers::SolverDirect >> . The problem is that with around 2 DOFs the code is run on my own >> machine and on the cluster as well b

[deal.II] Re: Convergence problem arising for large number of DoFs

Hi all, I am attaching the sequential and parallel codes as well as parameters.prm file. It would be appreciated if you could compare tangent_matrix (the system_matrix of the elasticity part of the problem) of parallel and sequential codes to find out where I have ruined the S.P.D condition

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

Dear Wolfgang, Thanks for your help. I can reduce my problem to four 2D elements. I would like to plot the system_matrix of sequential and parallel codes to compare them but I am not sure how to do so. Can I loop over the elements of system_matrix and simply plot them? Thanks -- The deal.II

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

Hi All, After two months of struggling with the parallel code, I finally found the bug. I had made a stupid mistake, initializing the temporary distributed solution inside the Newton loop I have no word to thank all of you dear friends, Wolfgang and Daniel in particular, for your

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

Dear Daniel, Then I would expect that the solver should behave the same for both > matrices. Are you still running into the same problems using just 4 cells > with your parallel code? > Yes, the parallel code is not solved by SolverCG+SSOR even for only 4 cell. It is really weird to me that

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

Hi all, It seems that although before first call to solve(in the zero newoton iteration) very few system matrix components are zero but after first solving in the first Newoton iteration, most of the system_matrix components are zero except all the diagonal components and few off-diagonal

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

C-5, Bruno Turcksin wrote: > > 2016-10-19 11:51 GMT-04:00 Hamed Babaei <hamedb...@gmail.com >: > > > I need to compute the determinant of system_matrix to check if its > positive > > or negative so that I know my system_matrix is positive definite or not. > Th

[deal.II] How to use Trilinos instead of Petsc in step-40

Hi friends, I want to use Trilinos instead of Petsc in my parallel code which is based on step-40. I guess some changes should be made in the following lines of the include files part: namespace LA { #if defined(DEAL_II_WITH_PETSC) && !(defined(DEAL_II_WITH_TRILINOS) &&

Re: [deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

Hi Daniel, I hope you are doing well. I've been struggling to run step-40 using Trilinos instead of Petsc. I appreciate it if you could let me know which parts of the code should be changed and how. Documentation in the include part says : " uncomment the following #define if you have PETSc

Re: [deal.II] How to addapt MappingQEulerian class for Parallel codes using the PETSc wrapper classes

Dear Timo, Regarding using MappingQEulerian class in parallel, I did what you said for the vector type template argument. It works when I run the code on my own machine but I got the following error when I run it on cluster: An error occurred in line <1480> of file in function

[deal.II] Re: How to apply boundary values for a particular point on the boundary instead of the whole boundary surface

Paul linked), I wrote the following >> method that you and maybe others will find useful. >> >> It takes in a vector containing the list of components of a field that >> need point constraints (rigidBodyModeComponents) and adds a constraint >> where needed: >> &

[deal.II] Direct Solvers in Parallel

Hi friends, I am parallelizing a code similar to step-44 in which it is possible to use either an iterative solver SolverCG or a direct solver, SparseDirectUMFPACK. I have used the latter in the non-parallel code and works great. Using iterative solvers like SolverCG I have problem in

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

Dear Wolfgang, In attach you shall find the bilinear form and the assemble part of the code as well. Thanks, On Friday, October 21, 2016 at 11:14:52 AM UTC-5, Wolfgang Bangerth wrote: > > > > On Thursday, October 20, 2016 at 9:48:55 PM UTC-5, Wolfgang Bangerth > wrote: > > > > What is

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

Dear Daniel, Please look at the pdf file attached. Thanks On Friday, October 21, 2016 at 4:51:22 PM UTC-5, Daniel Arndt wrote: > > Hamed, > > At least I can't open your file in a way to clearly see what your > bilinearform is, but could just guess from the implementation. Can you > either

