[deal.II] How to report a progress of KrylovSchur solver

[Loylick]

Hi everyone, 
I solve some eigenvalue problem with SLEPcWrappers::SolverKrylovSchur 
solver.
I takes several hours to accomplish the task and I wonder if there is a way 
to report a progress back from the solver to show for example a number of 
iterations passed?

Alex

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

[Loylick]

Thank you, Wolfgang

It was very helpful. I've resolved the issue.

Alex

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[deal.II] output vector solution to vtk file

[Loylick]

Hi!

I solve elasticity equations where I have a vector-valued eigen functions. 
I've encountered such a problem when I output my solution to a vtk file. 
Each eigen function is output as 3 scalar arrays: eigenfunction_n_0, 
eingenfunction_n_1, eingenfunction_n_2. Where 0,1,2 stand for x,y,z 
component of the eingenfuction n. I'd like it to be a vector  
eingenvector_n = i*eigenfunction_n_0 + j*eigenfunction_n_1 + 
k*eigenfunction_n_2 (i,j,k - unit vectors for x,y,z axis) so that when I 
import this file to Paraview program I would see one picture per one 
eingenfunction rather than having 3 scalar pictires per 1 function. Tell me 
please if it is possible to generate such a vtk file with dealii?

Alex

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Re: [deal.II] how to remove rows from system matrix

[Loylick]

Thanks again this example will help me in future. Am I missing something or 
how FE_Enriched would help me to handle a singular matrix? 
I thought that this class just helps to integrate over discontinuous 
domains and it has nothing to do with zero degrees of freedom that I have 
in voids.

среда, 29 августа 2018 г., 15:27:03 UTC+3 пользователь Jean-Paul Pelteret 
написал:
>
>
>  As for examples of the FE_Enriched class, although there are no tutorials 
> that use it as of yet you can still look in the test directory for usable 
> code snippets, e.g. tests/fe/fe_enriched*.cc 
> 
>
>
> I see that there is an equivalent of step-36 that uses FE_Enriched. It can 
> be found here 
> 
> .
>

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Re: [deal.II] how to remove rows from system matrix

[Loylick]

> Well, I guess you could search for all support points of enriched DoFs 
> that lie outside of your domain of interest and add a homogeneous 
> constraint for them to the AffineConstraints object. The 
> DoFTools::map_dofs_to_support_points 
> 
>  and DoFTools::map_support_points_to_dofs 
> 
>  functions 
> may be of some use.
>
> Thanks, I'll try that.

By the way, have you looked at the FE_Enriched 
>  class? 
> It seems to me like its built for applications similar to this one.
>

I started with the code published in 
https://journals.ub.uni-heidelberg.de/index.php/ans/article/view/22317 and
adopted it for my problem. Since you had removed Step-47 tutorial it is 
hard to figure out how to use FE_Enriched class.
So using FE_Enriched will be my next step.

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[deal.II] Re: Inhomogeneous neumann bc for step-20

[Loylick]

if you formulate a weak form for your problem you will see a boundary 
integral from grad(u),
in step-20 it is equal to zero, since you changed the BC you should take 
into account this
term in a weak form too.

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Re: [deal.II] how to remove rows from system matrix

[Loylick]

>What does the literature suggest how to handle this situation? 
>
 
 The literature says, I cite: "The nodes that lie inside the void and whose 
nodal support is
 not intersected by the void are removed from the calculations. This is 
performed usually by removing
 the DOFs associated with those nodes from the system of equations and 
solving the system
 only for the remaining DOFs."  The question is how to realise it with 
dealii tools by constrainment of
zero degrees of freedom?



> > Here is a picture of a void with enriched nodes. Blue triangls are 
> enriched 
> > with Heaviside function, red rectangles are zero degrees of freedom. 
> > When there are no whole cells inside a void (only cells intersected by 
> the 
> > boundary are inside a void) I have a regular solution. 
>
> You mean you have a solution for the blue cases but not the red ones? 
>

 I mean that if my mesh is coarse so that I have only intersected cells 
(with blue nodes) in a void, I get a solution
by putting them to be zero inside a void. Enrichment function does the job 
in this case. I showed an example of such
a coarse mesh in the picture beneath.

