[Nek5000-users] Vanishing Jacobians while using moving mesh

Thu Feb 16 06:28:29 CST 2012

PS -- an example of the results can be found here:

   www.mcs.anl.gov/~fischer/ocyl.gif

On Thu, 16 Feb 2012, 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 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 ...
>>>> 
>>>> 
>>>> _______________________________________________
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>>>> 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
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>