Re: [deal.II] Re: Trouble with VisIt 2.11

2016-11-02 Thread Praveen C 
So the VisIt people said they forgot to include the xdmf plugin in v2.11
and we have to wait for the next release to get it back. Meanwhile an
alternative is suggested, see

https://elist.ornl.gov/pipermail/visit-users/2016-November/019322.html

Best
praveen


On Tue, Nov 1, 2016 at 4:07 PM, Praveen C  wrote:

>
> On Thu, Oct 27, 2016 at 12:53 PM, 'Uwe Köcher' via deal.II User Group <
> dealii@googlegroups.com> wrote:
>
>> Dear Praveen,
>>
>> I do not use visit, but deal.II + hdf5 + paraview. Your attached file can
>> be opened with paraview.
>> But this does not mean, that we have a correct implementation within
>> deal.II, but I suppose it has
>> something to do with your visit versions or installations.
>>
>> Kind regards
>>   Uwe
>>
>
> Thanks Uwe for testing with paraview. I have Paraview but dont really like
> it. I used the VisIt mac binary, so it may be a bug in VisIt itself. For
> now I have gone back to previous version of VisIt. I will post to visit
> list about this.
>
> Best
> praveen
>

-- 
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.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] GridGeneration

2016-11-02 Thread Wolfgang Bangerth 

On 11/02/2016 05:54 PM, benhour.amiria...@gmail.com wrote:

I want to use half_hyper_ball for my domain. Unfortunately, I cannot refine
the mesh around the center. I attached my geometry below. The code that I am
using has been written as follows:
Point <2> center;
  const double radius = 30e-9;
  GridGenerator::half_hyper_ball(triangulation,
center,
radius);
  triangulation.set_all_manifold_ids(0);
  const SphericalManifold<2> manifold_description(center);
  triangulation.set_manifold (0, manifold_description);
  GridTools::copy_boundary_to_manifold_id(triangulation);
  triangulation.refine_global (4);
  triangulation.set_manifold (0);
  const double angle = numbers::PI / 2.0;
  GridTools::rotate (angle, triangulation);

I have doubt related to the fact that the SpericalManifold cannot be used for
the cell containing the center of the coordinate system and consider it as a
singular point. It would be very kind of you if you let me know what I should
use instead?


Benhour,
there is a lengthy discussion of how to deal with essentially your situation 
in the "Possibilities for extensions" section of step-6.


Best
 W.

--

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
--- 
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.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Re: hp convergence for non-linear solver.

2016-11-02 Thread Wolfgang Bangerth 

On 11/02/2016 07:17 PM, Jaekwang Kim wrote:


I'd like check the visualized error per cell.
Is there any module in deal.ii that enables this...?



Yes, you just need to create a vector with as many entries as there are cell 
(e.g., the output of VectorTools::integrate_difference) and attach that to the 
DataOut object you have. step-27 shows how to do that, but it in essence works 
just like for vectors that have as many entries as there are DoFs.


Best
 W.

--

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
--- 
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.
For more options, visit https://groups.google.com/d/optout.

[deal.II] Re: How can I find the neighbouring element if I'm on a given face in a given cell?

2016-11-02 Thread smetcalfephd 
That looks good! Thanks for the help.

Stephen

On Wednesday, 2 November 2016 18:36:02 UTC+1, Bruno Turcksin wrote:

> Stephen,
>
> On Wednesday, November 2, 2016 at 1:20:58 PM UTC-4, smetca...@gmail.com 
>  wrote:
>
>> I'm currently implementing a blow-up problem with space-time adaptivity 
>> controlled by a derived pointwise a posteriori error bound and I'm having 
>> trouble implementing the estimator (previously, I just used meshworker and 
>> it did most of the work for me but you cannot use such an approach for 
>> pointwise spatial estimators). I've got it correctly looping over cells and 
>> also got it looping over all faces and correctly calculating the value of 
>> the estimator on the *boundary faces*, however, I'm not entirely sure 
>> how if I'm on a given face in a given cell I can obtain the values I need 
>> from the neighbouring element. In particular, I'm not sure how to locate 
>> the neighbour (I think once I have it I can work over it with FEFaceValues 
>> without any issues!). I'm sure the answer is obvious but I just can't find 
>> it.
>>
> You can use neighbor 
> http://www.dealii.org/8.4.1/doxygen/deal.II/classCellAccessor.html#acec7a480d2bcdd506a3350dd9ec3cfeb
>  
> to get the neighbor of a cell. Is that what you are looking for?
>
> Best,
>
> Bruno
>

-- 
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.
For more options, visit https://groups.google.com/d/optout.

[deal.II] Re: How can I find the neighbouring element if I'm on a given face in a given cell?

