Re: [deal.II] Spectral Methods using dealii

[陈敏]

Dear Wolfgang Bangerth

I found "FE_DGQLegendre" in dealii, and I think it is the spectral methods
but use discontinous Galerkin. I also found "FESeries::Legendre", this
class provide the transformation
<https://www.dealii.org/current/doxygen/deal.II/classFESeries_1_1Legendre.html#ae2dae601bf1167c237969be15c66d7fd:~:text=%E2%97%86-,precalculate_all_transformation_matrices,-()>
between the  polynomial space and physical space. But it lack tutorial of
the two classes.

Best
Chen

陈敏  于2024年6月23日周日 18:53写道：

> Dear Wolfgang Bangerth
>
> I learn spectral methods from the book "Hesthaven, Nodal Discontinuous
> Galerkin Methods, 2008". This book focuses on the Nodal Discontinuous
> Galerkin Methods, and use Legendre polynomials to expanse the solution of a
> nodal element on a polynomial space like the followed equations[Page 53 of
> the book]:
> [image: image.png]
> ψn is the Legendre polynomial basis on polynomial space, and *lik is the 
> *lagrangian
> polynomial basis on physical space. There will be a transform between the
> two spaces by projection.
>
> Anyway, if I want to implement a spectral method in dealii, I just need to
> use Legendre polynomial basis and do quadrature on Legendre-Gauss-Lobatto
> (LGL) quadrature points?
>
> Thanks!
>
> Best
> Chen
>
> Wolfgang Bangerth  于2024年6月19日周三 07:08写道：
>
>> On 6/15/24 09:51, 陈敏 wrote:
>> >
>> >   I have a question of Spectral Methods using dealii. As far as I know,
>> we can
>> > you the Legendre function and some other Orthogonal polynomials as
>> basis
>> > function in dealii. But we need the projection from polynomial space to
>> > physical space, how to do the projection in dealii?
>>
>> I am not familiar with the term "projection from polynomial space to
>> physical
>> space". Do you mean the transformation from reference cell to a
>> particular
>> cell of the mesh? If not, can you elaborate?
>>
>> Best
>>   Wolfgang
>>
>> –
>> --
>> 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
>> —
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>> .
>>
>

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Re: [deal.II] Spectral Methods using dealii

[陈敏]

Dear Wolfgang Bangerth

I learn spectral methods from the book "Hesthaven, Nodal Discontinuous
Galerkin Methods, 2008". This book focuses on the Nodal Discontinuous
Galerkin Methods, and use Legendre polynomials to expanse the solution of a
nodal element on a polynomial space like the followed equations[Page 53 of
the book]:
[image: image.png]
ψn is the Legendre polynomial basis on polynomial space, and *lik is
the *lagrangian
polynomial basis on physical space. There will be a transform between the
two spaces by projection.

Anyway, if I want to implement a spectral method in dealii, I just need to
use Legendre polynomial basis and do quadrature on Legendre-Gauss-Lobatto
(LGL) quadrature points?

Thanks!

Best
Chen

Wolfgang Bangerth  于2024年6月19日周三 07:08写道：

> On 6/15/24 09:51, 陈敏 wrote:
> >
> >   I have a question of Spectral Methods using dealii. As far as I know,
> we can
> > you the Legendre function and some other Orthogonal polynomials as basis
> > function in dealii. But we need the projection from polynomial space to
> > physical space, how to do the projection in dealii?
>
> I am not familiar with the term "projection from polynomial space to
> physical
> space". Do you mean the transformation from reference cell to a particular
> cell of the mesh? If not, can you elaborate?
>
> Best
>   Wolfgang
>
> –
> --
> 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
> —
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> https://groups.google.com/d/msgid/dealii/9cc4ed3b-3c65-4071-b1e8-918de2373470%40colostate.edu
> .
>

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[deal.II] Spectral Methods using dealii

[陈敏]

Dear all

 I have a question of Spectral Methods using dealii. As far as I know, we
can you the Legendre function and some other Orthogonal polynomials as
basis function in dealii. But we need the projection from polynomial space
to physical space, how to do the projection in dealii? Or Are there some
misunderstanding of Spectral Methods?

Best
Chen

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Re: [deal.II] Re: gmsh imported into dealii

[陈敏]

You should not add Physical Surface("inner wall surface", 776) of interface
in gmsh,

This interface can be determined by the step-46, this is the drawback of
dealii as I know.



王艺康  于2024年6月13日周四 14:27写道：

> Hello，
> Sure. I just use GridIN to read the grid.
>
> using namespace dealii;
> void run()
> {
>
> Triangulation<3> triangulation;
> GridIn<3> grid_in;
> grid_in.attach_triangulation(triangulation);
>
> {
> std::string   filename = "heart_have_thickness(1).msh";
> std::ifstream file(filename);
> Assert(file, ExcFileNotOpen(filename.c_str()));
> grid_in.read_msh(file);
> }
>
> }
>
>  int main()
>  {
>
>  run();
>
>  }
>
> On Wednesday, June 12, 2024 at 10:46:04 PM UTC+8 blais...@gmail.com wrote:
>
>> Can you provide the GMSH code and a small executable that tries to
>> achieve what you are doing? I can take a look and figure out what is the
>> issue :)
>>
>>
>> On Wednesday, June 12, 2024 at 3:08:19 a.m. UTC-4 yikangw...@gmail.com
>> wrote:
>>
>>> Hollo,
>>> I tried your suggestion but dealii still reports an error. I don't think
>>> it has anything to do with the grid type, it also errors when I only use
>>> Gridin.
>>>
>>> Wang
>>>
>>> On Friday, June 7, 2024 at 11:32:16 PM UTC+8 blais...@gmail.com wrote:
>>>
 Loading a tet mesh works if you set-up your Mapping/FE accordingly,
 this is a feature we use extensively.


 On Wednesday, June 5, 2024 at 1:28:20 p.m. UTC+1 bruno.t...@gmail.com
 wrote:

> Wang,
>
> Are you loading a hex mesh or a tet mesh? I don't know if loading a
> tet mesh works.
>
> Best,
>
> Bruno
>
> Le mar. 4 juin 2024 à 21:12, 王艺康  a écrit :
>
>> Bruno,
>> In fact that's what I did. The error is the same for regenerated
>> meshes entered into dealii. I redrew a simple geometry again without
>> defining any physical information still the same error. I don't 
>> understand
>> why this is wrong, if I generate only the fluid-solid coupling interface 
>> to
>> the external contour (solid domain) mesh there is no problem, but the 
>> same
>> error occurs when I generate only the internal (fluid domain).
>>
>> Wang
>>
>>
>> [image: 捕获1.PNG][image: 捕获2.PNG]
>> [image: 捕获3.PNG]
>> [image: 捕获4.PNG]
>>
>>
>> On Tuesday, June 4, 2024 at 10:28:21 PM UTC+8 bruno.t...@gmail.com
>> wrote:
>>
>>> Wang,
>>>
>>> Do you have a geo file that describes the geometry? Can you remove
>>> the "Physical Surface" lines in the geo file and regenerate the mesh.
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> Le mar. 4 juin 2024 à 10:13, 王艺康  a écrit :
>>>
 Hello,
 Thank you very much for your reply. That's what I thought at first,
 but I was wrong, when I removed the corresponding physical group it was
 still the same error. I think gmsh automatically sets the coupling
 interface to solid when drawing the model body mesh, but I don't know 
 how
 to change it. I didn't learn gmsh deep enough.

