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

2020-09-03 Thread 'Maxi Miller' via deal.II User Group
Another issue I have is for the following code piece, where I basically have to rescale every part of the solution by a different factor (due to using unitless variables in the calculation): const ComponentMask surface_A_mask = fe.component_mask(surface_A); const ComponentMask surface_B_mask =

[deal.II] Scaling behavior of Matrix-Free test program

2020-03-02 Thread 'Maxi Miller' via deal.II User Group
I wrote a small test program for solving a non-linear equation using the RK4-solver implemented in deal.II, and assembling the right hand side using the matrix-free framework (code is attached). Afterwards I wanted to check the scaling behavior, after it should serve as a base for a larger

Re: [deal.II] Using data from external matrix as source for calculations done with deal.II - best approach?

2020-02-27 Thread 'Maxi Miller' via deal.II User Group
After additional tests I noticed that I'm not only overwriting the target_component-component with the new values, but also the other components, but with 0 instead. But instead I do not want to touch them. How can I do that (if possible)? Thanks! Am Donnerstag, 27. Februar 2020 17:00:12 UTC+1

Re: [deal.II] Using data from external matrix as source for calculations done with deal.II - best approach?

2020-02-27 Thread 'Maxi Miller' via deal.II User Group
Yes, the lambda worked, thanks! Am Donnerstag, 27. Februar 2020 17:00:12 UTC+1 schrieb Wolfgang Bangerth: > > > > | > > Functions::InterpolatedTensorProductGridData > interpolator(this->coordinate_values, > > >

Re: [deal.II] Using data from external matrix as source for calculations done with deal.II - best approach?

2020-02-27 Thread 'Maxi Miller' via deal.II User Group
39:23 UTC+1 schrieb Wolfgang Bangerth: > > On 1/23/20 7:29 AM, 'Maxi Miller' via deal.II User Group wrote: > > > > Why would you want to project when you can interpolate? That seems > > unnecessarily expensive :-) > > > > I would like to have the

Re: [deal.II] Difference between laplace-application through a matrix and through get_function_gradients()

2020-01-30 Thread 'Maxi Miller' via deal.II User Group
as I can see) nothing which can be used by others, I decided to delete the question. Therefore, the original question is not relevant anymore, either. Thanks! Am Mittwoch, 29. Januar 2020 23:19:50 UTC+1 schrieb Wolfgang Bangerth: > > On 1/20/20 7:59 AM, 'Maxi Miller' via deal.II User Group

Re: [deal.II] Using data from external matrix as source for calculations done with deal.II - best approach?

2020-01-23 Thread 'Maxi Miller' via deal.II User Group
Am Mittwoch, 22. Januar 2020 19:23:52 UTC+1 schrieb Wolfgang Bangerth: > > On 1/22/20 11:17 AM, 'Maxi Miller' via deal.II User Group wrote: > > As source term for calculations I am using data which is written in an > > external matrix (because it has been calcula

[deal.II] Using data from external matrix as source for calculations done with deal.II - best approach?

2020-01-22 Thread 'Maxi Miller' via deal.II User Group
As source term for calculations I am using data which is written in an external matrix (because it has been calculated by an external function), together with the x- and y-values for each matrix entry. My current approach for using this data is to use an interpolation function from GSL, and

[deal.II] Usage of vdSin/similar functions from the MKL together with VectorizedArray

2020-01-22 Thread 'Maxi Miller' via deal.II User Group
As described in step-48 it is possible to use vectorized functions, such as the function vdSin() from the MKL-library from Intel, together with VectorizedArray-variables. Unfortunately I could not find any example about how I can do that. Is the approach to simply use a code similar to

[deal.II] Re: Implementation of a solver for the non-linear diffusion equation using the TimeStepping-Class

2020-01-22 Thread 'Maxi Miller' via deal.II User Group
Found my mistake, I was iterating over the wrong things. Am Sonntag, 19. Januar 2020 14:54:16 UTC+1 schrieb Maxi Miller: > > I added a small MWE-code to the question, to make debugging easier. > Switching between the linear heat equation and the non-linear heat equation > can be done using the

Re: [deal.II] Re: Application of inverse mass matrix in matrix-free context using cell_loop instead of scale()

2020-01-20 Thread 'Maxi Miller' via deal.II User Group
om/dealii/dealii/blob/b84270a1d4099292be5b3d43c2ea65f3ee005919/tests/matrix_free/pre_and_post_loops_01.cc#L100-L121 >> ? >> >> Best, >> Daniel >> >> Am Sa., 18. Jan. 2020 um 12:05 Uhr schrieb 'Maxi Miller' via deal.II User >> Group : >&g

[deal.II] Difference between laplace-application through a matrix and through get_function_gradients()

2020-01-20 Thread 'Maxi Miller' via deal.II User Group
When applying the laplace operator to my solution vector, what is the difference between forming an explicit matrix containing the laplace operator by using template void LaplaceProblem::assemble_mass_matrix (){ TimerOutput::Scope t(computing_timer, "Mass matrix assembly");

[deal.II] Extension of gather_evaluate for read_dof_values_plain()?

