[FLASH-USERS] How can I modify the LaserSlab example to calculate B fields?

Thu May 28 17:58:00 EDT 2020

Just saw Ben's email, so that should solve the problem. You probably still
want to fix the 'shockDetect' parameter as well.

I just wanted to add that the log file contains a lot of useful
information. As sanity checks, the log file includes the setup command that
was used (this will help tell you if you're using the correct executable),
and a list of all runtime parameters (this will help tell you if the code
is reading in your par file correctly).

On Thu, May 28, 2020 at 4:40 PM Eddie Hansen <ehansen at pas.rochester.edu>
wrote:

> This shouldn't resolve the issue, but you have 'shockDetect' defined twice
> in your par file. The 2nd instance is set to false, so shock detection is
> likely turned off. This would cause the Biermann source to be calculated
> everywhere, including at shocks, which would potentially lead to
> erroneously large values.
>
> Could you also attach your log file so we can at least verify that the run
> is using the correct setup, units, and runtime parameters?
>
> On Thu, May 28, 2020 at 3:11 PM Anthony Raymond <raymonda at fusion.gat.com>
> wrote:
>
>> Hello all,
>>
>> If I could resurrect this subject, I'm wondering if someone wouldn't mind
>> guiding me in the right direction regarding a new issue which cropped up:
>> despite activating the Biermann battery calculations and outputting the
>> magnetic field outputs, the outputs are filled with zeros for all
>> components over all time throughout the laserslab simulation.
>>
>> The .par file is attached to this email, and the setup command used was:
>>
>> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16
>> +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6
>> -parfile=example.par
>>
>> This represents a simple series of modifications to the original
>> LaserSlab example with the goal of calculating and outputting the magnetic
>> field induced by non-parallel density and temperature gradients, for
>> educational purposes. The LaserSlab directory was copied into the magnetoHD
>> directory as well and run from that location, following advice from another
>> FLASH user.
>>
>> It was my expectation to see an azimuthal magnetic field surrounding the
>> laser/plasma interaction spot, but I suppose I'm missing something in
>> setting up the simulation.
>>
>> Just curious if someone wouldn't mind pointing me in the right direction.
>>
>> Thanks and all the best,
>> Tony
>>
>>
>>
>>  ----- Original Message -----
>> > From: "shz133" <shz133 at eng.ucsd.edu <mailto:shz133 at eng.ucsd.edu>>
>> > To: "Anthony Raymond" <raymonda at fusion.gat.com <mailto:
>> raymonda at fusion.gat.com>>
>> > Sent: Wednesday, May 27, 2020 1:06:18 PM
>> > Subject: Re: [FLASH-USERS] How can I modify the LaserSlab example to
>> calculate B fields?
>> >
>> > Hi Tony,
>> >
>> > Have you checked the chk file? Did you see magx, magy, magp?
>> >
>> > Shu
>> >
>> >> On May 27, 2020, at 12:39 PM, Anthony Raymond <raymonda at fusion.gat.com
>> <mailto:raymonda at fusion.gat.com>> wrote:
>> >>
>> >> Thanks for the reply. I took your advice and copied my entire
>> LaserSlab directory into the magnetoHD directory, then ran
>> >>
>> >> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16
>> +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6
>> -parfile=example.par
>> >>
>> >> then CD's into object, ran "make", then ran the simulation.
>> >>
>> >> However, when I run h5info in matlab on the first hdf5 file that is
>> generated, I don't see any entries referencing the magnetic field.
>> >>
>> >> I wonder if I'm still doing something incorrectly?
>> >>
>> >> Thanks and all the best,
>> >> Tony
>> >>
>> >>
>> >> ----- Original Message -----
>> >> From: "Marissa B. P. Adams" <marissa at flash.uchicago.edu <mailto:
>> marissa at flash.uchicago.edu><mailto:marissa at flash.uchicago.edu <mailto:
>> marissa at flash.uchicago.edu>>>
>> >> To: "Anthony Raymond" <raymonda at fusion.gat.com <mailto:
>> raymonda at fusion.gat.com> <mailto:raymonda at fusion.gat.com <mailto:
>> raymonda at fusion.gat.com>>>
>> >> Cc: "flash-users" <flash-users at flash.uchicago.edu <mailto:
>> flash-users at flash.uchicago.edu> <mailto:flash-users at flash.uchicago.edu
>> <mailto:flash-users at flash.uchicago.edu>>>
>> >> Sent: Wednesday, May 27, 2020 11:34:51 AM
>> >> Subject: Re: [FLASH-USERS] How can I modify the LaserSlab example to
>> calculate B fields?
>> >>
>> >> Hi Anthony,
>> >>
>> >> ******First: Did you make a copy of the LaserSlab problem in magnetoHD
>> ? See section 34.2 in the user manual for examples. Try that again but then
>> do effectively the same setup script you did:
>> >>
>> >> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16
>> +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6
>> -parfile=example.par
>> >>
