[FLASH-USERS] Laserslab: problem with hydrogen IONMIX/ energy groups and computed dt is not positive
Stylianos Passalidis
stylianos.passalidis at sorbonne-universite.fr
Mon Jan 11 12:46:45 EST 2021
Hello all
We have compiled and ran a customised version Laserslab with the
example3d.par and everything seems to work. On the contrary when we
want to use hydrogen instead of helium and/or aluminum we encounter a
number of errors, different ones each time we use a different EOS tab file.
* IONMIX h-100grp-lte.imx
We have set it up with the ./setup custom_Laserslab -auto -3d
+hdf5typeio species=cham,targ +mtmmmt +laser +uhd3t +mgd
mgd_meshgroups=100 -parfile=custom_3d.par +pm4dev
and I take a succesfull make.
In the custom_3d.par i have declared 100
rt_mgdNumGroups = 100
#rt_mgdBoundEntry = "grbd_manual"
rt_mgdBounds_1 = 0.0
rt_mgdBounds_2 = 0.00139292180089
rt_mgdBounds_3 = 0.001564702535
...
rt_mgdBounds_100 = 124.0/
rt_mgdBounds_101 = 10000.
acquired from the
FLASH4.6.1/source/Simulation/SimulationMain/radflaHD/SupernovaRad1D/flash_working.par
Then when I ran it I receive the following error, relevant to IONMIX /
Opacity energy group mismatch, bold in the output flow! Lasslab.log
attached for further information!
[itazes at login01 object]$ mpirun -np 2
/users/pr007/itazes/FLASH4.6.1/object/flash4
...
Grid_init: resolution based on runtime params:
lrefine dx dy dz
3 0.003 0.003 0.003
4 0.001 0.001 0.001
5 6.250E-04 6.250E-04 6.250E-04
MaterialProperties initialized
Cosmology initialized
[eos_tabBrowseIonmixTables] IONMIX file found: h-100grp-lte.imx
Grid_init: resolution based on runtime params:
lrefine dx dy dz
3 0.003 0.003 0.003
4 0.001 0.001 0.001
5 6.250E-04 6.250E-04 6.250E-04
MaterialProperties initialized
Cosmology initialized
[eos_tabBrowseIonmixTables] IONMIX file found: h-100grp-lte.imx
in eos_inittabulated, tableName = h-100grp-lte.imx
in eos_inittabulated, groupName = -none-
in eos_inittabulated, tableName = h-100grp-lte.imx
in eos_inittabulated, groupName = -none-
[eos_tabBrowseIonmixTables] IONMIX file found: h-100grp-lte.imx
[eos_tabBrowseIonmixTables] IONMIX file found: h-100grp-lte.imx
in eos_inittabulated, tableName = h-100grp-lte.imx
in eos_inittabulated, groupName = -none-
in eos_inittabulated, tableName = h-100grp-lte.imx
in eos_inittabulated, groupName = -none-
RadTrans initialized
[EnergyDeposition_init] INFO: Using ed_irradVar= 16
ed_irradVarName=lase
RadTrans initialized
[EnergyDeposition_init] INFO: Using ed_irradVar= 16
ed_irradVarName=lase
Source terms initialized
Source terms initialized
iteration, no. not moved = 0 0
refined: total leaf blocks = 8
refined: total blocks = 9
[amr_morton_process]: Initializing surr_blks using standard orrery
implementation
iteration, no. not moved = 0 0
refined: total leaf blocks = 8
refined: total blocks = 9
[amr_morton_process]: Initializing surr_blks using standard orrery
implementation
INFO: Grid_fillGuardCells is ignoring masking.
INFO: Grid_fillGuardCells is ignoring masking.
iteration, no. not moved = 0 0
refined: total leaf blocks = 64
refined: total blocks = 73
iteration, no. not moved = 0 0
refined: total leaf blocks = 64
refined: total blocks = 73
Finished with Grid_initDomain, no restart
Driver_abort called. See log file for details.