2020-01-19 Thread 'Maxi Miller' via deal.II User Group
Currently gather_evaluate is a replacement for the combination of read_dof_values() and evaluate(), but it can not be used if one has to use read_dof_values_plain() instead. Therefore I was wondering if it was not implemented simply due to a lack of time, or because it is more difficult to

[deal.II] Re: Implementation of a solver for the non-linear diffusion equation using the TimeStepping-Class

2020-01-19 Thread 'Maxi Miller' via deal.II User Group
I added a small MWE-code to the question, to make debugging easier. Switching between the linear heat equation and the non-linear heat equation can be done using the constexpr-variable use_nonlinear in line 79. Furthermore, I changed the solution from exp(-pi^2*t) to exp(-2 * pi^2 * t), and

Re: [deal.II] Re: Application of inverse mass matrix in matrix-free context using cell_loop instead of scale()

2020-01-19 Thread 'Maxi Miller' via deal.II User Group
x_free/pre_and_post_loops_01.cc#L100-L121 > ? > > Best, > Daniel > > Am Sa., 18. Jan. 2020 um 12:05 Uhr schrieb 'Maxi Miller' via deal.II User > Group >: > >> I tried implementing it as >> data.cell_loop(::local_apply_cell, >>

[deal.II] Re: Application of inverse mass matrix in matrix-free context using cell_loop instead of scale()

2020-01-18 Thread 'Maxi Miller' via deal.II User Group
I tried implementing it as data.cell_loop(::local_apply_cell, this, dst, src, //true, [&](const unsigned int start_range, const unsigned int end_range){

[deal.II] Re: Application of inverse mass matrix in matrix-free context using cell_loop instead of scale()

2020-01-18 Thread 'Maxi Miller' via deal.II User Group
I.e. I should add an elementwise multiplication with the inverse mass matrix vector as postprocessing function? -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because

[deal.II] Application of inverse mass matrix in matrix-free context using cell_loop instead of scale()

2020-01-18 Thread 'Maxi Miller' via deal.II User Group
In step-48 the inverse mass matrix is applied by moving the inverse data into a vector and applying the function scale(), i.e. as in the following code: data.cell_loop(::local_apply_cell, this, dst, src,

[deal.II] Implementation of non-linear diffusion equation using the TimeStepping-Class and matrix-free routines

2020-01-18 Thread 'Maxi Miller' via deal.II User Group
I tried to implement a solver for the non-linear diffusion equation (\partial_t u = grad(u(grad u)) - f) using the TimeStepping-Class, the EmbeddedExplicitRungeKutta-Method and (for assembly) the matrix-free approach. For initial tests I used the linear heat equation with the solution u =

[deal.II] Implementation of a solver for the non-linear diffusion equation using the TimeStepping-Class

2020-01-18 Thread 'Maxi Miller' via deal.II User Group
I tried to implement a solver for the non-linear diffusion equation (\partial_t u = grad(u(grad u)) - f) using the TimeStepping-Class, the EmbeddedExplicitRungeKutta-Method and (for assembly) the matrix-free approach. For initial tests I used the linear heat equation with the solution u =

Re: [deal.II] Segfault when calling gather_evaluate() or read_dof_values_plain()

2020-01-14 Thread 'Maxi Miller' via deal.II User Group
either use a diagonal > mass matrix (see step-48) or use the cellwise inverse as a preconditioner > (when combined with suitable scaling) and solve the mass matrix iteratively. > > Best, > Martin > On 14.01.20 10:49, 'Maxi Miller' via deal.II User Group wrote: > > I could narrow it

Re: [deal.II] Segfault when calling gather_evaluate() or read_dof_values_plain()

2020-01-14 Thread 'Maxi Miller' via deal.II User Group
vec.partitioner $3 = std::shared_ptr (use count 3 , weak count 0) = {get() = 0x7a60c0} i.e. no null ptr. Could the problem be there, or somewhere else? Thanks! Am Montag, 13. Januar 2020 21:41:54 UTC+1 schrieb Wolfgang Bangerth: > > On 1/13/20 8:41 AM, 'Maxi Miller' via deal.II User Group wr

[deal.II] Segfault when calling gather_evaluate() or read_dof_values_plain()

2020-01-13 Thread 'Maxi Miller' via deal.II User Group
I tried to implement a RK4-solver similar to the upcoming example 67 using the matrix-free technique, and compare it to other solvers I wrote earlier. For this purpose I chose the classical heat-equation for testing. When running the attached example, though, I get a segfault when calling

[deal.II] Re: "fatal error: MueLu_CreateEpetraPreconditioner.hpp: No such file or directory" when compiling with Trilinos

2020-01-10 Thread 'Maxi Miller' via deal.II User Group
I ran into several other compilation problems with that trilinos version, thus I decided to try the suggested patch instead. Am Donnerstag, 9. Januar 2020 16:31:21 UTC+1 schrieb Bruno Turcksin: > > Hi, > > This is a known problem with the development version of Trilinos >

[deal.II] "fatal error: MueLu_CreateEpetraPreconditioner.hpp: No such file or directory" when compiling with Trilinos