 Wang

 On Tuesday, June 4, 2024 at 8:28:07 PM UTC+8 bruno.t...@gmail.com
 wrote:

> Hello,
>
> Deal.II associates the physical group of a face with a boundary
> id. You need to remove the physical group that are associated with 
> interior
> faces.
>
> Best,
>
> Bruno
>
> On Tuesday, June 4, 2024 at 3:28:05 AM UTC-4 yikangw...@gmail.com
> wrote:
>
>> I drew the model in gmsh but importing to dealii is giving me an
>> error.This step error occurs when importing a model.
>>
>> The violated condition was:
>> boundary_id != numbers::internal_face_boundary_id
>> Additional information:
>> The input arguments for creating a triangulation specified a
>> boundary
>> id for an internal face. This is not allowed.
>>
>>
>>
>> Here only a part of the mesh is shown (the outer contour also
>> generates the mesh),the error should occur at the interface of the 
>> two
>> bodies, but I don't know how to fix it. This model will be used for
>> fluid-solid coupling, where the interior is the fluid domain and the
>> contours are the solid domain.
>> [image: 捕获.PNG]
>>
>>
>>
>> --
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Re: [deal.II] "constraints for degree of freedom ... should not be stored ... " after SolutionTransfer

[陈敏]

Hi Simon

you can write function of setup_system like other tutorial setp, after
refine mesh, rerun function of setup_system().

Best
Chen

Simon  于2024年6月10日周一 14:13写道：

> No, the program that produced the error is serial not parallel.
>
> Best,
> Simon
>
> Wolfgang Bangerth schrieb am Montag, 10. Juni 2024 um 04:30:33 UTC+2:
>
>> On 6/8/24 07:51, Simon wrote:
>> >
>> > Before refinement, dofHandler stored 138 DoFs, after refinement 202.
>> >
>> > I could not reproduce the error on a minimal example.
>> > However, it is not clear to me why
>> > make_hanging_constraints() reports an error associated with dof index
>> 167,
>> > if I cleared the constraints object before hand and can be certain that
>> my
>> > DoFHandler has 202 DoFs.
>> > So the sequence of distributing DoFs, followed by clearing constraints
>> and
>> > calling make hanging node constraints should work independently of how
>> my
>> > program arrived at these lines of code. Is this not true?
>> >
>> > Any general hints as for the problem source and narrowing down the
>> problem?
>>
>> Did you initialize the AffineConstraints object with index sets for the
>> locally owned and/or locally relevant DoFs? If so, you will have to
>> re-initialize it with the now larger/different number of DoFs you have
>> after
>> mesh refinement.
>>
>> Best
>> W.
>>
>> --
>> 
>> Wolfgang Bangerth email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>
>> --
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> 
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>

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Re: [deal.II] Pressure load on a plate upper surface in solid mechanics

[陈敏]

One more thing:
you should loop over q point before loop over dof.

Léonhard YU  于2024年6月8日周六 18:14写道：

> Dear all,
>  I am working on impose constant pressure load on a plate's upper surface.
> The code is derived from step-18 and attached below. But I found that the
> diplacement is not right, and it varies when the number of face elements
> changes. I am thinking about something wrong with the loading but I do not
> have any idea. Thanks a lot if you can help me.
> The constant pressure is 1e-2 and the boundary_id for loading is
> bc_uppersurface. The codes attached below:
>
> for (const auto &cell : dof_handler.active_cell_iterators())
> if (cell->is_locally_owned())
> {
> cell_matrix = 0;
> cell_rhs= 0;
>
> fe_values.reinit(cell);
> for (unsigned int i = 0; i < dofs_per_cell; ++i)
> for (unsigned int j = 0; j < dofs_per_cell; ++j)
> for (unsigned int q_point = 0; q_point < n_q_points; ++q_point)
> {
> const SymmetricTensor<2, dim>
> eps_phi_i = get_strain(fe_values, i, q_point),
> eps_phi_j = get_strain(fe_values, j, q_point);
>
> cell_matrix(i, j) += (eps_phi_i *//
> stress_strain_tensor * //
> eps_phi_j  //
> ) *//
> fe_values.JxW(q_point); //
> }
>
> // pressure load
> for (const auto &face : cell->face_iterators())
> {
> if (face->at_boundary() && (face->boundary_id() ==
> bc_uppersurface))
> {
> fe_face_values.reinit(cell, face);
> for (unsigned int i = 0; i < dofs_per_cell; ++i)
> {
> const unsigned int component_i =
> fe.system_to_component_index(i).first;
> for (unsigned int face_q_point = 0; face_q_point <
> face_n_q_point; ++face_q_point)
> {
> Tensor<1,dim> dir;
> dir = fe_face_values.normal_vector(face_q_point);
> Point point_dof =
> fe_face_values.quadrature_point(face_q_point);
> const double magnitude = 1e-2;
> const Tensor<1, dim> traction = -1.0 * magnitude * dir;
> cell_rhs(i) +=
> fe_face_values.shape_value(i, face_q_point) *
> traction[component_i] *
> fe_face_values.JxW(face_q_point);
> }
> }
> }
> }
> }
>
> Best Regards
>
> --
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> 
> .
>

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Re: [deal.II] Pressure load on a plate upper surface in solid mechanics

[陈敏]

Hi  Léonhard

Your solution may not Converge to a mesh-independent solution.

Best
Chen

Léonhard YU  于2024年6月8日周六 18:14写道：

> Dear all,
>  I am working on impose constant pressure load on a plate's upper surface.
> The code is derived from step-18 and attached below. But I found that the
> diplacement is not right, and it varies when the number of face elements
> changes. I am thinking about something wrong with the loading but I do not
> have any idea. Thanks a lot if you can help me.
> The constant pressure is 1e-2 and the boundary_id for loading is
> bc_uppersurface. The codes attached below:
>
> for (const auto &cell : dof_handler.active_cell_iterators())
> if (cell->is_locally_owned())
> {
> cell_matrix = 0;
> cell_rhs= 0;
>
> fe_values.reinit(cell);
> for (unsigned int i = 0; i < dofs_per_cell; ++i)
> for (unsigned int j = 0; j < dofs_per_cell; ++j)
> for (unsigned int q_point = 0; q_point < n_q_points; ++q_point)
> {
> const SymmetricTensor<2, dim>
> eps_phi_i = get_strain(fe_values, i, q_point),
> eps_phi_j = get_strain(fe_values, j, q_point);
>
> cell_matrix(i, j) += (eps_phi_i *//
> stress_strain_tensor * //
> eps_phi_j  //
> ) *//
> fe_values.JxW(q_point); //
> }
>
> // pressure load
> for (const auto &face : cell->face_iterators())
> {
> if (face->at_boundary() && (face->boundary_id() ==
> bc_uppersurface))
> {
> fe_face_values.reinit(cell, face);
> for (unsigned int i = 0; i < dofs_per_cell; ++i)
> {
> const unsigned int component_i =
> fe.system_to_component_index(i).first;
> for (unsigned int face_q_point = 0; face_q_point <
> face_n_q_point; ++face_q_point)
> {
> Tensor<1,dim> dir;
> dir = fe_face_values.normal_vector(face_q_point);
> Point point_dof =
> fe_face_values.quadrature_point(face_q_point);
> const double magnitude = 1e-2;
> const Tensor<1, dim> traction = -1.0 * magnitude * dir;
> cell_rhs(i) +=
> fe_face_values.shape_value(i, face_q_point) *
> traction[component_i] *
> fe_face_values.JxW(face_q_point);
> }
> }
> }
> }
> }
>
> Best Regards
>
> --
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> 
> .
>

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Re: [deal.II] dealii Installation

[陈敏]

Hi wang

Ubuntu 16 is too outdate, and you can do something like:

   1. use new version of ubuntu, ubuntu 2004, ubuntu 22.04 for example
   2. install a new gcc compiler which support new c++ Standard
   3. use spack to install dealii
   4. install old version of dealii (dealii 9.0.0 for example) in ubuntu 16

