This may be a stupid questions, but I get no idea how to do this.
I followed the tutorial and finally generate analysis filed Data/states/mpas.3dvar.2019-08-08_12.00.00.nc.
I tried to take this file as MPAS model initial condition，but It didnot success. The whole processes are as follow:
The streams.atmosphere is:
<streams>
<immutable_stream name="static"
type="input"
filename_template="x1.256002.init.nc"
input_interval="initial_only" />
<immutable_stream name="input"
type="input"
filename_template="Data/states/mpas.3dvar.$Y-$M-$D_$h.$m.$s.nc"
input_interval="initial_only" />
<immutable_stream name="restart"
type="input;output"
io_type="pnetcdf,cdf5"
filename_template="restart.$Y-$M-$D_$h.$m.$s.nc"
input_interval="initial_only"
clobber_mode="overwrite"
output_interval="0_06:00:00" />
<stream name="output"
type="output"
io_type="pnetcdf,cdf5"
filename_template="history.$Y-$M-$D_$h.$m.$s.nc"
clobber_mode="overwrite"
input_interval="initial_only"
output_interval="0_06:00:00" >
<file name="stream_list.atmosphere.output"/>
</stream>
<stream name="diagnostics"
type="output"
filename_template="diag.$Y-$M-$D_$h.$m.$s.nc"
clobber_mode="overwrite"
output_interval="none" >
<file name="stream_list.atmosphere.diagnostics"/>
</stream>
<stream name="surface"
type="none"
filename_template="x1.256002.sfc_update.nc"
filename_interval="none"
input_interval="none" >
<file name="stream_list.atmosphere.surface"/>
</stream>
<immutable_stream name="iau"
type="none"
filename_template="x1.256002.AmB.$Y-$M-$D_$h.$m.$s.nc"
filename_interval="none"
packages="iau"
input_interval="none" />
<!--immutable_stream name="da_state"
type="output"
io_type="pnetcdf,cdf5"
clobber_mode="truncate"
filename_template="mpasout.$Y-$M-$D_$h.$m.$s.nc"
output_interval="0_06:00:00" /-->
</streams>
and the namelist.atmosphere is:
&nhyd_model
config_time_integration_order = 2
config_dt = 240
config_start_time = "2019-08-08_12:00:00"
config_run_duration = '0_24:00:00'
config_split_dynamics_transport = true
config_number_of_sub_steps = 2
config_dynamics_split_steps = 3
config_h_mom_eddy_visc2 = 0.0
config_h_mom_eddy_visc4 = 0.0
config_v_mom_eddy_visc2 = 0.0
config_h_theta_eddy_visc2 = 0.0
config_h_theta_eddy_visc4 = 0.0
config_v_theta_eddy_visc2 = 0.0
config_horiz_mixing = '2d_smagorinsky'
config_len_disp = 48000.0
config_visc4_2dsmag = 0.05
config_w_adv_order = 3
config_theta_adv_order = 3
config_scalar_adv_order = 3
config_u_vadv_order = 3
config_w_vadv_order = 3
config_theta_vadv_order = 3
config_scalar_vadv_order = 3
config_scalar_advection = true
config_positive_definite = false
config_monotonic = true
config_coef_3rd_order = 0.25
config_epssm = 0.1
config_smdiv = 0.1
/
&damping
config_zd = 22000.0
config_xnutr = 0.2
/
&io
config_pio_num_iotasks = 0
config_pio_stride = 1
/
&decomposition
config_block_decomp_file_prefix = 'x1.256002.graph.info.part.'
/
&restart
config_do_restart = false
/
&printout
config_print_global_minmax_vel = true
config_print_detailed_minmax_vel = true
/
&IAU
config_IAU_option = 'off'
config_IAU_window_length_s = 21600.
/
&physics
config_sst_update = false
config_sstdiurn_update = false
config_deepsoiltemp_update = false
config_radtlw_interval = '00:30:00'
config_radtsw_interval = '00:30:00'
config_bucket_update = 'none'
config_physics_suite = 'mesoscale_reference'
/
&soundings
config_sounding_interval = 'none'
/
&assimilation
config_jedi_da = false
/
However, the model can’t run. It says CRITICAL ERROR: NaN detected in 'w' field.
