[deal.II] Re: Multi-physics implementation

[Ray Mclaren]

Mr. Simon

thank you for your response, It was exactly what I was looking for. 

On Tuesday, September 22, 2020 at 5:01:42 PM UTC+9 simon...@gmail.com wrote:

> Hi,
> I would do it like this:
>
>   // Setup two DoFHandlers, one for the heat and one for Allen-Cahn
>   DoFHandler heat_dof_handler(triangulation);
>   DoFHandler allen_cahn_dof_handler(triangulation);
>
>// Solve for this first
>   Vector heat_solution;
>
>   // Lots of things in between here...
>
>   // When assembling for allen_cahn, create two FEValues objects.
>   FEValues fe_values(allen_cahn_element, quadrature, update_flags);
>   FEValues heat_fe_values(heat_element, quadrature, update_values);
>
>   for (auto cell : allen_cahn_dof_handler.active_cell_iterators())
> {
>   // Cast to an iterator on the heat_dof_handler
>   typename DoFHandler::active_cell_iterator heat_cell(
> , cell->level(), cell->index(), _dof_handler);
>
>   // Call reinit with the corresponding cells.
>   fe_values.reinit(cell);
>   heat_fe_values.reinit(heat_cell);
>
>   // Get the heat values at the quadrature points using heat_fe_values
>   std::vector heat_values(heat_element.dofs_per_cell);
>   heat_fe_values.get_function_values(heat_solution, heat_values);
>
>   // Assemble the system using fe_values here ...
> }
>
> Best,
> Simon
> On Tuesday, September 22, 2020 at 2:31:01 AM UTC+2 mclaren...@gmail.com 
> wrote:
>
>> Hi,
>> I have a question regrading multi-physics problem implementation.
>>
>> I am developing a program that will solve the steady-state thermal 
>> conduction (laplace) first and then the allen-Cahn equation.
>>
>> both of the problems are solved on the same mesh, however due to the 
>> nature of my specific implementation they solved separately. To solve the 
>> allen-Cahn equation, I need to evaluate temperature dependent functions at 
>> each node in the domain.
>>
>> Hence, they only share the same triangulation, but everything else is 
>> separate.
>>
>> My question is, how to use the solution vector from the thermal 
>> conduction (the temperature) in the assembly of the allen-cahn equation ?
>>
>>  how to access the temperature at these nodes and make sure that they are 
>> synchronized ? 
>>
>> thank you
>>
>>

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Re: [deal.II] Re: .msh file triangulation failed

[yuesu jin]

Dear Bruno,
  Sorry for the late reply. Here is flooding, I was driving home hours
before. You are right, in the linux version of gmsh, it always gives the
error message that cannot find the corresponding vertex, but actually I do
nothing on the cell. It is the 1e-7 rounding error that makes the system
very unstable. Thank you again for your patience and kindness. Have a good
day!
Best regards,
Yuesu

On Tue, Sep 22, 2020 at 10:55 AM Bruno Turcksin 
wrote:

> Honestly I don't know. I wonder if the terms -1e-07 are the problem. I
> told you to remove  SetFactory("OpenCASCADE") because it was the only
> difference with my .geo files.
>
> Bruno
>
> Le mar. 22 sept. 2020 à 11:20, yuesu jin  a écrit :
> >
> > Dear Bruno,
> >   The problem was solved after I removed the
> 'SetFactory("OpenCASCADE")'.  Here are two mesh files with and without
> 'SetFactory("OpenCASCADE")'. Could you tell me why this command made the
> system unable to work? Thank you very much for your help!
> > Best regards,
> > Yuesu
> >
> >
> >
> > On Tue, Sep 22, 2020 at 10:01 AM Bruno Turcksin <
> bruno.turck...@gmail.com> wrote:
> >>
> >> Hmmm. Can you try without the SetFactory("OpenCASCADE"); and can you
> >> send me your .msh
> >>
> >> Bruno
> >>
> >> Le mar. 22 sept. 2020 à 10:45, yuesu jin  a
> écrit :
> >> >
> >> > Dear Bruno,
> >> >I did some modification according to your suggestion :
> >> > 
> >> > Physical Volume("4") = {1};
> >> > //+
> >> > Physical Surface("0") = {4, 3, 2, 5, 1, 6};
> >> > 
> >> > I add all external surfaces in one physical group and the volume in
> another group. But the error message remains the same.  I tried a few types
> of grouping combinations, the error message did not change.
> >> > Best regards,
> >> > Yuesu
> >> >
> >> > On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin <
> bruno.turck...@gmail.com> wrote:
> >> >>
> >> >> You don't want to set the physical groups for the curves and the
> >> >> points. This means nothing in deal.II. A vertex does not have a
> >> >> boundary ID. You need all the external surfaces and the volume to
> have
> >> >> a physical group. That's it.
> >> >>
> >> >> Bruno
> >> >>
> >> >> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a
> écrit :
> >> >> >
> >> >> > Dear Bruno,
> >> >> >   Thank you for your help! I added physical groups for volume,
> surfaces, curves, and points. But the problem remains the same.  The
> modified geo file is attached below.
> >> >> > Best regards,
> >> >> > Yuesu
> >> >> >
> >> >> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin <
> bruno.turck...@gmail.com> wrote:
> >> >> >>
> >> >> >>
> >> >> >> Yuesu,
> >> >> >>
> >> >> >> I had the same problem recently. Our gmsh reader assumes that the
> user has set boundary id and material id to the mesh. It looks like you
> don't have those and so the file is read incorrectly.
> >> >> >>
> >> >> >> Best,
> >> >> >>
> >> >> >> Bruno
> >> >> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4
> jinyu...@gmail.com wrote:
> >> >> >>>
> >> >> >>> Dear all,
> >> >> >>>   I have one problem when I try to input the .msh file with
> grid_in function. The error message is :
> >> >> >>>
> >> >> >>> *
> >> >> >>>
> >> >> >>> Exception on processing:
> >> >> >>>
> >> >> >>> 
> >> >> >>> An error occurred in line <3139> of file
>  in function
> >> >> >>> static void
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
> std::vector >&, const std::vector,
> std::allocator > >&, const dealii::SubCellData&,
> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
> >> >> >>> The violated condition was:
> >> >> >>> false
> >> >> >>> Additional information:
> >> >> >>> While trying to assign a boundary indicator to a line: the
> line with end vertices -1 and 0 does not exist.
> >> >> >>> 
> >> >> >>>
> >> >> >>> I attached the gmsh .geo file in this email. There is no vertex
> -1 actually. Could you tell me what's wrong with my mesh generation?
> >> >> >>>
> >> >> >>> Thank you very much!
> >> >> >>> Best regards,
> >> >> >>>
> >> >> >>> --
> >> >> >>> Yuesu Jin,
> >> >> >>> Ph.D student,
> >> >> >>> University of Houston,
> >> >> >>> College of Natural Sciences and Mathematics,
> >> >> >>> Department of Earth and Atmospheric Sciences,
> >> >> >>> Houston, Texas 77204-5008
> >> >> >>> 346-404-2062
> >> >> >>>
> >> >> >> --
> >> >> >> 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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> Google Groups "deal.II User Group" group.
> >> >> >> To unsubscribe from this group and stop receiving emails from it,
> 