Best
Chen

王艺康  于2024年5月28日周二 21:07写道：

> Hello, everyone.
> I'm having a problem installing dealii with candi.I'm installing
> dealii-9.5.1 on Ubuntu 16.0.4 via candi, only then all the dependencies I
> need can be downloaded and installed correctly but I get an error when
> installing dealii.
>
>
>
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:
> In instantiation of ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >
> dealii::GridTools::internal::guess_owners_of_entities(MPI_Comm, const
> std::vector > >&, const
> std::vector&, double) [with int spacedim = 1; T =
> dealii::Point<1>; MPI_Comm = int]’:
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:6195:71:
>   required from
> ‘dealii::GridTools::internal::DistributedComputePointLocationsInternal spacedim>
> dealii::GridTools::internal::distributed_compute_point_locations(const
> dealii::GridTools::Cache&, const
> std::vector >&, const
> std::vector > >&, const
> std::vector&, double, bool, bool) [with int dim = 1; int spacedim =
> 1]’
> /home/hj/dealii-candi/home/hj/wyk/candi/build/deal.II-v9.5.1/source/grid/grid_tools.inst:1289:12:
>   required from here
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:5970:67:
> error: converting to ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >’ from initializer list would use explicit
> constructor ‘constexpr std::tuple< 
> >::tuple(_UElements&& ...) [with _UElements = {std::vector std::allocator >, std::vector std::allocator >, std::vector std::allocator >};  = void; _Elements
> = {std::vector >,
> std::vector >,
> std::vector >}]’
>return {std::move(ranks), std::move(ptr), std::move(indices)};
>^
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:
> In instantiation of ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >
> dealii::GridTools::internal::guess_owners_of_entities(MPI_Comm, const
> std::vector > >&, const
> std::vector&, double) [with int spacedim = 2; T =
> dealii::Point<2, double>; MPI_Comm = int]’:
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:6195:71:
>   required from
> ‘dealii::GridTools::internal::DistributedComputePointLocationsInternal spacedim>
> dealii::GridTools::internal::distributed_compute_point_locations(const
> dealii::GridTools::Cache&, const
> std::vector >&, const
> std::vector > >&, const
> std::vector&, double, bool, bool) [with int dim = 1; int spacedim =
> 2]’
> /home/hj/dealii-candi/home/hj/wyk/candi/build/deal.II-v9.5.1/source/grid/grid_tools.inst:1388:12:
>   required from here
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:5970:67:
> error: converting to ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >’ from initializer list would use explicit
> constructor ‘constexpr std::tuple< 
> >::tuple(_UElements&& ...) [with _UElements = {std::vector std::allocator >, std::vector std::allocator >, std::vector std::allocator >};  = void; _Elements
> = {std::vector >,
> std::vector >,
> std::vector >}]’
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:
> In instantiation of ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >
> dealii::GridTools::internal::guess_owners_of_entities(MPI_Comm, const
> std::vector > >&, const
> std::vector&, double) [with int spacedim = 3; T =
> dealii::Point<3, double>; MPI_Comm = int]’:
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:6195:71:
>   required from
> ‘dealii::GridTools::internal::DistributedComputePointLocationsInternal spacedim>
> dealii::GridTools::internal::distributed_compute_point_locations(const
> dealii::GridTools::Cache&, const
> std::vector >&, const
> std::vector > >&, const
> std::vector&, double, bool, bool) [with int dim = 1; int spacedim =
> 3]’
> /home/hj/dealii-candi/home/hj/wyk/candi/build/deal.II-v9.5.1/source/grid/grid_tools.inst:1487:12:
>   required from here
> /home/hj/dealii-candi/home/hj/wyk/candi/deal.II-v9.5.1/source/grid/grid_tools.cc:5970:67:
> error: converting to ‘std::tuple std::allocator >, std::vector std::allocator >, std::vector std::allocator > >’ from initializer list would use explicit
> constructor ‘constexpr std::tuple< 
> >::tuple(_UElements&& ...) [with _UElements = {std::vector std::allocator >, std::vector std::allocator >, std::vector std::alloca

Re: [deal.II] Output domain id for different parts of the domain

[陈敏]

Dear Daniel Arndt



Thank you for your reply, it is really helpfull and appreciated!

Best
Chen

Daniel Arndt  于2024年4月29日周一 23:31写道：

> Chen,
>
> Have a look at how the subdomain id is added to the output results in
> step-40 (
> https://www.dealii.org/current/doxygen/deal.II/step_40.html#LaplaceProblemoutput_results
> ).
>
> Best,
> Daniel
>
> On Mon, Apr 29, 2024 at 9:23 AM 陈敏  wrote:
> >
> > Dear all
> >
> > I'm dealing with a fluid-structure interaction problem, and I want ot
> output the domain id to the cell to the vtk/vtu result files. By the way,
> partitioning the fluid and solid domain by the id can be very convenient in
> paraview. But I don't know how to output the domain id when using dealii.
> Could anyone help me?
> >
> >
> > Best regards
> > Chen
> >
> > --
> > 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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> .
>

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[deal.II] Output domain id for different parts of the domain

[陈敏]

Dear all

I'm dealing with a fluid-structure interaction problem, and I want ot
output the domain id to the cell to the vtk/vtu result files. By the
way, partitioning the fluid and solid domain by the id can be
very convenient in paraview. But I don't know how to output the domain id
when using dealii. Could anyone help me?


Best regards
Chen

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Re: [deal.II] Gridin_COMSOL_mphtxt cannot import my mesh

[陈敏]

Yufei Fang:

