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

Hamed, [...] > I am going to do the same as Bastian, namely periodic boundary condition > for displacement such that u( 0, y ) = u( 1, y ) + *lambda ,* > * so I used the recommended above code by Bastian for applying > inhomogenity to predefined periodicity, in order to have reletive >

[deal.II] Re: Periodic Boundary Condition

Hamed, 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 condition in Meshworker.

Sudarshan, J-P is right. You can use constraints within the MeshWorker framework and hence also periodic boundary conditions. In more detail, you have to provide the assembler with the ConstraintMatrix. In addition to step-45 for periodic boundary conditions, you should also have a look to

[deal.II] Re: hp HDG in deal.II

Samuel, I am attempting to implement a hp hybridized dg-method for solving > ellipctic problems in deal.II. I am relying on steps 27 and 51 of the > deal.II tutorial programs. However, when I try to group some FE_FaceQ > elements in an hp::FeCollection and distribute the degrees of freedom, I

[deal.II] Re: Periodic Boundary Condition

Hamed, Am Dienstag, 15. November 2016 19:09:18 UTC+1 schrieb Hamed Babaei: > > 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

[deal.II] Re: Very basic question on setting boundary id

Jaekwang, It seems that you are missing constraints.distribute(solution); after solving the linear system. The constrained dofs are set to zero during assembly and this call is necessary to get the correct values for these in the solution as well. You might want to have a look at

[deal.II] Re: storing sparse matrix in .txt and scan in Matlab

Anup, > >> 1. if the way of writing the sparse matrix on a .txt file is appropriate >> for post-processing in matlab, if not, please suggest >> a way; >> > > There are three print functions in the deal.II SparseMatrix. As explained > in the documentation >

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

Hamed, Using the print function of Sparsematrix class (Thanks to Daniel for > letting me know that) I printed the elements of system_matrix for both > sequential and parallel codes. > I reduced the problem to only 54 DoFs. It seems that both system_matrices > are symmetric and Identical

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

Hamed, 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? > All of the matrix classes

[deal.II] Re: Visit error...?

Kyusik, Am Donnerstag, 3. November 2016 10:51:20 UTC+1 schrieb hank...@gmail.com: > > Hi all, > > I'm trying to calculate absolute values of (exact_solution - > numeric_solution) and visualize it using Visit. > > So, I added the following in my code. > > error = solution; > error -=

[deal.II] Re: Extra layer around mesh

Joel, Same error with your changes. I searched for subdivided in > http://www.dealii.org/developer/doxygen/deal.II/changes_between_8_3_and_8_4.html > > and found under specific improvements, that subdivided_parallelepiped > produced the wrong boundary indicators. Could this be the reason, why

[deal.II] Re: hp convergence for non-linear solver.

Jaekwang, [...] > > VectorTools::integrate_difference > (dof_handler,solution,Solution(), > >difference_per_cell > *,QGauss(degree+**2**)*,VectorTools::L2_norm); > somegthing that immediately comes to mind is that you don't use a non-default Mapping

Re: [deal.II] computing some other output quantity after solution is calculated.

Kyusik, [...] > 3. I calculated l2 norm > Difference = solution; > Difference -= exact_solution; > norm = Difference.l2norm(); > > But, according to what you mentioned, I calculated l2norm of U_i-U_i_exact > not l2norm of u_h(x)-u_h_exact(x) > Yes, this gives you the l2-norm of U_i-U_i_exact

[deal.II] Re: computing some other output quantity after solution is calculated.