>> >>> On May 27, 2020, at 14:07, Anthony Raymond <raymonda at fusion.gat.com
>> <mailto:raymonda at fusion.gat.com>> wrote:
>> >>>
>> >>> Hello all,
>> >>>
>> >>> Thank you in advance for the help!
>> >>>
>> >>> I am simply running the LaserSlab and want to keep track of the
>> Biermann battery magnetic field induced by the laser-plasma interaction.
>> >>>
>> >>> Taking the advice in the manual, I added the following lines to the
>> top of my example.par script:
>> >>>
>> >>> hy_useBiermann = .true.
>> >>> hy_biermannSource = .true.
>> >>> conserveAngField =.true.
>> >>> shockDetect = .true.
>> >>>
>> >>> and added +usm3t to the setup script (removing +uhd3t):
>> >>>
>> >>> ./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio
>> species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6
>> -parfile=example.par
>> >>>
>> >>> At the bottom of the example.par file, I need to somehow tell FLASH
>> to output the magnetic field components. From the manual, it seems like
>> this should be done by adding:
>> >>>
>> >>>
>> >>> plot_var_10          = "grbx"
>> >>> plot_var_11          = "grby"
>> >>> plot_var_12          = "grbz"
>> >>>
>> >>
>> >> Continuing for purposes of caution for you…. I think this is true if
>> you’re using the hybrid solver for a combo with PIC usage. Re: section
>> 20.1.2.3. Is that what you want to use?
>> >>
>> >> I would recommend trying:
>> >>
>> >> plot_var_10  = “magx”
>> >> plot_var_11  = “magy”
>> >> plot_var_12  = “magz”
>> >>
>> >> instead if using the hybrid version of the code isn’t your original
>> intent right now. You’ll probably want to assign those gr* variables in the
>> Config file, as well as learn how to use that component of the code/learn
>> what limitations it may have. I’ve never tried to use the hybrid stuff, so
>> someone else may wanna chime in.
>> >>
>> >> You can also try looking at the “*chk*” or checkpoint files. They
>> store all of the UNK in there. They’re very large files though, so it is
>> often suggested to not print so many. That means that both mag* and gr*
>> should be stored in there (gr* only if associated hybrid units/modules are
>> also used).
>> >>
>> >>>
>> >>> I let the simulation run, and am trying to find the magnetic field
>> data in the resulting hdf5 outputs. However, they don't appear to be in
>> there. If I run in h5info(filename) in matlab, I find the datasets for
>> density, temperature, etc., but no magnetic field info.
>> >>>
>> >>> Could someone please suggest what I might be doing incorrectly?
>> >>>
>> >>> I've attached the par file that I used to this email.
>> >>
>> >>
>> >> Correct me if I am wrong but from the looks of your example.par you
>> may not printing any checkpoint files (sorry it is very hot and I don’t
>> have AC so my brain is fried, almost literally).
>> >>
>> >> .
>> >> .
>> >> .
>> >> ### Checkpoint Options  ###
>> >> checkpointFileIntervalTime = 1.0
>> >> checkpointFileIntervalStep = 1000
>> >>
>> >> ### Plot Options ###
>> >> plotFileNumber       = 0
>> >> plotFileIntervalStep = 100
>> >> plotFileIntervalTime = 0.01e-09
>> >> .
>> >> .
>> >> .
>> >> tmax           = 2.0e-09
>> >>
>> >> How many time steps did the simulation take? Did it make it to a
>> checkpoint? You can look at the UNK variables that are being used using
>> h5ls or VisIt.
>> >>
>> >>>
>> >>> Thanks and all the best,
>> >>> Tony
>> >>> <example.par>
>> >>
>> >>
>> >> With washed hands,
>> >> Marissa
>> >>
>> >>
>> >> %———————————————————%
>> >> Marissa B. P. Adams
>> >> (she/her/hers)
>> >> Phd Candidate, University of Rochester
>> >> E-mail: madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>
>> <mailto:madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>>
>> <mailto:madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>
>> <mailto:madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>>>
>> >> Website: https://www.pas.rochester.edu/~madams <
>> https://www.pas.rochester.edu/~madams><
>> https://www.pas.rochester.edu/~madams <
>> https://www.pas.rochester.edu/~madams>> <
>> http://www.pas.rochester.edu/~madams <
>> http://www.pas.rochester.edu/~madams><
>> http://www.pas.rochester.edu/~madams <
>> http://www.pas.rochester.edu/~madams>>>
>> >> Twitter:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=>
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=>
>> > <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=>
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=>
>> >>
>> >> Current Location:
>> >> My 400 sq. ft. apartment
>> >> 371 Bausch and Lomb Hall
>> >> University of Rochester
>> >> Rochester, NY 14627
>
>
>
> --
> Eddie Hansen, PhD
> Postdoctoral Associate
> University of Rochester
> 607-341-6126 | Flash Center
>

-- 
Eddie Hansen, PhD
Postdoctoral Associate
University of Rochester
607-341-6126 | Flash Center
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