The selection of exporting data should by careful.
[image: image.png]
Chen

Yufei Fang  于2024年3月27日周三 20:12写道：

> Dear Professor Bangerth,
> I appreciate the effort and time you dedicated to reviewing and addressing
> the error I encountered. Your guidance has been beneficial. Following your
> advice, I have updated the mesh file to incorporate triangles. The file now
> has the following structure:
> """
> 3 # number of vertices per element
> 16308 # number of elements
> # Elements
> 0 2 1
> 3 1 2
> 1 3 5
> ...
> """
> However, this modification has led to a new error message:
> """
> An error occurred in line <1557> of file
> 
> in function
> void dealii::GridIn::read_comsol_mphtxt(std::istream&)
> [with int dim = 2; int spacedim = 3; std::istream =
> std::basic_istream]
>
> *The violated condition was: s == "4 Mesh"*
> Additional information:
> You are trying to use functionality in deal.II that is currently not
> implemented. In many cases, this indicates that there simply didn't
> appear much of a need for it, or that the author of the original code
> did not have the time to implement a particular case. If you hit this
> exception, it is therefore worth the time to look into the code to
> find out whether you may be able to implement the missing
> functionality. If you do, please consider providing a patch to the
> deal.II development sources (see the deal.II website on how to
> contribute).
>
> Stacktrace:
> ---
> #0
>  
> /dssg/opt/icelake/linux-centos8-icelake/gcc-9.3.0/dealii-9.4.0/install/deal/lib/libdeal_II.g.so.9.4.0:
> dealii::GridIn<2, 3>::read_comsol_mphtxt(std::istream&)
> #1  ./test: run3D()
> #2  ./test: main
> 
> """
> Attached are my updated .mphtxt and .cc files. Could you kindly assist in
> identifying the source of the issue?
> On Friday, March 22, 2024 at 11:11:25 AM UTC+8 Wolfgang Bangerth wrote:
>
>>
>> Yufei:
>> I looked at your input file, and the error message is correct. The
>> relevant
>> part of 3D.mphtxt looks as follows:
>>
>> ```
>> 1 # number of element types
>>
>> # Type #0
>>
>> 3 edg # type name
>>
>>
>> 2 # number of vertices per element
>> 24584 # number of elements
>> # Elements
>> 0 1
>> 2 1
>> ...
>> ```
>>
>> What this part of the file says is "there is only one type of cells",
>> "all
>> cells have type 3 (edges)" where edge=1d line segments, and "here are
>> 24584
>> cells of this type", with each of the line segments described by two
>> vertex
>> numbers.
>>
>> In other words, the file you saved only contains line segments in 3d, but
>> no
>> quadrilaterals or triangles. You'll have to figure out how to save the
>> information you really want, namely cells, rather than just these edges.
>>
>> Best
>> W.
>>
>>
>>
>> On 3/10/24 23:50, Yufei Fang wrote:
>> > *** Caution: EXTERNAL Sender ***
>> >
>> > Sir Chen, thanks for your reply,
>> > I changed the code to
>> > "
>> > Triangulation<2,3> triangulation;
>> > GridIn<2,3> grid_in;
>> > "
>> > However, it still doesn't work, and the error message is the same as
>> before:
>> > "
>> > An error occurred in line <2264> of file
>> >  in function
>> > static void
>> >
>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> std::vector >&, const
>> std::vector >&, const dealii::SubCellData&,
>> dealii::Triangulation&) [with int dim = 2; int spacedim = 3]
>> > The violated condition was:
>> > cells.size() > 0
>> > Additional information:
>> > No cells given
>> > "
>> > 😭
>> > Here is my .mphtxt, can you help me check where the problem is?
>> >
>> > On Friday, March 8, 2024 at 3:57:14 PM UTC+8 hkch...@gmail.com wrote:
>> >
>> > Hi Yufei Fang,
>> >
>> > changing the origin code to the followeing will be  ok.
>> >
>> >
>> > void run3D()
>> > {
>> > Triangulation<2,3> triangulation;
>> > GridIn<2,3> grid_in;
>> >
>> > grid_in.attach_triangulation(triangulation);
>> > std::ifstream input_file("../resource/3D.mphtxt");
>> > grid_in.read_comsol_mphtxt(input_file);
>> >
>> > std::ofstream out("grid3D.vtk");
>> > GridOut   grid_out;
>> > grid_out.write_vtk(triangulation, out);
>> > std::cout << "Grid written to grid.vtk" << std::endl;
>> > }
>> >
>> > int main()
>> > {
>> > run3D();
>> > }
>> >
>> >
>> > Chen
>> >
>> > Yufei Fang  于2024年3月6日周三 17:48写道：
>> >
>> > I'm trying to import the mesh from COMSOL to triangulation.
>> >
>> > comsol_4IaAE9lQVf.png
>> > it's an air-supported membrane structure, the mesh consists of free
>> > triangular or free quad. both are failed.
>> > *here is my code:*
>> > "
>> > void run3D()
>> > {
>> > Triangulation<3> triangulation;
>> > GridIn<3> grid_in;
>> > grid_in.attach_triangulation(triangulation);
>> > std::ifstream input_file("../resource/3D.mphtxt");
>> > grid_in.read_comsol_mphtxt(input_file);
>> >
>> > std::ofstream out("grid3D.vtk");
>> > GridOut   grid_out;
>> > grid_out.write_vtk(triangulation, out);
>> > std

Re: [deal.II] Gridin_COMSOL_mphtxt cannot import my mesh

[陈敏]

Hi Yufei Fang,

changing the origin code to the followeing will be  ok.


void run3D()
{
Triangulation<2,3> triangulation;
GridIn<2,3> grid_in;
grid_in.attach_triangulation(triangulation);
std::ifstream input_file("../resource/3D.mphtxt");
grid_in.read_comsol_mphtxt(input_file);

std::ofstream out("grid3D.vtk");
GridOut   grid_out;
grid_out.write_vtk(triangulation, out);
std::cout << "Grid written to grid.vtk" << std::endl;
}

int main()
{
run3D();
}


Chen

Yufei Fang  于2024年3月6日周三 17:48写道：

> I'm trying to import the mesh from COMSOL to triangulation.
>
> [image: comsol_4IaAE9lQVf.png]
> it's an air-supported membrane structure, the mesh consists of free
> triangular or free quad. both are failed.
> *here is my code:*
> "
> void run3D()
> {
> Triangulation<3> triangulation;
> GridIn<3> grid_in;
> grid_in.attach_triangulation(triangulation);
> std::ifstream input_file("../resource/3D.mphtxt");
> grid_in.read_comsol_mphtxt(input_file);
>
> std::ofstream out("grid3D.vtk");
> GridOut   grid_out;
> grid_out.write_vtk(triangulation, out);
> std::cout << "Grid written to grid.vtk" << std::endl;
> }
>
> int main()
> {
> run3D();
> }
> "
> the error is:
> "
> An error occurred in line <2264> of file
>  in function
> static void
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
> std::vector >&, const
> std::vector >&, const dealii::SubCellData&,
> dealii::Triangulation&) [with int dim = 3; int spacedim = 3]
> The violated condition was:
> cells.size() > 0
> Additional information:
> No cells given
> "
> my question is:
> 1. how to import such a mesh into dealii;
> 2. the tutorial said triangular and tetrahedral cannot be imported in
> dealii, but i can import triangular or tetrahedral element by
> gridin_COMSOL_mphtxt, is it controdicory?
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
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> 
> .
>

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Re: [deal.II] ibpetsc.so.3.019 not found

[陈敏]

Hi Jai

You can add the path of libpetsc.so to the environment variable
“LD_LIBRARY_PATH”.

Best
Chen

Wolfgang Bangerth  于2023年11月30日周四 13:05写道：

> On 11/29/23 20:51, Jai wrote:
> > The exeuctable  of step-5 and 15 got generated without error and while
> > running, I am getting the following error. ./step-5: error while loading
> > shared libraries: libpetsc.so.3.019: cannot open shared object file: No
> such
> > file or directory. How to resolve it. I am using Intel.
>
> Jai: You already asked this in a github issue at
>https://github.com/dealii/dealii/issues/16308
> Bruno asked for more information. There is nothing we can help you if you
> simply repeat the question without providing what Bruno already asked for.
>
> Best
>   WB
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
> --
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> .
>

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[deal.II] A question on dealii tutorial step-35

[陈敏]

Dear all,

I have a question on the step-35
 when I learn it.
the step use project method to solve NS equation. And for updating the
pressure step, there is a Rotational Form
.
In the function of update_pressure(const bool reinit_prec), it seem it plus
the rotational term(+1/Re*div u), while the formula is minus(-1/Re*div u),
the pres_tmp is calculated at projection_step
,
and is pres_tmp is (div u).

I want to know why here is plus not minus. Maybe the minus sign was
included in the original code I didn't notice or understand.

Could anyone help me out?

Best,
Chen

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Re: [deal.II] Request of Step-77-snes.cc File

[陈敏]

Hi Lex Lee,

The file is here:
https://github.com/dealii/dealii/blob/master/tests/petsc/step-77-snes.cc

Best
Chen

Lex Lee  于2023年8月7日周一 13:22写道：

> Hello Deal.ii main developers,
>
> I noticed the webpage for tutorial step-77 here (
> https://www.dealii.org/current/doxygen/deal.II/step_77.html) writes:  "let
> us point out that a version of this program that uses SNES instead of
> KINSOL is available as part of the test suite, in the file
> tests/petsc/step-77-snes.cc."
>
> It seems that there exits a code file with no bugs called step-77-snes.cc.
> I checked a lot on my local computer and I am pretty sure there is no such
> files. Does this file really exists? If yes, could you kindly share me the
> complete code file?
>
> I am learing Jacobian-free Newton Krylov method, and want to play with
> PETSc(snes) library. Thanks a lot.
>
> Best,
>
> Lex Lee
>
>
> --
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> 
> .
>

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Re: [deal.II] does deal.ll support order 8 elements?

[陈敏]

Dear  ztdep ,

I changed the order of fe_q to 10 order in step-5(example/step-5/step5.cc:
line 119). After compile and run, it can work well. So the deal.ii at least
support 10 order Lagrange element.

