[Nek5000-users] Vanishing Jacobians while using moving mesh

Wed Feb 15 10:58:18 CST 2012

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
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> >
>
>
>
> --
> Josh Camp
>
> "All that is necessary for the triumph of evil is that good men do
> nothing" -- Edmund Burke
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