[deal.II] How to apply boundary values for a particular point on the boundary instead of the whole boundary surface

Hi friends, For an elastic problem, I am going to apply zero boundary displacements for three specific points on the center of -x, -y and -z planes of a cubic domain. I have already done this but for the boundary surface not a boundary point (the same as incremental_boundary_displacement in

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

Dear Wolfgang, On Thursday, October 20, 2016 at 9:48:55 PM UTC-5, Wolfgang Bangerth wrote: > > What is the norm of the first right hand side? You now set the tolerance > in > the first iteration to a fixed value of 1e-16, but how does this compare to > the previous value of

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

Hi everyone, Thank you all for your incredible guides. It seems that I've been choosing wrong solver for my problem. Since my problem has some sort of instability in its nature, although my system_matrix is symmetric, it is not necessarily positive definite. So I have two questions: First, Is

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

:37 AM UTC-4, Hamed Babaei wrote:It > seems that I've been choosing wrong solver for my problem. Since my problem > has some sort of instability in its nature, >> >> although my system_matrix is symmetric, it is not necessarily positive >> definite. So I have two questio

[deal.II] Periodic Boundary Condition

Hi all, Following step-45, I am going to implement periodic boundary condition on my code for a Thermo-elastic problem, in which the thermal and elastic parts are solved separately (I have two different dof_handelers for temprature and displacement fields without any block structure). I am

[deal.II] Re: Periodic Boundary Condition

Dear Daniel, As you can see my assembly in the first post, my system_matrix and system_rhs are not made directly from cell_system_matrix or cell_system_rhs, but they are the result of some manipulations on mass_matrix, laplase_matrix and nl_matrix (the same approach as step_25) that have

[deal.II] Re: Periodic boundary conditions seem to be not applied

Dear Bastian and Daniel, > That's what I was assuming. So yesterday I did it with this code : > // This block add to the periodicity constraint the little > compression we want > { > IndexSet selected_dofs_left; > std::set< types::boundary_id > boundary_ids_left=

[deal.II] Re: Periodic Boundary Condition

In addition I just tried to apply periodic boundary condition constraints at the end of assembly using, void ConstraintMatrix::condense. However, it seems this function doesn't work with TrilinosWrappers::sparsematrix but dealii ones. Thanks -- The deal.II project is located at

[deal.II] Re: Periodic boundary conditions seem to be not applied

Daniel, You are completely right. The problem was resolved applying your comment. Thank you very much, Hamed -- 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

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

Dear Bruno, I mean non of the standard preconditioners helped to make it converged. On Monday, October 31, 2016 at 3:13:35 PM UTC-5, Bruno Turcksin wrote: > > Hamed, > > 2016-10-31 15:56 GMT-04:00 Hamed Babaei <hamedb...@gmail.com >: > > > I have already checked SS

[deal.II] Re: Convergence problem arising for large number of DoFs

n Monday, October 31, 2016 at 2:14:38 PM UTC-5, Bruno Turcksin wrote: > > Hamed, > > On Monday, October 31, 2016 at 3:01:20 PM UTC-4, Hamed Babaei wrote: >> >> This error message can indicate that you have simply not allowed a >> sufficiently large number of iterations for

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

be solved by the same solver or System_matrix features may change through palatalization. Thanks, On Wednesday, November 2, 2016 at 9:29:54 AM UTC-5, Bruno Turcksin wrote: > > Hamed, > > 2016-11-02 10:22 GMT-04:00 Hamed Babaei <hamedb...@gmail.com >: > > > It seems that my

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

system_matrix is not s.p.d any more although in sequential code it was. Thanks for your time, Hamed On Wednesday, November 2, 2016 at 8:00:23 AM UTC-5, Wolfgang Bangerth wrote: > > On 11/01/2016 10:31 AM, Hamed Babaei wrote: > > > > I mean non of the standard preconditioners helped to

Re: [deal.II] Re: what do SolverControl do for Direct Solvers?