----------------------------------------------------------------------
Beginning MPAS-atmosphere Output Log File for task 0 of 54
Opened at 2022/09/16 15:29:27
----------------------------------------------------------------------
Using default double-precision reals
Reading namelist from file namelist.atmosphere
*** Encountered an issue while attempting to read namelist record limited_area
The following values will be used for variables in this record:
config_apply_lbcs = F
----- Setting up physics suite 'mesoscale_reference' -----
config_microp_scheme = mp_wsm6
config_convection_scheme = cu_ntiedtke
config_pbl_scheme = bl_ysu
config_gwdo_scheme = bl_ysu_gwdo
config_radt_cld_scheme = cld_fraction
config_radt_lw_scheme = rrtmg_lw
config_radt_sw_scheme = rrtmg_sw
config_sfclayer_scheme = sf_monin_obukhov
config_lsm_scheme = noah
----- Setting up package variables -----
mp_kessler_in = F
mp_thompson_in = F
mp_wsm6_in = T
cu_grell_freitas_in = F
cu_kain_fritsch_in = F
cu_tiedtke_in = T
bl_mynn_in = F
bl_ysu_in = T
Reading streams configuration from file streams.atmosphere
WARNING: In file streams.atmosphere, output-only stream "output" has the "input_interval" attribute.
Found mesh stream with filename template x1.256002.init.nc
Using default io_type for mesh stream
** Attempting to bootstrap MPAS framework using stream: static
Bootstrapping framework with mesh fields from input file 'x1.256002.init.nc'
* Requested field rainprod is deactivated due to packages, or is a scratch variable.
* Requested field evapprod is deactivated due to packages, or is a scratch variable.
* Requested field nt_c is deactivated due to packages, or is a scratch variable.
* Requested field mu_c is deactivated due to packages, or is a scratch variable.
* Requested field nca is deactivated due to packages, or is a scratch variable.
* Requested field cubot is deactivated due to packages, or is a scratch variable.
* Requested field cutop is deactivated due to packages, or is a scratch variable.
* Requested field w0avg is deactivated due to packages, or is a scratch variable.
* Requested field qcg is deactivated due to packages, or is a scratch variable.
* Requested field sh3d is deactivated due to packages, or is a scratch variable.
* Requested field qke is deactivated due to packages, or is a scratch variable.
* Requested field qke_adv is deactivated due to packages, or is a scratch variable.
* Requested field cov is deactivated due to packages, or is a scratch variable.
* Requested field qsq is deactivated due to packages, or is a scratch variable.
* Requested field tsq is deactivated due to packages, or is a scratch variable.
* Requested field tke_pbl is deactivated due to packages, or is a scratch variable.
* Requested field el_pbl is deactivated due to packages, or is a scratch variable.
* Requested field ch is deactivated due to packages, or is a scratch variable.
* Requested field k22_shallow is deactivated due to packages, or is a scratch variable.
* Requested field kbcon_shallow is deactivated due to packages, or is a scratch variable.
* Requested field ktop_shallow is deactivated due to packages, or is a scratch variable.
* Requested field ktop_deep is deactivated due to packages, or is a scratch variable.
* Requested field xmb_total is deactivated due to packages, or is a scratch variable.
* Requested field xmb_shallow is deactivated due to packages, or is a scratch variable.
* Requested field qc_cu is deactivated due to packages, or is a scratch variable.
* Requested field qi_cu is deactivated due to packages, or is a scratch variable.
* Requested field rqrcuten is deactivated due to packages, or is a scratch variable.
* Requested field rqscuten is deactivated due to packages, or is a scratch variable.
* Requested field rniblten is deactivated due to packages, or is a scratch variable.
* Requested field scalars_amb is deactivated due to packages, or is a scratch variable.
* Requested field u_amb is deactivated due to packages, or is a scratch variable.
* Requested field rho_amb is deactivated due to packages, or is a scratch variable.
* Requested field theta_amb is deactivated due to packages, or is a scratch variable.
* Requested field lbc_scalars is deactivated due to packages, or is a scratch variable.
* Requested field lbc_u is deactivated due to packages, or is a scratch variable.
* Requested field lbc_w is deactivated due to packages, or is a scratch variable.
* Requested field lbc_rho is deactivated due to packages, or is a scratch variable.
