[FLASH-USERS] Checkboard of Magnetic Monopoles

Tue Apr 17 23:50:08 EDT 2012

Hi Aaron again,

ENER_VAR should be the conservative TOTAL plasma energy including eint,
ekin and emag IN THE HYDRO unit. Please have a look at
hy_uhd_energyFix.F90 where the total plasma energy (i.e., eint+ekin+emag)
gets converted to the specific gas energy (i.e., (eint+ekin)/dens) and
stored in ENER_VAR.

However, if you are calling ENER_VAR OUTSIDE the hydro unit, for example
in your Cool.F90, then it only includes SPECIFIC eint and ekin.

Best,
Dongwook
=========================================
Dongwook Lee, Ph.D., Research Scientist
The Flash Center for Computational Science
The University of Chicago
5747 S. Ellis Ave., Room 319
Chicago, IL 60637
(773) 834-6830

> Hi Nathan,
>
> Thanks for the suggestion.  It tried adding magnetic energy, but it
> doesn't change the placement of the checkboards.  I'm not sure magnetic
> energy belongs in ENER_VAR because the related section in
> Simulation_initBlock reads:
>
>            ! total specific gas energy
>            enerZone = eintZone + ekinZone
>
> I have also tried turning EnergyFix on and off, but there it has no
> discernible effect.
>
> Thanks,
> Aaron
> ________________________________________
> From: Nathan Goldbaum [goldbaum at ucolick.org]
> Sent: Tuesday, April 17, 2012 2:29 PM
> To: Aaron Froese
> Subject: Re: [FLASH-USERS] Checkboard of Magnetic Monopoles
>
> Hi Aaron,
>
> This is a wild guess, but I think the error you're seeing is because
> you're not including the magnetic energy when you update the solnData
> vector.
>
> Instead of
>
> solnData(ENER_VAR,i,j,k) = ei + ek
>
> You should have
>
> solnData(ENER_VAR,i,j,k) = ei + ek + emag
>
> where
>
> emag =
> .5*dot_product(solnData(MAGX_VAR:MAGZ_VAR,i,j,k),solnData(MAGX_VAR:MAGZ_VAR,i,j,k))
>
> I suggest you look closely at hy_uhd_energyFix.F90 (located in
> source/physics/Hydro/HydroMain/unsplit/MHD_StaggeredMesh/) before you make
> further modifications.
>
> Hope that helps!  If any other users of the unsplit solver have a more
> solid understanding of what's happening in Aaron's simulation, please
> chime in.
>
> Cheers,
>
> Nathan Goldbaum
> Graduate Student
> Astronomy & Astrophysics, UCSC
> goldbaum at ucolick.org
> http://www.ucolick.org/~goldbaum
>
> On Apr 17, 2012, at 2:20 PM, Aaron Froese wrote:
>
>> Hi Mark,
>>
>> I have been able to recreate the checkboarding problem on the OrszagTang
>> example using the USM solver.  I have included the necessary changes,
>> which just involve including a modified cooling module to reduce the
>> local internal energy by a small factor each time step.  I have included
>> plots of divB at the first checkpoint for two cases: one with a static
>> AMR and the internal energy dropping by a factor of 1e-6 each time step,
>> the other with a dynamic AMR and the internal energy dropping by a
>> factor of 1e-3 each time step.  The monopoles always appear on the
>> borders of 8x8 squares.
>>
>> Thanks,
>> Aaron
>> ________________________________________
>> From: Mark L Richardson [Mark.L.Richardson at asu.edu]
>> Sent: Thursday, April 12, 2012 4:20 PM
>> To: Aaron Froese
>> Cc: flash-users at flash.uchicago.edu
>> Subject: Re: [FLASH-USERS] Checkboard of Magnetic Monopoles
>>
>> Hi Aaron,
>>  Are you able to overlay the grid so we can see how these features
>> relate to the blocksize?
>>
>> Cheers,
>>  -Mark
>>
>> On Thu, Apr 12, 2012 at 3:54 PM, Aaron Froese
>> <aaron.froese at generalfusion.com<mailto:aaron.froese at generalfusion.com>>
>> wrote:
>> I am using the USM MHD solver with flash3 and I noticed that I am
>> getting very large magnetic monopoles appearing in my solution, of the
>> same order as the magnetic fields.  The monopoles appear in a somewhat
>> random checkboard-like pattern, which I believe has something to do with
>> the block-structure of the mesh.  I have attached two plots which show
>> the magnitude of divb and posted copies online in case the mailing list
>> does not allow file attachments.
>>
>> Cylindrical Shell Compression 2D - abs(divb)
>> http://oi40.tinypic.com/1zeihbp.jpg
>>
>> Spherical Shell Compression 3D - abs(divb)
>> http://oi39.tinypic.com/34grldv.jpg
>>
>> The central circle where the checkboard pattern appears is the only
>> volume that is magnetized.  I am using a static AMR mesh with a uniform
>> resolution across the magnetized volume, and less refinement in the
>> surrounding non-magnetized fluid.  Has anyone observed similar
>> behaviour?  It is definitely numerical in nature, but I do not know what
>> part of the code is responsible..
>>
>> Thanks,
>> Aaron
>>
>>
>>
>> --
>> Mark Richardson,
>> Mark.L.Richardson at asu.edu<mailto:Mark.L.Richardson at asu.edu>
>> Ph.D. Candidate: Astrophysics
>> PSF 271
>> School of Earth and Space Exploration
>> Arizona State University
>> 480 318-4449
>> www.public.asu.edu/~mlricha4<http://www.public.asu.edu/~mlricha4>
>>
>>
>>
>> !DSPAM:10175,4f8ddebf128361398417114!
>> <OrszagTang-Cool-AMR_abs-divb.png><OrszagTang-Cool-uniform_abs-divb.png><Cool.F90><Config>
>