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This would imply there is an inconsistency in applying physics
operators.<br>
<br>
I think there exist a (PARAMESH?) option enforcing evolving all blocks
in the simulation, if necessary. A local modification might be more
efficient, though.<br>
<br>
In the latter case, the next question I would have is whether all
blocks coarser than parent blocks do have valid data.<br>
<br>
Tomek<br>
--<br>
Ross Parkin wrote:
<blockquote
cite="mid:20090409092216.no1u2btipsg08kk4@webmail.leeds.ac.uk"
type="cite">
<pre wrap="">Hi Seyit,
Quoting Seyit Hocuk <a class="moz-txt-link-rfc2396E" href="mailto:seyit@astro.rug.nl"><seyit@astro.rug.nl></a>:
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
</blockquote>
<pre wrap=""><!---->
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
</pre>
<blockquote type="cite">
<pre wrap="">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!
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
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