[FLASH-USERS] WARNING after gc filling problem

[Klaus Weide]

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