* Requested field lbc_theta is deactivated due to packages, or is a scratch variable.
Parsing run-time I/O configuration from streams.atmosphere ...
----- found immutable stream "static" in streams.atmosphere -----
filename template: x1.256002.init.nc
filename interval: none
direction: input
reference time: initial_time
record interval: -
input alarm: initial_only
----- found immutable stream "input" in streams.atmosphere -----
filename template: Data/states/mpas.3dvar.$Y-$M-$D_$h.$m.$s.nc
filename interval: none
direction: input
reference time: initial_time
record interval: -
input alarm: initial_only
----- found immutable stream "restart" in streams.atmosphere -----
filename template: restart.$Y-$M-$D_$h.$m.$s.nc
filename interval: 0_06:00:00
clobber mode: overwrite
I/O type: Parallel-NetCDF (CDF-5, large variable support)
direction: input, output
reference time: initial_time
record interval: -
input alarm: initial_only
output alarm: 0_06:00:00
----- found immutable stream "iau" in streams.atmosphere -----
filename template: x1.256002.AmB.$Y-$M-$D_$h.$m.$s.nc
filename interval: none
direction: none
reference time: initial_time
record interval: -
package: iau
----- found stream "output" in streams.atmosphere -----
filename template: history.$Y-$M-$D_$h.$m.$s.nc
filename interval: 0_06:00:00
clobber mode: overwrite
I/O type: Parallel-NetCDF (CDF-5, large variable support)
direction: output
reference time: initial_time
record interval: -
output alarm: 0_06:00:00
----- found stream "diagnostics" in streams.atmosphere -----
filename template: diag.$Y-$M-$D_$h.$m.$s.nc
filename interval: none
clobber mode: overwrite
direction: output
reference time: initial_time
record interval: -
output alarm: none
----- found stream "surface" in streams.atmosphere -----
filename template: x1.256002.sfc_update.nc
filename interval: none
direction: none
reference time: initial_time
record interval: -
----- done parsing run-time I/O from streams.atmosphere -----
** Validating streams
Reading dimensions from input streams ...
----- reading dimensions from stream 'static' using file x1.256002.init.nc
nCells = 256002
nEdges = 768000
nVertices = 512000
TWO = 2
maxEdges = 10
maxEdges2 = 20
R3 = 3
vertexDegree = 3
nVertLevelsP1 = 42
nVertLevels = 41
FIFTEEN = 15
nMonths = 12
----- reading dimensions from stream 'input' using file Data/states/mpas.3dvar.2019-08-08_12.00.00.nc
nVertLevels = 41
nCells = 256002
nEdges = 768000
nVertLevelsP1 = 42
nSoilLevels = 4
----- reading dimensions from stream 'restart' using file restart.2019-08-08_12.00.00.nc
nVertLevels = 41
nCells = 256002
nEdges = 768000
nVertices = 512000
TWO = 2
maxEdges = 10
maxEdges2 = 20
R3 = 3
vertexDegree = 3
nVertLevelsP1 = 42
FIFTEEN = 15
nLags = 140
nOznLevels = 59
nMonths = 12
nSoilLevels = 4
----- skipping inactive stream 'iau'
*** unable to open input file lbc.2019-08-08_12.00.00.nc for stream 'lbc_in'
----- reading dimensions from stream 'da_state' using file mpasout.2019-08-08_12.00.00.nc
nVertLevels = 41
nCells = 256002
nEdges = 768000
nVertLevelsP1 = 42
nSoilLevels = 4
----- done reading dimensions from input streams -----
Processing decomposed dimensions ...
----- done processing decomposed dimensions -----
Assigning remaining dimensions from definitions in Registry.xml ...
THREE = 3
TWENTYONE = 21
nAerLevels = 29 (naerlev)
cam_dim1 = 4 (camdim1)
nVertLevelsP2 = 43
nIsoLevelsT = 5
nIsoLevelsZ = 13
----- done assigning dimensions from Registry.xml -----
WARNING: Variable cldfrac not in input file.
WARNING: Variable re_cloud not in input file.
WARNING: Variable re_ice not in input file.
WARNING: Variable re_snow not in input file.
WARNING: Variable pressure_p not in input file.
WARNING: Variable pressure_base not in input file.
WARNING: Variable rho_base not in input file.
