Re: [deal.II] Eigenvalues and Eigenvectors of BlockSparse Matrix

2020-09-23 Thread Jean-Paul Pelteret
Hi Animesh, Although in that code-gallery example the system is assembled into a BlockSparseMatrix, the system actually has only one block. So you can retrieve the underlying SparseMatrix (and Vector for the RHS) via tangent_matrix.block(u_dof, u_dof); system_rhs.block(u_dof); and use them

Re: [deal.II] Multi-physics implementation

2020-09-22 Thread Jean-Paul Pelteret
Hi Ray, I’m happy to see that Simon has already given a great explanation as to how to solve your problem. It’s probably more on point than the code that mentioned that I would direct you towards. So it really was worthwhile asking the question again here :-) Best, Jean-Paul > On 22 Sep

Re: [deal.II] Separated domains in load balanding

2020-09-15 Thread Jean-Paul Pelteret
Ah, I was just busy writing what Wolfgang said. You can find more info on custom partitions for parallel::shared::Triangulation here: https://dealii.org/current/doxygen/deal.II/classparallel_1_1shared_1_1Triangulation.html#a686a3453dfec098eb64d1510aa1716e1

Re: [deal.II] Can not access the files for Quasi-Static Finite-Strain Compressible Elasticity program

2020-09-10 Thread Jean-Paul Pelteret
Timo, I think that what Animesh is referring to relates to this issue: https://github.com/dealii/dealii/issues/10295 None of the hyperlinks inside the code gallery documentation are working. J-P > On 10 Sep 2020, at 20:25, Timo Heister wrote: >

Re: [deal.II] extract_dofs() extremely slow in for single-thread run?

2020-09-02 Thread Jean-Paul Pelteret
disables the reinit()-call, and I have > to call cell->is_locally_owned(), instead of cell->locally_owned(). > Thanks! > > Jean-Paul Pelteret schrieb am Dienstag, 1. September 2020 um 20:28:18 UTC+2: > Hi, > > 30-40% of the runtime for this operation seems a bit excessiv

Re: [deal.II] Re: Thermal Modelling of Additive Manufacturing Process

2020-09-02 Thread Jean-Paul Pelteret
Dear Pushkar, Indeed, as Bruno said, it’s hard to understand what information you’re looking for. This can certainly be done with deal.II, as it’s a topic of research that my former colleague has been working on for some time:

Re: [deal.II] extract_dofs() extremely slow in for single-thread run?

2020-09-01 Thread Jean-Paul Pelteret
Hi, 30-40% of the runtime for this operation seems a bit excessive to me. Maybe you should try using the FEValuesExtractors in conjunction with FEValues in order to get the solution at the quadrature points. If you want the solution at the support points, then you can just create a quadrature

Re: [deal.II] How to extract nodes/vertices at the interface of two domains?

2020-09-01 Thread Jean-Paul Pelteret
Dear Behrooz, I guess that the first thing that you need to be able to do is to traverse the mesh until you can get an iterator and index to the cell face that you’re interested in. If the manifold already has some sort of ID associated with it, then you can just do something like

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-21 Thread Jean-Paul Pelteret
ssors(perhaps 4) and if even that doesn't work, then I will try it > in serial. > > Best, > Aaditya > > On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote: > Hi Aaditaya, > > I don’t think that I’ve ever seen anyone have this problem before. We

Re: [deal.II] deal.ii Installation : expand_instantiations Error

2020-08-21 Thread Jean-Paul Pelteret
Hi Aaditaya, I don’t think that I’ve ever seen anyone have this problem before. We build the expand_instantiations binary, and its supposed to be used when expanding files in which we define various combinations of template parameters to instantiate templates within the library. If you’re

Re: [deal.II] Nested reverse and forward-mode Sacado memory leak

2020-08-12 Thread Jean-Paul Pelteret
theoretically. Turns out, it was a bottleneck in my code, so I need > sacado_rad_fad. Might just switch the AD package. > > Thanks again, following-up with a documentation PR > https://github.com/dealii/dealii/pull/10818 > <https://github.com/dealii/dealii/pull/10818> >

Re: [deal.II] Nested reverse and forward-mode Sacado memory leak

2020-08-11 Thread Jean-Paul Pelteret
Hi Doug,Yes, sadly I have experienced the same but wasn’t able to allot the time to figure out if it was indeed a bug in Sacado (and maybe something that’s already been fixed upstream in a newer version of Trilinos than I was using) or something that we did. I’m really glad that you managed to

