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

2016-06-24 Thread luca.heltai
What J-P is suggesting is the following: Have a std_cxx11::shared_pointer solver member in your class, then if (!solver) { solver = std_cxx11::shared_pointer(new TrilinosWrappers::SolverDirect direct(…) ); solver->initialize (mass_matrix); } this will be done only once, and

Re: [deal.II] WorkStream and FEFieldFunction for projecting onto a (possibly) coarsened mesh

2016-05-20 Thread luca.heltai
Sam, I’d suggest you to use a shared pointer as member variable: std::shared_ptr > f_ptr; Then the first time you know how to construct the function, you do this as f_ptr = std::shared_ptr > (new FEFieldFunction<…>(here your construction objects); you

Re: [deal.II] WorkStream and FEFieldFunction for projecting onto a (possibly) coarsened mesh

2016-05-20 Thread luca.heltai
As long as the solution vector is the same (say current_solution), this will work. Should you need to get another solution at next time step, just repeat the > f_ptr = std::shared_ptr > (new FEFieldFunction<…>(here > your construction objects); phase, and the previous one

Re: [deal.II] SphericalManifold and accuracy problem

2016-08-10 Thread luca.heltai
, but dont know where to begin. Give me some places > where I should start looking. I suppose I should start with MappingQ and > MappingQGeneric. > > My shallow water project is stuck due to this, so I am really keen to resolve > this issue. > > Best > praveen > > On

Re: [deal.II] solve on mesh imported through opencascade interface

2016-06-29 Thread luca.heltai
Dear Tom, you’re not doing anything wrong. The Manifold/Boundary interfaces are undergoing a lot of restructuring, and you hit a problem of backward compatibility implementation… Your issue is in the following lines of code, that were inserted to maintain backward compatibility between

Re: [deal.II] Neumann vector conditions

2017-02-17 Thread luca.heltai
> On 17 Feb 2017, at 14:46, Franco Milicchio wrote: > > I agree I have a translation problem here. In practice, I am integrating a > weak problem as this (in Fenics' UFL terms, but easy to recognize): > > > inner( sigma(u), eps(v) ) * dx = inner(f, v) * dx +

Re: [deal.II] Recommendation: BCs in config

2017-02-13 Thread luca.heltai
Actually, you have some alternatives… Take a look at this class: https://github.com/mathLab/deal2lkit/blob/master/include/deal2lkit/parsed_mapped_functions.h It does something similar to what you are asking for. (documentation here:

Re: [deal.II] Neumann vector conditions

2017-02-17 Thread luca.heltai
Dear Franco, I think there is a problem in your formulation… You are integrating u_i n_i f_i and while you can certainly come up with good reasons for this to work out, I’m unsure about what you want to achieve. If your boundary conditions are ((grad(u)).n,v) = u_i,j n_j v_i and you

Re: [deal.II] Re: Proper use of CompositionManifold

2016-09-22 Thread luca.heltai
For future reference, if you are in doubt on how to use a single class/function, you can skim through the directory tests, i.e., tests/manifold/composition_manifold_* would have shown to you an example which is identical to what you are trying to achieve, and in general it contains very

Re: [deal.II] Re: PolarManifold vs SphericalManifold

2016-09-22 Thread luca.heltai
Yes. This is a problem inherent with the fact that it is not possible to approximate a sphere with a single chart without singularities. On the other hand, the manifold you use to describe the top and bottom part of the sphere are not continuous, so the triangulation gets confused when you add

Re: [deal.II] Relation of FE_Q support points and quadrature points

2016-11-23 Thread luca.heltai
Now I have to figure out some other way to do this efficiently. I want to > avoid use of get_function_values. > > Best > praveen > > On Wed, Nov 23, 2016 at 3:27 PM, luca.heltai <luca.hel...@gmail.com> wrote: > Not necessarily. In fact the ordering is reshuffled so

Re: [deal.II] ifem

2016-12-17 Thread luca.heltai
Dear Joaquin, as I wrote to you on one of my previous emails, the repository https://github.com/luca-heltai/ans-ifem contains a branch that compiles correctly, without those warnings, on the development version of deal.II. There are some more warnings due to the deprecation of the ‘sadd’

Re: [deal.II] using FEValues extractor for a

2016-12-17 Thread luca.heltai
Dear Anup, one option you have is to use a Triangulation. I would still use two scalar extractors: const FEValuesExtractors::Scalar u_x const FEValuesExtractors::Scalar u_y Tensor<2,dim+1> gradient; gradient[0] = fe_values_ref[u_x].gradient(k, q_point) gradient[1] =

[deal.II] Re: deal.ii from candi

2016-11-30 Thread luca.heltai
Ciao Dirk, unfortunately not. I’m forwarding your mail to the mailing list. Maybe someone there has a better idea… L. > On 29 Nov 2016, at 19:19, Dirk Peschka wrote: > > > Hey Luca, > > duing the petsc compilation, when making mumps, I get some strange > errors

Re: [deal.II] How can I resize a std::vector<Functions::ParsedFunction>?