WARNING: Variable theta_base not in input file.
WARNING: Variable refl10cm_max not in input file.
WARNING: Variable lai not in input file.
WARNING: Variable sfc_albbck not in input file.
WARNING: Variable sfc_albedo not in input file.
WARNING: Variable sfc_albedo_seaice not in input file.
WARNING: Variable sfc_emibck not in input file.
WARNING: Variable mavail not in input file.
WARNING: Variable sfc_emiss not in input file.
WARNING: Variable thc not in input file.
WARNING: Variable ust not in input file.
WARNING: Variable xicem not in input file.
WARNING: Variable z0 not in input file.
WARNING: Variable znt not in input file.
WARNING: Variable snowc not in input file.
WARNING: Variable tmn not in input file.
WARNING: Variable seaice not in input file.
WARNING: Variable dzs not in input file.
WARNING: Variable zs not in input file.
WARNING: Variable ter not in input file.
WARNING: Variable h_oml_initial not in input file.
Checking consistency of limited-area settings...
- config_apply_lbcs = F
- Maximum value in bdyMaskCell = 0
----- done checking limited-area settings -----
DT_RADTLW =1800.00000000000
DT_RADTSW =1800.00000000000
DT_CU =240.000000000000
DT_PBL =240.000000000000
IMS =1 IME =4739
JMS =1 JME =1
KMS =1 KME =42
IDS =1 IDE =4740
JDS =1 JDE =2
KDS =1 KDE =42
ITS =1 ITE =4739
JTS =1 JTE =1
KTS =1 KTE =41
--- specifics on cloud microphysics option microp_scheme = mp_wsm6
--- dt_microp = 240.000000000000
--- n_microp = 1
--- has_reqc = 0
--- has_reqi = 0
--- has_reqs = 0
skipping over lutype = OLD
skipping over lutype = USGS
landuse type = MODIFIED_IGBP_MODIS_NOAH found 33 categories 2 seasons
--- initialize NOAH LSM tables
skipping over lutype = USGS
landuse type = MODIFIED_IGBP_MODIS_NOAH found 20 categories
end read VEGPARM.TBL
input soil texture classification = STAS
soil texture classification = STAS found 19 categories
end read SOILPARM.TBL
end read GENPARM.TBL
--- end initialize NOAH LSM tables
min/max of meshScalingDel2 = 1.00000000000000 1.00000000000000
min/max of meshScalingDel4 = 1.00000000000000 1.00000000000000
Timing for diagnostic computation: 2.48376270569861 s
Timing for stream output: 9.88402289245278 s
Begin timestep 2019-08-08_12:00:00
--- time to update background surface albedo, greeness fraction.
--- time to run the LW radiation scheme L_RADLW =T
--- time to run the SW radiation scheme L_RADSW =T
--- time to run the convection scheme L_CONV =T
--- time to update the ozone climatology for RRTMG radiation codes
--- time to apply limit to accumulated rainc and rainnc L_ACRAIN =F
--- time to apply limit to accumulated radiation diags. L_ACRADT =F
--- time to calculate additional physics_diagnostics =F
split dynamics-transport integration 3
global min w: 0.100000000000000E+21 k=-1, 0.00000000000000 lat, 0.00000000000000 lon
global max w: -0.100000000000000E+21 k=-1, 0.00000000000000 lat, 0.00000000000000 lon
global min u: 0.100000000000000E+21 k=-1, 0.00000000000000 lat, 0.00000000000000 lon
global max u: -0.100000000000000E+21 k=-1, 0.00000000000000 lat, 0.00000000000000 lon
global max wsp: -0.100000000000000E+21 k=-1, 0.00000000000000 lat, 0.00000000000000 lon
CRITICAL ERROR: NaN detected in 'w' field.
But I checked my file. it didnot contain NaN values.
(base) [cym@node1]~/tutorials/mpas-jedi-lekima% cat checknan.ncl
begin
f=addfile("Data/states/mpas.3dvar.2019-08-08_12.00.00.nc","r")
w=f->w
print("any(isnan_ieee(w))")
print(any(isnan_ieee(w)))
end
(base) [cym@node1]~/tutorials/mpas-jedi-lekima% ncl checknan.ncl
Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) any(isnan_ieee(w))
(0) False
Maybe I made some mistake?