[FLASH-USERS] Problems Simulating Partially Ionized Plasma with USM

[Patrick Rieser]

First of all, thanks a lot for your answers, they were quite useful!

It actually was quite easy to active the Ionize unit, despite the fact, 
that the ma28 library would not compile, but i copied the one from flash 
4b and it solved the problem.

Flash seems to recognize the Ionize unit just fine and tries to 
initialize the species but when i try to do some plots, all the species 
have a constant value of 1e-10 over the whole volume (done with VisIT). 
This does not change with time - from redshift 99 down to 2. The 
temperature ranges form ~10e-1 to 10e7 and the density from 10e-31 to 
10e-25 over the volume. Could the densities be too low for the 
Ionize/Multispecies unit to work? There also seems to be something wrong 
with the Initially defined values of the species (table below).


 From the log file:

Initially defined values of species:
Name     Index          Total   Positive  Neutral   Negative  bind Ener 
Gamma
elec        25      -9.99E+02 -9.99E+02 -9.99E+02 -9.99E+02 -9.99E+02 
-9.99E+02
h           26       1.00E+00  1.00E+00 -9.99E+02 -9.99E+02 -9.99E+02  
1.67E+00
he          27       4.00E+00  2.00E+00 -9.99E+02 -9.99E+02 -9.99E+02  
1.67E+00
he1         28      -9.99E+02 -9.99E+02 -9.99E+02 -9.99E+02 -9.99E+02 
-9.99E+02
he2         29      -9.99E+02 -9.99E+02 -9.99E+02 -9.99E+02 -9.99E+02 
-9.99E+02


Thanks a lot in advance!

Greetings,
Patrick




Am 11.05.2012 03:33, schrieb Klaus Weide:
> Patrick,
>
> Below I have added various comments. These may or may not help you
> directly, and I am not addressing any aspects of your problem specific to
> the MHD solver.  Read references to "Hydro" below as "Hydro or MHD
> implementation".
>
> On Thu, 10 May 2012, Patrick Rieser wrote:
>
>> So I am using a little bit modified Flash 3.3 to do simulations on galaxy
>> cluster for my master thesis. We have got a MHD setup using USM. By now there
>> are two species defined, H and He and the calculations are done with the
>> assumption of full ionization. So now my part is to extend the simulation that
>> a partially ionized gas can be calculated with neutral parts H and He, and
>> ionized parts H+, He+ and He++. After each time step the ionization of those
>> particles should be recalculated. My plan has been to modify the USM solver. I
>> thought of integrating two different densities, one for the neutral and one
>> for the ionized particles.
> Note that when you have species defined, the Hydro and MHD solvers should
> in effect already integrate several densities, without any further effort:
> namely, partial densities for the various species as well as the usual
> total density.  (This is basically done by advecting the mass fractions.)
>
>> Then add source terms to the flow vectors of the
>> USM solver. To get those source terms I would have to modify EOS equations.
>>
>> Even though I did quite some reading about multifluid MHD and spend quite some
>> time playing with flash and it's source code I can't get my head around some
>> thing:
>>
>> 1) I recently stumbled over the Ionization module in flash. But I am not quite
>> sure if I can use it to do what I want and would not have to modify the EOS
>> and USM modules, but change the setup of our simulation. This is because of 2)
> In principle, you should be able to use the Ionize unit; if not in its
> current form (with the existing sets of species and rates) then at least
> some modification that does essentially the same things.  (There are some
> things going on in the existing implementation that I don't properly
> understand - like how mass fractions for hydrogen and electrons are
> determined, and why there is a mass fraction for the electrons at all -
> and they may not be appropriate for your application.  Note that according
> to the Users Guide (16.2.1), "the source term in the NEI unit
> implementation is adequate to solve the problem for optically thin plasma
> in the ``coronal'' approximation; just collisional ionization,
> auto-ionization, radiative recombination, and dielectronic recombination
> are considered.")
>
> Above you wrote: "After each time step the ionization of those particles
> should be recalculated." This gives the impression that you want the
> ionization levels to adapt to the updated state (incl. temperature)
> instantaneously after Hydro or MHD has moved the fluid around. That would
> be just the "Eqi" implementation of the Ionize unit. You would use the
> "Nei" implementation if you wanted to take account of non-equilibrium
> ionization instead.
>
>> 2) I read the PhD thesis from Dongwook Lee describing the Unsplit scheme for
>> multidimensional MHD and tried to pick apart the USM source code but I can't
>> really find out how flash handles (multi) species, density and Ionization in
>> the USM solver. Does USM work with the Ionization module? If so, can USM
>> handle neutral species and the partially ionized plasma? Do I just have to
>> implement the Ionized module in the simulation then?
> For comparison and for reference, here is how variable ionization is
> represented in FLASH in 3T (three temperature) mode, in contrast to the
> approach taken in the Ionize unit. I don't mean to imply that you should
> use FLASH in this mode, just to present an alternative approach that is
> actually being used.
>
>    * No need to use the Ionize unit; as it is, it wouldn't work right with
>      3T mode anyway.
>
>    * Electrons are not represented as a FLASH "species"; the number
>      density of electrons is computed by the 3T Eos implementation
>      instead, and is (usually) an output from Eos calls.
>      The Zfree (number of free electron per ion) used in these 3T Eos
>      implementations can be a fixed property of a material or based
>      on a (T_ele,rho) table and/or a combination of contributions
>      from different species.
>
>    * Each FLASH "species" represents the mass fraction of one "material"
>      (i.e. here, one element), not of one ionization level of one element.
>      In your simulations you would have only two species, H_SPEC and
>      HE_SPEC.
>
>    * The code keeps track of specific internal energy of the electron component
>      of the fluid, or equivalently electron temperature T_ele (in addition
>      to T_ion, T_rad), in addition to combined (total) energy.
>      Since Zfree depends on T_ele, ionization is currently assumed
>      in equilibrium with electron thermal energy (but electrons and ion
>      thermal energy need not be in equilibrium).
>
>
> I hope this is of some use.
>
> Klaus