Re: [deal.II] PETSC issue while trying to run step-18

[Daniel Arndt]

https://dealii.org/developer/readme.html#configuration-options says to call
cmake with -DPETSC_DIR=/path/to/petsc -DPETSC_ARCH=architecture.
I normally just set the environment variable PETSC_DIR and configure
deal.II with -DDEAL_II_WITH_PETSC=ON

Best,
Daniel

Am Di., 22. Sept. 2020 um 12:29 Uhr schrieb krishan...@gmail.com <
krishanu.se...@gmail.com>:

>
> Hello,
>
> I tried to run step-18 and initially received the following error message:
>
>  Error! This tutorial requires a deal.II library that was configured with
>   the following options:
>
>   DEAL_II_WITH_MPI = ON
>   DEAL_II_WITH_PETSC = ON
>   DEAL_II_PETSC_WITH_COMPLEX = OFF
>
>   However, the deal.II library found at
>   /home/krishanu/Google_Drive/dealii/dealii_920/library_dealii_920 was
>   configured with these options
>
>   DEAL_II_WITH_MPI = OFF
>   DEAL_II_WITH_PETSC = OFF
>   DEAL_II_PETSC_WITH_COMPLEX =
>
>   which conflict with the requirements.
>
> So, I used the following commands (from this link:
> https://www.dealii.org/current/external-libs/petsc.html) to install PETSC:
>
> tar xvzf petsc-x-y-z.tar.gz cd petsc-x-y-z
> export PETSC_DIR=`pwd`
> export PETSC_ARCH=x86_64
> ./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1
> --download-hypre=1
> make
> make test
>
> Then used the following commands to build, configure and install deal.ii
>
> mkdir build
> cd build
> cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II
>
> But it seems that deal.ii did not auto detect PETSC and MPI as it showed
> the following among other configured features:
>
> Configured Features (DEAL_II_ALLOW_BUNDLED = ON,
> DEAL_II_ALLOW_AUTODETECTION = ON):
>
> #  ( DEAL_II_WITH_MPI = OFF )
> #  ( DEAL_II_WITH_PETSC = OFF )
>
> I am wondering what I might be missing here. Could anyone please help?
>
>
> --
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> 
> .
>

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[deal.II] Re: Multi-physics implementation

[simon...@gmail.com]

Hi,
I would do it like this:

  // Setup two DoFHandlers, one for the heat and one for Allen-Cahn
  DoFHandler heat_dof_handler(triangulation);
  DoFHandler allen_cahn_dof_handler(triangulation);

   // Solve for this first
  Vector heat_solution;

  // Lots of things in between here...

  // When assembling for allen_cahn, create two FEValues objects.
  FEValues fe_values(allen_cahn_element, quadrature, update_flags);
  FEValues heat_fe_values(heat_element, quadrature, update_values);

  for (auto cell : allen_cahn_dof_handler.active_cell_iterators())
{
  // Cast to an iterator on the heat_dof_handler
  typename DoFHandler::active_cell_iterator heat_cell(
, cell->level(), cell->index(), _dof_handler);

  // Call reinit with the corresponding cells.
  fe_values.reinit(cell);
  heat_fe_values.reinit(heat_cell);

  // Get the heat values at the quadrature points using heat_fe_values
  std::vector heat_values(heat_element.dofs_per_cell);
  heat_fe_values.get_function_values(heat_solution, heat_values);

  // Assemble the system using fe_values here ...
}

Best,
Simon
On Tuesday, September 22, 2020 at 2:31:01 AM UTC+2 mclaren...@gmail.com 
wrote:

> Hi,
> I have a question regrading multi-physics problem implementation.
>
> I am developing a program that will solve the steady-state thermal 
> conduction (laplace) first and then the allen-Cahn equation.
>
> both of the problems are solved on the same mesh, however due to the 
> nature of my specific implementation they solved separately. To solve the 
> allen-Cahn equation, I need to evaluate temperature dependent functions at 
> each node in the domain.
>
> Hence, they only share the same triangulation, but everything else is 
> separate.
>
> My question is, how to use the solution vector from the thermal conduction 
> (the temperature) in the assembly of the allen-cahn equation ?
>
>  how to access the temperature at these nodes and make sure that they are 
> synchronized ? 
>
> thank you
>
>

-- 
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[deal.II] .msh file triangulation failed

[yuesu jin]

Dear all,
  I have one problem when I try to input the .msh file with grid_in
function. The error message is :

*

Exception on processing:


An error occurred in line <3139> of file
 in function
static void
dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
std::vector >&, const std::vector,
std::allocator > >&, const dealii::SubCellData&,
dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
The violated condition was:
false
Additional information:
 *   While trying to assign a boundary indicator to a line: the line with
end vertices -1 and 0 does not exist.*


I attached the gmsh .geo file in this email. There is no vertex -1
actually. Could you tell me what's wrong with my mesh generation?

Thank you very much!
Best regards,

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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tank.geo
Description: Binary data

Re: [deal.II] step-1 Error

[luca.heltai]

If he’s running from the deal.II terminal, he should have the module command 
(it is part of the spack installation). 