On Friday, October 28, 2016 at 7:59:06 AM UTC-5, Bruno Turcksin wrote: > > Hamed, > > 2016-10-27 19:03 GMT-04:00 Hamed Babaei <hamedb...@gmail.com >: > > > I've been using the default one, Amesos_KLU, and I checked > > Amesos_Superludist but trilinos doesn't rec

[deal.II] Convergence problem arising for large number of DoFs

Hi all, I have parallelized a code in which I use GMRES or Bicgstab solvers with BlockJacobi preconditioner for a symmetric but not possitive-difinite system matrix. The problem is that it converges for 15 DoFs and fewer (on 1 node with 16 processor) but does'nt converge for larger number

[deal.II] Problem with PETScWrappers::SolverCG

Hi freinds, I have parallelized a code for a Thermoelastic problem based on step-40 . Although the non-parallel code works for all the initial values and boundary conditions, the parallel one fails giving this error : "PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably

[deal.II] Re: How to use Trilinos instead of Petsc in step-40

Another point I need to mention is that I had the same problem when as my first try of parallelization, I paralleled a much simpler code, the step-25, based on the step-40 . I received the same Segmentation Violation error from Petsc. At that time, I replaced PreconditionerAMG with

[deal.II] Re: How to use Trilinos instead of Petsc in step-40

Pelteret wrote: > > Hi Hamad, > > Can you please tell us which version of deal.II you are using, and provide > us with the installation logs? > > Regards, > J-P > > On Friday, October 14, 2016 at 11:51:09 PM UTC+2, Hamed Babaei wrote: >> >> Hi friends, >

[deal.II] Re: Periodic boundary conditions seem to be not applied

Dear Daniel, I have applied periodic boundary condition on displacement field for a square 2D domain and in order to apply boundary displacement I want to consider relative displacement between pair faces, namely, u_x (0,y)=u_x(L,y)+delta_x and u_y (x,0)=u_y(x,L)+delta_y , using

[deal.II] Re: Periodic boundary conditions seem to be not applied

I just realized that the problem comes from that part of the code that applies relative displacement between bottom and top faces, since there is not corner element distortion when having u_x (0,y)=u_x(L,y)+delta_x and I uncomment the second part of the code namely, { IndexSet

[deal.II] Re: Periodic boundary conditions seem to be not applied

Dear Daniel, > I would suggest you to look at the constraints in the ConstraintMatrix > using ConstraintMatrix::print[1] for a mesh consisting of has few cells as > possible. > Using DoFTools::map_dofs_to_support_points[2] you can then verify that > these are correct. > Issuing "

[deal.II] Alternative for ConstraintMatrix::condense in parallel codes?

Hi all, I have used* constraints.condense* function in a serial code to apply periodic constraints on system_matrix and system_rhs after their assembly in which I do not use *constraints.distribute_local_to_global* for cell_matrix and cell_rhs but I first assemble mass_matrix , laplace_matrix,

[deal.II] Re: Periodic boundary conditions seem to be not applied

Dear Daniel and Timo, Thank you very much for your advises. I have figured out the problem with the periodic constraints but I do not know where this problem comes from. Let me explain the issue more. As I mentioned earlier, I have applied periodic BC for displacement field and I want to apply

[deal.II] Re: Periodic boundary conditions seem to be not applied

Dear Daniel, > It seems that you are now constraining all the components, i.e. > u_x(0,y)=u_x(L,y) and u_y(0,y)=u_y(L,y). > Is this really what you want to do? Otherwise, you should have a > ComponentMask in your call to > DoFTools::make_periodicity_constraints as well, i.e. > > You are

[deal.II] Re: Periodic boundary conditions seem to be not applied

Dear Daniel, I just resolved the problem. Because constraints.close function resolves chains of constraints, It interfered with set_inhomogeinity process. So I had to issue constraints.close before applying inhomogeinities. Thank you very much for your helpful hints. I appreciate it. Hamed

