[Nek5000-users] genmap, ABORT: SELF-CHK

[nek5000-users at lists.mcs.anl.gov]

Hi Paul and Katie,

Thank you for your help. Your suggestion of compressing a regular grid 
in the .usr file is very interesting and I will certainly look into it 
during the rest of my study. The scripts to generate an O-grid would 
also be of great interest.

Thanks again,

Holly


Le 26/06/2013 22:14, Paul Fischer a écrit :
>
>
> Hi Holly,
>
> Attached is a tarfile with a script "mkmesh" and a .usr file
> that will take a regular square grid and compress it near the
> center. Compression has two components:
>
> 1) a tensor-product compression, similar to what you had
>
> 2) a pseudo-orthogonal grid concentration
>
> The purpose of the second part is to avoid very high aspect
> ratio cells, which really impact the conditioning of the linear
> systems and consequently the iteration counts.
>
> On this latter point, let me make a couple of comments/questions.
>
> In your original script you had a compression factor of 0.7,
> extended over 50 elements, which would give a largest to smallest
> ratio of ~ 1.e-8 and you would end up with an aspect ratio of
> approximately 1.e-6.
>
> My guess is that you have something very near the origin that you
> are trying to resolve and are not interested in the far field.
> Because of the difficulties with high-aspect ratio elements
> (which is common to all discretizations, but see pp. 24-26
> of www.mcs.anl.gov/~fischer/pubhtml/jcp97.pdf for a discussion
> related to the SEM), it might be of interest to consider an O-grid,
> i.e., a cylinder, in which you can easily focus resolution and
> maintain near unit aspect-ratio throughout the domain. Attached
> is an example mesh (in t.t2.gz). I can also provide the scripts
> used to generate this, if of interest.
>
> Paul
>
>
>
>
> On Wed, 26 Jun 2013, nek5000-users at lists.mcs.anl.gov wrote:
>
>>
>> Hi Holly,
>>
>> I've posted this back to the list since it doesn't involve big
>> data files and the resolution of the problem might be of interest
>> to others.
>>
>> I think I see what's going on and have a couple ideas to fix it.
>>
>> Most likely, the reduction attained with 50 elements and a geomtric 
>> progression of 0.7 is wreaking havoc either in the .rea file or in
>> the tolerances within genmap. A significant issue here is that
>> the file format in the .rea file is in limited precision --- I think
>> we can change that with little difficulty and still be compatible
>> with the workflow. We'll look into that on our end.
>>
>> A reasonable work-around, which is what I typically do, would be
>> to rescale your element coordinates inside nek, and just use a 
>> uniform mesh as the input. I'll send along some code on how to
>> do this shortly --- along with another approach that will also
>> give you focused resolution at the origin without the high aspect
>> ratio elements that will result from the tensor-product approach
>> used here.
>>
>> Paul
>>
>>
>>
>> On Wed, 26 Jun 2013, Holly Johnson wrote:
>>
>>> Hi Paul,
>>>
>>> My mesh is actually quite simple, I've had to reduce it from a much 
>>> more complicated version because Visit couldn't handle the number of 
>>> elements I was using.
>>>
>>> This is my .box file :
>>>
>>> linear.rea
>>> 2
>>> 1
>>> #
>>> # linear.box
>>> #
>>> Box
>>> -50 -50
>>> -3. 0. 0.7
>>> -3. 0. 0.7
>>> SYM, ,v ,
>>> Box
>>> -50 -50
>>> -3. 0. 0.7
>>> 0. 3. 1.3
>>> SYM, , ,O
>>> Box
>>> -50 -50
>>> 0. 3. 1.3
>>> -3. 0. 0.7
>>> ,SYM,v ,
>>> Box
>>> -50 -50
>>> 0. 3. 1.3
>>> 0. 3. 1.3
>>> ,SYM, ,O
>>>
>>> I get the error for any mesh tolerance value when the scaling 
>>> coefficients are _<_ 0.7 or _>_ 1.3. However it works fine for 
>>> _>_0.8 and _<_1.2. I assume therefore it is that the elements of the 
>>> mesh near the center of the grid are just too small?
>>>
>>> Thanks again for your help,
>>>
>>> Holly
>>>
>>> Holly Johnson
>>> Masters Student at ONERA - DAFE
>>> D�partement d'A�rodynamique Fondamentale et Exp�rimentale
>>> 8, Rue des Vertugadins
>>> 92190 - Meudon - France
>>>
>>
-- 
Holly Johnson
Masters Student at ONERA - DAFE
Département d'Aérodynamique Fondamentale et Expérimentale
8, Rue des Vertugadins
92190 - Meudon - France