Re: [deal.II] Error in the second derivative of solution...?

[hanks0227]

Dr. Wolfgang Bangerth,

Thank you very much for your kind reply.

But, could I have one more question?

>
> I don't know whether the problem really comes from that, but you can't 
> take 
> the second derivative of a finite element solution without problem. The 
> issue 
> is that it exists, of course, in the interior of elements.


I just had a good idea for the calculation q without second derivative 
yesterday.

But I need the surface integral of divergence of f(R,solution)*grad_solution

where f is function of position and solution.


So my new question is , in deal.II, could I get local divergence of certain 
function to get surface integral?

Thank you.

Kyusik.


>
>
>
>

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Re: [deal.II] Error in the second derivative of solution...?

[Wolfgang Bangerth]

On 05/14/2017 01:57 AM, hanks0...@gmail.com wrote:


I guess this problem comes from the second derivatives of solution.


I don't know whether the problem really comes from that, but you can't take 
the second derivative of a finite element solution without problem. The issue 
is that it exists, of course, in the interior of elements. But it is a 
delta-function like thing at the interfaces between cells because the finite 
element solution is continuous but not continuously differentiable across the 
interface (it has a "kink"), and consequently the second derivative consists 
of delta functions. I suppose you are not taking them into account in your 
formulation.


If you do need second derivatives, you need to either use a C^1 element (quite 
difficult to do), or use a mixed formulation in which you rewrite the equation 
 -Delta q = f  into

  u + nabla q = 0
  -div u  = -f
and then use a continuous element for the variable u. This way u=-grad q,
and Delta q = -div u, which you can compute because u is continuous.

Best
 W.

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   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Getting error during cmake configuration step and later during make run

[Vikram Bhamidipati]

I am new to dealii. I installed deal.II 8.5.0 using the dmg package from 
dealii website on mac OS Sierra. When I tried to configure I got this error:

CMake Error at 
/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/Cellar/cmake/3.7.2/share/cmake/Modules/CMakeTestCXXCompiler.cmake:44
 
(message):
  The C++ compiler
  "/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/mpicxx" is
  not able to compile a simple test program.

  It fails with the following output:

   Change Dir: 
/Users/vikramb/Documents/dealII/svn_co/deal.II/examples/step-1/CMakeFiles/CMakeTmp

  

  Run Build Command:"/usr/bin/make" "cmTC_5fce3/fast"

  /Applications/Xcode.app/Contents/Developer/usr/bin/make -f
  CMakeFiles/cmTC_5fce3.dir/build.make CMakeFiles/cmTC_5fce3.dir/build

  Building CXX object CMakeFiles/cmTC_5fce3.dir/testCXXCompiler.cxx.o

  /Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/mpicxx -o
  CMakeFiles/cmTC_5fce3.dir/testCXXCompiler.cxx.o -c
  
/Users/vikramb/Documents/dealII/svn_co/deal.II/examples/step-1/CMakeFiles/CMakeTmp/testCXXCompiler.cxx


  make[1]: *** [CMakeFiles/cmTC_5fce3.dir/testCXXCompiler.cxx.o] Illegal
  instruction: 4

  make: *** [cmTC_5fce3/fast] Error 2

To workaround this I changed the CXX compiler option though ccmake. I was 
able to successfully configure and build. However when I ran I got this 
error:

make[3]: *** [CMakeFiles/run] Illegal instruction: 4
make[2]: *** [CMakeFiles/run.dir/all] Error 2
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
make: *** [run] Error 2

Can anyone tell what I am not doing right?

Thanks,
Vikram

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[deal.II] Re: Step-42

[benhour . amirian66]

Hi Daniel,
I tried with version 8.4.1 and also the new version, 8.5, however it does 
not run at all. The errors that I got are given as below:
make[3]: *** [CMakeFiles/run] Error 1
make[2]: *** [CMakeFiles/run.dir/all] Error 2
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
make: *** [run] Error 2

Thanks,
Ben

On Sunday, May 14, 2017 at 5:25:36 PM UTC-5, Daniel Arndt wrote:
>
> Ben,
>
> I really appreciate it if you let me know how I can run step 42 because 
>> whenever I ran it, I got two error without any information about that. This 
>> is exactly the same with "goal oriented mesh adaptivity in elastoplasticity 
>> proiblems" example which is written by Shahram. Looking forward to hearing 
>> from you.
>>
> Which version of deal.II are you using? Can you provide us with the errors 
> you get?
>
> Best,
> Daniel
>

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[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

[Daniel Arndt]

Hamed,
 

> To the best of my knowledge, GridGenerator::subdivided_hyper_rectangle 
>> generates a coarsest level mesh (i.e. all cells have level = 0) with the 
>> given discretisation in each coordinate direction. 
>>
>
> It seems that GridGenerator::subdivided_hyper_rectangle needs repetition 
> argument and complete mesh generation in one step. so cells have level=1 .
>
As far as I see, GridGenerator::subdivided_hyper_rectangle only calls 
"Triangulation::create_triangulation" and hence creates a coarse 
triangulation.
Can you confirm either?

