[deal.II] Re: changing step-25 based on step-40

2016-06-07 Thread Jean-Paul Pelteret
> On Tuesday, June 7, 2016 at 11:26:02 AM UTC-5, Jean-Paul Pelteret wrote: >> >> The one thing that I've noticed is that you're not using a constraint >> matrix, as is done in step-40: >> constraints.clear >> <https://dealii.org/8.4.0/doxygen/deal.II/cla

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

2016-06-07 Thread Jean-Paul Pelteret
Hi Bastien, There are a few potential problems here. 1. You're only refining cells along the top edge of your domain. Periodic boundaries can only have a difference of 1 refinement level between pairs of faces. 2. You may not be colouring any of your boundaries. This should be a

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

2016-06-07 Thread Jean-Paul Pelteret
periodic_faces, >> match_periodic_face_pairs...) work together, so I could not make my >> constraints work. >> But I think that here lays the solution. So I tried to collect my >> periodic faces before any refinement, with the normal function of >> GridTools. This ti

[deal.II] Re: deal.ii and Trilinos

2016-06-07 Thread Jean-Paul Pelteret
Hi Marco, Thats a good question. It doesn't look like its explicitly documented anywhere as to which packages deal.II *requires* Trilinos to be built with (i.e. utilises directly or offers some wrapped functionality for). I'll make a note to do this on the GitHub repository. Hints to the

[deal.II] Re: tensor contraction problem

2016-06-12 Thread Jean-Paul Pelteret
Hi Anup, What version of deal.II are you using? In the documentation for version 8.4.0 such a function certainly exists . Anyway, in this case its probably unnecessary to explicitly specify the

[deal.II] Re: tensor product and polar decomposition

2016-06-10 Thread Jean-Paul Pelteret
For the second question, if I'm not mistaken you must first compute the square root of the eigenvalues of C=F^{T}.F from which you can construct U or V. Thereafter its trivial to compute R. One way that you can do the eigenvalue computation is with the GNU scientific library (GSL). Otherwise

Re: [deal.II] Re: tensor product and polar decomposition

2016-06-11 Thread Jean-Paul Pelteret
on rules applies for two > 'SymmetricTensors' > as well, am I right? > > Thank you very much, > > Regards, > Anup. > > On Fri, Jun 10, 2016 at 1:36 PM, Jean-Paul Pelteret <> wrote: > >> For the first question, if the tensors are of type Tensor<rank,dim> t

[deal.II] Re: deal__ paper on wave propagation

2016-05-26 Thread Jean-Paul Pelteret
Have you had a look at this list of publications that acknowledge deal.ii? On Friday, May 27, 2016 at 1:21:52 AM UTC+2, Poonam Saini wrote: > > Hi All, > > can some one suggest research paper and code using dealii for wave > propagation? > Thanks in

[deal.II] Re: non-homogeneous dirichlet boundary with constraint matrix. Get zero solution on the boundary.

2016-06-16 Thread Jean-Paul Pelteret
No problem! I'm glad that you managed to figure it out :-) On Friday, June 17, 2016 at 7:09:08 AM UTC+2, Anders Ström wrote: > > yes, this solved it. I was going to marked as solved or close it but I > couldn't figure out how. > > Den måndag 13 juni 2016 kl. 08:17:25 UTC+2

[deal.II] Re: TrilinosWrappers::SolverDirect

2016-06-24 Thread Jean-Paul Pelteret
Praveen, >From what I can discern, it seems that you've posted this twice: https://groups.google.com/forum/#!topic/dealii/4TRWnmMywRI Do you have any objections to me deleting this post? J-P On Friday, June 24, 2016 at 8:37:45 AM UTC+2, Praveen C wrote: > > Dear all > > I am using the new

[deal.II] Re: On using TrilinosWrappers::SolverDirect

2016-06-24 Thread Jean-Paul Pelteret
Praveen, I think that the problem is that you have an object that contains MPI data (like a MPI communicator) that is still in use/existence at the time that MPI_FINALIZE is called (generally by the Utilities::MPI::MPI_InitFinalize

[deal.II] Re: fourth order tensor

2016-05-24 Thread Jean-Paul Pelteret
Dear Anup, The subtle difference has to do with the symmetry of the tensors. In the first line of the notation, \mathcal{I} is defined such that A_{ab} = I_{abcd} A_{cd} = [\delta_{ac}\delta_{bd}] A_{cd} and A_{ba} = \bar{I}_{abcd} A_{cd} = [\delta_{ad}\delta_{bc}] A_{cd} . These respectively

