[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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>>> >
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>>> **>
>>>
>>>
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