Best,
Daniel

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[deal.II] Re: Step-42

[Daniel Arndt]

Ben,

I really appreciate it if you let me know how I can run step 42 because 
> whenever I ran it, I got two error without any information about that. This 
> is exactly the same with "goal oriented mesh adaptivity in elastoplasticity 
> proiblems" example which is written by Shahram. Looking forward to hearing 
> from you.
>
Which version of deal.II are you using? Can you provide us with the errors 
you get?

Best,
Daniel

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[deal.II] Re: Adding periodicity to a thin sample with one element in thickness direction

[Hamed Babaei]

Dear Jean-Paul,

Thank you for your prompt help.

Although I don't really understand your specific question, I am guessing 
> that you were wondering if its possible to use the "repetitions" parameter 
> to bias the initial mesh gradation before adding periodicity (since the 
> periodic face pairs must be chosen on the on the coarsest mesh).
>
 
Yes, you are right. In fact, I do not want to refine the mesh but generate 
the initial mesh in away that mesh discritisation is done after adding 
periodicity.
 

> To the best of my knowledge, GridGenerator::subdivided_hyper_rectangle 
> generates a coarsest level mesh (i.e. all cells have level = 0) with the 
> given discretisation in each coordinate direction. 
>

It seems that GridGenerator::subdivided_hyper_rectangle needs repetition 
argument and complete mesh generation in one step. so cells have level=1 .
 

> You could also consider using anisotropic refinement (see step-30 
> ), but this 
> feature is not so commonly used (as far as I can tell) and it is not 
> supported by all Triangulations 
> 
> .
>

Since my code is parallel, I am wondering what is the alternative for me.


Thanks and regards,
Hamed
 

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Re: [deal.II] Re: method/function from Triangulation class that returns a vertex

[Bhanu Teja]

Thanks for the clarification Prof. Bangerth and Prof. Jean Paul.

On Friday, May 12, 2017 at 6:16:08 PM UTC+5:30, Wolfgang Bangerth wrote:
>
> On 05/12/2017 02:22 AM, Jean-Paul Pelteret wrote: 
> > 
> > By Vertex, I meant the geometric quantity only. As I have used first 
> order 
> > scalar basis functions i.e FE_Q<2> fe(1) to distribute the degrees 
> of 
> > freedom by dof_handler.distribute_dofs(fe);. I expect 'n_dofs = 
> > n_vertices' and also the finite element nodes to be residing 
> directly on 
> > the geometric vertices.  So when I use  'vertices = 
> > triangulation.get_vertices();' I expect the number of 
> elements(Points) in 
> > vertices array to be equal to the number of nodes(geometric 
> vertices) in 
> > my mesh. 
> > 
> > 
> > This is all correct. 
>
> But only somewhat. While it is true that their *number* is the same, 
> vertices 
> are not necessarily numbered consecutively. So the largest vertex index is 
> not 
> necessarily equal to the largest dof index. And they are definitely not 
> numbered so that vertex_index=dof_index. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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[deal.II] Step-42

[benhour . amirian66]

Dear All,
I really appreciate it if you let me know how I can run step 42 because 
whenever I ran it, I got two error without any information about that. This 
is exactly the same with "goal oriented mesh adaptivity in elastoplasticity 
proiblems" example which is written by Shahram. Looking forward to hearing 
from you.

Thanks,
Ben

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Re: [deal.II] How to implement total remeshing

[Wolfgang Bangerth]

On 05/14/2017 01:01 AM, Amir Pasha wrote:

Thank you. Is there any representative example for Mesquite application or
total remeshing?


None in deal.II that I know of. But Mesquite surely has some tutorials.

Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Re: Crack propagation

[Jack]

Hi Daniel,

Thank you very much!

