[Nek5000-users] Vanishing Jacobians while using moving mesh

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Thu Feb 16 08:26:25 CST 2012 

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> wrote:

>
> PS -- an example of the results can be found here:
>
>  www.mcs.anl.gov/~fischer/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>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>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>>
>>> 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>>
>>>> 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>
>>>>> 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
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>>>>
>>>>
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