Re: [deal.II] ABOUT OUTPUT IN PARALLEL

2020-07-29 Thread Jean-Paul Pelteret
Hi, The problem is most likely that you’ve got on (static) variable “times_and_names” that is referencing two completely different of output files. This means that for every tilmestep, you’ve now got two entries in this file and Paraview probably doesn’t know what to do with it. You can easily

Re: [deal.II] omp_simd error in step-67 when installing deal.ii 9.2.0 with spack

2020-07-22 Thread Jean-Paul Pelteret
Hi Ester, There’s a quick workaround for this. You should just edit this line of the deal.II spack package: https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py#L252

Re: [deal.II] About metallic ductile damage

2020-06-09 Thread Jean-Paul Pelteret
Dear Itachi, To supplement what Bruno has already mentioned, deal.II provides some of the tools what you might find useful to implement constitutive laws or specific governing equations. To get some feeling as to what is possible, I would suggest that you take a look through the list of

Re: [deal.II] Deal.ii installation

2020-06-09 Thread Jean-Paul Pelteret
Dear Prasad, I’m glad to hear that you solved your problem. I must say, though, that the problem and the solution only seems to me to be tangentially related. Although neither you, I, nor probably anyone else could have guessed from the cryptic and nondescript error message, you were probably

Re: [deal.II] Particle Class Implementation

2020-06-09 Thread Jean-Paul Pelteret
Dear Victoria, You’re on the right track, but it looks like you got the syntax a bit wrong. To create a particle you need to write something like Particles::Particle particle; You’ll note that the specific constructor that is called is inferred from the arguments given to the instance of the

Re: [deal.II] preconditioner for three block matrix

2020-06-02 Thread Jean-Paul Pelteret
Dear Zeb, To expand on what Wolfgang said in his previous email, we have a page that provides some hints on how to formulate a question that you can then engage the community with. Please give it a read, and have another go at asking

Re: [deal.II] Resolving with different RHS

2020-06-02 Thread Jean-Paul Pelteret
Hi Andreas, I concur with Simon. Additionally, if you’re using the Trilinos linear algebra classes, then the TrilinosWrappers::SolverDirect solver will do the same https://dealii.org/developer/doxygen/deal.II/classTrilinosWrappers_1_1SolverDirect.html#a6c0fecc921bc93f2c005e265cfbdd882

Re: [deal.II] problem measure() for quads

2020-05-29 Thread Jean-Paul Pelteret
Hi Andreas, Thanks for being willing to make a pull request of this. The basic instructions for how to do so are listed in our FAQ, https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#i-found-a-typo-or-a-bug-and-fixed-it-on-my-machine-how-do-i-get-it-included-in-dealii

Re: [deal.II] vertex and dofcells

2020-05-26 Thread Jean-Paul Pelteret
Dear Alberto, Quick answer: There’s a entry in the FAQ that may answer your question: https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#how-do-i-get-the-degree-of-freedom-indices-at-vertices

Re: [deal.II] How to download deal ii 8.2.1 virtual machine image

2020-05-01 Thread Jean-Paul Pelteret
for sending the link for previous versions. Should I download all the > files or the .tar.gz file is enough to install an 8.2.1 version. > > Thanks & Regards > Ajith > > > On Fri, May 1, 2020 at 2:21 PM Jean-Paul Pelteret <mailto:jppelte...@gmail.com>> wrote:

Re: [deal.II] How to download deal ii 8.2.1 virtual machine image

2020-05-01 Thread Jean-Paul Pelteret
Dear Ajith, To supplement what has been said before, older versions of deal.II can be found on the GitHub release page and our mirror: https://github.com/dealii/dealii/releases https://dealii.43-1.org/downloads/ It

Re: [deal.II] My machine did't manage to run Deal.II

2020-04-28 Thread Jean-Paul Pelteret
Dear Wilmar, Indeed, Francis has the right suggestion, although I’m a bit worried that its still not going to help you (unless writing into swap is something that you’d consider). A similar question had been asked a couple of years ago, and the answer that they got at the time was that > 1GB

Re: [deal.II] discrepancy in step-44 material model between implementation and formula.

