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

2020-04-14 Thread James Gorman 
Jean-Paul,

The boundary ID output from the four different calculations are as follows 
(before any boundary IDs are set to 6):

1) 3D, no imported mesh: equal numbers for boundary IDs 0, 1, 2, 3, 4, and 
5. This calculation converges to a solution (as expected). 
2) 2D, no imported mesh: equal numbers for boundary IDs 0, 1, 2, and 3. 
This calculation converges to a solution (as expected). 
3) 3D, imported mesh: some boundary IDs are 1 and 2, while most boundary 
IDs are 3. This calculation converges to a solution.
4) 2D, imported mesh: all boundary IDs are 0. This calculation does not 
converge to a solution.

After cycling through all of the face cells and using set_boundary_id(), 
each calculation (correctly) has 6 as a boundary ID for some number of 
faces.

With the information above and your comments, I take it that boundary ID = 
0 means the boundary is traction-free and no dirichlet BC is specified? 
Assuming this is the case, then it makes sense there would be no 
convergence. It also means that the 3D calculation with the imported mesh 
is not the same as the original. I have not yet determined why I cannot 
read the .vtu output files in Paraview, which is why I did not know this 
before (I could only tell it converged to a solution).

I do find it interesting that the two meshes were not imported with the 
same boundary IDs. I guess in the future I should assume that all boundary 
IDs are zero and reset them for each calculation? Also, is there a quick 
reference guide for what each boundary ID means? I have not yet found such 
a reference on the deal.ii website.

Thank you for your help,
James

On Monday, April 13, 2020 at 3:26:14 AM UTC-4, Jean-Paul Pelteret wrote:
>
> It might be that one of the constrained boundaries is not traction free...
>
>
> Correction: This should have read "It might be that one of the constrained 
> boundaries is *now* traction free..."
>
>

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[deal.II] deal.II Newsletter #118

2020-04-14 Thread Rene Gassmoeller 
Hello everyone!

This is deal.II newsletter #118.
It automatically reports recently merged features and discussions about the 
deal.II finite element library.


## Below you find a list of recently proposed or merged features:

#9887: Add Tvmult to Petsc PreconditionJacobi (proposed by dangars) 
https://github.com/dealii/dealii/pull/9887

#9886: Remove deprecated LinearAlgebra::distributed::Vector member functions 
(proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9886

#9885: Add warning to ParameterHandler::parse_input() (proposed by peterrum) 
https://github.com/dealii/dealii/pull/9885

#9884: Fix an indexing bug with multiple postprocessors (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/9884

#9883: Finish step-50 (proposed by tcclevenger) 
https://github.com/dealii/dealii/pull/9883

#9882: Remove FiniteElement::[has|get]_generalized_face_support_points 
(proposed by masterleinad) https://github.com/dealii/dealii/pull/9882

#9881: Tiny Cmake documentation fix (proposed by rezarastak; merged) 
https://github.com/dealii/dealii/pull/9881

#9880: Avoid doxygen warnings (proposed by masterleinad) 
https://github.com/dealii/dealii/pull/9880

#9879: Center comment (proposed by dangars; merged) 
https://github.com/dealii/dealii/pull/9879

#9877: update included std headers in number.h and types.h (proposed by 
rezarastak; merged) https://github.com/dealii/dealii/pull/9877

#9876: Don't parse *.cc files with doxygen (proposed by masterleinad) 
https://github.com/dealii/dealii/pull/9876

#9875: Remove MatrixFree::DoFHandlers::level (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/9875

#9874: Merge MatrixFree::internal_reinit for DoFHandler and hp::DoFHandler 
(proposed by peterrum; merged) https://github.com/dealii/dealii/pull/9874

#9873: Document time stepping methods to tutorial summary. (proposed by 
jppelteret) https://github.com/dealii/dealii/pull/9873

#9872: doxygen: enable private again (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9872

#9871: Minor fixes to get_boundary_ids_01 (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/9871

#9870: Fix three tests (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/9870

#9869: Fix a doxygen table. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/9869

#9868: Add support for building using CCache (proposed by jppelteret) 
https://github.com/dealii/dealii/pull/9868

#9866: Fix gcc warning in TBB (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/9866

#9865: Improve CMake documentation for google search (proposed by dangars; 
merged) https://github.com/dealii/dealii/pull/9865

#9864: CI: github actions: checkout@v2 (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9864

#9863: Use #ifdef to guard std::async in step-69 (proposed by dangars; merged) 
https://github.com/dealii/dealii/pull/9863

#9862: refactoring of ParameterAcceptor::initialize() (proposed by nfehn) 
https://github.com/dealii/dealii/pull/9862

#9861: Improve CellWeights documentation (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/9861

#9860: Remove more deprecations (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/9860

#9859: Some doxygen fixes (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/9859