[image: MeshCoarse.png] 


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[deal.II] Re: Inhomogeneous neumann bc for step-20

[Loylick]

ingomogeneous neumann BC are imposed through including them into a 
stiffness matrix. 
You should not use MatrixTools::apply_boundary_values for this purpose I 
guess.
Look the Step-7 trutorial for the info on how to calculate boundary 
integral for neumann BC.



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[deal.II] Re: step-8

[Loylick]

Essentially, there is no need in changing anything in assemble_system  
function from step-8, 
at least for stiffness matrix. You should change boundary conditions and 
triangulation to suit for your task,
that is all. However you should not mix up Young's modulus with Lame 
parameters which are used in the program.
if lambda and mu stay there, they have to stay there :). There is a great 
table with identities between
different modulus and parameters of elasticity at 
https://en.wikipedia.org/wiki/Lam%C3%A9_parameters.

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[deal.II] Re: step-8

[Loylick]

Essentially There is no need in changing anything in assemble_system  
function from step-8. 
At least for stiffness matrix, you should change boundary conditions and 
triangulation to suit for your task,
that is all. However you should not mix up Young's modulus with Lame 
parameters which are used in the program.
if lambda and mu stay there, they have to stay there :). There is a great 
table with identies between
different modulus and parameters in elasticity at 
https://en.wikipedia.org/wiki/Lam%C3%A9_parameters.

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Re: [deal.II] how to remove rows from system matrix

[Loylick]

Thank you, Wolfgang, for your suggestion. I've read step-11 tutorial but I 
still can not figure out what kind of constraints I can impose in my case.
Here is a picture of a void with enriched nodes. Blue triangls are enriched 
with Heaviside function, red rectangles are zero degrees of freedom.
When there are no whole cells inside a void (only cells intersected by the 
boundary are inside a void) I have a regular solution. If at least one cell
is inside a void entirly (no intersection with void's boundary) I get a 
singular matrix. Correct me if I'm wrong, I think I could put one (or some) 
of enriched nodes 
inside a void to be zero and constrain red rectangle nodes to be equal to 
some neighbor nodes with enrichment. Or I'm missing something and there is 
a "right"
way to treat this case?

[image: enrichedNodes.png] 

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[deal.II] how to remove rows from system matrix

[Loylick]

Hi!
I'm trying to implement XFEM method for elasticity problem with voids. I 
use FE_Collection:
fe_collection.push_back (FESystem (FE_Q(1), 1, FE_Nothing(), 
1));
fe_collection.push_back (FESystem (FE_Q(1), 1, FE_Q(1), 1));

Triangulation remains always unchanged, I do not cut voids in the mesh. 
Instead I use enriching function V(x) which is 0 inside voids and 1 
elsewhere.
So I get a singular matrix with zero degrees of freedom inside voids. For 
this system to be solved I should eliminate rows corresponding to zero 
degrees of freedom
from my system matrix. I need your advise how to implement it in dealii in 
an optimal way. I do not know beforehand how many rows are to be removed so 
initially I allocate my sparsity pattern as:
DynamicSparsityPattern dsp(dof_handler.n_dofs(), dof_handler.n_dofs());
Or maybe there are some other techniques to deal with this kind of problem 
that I'm not aware of. I would appreciate any suggestion on how it could be 
solved.

Alex

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[deal.II] current state of XFEM implementation in dealii

[Loylick]

Hello!
 
I'd like to ask about the current state of XFEM methode support in the 
Dealii library. I'm going to solve a crack detection problem in 2D. 
Is it possible to solve the problem by presently existing tools in Dealii 
or it will require some substatial extension and I'd better find another 
library
for this kind of problem?

Alex

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[deal.II] how to refine only the outer cells of a mesh?

[Loylick]

Hello!

I have hyper_ball triangulation refined couple of times globally. Now I 
want to refine only the cells which lay on the surface. In tutorial I've 
found the function refine_and_coarsen_fixed_number but I have not arrived 
at formulating the proper criteria. In examples you use a solution to buld 
the critaria to refine adaptively a mesh. What is the most simple way to 
make it?