Best regards
Chen

ztdep...@gmail.com  于2023年7月4日周二 20:26写道：

> does deal.ll support order 8 elements? what is the highest order element
> deal.ll support.
>
> --
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> 
> .
>

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Re: [deal.II] Issues about "could not locate a (sufficiently recent) version of deal.ii"

[陈敏]

Dear Zhengliu Zhou,

If you don't understand how to use cmake to install the dealii, changing
the installing approach to candi(https://github.com/dealii/candi) or spack(
https://github.com/dealii/dealii/wiki/deal.II-in-Spack) could be better.

Best,
Chen

Zhengliu Zhou  于2023年7月4日周二 14:10写道：

> Prof. Bangerth,
>   I am sorry to bother you again with such a trivial issue. Yet I
> still cannot resolve it. Below is a screenshot following your suggestion,
> but the same error remains. I suppose I didn't install something correctly?
> Thank you!
> [image: image.png]
>
> On Mon, Jul 3, 2023 at 9:22 PM Wolfgang Bangerth 
> wrote:
>
>> On 7/3/23 21:52, Zhengliu Zhou wrote:
>> > Thank you for your prompt reply. I fixed the two errors you
>> mentioned,
>> > but the error remained. Could it be caused by something else?
>>
>> Zhengliu,
>> what you are asked to provide is a path to a deal.II installation, not
>> "/path/to/deal.II". You need to replace this string by an actual
>> directory name.
>>
>> Best
>>   WB
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>
>> --
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>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>
>
> --
> Regards,
> Zhengliu
>
> --
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> .
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Re: [deal.II] the ordering of the vertex is changed after read in mesh

[陈敏]

Dear  ztdep ,

Given a schematic diagram could let me better understand the
question. Moreover, the sorting of grid nodes is generally positive in the
counterclockwise direction, and negative in the opposite direction.

Best
Chen

ztdep...@gmail.com  于2023年7月4日周二 19:49写道：

>
> I read in the mesh from "unv" file. but i found that the vertex ordering
> is changed.
> in the origin unv file :
> the vertex of a cell is
>  9 6 3 7.
> but in deall.ll it gives:
> 63  9  7
> I don't understand why this had happened.
>
> --
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> 
> .
>

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Re: [deal.II] Unable to refresh spack module

[陈敏]

Hi, Vinayak Vijay

I think installing dealii-9.4 with hdf5 using spack maybe some bug, you can
turn off the hdf5 by spack install dealii@9.4.0~hdf5.

Best
Chen

Vinayak Vijay  于2023年5月12日周五 17:23写道：

> Hello,
>
> In order to upgrade the version of dealii, i reinstalled the latest
> version of spack. I have been able to also install dealii using spack.
> However, when i use the command "spack module tcl refresh", i get the
> following error.
>
> ==> Error: Cannot use invalid module set default.Valid module set
> names are []
>
> If i just ignore this and perform "make run" of my code i get the
> following error:
>
> [ 14%] Linking CXX executable main
> /usr/bin/ld.gold: error: cannot find -lhdf5-shared
> collect2: error: ld returned 1 exit status
> make[3]: *** [CMakeFiles/main.dir/build.make:292: main] Error 1
> make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/main.dir/all] Error 2
> make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2
> make: *** [Makefile:137: run] Error 2
>
> I think these two errors are linked. Can someone point out what i should
> do now?
>
> Note: I was able to perfectly run dealii v9.3 befor this reinstallation.
>
> Thanks,
> Vinayak
>
> --
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> 
> .
>

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Re: [deal.II] Re: Trouble getting UMFPACK to work

[陈敏]

You can install lapack/blas of netlib version or openblas version or intel
mkl version

best
chen

On Wed, Jul 6, 2022 at 1:05 PM ME20D503 NEWTON  wrote:

> Dear Daniel,
> i am getting this while running cmake-DDEAL_II_WITH_UMFPACK=ON, can you
> please see  the highlighted output?
>
> 
>
>  No source or binary directory provided.  Both will be assumed to be the
>   same as the current working directory, but note that this warning will
>   become a fatal error in future CMake releases.
>
>
> -- This is CMake 3.16.3
> --
> -- Include /home/newton/fem/dealii-9.2.0/cmake/setup_external_macros.cmake
> -- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_add_flags.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_check_compiler_setup.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_check_cxx_compiler_bug.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_check_mpi_interface.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_clear_cmake_required.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_configure_feature.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_add_definitions.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_add_library.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_add_test.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_file.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_library.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_path.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_program.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_insource_setup_target.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_package_handle.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_pickup_tests.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_query_git_information.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_setup_target.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_decorate_with_stars.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_enable_if_links.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_enable_if_supported.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_enable_language_optional.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_evaluate_expression.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_expand_instantiations.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_filter_system_libraries.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_find_package.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_find_system_library.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_item_matches.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_purge_feature.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_register_feature.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_remove_duplicates.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_replace_flag.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_reset_cmake_required.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_set_if_empty.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_setup_source_list.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_setup_unity_target.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_strip_flag.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_switch_library_preference.cmake
> -- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_to_string.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_to_string_and_add_prefix.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_unset_if_changed.cmake
> -- Include
> /home/newton/fem/dealii-9.2.0/cmake/macros/macro_verbose_include.cmake
> --
> -- Include /home/newton/fem/dealii-9.2.0/cmake/setup_cached_variables.cmake
> -- Prepending ${CUDA_NVCC_FLAGS} to ${DEAL_II_CUDA_FLAGS}
> -- The CXX compiler identification is GNU 9.4.0
> -- The C compiler identification is GNU 9.4.0
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler A

Re: [deal.II] UMFPACK ISSUE.

[陈敏]

After run cmake, there is a log to tell you whether the UMFPACK have
configure with the dealii, you should give the log to us. The cmake log
file can be found in build/cmakefile/**.log as well.

Best
Chen

ME20D503 NEWTON  于2022年7月6日周三 12:38写道：

> Dear Luca,
>
> can help me out, what this error is trying to tell me?
>
> To call this function you need UMFPACK, but you configured deal.II
> without passing the necessary switch to 'cmake'. Please consult the
> installation instructions in doc/readme.html.
>
>
> On Tuesday, July 5, 2022 at 12:41:03 PM UTC+5:30 luca@gmail.com wrote:
>
>> This part of the message contains all the information you need to fix the
>> issue.
>>
>> Luca
>>
>> > Il giorno 5 lug 2022, alle ore 06:46, ME20D503 NEWTON <
>> me20...@iittp.ac.in> ha scritto:
>> >
>> > Additional information:
>> > To call this function you need UMFPACK, but you configured deal.II
>> > without passing the necessary switch to 'cmake'. Please consult the
>> > installation instructions in doc/readme.html.
>>
> --
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> 
> .
>

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[deal.II] python binding

[陈敏]

Dear all,

I compiled deal.ii with python binding. and I want to run the example of
step-49.ipynb. I have installed jupyter by pip3 install jupyter. Now, my
question is what should I do to run the step-49.ipynb？Add
"/path/todealii/lib/python3.8/site-packages/PyDealII/" to PYTHONPATH？

Best
Chen

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Re: [deal.II] Facing problem while installation deal.ii

[陈敏]

Dear Abhishek Nath Thakur

These are many examples showing how to use deal.ii, these are corresponding
documents on the official website
. But some of
these need external packages

not bundled in the deal.ii. you need to install them yourself. Finally, you
don't need to install all of the external packages, only the necessary
packages are needed according to your applications.

Best
Chen

Abhishek Nath Thakur  于2022年6月10日周五 15:57写道：

> Dear deal.ii users,
>
> I tried to install deal.ii 9.2.0 several times but every time i'm getting
> "dependencies not satisfied" (*image attached below*) due to which my
> installation stops at 52% everytime. I'm not sure if its an error or
> something else. So any help is appreciated
>
> Thank you in advance
>
>
> --
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> 
> .
>

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Re: [deal.II] [deal.ii] a small bug on the deal.ii document

[陈敏]

Hi Wolfgang,

The patch has been pushed to my fork "doc/fix_update_flags_h".

