[Nek5000-users] Vanishing Jacobians while using moving mesh

Thu Feb 16 06:26:05 CST 2012

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 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> 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> 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
>>> 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
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>
>
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