Kyusik, //by Han(To get psi0) > Vector::iterator max; > max=std::max_element(solution.begin(),solution.end()); > This can only work if you know that the maximum is attained at one of the support_points of your FiniteElement. In general, you can use VectorTools::integrate_difference to

Re: [deal.II] Re: boundary conditions

> > so the uniform flux from left and right of the rectangle implies periodic > boundary condition. But the K ( hydraulic conductivity) is a function of > (x,y). > If we want to enforce the periodic boundary condition, should we expect to > have a condition on K ? should K be periodic as well

[deal.II] Re: Error with the content "dealii::numbers::is_finite(sum)"

Benhour, are you running in serial or with more than one process? In the first case, I would suspect that your matrix is singular. Best, Daniel -- 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 ---

[deal.II] Re: boundary conditions

OK. So do I understand you correctly, that you are imposing Neumann boundary conditions on all *four* boundaries? In that case the solution is only unique up to a constant. It seems to my that in the problem I posed, the boundary condition is not > correct. > Can you be a bit more specific? How

[deal.II] Re: boundary conditions

Retired Replicant, H can be hydraulic head and K is the hydraulic conductivity. > Or H can be temperature with k being diffusion coefficient. > Have a look at step-7, if you just consider a diffusion problem. There Neumann boundary conditions are used on part of the boundary which is also

[deal.II] Re: Trouble with VisIt 2.11

Praveen, It's hard to tell from your description what is causing the error. At least, Visit has some internal problems and if you can open with a previous version, chances are high that this is a Visit issue. Can you open the file with Paraview or any other suitable program? Can you provide us

[deal.II] Re: How to use sacado package

Jaekwang, It seems that no fortran compiler is found. You should be able to configure Trilinos without fortran using -DTrilinos_ENABLE_Fortran:BOOL=OFF After that it's the usual make install [1]. Best, Daniel [1] https://www.dealii.org/developer/external-libs/trilinos.html Am Samstag, 22.

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

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 write it here (using LaTeX or similar) or upload the file as pdf again? Best, Daniel -- The deal.II project is located at

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

Hamed, which solvers do you think I can examin and see if they can be used instead > of SolverCG? > Running with the deal.II CG solver gives me An error occurred in line <424> of file in function void

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

Hamed, running your code with a Trilinos installation alone fails for me in line 1617 with An error occurred in line <279> of file in function void dealii::TrilinosWrappers::SolverBase::do_solve(const dealii::TrilinosWrappers::PreconditionBase&) The violated condition was: false

[deal.II] Re: Easy way to calculate second-deviatoric tensor

Jaekwang, >From this symmetric gradient tensor, do we have one easy way to calculate > the following "the second invariant of rate-of-strain tensor"? > There is SymmetricTensor::second_invariant [1] which is defined as I2 = 1/2[ (trace sigma)^2 - trace (sigma^2) ] and

Re: [deal.II] Derivatives (gradients) of Symmetric Tensors

Metin, I understand that the components are in space (x/y/z), > and (*shape_gradient_ptr++)[d] would be derivative of phi in each > direction; is that correct? > Yes, that is the derivative of the dth component in direction d. > > (compared to vectors) the implementation of divergence function

Re: [deal.II] Derivatives (gradients) of Symmetric Tensors

Metin, [...] > For the vectors, the implementation (for the else case) is as following; > > *for* (*unsigned* *int* shape_function=0; > >shape_function > { > > *for* (*unsigned* *int* d=0; d<*spacedim*; ++d) > >

[deal.II] Re: Vector-valued gradient of solution vector

Joel, Yes, this looks about right. I would really replace "std::vector double x,y,z" by "Vector x,y,z". In the end, entries in these vectors only make sense with the corresponding DoFHandler. This would also allow you to use these Vectors for postprocessing in deal.II. Best, Daniel -- The

[deal.II] Re: Vector-valued gradient of solution vector

Joel, I did try it, but I cant just change the local_velocity_values from a > std::vector> to std::vector. Then the > fe_values[velocities].get_function_values function doesnt compile. > That's true, but you should use std::vector and not std::vector, see also [1]. >

[deal.II] Re: More power outages

Everything should be available again. Am Mittwoch, 28. September 2016 15:19:15 UTC+2 schrieb sotelo...@gmail.com: > > it is already 28th, the server still down. is it going to take longer > than announced? > Edith > > On Monday, September 12, 2016 at 11:21:13 AM UTC-5, Guido Kanschat wrote: >>