Best
Chen

Wolfgang Bangerth  于2022年6月1日周三 20:24写道：

> On 6/1/22 03:00, hkch...@gmail.com wrote:
> >
> > I think the following formula is wrong for the position of the first
> left
> > square bracket: \sum_{q}[\J^{-1}(\hat{x}_q) rather \J^{-1}[(\hat{x}_q)
> >
> >
> https://www.dealii.org/current/doxygen/deal.II/group__UpdateFlags.html#:~:text=Second%2C%20this%20integral%20is%20then%20approximated%20through%20quadrature.%20This%20yields%20the%20formula
> >
>
> Hi Chen:
> yes, good eye!
>
> Would you like to take the opportunity to write a patch to fix this and
> become
> a contributor to deal.II? The source file from which the documentation you
> point to is generate is
>doc/doxygen/headers/update_flags.h
> and instructions on writing patches can be found at
>https://github.com/dealii/dealii/wiki/Contributing
>
> If you don't want to write such a patch yourself, let us know and we'll
> fix it
> ourselves!
>
> Best
>   Wolfgang
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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>

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Re: [deal.II] compile dealii with intel oneAPI

[陈敏]

Thank you, Matthias Maier!

I block the tab of the intel oneAPI, just using the bundled tab, and it
work right! Thank you so much!
Best
Chen

On Fri, May 13, 2022 at 1:48 AM Matthias Maier  wrote:

> Hi,
>
> Something went wrong with your setup - your error message suggests that
> tbb had been set up from the bundled directory and you end up mixing
> bundled tbb with external oneapi tbb, which cannot work.
>
> Would you mind sending us the detailed.log file found in your build
> directory? It contains a listing of the entire configuration including
> all libraries.
>
> Best,
> Matthias
>
>
>
> On Thu, May 12, 2022, at 05:30 CDT, 陈敏  wrote:
>
> > Hi, everyone
> > I compile the deal.ii-9.3.3 with the intel oneAPI version 2022.1.1.119
> > (intel compiler, intel MPI, intel mkl and intel TBB). And I compiled it
> > with the ReleaseAndDebug version. so in the dir of the installed deal.ii,
> > there are examples of step-X.release and step-X.debug. I can run the
> > step-9.release and step-9.debug right and get the results, but if I
> compile
> > the step-9.cc like
> >
> > mkdir build
> > cd build
> > cmake ..
> >  make
> >
> >
> > there are some error:
> >
> > In file included from
> > /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/tbb_machine.h:117,
> >  from
> > /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/atomic.h:32,
> >  from
> > /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/pipeline.h:24,
> >  from
> > /home/tfblab/dealii_9_3_3/include/deal.II/base/work_stream.h:34,
> >  from
> > /home/tfblab/dealii_9_3_3/examples/step-9/step-9.cc:52:
> >
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/tbb_stddef.h:409:14:
> > error: expected type-specifier before ‘split’
> >   409 | operator split() const { return split(); }
> >   |  ^
> > In file included from
> > /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/pipeline.h:25,
> >  from
> > /home/tfblab/dealii_9_3_3/include/deal.II/base/work_stream.h:34,
> >  from
> > /home/tfblab/dealii_9_3_3/examples/step-9/step-9.cc:52:
> > /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/task.h:139:9:
> error:
> > reference to ‘task_group_context’ is ambiguous
> >   139 | task_group_context& my_context;
> >
> >
> > The detailed error log is attached
> > It seems that I compile the step-9 with bundled tbb, but I compile dealii
> > with the intel oneAPI TBB actually, and the step-9.release can run right.
> > So why is there the error?
> >
> > Best,
> > Chen
>
> --
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[deal.II] compile dealii with intel oneAPI

[陈敏]

Hi, everyone
I compile the deal.ii-9.3.3 with the intel oneAPI version 2022.1.1.119
(intel compiler, intel MPI, intel mkl and intel TBB). And I compiled it
with the ReleaseAndDebug version. so in the dir of the installed deal.ii,
there are examples of step-X.release and step-X.debug. I can run the
step-9.release and step-9.debug right and get the results, but if I compile
the step-9.cc like

mkdir build
cd build
cmake ..
 make


there are some error:

In file included from
/home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/tbb_machine.h:117,
 from
/home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/atomic.h:32,
 from
/home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/pipeline.h:24,
 from
/home/tfblab/dealii_9_3_3/include/deal.II/base/work_stream.h:34,
 from
/home/tfblab/dealii_9_3_3/examples/step-9/step-9.cc:52:
/home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/tbb_stddef.h:409:14:
error: expected type-specifier before ‘split’
  409 | operator split() const { return split(); }
  |  ^
In file included from
/home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/pipeline.h:25,
 from
/home/tfblab/dealii_9_3_3/include/deal.II/base/work_stream.h:34,
 from
/home/tfblab/dealii_9_3_3/examples/step-9/step-9.cc:52:
/home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/task.h:139:9: error:
reference to ‘task_group_context’ is ambiguous
  139 | task_group_context& my_context;


The detailed error log is attached
It seems that I compile the step-9 with bundled tbb, but I compile dealii
with the intel oneAPI TBB actually, and the step-9.release can run right.
So why is there the error?

Best,
Chen

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Re: [deal.II] SparseDirectMUMPS before deal.ii 8.3.0

[陈敏]

Thanks, Praveen.

I think the SparseDIrectMUMPS in dealii-8.2.1 don't need run program
with mpirun
-np N ./Program just ./Program and MUMPS will run parallel controlling by
itself. can I control it by myself?

Best,
Chen

Praveen C  于2022年4月21日周四 16:14写道：

> You need this
>
> https://dealii.org/current/doxygen/deal.II/classConditionalOStream.html
>
> On 21-Apr-2022, at 1:30 PM, hkch...@gmail.com  wrote:
>
> Hi, everyone.
>
> I have installed the deal.ii version 8.2.1 to use SparseDirectMUMPS
> replace SparseDirectUMFPACK. It seems that I can run it in parallel like 
> mpirun
> -np 2 ./MyProgram, but standard IO std::cout is used in my code, what
> should I do to print log in terminal only once?
>
> Best,
> Chen
>
>
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Re: [deal.II] Supported matrix/vector to LinearOperator

[陈敏]

Thanks, Luca.

I learn a lot. Since I use TrilinosWrapper::MPI::Vector,
TrilinosWrapper::SolveDirect can't use in linear_operator.
Since I can't get the precondition from linear_operator directly, I will
creat a inverse_operator without precondition.

Best,
Chen

Luca Heltai  于2022年4月20日周三 15:25写道：

> > While I can't get the entity of the matrix, I want to get the
> precondition directly from a linear_operator.
>
>
> > SparseMatrix M;
> > auto op_M = linear_operator(M);
> > TrilinosWrapper::PreconditionILU prec_M(op_M);
>
> This you cannot do. It is the other way around. Preconditioners need
> matrices (linear operator only store information about the *action* of the
> matrix, or of the various operations. Think of it this way: A*B*C*D_inv is
> still a linear operator. What matrix should this return to you?)
>
> This is how you should use it, if you want your preconditioner to be a
> linear operator:
>
> TrilinosWrapper::PreconditionILU prec_M_mat(M);
> auto op prec_M = linear_operator(M, prec_M_mat);
>
> > Can I get the entity of matrix G by TrilinosWrapper::MPI::SparseMatrix G
> = op_G; or the precondition of op_G?
>
> Nope. This, again, does not make sense.
>
> A Matrix is a linear operator (therefore you can create a linear operator
> from a matrix), but a linear operator is just an action (therefore you
> cannot create a matrix from a linear operator).
>
> L
>
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[deal.II] Supported matrix/vector to LinearOperator

[陈敏]

Hi everyone,

When solving a block matrix system, the LinearOperator is a useful tool. My
question is whether the LinearOpertor supports Matrix type (the same as the
Vector type) like PETSCWrapper::MPI::SparseMatrix or
TrilinosWrapper::MPI::SparseMatrix?