[deal.II] Re: problem applying Dirichlet boundary condition

2016-07-28 Thread Jean-Paul Pelteret
Dear Anup, The clue is in the name of your class. You should be providing the incremental update \Delta d^{t} for the position on the Dirichlet boundary, but you're specifying the total displacement d^{t}. Also, you're applying the constraint at all Newton iterations. So, in effect, you're

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

2016-08-01 Thread Jean-Paul Pelteret
Dear Eshan, Sometimes it is necessary to manually remove CMakeCache.txt before reconfiguring a project. Can you try to do this and see if you have any further success? Regards, J-P On Monday, August 1, 2016 at 2:42:25 PM UTC+2, Ehsan wrote: > > Dear Daniel, > I checked the "detailed.log" file

[deal.II] Re: Scaling grid coordinates

2016-08-03 Thread Jean-Paul Pelteret
Hi Bruce, Yes there is, its called GridTools::scale . If you want to don't want to physically modify the grid again just for the purpose of writing it out after postprocessing, you

[deal.II] Re: Dirichlet constraint to a specific node

2016-07-17 Thread Jean-Paul Pelteret
Dear Anup, In addition to Daniel's approach, if you're using just linear shape functions then vertex_dof_index can also help here. See this post and this list of search results

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

2016-07-19 Thread Jean-Paul Pelteret
Dear Deepak, To the best of my knowledge, such functionality is not available in the library because, well, its not the normal type of information that one would be interested in. So you'll have to write the functionality yourself. What have you tried so far? How I would do it is by computing

[deal.II] Re: Expanding on tutorial Step-44 to include a plastic constitutive model

2016-07-20 Thread Jean-Paul Pelteret
Dear Samuel, Yes, it would definitely be possible to replace/augment the current constitutive law with a rate-dependent law. Beside a new definition of the stress and material tangent, you presumably also need to store some variables for you local problem and solve for them at the correct

[deal.II] Re: Expanding on tutorial Step-44 to include a plastic constitutive model

2016-07-20 Thread Jean-Paul Pelteret
You could do this in one of 2 ways: Either you need to do combine the ::update/assemble_XYZ and ::update_assemble_XYZ into a single function, or you can leave them as they are and replace the WorkSteam::run call by the appropriate manual cell loop, e.g. WorkStream::run

[deal.II] Re: Deal.II does not pass quick tests after installation

2016-07-11 Thread Jean-Paul Pelteret
Thanks for pointing that out David, I didn't see the picture in the reply. Since I can't edit the posts themselves, I've duplicated the post here and those that required "censoring". Nguyen's message follows: --- Dear Mr. Wells, I am sorry but if you would please kindly delete the

[deal.II] Re: geometry

2016-07-13 Thread Jean-Paul Pelteret
Dear Benhour, You could use one of the GridGenerator options to create a half circle, and then use GridGenerator::create_triangulation_with_removed_cells to remove the excess cells

[deal.II] Re: PETScWrappers::SparseDirectMUMPS solver error

2016-07-11 Thread Jean-Paul Pelteret
Dear Rajat, Unfortunately your question does not provide sufficient information for anyone to be able to help you. Although the error is in the solver, the source of the error could come from one of several places. Please see this post

[deal.II] Re: Geometry and boundary conditions

2016-07-07 Thread Jean-Paul Pelteret
Hi Benhour, Have you looked at any of the tutorials on geometry creation and solid mechanics? I believe that these specific points are covered there. Regards, J-P On Thursday, July 7, 2016 at 5:21:30 PM UTC+2, benhour.amiria...@gmail.com wrote: > > Dear Daniel, > Thanks very much for your

[deal.II] Re: Error durind checkpoint / restart using parallel distributed solution transfer

2016-07-07 Thread Jean-Paul Pelteret
;-) On Thursday, July 7, 2016 at 9:14:52 PM UTC+2, RAJAT ARORA wrote: > > Hello, > > Yes professor. I thought this might be helpful to anyone who gets a > similar error and is looking for a solution. > > On Wednesday, July 6, 2016 at 3:58:05 AM UTC-4, Jean-Paul Pelteret wrote: >>

[deal.II] Re: Triangulation.save() not working as expected

2016-07-08 Thread Jean-Paul Pelteret
Hi Rajat, I suspect that this might be related to this issue , but we should wait for confirmation from someone with more knowledge on how the triangulation class works. Regards, J-P On Friday, July 8, 2016 at 9:56:07 AM UTC+2, RAJAT ARORA wrote:

Re: [deal.II] Re: extract global node index (or DOF index) which belong to a specific boundary id

2016-06-30 Thread Jean-Paul Pelteret
y, April 2, 2016 at 11:09:51 PM UTC+4:30, bangerth wrote: >> >> On 04/02/2016 08:07 AM, Jean-Paul Pelteret wrote: >> > You can get the support points associated with the vertices using the >> > following method: >> > >> > | >> > cell-

[deal.II] Re: possible memory leak using TrilinosWrappers direct solver?