Alex

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[deal.II] Re: New nonzero at (3,3) caused a malloc when changing area of triangulation

[Loylick]

I've resolved the issue by adding a fragment of code that handles sparsity 
pattern.
DoFRenumbering::Cuthill_McKee (dof_handler);
hanging_node_constraints.clear();
DoFTools::make_hanging_node_constraints(dof_handler,
hanging_node_constraints); 
hanging_node_constraints.close();

DynamicSparsityPattern dsp(dof_handler.n_dofs(), dof_handler.n_dofs());
DoFTools::make_sparsity_pattern(dof_handler, dsp);
hanging_node_constraints.condense(dsp);
sparsity_pattern.copy_from(dsp);

stiffness_matrix.reinit(sparsity_pattern);
mass_matrix.reinit(sparsity_pattern);

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[deal.II] New nonzero at (3,3) caused a malloc when changing area of triangulation

[Loylick]

Hello!

I was experimenting with Dealii examples and stumbled on some error I can 
not find a reason for.
I modified the example step-36 by defining an area like a pyramid on top of 
a truncated pyramid.
I constructed the truncated pyramid from 5 simplexes and top pyramid of 2 
simplexes by merging
these 7 triangulations.
At running the program stops with the error:
./step-36.exe
   Number of active cells:   224
   Number of degrees of freedom: 327
[0]PETSC ERROR: - Error Message 
--
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: New nonzero at (3,3) caused a malloc
Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn 
off this check
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for 
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.5, Jan, 01, 2017
[0]PETSC ERROR: H:\Dev\install\solid\Release\step-36.exe on a 
arch-mswin-c-debug named LILA by loylick Sat Apr  1 06:46:54 2017
[0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc=0 
--with-mpi=0 --with-debugging=1 --download-f2cblaslapack=1
[0]PETSC ERROR: #1 MatSetValues_SeqAIJ() line 485 in 
H:\Dev\PETSC-~1.5\src\mat\impls\aij\seq\aij.c
[0]PETSC ERROR: #2 MatSetValues() line 1190 in 
H:\Dev\PETSC-~1.5\src\mat\INTERF~1\matrix.c



Exception on processing:


An error occurred in line <1403> of file 
 in function
add
The violated condition was:
ierr == 0
Additional information:
deal.II encountered an error while calling a PETSc function.
The description of the error provided by PETSc is "Argument out of range".
The numerical value of the original error code is 63.


Please give me a clue about what is going wrong in the program. I put the 
code into attach.

P.S. the same program with the truncated pyramid area constructed from 5 
simplexes (without top pyramid) works fine.

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/* -
 *
 * Copyright (C) 2009 - 2016 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 at
 * the top level of the deal.II distribution.
 *
 * -

 *
 * Authors: Toby D. Young, Polish Academy of Sciences,
 *  Wolfgang Bangerth, Texas A&M University
 */

// @sect3{Include files}

// As mentioned in the introduction, this program is essentially only a
// slightly revised version of step-4. As a consequence, most of the following
// include files are as used there, or at least as used already in previous
// tutorial programs:
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

// IndexSet is used to set the size of PETScWrappers::Vector:
#include 

// PETSc appears here because SLEPc depends on this library:
#include 
#include 

// And then we need to actually import the interfaces for solvers that SLEPc
// provides:
#include 

// We also need some standard C++:
#include 
#include 

// Finally, as in previous programs, we import all the deal.II class and
// function names into the namespace into which everything in this program
// will go:
namespace Step36
{
  using namespace dealii;

  // @sect3{The EigenvalueProblem class template}

  // Following is the class declaration for the main class template. It looks
  // pretty much exactly like what has already been shown in step-4:
  template 
  class EigenvalueProblem
  {
  public:
EigenvalueProblem (const std::string &prm_file);
void run ();

  private:
void make_grid_and_dofs ();
void assemble_system ();
unsigned int solve ();
void output_results () const;

Triangulation triangulation;
FE_Q  fe;
DoFHandlerdof_handler;

// With these exceptions: For our eigenvalue problem, we need both a
// stiffness matrix for the left hand side as well as a mass matrix 

Re: [deal.II] how to draw 1D plot

[Loylick]

Thank you, I thought that there was a more generic way of drawing 1D plots 
in Dealii.