2020-01-09 Thread 'Maxi Miller' via deal.II User Group
Hei, when trying to compile deal.II with one of the latest Trilinos-Versions, compilation fails with "fatal error: MueLu_CreateEpetraPreconditioner.hpp: No such file or directory", but the configuration process goes through without rising any problems. Which modules do I have to enable in

[deal.II] Usage of the AD framework for solving a time-dependent equation

2019-12-08 Thread 'Maxi Miller' via deal.II User Group
I tried to use the AD framework in my own codes (mainly for solving nonlinear equations), and therefore wrote a small test program for solving the linear diffusion equation (after I can calculate the jacobian by hand for that equation). Thus, my residual for the AD-jacobian is -0.5 * (\nabla

Re: [deal.II] Arpack solver reports 4294967295 iterations before converging

2019-10-11 Thread 'Maxi Miller' via deal.II User Group
Like this: https://github.com/dealii/dealii/pull/8899? Am Freitag, 11. Oktober 2019 16:42:24 UTC+2 schrieb Wolfgang Bangerth: > > On 10/11/19 7:22 AM, 'Maxi Miller' via deal.II User Group wrote: > > It is using the SolverControl-class for setting parameters such as the > >

Re: [deal.II] Arpack solver reports 4294967295 iterations before converging

2019-10-11 Thread 'Maxi Miller' via deal.II User Group
. Oktober 2019 07:35:41 UTC+2 schrieb Wolfgang Bangerth: > > On 10/9/19 7:47 AM, 'Maxi Miller' via deal.II User Group wrote: > > This number already comes from solver_control, given as > > > > solver_control.last_step (); > > Hm, that's really quite unfortunat

Re: [deal.II] Arpack solver reports 4294967295 iterations before converging

2019-10-09 Thread 'Maxi Miller' via deal.II User Group
This number already comes from solver_control, given as solver_control.last_step (); Am Montag, 7. Oktober 2019 15:33:29 UTC+2 schrieb Wolfgang Bangerth: > > On 10/7/19 5:32 AM, 'Maxi Miller' via deal.II User Group wrote: > > I implemented the changes in step-36 suggested in

[deal.II] Arpack solver reports 4294967295 iterations before converging

2019-10-07 Thread 'Maxi Miller' via deal.II User Group
I implemented the changes in step-36 suggested in the tutorial for using ARPACK instead of PETSc (as shown in the attachment). Now, the solver reports a convergence in 4294967295 iterations (with correct result), thus I assume a overflow/underflow bug. Is that something which I should report

Re: [deal.II] Create a LinearAlgebra::distributed::Vector from a LinearAlgebra::distributed::Vector

2019-09-23 Thread 'Maxi Miller' via deal.II User Group
> (In that case, no data is exchanged, and the vectors need to have > compatible locally owned dofs before calling.) > > Best, > Martin > On 23.09.19 17:07, 'Maxi Miller' via deal.II User Group wrote: > > When doing that in my code, I get the error > error: conversion from

Re: [deal.II] Create a LinearAlgebra::distributed::Vector from a LinearAlgebra::distributed::Vector

2019-09-23 Thread 'Maxi Miller' via deal.II User Group
When doing that in my code, I get the error error: conversion from ‘Vector’ to non-scalar type ‘Vector< float,[...]>’ requested thus I assume I have to implement it myself... Am Freitag, 13. September 2019 17:53:37 UTC+2 schrieb Wolfgang Bangerth: > > On 9/13/19 8:39 AM, 'Maxi

[deal.II] Create a LinearAlgebra::distributed::Vector from a LinearAlgebra::distributed::Vector

2019-09-13 Thread 'Maxi Miller' via deal.II User Group
In my program I have to reuse old solutions (due to time dependency), but would like to use them both as double values and float values (preconditioning does not require double values). Unfortunately my old solution is only given as a LinearAlgebra::distributed::Vector(), but I have to use a

Re: [deal.II] Requirements for citing deal.II

2019-09-11 Thread 'Maxi Miller' via deal.II User Group
Ok, will do that, thanks! Am Mittwoch, 11. September 2019 16:52:51 UTC+2 schrieb Wolfgang Bangerth: > > On 9/11/19 3:27 AM, 'Maxi Miller' via deal.II User Group wrote: > > In one of my side projects I include the library deal.II, but use it > > only for reading in parameter

[deal.II] Requirements for citing deal.II

2019-09-11 Thread 'Maxi Miller' via deal.II User Group
In one of my side projects I include the library deal.II, but use it only for reading in parameter files and printing out data in the HDF5 format. I included it mostly because it is in use in most of my main projects, and thus it already was available. Furthermore, being able to reuse parameter

Re: [deal.II] VectorTools::Compress() fails after mesh_loop and distribute_local_to_global

2019-09-02 Thread 'Maxi Miller' via deal.II User Group
u can not figure it out, can you make a minimal complete example I > can try? > > > On Tue, Aug 27, 2019 at 6:59 AM 'Maxi Miller' via deal.II User Group > > wrote: > > > > I am trying to assemble my residual/RHS by using mesh_loop: > >