2017-02-03 Thread Jean-Paul Pelteret
ssing line :-) So what you were witnessing was the gradual creation (over your *many* time steps) of a very large vector of strings. That's all! I hope that you find the simplicity of the solution pleasantly satisfying. Best, Jean-Paul On Thursday, February 2, 2017 at 8:35:25 PM UTC+1, Jean-Paul

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

2017-02-04 Thread Jean-Paul Pelteret
Seyed, Thats a compile-time error, not a run-time error. I bet that your output_results() function is marked as const, so you cannot modify the configurational_forces vector unless its mutable. But if you have any doubts, stick to what’s done in step-40. I’m not particularly familiar with the

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

2017-02-06 Thread Jean-Paul Pelteret
Dear Seyed, Daniel’s been nice enough to furnish you with more information, but at this point one of your deleted comments is quite telling to me: > Any ideas what could cause such a behavior? I am really not an expert yet to > dive deeply inside the deal.II parallel structure. As we explain

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

2017-02-06 Thread Jean-Paul Pelteret
> > Since Erik explicitly asks for a way to "get the degrees of freedom living > on the set of faces", I would still just modify the referenced code to > return face_iterators and access the corresponding DoFs using them. > You're 100% correct, I misread the question (well, rather I focussed

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

2017-02-03 Thread Jean-Paul Pelteret
Dear Seyed, For output purposes, the output vectors must contain values for both locally owned and locally relevant DoFs. This is because DataOut needs to output the solution for an entire patch (i.e. one whole cell) , which demands that it knows the solution at all of the DoFs in that cell.

[deal.II] Re: discontinuity and overlap of elements in 2D thermoelasticity problem using quadratic elements

2017-01-22 Thread Jean-Paul Pelteret
> On Saturday, January 21, 2017 at 4:53:13 AM UTC-6, Jean-Paul Pelteret > wrote: >> >> Dear Anup, >> >> Its possible that this is related to this issue >> <https://github.com/dealii/dealii/issues/2206>. Do you perhaps have a >> minimal test case that

[deal.II] Re: discontinuity and overlap of elements in 2D thermoelasticity problem using quadratic elements

2017-01-21 Thread Jean-Paul Pelteret
Dear Anup, Its possible that this is related to this issue . Do you perhaps have a minimal test case that reproduces the problem? Best, Jean-Paul On Saturday, January 21, 2017 at 4:07:00 AM UTC+1, Anup Basak wrote: > > Hello all, > > I have solved

[deal.II] Re: cannot call member function ‘void tbb::task::spawn(tbb::task&)’ without object

2017-01-30 Thread Jean-Paul Pelteret
Dear Lev, Can you please post your configuration and installation log files (`summary.log` and `detailed.log`)? Regards, Jean-Paul On Tuesday, January 31, 2017 at 4:47:30 AM UTC+1, Lev Karatun wrote: > > Hi, > > I was trying to install (to an empty directory) the newest version of > dealII

[deal.II] Re: bool ParameterHandler::read_input (const std::string &, const bool, const bool, const std::string &) DEAL_II_DEPRECATED

2017-01-29 Thread Jean-Paul Pelteret
Dear Vinayak, You must be using the developer version, right? This function has been deprecated and, I believe, is superseded by the function ParameterHandler::parse_input . I hope

[deal.II] Re: Assembly of material forces

2017-01-25 Thread Jean-Paul Pelteret
Dear Seyed, > My problem is not the theory. > Providing the theory is for our benefit (and therefore yours). No one here is necessarily an expert in what you're trying to accomplish. So, for all of your explanation, an equation or two might go a long way to help us understand exactly what

[deal.II] Re: Add heterogeneous parameters controlled by function on cells

2017-01-25 Thread Jean-Paul Pelteret
Dear Lam, There are a number of ways that you can do this. One approach would be to define a class that derives from the function class ; this is alluded to in step-8