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[deal.II] how to draw 1D plot

[Loylick]

Hi!

I was looking through the documentation but I could not figure out how to 
make graphic output of a simiple 1D plot like one I attached to this post.
I had to output my data to a file and draw the graph by hand to show it to 
you. My data are just two columns: X, Y. When I look at gnuplot file 
generated by
Dealii I see that it tries to draw my data as 2D plot.
Regards, Alex

MatrixOut matrix_out;
FullMatrix DBvsF;
DBvsF.reinit(2, 1000);
std::vector   frequency;


double w;
double e = parameters.get_double("dissip");
unsigned int l;
unsigned int sz = frequency.size()-1;

for ( l=0; l<1000 ;  l++) {
step = sqrt(w);
w+=step;
double val = log(DbAtFreq(w, &frequency, e));
DBvsF(0, l)= w;
DBvsF(1, l) = val;
}


   std::ofstream out("DBvsFrequency.plt");
   matrix_out.build_patches(DBvsF, "M");
   matrix_out.write_gnuplot(out);


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Re: [deal.II] square pyramid boundary

[Loylick]

Hi! Thanks for reply.

Following to 1) I have built my square pyramid from 2 simplexes end merged 
them. Next problem arose immediately. I realized that I did not quite 
understand which of set_boundary functions to use.  Is the following code 
enough or I should use some more sophisticated approach? Maybe 
set_all_boundary_ids will do better? 
<https://www.dealii.org/8.4.1/doxygen/deal.II/group__boundary.html#ga8fd51eb24101d7eec9a0337dc667e9a9>
typename Triangulation::active_cell_iterator 
<https://www.dealii.org/8.4.1/doxygen/deal.II/classTriaActiveIterator.html>
cell = tria.begin_active 
<https://www.dealii.org/8.4.1/doxygen/deal.II/classTriangulation.html#abef8795e729458954fd7301214012665>
(),
endc = tria.end 
<https://www.dealii.org/8.4.1/doxygen/deal.II/classTriangulation.html#a55aebb671467ea1367153f81463855ca>
();
for (; cell!=endc; ++cell)
{
   for (unsigned int face=0; face::faces_per_cell; ++face)
   {
  if (cell->face(face)->at_boundary())   
cell->face(face)->set_boundary_id(1);
   }
}


Dear Loylick,
>
> For these more complex grids that are not defined in GridGenerator, you 
> have a few options. You can:
> 1. Use other GridGenerator functions in conjunction with the 
> GridGenerator::merge_triangulations 
> <https://www.dealii.org/8.4.1/doxygen/deal.II/namespaceGridGenerator.html#a0dace8884c1510160d7b6cbb313523e9>
>  
> function so assemble it piece-wise
> 2. Use external meshing software, such as GMsh or Cubit
> 3. Construct the grid by hand, such as is demonstrated in step-14 
> <https://www.dealii.org/8.4.1/doxygen/deal.II/step_14.html#TheExercise_2_3class>
> .
>
> Regards,
> Jean-Paul
>
> On Monday, December 12, 2016 at 4:31:18 AM UTC+1, Loylick wrote:
>>
>> Hi Wolfgang!
>> To be precise I need the Triangulation object if it is what you call a 
>> *mesh*, that is it. 
>>
>

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Re: [deal.II] square pyramid boundary

[Loylick]

Hi Wolfgang!
To be precise I need the Triangulation object if it is what you call a 
*mesh*, that is it. 

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[deal.II] square pyramid boundary

[Loylick]

Hello!
I would like to know how to implement a square pyramid boundary with the 
Dealii library tools? I've looked through the examples but have not found 
anything alike. Examples are given mostly on hyper cube domains.

Alex

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