[deal.II] what to do with Neumann term in week formulation when applying Periodic Boundary Condition

Hi all, I am considering Periodic Boundary Condition for a problem which is very simillar to step-25. Before applying periodic condition, I considered homogeneous Newmann Boundary condition in external surfaces by simply omitting Neumann term in week formulation (v , n.grad(u) )=0. However,

[deal.II] Re: what to do with Neumann term in week formulation when applying Periodic Boundary Condition

Another Point I would like to mention is that I checked constant values for neumann_value( for example, 0.7) and the solver converges. So I think problem comes from the way I compute neumann_value from old_solution. I has followed step-7, in which non-homogeneous Neumann boundary values are

[deal.II] How to apply non-homogeneous Neumann boundary conditions when we do not have exact solution

Hello all, Following step-7 I am going to apply non-homogeneous Neumann boundary conditions. The problem is that, in step-7, Neumann value is computed using exact solution, however in real-life problems we do not know exact solution beforehand. Neumann value is computed in step-7 as follows:

[deal.II] Re: Periodic Boundary Condition

Dear Daniel, Happy new year. I wish a wonderful new year for you ! This is only (directly) possible if you are not using inhomogeneous > constraints. In that case, you can call > ConstraintMatrix::distribute_local_to_global separately for matrix and > right-hand side. > I am struggling to

[deal.II] Re: Periodic Boundary Condition

Dear Daniel, You can obtain local DoF values from a global FE vector using > FEValuesBase::get_function_values [1], create the right-hand side locally > as you wish and use ConstraintMatrix::distribute_local_to_global to create > the global right-hand side. This is outlined in step-21 for

[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

Dear Jean-Paul, Thank you for your prompt help. Although I don't really understand your specific question, I am guessing > that you were wondering if its possible to use the "repetitions" parameter > to bias the initial mesh gradation before adding periodicity (since the > periodic face pairs

[deal.II] Adding periodicity to a thin sample with one element in thickness direction

Hello, I want to apply periodic boundary condition on a 3D thin square plate with one element in the thickness direction. I have already used the following for meshing std::vector< unsigned int > repetitions(dim, 100); if (dim == 3) repetitions[dim-1] = 1;

[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

; that you're experiencing, I would say that this is an unexpected outcome. > > Regards, > Jean-Paul > > On Monday, May 15, 2017 at 3:40:20 PM UTC+2, Hamed Babaei wrote: >> >> Dear Daniel, >> >> As far as I see, GridGenerator::subdivided_hyper_rectangle on

[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

Hello all, You are right. I was running in debug mode, slowing down the code. Thank you very much for your incredible help. I appreciate your kindness and generosity to support the community. Best regards, Hamed -- The deal.II project is located at http://www.dealii.org/ For mailing

[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

Dear Daniel, As far as I see, GridGenerator::subdivided_hyper_rectangle only calls > "Triangulation::create_triangulation" and hence creates a coarse > triangulation. > Can you confirm either? > If GridGenerator::subdivided_hyper_rectangle creates a coarse triangulation, a question arises

[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

Hello all, I am so sorry, Wolfgang, if I failed to express my thoughts in a clear and proper manner. Let me restate my reply to J-P's comment, Hope it is better this time ! > I've attached a slightly amended version of your code that I think will > highlight what the perceived problem is.

[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

; Refinement iteration: 3 >> Finished. > > > Regards, > Jean-Paul > > On Tuesday, May 16, 2017 at 6:17:07 PM UTC+2, Hamed Babaei wrote: >> >> Dear Jean-Paul and Daniel, >> >> I provided a minimal code which demonstrates the issue. There is no >

Re: [deal.II] Re: Multiple Triangulations

Dear Dr. Bangert, Since you have hanging nodes, do you apply hanging node constraints to > the displacement field you then put into MappingQEulerian? > It turns out that I have not applied hanging node constraints properly. I just did so and the problem was solved. Thank you very much for

[deal.II] GridTools::collect_periodic_faces has problem with meshes generated by Gmsh or Abaqus when running in parallel.