The deal.II terminal exports the paths so that the module command is there. 
What version of the deal.II package is he using? On my system, this is the 
output I get:



bash-3.2$ module avail
--- 
/Applications/deal.II.app/Contents/Resources/spack/share/spack/modules/darwin-catalina-x86_64
 
adol-c/2.7.2   hwloc/1.11.11numdiff/5.9.0   
   xz/5.2.5 
arpack-ng/3.7.0-openblas   hypre/2.18.2-openblasoce/0.18.3  
   zlib/1.2.11  
assimp/4.0.1   intel-tbb/2020.2 openblas/0.3.10 
   
autoconf-archive/2019.01.06libc/1.0 openmpi/3.1.6   
   
autoconf/2.69  libffi/3.3   openssl/1.1.1g  
   
automake/1.16.2libsigsegv/2.12  p4est/2.2   
   
boost/1.73.0   libtool/2.4.6parmetis/4.0.3  
   
bzip2/1.0.8libxml2/2.9.10   perl/5.18.4 
   
cmake/3.17.1   m4/1.4.18
petsc/3.13.1-openblas-py2-py3  
dealii/9.2.0-openblas-py2-py3  matio/1.5.13 pkgconf/1.7.3   
   
diffutils/3.7  metis/5.1.0  python/3.7.7
   
environment-modules/4.5.1  mpc/1.1.0readline/8.0
   
expat/2.2.9mpfr/4.0.2   
slepc/3.13.3-openblas-py2-py3  
gdbm/1.18.1mumps/5.2.0-openblas sqlite/3.31.1   
   
gettext/0.20.2 muparser/2.2.6.1 
suite-sparse/5.3.0-openblas
ginkgo/1.1.0   nanoflann/1.2.3  sundials/3.2.1  
   
glm/0.9.7.1ncurses/6.2  
superlu-dist/6.3.0-openblas
gmp/6.1.2  netcdf-c/4.7.3   symengine/0.6.0 
   
gmsh/4.5.4-openblasnetcdf-cxx/4.2   tar/1.32
   
googletest/1.10.0  netgen/5.3.1 tcl/8.6.8   
   
gsl/2.5netlib-scalapack/2.0.2-openblas  tetgen/1.5.0
   
hdf5/1.10.6ninja/1.10.0-py2-py3 
trilinos/12.18.1-openblas  
bash-3.2$ 

 

> On 21 Sep 2020, at 22:51, Wolfgang Bangerth  wrote:
> 
> 
> Hi Luca,
> 
>> Are you running the terminal, or the deal.II application?
>> When you run the deal.II application, you are dropped into a terminal (with 
>> instructions) to run deal.II examples. Including how to set up your bashrc 
>> (or zshrc) to point to the deal.II
>> Installation/the module command.
> 
> He's running in the terminal that shows all of the instructions. The problem 
> is not that 'module load dealii' doesn't know how to load deal.II, but that 
> the 'module' command doesn't seem to exist on his system. That's what the 
> error message says:
>  bash: module: command not found
> 
> I can't seem to find any information (but also don't know where to look) on 
> how one can install the 'module' command or, more generally, which general 
> package 'module' would actually come from.
> 
> Any ideas?
> 
> Best
> W.
> 
> -- 
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>   www: http://www.math.colostate.edu/~bangerth/
> 
> -- 
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Re: [deal.II] Using DataOut when dim != spacedim

[Daniel Arndt]

Malhar,

the template arguments for DataOut are dim and DoFHandlerType where
DoFHandlerType defaults to DoFHandler
since you are using a DoFHandler<2, 3> object you need to specify the
second template argument explicitly, i.e.

DataOut<2, DoFHandler<2,3>> data_out;

You could have a look at step-38.

Best,
Daniel

Am Di., 22. Sept. 2020 um 01:37 Uhr schrieb Malhar T. <
malhar.ti...@gmail.com>:

> Hello All,
> I hope you are doing well !
>
> I am working on a surface patch in 3D (dim=2 & spacedim=3 and developed
> using ChartManifold<2,3> by following code similar to step-53
> ) and I
> would like to output the results into a vtk file. I am mostly following
> tutorials, as I am not really great with C++. So, initially I used the
> class DataOut and tried to specify the geometry using attach_dof_handler.
>
> This is how its defined,
>
> Triangulation<2, 3> triangulation;
> DoFHandler<2, 3>dof_handler;
>
> And output_results function was written as
>
> {
> DataOut data_out;
> data_out.attach_dof_handler(dof_handler);
> }
>
> But I got the error
>
>
> error: cannot convert ‘const dealii::DoFHandler<2, 3>’ to ‘const 
> dealii::DoFHandler<2, 2>&’
> note:   initializing argument 1 of ‘void 
> dealii::DataOut_DoFData patch_space_dim>::attach_dof_handler(const DoFHandlerType&) [with 
> DoFHandlerType = dealii::DoFHandler<2, 2>; int patch_dim = 2; int 
> patch_space_dim = 2]’
>
> I tried searching in the forum and came to know about DataOutFaces
> (through this post
> ), and I
> also looked at the step-61
> 
> tutorial on its implementation, but I got the same error again. I have a
> feeling that I am not understanding something very trivial, thus, any
> pointers would be really helpful.
>
> Thank You.
>
>
> I tried searching in the forum and came to know about DataOutFaces
> (through this post)
> , and I
> also looked at the step-61
> 
> tutorial on its implementation, but I got the same error again. I have a
> feeling that I am not understanding something very trivial, any pointers
> would be helpful. Thank You.
>
> --
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> 
> .
>

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Re: [deal.II] Re: .msh file triangulation failed

[yuesu jin]

Dear Bruno,
  Thank you for your help! I added physical groups for volume, surfaces,
curves, and points. But the problem remains the same.  The modified geo
file is attached below.
Best regards,
Yuesu

On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin 
wrote:

>
> Yuesu,
>
> I had the same problem recently. Our gmsh reader assumes that the user has
> set boundary id and material id to the mesh. It looks like you don't have
> those and so the file is read incorrectly.
>
> Best,
>
> Bruno
> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com
> wrote:
>
>> Dear all,
>>   I have one problem when I try to input the .msh file with grid_in
>> function. The error message is :
>>
>> *
>>
>> Exception on processing:
>>
>> 
>> An error occurred in line <3139> of file
>>  in function
>> static void
>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> std::vector >&, const std::vector,
>> std::allocator > >&, const dealii::SubCellData&,
>> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
>> The violated condition was:
>> false
>> Additional information:
>>  *   While trying to assign a boundary indicator to a line: the line
>> with end vertices -1 and 0 does not exist.*
>> 
>>
>> I attached the gmsh .geo file in this email. There is no vertex -1
>> actually. Could you tell me what's wrong with my mesh generation?
>>
>> Thank you very much!
>> Best regards,
>>
>> --
>> Yuesu Jin,
>> Ph.D student,
>> University of Houston,
>> College of Natural Sciences and Mathematics,
>> Department of Earth and Atmospheric Sciences,
>> Houston, Texas 77204-5008
>> 346-404-2062 <(346)%20404-2062>
>>
>> --
> 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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> 
> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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tank.geo
Description: Binary data

Re: [deal.II] step-1 Error

[Scott Ziegler]

I'm using version 9.0.0 of deal.ii. I have an older MacBook and it won't 
update past iOS 10.13.6. I downloaded the .dmg file and opened it/moved it 
into my applications but I haven't done anything else besides try to run 
the first example.

