[deal.II] Re: for help step-35 . flow around the cylinder
On 12/8/19 9:02 AM, hussan zeb wrote: > > > An error occurred in line <361> of file > in function > dealii::Point::Point(Number, Number, Number) [with int dim > = > 2; Number = double] > The violated condition was: > dim == 3 > Additional information: > You can only initialize Point<3> objects using the constructor that takes > three arguments. Point objects with dim!=3 require initialization with > the constructor that takes 'dim' arguments. > > Stacktrace: > --- > #0 ./step-35: dealii::Point<2, double>::Point(double, double, double) > #1 ./step-35: Step35::NavierStokesProjection<2>::run(bool, unsigned int) > #2 ./step-35: main > Hussan, we don't know what causes this without debugging the code you attach. But the error message is quite clear in explaining what is happening. One way or the other, you will have to learn to debug codes with a debugger so you can see where this kind of error happens and how to fix it. There are also video lectures on this topic. Why don't you use this relatively simple occasion as a way to learn a new skill? Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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 you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/9f55ca5f-d84b-2d7c-f1c7-3d562ccbd582%40colostate.edu.
Re: [deal.II] get_dof_indices() only works on active cells - blocks vector
Dear David,
Thank you for your quick reply.
Yes, I need the neighbour information of each cell to compute the boundary
integration in the DG formulation. Therefore, I get the neighbouring cell
in the loop of the active cell by using "const auto neighbor =
cell->neighbor(face_n)"; (similar to step 30).
I am quite sure that the problem is what you are describing, thus it occurs
only when I use the adaptative refinement.
The problem appears here:
#0 ./FEM-DGdeal: dealii::DoFCellAccessor,
false>::get_dof_indices(std::vector >&) const
#1 ./FEM-DGdeal: FEMwDG<2>::assemble_system(unsigned int)
#2 ./FEM-DGdeal: FEMwDG<2>::run(unsigned int, unsigned int, unsigned int,
unsigned int)
#3 ./FEM-DGdeal: main
And the part of the code where I call the get_dof_indices is this:
void FEMwDG::assemble_system(const unsigned int typecase)
{
const unsigned int dofs_per_cell = dof_handler.get_fe().dofs_per_cell;
std::vector local_dof_indices(dofs_per_cell);
std::vector
neighbor_dof_indices(dofs_per_cell);
const UpdateFlags update_flags = update_values | update_gradients |
update_quadrature_points |
update_JxW_values;
const UpdateFlags face_update_flags = update_values |
update_quadrature_points | update_JxW_values |
update_normal_vectors;
const UpdateFlags neighbor_face_update_flags = update_values;
FEValues fe_values(mapping, fe, quadrature, update_flags);
FEFaceValues fe_face_values(mapping, fe, face_quadrature,
face_update_flags);
FESubfaceValues fe_subface_values(mapping, fe, face_quadrature,
face_update_flags);
FEFaceValues fe_face_neighbor(mapping, fe,
face_quadrature,neighbor_face_update_flags);
FullMatrix ui_vi_matrix(dofs_per_cell, dofs_per_cell);
//matrix dominio
FullMatrix ue_vi_matrix(dofs_per_cell, dofs_per_cell);
FullMatrix ui_ve_matrix(dofs_per_cell, dofs_per_cell);
FullMatrix ue_ve_matrix(dofs_per_cell, dofs_per_cell);
Vector cell_vector(dofs_per_cell);
const FEValuesExtractors::Scalar verror(0);
const FEValuesExtractors::Scalar variable(1);
for (const auto : dof_handler.active_cell_iterators())
{
fe_values.reinit(cell); ui_vi_matrix = 0; cell_vector= 0;
//--DOMAIN
INTEGRATOR--
adv.assemble_cell_term(fe_values, ui_vi_matrix, cell_vector,
verror, variable,cell, typecase);
cell->get_dof_indices(local_dof_indices);
for (unsigned int face_n = 0; face_n <
GeometryInfo::faces_per_cell; ++face_n)
{
//-FACE AT THE
EXTERNAL
BOUNDARY-
const auto face = cell->face(face_n);
if (face->at_boundary())
{