* Error message is [op_readIonmixTables] ERROR: IONMIX / Opacity energy
group mismatch
Calling MPI_Abort() for shutdown in 2 seconds!*
Finished with Grid_initDomain, no restart
Driver_abort called. See log file for details.
* Error message is [op_readIonmixTables] ERROR: IONMIX / Opacity energy
group mismatch**
** Calling MPI_Abort() for shutdown in 2 seconds*!
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[54963,1],0]
Exit code: 1
--------------------------------------------------------------------------
[itazes at login01 object]$
* IONMIX4 h-imx-1grp.cn4
Furthermore, we decided to use the IONMIX4 hydrogen tabulated EOS file,
h-imx-1grp.cn4 setting it up with
We have set it up with the ./setup custom_Laserslab -auto -3d
+hdf5typeio species=cham,targ +mtmmmt +laser +uhd3t +mgd
mgd_meshgroups=1 -parfile=custom_3d.par +pm4dev
In this case we managed to surpass the IONMIX/ Opacity energy group
mismatch error in this case only 2 boundaries in our .par where used as
following:
rt_mgdNumGroups = 1
#rt_mgdBoundEntry = "grbd_manual"
rt_mgdBounds_1 = 1.0e-2
rt_mgdBounds_2 = 1
and we encounter another error:
Error message is [Diffuse]: computed dt is not positive! Aborting!
Calling MPI_Abort() for shutdown in 2 seconds,
bold in the output flow! Lasslab.log attached for further information!
We have already tried to play with the CFL value and lower it but
changed in out output
also we changed the value of
tdt_diff_factor = 1.0e+100 # Disable diffusion dt
but we do not really understand its purpose. FYI we attach the flash.par
we used
[itazes at login01 object]$ mpirun -np 1
/users/pr007/itazes/FLASH4.6.1/object/flash4
RuntimeParameters_read: ignoring unknown parameter "iGridSize"...
RuntimeParameters_read: ignoring unknown parameter "jGridSize"...
RuntimeParameters_read: ignoring unknown parameter "kGridSize"...
Grid_init: resolution based on runtime params:
lrefine dx dy dz
3 0.003 0.003 0.003
4 0.001 0.001 0.001
5 6.250E-04 6.250E-04 6.250E-04
MaterialProperties initialized
Cosmology initialized
[eos_tabBrowseIonmix4Tables] IONMIX4 file found: h-imx-1grp.cn4
[eos_tabBrowseIonmix4Tables] IONMIX4 file found: h-imx-1grp.cn4
in eos_inittabulated, tableName = h-imx-1grp.cn4
in eos_inittabulated, groupName = -none-
in eos_inittabulated, tableName = h-imx-1grp.cn4
in eos_inittabulated, groupName = -none-
RadTrans initialized
[EnergyDeposition_init] INFO: Using ed_irradVar= 16
ed_irradVarName=lase
Source terms initialized
iteration, no. not moved = 0 0
refined: total leaf blocks = 8
refined: total blocks = 9
[amr_morton_process]: Initializing surr_blks using standard orrery
implementation
INFO: Grid_fillGuardCells is ignoring masking.
iteration, no. not moved = 0 0
refined: total leaf blocks = 64
refined: total blocks = 73
Finished with Grid_initDomain, no restart
Ready to call Hydro_init
[Hydro_init] INFO: Turning shockDetect on because RiemannSolver is hybrid.
Hydro initialized
Gravity initialized
Driver_abort called. See log file for details.
