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

2016-06-08 Thread Daniel Arndt
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

Re: [deal.II] new shape function definition

2016-06-07 Thread Daniel Arndt
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: Periodic boundary conditions seem to be not applied

2016-06-07 Thread Daniel Arndt
>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

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

2016-05-25 Thread Daniel Arndt
Dear Rajat, After the mesh partitioning is done, in a parallel::distributed::Triangulation the local meshes are independent of each other. In particular, moving a vertex on one process does not change anything for all the other processes. Therefore, it is necessary to move the vertices of a

[deal.II] Re: Thermoelastic Problem

2016-06-07 Thread Daniel Arndt
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

2016-05-30 Thread Daniel Arndt
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: Read serial vector into a parallel vector

2016-06-20 Thread Daniel Arndt
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: Post-processing of solution (computing stress distribution)

2016-05-22 Thread Daniel Arndt
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

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

2016-05-23 Thread Daniel Arndt
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

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

2016-05-16 Thread Daniel Arndt
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

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

2016-07-28 Thread Daniel Arndt
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

[deal.II] Re: A question about velocity correction in Step-35

2016-07-30 Thread Daniel Arndt
Jiaqi, the algorithm in step-35 is the one that is proposed in "L. Timmermans, P. Minev, and F. Van De Vosse, “An approximate projec- tion scheme for incompressible flow using spectral elements”, International journal for numerical methods in fluids, vol. 22, no. 7, pp. 673–688, 1996." The

Re: [deal.II] Re: A question about velocity correction in Step-35

2016-07-31 Thread Daniel Arndt
Wolfgang, Interesting that this isn't even mentioned in the introduction to that > program, or anywhere else, for that matter. How did you find out? > A major part of my PhD thesis is based on these projection methods. Reading the literature this seems to be the first paper in which the

[deal.II] Re: time-dependent boundary conditions for distributed computations

2016-07-31 Thread Daniel Arndt
Marek, You would just set up your ConstraintMatrix anew. This is also the way it is done in step-44. 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 message

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

2016-08-03 Thread Daniel Arndt
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

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

2016-08-11 Thread Daniel Arndt
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: tests fail

2016-08-11 Thread Daniel Arndt
Giorgis, This looks like a problem with your PETSc installation. Can you confirm that it is installed correctly? Do any problems appear if you compile deal.II without PETSc? Best, Daniel Am Donnerstag, 11. August 2016 22:16:49 UTC+2 schrieb Giorgos Kourakos: > > Hi, > > I'm trying to compile a

[deal.II] Re: Data exchanges in IO

2016-08-12 Thread Daniel Arndt
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

2016-08-12 Thread Daniel Arndt
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: geometry

2016-07-13 Thread Daniel Arndt
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: Transferring solutions in distributed computing

2016-07-21 Thread Daniel Arndt
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

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

2016-07-21 Thread Daniel Arndt
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: geometry

2016-07-16 Thread Daniel Arndt
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

2016-07-17 Thread Daniel Arndt
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

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

2016-07-04 Thread Daniel Arndt
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: problems with installation ; Unknown CMake command "DEAL_II_ADD_LIBRARY"

2016-07-04 Thread Daniel Arndt
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: > >

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

2016-08-06 Thread Daniel Arndt
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] Re: Using create_point_source_vector() function with hp::DoFHandler

2016-07-28 Thread Daniel Arndt
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 the solution from one problem as a boundary condition in another problem with matching mesh on the boundary

2016-08-09 Thread Daniel Arndt
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

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

2016-06-30 Thread Daniel Arndt
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]

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

2016-07-01 Thread Daniel Arndt
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: Question about Dealii

2016-07-01 Thread Daniel Arndt
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

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

2016-06-20 Thread Daniel Arndt
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: Source of a constant residual error when a triangulation has hanging nodes

2017-02-01 Thread Daniel Arndt
Pasha, I have a code that works fine. Now, I am working to change the code > structure to use “workstream”. The new code works fine without adaptive > refinement. However, when the mesh is refined and the triangulation has > hanging node, a constant residual error remains during Newton

Re: [deal.II] Re: How to shift a ConstraintMatrix that initialized with IndexSet?