2017-03-22 Thread luca.heltai
Hi Alex, I’d use a vector of std::vector > v; which are light objects, and can be resized and reshaped. Whenever you do a push_back, you’d have to use v.push_back(std_cxx11::shared_pointer

Re: [deal.II] How can I resize a std::vector<Functions::ParsedFunction>?

2017-03-23 Thread luca.heltai
Resizing is fine. It is the equality that won’t work: function_pointers[f] = std::shared_ptr(new dealii::Functions::ParsedFunction())); is the correct way to do it. L. > On 23 Mar 2017, at 15:09, Alex Zimmerman wrote: > >

Re: [deal.II] Re: Unable to download dealii-8.4.1 for Mac

2017-04-09 Thread luca.heltai
Same here. I can download the package both from home and from my office. L. > On 8 Apr 2017, at 18:35, Daniel Arndt > wrote: > > Ana, > > I can't confirm your problem. Downloading works without issues. What browser > are you using? Do you get any

Re: [deal.II] Re: Finite Element Method for Two Phase Flow

2017-04-09 Thread luca.heltai
Or, you could use as a stable pair of finite elements the FE_Q(k)-FE_DGP(k-1) pair: D. Boffi and L. Gastaldi. On the quadrilateral Q2-P1 element for the Stokes problem. Int. J. Numer. Meth. Fluids, 39 (2002), 1001-1011. This pair of finite elements is known to produce consistently better

Re: [deal.II] Refining a hyper_ball with a spherical_manifold produces nan values

2017-04-26 Thread luca.heltai
This is actually not a bug. A spherical manifold is undefined on the center of the sphere/ball. You cannot attach set_all_manifold_ids of the spherical manifold and attach a spherical manifold to it, since the central cell (the one where the cell->center() coincides with the ball center) would

Re: [deal.II] Problem with compiling in macOS sierra, version 10.12.5

2017-06-05 Thread luca.heltai
If you don’t have XCode, then you don’t have XCode tools. You can download XCode from the App store. This error: > The CMAKE_C_COMPILER: > > > > > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc > > > > is not a full path to an existing

Re: [deal.II] Problem with compiling in macOS sierra, version 10.12.5

2017-06-05 Thread luca.heltai
Did you install xcode and xcode-tools? It looks like deal.II cannot find a lot of things… The application opens a terminal and tries to figure out if you did. Does the terminal open up with no issues? L. > On 5 Jun 2017, at 8:00, Sudarshan Kumar wrote: > > I have

Re: [deal.II] Problem with compiling in macOS sierra, version 10.12.5

2017-06-05 Thread luca.heltai
No need to restore to the old version. I have 10.12.5 myself. Can you try running xcode, and see if it asks you wether you want to upgrade the command line tools? L. > On 5 Jun 2017, at 8:22, Sudarshan Kumar wrote: > > > > On Monday, June 5, 2017 at 11:39:28 AM

Re: [deal.II] Compute jacobian at point (no quadrature point)

2017-06-14 Thread luca.heltai
Felix, also, if the point you want is not a quadrature point, you can exploit the following trick: Point my_point_in_reference_cell; std::vector quad(1, my_point_in_reference_cell); and then you can initialize an FEValues fev(fe, quad, update_inverse_jacobians); This will give you

Re: [deal.II] Refining a cylinder only in x

2017-09-19 Thread luca.heltai
Dear Lucas, you could use GridTools::remove_anisotropy Best, Luca. > On 18 Sep 2017, at 16:29, Lucas Campos wrote: > > Dear Bruno, > > You will find attached the resulting grids. While I originally expected to > find new divisions only along the x-direction, your

Re: [deal.II] Re: Deal for Mac OS 10.13

2017-10-11 Thread luca.heltai
Yes. It is trying to use the accelerate framework, but since it was installed using 10.12, it links to that one. If you install the 10.12 SDK you should have what you need. L. > On 11 Oct 2017, at 8:58, Alberto Salvadori wrote: > > Sure, I will. Am I

Re: [deal.II] Re: Isogeometric analysis

2017-11-22 Thread luca.heltai
Dear Yaakov, did you even try google? :) google search: dealii isogeometric analysis https://www.google.it/search?q=dealii+isogeometric+analyis_rd=cr=0=vTkVWvurIcOUaPbVr6AO gives you as a first result this repository: https://github.com/mathLab/IGA-dealii So far it supports single patch