fe_face_values.reinit(cell, face_n);
adv.assemble_boundary_term(fe_face_values,
ui_vi_matrix, cell_vector, verror, variable);
}
//-FACE AT THE
INTERNAL
BOUNDARY-
else
{
const auto neighbor = cell->neighbor(face_n);
if ((dim > 1) && (cell->index() <
neighbor->index()))
{
const unsigned int neighbor2
=cell->neighbor_face_no(face_n);
ue_vi_matrix = 0; ui_ve_matrix = 0; ue_ve_matrix
= 0;
fe_face_values.reinit(cell, face_n);
fe_face_neighbor.reinit(neighbor, neighbor2);
adv.assemble_face_term(fe_face_values,
fe_face_neighbor, ui_vi_matrix, ue_vi_matrix, ui_ve_matrix, ue_ve_matrix,
verror, variable, typecase);
neighbor->get_dof_indices(neighbor_dof_indices);
// ---LOCAL ASSEMBLE
--
for (unsigned int i = 0; i < dofs_per_cell; ++i)
for (unsigned int j = 0; j < dofs_per_cell; ++j)
{
system_matrix.add(local_dof_indices[i],
neighbor_dof_indices[j], ue_vi_matrix(i, j));
system_matrix.add(neighbor_dof_indices[i], local_dof_indices[j],
ui_ve_matrix(i, j));
system_matrix.add(neighbor_dof_indices[i],
neighbor_dof_indices[j], ue_ve_matrix(i, j));
}
}
}
}
Re: [deal.II] get_dof_indices() only works on active cells - blocks vector
Dear Juan, My best guess is that, at some point in the loop over all active cells, you are also doing some computations involving the neighbor of each cell. TriaAccessor::neighbor() returns the neighboring cell which has, at most, the same level number as the current cell: i.e., if the neighbor cell has been refined but the current cell has not, then trying to get the degrees of freedom from the neighbor will throw exactly this exception since the cell returned by the call to neighbor() is inactive. This is only a guess. Could you show us the part of your code that triggers this exception? That will help us give you a better answer :) Thanks, David On Fri, Dec 6, 2019 at 3:53 AM Juan Felipe Giraldo wrote: > > > Hi all! > > I am currently working on the linear advection problem by using a DG > formulation, similar to the problem in step 12 > https://www.dealii.org/current/doxygen/deal.II/step_12.html, but using a > mixed formulation as it is shown in step 20 > https://www.dealii.org/current/doxygen/deal.II/step_20.html. I can solve the > problem without problems using a global refinement, however, when I implement > an adaptative refinement I have the following problem after the 1st > refinement cycle > > An error occurred in line <3792> of file > > in function > void dealii::DoFCellAccessor lda>::get_dof_indices(std::vector&) const [with DoFHandlerType > = dealii::DoFHandler<2, 2>; bool level_dof_access = false] > The violated condition was: > this->active() > Additional information: > get_dof_indices() only works on active cells. > > > I have seen that some people had this problem a couple of years ago, but I > have not seen a proper solution to solve it. > > Anyone knows how can I solve it? > > Thank you so much, > > Regards, > > Juan Felipe Giraldo > > -- > 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 you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/38d23dcb-3028-45eb-a539-737e72c597b0%40googlegroups.com. -- 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 you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CABrTbYS7_D7cz8BVjObSSy3a6zAHMSCrwn75cj79XBVnOicCpw%40mail.gmail.com.
[deal.II] Usage of the AD framework for solving a time-dependent equation
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
u_1 + \nabla u_0)\cdot\nabla\varphi - \frac{1}{dt}(u_1 - u_0)\cdot\varphi,
with u_0 my current solution, and u_1 my solution for the next step. When
creating the jacobian by hand, I use the same approach as shown in example
33, and assume that u_1 = u_0 in my first step, resulting in
-0.5\cdot(\nabla\varphi_i\cdot\nabla\varphi_j) -
\frac{1}{dt}\cdot\varphi_i\cdot\varphi_j, and my right hand side is \nabla
u_0\cdot\nabla\varphi.