Re: [deal.II] Re: Add heterogeneous parameters controlled by function on cells

2017-01-26 Thread Jean-Paul Pelteret
day, January 25, 2017 at 2:47:18 PM UTC+1, Wolfgang Bangerth > wrote: >> >> On 01/25/2017 05:37 AM, Jean-Paul Pelteret wrote: >> > Dear Lam, >> > >> > There are a number of ways that you can do this. One approach would be >> to >> >

[deal.II] Re: Assembly of material forces

2017-01-26 Thread Jean-Paul Pelteret
Dear Seyed, On top of what Wolfgang has already said, I have a few more direct comments about what you posted a few days ago. > The computation of configurational forces is accomplished by the following > formula: > > > >

[deal.II] Re: question about a lage deformation model based on the updated Lagrangian foemolation

2017-01-27 Thread Jean-Paul Pelteret
figure > demonstrates the mesh with adaptive h-refinement. > > > On Thursday, January 26, 2017 at 12:23:09 AM UTC+3:30, Jean-Paul Pelteret > wrote: >> >> Dear H.B. >> >> For this mesh and deformation field, you can expect to run into this >> problem r

[deal.II] Re: question about a lage deformation model based on the updated Lagrangian foemolation

2017-01-27 Thread Jean-Paul Pelteret
e.g. Perhaps the mesh strategy I've sketched out *might* be more appropriate? On Friday, January 27, 2017 at 11:28:59 AM UTC+1, Jean-Paul Pelteret wrote: > > Hi H.B, > > I suppose its not entirely surprising, because performing local mesh > refinement doesn't really address

[deal.II] Re: question about a lage deformation model based on the updated Lagrangian foemolation

2017-01-25 Thread Jean-Paul Pelteret
Dear H.B. For this mesh and deformation field, you can expect to run into this problem regardless of whether you use the total or updated Lagrangian formulation. As you can see, with your updated formulation you run into an issue when the mapping Jacobian becomes singular (due to element

[deal.II] Re: hp::DoFHandler does not support parallel::distributed::Triangulation

2017-02-22 Thread Jean-Paul Pelteret
Hi Zhenlin, I concur with Denis - I regularly use the method that he's outlined in conjunction with hp::DoFHandler. Regards, Jean-Paul On Wednesday, February 22, 2017 at 9:53:26 AM UTC+1, Denis Davydov wrote: > > you can always partition regular triangulation by >

[deal.II] Re: Access specific element within a distributed triangulation

2017-02-24 Thread Jean-Paul Pelteret
Dear Seyed, There are no cell "numbers" in deal.II, only CellIDs to give some unique identifier to each cell. So its unclear to me as to exactly what you're trying to achieve here. Are you wanting the fourth cell iterator for

[deal.II] New: Physics module and solid mechanics code gallery example

2017-02-24 Thread Jean-Paul Pelteret
Dear all, It is my pleasure to announce the inception of a Physics module in the deal.II project. This module, and its associated namespaces, is dedicated providing some core functionality for computations commonly

[deal.II] Re: Access specific element within a distributed triangulation

2017-02-24 Thread Jean-Paul Pelteret
Hi Seyed, Nope, like I said, there's no such thing as a cell number in deal.II (at least in the sense that a cell knows its own "id" number). The cell->id() function returns a CellId

[deal.II] Re: Neumann vector conditions

2017-02-22 Thread Jean-Paul Pelteret
Hi Franco, Great, I'm glad that you managed to work it out! Best, Jean-Paul On Wednesday, February 22, 2017 at 12:58:45 PM UTC+1, Franco Milicchio wrote: > > Thanks guys, I've succeeded in making a full 3D example with your > suggestions. > > -- The deal.II project is located at

[deal.II] Re: Approximate Derivative Tensor functionality

2017-02-15 Thread Jean-Paul Pelteret
Hi Sumedh, The highlighted parts look suspicious: DerivativeApproximation::approximate_derivative_tensor(dof_handler, solution, cell, cell_grad, unsigned int); DerivativeApproximation::approximate_derivative_tensor(dof_handler, solution, cell, cell_hessian, unsigned int); You

[deal.II] Re: installation problem

2017-02-16 Thread Jean-Paul Pelteret
Dear Dip, The clue is in the message you posted: cannot create directory: /usr/local/share/deal.II/scripts. Maybe need > administrative privileges. You can try to set the install prefix to another directory that you have write access to, such as your home directory. I hope that this helps.