2020-04-27 Thread Jean-Paul Pelteret
will take the discussion beyond the scope of > the question I asked earlier. I will ask that later. Thank you once again. > > > Navneet R > > > > On Wed, Mar 18, 2020 at 3:56 AM Jean-Paul Pelteret <mailto:jppelte...@gmail.com>> wrote: > Dear Navneet, &

Re: [deal.II] Periodicity with simultaneous displacement controlled BCs

2020-04-27 Thread Jean-Paul Pelteret
Dear David, Indeed, Wolfgang is correct. I gather that you’re trying to produce the sort of displacement field that you see in the attached image. This reference > C. Miehe. Computational micro-to-macro transitions for discretized > micro-structures of hetero- geneous materials at finite

Re: [deal.II] Step 44: imported 2d mesh fails to converge to solution

2020-04-13 Thread Jean-Paul Pelteret
> It might be that one of the constrained boundaries is not traction free... Correction: This should have read "It might be that one of the constrained boundaries is now traction free..." -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

Re: [deal.II] Step 44: imported 2d mesh fails to converge to solution

2020-04-12 Thread Jean-Paul Pelteret
Dear James, To me, the most likely point of failure here relates to the application of boundary conditions. It might be that one of the constrained boundaries is not traction free, and so the problem is not free of rigid body modes. Can you please confirm that you apply the same numbering

Re: [deal.II] Adding the manifold ID to a DataOutFaces

2020-04-09 Thread Jean-Paul Pelteret
value. Maybe someone else on the mailing list knows more about this class, and could provide more hints? > On 10 Apr 2020, at 00:45, Jean-Paul Pelteret wrote: > > Hi Bruno, > > I haven’t used this class before, and admittedly haven’t gone digging too > deep for examples of w

Re: [deal.II] Adding the manifold ID to a DataOutFaces

2020-04-09 Thread Jean-Paul Pelteret
Hi Bruno, I haven’t used this class before, and admittedly haven’t gone digging too deep for examples of where its used. But here are a few examples (one tutorial and a couple from the test suite) that may be able to guide you in the right direction. At first glance, its seems to work

Re: [deal.II] Difficulty setting manifold with Opencascade using gmsh mesh + salome STEP (or IGES) - Step-54

2020-04-09 Thread Jean-Paul Pelteret
he functionnality I will add it to the >> FAQ. Thanks for adding this section. >> Best >> Bruno >> >> >> On Friday, 3 April 2020 16:11:05 UTC-4, Jean-Paul Pelteret wrote: >> Dear Bruno, >> >> I guess that it would be best to mention this in th

Re: [deal.II] Local tutorial installation missing some examples

2020-04-09 Thread Jean-Paul Pelteret
Hi Xuefeng, The list of tutorials that are contained in the latest release (currently 9.1.1, which you’re using) are shown on this page: https://www.dealii.org/current/doxygen/deal.II/Tutorial.html The tutorials that your find

Re: [deal.II] ABOUT ASSEMBLING RIGHT HAND SIDE

2020-04-07 Thread Jean-Paul Pelteret
Hi Xiang, You’ve also not mentioned whether you’re comparing vectors before or after you’ve distributed the constraints. Perhaps you get the same result if you call constraints.distribute() on both of your vectors? Best, Jean-Paul > On 07 Apr 2020, at 22:22, Wolfgang Bangerth wrote: > > On

Re: [deal.II] Difficulty setting manifold with Opencascade using gmsh mesh + salome STEP (or IGES) - Step-54

2020-04-03 Thread Jean-Paul Pelteret
ily available. Clearly I would not have found that out > without Luca's help. > Best > Bruno > > > On Friday, 3 April 2020 09:43:33 UTC-4, Jean-Paul Pelteret wrote: > Dear Bruno, > > I’m glad that you managed to solve this issue with Luca’s aid. I think that >

Re: [deal.II] Difficulty setting manifold with Opencascade using gmsh mesh + salome STEP (or IGES) - Step-54

2020-04-03 Thread Jean-Paul Pelteret
Dear Bruno, I’m glad that you managed to solve this issue with Luca’s aid. I think that the information and workflow that Luca gave was really valuable. Would you care to add this to the Wiki page? Best, Jean-Paul > On 03 Apr 2020, at 06:03, Bruno Blais wrote: > > Ciao Luca, > It works

Re: [deal.II] discrepancy in step-44 material model between implementation and formula.

2020-03-17 Thread Jean-Paul Pelteret
case of > three variable formulation and are independent hence , as . > > Regards, > Navneet R > > > > > On Fri, Mar 6, 2020 at 2:47 AM Jean-Paul Pelteret <mailto:jppelte...@gmail.com>> wrote: > Dear Naveet, > > I think that I see where thi

Re: [deal.II] Installation with spack - no access to adol-c

2020-03-17 Thread Jean-Paul Pelteret
Hi Konrad, Yes, we need some version of ADOL-C greater than 2.6.3, as we upstreamed some required patches to the project. I installed deal.II using Spack a few weeks ago, and didn’t run into any difficulty... but I see that the Gitlab project is indeed locked down, which is a bit surprising.

Re: [deal.II] discrepancy in step-44 material model between implementation and formula.

