[FLASH-USERS] Negative/zero densities and internal energies after filling gc

Thu Apr 9 04:22:16 EDT 2009

Hi Seyit,

Quoting Seyit Hocuk <seyit at astro.rug.nl>:

> Hi community,
>
> I've switched to Flash3.1.1a (from version 2.5), but when I try to run
> my setup, comparable to the Jeans setup, I encounter problems. If I am
> running without cooling and with a uniform grid (lref_max=lref_min),
> then everything seems ok. However, if I add the cooling module OR I
> have adaptive refinement, zero or negative densities/internal energies
> appear (or lower than the "small" values). These cause the refinement
> to be messed up and of course leads to crashes. The error outpusts are
> shown below. From there, I notice that the error might come from guard
> cell filling.
>
> I test the standard Jeans setup and the same problems occur.
> Just changing and adding in flash.par:
> lrefine_max = 5
> refine_cutoff_1 = 1.0
>
> On several occasions I have checked the Eos_wrapped.F90 file and found
> the location where it might go wrong;
> just before reading solnData eint/dens was ok, but after this the
> values are crazy. Btw., I don't use massFractions ad haven't
> implemented Multispecies and no species are initiated.
>
>        eosData(pres+1:pres+vecLen) = &
>             solnData(PRES_VAR,range(LOW,IAXIS):range(HIGH,IAXIS),j,k)
>        eosData(dens+1:dens+vecLen) = &
>             solnData(DENS_VAR,range(LOW,IAXIS):range(HIGH,IAXIS),j,k)
>        eosData(temp+1:temp+vecLen) = &
>             solnData(TEMP_VAR,range(LOW,IAXIS):range(HIGH,IAXIS),j,k)
>        eosData(gamc+1:gamc+vecLen) = &
>             solnData(GAMC_VAR,range(LOW,IAXIS):range(HIGH,IAXIS),j,k)
>        eosData(eint+1:eint+vecLen) = energyInternal(1:vecLen)
>
>
>        call
> Eos(mode,vecLen,eosData)!,massFraction)!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>
> Another thing that I notice but is likely completely unrelated is, that
> with this latest Flash version, the upper level blocks are blocky and
> have absurd values. Though, the highest refined level is always ok.
> Could it be related, as it needs parent blocks for refinement? Then
> again, how is this related to cooling when there is no refinement. I
> double checked with Jeans and Sedov test problems; it was the same
> thing.
>

I can't help you with the Jeans simulation but I have noticed a  
similar problem with the coarsest level blocks when you are using  
source terms. Specifically, my problem was that blocks on the coarsest  
refinement level were not being acted on by source terms. I tracked  
down the root of this problem; it seems that the blockList passed from  
Driver_evolveFlash into Driver_sourceTerms is only for leaf blocks and  
not all blocks. You can get around this by adding a call to  
Grid_getlistofblocks and requesting all blocks before you start  
applying source terms. I hope this helps.

Cheers,

Ross Parkin

>
> Some info on my environment:
> Kernel: Centos 5.2
> Machine: Linux ulubey 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST
> 2008 x86_64 x86_64 x86_64 GNU/Linux
> ifort version: (IFORT) 10.1 20080602
> hdf5 version: 1.8.1
> MPICH version. 2-1.0.7
> gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)
>
>
>
>
> A snippet from the log file when the warnings appear.
>
> [GRID amr_refine_derefine] min leaf blks 76    max leaf blks 76    tot
> leaf blks 76
> [ 04-08-2009  18:10:42.268 ] [GRID amr_refine_derefine]: refinement complete
> [ 04-08-2009  18:10:42.273 ] WARNING after amr_prolong: min.
> unk(EINT_VAR)=6685180.741266931 PE=0 block=18 type=1
> [ 04-08-2009  18:10:42.274 ] step: n=37 t=1.414748E+12 dt=1.000000E+11
> [ 04-08-2009  18:10:42.279 ] WARNING after gc filling: min.
> unk(EINT_VAR)=6162624.299265089 PE=0 block=18 type=1
> [ 04-08-2009  18:10:42.297 ] WARNING after gc filling: min.
> unk(EINT_VAR)=6174477.607051291 PE=0 block=18 type=1
> .
> .
> [ 04-08-2009  18:10:42.939 ] WARNING after gc filling: min.
> unk(EINT_VAR)=6274674.035376545 PE=0 block=32 type=1
> [ 04-08-2009  18:10:42.939 ] WARNING after gc filling: min.
> unk(EINT_VAR)=6259353.579602077 PE=0 block=33 type=1
> [ 04-08-2009  18:10:42.992 ] [gr_hgRecordNodeTypeState] max refine level =: 5
> [ 04-08-2009  18:10:43.054 ] [IO_writeCheckpoint] open: type=checkpoint
> name=xSH-A1_hdf5_chk_0002
> [ 04-08-2009  18:10:43.059 ] [IO_writeCheckpoint] close:
> type=checkpoint name=xSH-A1_hdf5_chk_0002
> [ 04-08-2009  18:10:43.059 ] step: n=40 t=2.014748E+12 dt=1.000000E+11
> [ 04-08-2009  18:10:43.064 ] WARNING after gc filling: min.
> unk(EINT_VAR)=5604765.671211276 PE=0 block=18 type=1
> [ 04-08-2009  18:10:43.083 ] WARNING after gc filling: min.
> unk(EINT_VAR)=5320601.064666561 PE=0 block=18 type=1
> [ 04-08-2009  18:10:43.112 ] [gr_hgRecordNodeTypeState] max refine level =: 5
> [ 04-08-2009  18:10:43.161 ] WARNING after gc filling: min.
> unk(DENS_VAR)=-0.7514521682254683594983E-21 PE=0 block=8 type=2
> [ 04-08-2009  18:10:43.161 ] WARNING after gc filling: min.
> unk(DENS_VAR)=-0.1537578263572373951611E-20 PE=0 block=13 type=2
>
>
>
> Another snippet from the log file when the crash occurs (more frequent
> for cooling runs).
>
> [ 04-08-2009  17:51:23.737 ] [IO writePlotfile] open: type=plotfile
> name=xSH-A1_hdf5_plt_cnt_0000
> [ 04-08-2009  17:51:23.738 ] [IO_writePlotfile] close: type=plotfile
> name=xSH-A1_hdf5_plt_cnt_0000
> [ 04-08-2009  17:51:23.738 ] [Driver_evolveFlash]: Entering evolution loop
> [ 04-08-2009  17:51:23.739 ] step: n=1 t=0.000000E+00 dt=1.000000E+02
> [ 04-08-2009  17:51:23.776 ] [gr_hgRecordNodeTypeState] max refine level =: 4
> [Eos_wrapped] ERROR Density or Internal Energy are zero after a call to EOS!
> [ 04-08-2009  17:51:23.816 ] [DRIVER_ABORT]: Driver_abort() called by
> PE           0
> [ 04-08-2009  17:51:23.816 ] abort_message: [Eos_wrapped] ERROR Density
> or Internal Energy are zero after a call to EOS!