Re: [deal.II] A cube rather than a ball with GridGenerator::hyper_ball

2017-11-17 Thread luca.heltai
Dear Alberto, > GridGenerator::hyper_ball ( triangulation, center, cell_radius ); > > static SphericalManifold volume_boundary; > > > triangulation.refine_global ( 3 ); > > triangulation.set_all_manifold_ids_on_boundary(0); > > triangulation.set_manifold (0, volume_boundary);

Re: [deal.II] New Mac OSX brew package

2017-11-09 Thread luca.heltai
It does not compile, anyway… :D Maybe Denis can help: I get the following when trying to compile pkg-config using gcc installed with spack: In file included from /System/Library/Frameworks/Security.framework/Headers/AuthSession.h:32:0, from

Re: [deal.II] Re: New Mac OSX brew package

2017-11-09 Thread luca.heltai
Oh, and naturally ’s/brew/spack/g’ in my previous email. clang --version Apple LLVM version 9.0.0 (clang-900.0.38) Target: x86_64-apple-darwin17.0.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin and gfortran --version

Re: [deal.II] A few questions

2017-11-08 Thread luca.heltai
>> — Are there any applications with immersed FEM (cut-cell, etc.) with deal.II? Yes. There are at least two open source codes, published on “Archive of Numerical Software”: http://journals.ub.uni-heidelberg.de/index.php/ans/issue/view/2930 "Carraro, Wetterauer: On the implementation of the

[deal.II] Sixth deal.II Users and Developers Workshop - 23 --27 July 2018, Trieste, Italy

2017-12-11 Thread luca.heltai
Dear all, registration is now open for the Sixth deal.II Users and Developers Workshop, to be held in Trieste@SISSA, from July 23 to July 28. http://indico.sissa.it/e/sixth-dealii-workshop The program includes invited talks and discussions by users and developers of the deal.II library in

Re: [deal.II] Re: Why does the L2-norm increase when the number of nodes becomes too large?

2017-12-20 Thread luca.heltai
M… I’m actually not sure it’s a bug… The point where the error starts growing is at 10e-12. This is basically machine precision, considering the fact that you are computing the L2 error. After you have reached machine precision, any addition you make to that, is just roundoff error

Re: [deal.II] Re: cmake . returns error on MAC OS XI Captain version 10.11.6 upon compiling dealii-8.5.0-brew.dmg

2018-05-11 Thread luca.heltai
The deal.II source directory can be found under /Applications/deal.II-9.0.0.app/Contents/Resources/spack/src/deal.II-9.0.0 There you will find the examples directory. In the new package (that I’m building right now), you’ll also have in the usual location. Best, Luca. > On 12 May 2018, at

Re: [deal.II] Re: Mac testers wanted

2018-05-11 Thread luca.heltai
t; Denis > > On Sunday, May 6, 2018 at 11:51:19 AM UTC+2, Luca Heltai wrote: > Sorry. The address is the following: > > https://github.com/dealii/dealii/releases/v9.0.0-rc2 > > Luca > > Il giorno 06 mag 2018, alle ore 11:30, luca.heltai <luca@gmail.com> ha

[deal.II] Mac testers wanted

2018-05-06 Thread luca.heltai
Dear all, I have just uploaded a new package for deal.II-9.0.0-rc2 here: https://github.com/dealii/dealii/releases/edit/v9.0.0-rc2 This was compiled with Apple clang 9.1.0, and gfortran from gcc 7.3. Please test, and let me know if everything is ok. Best, Luca. -- The deal.II project is

[deal.II] Sixth deal.II Users and Developers Workshop

2018-05-23 Thread luca.heltai
Dear All, the deadline for the submission of talks proposal for the “Sixth deal.II Users and Developers Workshop” is on the 23 of June (one month from now). You are invited to register and submit an abstract through the online procedure: http://indico.sissa.it/e/sixth-dealii-workshop If you

[deal.II] New package for mac - v9.1.0-pre-002bd21ce6

2018-05-27 Thread luca.heltai
Dear all, thanks for the feedback. Here you’ll find a new version of the deal.II package, made with spack, and compiled with clang@6.0.0, and gfortran@8.1: https://github.com/luca-heltai/dealii/releases/tag/v9.1.0-pre-002bd21ce6 The package is independent on apple compilers, should work on

Re: [deal.II] confusing result when re-read a mesh in gmsh format

2018-04-30 Thread luca.heltai
The problem is that you cannot read a mesh with hanging nodes. If you have a mesh with hanging nodes, all faces with a hanging node are actually boundary faces, so in your picture, all faces that are between a refined and an unrefined cells, are actually boundary faces, i.e., they are

