[Nek5000-users] Vanishing Jacobians while using moving mesh

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Mon Feb 27 10:23:47 CST 2012


Hi Paul,

Sorry for the late reply.

That would be great. I will get back once I start with 3D runs.

Regards,
Pradeep

On Tue, Feb 21, 2012 at 7:13 AM, <nek5000-users at lists.mcs.anl.gov> wrote:

>
> Hi Pradeep,
>
> There was one thing that I'd intended to mention regarding mesh motion.
>
> The file that I set up uses the most general ALE formulation,
> where the mesh velocity is computed through an elasticity solver.
> The performance for this solver has not been optimized, but there
> are several tricks we can use to make it faster.   At the moment,
> I would guess that well over half the time is spent in this solver,
> which could be an issue if you plan to look at 3D problems.  As
> you get into production runs we should examine the performance and
> optimize if necessary.
>
> Regards,
>
> Paul
>
>
>
> On Thu, 16 Feb 2012, nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>wrote:
>
>  Hi Paul,
>>
>> Thank you so much for your help!
>>
>> Regards,
>> Pradeep
>>
>> On Thu, Feb 16, 2012 at 7:28 AM, <nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>>
>> wrote:
>>
>>
>>> PS -- an example of the results can be found here:
>>>
>>>  www.mcs.anl.gov/~fischer/ocyl.****gif<http://www.mcs.anl.gov/~fischer/ocyl.**gif>
>>> <http://www.mcs.anl.gov/%**7Efischer/ocyl.gif<http://www.mcs.anl.gov/%7Efischer/ocyl.gif>
>>> >
>>>
>>>
>>>
>>>
>>> On Thu, 16 Feb 2012, nek5000-users at lists.mcs.anl.****gov<
>>> nek5000-users at lists.mcs.**anl.gov <nek5000-users at lists.mcs.anl.gov>
>>> >wrote:
>>>
>>>
>>>  Hi Pradeep,
>>>>
>>>> Attached is a case that appears to work.  Hope this helps.
>>>>
>>>> Paul
>>>>
>>>>
>>>> On Wed, 15 Feb 2012, nek5000-users at lists.mcs.anl.****gov<
>>>> nek5000-users at lists.mcs.**anl.gov <nek5000-users at lists.mcs.anl.gov>
>>>> >wrote:
>>>>
>>>>  Thanks Paul and Josh,
>>>>
>>>>>
>>>>> I shall start by making the modification in the rea file and trying
>>>>> visit
>>>>> 2.3.2
>>>>>
>>>>> Regards,
>>>>> Pradeep
>>>>>
>>>>> On Wed, Feb 15, 2012 at 9:39 AM, <nek5000-users at lists.mcs.anl.****gov<
>>>>> nek5000-users at lists.mcs.**anl.gov <nek5000-users at lists.mcs.anl.gov>>>
>>>>> wrote:
>>>>>
>>>>>  Pradeep,
>>>>>
>>>>>>
>>>>>> Which version of Visit are you using?  We have experienced similar
>>>>>> issues with version 2.4 when viewing 2D meshes.  If this is the case,
>>>>>> try using 2.3.2 and see if you have the same problem.
>>>>>>
>>>>>> Josh
>>>>>>
>>>>>> On Tue, Feb 14, 2012 at 8:08 AM,  <nek5000-users at lists.mcs.anl.***
>>>>>> *gov<nek5000-users at lists.mcs.**anl.gov<nek5000-users at lists.mcs.anl.gov>
>>>>>> >>
>>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>  Hi Neks,
>>>>>>>
>>>>>>> I'm trying to simulate 2D flow over an oscillating cylinder using
>>>>>>> moving
>>>>>>> mesh, and tried to set up a test case by looking at the peris
>>>>>>> example.
>>>>>>> I
>>>>>>> however am getting vanishing Jacobians after the first few timesteps.
>>>>>>>
>>>>>>> I am modifying the the boundary velocity of the cylinder in userbc
>>>>>>>
>>>>>>>  instead
>>>>>>
>>>>>>  of userchk (as in the peris example). Would it be possible for you to
>>>>>>>
>>>>>>>  look
>>>>>>
>>>>>>  at my .usr file and tell me what I am doing wrong?
>>>>>>>
>>>>>>> I have attached the .rea, .usr, and SIZE with this mail.
>>>>>>>
>>>>>>> Further, when I try to view the mesh of the output (or the xyz fld
>>>>>>> outputfile) in visit, visit crashes with the following error:
>>>>>>> VisIt's viewer exited abnormally! Aborting the Graphical User
>>>>>>> Interface.
>>>>>>>
>>>>>>> Lastly, would it be possible to simulate moving walls with large
>>>>>>> deformations (i.e. where multiple elements get deformed), where the
>>>>>>> deformation is known ahead of time? (eg. a flapping aerofoil)
>>>>>>>
>>>>>>> Thank you for your help!
>>>>>>>
>>>>>>> Regards,
>>>>>>> Pradeep
>>>>>>>
>>>>>>> Extract from logfile:
>>>>>>>
>>>>>>>       60 U-PRES gmres:    100  7.5345E+42  1.0000E-02  4.0062E+57
>>>>>>> 6.7556E-03  1.5093E-02
>>>>>>>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179