* Error message is [Diffuse]: computed dt is not positive! Aborting!**
** Calling MPI_Abort() for shutdown in 2 seconds!*
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[52177,1],0]
Exit code: 1
--------------------------------------------------------------------------
[itazes at login01 object]$
Stelios
--
Stylianos Passalidis
Phd candidate
Laboratory of Physical Chemistry - Matter and Radiation
Sorbonne Université
4 place Jussieu, 75005 Paris
Bureau 111, Corridor 43-44
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20210111/3e8b9f96/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: h-100grp-lte_imx-lasslab.log
Type: text/x-log
Size: 1570174 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20210111/3e8b9f96/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: h-imx-1grp_cn4-lasslab.log
Type: text/x-log
Size: 3831884 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20210111/3e8b9f96/attachment-0001.bin>
-------------- next part --------------
run_comment = "3D Laser Example Simulation"
log_file = "lasslab.log"
basenm = "lasslab_"
# This particular parfile is used as an example parfile that is
# described in detail in the users guide.
# Setup options for this example simulation are:
# ./setup -auto LaserSlab -noc -3d +pm4dev +hdf5typeio
# -nxb=16 -nyb=16 -nzb=16 +mtmmmt +laser +mgd
# +uhd3t species=cham,targ mgd_meshgroups=6
# -parfile=example3d.par
#########################
# OUTPUT PARAMETERS #
#########################
### Checkpoint Options ###
checkpointFileIntervalTime = 1.0
checkpointFileIntervalStep = 60
### Plot Options ###
plotFileNumber = 0
plotFileIntervalStep = 20
plot_var_1 = "dens"
plot_var_2 = "depo"
plot_var_3 = "tele"
plot_var_4 = "tion"
plot_var_5 = "ye "
plot_var_6 = "sumy"
### Restart Options ###
restart = .false.
checkpointFileNumber = 0
########################################
# #
# RADIATION/OPACITY PARAMETERS #
# #
########################################
rt_useMGD = .true.
rt_mgdNumGroups = 100
rt_mgdBoundEntry = "grbd_manual"
rt_mgdBounds_1 = 0.0
rt_mgdBounds_2 = 0.00139292180089
rt_mgdBounds_3 = 0.001564702535
rt_mgdBounds_4 = 0.00175766796203
rt_mgdBounds_5 = 0.00197443066374
rt_mgdBounds_6 = 0.00221792541603
rt_mgdBounds_7 = 0.00249144892318
rt_mgdBounds_8 = 0.00279870445235
rt_mgdBounds_9 = 0.00314385197252
rt_mgdBounds_10 = 0.00353156447686
rt_mgdBounds_11 = 0.00396709125087
rt_mgdBounds_12 = 0.00445632894312
rt_mgdBounds_13 = 0.00500590140066
rt_mgdBounds_14 = 0.00562324935008
rt_mgdBounds_15 = 0.00631673113837
rt_mgdBounds_16 = 0.00709573589759
rt_mgdBounds_17 = 0.00797081066543
rt_mgdBounds_18 = 0.0089538031828
rt_mgdBounds_19 = 0.0100580223018
rt_mgdBounds_20 = 0.0112984181758
rt_mgdBounds_21 = 0.0126917846715
rt_mgdBounds_22 = 0.0142569867429
rt_mgdBounds_23 = 0.0160152158462
rt_mgdBounds_24 = 0.0179902768533
rt_mgdBounds_25 = 0.0202089103493
rt_mgdBounds_26 = 0.0227011546757
rt_mgdBounds_27 = 0.0255007526235