Re: [deal.II] New deal.II 8.5.1 is 20% slower than deal.II 8.0.0

2017-12-30 Thread luca.heltai
If all you are solving is a two dimensional problem, you could encode your “get_function_values” into a matrix vector multiplication to drastically improve the situation. I’m thinking of a matrix of size (n_quadrature_points x n_active_cells) x n_dofs, and then you slice the results cellwise

Re: [deal.II] New deal.II 8.5.1 is 20% slower than deal.II 8.0.0

2017-12-31 Thread luca.heltai
multiplication (maybe with one identical Vandermonde matrix). L. > On 31 Dec 2017, at 6:09, Praveen C <cprav...@gmail.com> wrote: > > > >> On 30-Dec-2017, at 11:40 PM, luca.heltai <luca.hel...@gmail.com> wrote: >> >> I’m thinking of a matrix of siz

Re: [deal.II] Re: Creation of own CMakeLists.txt

2018-01-11 Thread luca.heltai
Take a look at this: https://github.com/luca-heltai/bare-dealii-app it is a bare structure, for medium to large size problems, with separate source/include/tests directories, that support travis CI integration. L. > On 11 Jan 2018, at 15:52, 'Maxi Miller' via deal.II User Group >

Re: [deal.II] Neighbors search within a particular radius of an element

2018-01-25 Thread luca.heltai
You could use KDTree, based on nanoflann. If you installed the development version of dealii with NANOFLANN support, then you’d have access to algorithms that work in order log(N) complexity for each search, and N log(N) to build the tree. You’d have to massage it a little, as at the moment

Re: [deal.II] Automatic refinement with minimal level of refinement

2018-02-19 Thread luca.heltai
After you have created your coarse mesh, you could GridTools::flatten_triangulation it. This will create a brand new coarse triangulation, containing only all your active cells. L. > On 19 Feb 2018, at 13:35, Lucas Campos wrote: > > Dear all, > > I am creating a mesh

Re: [deal.II] OpenCASCADE Technology (OCCT) 7.2.0 coming to Debian - implications for deal.II

2018-03-13 Thread luca.heltai
Kurt, in principle deal.II does not require OCE. It can work also with OCCT (it will use whatever it finds available, unless someone changed this behaviour). When OCCT will be packaged into debian, I’m sure we can make dealii use that instead of OCE. Best, Luca. > On 11 Mar 2018, at 4:29,

[deal.II] Postdoc @ SISSA mathLab, Trieste -- numerical modeling and simulation of nanometric electronic devices

2018-03-20 Thread luca.heltai
Dear all, the following announcement may be of interest to you or to some of your students. We are actively seeking for a deal.II experienced programmer ASAP! Best, Luca. -- A one year postdoctoral position is available at SISSA @ mathLab, starting from May 1, 2018 (see

Re: [deal.II] Compilation problems with MS Visual Studio, 2017

2018-10-12 Thread luca.heltai
Dear Rochan, you can find prebuilt static binaries of deal.II 8.5.0 for windows, with no external libraries, here: https://github.com/luca-heltai/dealii/releases/tag/9.5.pre-windows I also know of people that successfully compiled and used deal.II 9.0.0 on windows. L. > On 12 Oct 2018, at

Re: [deal.II] Help on manifold ids

2018-11-12 Thread luca.heltai
Dear Earl, setting the Manifold should be done *before* you do refinment. The line you added at the end, tria.execute_coarsening_and_refinement(), is not doing any refinement, so you don’t see the effect of your set_manifold_id() call. What happens if you refine globally once more after

Re: [deal.II] advice on import from STEP format

2018-10-01 Thread luca.heltai
Dear Marek, > On 29 Sep 2018, at 22:58, Marek Čapek wrote: > > Hi, > I have a geometry in step file format. I would like to import it and generate > from it a mesh digestible by dealii GridIn functions. > I followed step-54, modifying thefunction read_domain > >

Re: [deal.II] Cylinder by extrusion

2018-09-21 Thread luca.heltai
Dear Riku, this is not (yet) supported by deal.II. You will have to attach manually a CylindricalManifold after extrusion. The library does not know yet how to compute the extrusion of a general manifold object, therefore it removes all manifold objects from the extruded triangulation (as

Re: [deal.II] Saving boundary faces in half_hyper_shell to msh file

2018-11-18 Thread luca.heltai
Dear Praveen, this is actually a feature, and not a bug. The reason is that, by default, deal.II generates triangulations with boundary id = 0. If you don’t specify a boundary id in the gmsh file, then all boundary faces get boundary id = 0. This allows us to save space in the output grid,