[deal.II] Re: Neumann vector conditions

2017-02-16 Thread Jean-Paul Pelteret
Dear Franco, Super quick answer: Step-44 demonstrates how to implement the Neumann BC for elasticity . Best, Jean-Paul On Thursday, February 16, 2017 at 6:22:06 PM UTC+1, Franco Milicchio wrote: > > Dear

[deal.II] Re: Approximate Derivative Tensor functionality

2017-02-15 Thread Jean-Paul Pelteret
Dear Sumedh, The following works for me with version 8.4.1. For some reason it is necessary to supply some template arguments to this function - this could probably be improved. I'll open an issue about this. #include #include #include #include #include #include #include using

Re: [deal.II] Re: How to solve a linear system with two RHS and a same matrix?

2017-01-18 Thread Jean-Paul Pelteret
or5printERSojbb+0x126) > > [0x7fd462513f60] > [pasha:03624] [21] > ./FEM(_ZN3FEMILi2EE26assemble_large_deformationEb+0x2327) [0x560017] However, maybe this is not the case and some else has some other ideas. On Wednesday, January 18, 2017 at 10:37:48 AM UTC+1, Jean-Paul Pelteret

Re: [deal.II] Re: How to solve a linear system with two RHS and a same matrix?

2017-01-18 Thread Jean-Paul Pelteret
::MPI::Vector> > q_mapping(1, dof_handler, rel_solution2.block(0)); > > > Thank you > Pasha > > On Wednesday, January 18, 2017 at 1:07:48 PM UTC+3:30, Jean-Paul Pelteret > wrote: > Dear Pasha > > I think that there are two problems with how you'v

Re: [deal.II] Re: How to solve a linear system with two RHS and a same matrix?

2017-01-18 Thread Jean-Paul Pelteret
Great, thanks a lot. I've added it to the issue on GitHub that I opened this morning. So clearly the problem is elsewhere. Have you tried passing a normal MPI::Vector to the Eulerian map instead of the MPI::BlockVector that you had used in the

Re: [deal.II] Re: How to solve a linear system with two RHS and a same matrix?

2017-01-19 Thread Jean-Paul Pelteret
r time and consideration > Pasha > > On Wednesday, January 18, 2017 at 4:59:44 PM UTC+3:30, Jean-Paul Pelteret > wrote: >> >> Great, thanks a lot. I've added it to the issue >> <https://github.com/dealii/dealii/issues/3821> on GitHub that I opened >>

Re: [deal.II] Re: Elastic energy computation

2017-01-16 Thread Jean-Paul Pelteret
Dear Seyed, These two things are very different, and cannot be compared with one another. The “strain” in the assembly routine stems from the weak form, which is presented in the introduction to the tutorial. If one considers a variational approach, is coincides with the variation of the

[deal.II] Re: Elastic energy computation

2017-01-16 Thread Jean-Paul Pelteret
Dear Seyed, There are two get_strain() functions in step-18. The first computes the symmetric part of the shape function gradients, and the second computes the small strain tensor. To store the values of the

[deal.II] Re: How to solve a linear system with two RHS and a same matrix?

2017-01-17 Thread Jean-Paul Pelteret
Dear Pasha, At first glance, it would appear that there is a further ConstraintMatrix::distribute_local_to_global function designed with this in mind. It takes in the local_matrix but

[deal.II] Re: Computation of shape function gradients at the reference cell

2017-01-17 Thread Jean-Paul Pelteret
Dear Tulio, This is the type of information that you can get directly from the chosen FiniteElement, e.g. this function provides the shape function gradient on the unit cell. You could

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

2017-02-26 Thread Jean-Paul Pelteret
Dear Pasha, I must correct my answer by replacing "residual vector" by "internal force > vector" Ok, great. So this is a slightly different situation. I was going to say that I think that we're cross-talking here, and you saved me from sketching out a whole bunch of equations to clarify

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

2017-02-26 Thread Jean-Paul Pelteret
* $Id: step-44.cc 30526 2013-08-29 20:06:27Z felix.gruber $ * * Copyright (C) 2010 - 2013 by the deal.II authors and * & Jean-Paul Pelteret and Andrew McBride * * This file is part of the deal.II library. * * The deal.II library is free sof

[deal.II] Re: Announcing the deal.II Code Gallery

2017-02-28 Thread Jean-Paul Pelteret
Wolfgang's answer to Michael's question from a duplicate post: > Just check out the code gallery git repository in a directory parallel to > the > examples/ directory and build the deal.II documentation as described in > the > readme. It will pick up the code gallery and create joint