rt_mgdBounds_28 = 0.028645608281
rt_mgdBounds_29 = 0.0321783002214
rt_mgdBounds_30 = 0.036146657979
rt_mgdBounds_31 = 0.0406044096197
rt_mgdBounds_32 = 0.0456119091707
rt_mgdBounds_33 = 0.0512369537614
rt_mgdBounds_34 = 0.0575557015368
rt_mgdBounds_35 = 0.0646537027712
rt_mgdBounds_36 = 0.0726270581439
rt_mgdBounds_37 = 0.0815837198575
rt_mgdBounds_38 = 0.0916449532157
rt_mgdBounds_39 = 0.102946978448
rt_mgdBounds_40 = 0.115642815014
rt_mgdBounds_41 = 0.129904353346
rt_mgdBounds_42 = 0.145924682102
rt_mgdBounds_43 = 0.16392070241
rt_mgdBounds_44 = 0.18413606452
rt_mgdBounds_45 = 0.206844466613
rt_mgdBounds_46 = 0.232353360435
rt_mgdBounds_47 = 0.261008113919
rt_mgdBounds_48 = 0.293196687168
rt_mgdBounds_49 = 0.329354885085
rt_mgdBounds_50 = 0.369972257795
rt_mgdBounds_51 = 0.415598728716
rt_mgdBounds_52 = 0.466852040042
rt_mgdBounds_53 = 0.524426116424
rt_mgdBounds_54 = 0.589100460101
rt_mgdBounds_55 = 0.66175070467
rt_mgdBounds_56 = 0.743360470395
rt_mgdBounds_57 = 0.835034681561
rt_mgdBounds_58 = 0.938014526168
rt_mgdBounds_59 = 1.05369426053
rt_mgdBounds_60 = 1.18364008626
rt_mgdBounds_61 = 1.32961135529
rt_mgdBounds_62 = 1.49358438992
rt_mgdBounds_63 = 1.67777924048
rt_mgdBounds_64 = 1.88468974286
rt_mgdBounds_65 = 2.11711728286
rt_mgdBounds_66 = 2.37820872447
rt_mgdBounds_67 = 2.67149901564
rt_mgdBounds_68 = 3.00095904835
rt_mgdBounds_69 = 3.37104942099
rt_mgdBounds_70 = 3.78678083095
rt_mgdBounds_71 = 4.25378191503
rt_mgdBounds_72 = 4.7783754562
rt_mgdBounds_73 = 5.36766398854
rt_mgdBounds_74 = 6.02962595928
rt_mgdBounds_75 = 6.77322374993
rt_mgdBounds_76 = 7.60852501903
rt_mgdBounds_77 = 8.54683900939
rt_mgdBounds_78 = 9.60086966525
rt_mgdBounds_79 = 10.7848876325
rt_mgdBounds_80 = 12.1149234705
rt_mgdBounds_81 = 13.6089846921
rt_mgdBounds_82 = 15.2872995691
rt_mgdBounds_83 = 17.1725910053
rt_mgdBounds_84 = 19.2903841847
rt_mgdBounds_85 = 21.6693521601
rt_mgdBounds_86 = 24.3417040605
rt_mgdBounds_87 = 27.3436211748
rt_mgdBounds_88 = 30.7157468143
rt_mgdBounds_89 = 34.5037365874
rt_mgdBounds_90 = 38.7588765361
rt_mgdBounds_91 = 43.5387775043
rt_mgdBounds_92 = 48.908155137
rt_mgdBounds_93 = 54.939706074
rt_mgdBounds_94 = 61.7150921977
rt_mgdBounds_95 = 69.3260462632
rt_mgdBounds_96 = 77.8756138787
rt_mgdBounds_97 = 87.4795486529
rt_mgdBounds_98 = 98.2678793959
rt_mgdBounds_99 = 110.386670595
rt_mgdBounds_100 = 124.0
rt_mgdBounds_101 = 10000.
#rt_mgdNumGroups = 6
#rt_mgdBounds_1 = 1.0e-01
#rt_mgdBounds_2 = 1.0e+00
#rt_mgdBounds_3 = 1.0e+01
#rt_mgdBounds_4 = 1.0e+02
#rt_mgdBounds_5 = 1.0e+03
#rt_mgdBounds_6 = 1.0e+04
#rt_mgdBounds_7 = 1.0e+05
rt_mgdFlMode = "fl_harmonic"
rt_mgdFlCoef = 1.0
rt_mgdXlBoundaryType = "vacuum" #"reflecting"
rt_mgdXrBoundaryType = "vacuum"
rt_mgdYlBoundaryType = "vacuum"
rt_mgdYrBoundaryType = "vacuum" #"reflecting"
rt_mgdZlBoundaryType = "vacuum" #"reflecting"
rt_mgdZrBoundaryType = "vacuum" #"reflecting"
useOpacity = .true.