Re: [deal.II] Saving boundary faces in half_hyper_shell to msh file

2018-11-18 Thread luca.heltai
Did you use the option “colorize=on”? L. > On 18 Nov 2018, at 10:45, Praveen C wrote: > > > >> On 18-Nov-2018, at 2:59 PM, luca.heltai wrote: >> >> Dear Praveen, >> >> this is actually a feature, and not a bug. The reason is that, by def

Re: [deal.II] issues with manifold id (at least in codim-1) revealed by PR 7775

2019-03-13 Thread luca.heltai
I believe the first point is a bug of the read_ucd function. I opened an issue for this (https://github.com/dealii/dealii/issues/7802) The second point, however, is a feature. What should you do when two material ids meet? I think it is the responsability of the user to make sure that the

Re: [deal.II] Difference between MeshWorker::mesh_loop and WorkStream::run

2019-03-18 Thread luca.heltai
Take a look at this PR for a few examples of usage of mesh_loop: https://github.com/dealii/dealii/pull/7806 The function WorkStream::run takes (a minimum of) 5 arguments: WorkStream::run(cell, endc, cell_worker, copier, scratch, copy); initial and final iterator, a worker function, a copier

Re: [deal.II] New FiniteElement; Cohesive-zone model; A-FEM

2019-03-18 Thread luca.heltai
You may also find useful this link: https://journals.ub.uni-heidelberg.de/index.php/ans/issue/view/2930 where the authors implement XFEM in deal.II to model interface problems. L. > On 18 Mar 2019, at 9:39, Daniel Arndt > wrote: > > James, > > I am a graduate student who will be defending

Re: [deal.II] issues with manifold id (at least in codim-1) revealed by PR 7775

2019-03-19 Thread luca.heltai
Nicola, what would you think of a function in GridTools like GridTools::propagate_internal_manifold_ids(tria, disambiguation_function) that would loop over all cells, loop over all faces, check if the neighbor manifold id is the same of this cell, and i) the two ids are the same: assign the

Re: [deal.II] Difference between MeshWorker::mesh_loop and WorkStream::run

2019-03-19 Thread luca.heltai
> Is there a reason then that there are several examples using > integration_loop(), but (afaik) only one using mesh_loop? Yes. mesh_loop is more recent w.r.t. integration_loop. mesh_loop was introduced to address some of the oddities that are in integration_loop, that make its use somewhat

Re: [deal.II] Mass matrix for a distributed vector problem

2019-04-12 Thread luca.heltai
If you plan to use any domain that is not a square (or an affine transformation), you have to make sure you integrate exactly the product of two polynomials of order degree and of the determinant of the Jacobian. This last term is constant only for simple meshes, but it is the square root of a

Re: [deal.II] Mass matrix for a distributed vector problem

2019-04-11 Thread luca.heltai
You are integrating using two quadrature points per direction. Can you raise that to (2*fe.degree+1)? L. > On 11 Apr 2019, at 10:58, bobspar...@gmail.com wrote: > > Dear all, > > First of all, thanks for the awesome library. I am starting to learn deal.II, > and it is great! The

Re: [deal.II] Mass matrix for a distributed vector problem

2019-04-12 Thread luca.heltai
Wolfgang, is that true also for mass matrices? I’d agree with you for stiffness matrices, but I’d surprised this worked ok for mass matrices as well. If so, I’ve always been over integrating in my life… :) L. > On 12 Apr 2019, at 21:15, Wolfgang Bangerth wrote: > > On 4/12/19 8:41 AM,

Re: [deal.II] Interpolate correct solution onto mesh using interpolate() with FE_Bernstein elements

2019-05-16 Thread luca.heltai
> On 16 May 2019, at 9:16, 'Maxi Miller' via deal.II User Group > wrote: > > I would like to use the interpolate()-function to interpolate the correct > function onto my mesh for comparison during some simple tests. This works > fine when using FE_Q-elements, but fails when using

Re: [deal.II] obtaining an ellipsoid grid and manifold from GridGenerator::hyper_sphere() and a subclass of ChartManifold

2019-06-05 Thread luca.heltai
Did you look at this class? https://www.dealii.org/developer/doxygen/deal.II/classEllipticalManifold.html It is in deal.II 9.1.0… L. > On 3 Jun 2019, at 12:54, SebG wrote: > > Hi Thomas, hi Luca, > > I would like to re-generate the ellipsoidal with deal.ii 9.0.1 but the > interfaces of the

Re: [deal.II] obtaining an ellipsoid grid and manifold from GridGenerator::hyper_sphere() and a subclass of ChartManifold

2019-06-13 Thread luca.heltai
Dear Sebastian, have you tried using a simple SphericalManifold for your problem? The way spherical manifold works is by interpolating *both* the radius and the angles, so that points intermediate between two points with different radii get an average radius between the two. This may not be

Re: [deal.II] Extracting volume data to the boundary

2019-09-11 Thread luca.heltai
Alberto, be aware of the fact that, when you extract the boundary mesh, the orientation of the cells may be different w.r.t. to the corresponding face on the volumetric mesh. In other words, using FEValues codim_one(…); FEFaceValuescodim_zero(…); codim_one.reinit(codim_one_cell);

[deal.II] Re: What is the path to the dealii installation directory in a containerized version?