Regards,

Jack

在 2017年5月14日星期日 UTC+8下午5:07:26，Daniel Arndt写道：
>
> Jack,
>
> have a look at https://github.com/tjhei/cracks
>
> Best,
> Daniel
>
> Am Freitag, 12. Mai 2017 07:57:06 UTC+2 schrieb Jack:
>>
>> Hi S. A. Mohseni,
>>
>> I'm also interested on the cracking mechanics, where is such an example 
>> for crack propagation ? 
>>
>> Thanks !
>>
>> 在 2017年3月30日星期四 UTC+8下午9:13:16，Seyed Ali Mohseni写道：
>>>
>>> Dear Timo Heister and Thomas Wick,
>>>
>>> I am trying to run your phase-field crack propagation example, namely 
>>> the single edge notched tension test, with less than 9 Gauss points. 
>>> Hence, the fe variable is initialized using FE_Q(degree) where 
>>> degree cannot be 0. This means degree should always be >1 here in order to 
>>> make things work, but how can one compute the examples with 1 or 4 Gauss 
>>> points? Is the code not suited for what I am trying to achieve or where are 
>>> the parts I have to change in order to make it work for less integration 
>>> points. To be honest, I don't even see the point of having 9 integration 
>>> points for a 4-noded quadrilateral or am I overseeing something?
>>>
>>> Thank you in advance.
>>>
>>> Kind regards,
>>> S. A. Mohseni  
>>>
>>

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Re: [deal.II] AssertDimension (partition_blocks[partition], task_info.n_blocks) when calling MatrixFree::reinit() for finest level in GMG

[Denis Davydov]

Correct!

> On 14 May 2017, at 10:50, Daniel Arndt  
> wrote:
> 
> Denis,
> 
> this is solved by https://github.com/dealii/dealii/pull/4376, isn't it?
> 
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[deal.II] Re: Crack propagation

[Daniel Arndt]

Jack,

have a look at https://github.com/tjhei/cracks

Best,
Daniel

Am Freitag, 12. Mai 2017 07:57:06 UTC+2 schrieb Jack:
>
> Hi S. A. Mohseni,
>
> I'm also interested on the cracking mechanics, where is such an example 
> for crack propagation ? 
>
> Thanks !
>
> 在 2017年3月30日星期四 UTC+8下午9:13:16，Seyed Ali Mohseni写道：
>>
>> Dear Timo Heister and Thomas Wick,
>>
>> I am trying to run your phase-field crack propagation example, namely the 
>> single edge notched tension test, with less than 9 Gauss points. 
>> Hence, the fe variable is initialized using FE_Q(degree) where 
>> degree cannot be 0. This means degree should always be >1 here in order to 
>> make things work, but how can one compute the examples with 1 or 4 Gauss 
>> points? Is the code not suited for what I am trying to achieve or where are 
>> the parts I have to change in order to make it work for less integration 
>> points. To be honest, I don't even see the point of having 9 integration 
>> points for a 4-noded quadrilateral or am I overseeing something?
>>
>> Thank you in advance.
>>
>> Kind regards,
>> S. A. Mohseni  
>>
>

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Re: [deal.II] AssertDimension (partition_blocks[partition], task_info.n_blocks) when calling MatrixFree::reinit() for finest level in GMG

[Daniel Arndt]

Denis,

this is solved by https://github.com/dealii/dealii/pull/4376, isn't it?

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Re: [deal.II] How to implement total remeshing

[Amir Pasha]

Thank you. Is there any representative example for Mesquite application or 
total remeshing?

On Saturday, May 13, 2017 at 6:43:50 PM UTC+4:30, Wolfgang Bangerth wrote:
>
> On 05/13/2017 01:08 AM, Amir Pasha wrote: 
> > Dear all 
> > 
> > I want to implement a total remeshing technique when large deformations 
> are 
> > involved. I am using the updated Lagrangian method so that the 
> integration is 
> > performed at current configuration (mesh is moved to current 
> configuration) to 
> > simulate a material damage process. Due to material damage, deformation 
> is 
> > localized in a narrow band and mesh is distorted in the damaged area. 
> What are 
> > the general step for implementation total remeshing? 
> > 
> > 1) Create a new mesh based on the current configuration using an 
> external 
> > library such as gmesh 
> > 2) Move the old mesh to the initial configuration 
> > 3) Transfer data to the new mesh 
>
> Yes, these are the steps. None of them are entirely trivial, though for 
> the 
> last step you can at least use the FEFieldFunction class if you store both 
> the 
> old and the new mesh. 
>
> You may also want to think about using a mesh improvement library instead 
> of 
> completely remeshing. Take a look at the Mesquite library that's part of 
> Trilinos, for example. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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