On Tuesday, September 22, 2020 at 6:05:23 AM UTC-6 luca@gmail.com wrote:

> If he’s running from the deal.II terminal, he should have the module 
> command (it is part of the spack installation). 
>
> The deal.II terminal exports the paths so that the module command is 
> there. What version of the deal.II package is he using? On my system, this 
> is the output I get:
>
>
>
> bash-3.2$ module avail
> --- 
> /Applications/deal.II.app/Contents/Resources/spack/share/spack/modules/darwin-catalina-x86_64
>  
> 
> adol-c/2.7.2 hwloc/1.11.11 numdiff/5.9.0 xz/5.2.5 
> arpack-ng/3.7.0-openblas hypre/2.18.2-openblas oce/0.18.3 zlib/1.2.11 
> assimp/4.0.1 intel-tbb/2020.2 openblas/0.3.10 
> autoconf-archive/2019.01.06 libc/1.0 openmpi/3.1.6 
> autoconf/2.69 libffi/3.3 openssl/1.1.1g 
> automake/1.16.2 libsigsegv/2.12 p4est/2.2 
> boost/1.73.0 libtool/2.4.6 parmetis/4.0.3 
> bzip2/1.0.8 libxml2/2.9.10 perl/5.18.4 
> cmake/3.17.1 m4/1.4.18 petsc/3.13.1-openblas-py2-py3 
> dealii/9.2.0-openblas-py2-py3 matio/1.5.13 pkgconf/1.7.3 
> diffutils/3.7 metis/5.1.0 python/3.7.7 
> environment-modules/4.5.1 mpc/1.1.0 readline/8.0 
> expat/2.2.9 mpfr/4.0.2 slepc/3.13.3-openblas-py2-py3 
> gdbm/1.18.1 mumps/5.2.0-openblas sqlite/3.31.1 
> gettext/0.20.2 muparser/2.2.6.1 suite-sparse/5.3.0-openblas 
> ginkgo/1.1.0 nanoflann/1.2.3 sundials/3.2.1 
> glm/0.9.7.1 ncurses/6.2 superlu-dist/6.3.0-openblas 
> gmp/6.1.2 netcdf-c/4.7.3 symengine/0.6.0 
> gmsh/4.5.4-openblas netcdf-cxx/4.2 tar/1.32 
> googletest/1.10.0 netgen/5.3.1 tcl/8.6.8 
> gsl/2.5 netlib-scalapack/2.0.2-openblas tetgen/1.5.0 
> hdf5/1.10.6 ninja/1.10.0-py2-py3 trilinos/12.18.1-openblas 
> bash-3.2$ 
>
>
>
> > On 21 Sep 2020, at 22:51, Wolfgang Bangerth  
> wrote:
> > 
> > 
> > Hi Luca,
> > 
> >> Are you running the terminal, or the deal.II application?
> >> When you run the deal.II application, you are dropped into a terminal 
> (with instructions) to run deal.II examples. Including how to set up your 
> bashrc (or zshrc) to point to the deal.II
> >> Installation/the module command.
> > 
> > He's running in the terminal that shows all of the instructions. The 
> problem is not that 'module load dealii' doesn't know how to load deal.II, 
> but that the 'module' command doesn't seem to exist on his system. That's 
> what the error message says:
> > bash: module: command not found
> > 
> > I can't seem to find any information (but also don't know where to look) 
> on how one can install the 'module' command or, more generally, which 
> general package 'module' would actually come from.
> > 
> > Any ideas?
> > 
> > Best
> > W.
> > 
> > -- 
> > 
> > Wolfgang Bangerth email: bang...@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+un...@googlegroups.com.
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> https://groups.google.com/d/msgid/dealii/98392d90-dbd8-8213-26f8-6a0c3c844623%40colostate.edu
> .
>
>

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Re: [deal.II] Using DataOut when dim != spacedim

[luca.heltai]

Dear Malhar, 

just as you did for the Triangulation and the DoFHandler, also DataOut should 
be instantiated with <2,3>, i.e., 

not 

DataOut<2> …


but 


DataOut<2,3> …

Best,
Luca.


> On 22 Sep 2020, at 7:37, Malhar T.  wrote:
> 
> Hello All,
> I hope you are doing well !
> 
> I am working on a surface patch in 3D (dim=2 & spacedim=3 and developed using 
> ChartManifold<2,3> by following code similar to step-53) and I would like to 
> output the results into a vtk file. I am mostly following tutorials, as I am 
> not really great with C++. So, initially I used the class DataOut and tried 
> to specify the geometry using attach_dof_handler. 
> 
> This is how its defined,
> Triangulation<2, 3
> > triangulation;
> DoFHandler<
> 2, 3
> >dof_handler;
> 
> And output_results function was written as
> {
> DataOut data_out;
> data_out.attach_dof_handler(dof_handler);
> }
> 
> But I got the error
> 
> error: cannot convert ‘
> const dealii::DoFHandler<2, 3>’ to ‘const dealii::DoFHandler<2, 2
> >&’
> note:   initializing argument 
> 1 of ‘void dealii::DataOut_DoFData patch_space_dim>::attach_dof_handler(const DoFHandlerType&) [with 
> DoFHandlerType = dealii::DoFHandler<2, 2>; int patch_dim = 2; int 
> patch_space_dim = 2
> ]’
> 
> I tried searching in the forum and came to know about DataOutFaces (through 
> this post), and I also looked at the step-61 tutorial on its implementation, 
> but I got the same error again. I have a feeling that I am not understanding 
> something very trivial, thus, any pointers would be really helpful. 
> 
> Thank You.
> 
> 
> 
> -- 
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[deal.II] Re: .msh file triangulation failed

[Bruno Turcksin]

Yuesu,

I had the same problem recently. Our gmsh reader assumes that the user has 
set boundary id and material id to the mesh. It looks like you don't have 
those and so the file is read incorrectly.

Best,

Bruno
On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com wrote:

> Dear all,
>   I have one problem when I try to input the .msh file with grid_in 
> function. The error message is :
>
> *
>
> Exception on processing:
>
> 
> An error occurred in line <3139> of file 
>  in function
> static void 
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>  
> std::vector >&, const std::vector, 
> std::allocator > >&, const dealii::SubCellData&, 
> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
> The violated condition was: 
> false
> Additional information: 
>  *   While trying to assign a boundary indicator to a line: the line with 
> end vertices -1 and 0 does not exist.*
> 
>
> I attached the gmsh .geo file in this email. There is no vertex -1 
> actually. Could you tell me what's wrong with my mesh generation?
>
> Thank you very much!
> Best regards,
>
> -- 
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008

> 346-404-2062 <(346)%20404-2062>
>
>

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Re: [deal.II] Issue with unstructured hex mesh

[Wolfgang Bangerth]

On 9/22/20 10:41 AM, Paras Kumar wrote:
As can be seen in figures 7 & 8 of the attached report, a further refinement 
results in relatively smoother contours, but the irregularities are still not 
eliminated.


