[FLASH-USERS] WARNING after gc filling: min. unk(DENS_VAR)=0
Gary F Forjan
gforjan at gmu.edu
Wed Jul 7 21:05:45 EDT 2010
Hello Flash Users
I previously reported the problem below and would like to let everyone know that with much help from Klaus the problem was found and resolved. Although it seemed that there was something wrong with the way the boundary conditions were set up, it actually had to do with the declaration and initialization of the species in my experiment. I was trying to implement a simple proton-electron plasma which was easy to do in FLASH2.5 as it used the /materials/composition/prot+elec module to create a two-fluid proton/electron composition. The radloss Config file just declared NUMSPECIES 2. There were no inconsistencies or clashes. However, for FLASH3.2, I simply added in the heating and cooling routines from the Flash_Supplementary_Units without realizing that FLASH3.2 already includes hydrogen and electron species. The end result is that I had five species in my simulation. While I initially saw this, the error below plus the fact that the simulation ran with a uniform grid (lrefine_
min = lrefine_max) led me to believe the problem was in how I set up the boundary conditions. With some code changes to the Heat.F90, Cool.F90 and Radloss/Config file provided by Klaus, I rebuilt a new Flash executable and re-ran my experiment. The problem with the zero density after call to EOS no longer appeared when the adaptive mesh was used instead of uniform grid.
Kunal - Not sure if the problem I just had is related to your problem with the Sedov explosion experiment but perhaps it will give you some ideas about what can generate this kind of error.
On a side note, concerning plane parallel gravity, I noticed that the Gravity_accelOneRow.F90 file in the /Gravity/GravityMain/PlanePar directory does not initialize the values of the indexes j and k to the pos(:) argument as in other implementations of this routine. Maybe it's not an issue but I thought I would point it out.
Many thanks, Klaus, for helping solve this problem!
Gary
Dr. Gary Forjan
Department of Computational and Data Sciences
George Mason University, Fairfax, Va
gforjan at gmu.edu
----- Original Message -----
From: Gary F Forjan <gforjan at gmu.edu>
Date: Tuesday, May 11, 2010 6:46 am
Subject: [FLASH-USERS] WARNING after gc filling: min. unk(DENS_VAR)=0
> Hello Everyone
>
> This is an old problem I never managed to solve but had to leave
> to work on something else. I'm back to it now and would
> appreciate some help. I am simulating a solar coronal loop
> structure with heating, radiative cooling, and semi-circular
> gravity in FLASH 3.2. The simulation is one-dimensional with a
> user-defined xl boundary condition and a reflecting xr boundary
> condition. I have set up the user-defined boundary condition by
> modifying the Grid_applyBCEdge.F90 routine very much like the
> WindTunnel example. I know that when Grid_applyBCEdge is called,
> it is seeing the correct negative integer value (-38) for a user-
> defined boundary condition from the constants.h file. The
> simulation runs when I set lrefine_min = lrefine_max for a uniform
> grid and appears to give a correct physical solution. But when I
> try to run with adaptive mesh refinement, say lrefine_min = 1 and
> lrefine_max = 6, I get the error shown below that my density and
> internal enery are zero after the cal
> l to Eos. I believe this is occurring in the call to Eos_wrapped
> in gr_expandDomain.F90. I have attached my Config file and
> parameter file and would appreciate any ideas as to where to look
> to track down this error. Thanks, Gary.
>
> Dr. Gary Forjan
> Department of Computational and Data Sciences
> George Mason University, Fairfax, Va
> gforjan at gmu.edu
>
> *** Error printout follows ***
>
> Grid_applyBCEdge.F90 initialization:
> sim_rho0Chr = 4.038226615193243E-013
> sim_TChr = 30000.0000000000
> sim_Gamma = 1.66670000000000
> sim_p0Chr = 2.00000000000000
> bcType = -38
> iteration, no. not moved = 0 4
> iteration, no. not moved = 1 2
> iteration, no. not moved = 2 0
> refined: total leaf blocks = 6
> refined: total blocks = 11
> WARNING after gc filling: min.
> unk(DENS_VAR)=0.000000000000000000000 PE=2 block=1
> type=1
>
> 1 2.32E-15 2.24E-15 2.16E-15 2.08E-15 2.01E-15 1.94E-15 1.87E-
> 15 1.80E-15 1.74E-15 1.68E-15 1.62E-15 1.56E-15 0.0 0.0
> 0.0 0.0
>
> WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000
> PE=2 block=1 type=1
>
>
> 1 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14
> 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 0.0
> 0.0 0.0 0.0
>
> WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000
> PE=2 block=1 type=1
>
>
> 1 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14
> 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 0.0
> 0.0 0.0 0.0
>
> DRIVER_ABORT:
> [Eos_putData] ERROR Density or Internal Energy are zero after a
> call to EOS!
> WARNING after gc filling: min.
> unk(DENS_VAR)=0.000000000000000000000 PE=6 block=1
> type=1
>
> 1 0.0 0.0 0.0 0.0 4.76E-16 4.59E-16 4.43E-
> 16 4.27E-16 4.12E-16 3.98E-16 3.83E-16 3.70E-16 3.57E-16 3.44E-16
> 3.32E-16 3.20E-1
> 6
> WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000
> PE=6 block=1 type=1
>
>
> 1 0.0 0.0 0.0 0.0 2.24E+14 2.24E+14
> 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14
> 2.24E+14 2.24E+14 2.24E+1
> 4
> WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000
> PE=6 block=1 type=1
>
>
> 1 0.0 0.0 0.0 0.0 2.24E+14 2.24E+14
> 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14 2.24E+14
> 2.24E+14 2.24E+14 2.24E+1
> 4
> DRIVER_ABORT:
> [Eos_putData] ERROR Density or Internal Energy are zero after a
> call to EOS!
> rank 6 in job 1 r2i0n13_59888 caused collective abort of all ranks
> exit status of rank 6: return code 1
> rank 2 in job 1 r2i0n13_59888 caused collective abort of all ranks
> exit status of rank 2: return code 1
>
>
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