### SET CHAMBER (HELIUM) OPACITY OPTIONS ###
op_chamAbsorb = "op_tabpa"
op_chamEmiss = "op_tabpe"
op_chamTrans = "op_tabro"
op_chamFileType = "ionmix"
op_chamFileName = "h-100grp-lte.imx"
### SET TARGET (ALUMINUM) OPACITY OPTIONS ###
op_targAbsorb = "op_tabpa"
op_targEmiss = "op_tabpe"
op_targTrans = "op_tabro"
op_targFileType = "ionmix"
op_targFileName = "h-100grp-lte.imx"
############################
# #
# LASER PARAMETERS #
# #
############################
useEnergyDeposition = .true.
ed_maxRayCount = 160000
ed_gradOrder = 2
### LASER IO OPTIONS ###
ed_useLaserIO = .true.
ed_laserIOMaxNumberOfPositions = 10000
ed_laserIOMaxNumberOfRays = 128
ed_computeGradNeleX = .false.
ed_computeGradNeleZ = .false.
### SETUP LASER PULSES ###
ed_numberOfPulses = 3
# Define Pulse 1:
ed_numberOfSections_1 = 2
ed_time_1_1 = 0.0
ed_time_1_2 = 1.4e-09
ed_power_1_1 = 35000000000 #1.3e+07
ed_power_1_2 = 35000000000 #(375mJ/5ns) #1.3e+07
# Define Pulse 2:
ed_numberOfSections_2 = 5
ed_time_2_1 = 0.0
ed_time_2_2 = 1.6e-09
ed_time_2_3 = 1.65e-09
ed_time_2_4 = 1.7e-09
ed_time_2_5 = 3.0e-09
ed_power_2_1 = 1.3e+07
ed_power_2_2 = 1.3e+07
ed_power_2_3 = 3.13e+08
ed_power_2_4 = 1.3e+07
ed_power_2_5 = 1.3e+07
# Define Pulse 3:
ed_numberOfSections_3 = 5
ed_time_3_1 = 0.0
ed_time_3_2 = 1.6e-09
ed_time_3_3 = 1.65e-09
ed_time_3_4 = 1.7e-09
ed_time_3_5 = 3.0e-09
ed_power_3_1 = 2.333333e+07
ed_power_3_2 = 2.333333e+07
ed_power_3_3 = 6.233333e+08
ed_power_3_4 = 2.333333e+07
ed_power_3_5 = 2.333333e+07
### SETUP LASER BEAM ###
ed_numberOfBeams = 1
# Setup Gaussian Beam:
ed_lensX_1 = -0.2
ed_lensY_1 = 400.0e-04
ed_lensZ_1 = 200.0e-04
ed_targetX_1 = 0.0
ed_targetY_1 = 400.0e-04
ed_targetZ_1 = 200.0e-04
ed_targetSemiAxisMajor_1 = 0.75e-03
ed_targetSemiAxisMinor_1 = 0.75e-03
ed_semiAxisMajorTorsionAxis_1 = "z"
ed_semiAxisMajorTorsionAngle_1 = 0.0
ed_pulseNumber_1 = 1
ed_wavelength_1 = 1.053 #1.053
ed_crossSectionFunctionType_1 = "gaussian2D" # 2D Gaussian Beam
ed_gridType_1 = "square2D"
ed_gaussianExponent_1 = 1.0
ed_gaussianRadiusMajor_1 = 1.201122e-03
ed_gaussianRadiusMinor_1 = 1.201122e-03
ed_lensSemiAxisMajor_1 = 3.0e-03
ed_numberOfRays_1 = 25000 #100000
### Conduction parameters ###
useDiffuse = .true.
useConductivity = .true.
diff_useEleCond = .true.
diff_eleFlMode = "fl_larsen"
diff_eleFlCoef = 0.06
diff_thetaImplct = 1.0
diff_eleXlBoundaryType = "neumann"
diff_eleXrBoundaryType = "neumann"
diff_eleYlBoundaryType = "vacuum"
diff_eleYrBoundaryType = "neumann"
diff_eleZlBoundaryType = "neumann"
diff_eleZrBoundaryType = "neumann"
### Heat-Exchange parameters ###
useHeatexchange = .true.