OK, that's good to know at least as a check that your program is doing 
something right.



This approach would probably not be applicable for our use-case since, we  
need to model the interface between the filler and the matrix regions accurately.


Then I'm afraid I'm out of ideas short of using a program that can actually 
create hex meshes :-(


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Issue with unstructured hex mesh

[Wolfgang Bangerth]

On 9/22/20 4:27 PM, Wolfgang Bangerth wrote:

I wished every student project were as comprehensively explored! :-)


I tacitly assumed that Maurice Rohracker is your student. I didn't mean to 
imply that the work you're doing is at the "student level" -- quite the 
contrary: What your reports show is just really impressive!


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Issue with unstructured hex mesh

[Wolfgang Bangerth]

On 9/22/20 11:09 AM, Paras Kumar wrote:
In order to verify if the "improper" modeling of the curved particle surface 
due to the reason you explained above, is the cause for this irregularities, 
we tried with a cubic particle, thereby eliminating the above issue, but still 
observe irregularities in the stress contour on the particle surface, cf. 
Figures 3-5 of the attachment.  With this observation, we could probably 
conclude that improper modeling of the curved geometry is not the only reason 
for the irregularities.


I know this isn't helpful from the perspective of actually solving your 
problem, but: Excellent work testing out different hypotheses and validating 
every step of your work. What you show here is a model of how one builds 
numerical solutions: If there is something that seems odd, one systematically 
simplifies the simulation (sphere -> cube), and then cross checks different 
approaches (tets vs hexes vs uniform discretization) until it's clear what the 
issue is. I wished every student project were as comprehensively explored! :-)


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Multi-physics implementation

[Jean-Paul Pelteret]

Hi Ray,

I’m happy to see that Simon has already given a great explanation as to how to 
solve your problem. It’s probably more on point than the code that mentioned 
that I would direct you towards. So it really was worthwhile asking the 
question again here :-)

Best,
Jean-Paul

> On 22 Sep 2020, at 16:03, Ray Mclaren  wrote:
> 
> Mr. Simon
> 
> thank you for your response, It was exactly what I was looking for. 
> 
> On Tuesday, September 22, 2020 at 5:01:42 PM UTC+9 simon...@gmail.com 
>  wrote:
> Hi,
> I would do it like this:
> 
>   // Setup two DoFHandlers, one for the heat and one for Allen-Cahn
>   DoFHandler heat_dof_handler(triangulation);
>   DoFHandler allen_cahn_dof_handler(triangulation);
> 
>// Solve for this first
>   Vector heat_solution;
> 
>   // Lots of things in between here...
> 
>   // When assembling for allen_cahn, create two FEValues objects.
>   FEValues fe_values(allen_cahn_element, quadrature, update_flags);
>   FEValues heat_fe_values(heat_element, quadrature, update_values);
> 
>   for (auto cell : allen_cahn_dof_handler.active_cell_iterators())
> {
>   // Cast to an iterator on the heat_dof_handler
>   typename DoFHandler::active_cell_iterator heat_cell(
> , cell->level(), cell->index(), _dof_handler);
> 
>   // Call reinit with the corresponding cells.
>   fe_values.reinit(cell);
>   heat_fe_values.reinit(heat_cell);
> 
>   // Get the heat values at the quadrature points using heat_fe_values
>   std::vector heat_values(heat_element.dofs_per_cell);
>   heat_fe_values.get_function_values(heat_solution, heat_values);
> 
>   // Assemble the system using fe_values here ...
> }
> 
> Best,
> Simon
> On Tuesday, September 22, 2020 at 2:31:01 AM UTC+2 mclaren...@gmail.com 
>  wrote:
> Hi,
> I have a question regrading multi-physics problem implementation.
> 
> I am developing a program that will solve the steady-state thermal conduction 
> (laplace) first and then the allen-Cahn equation.
> 
> both of the problems are solved on the same mesh, however due to the nature 
> of my specific implementation they solved separately. To solve the allen-Cahn 
> equation, I need to evaluate temperature dependent functions at each node in 
> the domain.
> 
> Hence, they only share the same triangulation, but everything else is 
> separate.
> 
> My question is, how to use the solution vector from the thermal conduction 
> (the temperature) in the assembly of the allen-cahn equation ?
> 
>  how to access the temperature at these nodes and make sure that they are 
> synchronized ? 
> 
> thank you
> 
> 
> -- 
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> 
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[deal.II] deal.II Newsletter #135

[Rene Gassmoeller]

Hello everyone!

This is deal.II newsletter #135.
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:

#10949: Replace __restrict by DEAL_II_RESTRICT (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/10949

#10948: Fix step 68 animations (proposed by blaisb; merged) 
https://github.com/dealii/dealii/pull/10948

#10946: Remove n_face_orientations template argument within FEEvaluation 
(proposed by peterrum) https://github.com/dealii/dealii/pull/10946

#10944: Fix comping with ICC (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/10944

#10943: Fix 'and and' -> 'and'. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10943

#10942: [step-19] Correct & simplify some computations (proposed by 
kronbichler) https://github.com/dealii/dealii/pull/10942

#10940: Cleanup quadrature (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/10940

#10938: Fix some more gcc-10 warnings (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/10938

#10937: Add note to Triangulation::create_triangulation (proposed by peterrum; 
merged) https://github.com/dealii/dealii/pull/10937

#10936: Fix SCALAPACK tests again (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/10936

#10935: Avoid gcc-10 warning about deprecated parallel::Triangulation (proposed 
by masterleinad; merged) https://github.com/dealii/dealii/pull/10935

#10933: Fix broken link to muParser website (proposed by elauksap; merged) 
https://github.com/dealii/dealii/pull/10933

#10932: Step 74: Symmetric interior penalty Galerkin (SIPG) method for 
Poisson's equation (proposed by zjiaqi2018) 
https://github.com/dealii/dealii/pull/10932

#10931: Add some functions to FEEvaluation (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/10931

#10930: Also install missing files from the code gallery. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/10930

#10929: Use proper grammar. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10929

#10927: Provide more general factory class for FEEvaluation (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/10927

#10926: step-69: Remove boundary c_ij fix (proposed by tamiko) 
https://github.com/dealii/dealii/pull/10926

#10925: Better link to what one can do with iterators. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/10925