2020-03-05 Thread Jean-Paul Pelteret
Dear Naveet, I think that I see where things are not explained completely clearly. The sections “Hyperelastic materials”, “Neo-Hookean materials”, and “Elasticity tensors” all describe the theory for compressible materials. This is specifically mentioned in the “Neo-Hookean materials” part,

Re: [deal.II] Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-11 Thread Jean-Paul Pelteret
Hi Vachan, If you’re still not having any luck with this, then maybe you’d consider investigating deal.II through Spack. There’s in fact a whole section in their documentation dedicated to explaining how package installation is done on Cray systems:

Re: [deal.II] Macro periodic boundary condition for a elasticity equation

2020-02-10 Thread Jean-Paul Pelteret
Hi Lukas, If I’ve interpreted your emails correctly, you’ve mentioned two distinct things here, namely (1) the imposition of periodic displacement fluctuation field (thereby, in essence, prescribing a macroscopic average deformation gradient, with stress unknown) or (2) the imposition of a

Re: [deal.II] Instantiation problem for Utilities::MPI::sum (const ArrayView< const T > , const MPI_Comm _communicator, const ArrayView< T > )

2020-01-27 Thread Jean-Paul Pelteret
Dear Feimi, On first glance, it looks like the object you send in as the first argument to this function has the wrong type. The function expects an ArrayView< const int >, but you are passing it an ArrayView< int >. That’s the first thing that I spotted, but hopefully its just this that’s an

Re: [deal.II] Different shape representations with manifolds on the same triangulation

2020-01-19 Thread Jean-Paul Pelteret
er" > triangulation and > apply different mappings (alpha_m) to the cell iterator as we loop. > > Maybe this is not currently possible? > > Thanks in advance, > > Juan Carlos Araújo, > > > On Wednesday, 15 January 2020 22:19:46 UTC+1, Jean-Paul Pelter

Re: [deal.II] Using solution on from one FE problem as a boundary condition for another

2020-01-15 Thread Jean-Paul Pelteret
Hey Ernesto, I’ve used the approach outlined by Wolfgang and Daniel in my own work (multi physics problems, single DoFHandler with BC’s being transferred between a primary and secondary problem solved on subsets of the domain). Overall, it works really well so I’d back up their suggestion and

Re: [deal.II] Facilities for computing the "goodness" of a mesh (i.e. something like a mesh-quality indicator)

2020-01-15 Thread Jean-Paul Pelteret
Dear Krishna, There is also this long-standing pull request https://github.com/dealii/dealii/pull/8196 that hooks into the Verdict library to do mesh quality assessment. One day, hopefully in the not too distant future, I’ll get back to integrating

Re: [deal.II] Application for the use in continuum mechanics

2020-01-07 Thread Jean-Paul Pelteret
I suspect that he will chime in himself at some point, but you may also > want to look at the functionality Jean-Paul Pelteret has implemented for > the last release that allows you to just specify a stored energy and > then get the residual and Newton matrix out of this by automatic > differentiatio

Re: [deal.II] Monolithic coupling, staggered coupling, multiphysics capabilities

2020-01-07 Thread Jean-Paul Pelteret
To add to what Wolfgang said, there are a multitude of papers in our publication list https://dealii.org/publications.html that mention electro-active polymers and magneto-active polymers. You might wish to look there to see what has been accomplished in

Re: [deal.II] SOS - UNABLE to complete coding assignment 1 of Coursera - problems with UMFPACK - sparsity issues

2020-01-07 Thread Jean-Paul Pelteret
Hi Jordi, Indeed, it is as Wolfgang says. Unfortunately none of the developers know this course, or how to what extent deal.II is used in it. It was good timing that I was able to help you out during the vacation period (and you’re most welcome for that, if it did assist you), but time is

Re: [deal.II] SOS - UNABLE to complete coding assignment 1 of Coursera - problems with UMFPACK - sparsity issues

2020-01-03 Thread Jean-Paul Pelteret
f > the Jacobian in the basis gradients but, for 1d and 2d this has not to be > affecting due to the same spacing between nodes. Can you somehow "decript" > your answer a little bit, I am really struggling with this assignment XD > > Kind regards and thanks again! > &g

Re: [deal.II] SOS - UNABLE to complete coding assignment 1 of Coursera - problems with UMFPACK - sparsity issues

2019-12-29 Thread Jean-Paul Pelteret
Dear Jordi, Firstly, welcome to the forum. Well, as this is a course assignment I think that its fair to assume that some course mentor should be available to guide you toward the solution to the problem. You say that you’ve had no luck on the course site forum — that’s a bit poor. Anyway, I