[deal.II] Re: Vector-valued gradient of solution vector

Joel, Its been a week since my latest post, I was just wondering if you could > help me. > Did you try what I suggested? What were the problems? Looking at the latest files you sent, local_velocity_values has still not the type std::vector and you are still using for (unsigned int

[deal.II] Re: how to get 3D structured mesh from rotated 2D mesh in dealii

Marek, [...] I would like to process it in dealii by rotating it around y-axis, to > get 3D grid. > Is it possible in dealii? > No, there is no such function yet. > [...] > My objective is the mesh in the file the attached file perf_chamber.png, > which was obtained by merging > the inner

[deal.II] Re: periodic boundary conditions

Juan, [...] > 1) My first question is about how the "direction" works, is it 1 > correspond to "x" and 2 corresponds to "y"? > No, direction 0/1/2 means that the support_points of the dofs to be identified just differ in the x-/y-/z-component. What you are doing should be perfectly fine. >

[deal.II] Re: Input Q2 element generated by Gmsh using Gridin

Chenchen, We only support to read in meshes that are not refined. Translated to your situation this means that you are only able to use Q1 meshes as initial grid. Of course, you can then use triangulation.set_manifold to define the correct behavior when you refine your mesh within dealii along

[deal.II] Re: Can we say that the higher order method, the more accurate?

Jaekwang, Have a look at step-10. There you see how the order of the mapping influences the error. Basically, you have to set the mapping for your FEValues objects, when you compute error via integrate_difference and when you project or interpolate some Function to an FE Vector. Best, Daniel

Re: [deal.II] VectorTools::integrate_difference function

...of course I meant dof_handler.distribute_dofs(). Does the DoFhandler know at this point about the Trinagulation? Best, Daniel Am Dienstag, 20. September 2016 17:58:02 UTC+2 schrieb Daniel Arndt: > > Jaekwang, > > This seems to be unrelated. Did you setup the Triangulation be

Re: [deal.II] VectorTools::integrate_difference function

Jaekwang, This seems to be unrelated. Did you setup the Triangulation before calling fe.distribute_dofs()? Best, Daniel Am Dienstag, 20. September 2016 17:04:02 UTC+2 schrieb JAEKWANG KIM: > > yes...I tried that before, but I get an error message as follow.. > > As you mentioned, I first

[deal.II] Re: Vector-valued gradient of solution vector

Joel, > [...] > for (unsigned int q_index=0; q_indexfor (unsigned int i=0; i { > velocity[local_dof_indices[i]] = local_velocity_values[q_index]; > } > > Here you assign the same Tensor<1,dim> at all DoFs

[deal.II] Re: A*diag(V) with mmult?

Franck, One possibility is to use A.mmult(C,B,V) where B is an IdentityMatrix. Another way is to create an IdentityMatrix B, modify its entries suitably and use A.mmult(C,B). A third approach would be to just write the the scaling yourself. Best, Daniel Am Sonntag, 18. September 2016 18:01:17

[deal.II] Re: Can we say that the higher order method, the more accurate?

Jaekwank, You would indeed expect significantly better results with higher polynomial degree on the same mesh, if the solution is sufficiently regular. What kind of mesh are you using? Are you resolving all the boundary layers suitably? Are you using a Mapping of the same order as your velocity

[deal.II] Re: How to find all the partial derivatives of the solution polynomial in deal.II

Jiaqi, Currently you can access first, second and third partial derivatives in FEValues. The FiniteElement class also implements fourth derivatives. If this is sufficient for your purposes, then using FEValues*::third_derivative should be fine for you. I don't see a easier way at the moment.