>>>>>>>  16
>>>>>>>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179
>>>>>>>  16
>>>>>>>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179
>>>>>>>  16
>>>>>>>  ERROR:  alphad .le. 0 in econjp -1.31175831444004495E+179
>>>>>>>  16
>>>>>>>         60  DNORM, DIVEX  1.18120867781751263E+043
>>>>>>> 7.53448962619089522E+042
>>>>>>>        60   6.0000E-02  1.6697E-02 Fluid done
>>>>>>>    DT/DTCFL/DTFS/DTINIT   0.635E-45   0.635E-45   0.000E+00
>>>>>>> 0.100E-02
>>>>>>> Step     61, t= 6.0800000E-02, DT= 8.0000000E-04, C=*******
>>>>>>> 2.2667E-01
>>>>>>> 1.8287E-02
>>>>>>>            Solving for fluid
>>>>>>>
>>>>>>>
>>>>>>>   3  ERROR:  Vanishing Jacobian near      2th node of element
>>>>>>>
>>>>>>>  3.
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>   2  ERROR:  Vanishing Jacobian near      2th node of element
>>>>>>>
>>>>>>>  1.
>>>>>>
>>>>>>   2.27348348709230109E+081 -5.12478988977734591E+080
>>>>>>>  -2.60483379627720531E+079  3.21465902039155941E+039
>>>>>>>   3 xyz:  -5.30056E+39  -5.84642E+39
>>>>>>>   3 xyz:  -5.24850E+39  -6.93109E+39
>>>>>>>
>>>>>>>
>>>>>>>   3  ERROR:  Vanishing Jacobian near      2th node of element
>>>>>>>
>>>>>>>  4.
>>>>>>
>>>>>>    2 xyz:   1.25061E+38   4.64957E+39
>>>>>>>  9.79493533554062390E+080 -3.01548938509156252E+080
>>>>>>>   2 xyz:  -2.46589E-08  -5.64092E-01
>>>>>>>
>>>>>>>
>>>>>>>   3 xyz:  -5.30056E+39  -5.84642E+39
>>>>>>>   3 xyz:  -5.24850E+39  -6.93109E+39
>>>>>>>   2  ERROR:  Vanishing Jacobian near      3th node of element
>>>>>>>
>>>>>>>  2.
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>   3  ERROR:  Vanishing Jacobian near      2th node of element
>>>>>>>
>>>>>>>  5.
>>>>>>
>>>>>>   1.43125817410005932E+039 -6.03607926692375119E+038
>>>>>>>  5.54918579647991880E+039 -1.67302572815141788E+039
>>>>>>>   3 xyz:  -5.30056E+39  -5.84642E+39
>>>>>>>   2 xyz:  -2.46589E-08  -5.64092E-01
>>>>>>>   3 xyz:  -5.24850E+39  -6.93109E+39
>>>>>>>
>>>>>>>
>>>>>>>   3  ERROR:  Vanishing Jacobian near      2th node of element
>>>>>>>
>>>>>>>  6.
>>>>>>
>>>>>>    2 xyz:  -3.07794E-08  -7.04112E-01
>>>>>>>
>>>>>>>
>>>>>>>   2  ERROR:  Vanishing Jacobian near      7th node of element
>>>>>>>
>>>>>>>  7.
>>>>>>
>>>>>>   8.35923896949543198E+038 -3.55455289325888722E+038
>>>>>>>   3 xyz:  -5.30056E+39  -5.84642E+39
>>>>>>>  1.21747337192549314E+039 -1.79454406120891328E+038
>>>>>>>   3 xyz:  -5.24850E+39  -6.93109E+39
>>>>>>>   2 xyz:  -5.66434E-08  -1.29581E+00
>>>>>>>   2 xyz:  -6.27639E-08  -1.43583E+00
>>>>>>>
>>>>>>>
>>>>>>>   2  ERROR:  Vanishing Jacobian near      9th node of element
>>>>>>>
>>>>>>>  8.
>>>>>>
>>>>>>   1.17802538305091326E+039 -4.21489851051369387E+038
>>>>>>>   2 xyz:  -6.55671E-08  -1.49996E+00
>>>>>>>   2 xyz:  -3.25016E+38   4.93026E+39
>>>>>>>  call outfld: ifpsco: F
>>>>>>>
>>>>>>>      61  6.0800E-02 Write checkpoint:
>>>>>>>
>>>>>>>      61  6.0800E-02 OPEN:
>>>>>>> xyzcyl2.fld01
>>>>>>>  Jac error 1, setting p66=4, ifxyo=t
>>>>>>>
>>>>>>> call exitt: dying ...
>>>>>>>
>>>>>>>
>>>>>>> ______________________________****_________________
>>>>>>> Nek5000-users mailing list
>>>>>>> Nek5000-users at lists.mcs.anl.****gov <Nek5000-users at lists.mcs.anl.**
>>>>>>> gov <Nek5000-users at lists.mcs.anl.gov>>
>>>>>>> https://lists.mcs.anl.gov/****mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users>
>>>>>>> **<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>>>>> **>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Josh Camp
>>>>>>
>>>>>> "All that is necessary for the triumph of evil is that good men do
>>>>>> nothing" -- Edmund Burke
>>>>>> ______________________________****_________________
>>>>>> Nek5000-users mailing list
>>>>>> Nek5000-users at lists.mcs.anl.****gov <Nek5000-users at lists.mcs.anl.**
>>>>>> gov <Nek5000-users at lists.mcs.anl.gov>>
>>>>>> https://lists.mcs.anl.gov/****mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users>
>>>>>> **<https://lists.mcs.anl.gov/**mailman/listinfo/nek5000-users<https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>>>>>> **>
>>>>>>
>>>>>>
>>>>>>   ______________________________****_________________
>>>>
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