2019-07-31 Thread luca.heltai
Jhon, the path is there, and it is correct. The message is telling you that you are in a directory containing developement version of the examples. If you inspect the CMakeLists.txt of the example you are trying to compile, it tells you: FIND_PACKAGE(deal.II 9.2.0 QUIET HINTS

[deal.II] Postdoc Position (deal.II related), International School for Advanced Studies, Trieste, Italy

2019-08-05 Thread luca.heltai
Dear all, I’d like to advertise an opening for a Postdoctoral position (18 months) in my group, to work with and on deal.II. The deadline is pretty tight… please send me a private message if you are interested. Luca. --- Title of the position: Adaptive methods for solving multi-physics

[deal.II] 4 PhD Positions @ SISSA, Trieste

2019-08-09 Thread luca.heltai
Dear All, I would like to bring at your attention that the deadline to apply for a Phd position in Mathematical Analysis, Modelling and Applications at SISSA, Scuola Internazionale Superiore di Studi Avanzati Trieste, Italy is August 22nd, 2019 at noon (Rome time). Applied mathematics

Re: [deal.II] Associating a MappingManifold with a Manifold

2019-11-12 Thread luca.heltai
You don’t need to do anything special. Just create a MappingManifold, and pass it where required. The manifold that is used is the one associated to the triangulation. You don’t need to associate it to the Mapping, since the mapping is used on *all* objects of the triangulation, and it will

Re: [deal.II] Associating a MappingManifold with a Manifold

2019-11-16 Thread luca.heltai
> CylindricalManifold<2> cylman(0); > triangulation.set_manifold(numbers::flat_manifold_id, cylman); The flat_manifold_id is usually reserved for the flat manifold, and yours is not a flat manifold. Setting the flat manifold to the cylindrical manifold implies You should set the manifold

Re: [deal.II] deal stopped working with latest macOS update (10.15)

2019-12-03 Thread luca.heltai
; *** > [100%] Built target release > bash-3.2$ make > Scanning dependencies of target step-20 > [ 50%] Building CXX object CMakeFiles/step-20.dir/step-20.cc.o > [100%] Linking CXX executable step-20 > [100%] Built target step-20 > bash-3.2$ ./step-20 > Illegal instruction: 4 &g

Re: [deal.II] get_dof_indices() only works on active cells - blocks vector

2019-12-09 Thread luca.heltai
Dear Juan, The logic you should use is: when your neighbour is finer, you should not assemble the full face term from the coarse neighbour. Instead, you have to assemble your DG terms using a FESubfaceValues initialized with the correct arguments on the coarse face, to match *each* of the fine

Re: [deal.II] deal stopped working with latest macOS update (10.15)

2019-12-06 Thread luca.heltai
tel 030 3711239 > fax 030 3711312 > > e-mail: > alberto.salvad...@unibs.it > web-page: > http://m4lab.unibs.it/faculty.html > > > > On Fri, Dec 6, 2019 at 11:18 AM luca.heltai wrote: > Alberto, > > this may be related to different hardware and diffe

Re: [deal.II] deal stopped working with latest macOS update (10.15)

2019-12-06 Thread luca.heltai
member having some issues with XCode > during the installation. I thought it had automatically updated correctly, > but on closer inspection there was an error message (nothing an online search > couldn't solve). > > Ester > > > El dimarts, 3 desembre de 2019 11:08:57 UTC-5, luca.he

Re: [deal.II] deal stopped working with latest macOS update (10.15)

2019-12-06 Thread luca.heltai
t on closer inspection there was an error message (nothing an online search > couldn't solve). > > Ester > > > El dimarts, 3 desembre de 2019 11:08:57 UTC-5, luca.heltai va escriure: > I have not updated to the latest version yet. They changed clang, xcode, and > a

Re: [deal.II] Docker MPI

2019-10-25 Thread luca.heltai
You can do export PATH=$(spack location -i mpich)/bin:$PATH to prepend the path of mpich to your PATH. This is not done automatically. Alternatively, you could also run, as root: cd /usr/local spack view add . mpich which aliases all mpi commands to /usr/local/bin I usually do this in a

Re: [deal.II] deal stopped working with latest macOS update (10.15)

2019-10-25 Thread luca.heltai
Dear Ester, please take a look at the release page: https://github.com/dealii/dealii/releases/tag/v9.1.1 There is a package for Mac OS Catalina. In Catalina, permissions are much more restrictive, and you’ll have to explicitly enable the application to run (the first time), by right clicking