[deal.II] Re: Using constraints for already assembled RHS

Rajat, The first equation is the usual equilibrium equation. It is solved to give > displacements. The stiffness matrix is then multiplied by this global > displacement vector to give the global traction vector which forms the rhs > for the second equation. > The easiest solution to deal with

Re: [deal.II] singularity error due to 1/0

Kyusik, Can you summarize what you have tried and which errors/problems you got with these approaches? What exactly do you mean with "csc(theta) or sec(theta) can't be used in cylindrical coord system"? Best, Daniel Am Freitag, 9. September 2016 06:17:44 UTC+2 schrieb hank...@gmail.com: > >

[deal.II] Re: nearest neighbor

Joel, In GridTools::find_cells_adjacent_to_vertex(dof_handler,center_id) you need to give the number of the vertex_number as center_id, not the number of the degree of freedom. Then, you want to use Quadrature quadrature_formula(dof_handler.get_fe().get_unit_support_points()); to create a

[deal.II] Re: Neumann condtitions in the mixed space setting

Eldar, As you already found out, interpolate_boundary_values can only be used with a ComponentMask if the element you are using is primitive. Therefore, the workaround you are using seems to be suitable for the moment. Since BDM1 is div-conforming, project_boundary_values and

[deal.II] Re: where and how should I use the MeshWorker class? how should I do to implement DG without MeshWorker?

An old version of step-12[1] has an implementation that doesn't use MeshWorker. In my opinion, it is covenient to use MeshWorker if you can when you want to consider discontinuous ansatz spaces due to the different cases that can occur for face contributions. If you want or need to use more

[deal.II] Re: Vector-valued gradient of solution vector

I do that? > > Best, > Joel > > On Friday, August 12, 2016 at 5:35:07 PM UTC+2, Daniel Arndt wrote: >> >> Joel, >> >> Yes the matrix you are assembling is a vector-valued mass matrix now. >> For me your code is failing with >> >> void dealii::FEValuesBa

Re: [deal.II] Re: Getting number of hanging support points

Deepak, I am aware of the fact that ConstraintMatrix.n_constraints() gives the > number of hanging nodes for h-refinement, but if I only use p-refinement, > can it give the number of hanging support points occurring due to the > difference in the order of bases between two adjacent elements? I

[deal.II] Re: [dealii-developers] dealii.org website down?

dealii.org is online again. Am Mittwoch, 17. August 2016 19:33:48 UTC+2 schrieb Wolfgang Bangerth: > > On 08/17/2016 11:30 AM, thomas stephens wrote: > > Currently unable to load https://www.dealii.org/ along with tutorials > > (problem began at approximately 12:30pm ETD) > > Yes, there is a

[deal.II] Re: Data exchanges in IO

Bruce, The p_local_solution vector is filled with values as the result of solving > a linear equation, p_local_rho is filled with values by looping over > individual elements and assigning values calculated from other quantities. > Part of the reason the p_local_rho vector doesn't have ghost

[deal.II] Re: Vector-valued gradient of solution vector

Joel, Yes the matrix you are assembling is a vector-valued mass matrix now. For me your code is failing with void dealii::FEValuesBase::get_function_gradients(const InputVector&, std::vector >&) const [with

[deal.II] Re: Vector-valued gradient of solution vector

Joel, Does the equation you want to solve for have multiple components? Otherwise it would not make sense to multiply in the right hand side something with a gradient. If you want to project the gradient into a vector valued finite element ansatz space, then the matrix you are assembling looks

[deal.II] Re: Using the solution from one problem as a boundary condition in another problem with matching mesh on the boundary

can somehow evaluate the boundary > conditions? Or what would a better approach be? > > On Saturday, July 30, 2016 at 1:38:06 PM UTC+3, Daniel Arndt wrote: >> >> krei, >> >> If you want to solve different PDEs on different domains that can be >&g

Re: [dealii-developers] step 47

You might want to have a look at http://journals.ub.uni-heidelberg.de/index.php/ans/article/view/22317/23996 This seems to be quite similar. Best, Daniel Am Dienstag, 9. August 2016 19:28:51 UTC+2 schrieb bangerth: > > On 08/08/2016 11:55 PM, sella...@gmail.com wrote: > > I am a new user of

[deal.II] Re: Undefined reference to `tbb::interface5::internal::task_base::destroy(tbb::task&)

It seems that there is something wrong with your TBB installation. Which version of TBB are you using? Could you send your "detailed.log" file located in the deal.II build directory? TBB is also bundled with deal.II and you can force to use that via $ cmake -DDEAL_II_FORCE_BUNDLED_THREADS=ON .

