Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Daniel Arndt]

Hamed,

running your code with a Trilinos installation alone fails for me in line 
1617 with

An error occurred in line <279> of file 
 in function
void dealii::TrilinosWrappers::SolverBase::do_solve(const 
dealii::TrilinosWrappers::PreconditionBase&)
The violated condition was:
false
Additional information:
AztecOO::Iterate error code -2: numerical breakdown

and the same for no preconditioner. The same holds for PETSc. It seems that 
you should review if this matrix is assembled correctly and that CG is 
appropriate, i.e. is this matrix symmetric and positive definite?

I can't reproduce your error

"PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range"

running with a developer version.

Best,
Daniel


Am Montag, 17. Oktober 2016 04:47:32 UTC+2 schrieb Wolfgang Bangerth:
>
> On 10/16/2016 03:46 PM, Hamed Babaei wrote: 
> > Another point I need to mention is that I had the same problem when as 
> my 
> > first try of parallelization, I paralleled a much simpler code, the 
> step-25, 
> > based on the step-40 . 
> > I received the same Segmentation Violation error from Petsc. At that 
> time, I 
> > replaced PreconditionerAMG with PreconditionerJacobi and the problem 
> resolved. 
>
> This does not help right now, but as a general rule, it is far simpler to 
> debug things when you have a small, simple program that when you have a 
> large, 
> complicated one. In your case, you had a problem you didn't understand, 
> and 
> you chose to address it in a way that papered over it, rather than 
> properly 
> fixed it based on an understanding of what is going on. It is a truism 
> that 
> this sort of issue will come back at some time. 
>
> In other words, if you have a problem, debug it until you understand what 
> the 
> problem is, and then fix it the right way. Don't paper over it. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] trouble running new step-55

['Franck Kalala' via deal.II User Group]

Thank you Martin


Where is developer version 8.5.0-pre?
I installed dealii using candi, which I find very easy.
candi can install dev version 8.5.0-pre?

Cheers

Franck

2016-10-17 12:29 GMT+02:00 Martin Kronbichler 
:

> Dear Franck,
>
> I justed checked on my machine and it works both on an installation that
> only provides Trilinos and on an installation that has both (and where
> PETSc is selected). It looks like your installation is 8.4.0 whereas I
> think that step-55 requires the current developer version 8.5.0-pre. The
> compile error complains about missing classes in the LA::MPI namespaces
> which might be related to some changes we have done recently. Can you check
> with the developer version?
>
> Best,
> Martin
>
> On 17.10.2016 12:12, 'franck75' via deal.II User Group wrote:
>
> I am having trouble when trying to  run new step-55.
>
> I am having a very long error message. Here is one piece (see attached
> file).
>
> Does anyone able to run it?
>
> Best
> Franck
>
>
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[deal.II] Re: Solution Components of a Vector valued problem

[Jean-Paul Pelteret]

Dear Lisa,

A quick google search returned GridTools::find_cells_adjacent_to_vertex 

 
. Is this what you're looking for?

Regards,
J-P

On Monday, October 17, 2016 at 1:01:57 PM UTC+2, Lisa Collins wrote:
>
> Hello,
>
> Thanks for the reply.
> I did it with iteration over all cells and vertexes of each cell.
> Is there any effective way to do it without iteration over cells? 
> For example something like inverse of cell->vertex_dof_index 
> 
>  
> which gets the global index and points to the first cell which which the 
> corresponding index belongs to.
>
> Thanks.
> Lisa
>
> On Friday, October 14, 2016 at 1:36:19 PM UTC+2, Jean-Paul Pelteret wrote:
>>
>> Dear Lisa,
>>
>> You should have a look at some of the previous discussions on the use of 
>> the cell->vertex_dof_index 
>> 
>>  function 
>> (as well as its documentation 
>> );
>>  
>> this provides an easy link between vertices and degrees of freedom.
>>
>> Regards,
>> J-P
>>
>> On Friday, October 14, 2016 at 1:20:29 PM UTC+2, Lisa Collins wrote:
>>>
>>> Hallo,
>>> Thanks for both replies.
>>> In general, from a solution vector, how can I extract u_x, u_y, and T 
>>> nodal values corresponding to a specific node?
>>> Best regards.
>>> Lisa
>>>
>>> On Thursday, October 13, 2016 at 1:05:08 PM UTC+2, Lisa Collins wrote:

 Hello,

 Dealing with vector valued problems in deal ii is a bit confusing for 
 me.
 I have a question regarding the solution vector (S).
 If we have a problem with 20 nodes and 3 dofs per node (u_x , u_y , and 
 T temperature) can we always say that:

 S[0] = u_x of node A
 S[1] = u_y of node A
 S[2] = T of node A

 S[3] = u_x of node B
 S[4] = u_y of node B
 S[5] = T of node B

 and so on.