2017-02-06 Thread Daniel Arndt
Ce Qin, This finally made its way into the developer version via PR #3722 . The approach we finally came up with is to also shift the local indices when shifting the ConstraintMatrix objects.[1] Merging two ConstraintMatrix objects also merges the

[deal.II] Re: Synchronization issue for parallel computation of material forces

2017-02-06 Thread Daniel Arndt
Seyed, your results look like the ghost values are wrong. My first guess would be that you are still using a completely distributed vector (one initialized with locally_owned_dofs only) instead of a ghosted one (initialized with locally_owned_dofs and locally_relevant_dofs). Can you confirm

[deal.II] Re: neighboring faces on the boundary

2017-02-06 Thread Daniel Arndt
> > We actually already have a function that can do 1/2 the job for you, > namely GridTools:: compute_active_cell_halo_layer > . > > In this instance your predicate would be whether the

[deal.II] Re: Assembly of material forces

2017-01-25 Thread Daniel Arndt
Seyed, What exactly are you trying to do? Which equations are you considering? How would what you want to do look in formulas? The information you provide are much too high-level to expect a useful answer. [...] > Conclusion: It would be great, if you can at least guide me to the correct >

[deal.II] Re: Postprocessing using the same variable twice

2017-01-22 Thread Daniel Arndt
> > Is it possible to output the magnitude of displacements and its components > all together? > > std::vector > data_component_interpretation(dim, DataComponentInterpretation:: > component_is_part_of_vector); > > The above allows me to output the displacements as a vector field and > shows

[deal.II] Re: Matrix tools in MatrixCreator namespace

2017-02-16 Thread Daniel Arndt
Sumedh, I want to use the *create_mass_matrix* and *create_laplace_matrix* > functionality of MatrixCreator namespace. The function prototype here > requires to pass a pointer (which is by default 0 meaning that there is no > variable coefficient associated with variable or laplace of

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

2016-08-19 Thread Daniel Arndt
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: Derivative of a scalar function in the code

2016-08-15 Thread Daniel Arndt
Benhour, What exactly is your problem? Lots of the examples programs, i.e. step-14, step-15, step-18, step-31, step-32, step-35, step-43 and step-44, use FEValues::get_function_gradients. Best, Daniel Am Montag, 15. August 2016 03:13:14 UTC+2 schrieb benhour@gmail.com: > > Dear All, > I

[deal.II] Re: nearest neighbor

2016-09-07 Thread Daniel Arndt
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

2016-08-31 Thread Daniel Arndt
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: Using constraints for already assembled RHS

2016-09-12 Thread Daniel Arndt
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

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

2016-09-16 Thread Daniel Arndt
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.

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

2016-09-09 Thread Daniel Arndt
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: Vector-valued gradient of solution vector

2016-09-29 Thread Daniel Arndt
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

2016-09-28 Thread Daniel Arndt
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]. >

Re: [deal.II] how to use solution.

2016-10-05 Thread Daniel Arndt
Kyusik, As Wolfgang already mentioned, you want to use FEValues::get_function_values() to extract from a global FE Vector the local values at the quadrature points in the cell you are on. These quadrature points normally don't coincide with with the mapped unit support points of the

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

2016-10-04 Thread Daniel Arndt
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] Re: how to get 3D structured mesh from rotated 2D mesh in dealii

2016-10-04 Thread Daniel Arndt
Marek, Only the vertices with indices in considered_vertices are tested for >> equality. This speeds up the algorithm, which is quadratic and thus quite >> slow to begin with. However, if you wish to consider all vertices, simply >> pass an empty vector. >> > > i.e. I have assumed it is

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

2016-09-20 Thread Daniel Arndt
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: Can we say that the higher order method, the more accurate?

2016-09-20 Thread Daniel Arndt
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

2016-09-20 Thread Daniel Arndt
...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

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

2016-09-21 Thread Daniel Arndt
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: A*diag(V) with mmult?

2016-09-18 Thread Daniel Arndt
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?

2016-09-18 Thread Daniel Arndt
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: Vector-valued gradient of solution vector

2016-09-19 Thread Daniel Arndt
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: periodic boundary conditions

2016-09-22 Thread Daniel Arndt
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: [dealii-developers] dealii.org website down?

2016-08-18 Thread Daniel Arndt
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: where and how should I use the MeshWorker class? how should I do to implement DG without MeshWorker?

2016-08-27 Thread Daniel Arndt
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: assembling individual block step 43

2016-08-27 Thread Daniel Arndt
Dear Franck, > I am looking at step-43 using different method. I do a semi discretization > in space and end up with an ode for the saturation and use different > technique for time integration for the saturation. > > For this I will need to assemble the matrix H after solving for the >

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

2016-08-22 Thread Daniel Arndt
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

[deal.II] Re: Neumann bc in step-20

2016-09-29 Thread Daniel Arndt
Erik, Am Donnerstag, 29. September 2016 07:32:04 UTC+2 schrieb Erik Svensson: > > Hi, > > I’m trying to implement homogeneous Neumann bc on part of the boundary in > tutorial example step-20. > > The Neumann bc should be imposed strongly (as for Dirichlet bc in normal, > non-mixed,