Hi All, I'm having problem when applying periodicity on meshes generated with Gmsh or Abaqus. The problem arises when I run in parallel (in serial it works) getting the following error: void dealii::GridTools::match_periodic_face_pairs(std::set >&,

[deal.II] Re: GridTools::collect_periodic_faces has problem with meshes generated by Gmsh or Abaqus when running in parallel.

Dear Dr. Arndt, Thank you very much for your help. The problem was resolved applying your comment. I was setting the indicators running over locally owned cells not all the cells. Best regards, Hamed On Saturday, February 17, 2018 at 11:20:32 AM UTC-6, Daniel Arndt wrote: > > Hamed, > > for

Re: [deal.II] Trouble using VectorTools::interpolate_based_on_material_id

Dear Wolfgang, Thank you for opening the Github issue. I've been looking around the function implementation and will be trying to figure out the issue. I will update you once I have some understanding. Regards, -- The deal.II project is located at http://www.dealii.org/ For mailing

Re: [deal.II] Trouble using VectorTools::interpolate_based_on_material_id

Dear Wolfgang: Thank you for your time addressing this issue. -- 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

[deal.II] Re: Trouble using VectorTools::interpolate_based_on_material_id

I just realized I made a mistake and uploaded the executable instead of the mini code itself! It is uploaded again here. On Monday, December 10, 2018 at 11:17:40 AM UTC-6, Hamed Babaei wrote: > > Hello, > > I would like to forcefully determine the solution at some regions of

Re: [deal.II] Trouble using VectorTools::interpolate_based_on_material_id

Dear Wolfgang, In the meanwhile that the VectorTools::interpolate_based_on_material_id function is taking care of, I just did the same through the following code to change my solution vector in the specific regions with designated material_id, which may be used by those who have the same issue

Re: [deal.II] Trouble using VectorTools::interpolate_based_on_material_id

Dear Wolfgang, > In other words, there are no NaNs for me. What do you get? And what > version of > deal.II are you using? > Thank you very much for your help. In fact, what you got is for the case that the material_id for the entire domain (both half of cubes) is included in

Re: [deal.II] Trouble using VectorTools::interpolate_based_on_material_id

I forgot to mention that I am using deal.ii 9.0.0 version. Thanks -- 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

Re: [deal.II] SymmetricTensor rank 6 implementation issue

Dear Wolfgang, I believe it will be less time-consuming if I simply avoid using the SymmetricTensor class and use the Tensor class instead and insert the symmetric elements manually. Thanks anyway for your incredible support! -- The deal.II project is located at http://www.dealii.org/ For

[deal.II] SymmetricTensor rank 6 implementation issue

Hello, I am planning to use a symmetric tensor rank-6 for third-order elastic constants in a nonlinear elasticity code. The tensor is supposed to be symmetric within each three pair indices as well as all possible orders of pair permutations. Namely, C_ijklmn = C_jiklmn = C_ijlkmn = C_ijklnm

[deal.II] Re: SymmetricTensor rank 6 implementation issue

add #include We cannot > do explicit instantiation for every thing so if you have something that is > less common you need the extra include. > > Best > > Bruno > > On Friday, May 3, 2019 at 4:07:56 PM UTC-4, Hamed Babaei wrote: >> >> Hello, >> >&

[deal.II] Re: SymmetricTensor rank 6 implementation issue

Dear Bruno, Thank you very much for your hint. I added the extra include but it did not help and I am still getting the same error! I am wondering what other things I may want to try? Thanks -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

[deal.II] Problem with the installation of deal.II v9.2.0 using Candi

Hello everyone, I'm trying to install the last version of deal.II using candi shell script. I have used it multiple times before and it worked well as I install all prerequisite packages as it suggests. However, I get the following error this time. I appreciate it if anyone could let me know