[deal.II] VectorTools::Compress() fails after mesh_loop and distribute_local_to_global

2019-08-27 Thread 'Maxi Miller' via deal.II User Group
I am trying to assemble my residual/RHS by using mesh_loop: evaluation_point = present_solution; extension_vector = newton_update; extension_vector *= alpha; evaluation_point += extension_vector; residual.reinit(locally_owned_dofs, mpi_communicator);

[deal.II] Mixed-precision algorithms in deal.II

2019-08-26 Thread 'Maxi Miller' via deal.II User Group
I tried to implement a simple mixed-precision algorithm in deal.II, which creates my matrix using float values, and my vectors using double values. Unfortunately, the function distribute_local_to_global(cell_matrix, cell_rhs, local_dof_indices, system_matrix, system_rhs) does not support mixed

[deal.II] Creation of diagonal matrix for the heat equation in a matrix-free context

2019-08-02 Thread 'Maxi Miller' via deal.II User Group
Following step-37 I tried to extend it for non-linear equations, using a jacobian approximation for the "matrix" (which can be written as Jv = (F(u + ev) - F(u)) * 1/e, with e a small value (~1e-6), F() the residual of the function, u the current solution, v the krylov vector obtained from the

Re: [deal.II] Re: MGTransferMatrixFree<> interpolate_to_mg() fails with segfault, when compiled in release mode

2019-08-01 Thread 'Maxi Miller' via deal.II User Group
Found my mistake, I forgot to call mg_transfer.build(dof_handler); before doing anything with it. Am Donnerstag, 1. August 2019 09:02:15 UTC+2 schrieb Maxi Miller: > > Hei, > the program crashes in release mode way before it crashes in debug mode. > The code shown is completely from the

Re: [deal.II] Re: MGTransferMatrixFree<> interpolate_to_mg() fails with segfault, when compiled in release mode

2019-08-01 Thread 'Maxi Miller' via deal.II User Group
Hei, the program crashes in release mode way before it crashes in debug mode. The code shown is completely from the deal.II-library, with some added std::cout<<-lines. The only code written by myself is in main.cc, but the crash happens in the code from the library. Am Donnerstag, 1. August

[deal.II] MGTransferMatrixFree<> interpolate_to_mg() fails with segfault, when compiled in release mode

2019-07-31 Thread 'Maxi Miller' via deal.II User Group
I am trying to implement a test program using the matrix-free method, combined with a geometric multigrid preconditioner. In my case my vmult/apply_add-function needs access to the solution from the last step. Thus I added a vector LinearAlgebra::distributed::Vector old_solution; which is

Re: [deal.II] Error on runnig the examples

2019-07-31 Thread 'Maxi Miller' via deal.II User Group
Apparently you did not install the library correct, there is no *.so-file in that folder. Maybe try to reinstall it? Am Mittwoch, 31. Juli 2019 09:38:17 UTC+2 schrieb Javad Hashemi: > > Dear Dr. Bangreth, > > I really appreciate your email. I checked the lib folder and you can see > the list of

Re: [deal.II] Access old solution(s) in MatrixFreeOperators::Base::apply_add()

2019-07-26 Thread 'Maxi Miller' via deal.II User Group
I found my mistake, I could not reuse the same partition for the main matrix and the MG-matrices, thus I had to add LinearAlgebra::distributed::Vector local_solution; mg_matrices[level].initialize_dof_vector(local_solution); //local_solution = solution;

[deal.II] Access old solution(s) in MatrixFreeOperators::Base::apply_add()

2019-07-26 Thread 'Maxi Miller' via deal.II User Group
I followed step-37 for creating a MatrixFreeOperator, but now I also would like to access a previous solution (which is needed during apply_add()), and stored using a LinearAlgebra::distributed::Vector. In step-48 there is an example which uses previous solutions, but here the solve-function is

Re: [deal.II] VMult-function in the MatrixFree-Framework

2019-07-24 Thread 'Maxi Miller' via deal.II User Group
/19 12:23 PM, 'Maxi Miller' via deal.II User Group wrote: > > My LinearOperator only provides a vmult-interface, nothing else, but for > > initializing the preconditioner I still need a sparse matrix, thus I can > not > > use the LinearOperator, as far as I understan

Re: [deal.II] VMult-function in the MatrixFree-Framework

2019-07-24 Thread 'Maxi Miller' via deal.II User Group
My LinearOperator only provides a vmult-interface, nothing else, but for initializing the preconditioner I still need a sparse matrix, thus I can not use the LinearOperator, as far as I understand. Or is there a way to use it? Am Mittwoch, 24. Juli 2019 17:28:14 UTC+2 schrieb Daniel Arndt: > >

Re: [deal.II] Matrix-free-method for an operator depending on input from solver

2019-07-24 Thread 'Maxi Miller' via deal.II User Group
vectors there. Given a > nonlinear field u that you linearize about, you could perturb it with e*v_i > and compute the local diagonal according to your formula. From what I > understand, you have the operator in an even more abstract way, so > collecting everything in one local