#10924: Better explain something in step-1. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10924

#10923: Make the tolerance in step-1 relative. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10923

#10922: Refactor access to FEEvaluationImpl and friends (proposed by 
kronbichler; merged) https://github.com/dealii/dealii/pull/10922

#10920: Fix multiple-component bug in FEFaceEvaluationImpl::integrate_scatter 
(proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/10920

#10919: Minor doc fixes. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10919

#10918: step-3: use a double for the RHS (proposed by tjhei; merged) 
https://github.com/dealii/dealii/pull/10918

#10915: step-50: fix the error estimator (proposed by zjiaqi2018; merged) 
https://github.com/dealii/dealii/pull/10915

#10912: Mark two functions 'noexcept'. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10912

#10911: Fix SCALAPACK tests (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/10911

#10898: Mention Code Complete as a resource. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10898

#10885: Python method for number of triangulation cells (proposed by agrayver; 
merged) https://github.com/dealii/dealii/pull/10885

#10703: Discuss the concept of superconvergence better. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/10703

#10417: Add inter-grid transfer operators (proposed by peterrum; merged) 
https://github.com/dealii/dealii/pull/10417

#10308: Step-68 : Particle tracking of a massless tracer in a vortical flow 
(proposed by blaisb; merged) https://github.com/dealii/dealii/pull/10308

#10301: step-19: A simple particles tutorial. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/10301


## And this is a list of recently opened or closed discussions:

#10947: Document pre-compiled polynomial degrees with FEEvaluation (opened) 
https://github.com/dealii/dealii/issues/10947

#10945: [step-19] Revise discussion about time stepping (opened) 
https://github.com/dealii/dealii/issues/10945

#10941: Implementing multi-physics problem (opened and closed) 
https://github.com/dealii/dealii/issues/10941

#10939: [step-59] Extend section on possibilities for extensions (opened) 

Re: [deal.II] Re: .msh file triangulation failed

[Bruno Turcksin]

Honestly I don't know. I wonder if the terms -1e-07 are the problem. I
told you to remove  SetFactory("OpenCASCADE") because it was the only
difference with my .geo files.

Bruno

Le mar. 22 sept. 2020 à 11:20, yuesu jin  a écrit :
>
> Dear Bruno,
>   The problem was solved after I removed the 'SetFactory("OpenCASCADE")'.  
> Here are two mesh files with and without 'SetFactory("OpenCASCADE")'. Could 
> you tell me why this command made the system unable to work? Thank you very 
> much for your help!
> Best regards,
> Yuesu
>
>
>
> On Tue, Sep 22, 2020 at 10:01 AM Bruno Turcksin  
> wrote:
>>
>> Hmmm. Can you try without the SetFactory("OpenCASCADE"); and can you
>> send me your .msh
>>
>> Bruno
>>
>> Le mar. 22 sept. 2020 à 10:45, yuesu jin  a écrit :
>> >
>> > Dear Bruno,
>> >I did some modification according to your suggestion :
>> > 
>> > Physical Volume("4") = {1};
>> > //+
>> > Physical Surface("0") = {4, 3, 2, 5, 1, 6};
>> > 
>> > I add all external surfaces in one physical group and the volume in 
>> > another group. But the error message remains the same.  I tried a few 
>> > types of grouping combinations, the error message did not change.
>> > Best regards,
>> > Yuesu
>> >
>> > On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin  
>> > wrote:
>> >>
>> >> You don't want to set the physical groups for the curves and the
>> >> points. This means nothing in deal.II. A vertex does not have a
>> >> boundary ID. You need all the external surfaces and the volume to have
>> >> a physical group. That's it.
>> >>
>> >> Bruno
>> >>
>> >> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
>> >> >
>> >> > Dear Bruno,
>> >> >   Thank you for your help! I added physical groups for volume, 
>> >> > surfaces, curves, and points. But the problem remains the same.  The 
>> >> > modified geo file is attached below.
>> >> > Best regards,
>> >> > Yuesu
>> >> >
>> >> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin 
>> >> >  wrote:
>> >> >>
>> >> >>
>> >> >> Yuesu,
>> >> >>
>> >> >> I had the same problem recently. Our gmsh reader assumes that the user 
>> >> >> has set boundary id and material id to the mesh. It looks like you 
>> >> >> don't have those and so the file is read incorrectly.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Bruno
>> >> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com 
>> >> >> wrote:
>> >> >>>
>> >> >>> Dear all,
>> >> >>>   I have one problem when I try to input the .msh file with grid_in 
>> >> >>> function. The error message is :
>> >> >>>
>> >> >>> *
>> >> >>>
>> >> >>> Exception on processing:
>> >> >>>
>> >> >>> 
>> >> >>> An error occurred in line <3139> of file 
>> >> >>>  in function
>> >> >>> static void 
>> >> >>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> >> >>>  std::vector >&, const 
>> >> >>> std::vector, std::allocator > 
>> >> >>> >&, const dealii::SubCellData&, dealii::Triangulation<3, spacedim>&) 
>> >> >>> [with int spacedim = 3]
>> >> >>> The violated condition was:
>> >> >>> false
>> >> >>> Additional information:
>> >> >>> While trying to assign a boundary indicator to a line: the line 
>> >> >>> with end vertices -1 and 0 does not exist.
>> >> >>> 
>> >> >>>
>> >> >>> I attached the gmsh .geo file in this email. There is no vertex -1 
>> >> >>> actually. Could you tell me what's wrong with my mesh generation?
>> >> >>>
>> >> >>> Thank you very much!
>> >> >>> Best regards,
>> >> >>>
>> >> >>> --
>> >> >>> Yuesu Jin,
>> >> >>> Ph.D student,
>> >> >>> University of Houston,
>> >> >>> College of Natural Sciences and Mathematics,
>> >> >>> Department of Earth and Atmospheric Sciences,
>> >> >>> Houston, Texas 77204-5008
>> >> >>> 346-404-2062
>> >> >>>
>> >> >> --
>> >> >> 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/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com.
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Yuesu Jin,
>> >> > Ph.D student,
>> >> > University of Houston,
>> >> > College of Natural Sciences and Mathematics,
>> >> > Department of Earth and Atmospheric Sciences,
>> >> > Houston, Texas 77204-5008
>> >> > 346-404-2062
>> >> >
>> >> > --
>> >> > The deal.II project is located at http://www.dealii.org/
>> >> > For 

[deal.II] PETSC issue while trying to run step-18

[krishan...@gmail.com]

Hello,

I tried to run step-18 and initially received the following error message:

 Error! This tutorial requires a deal.II library that was configured with
  the following options:

  DEAL_II_WITH_MPI = ON
  DEAL_II_WITH_PETSC = ON
  DEAL_II_PETSC_WITH_COMPLEX = OFF

  However, the deal.II library found at
  /home/krishanu/Google_Drive/dealii/dealii_920/library_dealii_920 was
  configured with these options

  DEAL_II_WITH_MPI = OFF
  DEAL_II_WITH_PETSC = OFF
  DEAL_II_PETSC_WITH_COMPLEX = 

  which conflict with the requirements.

