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

Wed Apr 8 13:23:32 EDT 2009

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.

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!

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