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

2016-08-25 Thread Jean-Paul Pelteret
Hi Deepak, Ok, so I've created a minimal working example to demonstrate what you're seeing here. I'm not sufficiently familiar with the p-refinement part of the hp functionality/implementation to tell whether this is truly the expected behaviour or not. I see that the examples and description

[deal.II] Re: Installation/Tutorial 1 Issue

2016-08-25 Thread Jean-Paul Pelteret
Hi Peter, How exactly did you compile the tutorial? Just for clarification, are you trying to use some custom build configuration or did you follow the standard guidelines (mentioned in the introduction to step-1 ),

[deal.II] Re: Tensor with variable components

2016-09-03 Thread Jean-Paul Pelteret
Dear Benhour, I'm afraid that your question falls out of the scope of those suitable for the forum (please see this post ). It is too vague and abstract, and to be honest you could spend some time constructing a small case to work

[deal.II] Re: modify solution vector

2016-09-02 Thread Jean-Paul Pelteret
Hi Ilya, You should have a look at some of the previous discussions on the use of the cell->vertex_dof_index function; this provides an easy link between vertices and degrees of freedom. In summary, and

[deal.II] Re: Failing to set up simple test configuration

2016-09-07 Thread Jean-Paul Pelteret
code is that is causing the error "Can't do > inplace edit on > /mnt/c/Users/Alexander/UbuntuShared/dimice-heat-dealii/build/tests/cylinder.debug/output: > > No such file or directory." Unfortunately I'm completely unfamiliar with > the test system and I have not a clue. &

[deal.II] Re: Failing to set up simple test configuration

2016-09-07 Thread Jean-Paul Pelteret
Great, glad that you sorted it out! By the way, there's recently been a discussion on GitHub related to running deal.II on windows. Its interesting to hear that you've got it running on Windows 10. Out of curiosity, how have you configured

Re: [deal.II] Re: variable time step in step44

2016-09-04 Thread Jean-Paul Pelteret
ep in the run() function how can I pass this new > time step, say 'delta_t' to the class 'Time' > to obtain other parameters like current_time etc. > > Thanks and regards, > Anup. > > On Wed, Aug 31, 2016 at 12:27 AM, Jean-Paul Pelteret <> wrote: > >> Dea

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

2016-08-30 Thread Jean-Paul Pelteret
Dear Joel, No, this functionality doesn't exist. However, you can create a quadrature rule with the quadrature points located at the support points (see the FAQ ),

[deal.II] Re: Failing to set up simple test configuration

2016-09-07 Thread Jean-Paul Pelteret
Hi Alex, numdiff: output: No such file or directory > /usr/bin/diff: output: No such file or directory > It appears that you might be missing some of the programs necessary to check your test's output against the "blessed" result. Can you you check that you have numdiff and diff installed and

[deal.II] Re: nearest neighbor

2016-09-01 Thread Jean-Paul Pelteret
Hi Joel, Do you mean the index to a vertex? And by nearest, do you mean the vertex that shares the shortest common edge with the specified vertex? If so, then no. But it shouldn't be hard to write such a function. You would need to find all cells that share the initial vertex (I believe this

[deal.II] Re: applying 3D mesh in step-20

2016-08-31 Thread Jean-Paul Pelteret
Dear Kyusik, If you open your original mesh file in Paraview (version 5.1 detects it as an AVS UCD file) and you clip the mesh to view its section, then I think you'll see the problem. Although the mesh looks fine from the outside, all of the inner vertices of your torus converge on an annulus

[deal.II] Re: applying 3D mesh in step-20

2016-08-31 Thread Jean-Paul Pelteret
ay If I use Prism cell instead of the Hexahedron cell in UCD > format?? Can the deal.II treat the Prism cell?? > > And, Do you also agree with that "SphericalManifold boundary" is not > related to this problem?? > > Thank you. > > Regard > Kyusik > > 2016년 8

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

2016-09-13 Thread Jean-Paul Pelteret
tion(y),2.0)+pow(solution(z),2.0); > } > > Where solution is the vector valued Vector that is 3 times bigger that the > scalar Vector called size. > > Best, > Joel > > On Tuesday, August 30, 2016 at 6:48:46 PM UTC+2, Jean-Paul Pelteret wrote: >> >> Dear

[deal.II] Re: After the calculation, Can the result be used??