Re: [deal.II] Step-42 -- Problem with Trilinos and P4EST

t;>> >>>> How should I solve this problem. >>>> Best regards. >>>> Ehsan >>>> >>>> On Monday, August 1, 2016 at 2:21:31 PM UTC+2, Ehsan wrote: >>>>> >>>>> Dear Daniel, >>>>&g

Re: [deal.II] Re: Using create_point_source_vector() function with hp::DoFHandler

Deepak, without a working example I can run, I don't see an obvious error. Note that there are two tests, namely "numerics/create_point_source_hp" and "hp/vectors_point_source_hp_01" that test `VectorTools::create_point_source` for hp. Maybe this helpful for debugging. Best, Daniel -- The

[deal.II] Re: Using create_point_source_vector() function with hp::DoFHandler

Deepak, could you provide us with a minimal example that shows your problem? Are you running in debug mode? What exactly does the program tell you when aborting? Best, Daniel -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

Re: [deal.II] Re: Transferring solutions in distributed computing

Junchao, It seems that the documentation is outdated for this piece of information. In fact, neither PETScWrapper::MPI::Vector nor TrilinosWrappers::MPI::Vector does have update_ghost_values. What you should do is exactly what is done in the few lines of step-42 you referenced. "solution =

[deal.II] Re: Transferring solutions in distributed computing

Junchao, You want to use parallel::distributed::SolutionTransfer instead if you are on a parallel::distributed::Triangulation Executing $ grep -r "parallel::distributed::SolutionTransfer" . in the examples folder, tells me that this object is used in step-32, step-42 and step-48. Have for

[deal.II] Re: geometry

Benhour, you can find a modification of step-3 in which the domain is a quarter circle attached. The four cells from GridGenerator::half_hyper_ball have been replaced by just three. The vertex (0,-radius) has been removed and all the remaining vertices with a negative y-component have been

[deal.II] Re: geometry

Benhour, It would be helpful if you tell us what the problem with the newly created problem is. Looking at the implementation of GridGenerator::half_hyper_ball [1], you can observe that there are cells which have vertices both with positive and negative y-components. This will likely lead to

[deal.II] Re: geometry

Benhour, Did you try what I suggested in https://groups.google.com/d/msg/dealii/QPLvZIQx7yw/LQ7t0-xWBgAJ ? Best, Daniel -- 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

[deal.II] Re: problems with installation ; Unknown CMake command "DEAL_II_ADD_LIBRARY"

Pablo, Did you see https://groups.google.com/forum/#!topic/dealii/rTx7Fea65dM ? Can you try without Opencascade and a clean build directory? Do you get this error also with the latest release tarball? Best, Daniel Am Montag, 4. Juli 2016 10:15:34 UTC+2 schrieb Pablo Perez del Castillo: > >

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

Ehsan, All I can say: After switching the order of arguments in SparseMatrix::add, your code runs for me with a recent developer version and Trilinos at least. Best, Daniel Am Montag, 4. Juli 2016 18:59:05 UTC+2 schrieb Ehsan Esfahani: > > Dear Professor Bangerth, > > Thanks for your response.