[deal.II] Matrix-free-method for an operator depending on input from solver

2019-07-24 Thread 'Maxi Miller' via deal.II User Group
I am currently trying to implement the JFNK-method in the matrix-free framework (by following step-37 and step-59) for solving nonlinear equations of the form F(u)=0. The method itself replaces the multiplication of the explicit jacobian J with the krylov vector v during solving with the

Re: [deal.II] VMult-function in the MatrixFree-Framework

2019-07-24 Thread 'Maxi Miller' via deal.II User Group
Is there then a way to use LinearOperator as Input for a preconditioner? Else I still have to form the full system matrix (which I would like to avoid). Am Mittwoch, 24. Juli 2019 13:43:09 UTC+2 schrieb Daniel Arndt: > > On the other hand, would it be sufficient to unroll the

Re: [deal.II] VMult-function in the MatrixFree-Framework

2019-07-24 Thread 'Maxi Miller' via deal.II User Group
Am Mittwoch, 24. Juli 2019 00:39:14 UTC+2 schrieb Daniel Arndt: > > Maxi, > > No, that code is the vmult-call I am using in my LinearOperator (and is >> used directly in my solve()-call). The calculate_residual()-function is >> similar to the function in step-15, with the difference, that I do

Re: [deal.II] Re: Matrix-Vector-multiplication on deal.II-grid

2019-07-23 Thread 'Maxi Miller' via deal.II User Group
the moving pulse. Is that possible? The matrix I was mentioning earlier would be a dense matrix, formed according to the DHT-method (i.e. no relation to FEM) Am Dienstag, 23. Juli 2019 22:35:57 UTC+2 schrieb Wolfgang Bangerth: > > On 7/22/19 1:32 AM, 'Maxi Miller' via deal.II User Group

Re: [deal.II] VMult-function in the MatrixFree-Framework

2019-07-23 Thread 'Maxi Miller' via deal.II User Group
No, that code is the vmult-call I am using in my LinearOperator (and is used directly in my solve()-call). The calculate_residual()-function is similar to the function in step-15, with the difference, that I do not provide alpha, but the vector, and return the calculated residual value. Thus,

Re: [deal.II] VMult-function in the MatrixFree-Framework

2019-07-23 Thread 'Maxi Miller' via deal.II User Group
My aim is to implement the jacobian approximation, i.e. (if F(u) = 0 is the function to solve) I wanted to implement dst = (F(current_solution + epsilon * src) - F(current_solution))/epsilon. In my LinearOperator, my code is LinearOperator jacobian_operator; jacobian_operator.vmult =

[deal.II] VMult-function in the MatrixFree-Framework

2019-07-23 Thread 'Maxi Miller' via deal.II User Group
In my project I already managed to replace the system_matrix in the solve()-call by a custom LinearOperator, but still I had to retain the matrix itself (for the preconditioner, for example). Thus I am now trying to use the MatrixFree-framework for that. Thus, some questions arose: - When

Re: [deal.II] Code tries to access DoF indices on artificial cells, even though those cells should not be artificial

2019-07-22 Thread 'Maxi Miller' via deal.II User Group
3 > Aquired function gradients on cell 3 > > > before crashing, indicating a problem on cell 1 1 0 3. As long as > cell->active() is false, I can not call the function is_artificial() for > checking if I am on an artificial cell. Is my if-loop correct, or did I > miss so

Re: [deal.II] Re: Matrix-Vector-multiplication on deal.II-grid

2019-07-22 Thread 'Maxi Miller' via deal.II User Group
On 7/12/19 11:28 AM, 'Maxi Miller' via deal.II User Group wrote: > > It is difficult to write it as a single integral. The operation is > similar to > > the split-step fourier method, i.e. transforming the column vector f(r) > once using > > g(rho)=2\pi\int_0^\infty

Re: [deal.II] Code tries to access DoF indices on artificial cells, even though those cells should not be artificial

2019-07-20 Thread 'Maxi Miller' via deal.II User Group
nction is_artificial() for checking if I am on an artificial cell. Is my if-loop correct, or did I miss something here? Am Freitag, 19. Juli 2019 18:01:03 UTC+2 schrieb Wolfgang Bangerth: > > On 7/19/19 9:59 AM, 'Maxi Miller' via deal.II User Group wrote: > > What do the parallel m

Re: [deal.II] Create a LinearOperator with a function instead of a matrix

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
mg, mg_transfer); and here I intent to replace all occurences of matrix_t with my custom LinearOperator (if that makes sense). Am Freitag, 19. Juli 2019 17:51:10 UTC+2 schrieb Wolfgang Bangerth: > > On 7/19/19 9:47 AM, 'Maxi Miller' via deal.II User Group wrote: > > What I did w

Re: [deal.II] Code tries to access DoF indices on artificial cells, even though those cells should not be artificial

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
... Am Freitag, 19. Juli 2019 17:53:05 UTC+2 schrieb Wolfgang Bangerth: > > On 7/19/19 9:49 AM, 'Maxi Miller' via deal.II User Group wrote: > > I can not use that function, else I will get > > An error occurred in line <3543> of file > > in function > >

Re: [deal.II] Code tries to access DoF indices on artificial cells, even though those cells should not be artificial