Re: [deal.II] Solve for eigenvalues for small matrix in serial

2019-12-19 Thread Jean-Paul Pelteret
Hi Pai, If you’ve got LAPACK installed then the LAPACKFullMatrix class is able to do the job for you. It has several methods implemented to compute eigenvalues, and you’d then use the eigenvalue()

Re: [deal.II] Instantiation of Vector< Sacado::Fad::DFad >

2019-09-17 Thread Jean-Paul Pelteret
H Doug and Wolfgang, At the time when we introduced the AD framework I took a stab at quickly adding support for to our Vector class. To summarise, I hit the same issue and couldn’t find an elegant solution past to get past it (so hopefully this is the only outstanding problem to add support

Re: [deal.II] Number of Lines in the Deal.ii Library

2019-08-10 Thread Jean-Paul Pelteret
-- > Language files blankcomment > code > --- > C++ 4842 114261 103709 > 399925 > C/C++ Header84 3254 3014

Re: [deal.II] Number of Lines in the Deal.ii Library

2019-07-30 Thread Jean-Paul Pelteret
Hi Jason, Sorry, replying to your message has been on my TODO list for quite some time. Thanks for sharing! Those numbers are certainly thought provoking. It would appear that we (being the collective community) have been putting in a few minutes here and there to write this FEM library :-D

Re: [deal.II] Different solution with different software

2019-07-30 Thread Jean-Paul Pelteret
e too hard on yourself. We’ve all made (and will continue to make) these sorts of mistakes from time to time :-) Best, Jean-Paul > On Thursday, July 25, 2019 at 7:28:13 PM UTC+2, Jean-Paul Pelteret wrote: > Dear Felix, > > I don’t claim to have read through your comprehensive document

Re: [deal.II] Different solution with different software

2019-07-25 Thread Jean-Paul Pelteret
Dear Felix, I don’t claim to have read through your comprehensive documentation of your issue in any detail, but one observation of your code is that you have a couple of suspect terms in your local matrix assembly. In particular, the terms of this form > 1/2/phiscale*(u_j_y-v_j_x) do not

Re: [deal.II] How can I get the global coordinate of Integrated Point

2019-07-17 Thread Jean-Paul Pelteret
Dear Jacob, You should have a look at step-8 , for example. In assemble_system() some local material properties are computed by evaluating some functions at all cell quadrature points: FEValues fe_values(fe, quadrature_formula,

Re: [deal.II] configuration with LAPACK/BLAS fails

2019-07-02 Thread Jean-Paul Pelteret
Hi Ahmad, Although I don’t have an answer for you, I just want to say that what you’re going here looks somewhat reasonable to me. Its unclear to me why this test would fail: /usr/bin/cc -DLAPACK_SYMBOL_CHECK -pthread-rdynamic CMakeFiles/cmTC_3cdf4.dir/src.c.o -o cmTC_3cdf4 -lgfortran

Re: [deal.II] Boundary conditions with the NedelecSZ element

2019-06-14 Thread Jean-Paul Pelteret
Dear Daniel, For non-primitive elements I believe its is necessary to use the project_boundary_values_() functions. So, maybe project_boundary_values_curl_conforming() or

Re: [deal.II] libraries for line search

2019-06-11 Thread Jean-Paul Pelteret
Dear Dhananjay, We have a family of line search algorithms implemented in the LineMinimization namespace (https://github.com/dealii/dealii/blob/master/include/deal.II/optimization/line_minimization.h

Re: [deal.II] how to get the inverse of a sparse matrix?

2019-06-06 Thread Jean-Paul Pelteret
ons to global block. I feel that this approach may not > work as I am dealing with continuous fields. > > I would be glad to know about your thoughts regarding this. > > Thanks, > Krishanu > > On Thursday, 6 June 2019 14:39:16 UTC-5, Jean-Paul Pelteret wrote: > Hi K

Re: [deal.II] how to get the inverse of a sparse matrix?

2019-06-06 Thread Jean-Paul Pelteret
Hi Krishna, One of my answers in this thread provides the solution you’re looking for, namely the suggestion of the LinearOperator class and its associated helper functions. Best, Jean-Paul > On 06 Jun 2019, at 19:41, Krishanu Sen wrote: > > Hello, > > I have a similar problem where

Re: [deal.II] Interface boundary attribute of partitioned meshes

2019-06-06 Thread Jean-Paul Pelteret
Dear Tom, You’ve come to the right place to ask your question but, occasionally, it takes some time for the right person to come along to be able to give a meaningful answer to it. I, for example, have no familiarity with Additive Schwarz methods, so I have no insights to share with you on

Re: [deal.II] Problem Solving BlockSparsematrix system blockwise

2019-05-20 Thread Jean-Paul Pelteret
Dear Gabriel, It looks to me like you forgot to dereference the shared pointer for the preconditioner. So, solver_gmres.solve( system_matrix.block(0,0), distributed_solution.block(0), rhs.block(0), *Mp_preconditioner); // <— here You probably have the same problem for the other call.

