[FLASH-USERS] WARNING after gc filling problem

[Gary F Forjan]

Hi Klaus

Thanks for the comments - I will try all your suggestions.  Since I think all compositions include electrons and hydrogen at a minimum, perhaps I do need to use the Multispecies unit to get a fully ionized proton/electron plasma.  I'll also see if using a uniform grid makes any difference. 

Thanks again, Gary


Gary Forjan
Department of Computational and Data Sciences
George Mason University, Fairfax, Va
gforjan at gmu.edu

----- Original Message -----
From: Klaus Weide <klaus at flash.uchicago.edu>
Date: Tuesday, September 15, 2009 9:39 am
Subject: Re: [FLASH-USERS] WARNING after gc filling problem

> On Tue, 15 Sep 2009, Gary F Forjan wrote:
> 
> > 
> > Thanks for the suggestion but compiling the code with the -O3 
> flag did not resolve the problem of zero values for the variables. 
> I have to think Klaus is right that something is wrong in 
> Paramesh but I am not sure what in my Config and flash.par file is 
> causing it.  Perhaps my composition.  I include only the line
> > 
> > REQUIRES Simulation/SimulationComposition/Ionize
> > 
> > in my Config file to implement a proton+elec plasma but the 
> Flash.h file shows that NSPECIES is defined as 5.  I am not sure 
> how FLASH determines that.
> 
> Hi Gary,
> 
> Yes, that NSPECIES number is strange.  You can try to find in 
> Flash.h 
> what those five species are supposed to be (look for XXX_SPECIES).
> 
> I am not very familiar with the Ionize code unit, but one obvious 
> thing 
> that is different between your FLASH3 build and a reference setup 
> (NeiTest) for Ionization is the following: your setup does not 
> include the 
> Multispecies unit (as shown in the "FLASH Units used" section of 
> your log 
> file).  So add a REQUESTS for that to you Config file and see what 
> happens.  You may then also have to use Eos/EosMain/Multigamma 
> instead of 
> Eos/EosMain/Gamma.
> 
> 
> Some other ideas to try:
> Add a 
>   REQUESTS Grid/GridBoundaryConditions
> explicitly to your Config file, before the
>   REQUESTS Grid/GridBoundaryConditions/OneRow
> you already have.  Normally this should always be implied, so this 
> is 
> unlikekly to do anything, but please try it anyway.
>  
> I have seen a similar effect (all guard cells filled with 0.0) in 
> the past 
> when the xl_boundary_type etc. string was misspelled in a .par 
> file, like
> "refecting".  Make sure that your Grid_applyBCEdge invocation sees 
> the 
> correct negative values for bcType (USER_DEFINED and REFLECTING as 
> defined 
> in constants.h).
> 
> If you force the Paramesh grid to be uniform (set 
> lrefine_min==lrefine_max), do you still see these errors?
> 
> Klaus
>