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
eitag, 19. Juli 2019 17:37:01 UTC+2 schrieb Wolfgang Bangerth: > > On 7/19/19 9:31 AM, 'Maxi Miller' via deal.II User Group wrote: > > Based on the stacktrace the problematic access happens within > mg_cell_worker(): > > ... > > which is guarded by the if-condition. &

Re: [deal.II] Create a LinearOperator with a function instead of a matrix

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
What I did was the replacement of system_matrix with a function, providing a vmult()-function. Now I would like to add a preconditioner based on that function to reduce the necessary GMRES-iterations. But until now most of the preconditioners require a matrix for initialization. Thus I wanted

Re: [deal.II] Create a LinearOperator with a function instead of a matrix

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
Bangerth: > > On 7/19/19 9:18 AM, 'Maxi Miller' via deal.II User Group wrote: > > Is it then possible to use this LinearOperator in a preconditioner? The > code > > works without one (i.e. PreconditionIdentity()), but the Iterations are > > increasing quite fast, thus negat

Re: [deal.II] Code tries to access DoF indices on artificial cells, even though those cells should not be artificial

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
p15::ScratchData<2> const&, Step15::CopyData const&, unsigned int, unsigned int) #13 ./MG_test: void dealii::MeshWorker::mesh_loop, true> >, Step15::ScratchData<2>, Step15::CopyData, dealii::TriaIterator, true> > >(dealii::TriaIterator, true> > const&

Re: [deal.II] Create a LinearOperator with a function instead of a matrix

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
Is it then possible to use this LinearOperator in a preconditioner? The code works without one (i.e. PreconditionIdentity()), but the Iterations are increasing quite fast, thus negating all speedup gained from the LinearOperator. I tried to find something in the examples, but only found data

[deal.II] Code tries to access DoF indices on artificial cells, even though those cells should not be artificial

2019-07-19 Thread 'Maxi Miller' via deal.II User Group
I am trying to port example 15 to a MPI-supported version, using the geometric multigrid method as preconditioner (to get more familiar with the implementation). I followed example 50 while doing that, but currently I get the error An error occurred in line <3866> of file

[deal.II] Create a LinearOperator with a function instead of a matrix

2019-07-16 Thread 'Maxi Miller' via deal.II User Group
I tried to follow the examples for setting up a LinearOperator (such as shown in Step-22 and Step-20), but instead of a matrix I wanted to provide my own function which should serve as vmult-function (i.e. a matrix-free linear operator). Is that possible? My initial test was the following code:

Re: [deal.II] Implicit stepping methods from the TimeStepping-namespace for large sparse matrices

2019-07-16 Thread 'Maxi Miller' via deal.II User Group
> function-type object that can be used for evaluating the inverse of the > Jacobians and the right-hand side. > You might also want to have a look at the test base/time_stepping_01 ( > https://github.com/dealii/dealii/blob/master/tests/base/time_stepping_01.cc > ). > > Best, &

[deal.II] Implicit stepping methods from the TimeStepping-namespace for large sparse matrices

2019-07-15 Thread 'Maxi Miller' via deal.II User Group
As far as I understand all implicit time-stepping methods in the TimeStepping-namespace take a function which invert the jacobian matrix and the mass matrix (combined). This is done using a sparse solver (UMFPACK). Is it that still possible for a larger system (10kk DoFs), or do I have to

[deal.II] Re: Matrix-Vector-multiplication on deal.II-grid

2019-07-12 Thread 'Maxi Miller' via deal.II User Group
It is difficult to write it as a single integral. The operation is similar to the split-step fourier method, i.e. transforming the column vector f(r) once using g(rho)=2\pi\int_0^\infty rf(r)J_0(2\pi\rho r)dr, multiplying it with a vector, and transforming it back using f(r) =

[deal.II] Matrix-Vector-multiplication on deal.II-grid

2019-07-12 Thread 'Maxi Miller' via deal.II User Group
Is it possible to "mis-"use the facilities of deal.II for calculating a NLS using the discrete hankel transformation? The idea here was to take an evenly refined grid, and calculate the values of each node column based on the values of the node column to the left/right times a constant matrix,

[deal.II] Re: Deal.II-Installation on Cluster fails

2019-07-12 Thread 'Maxi Miller' via deal.II User Group
Yes, that works, thanks! Am Donnerstag, 11. Juli 2019 17:01:21 UTC+2 schrieb Daniel Arndt: > > Maxi, > > Can you just try again with a recent commit? > > Best, > Daniel > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

Re: [deal.II] Elementwise multiplication of Tensors

2019-06-07 Thread 'Maxi Miller' via deal.II User Group
Something like this: https://github.com/dealii/dealii/pull/8307? Am Donnerstag, 6. Juni 2019 00:38:59 UTC+2 schrieb Wolfgang Bangerth: > > On 6/5/19 3:22 PM, 'Maxi Miller' via deal.II User Group wrote: > > is there a function for the elementwise multiplication of Tensors? I >

[deal.II] Elementwise multiplication of Tensors

2019-06-05 Thread 'Maxi Miller' via deal.II User Group
Hei, is there a function for the elementwise multiplication of Tensors? I could only find functions for the scalar product, but not the schur product. Thanks! -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