### Material and EOS parameters ###
eosModeInit = "dens_temp_gather"
eosMode = "dens_ie_recal_gather"
smallt = 1.0
smallx = 1.0e-99
eos_useLogTables = .false.
############################
# #
# HYDRO PARAMETERS #
# #
############################
# Use second order hybrid solver with minmod slope limiter. This
# essentially eliminates any Carbuncle instability.
order = 2 # Interpolation order (first/second/third/fifth order)
slopeLimiter = "vanLeer" # Slope limiters (minmod, mc, vanLeer, hybrid, limited)
LimitedSlopeBeta = 1. # Slope parameter for the "limited" slope by Toro
charLimiting = .true. # Characteristic limiting vs. Primitive limiting
use_avisc = .true. # use artificial viscosity (originally for PPM)
cvisc = 0.1 # coefficient for artificial viscosity
use_flattening = .false. # use flattening (dissipative) (originally for PPM)
use_steepening = .false. # use contact steepening (originally for PPM)
use_upwindTVD = .false. # use upwind biased TVD slope for PPM (need nguard=6)
RiemannSolver = "hybrid" # Roe, HLL, HLLC, LLF, Marquina, hybrid
entropy = .false. # Entropy fix for the Roe solver
shockDetect = .false. # Shock Detect for numerical stability
addThermalFlux = .false.
use_hybridOrder = .true.
# Hydro boundary conditions:
xl_boundary_type = "outflow" #"reflect"
xr_boundary_type = "outflow"
yl_boundary_type = "outflow"
yr_boundary_type = "outflow"
zl_boundary_type = "outflow" #"reflect"
zr_boundary_type = "outflow" #"reflect"
##########################
# INITIAL CONDITIONS #
##########################
sim_targetRadius = 0.0 #400.0e-04
sim_targetHeight = 00.0e-04 #50.0e-04
sim_vacuumHeight = 00.0e-04 #00.0e-04
# Target material defaults set for Aluminum at room temperature:
sim_rhoTarg = 2.7
sim_teleTarg = 290.11375
sim_tionTarg = 290.11375
sim_tradTarg = 290.11375
ms_targA = 26.9815386
ms_targZ = 13.0
ms_targZMin = 0.02
eos_targEosType = "eos_tab"
eos_targSubType = "ionmix"
eos_targTableFile = "h-100grp-lte.imx"
# Chamber material defaults set for Helium at pressure 1.6 mbar:
sim_rhoCham = 0.000287 #1ncr of 1053nm 0.00287 is 1ncr of 800 nm
sim_teleCham = 290.11375
sim_tionCham = 290.11375
sim_tradCham = 290.11375
ms_chamA = 1.00784
ms_chamZ = 1.0
eos_chamEosType = "eos_tab"
eos_chamSubType = "ionmix"
eos_chamTableFile = "h-100grp-lte.imx"
#######################
# TIME PARAMETERS #
#######################
tstep_change_factor = 1.10
cfl = 0.4
dt_diff_factor = 1.0e+100 # Disable diffusion dt
rt_dtFactor = 0.02
hx_dtFactor = 1.0e+100
tmax = 6.0e-09 #3.0e-09
dtmin = 1.0e-16
dtinit = 1.0e-15
dtmax = 3.0e-09
nend = 100000
#######################
# MESH PARAMETERS #
#######################
geometry = "cartesian"
# Domain size:
xmin = -400.0e-04 #-500.0e-04
xmax = 400.0e-04
ymin = 0.0
ymax = 800.0e-04
zmin = -400.0e-04
zmax = 400.0e-04
# NOFBS options:
#iProcs = 1
#jProcs = 1
#kProcs = 1
iGridSize = 16 #32
jGridSize = 16
kGridSize = 16 #32
# Total number of blocks:
nblockx = 1
nblocky = 1
nblockz = 1
lrefine_max = 3
lrefine_min = 1
refine_var_1 = "dens"
refine_var_2 = "tele"
More information about the flash-users
mailing list