Re: [deal.II] Convergence rate

2019-10-10 Thread luca.heltai
Dear Felix, by any chance, did you take a look at step 10? https://www.dealii.org/current/doxygen/deal.II/step_10.html This step explains a little bit what to do when you want to solve on curved domains with high order finite elements. In particular, you need to ensure that the mapping you

Re: [deal.II] Parallelizing step-33 with MPI

2019-12-22 Thread luca.heltai
Dear Ellen, you may want to compare with this: https://github.com/luca-heltai/dealii/pull/91/files#diff-acfb3c7b43e4935be016fda6ebdc5881 It is a parallel version of step-38, that never got into the library, written by one of our students, during a deal.II workshop in Trieste (held by Timo and

Re: [deal.II] number of cells sharing a line

2020-01-24 Thread luca.heltai
Nicola, I would simply do this by std::mapline(0)), unsigned int> line_count; for(const auto : tria.active_cell_iterators()) { for(unsigned int i=0; i< GeometryInfo::lines_per_cell; ++i) { const it = line_count.find(cell->line(i)); if(it !=

Re: [deal.II] "PETSc installation does not include a copy of the hypre package" while running the step-40 program

2020-01-26 Thread luca.heltai
Did you try the pre-compiled deal.II package? Both dealii-9.1.1-clang-9.0.0.dmg and dealii-9.1.1-catalina-haswell-ro.dmg.zip from https://github.com/dealii/dealii/releases/tag/v9.1.1 should work. Luca. > On 25 Jan 2020, at 21:29, Ihar Suvorau wrote: > > > Software: > • macOS

Re: [deal.II] problem with a projection using SphericalManifold

2020-01-22 Thread luca.heltai
Nicola, I think you are hitting a periodicity issue here. The points with angle 7/4 pi and 5/4 pi are at a distance (from pi/4) of 6/4 pi = -pi/2 (this is the shorter distance, and this is what is used in the code), and pi = -pi (this could be either -pi or pi, and it is in fact not well

Re: [deal.II] Deal.II on Docker

2020-03-14 Thread luca.heltai
By the way, the examples in the docker image are located under $(spack location -i dealii)/share/deal.II/examples i.e., you can go to cd $(spack location -i dealii)/share/deal.II/examples and from there, compile and run. Notice that they are not pre-compiled (they would just take up

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

2020-04-09 Thread luca.heltai
e? >> >> Best, >> Jean-Paul >> >>> On 03 Apr 2020, at 06:03, Bruno Blais wrote: >>> >>> Ciao Luca, >>> It works perfectly now even with regular GMSH triangulation (see movie). >>> Now I understand the difference a

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

2020-04-02 Thread luca.heltai
Bruno, it seems like you are attaching your faces to the *boundary* manifold. Let me try to explain what is happening. In the code for step-54, there is a wire that is used to describe the manifold of the *boundary* of the surface (a curve of dimension one embedded in dimension three). This

Re: [deal.II] Example not Compiling in deallii on Docker

2020-05-18 Thread luca.heltai
You are trying to compile the examples in the /usr/local directory. The default user in the dealii docker image is the “dealii” user, and it does not have write access to those directories. If you really want work inside the docker image, you should copy the directory of the example(s) you

Re: [deal.II] deal.ii 9.1.1 quit running after macOS Catalina update

2020-05-03 Thread luca.heltai
I’m updating my Mac, to see if I can reproduce. Best, Luca. > On 3 May 2020, at 9:47, Alberto Salvadori wrote: > > Dear community, > Luca in particular > > sorry for this bothering. It happened again, as on Dec. 2 , 2019 that after a > macOS update deal.ii 9.1.1 quit running. > There appears

Re: [deal.II] triangulation save not working for 1D domain

2020-06-07 Thread luca.heltai
incerely > Amaresh > > On Sun, Jun 7, 2020 at 8:39 PM luca.heltai wrote: > Amaresh, > > as the documentation states, parallel::distributed::Triangulation is not > implemented in 1d. Consequently, parallel::distributed::SolutionTransfer will > not work in 1d. > > Ar

Re: [deal.II] step 70 9.2 version

2020-06-05 Thread luca.heltai
Dear Heena, unfortunately, we failed in cherry picking a default value in the parameter file. The generated parameter handler tries to write output files in a `results` directory (as indicated in the default parameter file `set Output directory = results`), which however is not created by

Re: [deal.II] step 70 9.2 version

2020-06-05 Thread luca.heltai
Yes. On it. L. > On 5 Jun 2020, at 18:21, Wolfgang Bangerth wrote: > > On 6/5/20 10:19 AM, luca.heltai wrote: >> Wolfgang, it seems that indeed the default parameter file in 9.2 still >> contains `set Output directory = results`.:( > > Want to move that to the 9.2