Re: [deal.II] Adding TrilinosWrapper::BlockSparseMatrix

2019-05-06 Thread Jean-Paul Pelteret
Dear Gabriel, There is a function to do this operation https://dealii.org/9.0.0/doxygen/deal.II/classBlockMatrixBase.html#a9ee9987ece33a052d2b7a44034a8a01a So you should write this as

Re: [deal.II] Controllins fill-in, abs. tol and rel. tol or smoother and coarse solver of TrilinosWrappers::PreconditionAMG

2019-04-03 Thread Jean-Paul Pelteret
_ml.set("smoother: ifpack absolute threshold",ilu_atol); > parameter_ml.set("coarse: ifpack level-of-fill",ilu_fill); > parameter_ml.set("coarse: ifpack absolute threshold",ilu_atol); > preconditioner.initialize(system_matrix,parameter_ml); > > >

Re: [deal.II] Controllins fill-in, abs. tol and rel. tol or smoother and coarse solver of TrilinosWrappers::PreconditionAMG

2019-04-02 Thread Jean-Paul Pelteret
e. I have found the MULUE documentation, but it seems to be more tailored > around their XML interface? > > > Thank you so much, > Bruno > > > > On Tuesday, 12 March 2019 05:06:03 UTC-4, Jean-Paul Pelteret wrote: > Dear Bruno, > > I believe that my prop

Re: [deal.II] Installation problem

2019-03-23 Thread Jean-Paul Pelteret
Dear Wenguo, It looks like you’re linking deal.II, built as a shared library, against LAPACK, built as a static library. As the error message suggests, you’ll need to build LAPACK with the -fPIC flag in order to do this. As suggested here

Re: [deal.II] Accuracy of Dirichlet condition for p in step-20

2019-03-19 Thread Jean-Paul Pelteret
Dear Jane, > const Functions::ZeroFunction no_tang_bcs; This should be const Functions::ZeroFunction no_tang_bcs(n_components); Best, Jean-Paul -- 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] Finding the y-coordinate of the boundary during the assembly

2019-03-16 Thread Jean-Paul Pelteret
There’s a function to compute the bounding box in GridTools: https://www.dealii.org/current/doxygen/deal.II/namespaceGridTools.html#ae1ec55abefa31cf001fd29d8d4d993f1 > On 16 Mar 2019, at

Re: [deal.II] Interfacing deal.ii for solution, pre and post-processing

2019-03-15 Thread Jean-Paul Pelteret
Dear Muhammad, You can look at the documentation to the GridIn namespace for some ideas as to which software supports the generation of mesh files that deal.II can read, and the and GridOut

Re: [deal.II] Finding the y-coordinate of the boundary during the assembly

2019-03-15 Thread Jean-Paul Pelteret
Dear Jane, There is the BoundingBox class that could tell you the overall extents of the domain. So if your geometry is rectangular and not rotated then you could work out the difference between the y-coordinate of the top

Re: [deal.II] what is the different between VectorTools::point_value and fe_values.get_function_values()?

2019-03-14 Thread Jean-Paul Pelteret
Dear Pham, When you use the FEValuesExtractors in conjunction with the FEValues class using the operator[] like you’ve done here > fe_values[vector_re] then what is returned is an FEValuesViews type object. Since your vector_re extractor is of type FEValuesExtractors::vector, the returned

Re: [deal.II] Controllins fill-in, abs. tol and rel. tol or smoother and coarse solver of TrilinosWrappers::PreconditionAMG

2019-03-12 Thread Jean-Paul Pelteret
Dear Bruno, I believe that my proposed changes are working now, so you could always pull that branch from my repository and use it immediately. That might be the most convenient way for you to move forward. Thanks for being willing to share your findings wrt. AMG parameters. I think that

Re: [deal.II] Controllins fill-in, abs. tol and rel. tol or smoother and coarse solver of TrilinosWrappers::PreconditionAMG

2019-03-10 Thread Jean-Paul Pelteret
Dear Bruno, Indeed, it appears that one isn't able to change the settings passed to the AMG preconditioner other than those set by the AdditionalData object. Your only current alternative is to create the Teuchos::ParameterList yourself, which you can send in to the call to initialize()