So, I used the following commands (from this link: 
https://www.dealii.org/current/external-libs/petsc.html) to install PETSC:

tar xvzf petsc-x-y-z.tar.gz cd petsc-x-y-z
export PETSC_DIR=`pwd`
export PETSC_ARCH=x86_64
./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1 
--download-hypre=1
make
make test

Then used the following commands to build, configure and install deal.ii

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II

But it seems that deal.ii did not auto detect PETSC and MPI as it showed 
the following among other configured features:

Configured Features (DEAL_II_ALLOW_BUNDLED = ON, 
DEAL_II_ALLOW_AUTODETECTION = ON):

#  ( DEAL_II_WITH_MPI = OFF )
#  ( DEAL_II_WITH_PETSC = OFF )

I am wondering what I might be missing here. Could anyone please help?


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Re: [deal.II] Re: .msh file triangulation failed

[yuesu jin]

Dear Bruno,
   I did some modification according to your suggestion :



*Physical Volume("4") = {1};//+Physical Surface("0") = {4, 3, 2, 5, 1, 6};*

I add all external surfaces in one physical group and the volume in another
group. But the error message remains the same.  I tried a few types of
grouping combinations, the error message did not change.
Best regards,
Yuesu

On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin 
wrote:

> You don't want to set the physical groups for the curves and the
> points. This means nothing in deal.II. A vertex does not have a
> boundary ID. You need all the external surfaces and the volume to have
> a physical group. That's it.
>
> Bruno
>
> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
> >
> > Dear Bruno,
> >   Thank you for your help! I added physical groups for volume, surfaces,
> curves, and points. But the problem remains the same.  The modified geo
> file is attached below.
> > Best regards,
> > Yuesu
> >
> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin 
> wrote:
> >>
> >>
> >> Yuesu,
> >>
> >> I had the same problem recently. Our gmsh reader assumes that the user
> has set boundary id and material id to the mesh. It looks like you don't
> have those and so the file is read incorrectly.
> >>
> >> Best,
> >>
> >> Bruno
> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com
> wrote:
> >>>
> >>> Dear all,
> >>>   I have one problem when I try to input the .msh file with grid_in
> function. The error message is :
> >>>
> >>> *
> >>>
> >>> Exception on processing:
> >>>
> >>> 
> >>> An error occurred in line <3139> of file
>  in function
> >>> static void
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
> std::vector >&, const std::vector,
> std::allocator > >&, const dealii::SubCellData&,
> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
> >>> The violated condition was:
> >>> false
> >>> Additional information:
> >>> While trying to assign a boundary indicator to a line: the line
> with end vertices -1 and 0 does not exist.
> >>> 
> >>>
> >>> I attached the gmsh .geo file in this email. There is no vertex -1
> actually. Could you tell me what's wrong with my mesh generation?
> >>>
> >>> Thank you very much!
> >>> Best regards,
> >>>
> >>> --
> >>> Yuesu Jin,
> >>> Ph.D student,
> >>> University of Houston,
> >>> College of Natural Sciences and Mathematics,
> >>> Department of Earth and Atmospheric Sciences,
> >>> Houston, Texas 77204-5008
> >>> 346-404-2062
> >>>
> >> --
> >> 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/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com
> .
> >
> >
> >
> > --
> > Yuesu Jin,
> > Ph.D student,
> > University of Houston,
> > College of Natural Sciences and Mathematics,
> > Department of Earth and Atmospheric Sciences,
> > Houston, Texas 77204-5008
> > 346-404-2062
> >
> > --
> > 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 a topic in the
> Google Groups "deal.II User Group" group.
> > To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/dealii/HmoTVW7YfAw/unsubscribe.
> > To unsubscribe from this group and all its topics, send an email to
> dealii+unsubscr...@googlegroups.com.
> > To view this discussion on the web visit
> https://groups.google.com/d/msgid/dealii/CA%2B25a%3DLt6Dknw5DzkL0SCjozogiVoEVZQp%3DeurYpBWiUrCrLiQ%40mail.gmail.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
> ---
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 

Re: [deal.II] Re: .msh file triangulation failed

[Bruno Turcksin]

You don't want to set the physical groups for the curves and the
points. This means nothing in deal.II. A vertex does not have a
boundary ID. You need all the external surfaces and the volume to have
a physical group. That's it.

Bruno

Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
>
> Dear Bruno,
>   Thank you for your help! I added physical groups for volume, surfaces, 
> curves, and points. But the problem remains the same.  The modified geo file 
> is attached below.
> Best regards,
> Yuesu
>
> On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin  
> wrote:
>>
>>
>> Yuesu,
>>
>> I had the same problem recently. Our gmsh reader assumes that the user has 
>> set boundary id and material id to the mesh. It looks like you don't have 
>> those and so the file is read incorrectly.
>>
>> Best,
>>
>> Bruno
>> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com wrote:
>>>
>>> Dear all,
>>>   I have one problem when I try to input the .msh file with grid_in 
>>> function. The error message is :
>>>
>>> *
>>>
>>> Exception on processing:
>>>
>>> 
>>> An error occurred in line <3139> of file 
>>>  in function
>>> static void 
>>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>>>  std::vector >&, const std::vector, 
>>> std::allocator > >&, const dealii::SubCellData&, 
>>> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
>>> The violated condition was:
>>> false
>>> Additional information:
>>> While trying to assign a boundary indicator to a line: the line with 
>>> end vertices -1 and 0 does not exist.
>>> 
>>>
>>> I attached the gmsh .geo file in this email. There is no vertex -1 
>>> actually. Could you tell me what's wrong with my mesh generation?
>>>
>>> Thank you very much!
>>> Best regards,
>>>
>>> --
>>> Yuesu Jin,
>>> Ph.D student,
>>> University of Houston,
>>> College of Natural Sciences and Mathematics,
>>> Department of Earth and Atmospheric Sciences,
>>> Houston, Texas 77204-5008
>>> 346-404-2062
>>>
>> --
>> 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/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com.
>
>
>
> --
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008
> 346-404-2062
>
> --
> 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 a topic in the Google 
> Groups "deal.II User Group" group.
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> To unsubscribe from this group and all its topics, send an email to 
> dealii+unsubscr...@googlegroups.com.
> To view this discussion on the web visit 
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Re: [deal.II] Re: .msh file triangulation failed