[deal.II] Re: Question about Dealii

Hamed, Have a look at how temporary non-ghosted vectors are used in step-40. Similar to VectorTools::interpolate the solution vector in SolverCG::solve must not be ghosted. Best, Daniel Am 07/01/2016 um 01:15 AM schrieb Hamed Babaei: > Hi Daniel, > > I hope you are doing well. > I got an error

[deal.II] Re: Extract boundary DoFs using DoFTools::extract_boundary_dofs() and Indexset for parallel distributed triangulation

Pasha, First of all: The sum of values in the right-hand side vector only corresponds to a sum of values of the represented right-hand side function, if you use interpolating Finite Elements (such as FE_Q). Furthermore, you have to be sure that you are really interested in the values and not

[deal.II] Re: Extract boundary DoFs using DoFTools::extract_boundary_dofs() and Indexset for parallel distributed triangulation

Dear ?, dealii::IndexSet::ElementIterator::operator*() returns the stored global_dof_index [1]. Therefore, all you have to do is to dereference index: dealii::types::global_dof_index gdi = *index Best, Daniel [1]

Re: [deal.II] Re: Read serial vector into a parallel vector

Praveen, Am Montag, 20. Juni 2016 18:05:12 UTC+2 schrieb Praveen C: > > Hello Daniel > > I have a normal Triangulation and I solve on this using a Vector. > I could save this to file calling Vector::print. > > Is it now possible to read this into a TrilinosWrappers::MPI::Vector ? > No, there is

[deal.II] Re: Read serial vector into a parallel vector

Praveen, I solve a PDE in serial and save the solution to file. > Do you mean that your triangulation is not a parallel::distributed::Triangulation or that you are simply running with one process? > Is there a way to now read this solution into a > TrilinosWrappers::MPI::Vector object ? >

[deal.II] Re: Using the solution nodal values at previous time steps

Mohammad, first of all const double old_s = old_solution_values[q_point](1); const double old_s = old_solution_values0[q_point](1); const double old_s = old_solution_values1[q_point](1); looks weird. Are you redefining old_s all the time? Apart from that it looks so far good to me. Can

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

>else if (face_center[0] == 0) //Left >>> cell->face(f)->set_boundary_id (1); >>>else if (face_center[0] == 1) //Right >>> cell->face(f)->set_boundary_id (3); >>>else //No way >>> cell-&g

Re: [deal.II] new shape function definition

Bastien, as there already is the Polynomial class HermiteInterpolation you should create a new FiniteElement based on a TensorProductPolynomial. A good way might be to copy FE_Q_Base and modify it accordingly. Of course you need to think about how to interpolate values using this element, how

[deal.II] Re: Thermoelastic Problem

d stored on a quadrature > point related to elastic problem DofHandler, in order to solve > stress-induced heat equation problem. In other words, I don't know how to > exchange information between two equation. > > Thanks, > Hamed > > On Friday, June 3, 2016 at 3:40:28

[deal.II] Re: Doubt in Mesh Movement Step 42

ing that the dof is a locally owned dof by using the is_element > of the indexset of locally owned dofs help ? > Will this be slow ? > > > On Wednesday, May 25, 2016 at 7:19:27 AM UTC-4, Daniel Arndt wrote: >> >> Dear Rajat, >> >> After the mesh partitioning is done,

[deal.II] Re: Post-processing of solution (computing stress distribution)

Hey David, Yes, this won't work since FEValues need a cell to reinit to get mapping > data. I looded at the class DataPostprocessor as you mentioned, but don't > quite understand the parameters passed to compute_derived_quantities_vector > method. I don't understand what exactly is the

[deal.II] Re: Post-processing of solution (computing stress distribution)

David, the code snippet you posted is not going to work. You can't use a FEValues without initializing it with a cell_iterator. If all the information you need for your postprocessing is contained in a data vector based on a single DoFHandler, then DataPostprocessor is what you want to use. If

Re: [deal.II] Help with interpretation of PETSc and SLEPc error message.

Dear David, for debugging your code you should start with simplifying your code as much as possible to see what is going wrong. In particular, you should try with not refining your mesh and confirm that the assembled matrices look as they should. Can you modify the parameters in such a way that

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