Re: [deal.II] triangulation save not working for 1D domain

2020-06-07 Thread luca.heltai
Amaresh, as the documentation states, parallel::distributed::Triangulation is not implemented in 1d. Consequently, parallel::distributed::SolutionTransfer will not work in 1d. Are you running your code in debug mode? In debug mode several assertions are throw when you try to instantiate a 1d

Re: [deal.II] GMesh 1D mesh input error

2020-06-24 Thread luca.heltai
This may be a problem with your physical ids. Can you remove all physical ids from the geo file, and try to export a “bare” mesh, without material id/boundary id information? I currently use vtk for all my needs. L. > On 24 Jun 2020, at 14:53, Victoria W. wrote: > > Hi David, > > Thank

[deal.II] New deal.II 9.2.0 package for MAC

2020-06-24 Thread luca.heltai
Dear All, there has been an issue with the deal.II Package which I hope I was able to resolve. The new mac package is in the same place of the old one https://github.com/dealii/dealii/releases/download/v9.2.0/dealii-9.2.0.dmg Would anyone with a mac try it out and tell me if they can run

Re: [deal.II] New deal.II 9.2.0 package for MAC

2020-06-29 Thread luca.heltai
le/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff' > [100%] Built target step-18 > bash-3.2$ ./step-18 > dyld: Library not loaded: libmetis.dylib > Referenced from: > /Users/albertosalvadori/Codes/dealii-9.2/examples/step-18/./step-18 > Reason: image not found > Abort

[deal.II] New docker image for deal.II 9.2.0

2020-07-15 Thread luca.heltai
Dear all, I’d like to inform you that we now have also docker images with deal.II 9.2.0, based on ubuntu bionic (18.04.1), and based on ubuntu focal (20.04.1). You can find them with docker pull dealii/dealii:v9.2.0-bionic docker pull dealii/dealii:v9.2.0-focal (dealii/dealii:latest) Best,

Re: [deal.II] Interest in a step-12-like DG tutorial but for the advection-diffusion equation?

2020-07-10 Thread luca.heltai
If you want to take some more inspiration using mesh_loop, ScratchData, and FEInterfaceData, you could take a look at this: https://github.com/dealii/dealii/blob/master/tests/meshworker/scratch_data_08.cc where the FEInterfaceValues which is now included in ScratchData is used to solve SIPG on

Re: [deal.II] KDTree implementation error

2020-07-24 Thread luca.heltai
KDTree needs nanoflann to be available. Did you compile deal.II with nanoflann exnabled? Check in the summary.log if DEAL_II_WITH_NANOFLANN is ON. RTree, on the other hand, does not require nanoflann, as it is included with boost (and it is faster than nanoflann). L. > On 24 Jul 2020, at

Re: [deal.II] KDTree implementation error

2020-07-24 Thread luca.heltai
Dear Heena, here is a snippet to achieve what you want: #include namespace bgi = boost::geometry::index; … Point<2> p0; const auto tree = pack_rtree(tria.get_vertices()); for (const auto : tree | bgi::adaptors::queried(bgi::nearest(p0, 3))) // do something with p

Re: [deal.II] Particles and field interpolation error

2020-07-16 Thread luca.heltai
Ciao Franco, ParticleHandler was built with the intention of “losing” particles whenever they fall out of the domain. This is the default behaviour of the ParticleHandler, and unless you store a pointer to an existing particle somewhere, you should not be in trouble. If you iterate over the

Re: [deal.II] New docker image for deal.II 9.2.0

2020-07-16 Thread luca.heltai
t; amazingly helpful for those using Travis_CI for their deal.II derived codes > :). > > > On Wednesday, 15 July 2020 05:04:31 UTC-4, luca.heltai wrote: > Dear all, > > I’d like to inform you that we now have also docker images with deal.II > 9.2.0, based on ubuntu

Re: [deal.II] Particles and field interpolation error

2020-07-20 Thread luca.heltai
Dear Franco, what type of triangulation are you using? If you look at the code that is run with `update_cached_numbers` https://github.com/dealii/dealii/blob/9e50f3ac04d088a9d2ffa74a81f08348e7f98a65/source/particles/particle_handler.cc#L173 you will see that the numbers are updated (just as

Re: [deal.II] Particles and field interpolation error

2020-07-22 Thread luca.heltai
Dear Franco, you need read access to the locally active dofs, not just the locally owned dofs. Take a look at how things are done in step-70: the vector that is used to interpolate the field on the particles is a read-only ghosted vector, that contains the locally relevant dofs

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