Re: [deal.II] Error in the code

2019-03-08 Thread Jean-Paul Pelteret
Dear Muhammad, Can you confirm something: does the directory /media/muhammad/Data/Deal/dealii-8.3.0/ point to your source directory for deal.II, or the location of the installed library? Also, what does your CMakeLists.txt look like? If you are invoking autopilot like this

Re: [deal.II] Regarding billet proof jacket

2019-03-06 Thread Jean-Paul Pelteret
Dear Nitin, Your question is exceptionally broad, so its not possible to give you any meaningful answer or feedback on it. Perhaps you should take a looks at our guidelines for asking questions on the forum which are located here https://groups.google.com/forum/#!topic/dealii/GRZMUTLIm2I

Re: [deal.II] Shared memory parallelism of Trilinos

2019-03-05 Thread Jean-Paul Pelteret
Dear Bruno, > Thank you for the rapid and very detailed answer. This makes this community > so great. Bruno T. has given you far more insight into the inner workings of the Trilinos linear algebra packages than I’d have been able to (thanks :-) ), so I’m really glad that we were able to help

Re: [deal.II] Error installing complex_bessel library

2019-03-04 Thread Jean-Paul Pelteret
Dear Muhammad, This is not really a deal.II related question, but I’ll try to help you anyway. CMake is telling you that you don’t have a Fortran compiler installed, so you should install one. You should be able to do this with “sudo apt install gfortran “. I hope that this help you. Best,

Re: [deal.II] Shared memory parallelism of Trilinos

2019-03-04 Thread Jean-Paul Pelteret
Dear Bruno, > The suggested compilation options for Trilinos do not suggest the use of > OpenMP and the flag is not enabled by default. Can you please indicate where you read this? I’m looking at our documentation for interfacing to external libraries, i.e.

Re: [deal.II] Compile error with function compute_bounding_box on GCC 8.5

2019-03-01 Thread Jean-Paul Pelteret
Hi Reza, Thanks for letting us know about this problem. Yes, its best to report these types of issues directly on the GitHub repository :-) I’ve opened an issue based on the details that you given. You can track it here: https://github.com/dealii/dealii/issues/7771

Re: [deal.II] Can't find affineconstraints related header file

2019-02-28 Thread Jean-Paul Pelteret
Dear Chen, In deal.II version 9.0, affine constraints are applied using the ConstraintMatrix class (deal.II/lac/constraint_matrix.h). This class and header have been deprecated in the developer version, so if you’re using the developer version the ConstraintMatrix is typedef’d to

Re: [deal.II] Tutorial step-35 fails with my inp

2019-02-26 Thread Jean-Paul Pelteret
Dear Eugeny, Have you tried to increase the “max_iterations” in the parameter file? Basically, with the way the tutorial program is defined the solver is currently limited to use the number of iterations defined by the variable “vel_max_it”. This seems to be prescribed using a parameter file,

Re: [deal.II] Loading solution in step 6

2019-02-26 Thread Jean-Paul Pelteret
Ah, right, Thanks for the correction Wolfgang! > On 27 Feb 2019, at 06:58, Wolfgang Bangerth wrote: > > On 2/26/19 7:54 AM, Jean-Paul Pelteret wrote: >> >> Do you mean a 6-sided hexagon? Well, this is the sort of geometry that one >> might want to use a mesh genera

Re: [deal.II] Loading solution in step 6

2019-02-26 Thread Jean-Paul Pelteret
Dear John, > Another simple question is that how to obtain the triangulation of a > standard hexagonal in 2d? Do you mean a 6-sided hexagon? Well, this is the sort of geometry that one might want to use a mesh generation tool (e.g. GMSH, Cubit) for since you can’t trivially create a

Re: [deal.II] Position of a given node

2019-02-25 Thread Jean-Paul Pelteret
I wrote a small wiki entry for this this morning. You can see it here: https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#how-do-i-get-the-degree-of-freedom-indices-at-vertices

Re: [deal.II] Loading solution in step 6

2019-02-22 Thread Jean-Paul Pelteret
Dear John, You don’t say how you write this "solution-…txt” file, so its difficult to say exactly what the best course of action is. Do you know about the block_write() and block_read()

Re: [deal.II] How to get the coordinates of a given degree of freedom on an edge?

2019-02-22 Thread Jean-Paul Pelteret
Dear Kien, The problem that you’re facing (in the example that you gave us) is not one to do with deal.II itself, but rather C++ and how you’ve structured your code. When I build your code in debug mode, I see this warning: $ make Scanning dependencies of target problem [ 50%] Building CXX

Re: [deal.II] Parallel Nonlinear Poisson code in DEALII

2019-02-21 Thread Jean-Paul Pelteret
Dear Boron, As a new user, I’d like to welcome to the forum and deal.II! Am I correct that you only see this issue when executing your program in parallel? I think that the problem results from the way that you initialise the solution vector. That is, this line: >

Re: [deal.II] How to compute convergence rate of L2 norm of error without exact solution? And how to compute convergence rate of in different golobally refinement?