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

2016-09-25 Thread Daniel Arndt
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: Vector-valued gradient of solution vector

2016-09-27 Thread Daniel Arndt
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

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

2016-10-02 Thread Daniel Arndt
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: More power outages

2016-09-28 Thread Daniel Arndt
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: >>

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

2016-11-09 Thread Daniel Arndt
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

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

2016-11-10 Thread Daniel Arndt
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

[deal.II] Re: Trouble with VisIt 2.11

2016-10-23 Thread Daniel Arndt
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: Easy way to calculate second-deviatoric tensor

2016-10-17 Thread Daniel Arndt
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] Re: How to use Trilinos instead of Petsc in step-40

2016-10-18 Thread Daniel Arndt
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

[deal.II] Re: boundary conditions

2016-10-25 Thread Daniel Arndt
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: boundary conditions

2016-10-25 Thread Daniel Arndt
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: Error with the content "dealii::numbers::is_finite(sum)"

2016-10-25 Thread Daniel Arndt
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 ---

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

2016-10-21 Thread Daniel Arndt
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

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

2016-10-22 Thread Daniel Arndt
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.

[deal.II] Re: Problems with hanging nodes and "distribute_local_to_global"

2016-11-27 Thread Daniel Arndt
Heinrich, The way constraints are resolved in deal.II is as follows (related to *M. S. Shephard: Linear multipoint constraints applied via transformation as part of a direct stiffness assembly process. Int. J. Numer. Meth. Engrg., vol. 20 (1984), pp. 2107-2112.*): You have a linear system Ax=b

[deal.II] Re: Periodic boundary condition in Meshworker.

2016-11-16 Thread Daniel Arndt
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: Periodic Boundary Condition

2016-11-16 Thread Daniel Arndt
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

2016-11-15 Thread Daniel Arndt
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: hp HDG in deal.II

2016-11-16 Thread Daniel Arndt
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: Meshworker

2016-11-18 Thread Daniel Arndt
Sudarshan, template > void Step12::integrate_face_term (DoFInfo& dinfo1, DoFInfo& dinfo2, >CellInfo& info1, CellInfo& > info2) > { >const FEValuesBase& fe_v = info1.fe_values(); >const FEValuesBase& fe_v_neighbor = info2.fe_values();

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

2016-11-13 Thread Daniel Arndt
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

2016-11-13 Thread Daniel Arndt
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 >

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

2016-11-20 Thread Daniel Arndt
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: Meshworker

2016-11-20 Thread Daniel Arndt
Sudarshan, When I am at the face I need the solution at the interior quadrature > points as well. However from dinfo1.indices we could get the the dof > indices for the cell1. But is it possible to get the shape value at the > interior quadrature points ? > You can of course work

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

2016-11-01 Thread Daniel Arndt
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: Extra layer around mesh

2016-11-02 Thread Daniel Arndt
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: Visit error...?

2016-11-03 Thread Daniel Arndt
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 -=

Re: [deal.II] Re: boundary conditions

2016-10-28 Thread Daniel Arndt
> > 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: computing some other output quantity after solution is calculated.

2016-10-31 Thread Daniel Arndt
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

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

2016-11-01 Thread Daniel Arndt
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] Re: How to use Trilinos instead of Petsc in step-40

2016-10-17 Thread Daniel Arndt
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: problem in periodic boundary condition

2016-11-29 Thread Daniel Arndt
Anup, Looking at the resulting mesh after using grid_y_transform, the mesh is still rectangular. Therefore, it is not surprising that make_periodicity_constraints works without offset, but not with: Tensor<1, dim> offset; offset[dim-1] = width*tan_theta*scale;

[deal.II] Re: Tensor output via ConditionalOStream pcout

2016-12-09 Thread Daniel Arndt
Dear S. A. Mohseni, I found these definitions within symmetric_tensor.h. How can I access them? > They seem to allow output for my case. > [...] > You would just use the << operator, i.e. pcout << tensor Best, Daniel -- The deal.II project is located at http://www.dealii.org/ For mailing

[deal.II] Re: Tensor output via ConditionalOStream pcout

2016-12-15 Thread Daniel Arndt
Dear S.A. Mohseni, There is no need to duplicate code. ;-) FullMatrix also has a print function[1] and its implementation[2] is more or less identical to what you are doing. Best, Daniel [1] https://www.dealii.org/8.4.1/doxygen/deal.II/classFullMatrix.html#a6427bd9b23b03c590b9881c7dc551552

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

2016-12-11 Thread Daniel Arndt
Hamed, [...] > >4,5___6,7 > | | > | | > | | > |

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