2016-09-09 Thread Jean-Paul Pelteret
Hi Kyusik, If you mean that you want to extract the solution at the quadrature points then this certainly is possible. You can do with functions like those in FEValues::get_function_values

[deal.II] Re: Loading DoFHandler from Archive

2016-09-25 Thread Jean-Paul Pelteret
Hi Benjamin, I'm afraid that I don't have any knowledge of the save/load functionality in deal.II, but maybe someone who has experience with this part of the code (one of the ASPECT users, perhaps?) may be willing to comment on this. Just to clarify though - this is not a bug per se, but more

Re: [deal.II] Using p-refinement with high order elements

2016-10-07 Thread Jean-Paul Pelteret
ndary_values. Could you divert me to an example or discussion > where this is done. > > Best > Deepak > > On Fri, Oct 7, 2016 at 1:33 PM, Jean-Paul Pelteret <jppelte...@gmail.com> > wrote: > >> Hi Deepak, >> >> Its not pretty but at a glance this does look p

Re: [deal.II] Using p-refinement with high order elements

2016-10-07 Thread Jean-Paul Pelteret
n, I would like to know whether I can use > *Ve* > *ctorTools::create_point_source_vector *for the same? This function used > to help me for bilinear elements. > > Best regards > Deepak > > On Thu, Oct 6, 2016 at 8:10 PM, Jean-Paul Pelteret <> wrote: > >> Hi Deep

Re: [deal.II] Using p-refinement with high order elements

2016-10-08 Thread Jean-Paul Pelteret
ndices[2*v]] = 0; >> //system_rhs[global_dof_indices[2*v + 1]] = 1; >> } >> } >> >> I will check and get back with the updated code, in case I do not figure >> out the error :) >> >> Best r

Re: [deal.II] Using p-refinement with high order elements

2016-10-08 Thread Jean-Paul Pelteret
(v)[1] - 0.5) < 1e-12){ >> *system_rhs(cell->vertex_dof_index(v-1, 1)) = 0;* >>* system_rhs(cell->vertex_dof_index(v-1, 2)) = 1;* >> //system_rhs[global_dof_indices[2*v]] = 0; >> //system_rhs[global_dof_indices[2*v

Re: [deal.II] Using p-refinement with high order elements

2016-10-07 Thread Jean-Paul Pelteret
a point load. Would that still be possible with traction > boundary condition? > > Best, > Deepak > > On Fri, Oct 7, 2016 at 11:06 AM, Jean-Paul Pelteret <jppelte...@gmail.com> > wrote: > >> Dear Deepak, >> >> Its always easier to help debug a we

[deal.II] Re: Calculate surface integral over a boundary

2016-09-23 Thread Jean-Paul Pelteret
Hi Dragan, What is it that you're trying to evaluate? Although you don't specifically mention it, as you're wanting to do this in post-processing I presume that you're wanting to evaluate something to do with the solution? If so, then you can use the get_function_values

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

2016-08-27 Thread Jean-Paul Pelteret
Ha ha. Dammit, what a silly mistake :-) Thanks Wolfgang! On Friday, August 26, 2016 at 11:08:17 PM UTC+2, Wolfgang Bangerth wrote: > > On 08/25/2016 02:34 AM, Jean-Paul Pelteret wrote: > > Hi Deepak, > > > > Ok, so I've created a minimal working example to demonstrate

[deal.II] Re: Strange issue with KellyErrorEstimator functionality

2016-08-26 Thread Jean-Paul Pelteret
Dear Deepak, Have you run your code in debug mode to confirm that no errors are thrown? I have used the Kelly error estimator in the context of an hp problem with no issues. Have you tried increasing the number of face quadrature points (I notice that qrule starts at 1, but without knowing

[deal.II] Re: Unique (Continuous) Gradient at Edges/Vertices

2016-09-28 Thread Jean-Paul Pelteret
really elegant. It should work in principle. > I will try out to get around the FEFieldFunction and get back to this > thread afterwards. > > > Best, > Andreas > > > > Am Mittwoch, 28. September 2016 10:40:19 UTC+2 schrieb Jean-Paul Pelteret: >> >> Hi Andre

[deal.II] Re: Unique (Continuous) Gradient at Edges/Vertices

2016-09-28 Thread Jean-Paul Pelteret
Hi Andreas, I've had to do something similar in a different context. You could compute the L2-projection of the solution gradient using VectorTools::project. You'd need to define a new DoFHandler for the gradient components and define a function that returns the value of the solution gradient