2016-11-02 Thread Bruno Turcksin 
Stephen,

On Wednesday, November 2, 2016 at 1:20:58 PM UTC-4, smetcalfe...@gmail.com 
wrote:

> I'm currently implementing a blow-up problem with space-time adaptivity 
> controlled by a derived pointwise a posteriori error bound and I'm having 
> trouble implementing the estimator (previously, I just used meshworker and 
> it did most of the work for me but you cannot use such an approach for 
> pointwise spatial estimators). I've got it correctly looping over cells and 
> also got it looping over all faces and correctly calculating the value of 
> the estimator on the *boundary faces*, however, I'm not entirely sure how 
> if I'm on a given face in a given cell I can obtain the values I need from 
> the neighbouring element. In particular, I'm not sure how to locate the 
> neighbour (I think once I have it I can work over it with FEFaceValues 
> without any issues!). I'm sure the answer is obvious but I just can't find 
> it.
>
You can use neighbor 
http://www.dealii.org/8.4.1/doxygen/deal.II/classCellAccessor.html#acec7a480d2bcdd506a3350dd9ec3cfeb
 
to get the neighbor of a cell. Is that what you are looking for?

Best,

Bruno

-- 
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.
For more options, visit https://groups.google.com/d/optout.

[deal.II] How can I find the neighbouring element if I'm on a given face in a given cell?

2016-11-02 Thread smetcalfephd 

I'm currently implementing a blow-up problem with space-time adaptivity 
controlled by a derived pointwise a posteriori error bound and I'm having 
trouble implementing the estimator (previously, I just used meshworker and 
it did most of the work for me but you cannot use such an approach for 
pointwise spatial estimators). I've got it correctly looping over cells and 
also got it looping over all faces and correctly calculating the value of 
the estimator on the *boundary faces*, however, I'm not entirely sure how 
if I'm on a given face in a given cell I can obtain the values I need from 
the neighbouring element. In particular, I'm not sure how to locate the 
neighbour (I think once I have it I can work over it with FEFaceValues 
without any issues!). I'm sure the answer is obvious but I just can't find 
it.

Thanks for any help!

Stephen

-- 
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.
For more options, visit https://groups.google.com/d/optout.

[deal.II] Re: Extra layer around mesh

2016-11-02 Thread Daniel Arndt 
Joel,

Same error with your changes. I searched for subdivided in 
> http://www.dealii.org/developer/doxygen/deal.II/changes_between_8_3_and_8_4.html
>  
> and found under specific improvements, that subdivided_parallelepiped 
> produced the wrong boundary indicators. Could this be the reason, why it 
> doesnt work? Perhaps I need to update the version Im running.
>
Yes, this makes perfect sense. Either you update or you set the boundary 
indicators correctly yourself.

Best,
Daniel

-- 
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.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Changing geometry

2016-11-02 Thread A Banerjee 
I got my mistake. 

Thanks
Atanu

-- 
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.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Changing geometry

2016-11-02 Thread A Banerjee 
Yes. I agree. This was stupid question. 
Thanks
Atanu

-- 
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.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

2016-11-02 Thread Hamed Babaei 
Dear Wolfgang,

I wrote the sequential code first and It converged to the exact solution 
using SolverCG and SSOR preconditioner. 
However, the parallel code diverges at the first call to SolverCG but using 
GMRES or Bicgstab it works though up to 15 DoFs not more.

First and the most important question to me is what parallelization does to 
my system_matrix that it is not solved by SolverCG anymore. I guess the 
source of the problem is there.
Second, why it is solved by GMRES and Bicgstab for few DoFs (up to 15) 
and not more( for example, 1 million). 

It seems that my system_matrix is not s.p.d any more although in sequential 
code it was. 

Thanks for your time,
Hamed

On Wednesday, November 2, 2016 at 8:00:23 AM UTC-5, Wolfgang Bangerth wrote:
>
> On 11/01/2016 10:31 AM, Hamed Babaei wrote: 
> > 
> > I mean non of the standard preconditioners helped to make it converged. 
>
> Like Bruno mentioned, if the standard preconditioners don't work, then you 
> will need to think about more complicated ones. Take a look at my video 
> lectures on preconditioners, for example. 
>
> There is of course also the possibility that your matrix is not correct 
> and 
> indeed singular. In that case, you *have* to expect problems. Have you 
> verified that your numerical solutions converge to the exact ones for 
> small 
> problems? 
>
> 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+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

2016-11-02 Thread Wolfgang Bangerth 

On 11/01/2016 10:31 AM, Hamed Babaei wrote:


I mean non of the standard preconditioners helped to make it converged.


Like Bruno mentioned, if the standard preconditioners don't work, then you 
will need to think about more complicated ones. Take a look at my video 
lectures on preconditioners, for example.


There is of course also the possibility that your matrix is not correct and 
indeed singular. In that case, you *have* to expect problems. Have you 
verified that your numerical solutions converge to the exact ones for small 
problems?


Best
 W.

--

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
--- 
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.
For more options, visit https://groups.google.com/d/optout.

Re: [deal.II] Re: hp convergence for non-linear solver.

2016-11-02 Thread Wolfgang Bangerth 

On 11/01/2016 11:06 PM, Jaekwang Kim wrote:


do you have any other idea?



Output the errors per cell and visualize. Is there a pattern? Is the error 
localized on the boundary, for example?


Best
 W.

--

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
--- 
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.
For more options, visit https://groups.google.com/d/optout.