#9858: Fix two tests with roundoff problems (proposed by kronbichler; merged) 
https://github.com/dealii/dealii/pull/9858

#9857: Output more digits for test grid/grid_generator_01b (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/9857

#9856: Added windows build to github-ci (proposed by luca-heltai; merged) 
https://github.com/dealii/dealii/pull/9856

#9855: doxygen: extract everything (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9855

#9854: Update the cross compilation documentation (proposed by dangars; merged) 
https://github.com/dealii/dealii/pull/9854

#9852: Minor fixes to BoundingBox (proposed by simonsticko; merged) 
https://github.com/dealii/dealii/pull/9852

#9851: do not build release on github actions OSX (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9851

#9850: Document the mental model of DiscreteTime. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/9850

#9848: [CI]: add GitHub actions linux release build (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/9848

#9833: fixes issue 9722 by correctly writing time data into a aggregate pvd ... 
(proposed by krishnakumarg1984; merged) 
https://github.com/dealii/dealii/pull/9833

#9830: Doc of Tensor and SymmetricTensor improved. (proposed by rezarastak; 
merged) https://github.com/dealii/dealii/pull/9830

#9829: FETools: Add additional lexicographic_to_hierarchic_numbering functions 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/9829

#9817:

Re: [deal.II] Reading a Tensor from parameter file

2020-04-14 Thread Ahmad Shahba 
I don't know if it is the optimal way but I would use the following approach

   1. Read tensor components as Patterns::List
   2. Use  get
   

   method of ParameterHandler to read all tensor  components as one string
   into a string variable
   3. Use  split_string_list
   

  in the Utilities namespace to split the string into individual
   components (still all components are strings)
   4. Convert  string-type components into doubles using  string_to_double
   

in
   the Utilities namespace
   5. Use  Tensor
   

(const Tensor
   <
   rank_, dim, OtherNumber > ) to construct the tensor


On Tue, Apr 14, 2020 at 11:12 AM Paras Kumar 
wrote:

> Dear deal.II community,
>
> I am trying to read a second order tensor from a .prm file using the
> ParameterHandler functionalities. The tensor (for dim=3) is set in .prm
> file as
>
>   set macro def grad = 1.2|0.0|0.0|0.0|1.1|0.0|0.0|0.0|1.4
>
> and is currently read as a string using
> parameterHandler.declare_entry(
>   "macro def grad",
>   "1.0|1.0|1.0|1.0",
>   dealii::Patterns::Anything(),
>   "Macroscopic deformation gradient for homogenization");
>
> auto temp = parameterHandler.get("macro def grad");
> std::vector defGradComps;
> boost::algorithm::split(defGradComps,
> temp,
>boost::algorithm::is_any_of("|"));
> Assert(defGradComps.size() == dim * dim,
>dealii::ExcDimensionMismatch(defGradComps.size(),
> dim * dim));
>for (mncfrac::utilities::UnsignedIntType i = 0; i < dim; ++i)
>   for (mncfrac::utilities::UnsignedIntType j = 0; j < dim; ++j
> )
> this->problemSpecificParameters_.macroDefGrad_[i][j] =
>   std::stod(defGradComps[i * dim + j]);
>
>
> I am curious to know, if there is a smarter way (avoiding this manual
> copying by looping over the tensor entries) to do so using some other type
> of dealii::Patterns object or some other way.
>
> Thanks in advance and best regards,
> Paras Kumar
>
> --
> 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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> 
> .
>

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[deal.II] Reading a Tensor from parameter file

2020-04-14 Thread Paras Kumar 
Dear deal.II community,

I am trying to read a second order tensor from a .prm file using the 
ParameterHandler functionalities. The tensor (for dim=3) is set in .prm 
file as

  set macro def grad = 1.2|0.0|0.0|0.0|1.1|0.0|0.0|0.0|1.4

and is currently read as a string using 
parameterHandler.declare_entry(
  "macro def grad",
  "1.0|1.0|1.0|1.0",
  dealii::Patterns::Anything(),
  "Macroscopic deformation gradient for homogenization");

auto temp = parameterHandler.get("macro def grad");
std::vector defGradComps;
boost::algorithm::split(defGradComps,
temp,
   boost::algorithm::is_any_of("|"));
Assert(defGradComps.size() == dim * dim,
   dealii::ExcDimensionMismatch(defGradComps.size(),
dim * dim));
   for (mncfrac::utilities::UnsignedIntType i = 0; i < dim; ++i)
  for (mncfrac::utilities::UnsignedIntType j = 0; j < dim; ++j)
this->problemSpecificParameters_.macroDefGrad_[i][j] =
  std::stod(defGradComps[i * dim + j]);


I am curious to know, if there is a smarter way (avoiding this manual 
copying by looping over the tensor entries) to do so using some other type 
of dealii::Patterns object or some other way.

Thanks in advance and best regards,
Paras Kumar

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