Solving both systems should give me a value for \delta u, i.e. the update
for my current solution, such that u_1 = \delta u + u_0 (after the system
is linear).
Though, when running the code in the attachment, I get the correct result
(i.e. \delta u) for my hand-assembled system, but the solution I get for
the AD-generated jacobian is u_1, not \delta u. Did I misinterpret
something, or is there another bug in the code?
Thanks!
--
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
---
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"deal.II User Group" group.
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/* -
*
* Copyright (C) 2009 - 2019 by the deal.II authors
*
* This file is part of the deal.II library.
*
* The deal.II library is free software; you can use it, redistribute
* it, and/or modify it under the terms of the GNU Lesser General
* Public License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
* The full text of the license can be found in the file LICENSE.md at
* the top level directory of deal.II.
*
* -
*
* Author: Wolfgang Bangerth, Texas A University, 2009, 2010
* Timo Heister, University of Goettingen, 2009, 2010
*/
#include
#include
#include
#include
namespace LA
{
#undef DEAL_II_WITH_PETSC
#if defined(DEAL_II_WITH_PETSC) && !defined(DEAL_II_PETSC_WITH_COMPLEX) && \
!(defined(DEAL_II_WITH_TRILINOS) && defined(FORCE_USE_OF_TRILINOS))
using namespace dealii::LinearAlgebraPETSc;
# define USE_PETSC_LA
#elif defined(DEAL_II_WITH_TRILINOS)
using namespace dealii::LinearAlgebraTrilinos;
#else
# error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
#endif
} // namespace LA
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
constexpr double time_step = 0.0001;
namespace Step40
{
using namespace dealii;
template
class InitialCondition : public Function
{
public:
InitialCondition() : Function(1){
}
virtual double value(const Point , const unsigned int component) const override;
virtual Tensor<1, dim> gradient(const Point , const unsigned int component) const override;
};
template
double InitialCondition::value(const Point , const unsigned int) const{
const double x = p[0];
const double y = p[1];
return sin(M_PI * x) * sin(M_PI * y);
}
template
Tensor<1, dim> InitialCondition::gradient(const Point , const unsigned int) const{
const double x = p[0];
const double y = p[1];
Tensor<1, dim> return_value;
return_value[0] = M_PI * cos(M_PI * x) * sin(M_PI * y);
return_value[1] = M_PI * sin(M_PI * x) * cos(M_PI * y);
return return_value;
}
template
class LaplaceProblem
{
public:
LaplaceProblem();
void run();
private:
void setup_system();
void assemble_jacobian_by_hand_dynamic();
void assemble_jacobian_by_AD_dynamic();
void solve();
void solve_with_newton_hand();
void solve_with_newton_AD();
void refine_grid();
void output_results(const unsigned int cycle) const;
MPI_Comm mpi_communicator;
parallel::distributed::Triangulation triangulation;
FE_Q fe;
DoFHandler dof_handler;
IndexSet locally_owned_dofs;
IndexSet locally_relevant_dofs;
AffineConstraints constraints;
LA::MPI::SparseMatrix system_matrix, jacobian_matrix_AD, jacobian_matrix_hand, mass_matrix;
LA::MPI::Vector locally_relevant_solution,
locally_relevant_solution_AD,
locally_relevant_solution_hand;
LA::MPI::Vector system_rhs, residual_rhs_AD, residual_rhs_hand;
ConditionalOStream pcout;
TimerOutput
Re: [deal.II] deal stopped working with latest macOS update (10.15)