Best
Chen

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[deal.II] convert BlockSparseMatrix to SparseMatrix

[陈敏]

Hi everyone,

Is it possible to convert BlockSparseMatrix to SparseMatrix in deal.ii?
If so, Is it possible to convert LA::MPI::BlockSparseMatrix to
LA::MPI::SparseMatrix in deal.ii? and what should I do to dof_handler and
Sparse_pattern?

best,
chen

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[deal.II] convert linear_operator to SparseMatrix or get the inverse of linear_operator

[陈敏]

Hello team,
First, I got the linear_operator op_M(the matrix M). I want to get the
inverse of M named as M_inv. Because of the difficult of inverting the M
and that M is not symmetry, I used such codes to get M_inv:

> SparseMatrix M = op_M;

solver SolverGMRES> gmres(solver_control);

const auto M_inv = linear_operator(M, gmres, somepreconditioner);

 There are some questions on it：

   1. I don't know how to convert linear_operator to SparseMatrix,
   the code "SparseMatrix M = op_M;" get error.
   2. Whether could I get the M_inv directly by op_M using iterator method
   and don't need to convert linear_operator to SparseMatrix?
   3. Where I can find the support preconditioner for the iterator? it
   seems that the SolverGMRES don't supports the preconditoner of
   SparseILU and SparseDirectUMFPACK.

best regards
chen

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Re: [deal.II] Solving block system

[陈敏]

Thanks, Wolfgang Bangerth
PreconditionIdentity() is worked.
Best,
chen

Wolfgang Bangerth  于2022年4月6日周三 23:29写道：

> On 4/6/22 02:36, 陈敏 wrote:
> >   solver.solve(system_matrix, solution, system_rhs,
> > PETScWrappers::PreconditionNone());
> >
>
> Can you try to use PreconditionIdentity() instead?
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
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[deal.II] Solving block system

[陈敏]

Hi everyone,

I have a question on the solving of the block system that can solve a block
system without providing any preconditioner when using an iterator solver?
for example, PETScWrappers::PreconditionNone()?
Here is an error when I used the SolverFGMRES with PreconditionNone.
code:

> LA::MPI::BlockSparseMatrix   system_matrix;

LA::MPI::BlockVector   system_rhs, solution;


SolvorFGMRES solver(solver_control);

 solver.solve(system_matrix, solution, system_rhs,
> PETScWrappers::PreconditionNone());

error:

> /path/to/include/deal.II/lac/solver_hmres.h:1245:11: error: cannot comvert
> 'dealii::PETScWrappers::MPI::BlockVector'
> to'dealii::PETScWrappers::VectorBase&'

 1234preconditioner.vmult(z(j,x),v[j]);


Could anyone help me out？
Thank you！
Best,
chen

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[deal.II] Install error with p4est

[陈敏]

Dear all,

I want to use partition mesh with p4est, but p4est is difficult to install.
Can anyone give me some instructions on install p4est?

I install p4est following the install instructions from
https://dealii.org/current/external-libs/p4est.html*, *but still, some
errors occur:

> grep: /home/chen/p4est-build/FAST/src/p4est_config.h: 没有那个文件或目录
> Error: deal.II requires that p4est be built with zlib support. Please
> either ensure that zlib is installed in a standard location or add
> appropriate flags to LDFLAGS and CPPFLAGS to both calls to configure to
> describe where zlib's shared object files and headers are (e.g.,
> LDFLAGS="-L/path/to/shared-objects/" and
> CPPFLAGS="-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL -I/path/to/headers/").
>
the config.log is here.

One more question is that how to configure the p4est to appoint the
directory of zlib or the openmpi?

Best regards,
Chen

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config.log
Description: Binary data

Re: [deal.II] Re: Unable to Build Dealii on WSL Ubuntu 18.04

[陈敏]

Hi Sanket.Kulkarni,

Please check your deal.ii version, if it correspond with the deal.ii
version that prisms-plasticity used.
Since the header “…/tria_boundary_lib.h” have been removed in deal.ii 9.2.0.

Best,
Chen

On Wed, May 26, 2021 at 22:16 SANKET KULKARNI 
wrote:

> Hello,
> dealii is installed successfully, I want to install prisms-plasticity
> software and it is showing the following errors.
>
> Regards,
> Sanket.Kulkarni
>
> On Tue, May 25, 2021 at 4:04 PM Wolfgang Bangerth 
> wrote:
>
>> On 5/25/21 1:51 PM, SANKET KULKARNI wrote:
>> > I am not able to figure out how to resolve this issue since I am naive
>> in the
>> > Linux environment. Please can you help with this? My CMake command is
>> working
>> > fine. But the make install command is showing errors.
>>
>> Sanket,
>> what Marc is saying is that where you call
>>cmake -DCMAKE_INSTALL_PREFIX=/PATH/TO/DEALII/INSTALLATION .
>> you should replace /PATH/TO/DEALII/INSTALLATION by the name of the
>> directory
>> in which you want to install deal.II.
>>
>> That said, if you are new to linux, you would probably benefit from video
>> lectures 2.9 and 2.91 here:
>>https://www.math.colostate.edu/~bangerth/videos.html
>>
>> Best
>>   W.
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> --
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>> https://groups.google.com/d/forum/dealii?hl=en
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>>
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Re: [deal.II]Change from dealii-9.0.0 to deal.ii-9.2.0

[陈敏]

Dear David,
Thanks for your reply, it’s enough, I will read the document.
Sincerely,
Chen

On Fri, Apr 9, 2021 at 00:21 Wells, David  wrote:

> Hi Chen,
>
> No and yes - the same functionality has been moved into the Manifold
> classes, which are much more general than the old Boundary classes. For
> example, GridGenerator::hyper_ball automatically attaches a
> SphericalManifold to the boundary of the input Triangulation, which
> achieves the same result as attaching a HyperBallBoundary.
>
> More information is available at the module page:
>
> https://www.dealii.org/current/doxygen/deal.II/group__manifold.html
>
> Do you need to do anything more complex than generate a spherical
> geometry? If not, using SphericalManifold in place of HyperBallBoundary
> should do most of what you need to do (though, again, this is now done
> automatically by the grid generator functions).
>
> Best,
> David Wells
> ------
> *From:* dealii@googlegroups.com  on behalf of 陈敏
> 
> *Sent:* Thursday, April 8, 2021 12:14 PM
> *To:* dealii@googlegroups.com 
> *Subject:* [deal.II]Change from dealii-9.0.0 to deal.ii-9.2.0
>
> Dear all,
> From the website[The deal.II Library: Changes between Version 9.1.1 and
> 9.2.0
> <https://www.dealii.org/developer/doxygen/deal.II/changes_between_9_1_1_and_9_2_0.html>],
> I knew that  have been removed:
>
> Removed: The deprecated headers deal.II/grid/tria_boundary.h and
> deal.II/grid/tria_boundary_lib.h have been removed.
>
>
> In dealii-9.2.0, is there anyway to use some functions to realize the same
> function like the following codes which must include <
> deal.II/grid/tria_boundary_lib.h> and will work in dealii-9.0.0?
>
> *static* *const* HyperBallBoundary boundary(p,radius);
>   triangulation.set_boundary (80, boundary);
>
>
> Best,
> Chen
>
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[deal.II]Change from dealii-9.0.0 to deal.ii-9.2.0

[陈敏]

Dear all,
>From the website[The deal.II Library: Changes between Version 9.1.1 and
9.2.0
],
I knew that  have been removed:

Removed: The deprecated headers deal.II/grid/tria_boundary.h and
> deal.II/grid/tria_boundary_lib.h have been removed.