 Thanks.
 Lisa

>>>

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[deal.II] Re: Solution Components of a Vector valued problem

[Lisa Collins]

Hello,

Thanks for the reply.
I did it with iteration over all cells and vertexes of each cell.
Is there any effective way to do it without iteration over cells? 
For example something like inverse of cell->vertex_dof_index 

 
which gets the global index and points to the first cell which which the 
corresponding index belongs to.

Thanks.
Lisa

On Friday, October 14, 2016 at 1:36:19 PM UTC+2, Jean-Paul Pelteret wrote:
>
> Dear Lisa,
>
> You should have a look at some of the previous discussions on the use of 
> the cell->vertex_dof_index 
> 
>  function 
> (as well as its documentation 
> );
>  
> this provides an easy link between vertices and degrees of freedom.
>
> Regards,
> J-P
>
> On Friday, October 14, 2016 at 1:20:29 PM UTC+2, Lisa Collins wrote:
>>
>> Hallo,
>> Thanks for both replies.
>> In general, from a solution vector, how can I extract u_x, u_y, and T 
>> nodal values corresponding to a specific node?
>> Best regards.
>> Lisa
>>
>> On Thursday, October 13, 2016 at 1:05:08 PM UTC+2, Lisa Collins wrote:
>>>
>>> Hello,
>>>
>>> Dealing with vector valued problems in deal ii is a bit confusing for me.
>>> I have a question regarding the solution vector (S).
>>> If we have a problem with 20 nodes and 3 dofs per node (u_x , u_y , and 
>>> T temperature) can we always say that:
>>>
>>> S[0] = u_x of node A
>>> S[1] = u_y of node A
>>> S[2] = T of node A
>>>
>>> S[3] = u_x of node B
>>> S[4] = u_y of node B
>>> S[5] = T of node B
>>>
>>> and so on.
>>>
>>> Thanks.
>>> Lisa
>>>
>>

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Re: [deal.II] trouble running new step-55

[Martin Kronbichler]

Dear Franck,

I justed checked on my machine and it works both on an installation that 
only provides Trilinos and on an installation that has both (and where 
PETSc is selected). It looks like your installation is 8.4.0 whereas I 
think that step-55 requires the current developer version 8.5.0-pre. The 
compile error complains about missing classes in the LA::MPI namespaces 
which might be related to some changes we have done recently. Can you 
check with the developer version?


Best,
Martin


On 17.10.2016 12:12, 'franck75' via deal.II User Group wrote:

I am having trouble when trying to  run new step-55.

I am having a very long error message. Here is one piece (see attached 
file).


Does anyone able to run it?

Best
Franck


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[deal.II] Re: Easy way to calculate second-deviatoric tensor

[Daniel Arndt]

Jaekwang,

>From this symmetric gradient tensor, do we have one easy way to calculate 
> the following "the second invariant of rate-of-strain tensor"? 
>
There is SymmetricTensor::second_invariant [1] which is defined as I2 = 
1/2[ (trace sigma)^2 - trace (sigma^2) ]
and SymmetricTensor::first_invariant [1] which just the trace I_1=trace 
sigma. 
According to Wikipedia [2], your \Pi_\gamma can then be expressed as 
\Pi_\gamma^2 = 1/2(I1^2 -2 I2).

Best,
Daniel

[1] 
https://www.dealii.org/8.4.0/doxygen/deal.II/classSymmetricTensor.html#a7bbdfc57da6931de6a1757a0fa7ee982
 

[2] https://en.wikipedia.org/wiki/Invariants_of_tensors

>
> 
>
>
>
> Regards, 
>
> Jaekwang Kim 
>  
>

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