Re: [deal.II] Interpolation between FE_Q- and FE_Bernstein elements

2019-05-30 Thread 'Maxi Miller' via deal.II User Group
, it does not in the > second, a != b > I do not understand that behavior yet. > > Am Donnerstag, 30. Mai 2019 19:00:02 UTC+2 schrieb Wolfgang Bangerth: >> >> On 5/30/19 9:06 AM, 'Maxi Miller' via deal.II User Group wrote: >> > I wanted to write some

Re: [deal.II] Interpolation between FE_Q- and FE_Bernstein elements

2019-05-30 Thread 'Maxi Miller' via deal.II User Group
!= b Q(a)->B(b): Even though that worked in the first round, it does not in the second, a != b I do not understand that behavior yet. Am Donnerstag, 30. Mai 2019 19:00:02 UTC+2 schrieb Wolfgang Bangerth: > > On 5/30/19 9:06 AM, 'Maxi Miller' via deal.II User Group wrote: > > I wanted to

[deal.II] Interpolation between FE_Q- and FE_Bernstein elements

2019-05-30 Thread 'Maxi Miller' via deal.II User Group
I wanted to write some functions to convert my solution from using FE_Q-elements to FE_Bernstein-elements (and back). For that I wrote two functions, convert_feQ_to_feB() and convert_feB_to_feQ() (as listed in the attachment). When converting from FE_Q-elements to FE_Bernstein-elements, I get

Re: [deal.II] prepare_for_coarsening_and_refinement() for FE_Bernstein-elements

2019-05-29 Thread 'Maxi Miller' via deal.II User Group
I/classFE__Bernstein.html#ad881d4e04f5e699e4a8bda5b4e9f5265 > > that is impossible. Would an alternative solution be to interpolate > everything onto a grid using FE_Q-elements, transfer the result, and > interpolate the results back? > > Am Dienstag, 21. Mai 2019 03:

Re: [deal.II] prepare_for_coarsening_and_refinement() for FE_Bernstein-elements

2019-05-21 Thread 'Maxi Miller' via deal.II User Group
Dienstag, 21. Mai 2019 03:41:58 UTC+2 schrieb Wolfgang Bangerth: > > On 5/20/19 5:18 AM, 'Maxi Miller' via deal.II User Group wrote: > > Trying to transfer solutions from an old grid to a new grid with > > parallel::distributed::SolutionTransfer TrilinosWrappers::MPI::Vecto

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

2019-05-20 Thread 'Maxi Miller' via deal.II User Group
Donnerstag, 16. Mai 2019 22:00:23 UTC+2 schrieb luca.heltai: > > > > On 16 May 2019, at 9:16, 'Maxi Miller' via deal.II User Group < > dea...@googlegroups.com > wrote: > > > > I would like to use the interpolate()-function to interpolate the > correct function ont

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

2019-05-20 Thread 'Maxi Miller' via deal.II User Group
That works, thanks! Am Donnerstag, 16. Mai 2019 22:00:23 UTC+2 schrieb luca.heltai: > > > > On 16 May 2019, at 9:16, 'Maxi Miller' via deal.II User Group < > dea...@googlegroups.com > wrote: > > > > I would like to use the interpolate()-function to interpolat

[deal.II] prepare_for_coarsening_and_refinement() for FE_Bernstein-elements

2019-05-20 Thread 'Maxi Miller' via deal.II User Group
Trying to transfer solutions from an old grid to a new grid with parallel::distributed::SolutionTransfer> solution_transfer() and solution_transfer.prepare_for_coarsening_and_refinement() fails with An error occurred in line <71> of file <~/Downloads/git-files/dealii/source/ fe/fe_bernstein.cc>

Re: [deal.II] Applying boundary masks when using project_boundary_values()

2019-05-16 Thread 'Maxi Miller' via deal.II User Group
i.e. dirichlet-conditions on 0, neumann-conditions on 1, and similar stuff? Thanks! Am Donnerstag, 16. Mai 2019 19:20:59 UTC+2 schrieb Wolfgang Bangerth: > > On 5/15/19 8:37 AM, 'Maxi Miller' via deal.II User Group wrote: > > I have to replace VectorTools::interpolate_boundary_v

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

2019-05-16 Thread 'Maxi Miller' via deal.II User Group
'Maxi Miller' via deal.II User Group < > dea...@googlegroups.com > 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-elem

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

2019-05-16 Thread 'Maxi Miller' via deal.II User Group
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 FE_Bernstein elements. The error message I get is An error occurred in line <3098> of file

[deal.II] Applying boundary masks when using project_boundary_values()

2019-05-15 Thread 'Maxi Miller' via deal.II User Group
I have to replace VectorTools::interpolate_boundary_values with VectorTools::project_boundary_values at several places in my project. I could apply the boundary values only for certain parts in my FESystem using component masks, but I can not use those masks in project_boundary_values(). What