[deal.II] Re: Error in GridIn::read_abaqus for a mesh with two blocks

2016-10-25 Thread Jean-Paul Pelteret
, the UCD file and the resulting screenshot > from ParaView. > > > > Thank you! > > Oded > > > > P.S. > > I suggest you to upload the journal file to the wiki page – it may be > useful to other people. > > On Tuesday, October 25, 2016 at 4:09:22

[deal.II] Re: Modeling Stokes flow in and around a droplet using the approach of step-46

2016-10-30 Thread Jean-Paul Pelteret
Hi Oded, As you've observed, this class is not yet compatible with the hp::DoFHandler. If you'd like to try to extend it to support this case then we'd be happy accept a patch and to help you in doing so. Regards, J-P On Friday, October 28, 2016 at 11:54:27 PM UTC+2, Oded Yaakobi wrote: > >

[deal.II] Re: Question about Step 44 shape function gradient computations

2016-11-07 Thread Jean-Paul Pelteret
Dear Claire, You are right that this is a total Lagrangian formulation but that doesn't mean that one is restricted to defining the problem in terms of fully referential quantities. One can arrive at the same conclusion from a number of starting points, but ultimately its because we'd chosen

[deal.II] Re: Question about Step 44 shape function gradient computations

2016-11-08 Thread Jean-Paul Pelteret
Le lundi 7 novembre 2016 19:35:18 UTC+1, Jean-Paul Pelteret a écrit : >> >> Dear Claire, >> >> You are right that this is a total Lagrangian formulation but that >> doesn't mean that one is restricted to defining the problem in terms of >> fully referential quantit

[deal.II] Re: Learning Finite Element Method

2016-11-08 Thread Jean-Paul Pelteret
Dear Divya, Its incredibly difficult to answer your question because the answer is a deeply personal one. Instead of embarking on some long diatribe, I will simply encourage you to do your own research to find a set of resources that work for you. Understandably the lecture videos provided

Re: [deal.II] coordinates of dof (Q1)

2016-11-10 Thread Jean-Paul Pelteret
Dear Julian, In general its not easy to provide the functionality that you're looking for because not every degree-of-freedom is associated with a support point (e.g. the FE_DGPMonomial element) and let alone a vertex (e.g. an FE_Q of polynomial order 2 has DoFs with support points at face and

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-10 Thread Jean-Paul Pelteret
Dear Joaquin, It been a while since I've compiled trilinos manually, but if nothings changed since version 11.4 then your should be able to specify which MPI trilinos should be compiled against using the following cmake parameters: -D TPL_ENABLE_MPI:BOOL=ON \ > -D

[deal.II] Re: Defining tensor in different dim and spacedim

2016-10-19 Thread Jean-Paul Pelteret
Dear Benhour, Thank you for providing a little more context, but you still have not articulated what the actual problem is. What exactly do you mean by "I have some problem with defining elasticity matrices"? Please see this post ,

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

2016-10-14 Thread Jean-Paul Pelteret
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, > > I want to use Trilinos instead of Petsc in my parallel code which is based

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

2016-10-22 Thread Jean-Paul Pelteret
Thanks for sharing your solution, Stephen! On Saturday, October 22, 2016 at 1:43:29 PM UTC+2, Stephen DeWitt wrote: > > In case that link dies, here's the snippet of code: > > > // Set constraints to pin the solution if there are no Dirichlet BCs for a > component of a variable in an elliptic

Re: [deal.II] Re: Development history of deal.II

2016-10-22 Thread Jean-Paul Pelteret
Awesome, that looks to be it. Thanks! Cheers, J-P On Saturday, October 22, 2016 at 4:03:28 PM UTC+2, Matthias Maier wrote: > > > > Very cool :-) Is the tool that you used to make this freely available? > > The tool is gource if I am not absolutely mistaken. > > http://gource.io/ > > Best,

Re: [deal.II] Re: Development history of deal.II

2016-10-23 Thread Jean-Paul Pelteret
Thanks for pointing that out -- I didn't look in the comments and so I missed that useful command! For anyone who's interested, I had gource added to spack yesterday. On Saturday, October 22, 2016 at 10:19:36 PM UTC+2, Wolfgang Bangerth wrote: > > On

[deal.II] Re: Defining tensor in different dim and spacedim

2016-10-18 Thread Jean-Paul Pelteret
Dear Benhour, I'd like to help you but I really don't understand your question. Since its templated on the [space] dimension, the PointHistory class that you've displayed here is potentially suitable for either codimension 0 problems (dependent on your implementation of a constitutive law, of

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