[Bruno Turcksin]

Hmmm. Can you try without the SetFactory("OpenCASCADE"); and can you
send me your .msh

Bruno

Le mar. 22 sept. 2020 à 10:45, yuesu jin  a écrit :
>
> Dear Bruno,
>I did some modification according to your suggestion :
> 
> Physical Volume("4") = {1};
> //+
> Physical Surface("0") = {4, 3, 2, 5, 1, 6};
> 
> I add all external surfaces in one physical group and the volume in another 
> group. But the error message remains the same.  I tried a few types of 
> grouping combinations, the error message did not change.
> Best regards,
> Yuesu
>
> On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin  
> wrote:
>>
>> You don't want to set the physical groups for the curves and the
>> points. This means nothing in deal.II. A vertex does not have a
>> boundary ID. You need all the external surfaces and the volume to have
>> a physical group. That's it.
>>
>> Bruno
>>
>> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
>> >
>> > Dear Bruno,
>> >   Thank you for your help! I added physical groups for volume, surfaces, 
>> > curves, and points. But the problem remains the same.  The modified geo 
>> > file is attached below.
>> > Best regards,
>> > Yuesu
>> >
>> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin  
>> > wrote:
>> >>
>> >>
>> >> Yuesu,
>> >>
>> >> I had the same problem recently. Our gmsh reader assumes that the user 
>> >> has set boundary id and material id to the mesh. It looks like you don't 
>> >> have those and so the file is read incorrectly.
>> >>
>> >> Best,
>> >>
>> >> Bruno
>> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com 
>> >> wrote:
>> >>>
>> >>> Dear all,
>> >>>   I have one problem when I try to input the .msh file with grid_in 
>> >>> function. The error message is :
>> >>>
>> >>> *
>> >>>
>> >>> Exception on processing:
>> >>>
>> >>> 
>> >>> An error occurred in line <3139> of file 
>> >>>  in function
>> >>> static void 
>> >>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> >>>  std::vector >&, const 
>> >>> std::vector, std::allocator > 
>> >>> >&, const dealii::SubCellData&, dealii::Triangulation<3, spacedim>&) 
>> >>> [with int spacedim = 3]
>> >>> The violated condition was:
>> >>> false
>> >>> Additional information:
>> >>> While trying to assign a boundary indicator to a line: the line with 
>> >>> end vertices -1 and 0 does not exist.
>> >>> 
>> >>>
>> >>> I attached the gmsh .geo file in this email. There is no vertex -1 
>> >>> actually. Could you tell me what's wrong with my mesh generation?
>> >>>
>> >>> Thank you very much!
>> >>> Best regards,
>> >>>
>> >>> --
>> >>> Yuesu Jin,
>> >>> Ph.D student,
>> >>> University of Houston,
>> >>> College of Natural Sciences and Mathematics,
>> >>> Department of Earth and Atmospheric Sciences,
>> >>> Houston, Texas 77204-5008
>> >>> 346-404-2062
>> >>>
>> >> --
>> >> 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/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com.
>> >
>> >
>> >
>> > --
>> > Yuesu Jin,
>> > Ph.D student,
>> > University of Houston,
>> > College of Natural Sciences and Mathematics,
>> > Department of Earth and Atmospheric Sciences,
>> > Houston, Texas 77204-5008
>> > 346-404-2062
>> >
>> > --
>> > 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 a topic in the 
>> > Google Groups "deal.II User Group" group.
>> > To unsubscribe from this topic, visit 
>> > https://groups.google.com/d/topic/dealii/HmoTVW7YfAw/unsubscribe.
>> > To unsubscribe from this group and all its topics, send an email to 
>> > dealii+unsubscr...@googlegroups.com.
>> > To view this discussion on the web visit 
>> > https://groups.google.com/d/msgid/dealii/CA%2B25a%3DLt6Dknw5DzkL0SCjozogiVoEVZQp%3DeurYpBWiUrCrLiQ%40mail.gmail.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
>> ---
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>> To unsubscribe from this group and stop receiving emails from 

Re: [deal.II] Using DataOut when dim != spacedim

[Malhar Tidke]

Hello Luca,

I am sorry, I should have mentioned it in the question, I had tried it
earlier, but it leads to argument mismatch because, as Daniel has posted,
the second argument is DofHandlerType rather than spacedim. But, thank you
for your help. Appreciate it.

Best Regards,
Malhar

On Tue, Sep 22, 2020 at 5:33 PM luca.heltai  wrote:

> Dear Malhar,
>
> just as you did for the Triangulation and the DoFHandler, also DataOut
> should be instantiated with <2,3>, i.e.,
>
> not
>
> DataOut<2> …
>
>
> but
>
>
> DataOut<2,3> …
>
> Best,
> Luca.
>
>
> > On 22 Sep 2020, at 7:37, Malhar T.  wrote:
> >
> > Hello All,
> > I hope you are doing well !
> >
> > I am working on a surface patch in 3D (dim=2 & spacedim=3 and developed
> using ChartManifold<2,3> by following code similar to step-53) and I would
> like to output the results into a vtk file. I am mostly following
> tutorials, as I am not really great with C++. So, initially I used the
> class DataOut and tried to specify the geometry using attach_dof_handler.
> >
> > This is how its defined,
> > Triangulation<2, 3
> > > triangulation;
> > DoFHandler<
> > 2, 3
> > >dof_handler;
> >
> > And output_results function was written as
> > {
> > DataOut data_out;
> > data_out.attach_dof_handler(dof_handler);
> > }
> >
> > But I got the error
> >
> > error: cannot convert ‘
> > const dealii::DoFHandler<2, 3>’ to ‘const dealii::DoFHandler<2, 2
> > >&’
> > note:   initializing argument
> > 1 of ‘void dealii::DataOut_DoFData patch_space_dim>::attach_dof_handler(const DoFHandlerType&) [with
> DoFHandlerType = dealii::DoFHandler<2, 2>; int patch_dim = 2; int
> patch_space_dim = 2
> > ]’
> >
> > I tried searching in the forum and came to know about DataOutFaces
> (through this post), and I also looked at the step-61 tutorial on its
> implementation, but I got the same error again. I have a feeling that I am
> not understanding something very trivial, thus, any pointers would be
> really helpful.
> >
> > Thank You.
> >
> >
> >
> > --
> > 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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> .
>
> --
> The deal.II project is located at http://www.dealii.org/
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