It works very well. Thank you so much, Luca. Alberto *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Sat, Dec 7, 2019 at 7:23 AM luca.heltai wrote: > Dear Alberto, > > I’ve just finished uploading a new image: > > > https://github.com/dealii/dealii/releases/download/v9.1.1/dealii-9.1.1-clang-9.0.0.dmg > > This one is built with clang-9.0.0 (embedded in the image), and mpich. It > is still a temporary image, because symengine could not be installed ( > www.mpfr.org is down, and symengine depends on it), and neither could > netcdf. > > Can you see if this image works for you? > > The examples are in the path > > > /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/examples > > I quickly checked step-40, and it compiled and run fine. > > L. > > > On 6 Dec 2019, at 15:16, Alberto Salvadori > wrote: > > > > Hi Luca > > > > many thanks. I got this: > > > > bash-3.2$ spack arch > > shell-init: error retrieving current directory: getcwd: cannot access > parent directories: Operation not permitted > > shell-init: error retrieving current directory: getcwd: cannot access > parent directories: Operation not permitted > > shell-init: error retrieving current directory: getcwd: cannot access > parent directories: Operation not permitted > > shell-init: error retrieving current directory: getcwd: cannot access > parent directories: Operation not permitted > > darwin-catalina-ivybridge > > > > Thank you, I will do as you suggest. > > > > Alberto > > > > Alberto Salvadori > > Dipartimento di Ingegneria Meccanica e Industriale (DIMI) > > Universita` di Brescia, via Branze 43, 25123 Brescia > > Italy > > 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 different optimisation > configurations. > > > > What’s the output of: > > > > spack arch > > > > for you, in the deal.II terminal? > > > > I get: > > > > darwin-catalina-haswell > > > > If you get something different, then maybe the problem is there. I don’t > have a more recent mac (yet). It should arrive shortly, and then I should > be able to fix it also for you, I think. > > > > My initial suggestion still stands. I create the package using simply > “spack install dealii”. Try the following (in your dealii terminal): > > > > cd $SPACK_ROOT > > # git pull origin develop # Optional, if you want the latest versions of > all libraries > > spack install dealii@9.1.1 > > > > This will take some time, but should succeed. > > > > Luca. > > > > > > > On 5 Dec 2019, at 16:56, Alberto Salvadori > wrote: > > > > > > This is good, perhaps you can address how did you solved the issue. > > > I honestly have not done anything fancy: > > > > > > > > > 1 - downloaded dealii-9.1.1-catalina-haswell-ro.dmg.zip > > > 2 - drag and drop into applications > > > 3 - open the deal.ii.app > > > 4 - the outcome in attachment. > > > > > > I am using Xcode Version 11.2.1 (11B500), and macOS Catalina 10.15 > > > > > > Thank you! > > > > > > > > > > > > Il giorno martedì 3 dicembre 2019 17:45:13 UTC+1, Ester Comellas ha > scritto: > > > I'm also able to run step-20 succesfully, both in debug and release > modes. > > > > > > El dimarts, 3 desembre de 2019 11:33:40 UTC-5, Ester Comellas va > escriure: > > > Hi, > > > > > > I got deal.II-9.1.1 to work on macOS Catalina using the link Luca > provided. I'm running my parallel code using mpirun and everything works > smoothly. > > > > > > I don't recall the details, but I remember 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.heltai va escriure: > > > I have not updated to the latest version yet. They changed clang, > xcode, and a few other things. I’m assuming that the package I built on > catalina is no longer functional. > > > > > > I’ll get to it as quickly as I can. > > > > > > In the mean time, can you try to see if you can install deal.II using > spack? > > > > > > L. > > > > > > > On 2 Dec 2019, at 17:24, Alberto Salvadori > wrote: > > > > > > > > Dear community, > > > > Luca in particular > > > > > > > > I have installed the package for Mac OS Catalina that was pointed > out. > > > > In running the examples I noticed some unexpected errors > > > > > > > > Illegal instruction: 4 > > > > > > > > See below. > > > > > > > > Needless to say, the very same error comes out in running my own > code. > > > > Any help is appreciated > > > > > > > >