In dealii-9.2.0, is there anyway to use some functions to realize the same
function like the following codes which must include <
deal.II/grid/tria_boundary_lib.h> and will work in dealii-9.0.0?

*static* *const* HyperBallBoundary boundary(p,radius);
>   triangulation.set_boundary (80, boundary);


Best,
Chen

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Re: [deal.II] How to refine mesh in different field

[陈敏]

Dear Marc,

Thanks for your reply, I consider refinement and coarsening too.
I would read the step-46, I think it real helpful.

Best,
Chen

Marc Fehling  于2021年4月4日周日 上午11:54写道：

> Hi Chen,
>
> step-46
> 
> gives you a good example on how to perform grid refinement when coupling
> different kinds of equations in different parts of the domain. I would
> highly suggest reading this tutorial first.
>
> Do you only consider refinement or also coarsening? In case of coarsening,
> overwriting your error estimates with zeros (at the interface or anywhere
> else) is not a good solution as this would ultimately mean that these cells
> will be coarsened. It might make sense to set the values there to a
> different value here.
>
> Best,
> Marc
>
> On Saturday, April 3, 2021 at 8:48:48 AM UTC-6 hkch...@gmail.com wrote:
>
>> Dear deal.II community,
>>
>> In a fluid-structure interaction simulation, Computational domain was
>> divided into fluid domain and solid domain, for example, cell->material_id()
>> == 0 and cell->material_id() == 1(the way that deal.ii presents which
>> field the cell belong to) respectively, Now I want to refine the mesh in
>> fluid field and that in solid field separately in a fixed time interval.
>>
>> The tutorial guides, for example, tutorial step-40, show follow example
>> code:
>>
>> template 
>> void LaplaceProblem::refine_grid()
>> {
>> TimerOutput::Scope
>> 
>> t(computing_timer, "refine");
>> Vector
>> 
>> estimated_error_per_cell(triangulation.n_active_cells
>> 
>> ());
>> KellyErrorEstimator::estimate
>> 
>> (
>> dof_handler,
>> QGauss
>> (fe.degree
>> + 1),
>> std::map> ,
>> const Function
>>  *>(),
>> locally_relevant_solution,
>> estimated_error_per_cell);
>> parallel::distributed::GridRefinement::refine_and_coarsen_fixed_number
>> 
>> (
>> triangulation, estimated_error_per_cell, 0.3, 0.03);
>> triangulation.execute_coarsening_and_refinement
>> 
>> ();
>> }
>>
>> I think the code refines on the whole mesh domain, for my purpose, how to
>> change the code to meet me?
>> Could anyone help me out?
>>
>> Sincerely,
>> Chen
>>
> --
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> 
> .
>

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[deal.II] How to refine mesh in different field

[陈敏]

Dear deal.II community,

In a fluid-structure interaction simulation, Computational domain was
divided into fluid domain and solid domain, for example, cell->material_id()
== 0 and cell->material_id() == 1(the way that deal.ii presents which field
the cell belong to) respectively, Now I want to refine the mesh in fluid
field and that in solid field separately in a fixed time interval.

The tutorial guides, for example, tutorial step-40, show follow example
code:

template 
void LaplaceProblem::refine_grid()
{
TimerOutput::Scope

t(computing_timer, "refine");
Vector

estimated_error_per_cell(triangulation.n_active_cells

());
KellyErrorEstimator::estimate

(
dof_handler,
QGauss
(fe.degree +
1),
std::maphttps://dealii.org/developer/doxygen/deal.II/classunsigned_01int.html>,
const Function
 *>(),
locally_relevant_solution,
estimated_error_per_cell);
parallel::distributed::GridRefinement::refine_and_coarsen_fixed_number

(
triangulation, estimated_error_per_cell, 0.3, 0.03);
triangulation.execute_coarsening_and_refinement

();
}

I think the code refines on the whole mesh domain, for my purpose, how to
change the code to meet me?
Could anyone help me out?

Sincerely,
Chen

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[deal.II] Lapack Link Problem

[陈敏]

Hello all,
When I want to compile dealii with lapack ,
whatever how I set the dir of lapck, the CMAKE can;t find the lapack.(I
also set the lapack_dir in ccmake) error is following:
-

  Could not find the lapack library!

  Please ensure that a suitable lapack library is installed on your
computer.

  If the library is not at a default location, either provide some hints for
  autodetection,

  $ LAPACK_DIR="..." cmake <...>
  $ cmake -DLAPACK_DIR="..." <...>

  or set the relevant variables by hand in ccmake.

-
I run the command at shell:

sudo find / -name "lapack"

I get the path as follow:

/usr/lib/x86_64-linux-gnu/lapack

/home/chen/.local/lapack

first lapack maybe the version that installed through

sudo apt-get install libblas-dev liblapack-dev

second lapack is the version compiled by myself
there are some share lib in the dir:

:/usr/lib/x86_64-linux-gnu/lapack$ ls
liblapack.a  liblapack.so  liblapack.so.3  liblapack.so.3.9.0
~/.local/lapack$ ls
cmake  libblas.a  liblapack.a  pkgconfig

Could anyone help me?
Best,
Chen

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[deal.II] [deal.ii]mesh import problem

[陈敏]

Hi Deal.ii team,

I want to import the mesh file exported by gmsh.

First,I export mymodel.geo file to vtk file in gmsh, automatically,the
first line of the vtk is “# vtk DataFile Version 2.0” , so I change it to “ #
vtk DataFile Version 3.0”. However, an error is reported as follow:

libc++abi.dylib: terminating with uncaught exception of type
dealii::StandardExceptions::ExcMessage:

An error occurred in line <286> of file

in function
void dealii::GridIn<2, 2>::read_vtk(std::istream &) [dim = 2, spacedim
= 2]
The violated condition was:
false
Additional information:
While reading VTK file, unknown cell type encountered


*Then, I find out the CELLTYPE of VERTEX is recorded, Consequently, I
deleted the point record in CELLS and CELL_TYPES. But there are still
errors.*

libc++abi.dylib: terminating with uncaught exception of type
dealii::StandardExceptions::ExcNotImplemented:

An error occurred in line <257> of file

in function
void dealii::GridIn<2, 2>::read_vtk(std::istream &) [dim = 2, spacedim
= 2]
The violated condition was:
subcelldata.boundary_lines.size() == 0
Additional information:
You are trying to use functionality in deal.II that is currently not
implemented. In many cases, this indicates that there simply didn't appear
much of a need for it, or that the author of the original code did not have
the time to implement a particular case. If you hit this exception, it is
therefore worth the time to look into the code to find out whether you may
be able to implement the missing functionality. If you do, please consider
providing a patch to the deal.II development sources (see the deal.II
website on how to contribute).


*Other format are not imported successfully, for example, the inp format
get the errors as follows:*

Exception on processing internal UCD data:


An error occurred in line <857> of file

in function
void dealii::GridIn<2, 2>::read_ucd(std::istream &, const bool) [dim =
2, spacedim = 2]
The violated condition was:
false
Additional information:
While creating cell 0, you are referencing a vertex with index 0 but no
vertex with this index has been described in the input file.


libc++abi.dylib: terminating with uncaught exception of type
dealii::StandardExceptions::ExcMessage:

An error occurred in line <1064> of file

in function
void dealii::GridIn<2, 2>::read_abaqus(std::istream &, const bool) [dim
= 2, spacedim = 2]
The violated condition was:
false
Additional information:
Internal conversion from ABAQUS file to UCD format was unsuccessful.
More information is provided in an error message printed above. Are you
sure that your ABAQUS mesh file conforms with the requirements listed in
the documentation?


*Could anyone let me known how to import mesh ?*

Thank you,
Chen

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