[deal.II] Spline basìs function instead of gaussian basis function

2019-05-15 Thread 'Maxi Miller' via deal.II User Group
When using FE_Q-elements as basis function, Lagrange-polynoms are used, as far as I understand. Is it possible to replace those with B-splines as basis functions? -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

[deal.II] scratch_data_03.cc from test/meshworker produces strange results when refining adaptively

2019-05-01 Thread 'Maxi Miller' via deal.II User Group
I wanted to test the new ScratchData- and CopyData-Classes for DG-subfaces, and thus used Test 3 with a locally refined grid. The result shows significant distortions at the transitions between refinement levels. Should that be, or is that a bug? Or is it just the missing handling of subfaces

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-05-01 Thread 'Maxi Miller' via deal.II User Group
Am Dienstag, 30. April 2019 05:59:05 UTC+2 schrieb Wolfgang Bangerth: > > > Maxi, > > > What did you have to do? I was going to reproduce your problem today > by > > installing a Trilinos version that has NOX enabled. Is this moot > now, > > i.e., was it a bug in your code or

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-29 Thread 'Maxi Miller' via deal.II User Group
Am Montag, 29. April 2019 22:36:55 UTC+2 schrieb Wolfgang Bangerth: > > On 4/29/19 7:35 AM, 'Maxi Miller' via deal.II User Group wrote: > > Could get it to work, now the code works equally fine for one or several > > MPI threads. > > What did you have to do? I was

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-29 Thread 'Maxi Miller' via deal.II User Group
result in "Convergence failed". >> >> Am Samstag, 27. April 2019 05:43:47 UTC+2 schrieb Wolfgang Bangerth: >>> >>> On 4/26/19 2:28 PM, 'Maxi Miller' via deal.II User Group wrote: >>> > I think the current version is the smallest version I can get

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-29 Thread 'Maxi Miller' via deal.II User Group
ives a "Test passed", > using more threads will result in "Convergence failed". > > Am Samstag, 27. April 2019 05:43:47 UTC+2 schrieb Wolfgang Bangerth: >> >> On 4/26/19 2:28 PM, 'Maxi Miller' via deal.II User Group wrote: >> > I think the curre

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-29 Thread 'Maxi Miller' via deal.II User Group
m Samstag, 27. April 2019 05:43:47 UTC+2 schrieb Wolfgang Bangerth: > > On 4/26/19 2:28 PM, 'Maxi Miller' via deal.II User Group wrote: > > I think the current version is the smallest version I can get. It will > work > > for a single thread, but not for two or more thread

[deal.II] Re: Step 12, rewritten using ScratchData and CopyData

2019-04-29 Thread 'Maxi Miller' via deal.II User Group
After some tests it looks like as if the problem lies in the treatment of the subfaces. When refining the grid globally, everything works as expected, when refining adaptively, the ScratchData-Version fails. Thus I assume the problem lies there, but I can not see it in the code? -- The

[deal.II] Step 12, rewritten using ScratchData and CopyData

2019-04-26 Thread 'Maxi Miller' via deal.II User Group
I tried to rewrite step-12 using the recently introduced classes ScratchData and CopyData. In the first iteration, the results are similar, in the second iteration the new version gives wrong results, though. I compared the generated matrices and right hand side vectors, and they were

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-26 Thread 'Maxi Miller' via deal.II User Group
: > > On 4/26/19 1:59 AM, 'Maxi Miller' via deal.II User Group wrote: > > I tried to reduce it as much as possible while still being able to run, > > the result is attached. It still has ~600 lines, but I am not sure if I > > should remove things like the output-function? F

Re: [deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-26 Thread 'Maxi Miller' via deal.II User Group
as possible while removing unneccessary lines. Is that example usable? Am Freitag, 26. April 2019 05:12:39 UTC+2 schrieb Wolfgang Bangerth: > > On 4/25/19 10:13 AM, 'Maxi Miller' via deal.II User Group wrote: > > After running some tests, I ended up reducing the problem to the

[deal.II] Re: Integrating a deal.II-specific function in a NOX-Interface for MPI-threads

2019-04-25 Thread 'Maxi Miller' via deal.II User Group
After running some tests, I ended up reducing the problem to the transfer to and from the Epetra-vectors. I have to write an interface to the model (according to the instructions), and as shown in the code above. There I have Epetra-Vectors created by my interface, with a size of

[deal.II] Re: Error at Trilinos installation

2019-04-25 Thread 'Maxi Miller' via deal.II User Group
It looks as if you have to recompile Trilinos using the -fPIC-switch to create position independent code. Am Donnerstag, 25. April 2019 12:10:52 UTC+2 schrieb gabrie...@koeln.de: > > Hey everyone, > I have an error at compiling deal_ii_with_Trilinos=ON, which I dont > understand. > > First I

Re: [deal.II] Poisson test code fails for a fe-degree >= 2

2019-04-22 Thread 'Maxi Miller' via deal.II User Group
How exactly can I test the examples after modifying them, other than by running them? Am Sonntag, 7. April 2019 23:56:49 UTC+2 schrieb Wolfgang Bangerth: > > On 4/7/19 1:54 PM, 'Maxi Miller' via deal.II User Group wrote: > > Could do that, but not until Easter (Dead

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