2019-02-21 Thread Jean-Paul Pelteret
Hi Chucui, I can only offer you a very brief reply right now: You might want to look into the ConvergenceTable class to help you with (1). The introduction to the class directs you to some tutorials that indicate its

Re: [deal.II] Trouble getting UMFPACK to work

2019-02-20 Thread Jean-Paul Pelteret
Dear Darius, I just thought I’d ask whether you were able to solve your problem? Best, Jean-Paul > On 16 Feb 2019, at 05:22, Darius Barreto wrote: > > Dear Jean-Paul, > > Thanks for the reply. > > > > On Thursday, February 14, 2019 at 9:20:39 PM UTC+5:30,

Re: [deal.II] Trouble getting UMFPACK to work

2019-02-14 Thread Jean-Paul Pelteret
alii/wiki/deal.II-in-Spack>). I hope that this clarify what you need to do. Best, Jean-Paul > On 14 Feb 2019, at 08:16, Jean-Paul Pelteret wrote: > > Dear Darius, > > Your installation of deal.II has not been compiled with UMFPACK supplied as > an external library. The bund

Re: [deal.II] Trouble getting UMFPACK to work

2019-02-13 Thread Jean-Paul Pelteret
Dear Darius, Your installation of deal.II has not been compiled with UMFPACK supplied as an external library. The bundled version has also not been built, likely because you do not have the required dependencies installed. I believe that you need to have LAPACK installed for it to work, so you

Re: [deal.II] different results when compute integration with adaptive mesh

2019-02-11 Thread Jean-Paul Pelteret
Dear Chucui, Too add to all of the other comments, you can "sanity check” the result that you’re getting using this approach by performing the same calculations another way and comparing results. Specifically, you could easily calculate these norms by looping over all cells and integrating the

Re: [deal.II] Automatic Differentiation of the Finite Element Jacobian

2019-02-11 Thread Jean-Paul Pelteret
> The derivatives with respect to the > mesh points will be needed for optimization purposes. I’m not familiar with the algorithms used in shape optimisation, but one *possible* work-around if you need derivatives wrt. the mesh points on the finite element cell level would be to do the

Re: [deal.II] Automatic Differentiation of the Finite Element Jacobian

2019-02-05 Thread Jean-Paul Pelteret
Dear Doug, > Looking at the current implementation in fe_values, mapping_q_generic, and > local integrators, I see that it looks relatively easy to template the value > type since it is already partially templated. > > Is there a reason why those functions were not templates? No, its likely

Re: [deal.II] Warning messages about text-based stub files not syncing with library files when compiling on Mac.

2019-01-31 Thread Jean-Paul Pelteret
as A University > B.S. Nuclear Engineering > ––– > ––– > Cell:(682) 667-3646 > School Email: zach.ha...@tamu.edu <mailto:zach.ha...@tamu.edu> > Personal Email: zhardy1...@gmail.com <mailto:zhardy1...@gmail.com> > > -- > > > On Thu,

Re: [deal.II] Warning messages about text-based stub files not syncing with library files when compiling on Mac.

2019-01-31 Thread Jean-Paul Pelteret
h.ha...@tamu.edu> > Personal Email: zhardy1...@gmail.com <mailto:zhardy1...@gmail.com> > > -- > > > On Wed, Jan 30, 2019 at 11:57 PM Jean-Paul Pelteret <mailto:jppelte...@gmail.com>> wrote: > Dear Zachary, > > I googled this problem and it seems

Re: [deal.II] Warning messages about text-based stub files not syncing with library files when compiling on Mac.

2019-01-30 Thread Jean-Paul Pelteret
Dear Zachary, I googled this problem and it seems that, dependent on what version of Xcode and MacOS you’re running, there might be one of two solutions. Here’s a similar post on the Apple forums that outlines the two possibilities . The first

Re: [deal.II] command line compilation error on a linux machine using spack installation of deal.ii dev

2019-01-28 Thread Jean-Paul Pelteret
Dear Nicola, This is pretty strange, since you say that the same code compiles on other machines. From what I can tell from a brief search of this error message, it typically appears when there is a stray brace or comma or the like. Are you completely sure that source files on this problematic

Re: [deal.II] output vector solution to vtk file

2019-01-24 Thread Jean-Paul Pelteret
Dear Pham, Welcome to deal.II! Your observation is related to this frequently asked question . Basically, deal.II outputs the

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