[FLASH-USERS] multispecies ionmix not found

Thu Feb 13 01:52:55 EST 2020

Hi Marissa,

Great things are looking good so far. So far as I can see, the concept 
of different ions breaks down as it is solved as a single fluid. So the 
next step will likely need to be to go to the hybrid-PIC where the 2 ion 
species could be computed separately in the electron fluid. I've used a 
lot of PIC but in my current case it is far too computationally 
expensive to look at these multi-species dynamics over such a long 
time-scale at these temperatures. The documentation for the hybrid 
section is quite difficult to understand, with the examples even harder. 
Do yourself or any of your colleagues have experience setting up the 
hybrid problem? The 2 species would be initialised as cold, no e-field, 
no-b-field, just a target and energy deposition from a laser. For 
example, I see no simple way of specifiying the ion position such as in 
the laser-slab problem.

Sorry if I am spamming! But I appreciate the help.

All the best,

Aodhan

On 13/02/2020 11:02, Marissa Adams wrote:
> *This message is from an external sender. Please take care when 
> responding, clicking links or opening attachments.*
> Hi Aodhan,
>
> I am so glad I was able to help you. When it comes to pulling 
> information pertinent to each species you can multiply whatever 
> variable by the variables you have assigned to each species. These 
> variables in the original LaserSlab problem are referred to as "cham" 
> and "targ." The "cham" being a "pseudo-vacuum" (as aiming to solve 
> Maxwell's equations for light from the Eulerian perspective is another 
> problem on its own, so we place a fake material there at low density 
> to simulate vacuum), and "targ" is the species of the target, say Al 
> in the original case, or CH in yours. So you *can* acquire information 
> about CH.
>
> I thought (will admit I didn't google though) a bit more about your 
> problem in determining information from CH on C though. Perhaps you 
> can implement a numerical transition in the 
> Simulation_adjustEvolution.F90 routine? Or do some sort of weighting 
> on the "targ" species for C? I would recommend asking someone who is 
> more familiar with chemistry or equation of state under whatever 
> conditions you're dealing with at your institution. It could be cause 
> for a new and exciting collaboration.
>
> I hope this helps! Best of luck!
>
> Marissa
>
>
> On Wed, Feb 12, 2020, 19:07 Aodhan McIlvenny <amcilvenny01 at qub.ac.uk 
> <mailto:amcilvenny01 at qub.ac.uk>> wrote:
>
>     Hi Marissa,
>
>     Thanks for the help, it's now running.
>
>     I noticed this page in the manual previously, since it noted that
>     it tracked the average ionization and average atomic number only.
>     I was hoping that there would be a quick change to the input file
>     that allowed the output of each ion species within 1 material,
>     since the IONMIX file has a relative abundance of each ion
>     species, they must be being computed but maybe not output. I will
>     continue to look into this.
>
>     All the best,
>
>     Aodhan
>
>     On 13/02/2020 01:16, Marissa Adams wrote:
>>     *This message is from an external sender. Please take care when
>>     responding, clicking links or opening attachments.*
>>
>>
>>     On Wed, Feb 12, 2020 at 12:30 AM Aodhan McIlvenny
>>     <amcilvenny01 at qub.ac.uk <mailto:amcilvenny01 at qub.ac.uk>> wrote:
>>
>>         Hi all,
>>
>>         I have 2 questions which I hope are easy to answer; I am a
>>         bit stuck when trying to change the material in the laserslab
>>         example.
>>
>>           * I am trying to use the polystyrene ionmix4 file which is
>>             in the same format as the aluminium one however it
>>             returns an error that it can't be found. Any ideas why
>>             this is so?
>>
>>     Where are you running the executable? Perhaps you have not moved
>>     that particular file to the directory where you are running the
>>     ./flash4 executable. If you are running the executable in the
>>     /object/ directory where you have configured and made it, then
>>     the default Simulation module for the /LaserSlab/ problem will
>>     have not moved that particular file there. You can change this by
>>     editing the /Config/ file. For instance, I can see that in my
>>     version of the /LaserSlab/ problem, it will only copy these files
>>     to the object directory:
>>
>>     DATAFILES al-imx-002.cn4
>>
>>     DATAFILES al-imx-003.cn4
>>
>>     DATAFILES he-imx-005.cn4
>>
>>     e.g. Tables for aluminum and helium as found in the /Config/ file
>>     in //source/Simulation/SimulationMain/LaserSlab//
>>
>>           * Secondly, can I track the carbon and proton species
>>             separately from this one material? Ideally I would like
>>             to return the position and temperature of carbon and
>>             protons separately. Is there a partciular syntax for
>>             looking at each ion species from 1 material?
>>
>>     In order to track the in particular just the *carbon* elements of
>>     a plastic material such as CH, that will require your own
>>     scientific inquiry; from my naive experience, I've never heard of
>>     someone doing that in a Eulerian fluid code but I am sure I one
>>     can google it if it's been done. However, if you want to do
>>     standardized extractions of the species you're using as materials
>>     in FLASH, as well as acquire information such as the electron and
>>     ion densities, make sure you're using 3T and take a gander at
>>     page 539/section 34.7 of the user manual.
>>
>>         I have attached my .par file. I would much appreciate some
>>         help! I am using FLASH.4.6.2 and setup command was
>>
>>         ./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16
>>         +hdf5typeio species=cham,targ +mtmmmt +laser +uhd3t +mgd
>>         mgd_meshgroups=6 -parfile=VulcanTest2.par
>>
>>         Thanks in advance,
>>
>>         Aodhan
>>
>>
>>     Best,
>>     Marissa
>>
>>     -- 
>>     %---------------------------------------------%
>>     Marissa B. P. Adams
>>     (she/her/hers)
>>     Phd Candidate, University of Rochester
>>     NDVS, University of Chicago
>>     *E-mail:* marissa at flash.uchicago.edu
>>     <mailto:marissa at flash.uchicago.edu>
>>     *Website:* https://www.pas.rochester.edu/~madams
>>     <http://www.pas.rochester.edu/~madams>
>>     *Twitter:* https://twitter.com/mbpadams
>>     *Current Location:*
>>     553 ERC
>>     Flash Center for Computational Science
>>     5640 S. Ellis Ave, ERC 553
>>     Chicago, IL 60637
>
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