ROMS observations to DART observation sequences
Overview
The relationship between ROMS and DART is slightly different than most other models. ROMS has the ability to apply its
own forward operator as the model is advancing (a capability needed for variational assimilation) which produces
something the ROMS community calls ‘verification’ observations. The observation file that is input to ROMS is
specified by the s4dvar.in:OBSname variable. The verification obs are written out to a netcdf file whose name is
specified by the s4dvar.in:MODname variable. Since each ROMS model is advancing independently, a set of
verification observation files are created during a DART/ROMS assimilation cycle. This set of files can be converted
using convert_roms_obs to produce a DART observation sequence file that has precomputed forward operators (FOs).
convert_roms_obs can also convert s4dvar.in:OBSname,MODname files to a DART observation sequence file
that does not have the precomputed FOs.
The ROMS verification observation files must contain the obs_provenance as a global attribute and the following variables:
obs_lat, obs_lon, obs_depth
obs_value
obs_error
obs_time
NLmodel_value
obs_scale
obs_provenance
Note that the obs_provenance:flag_values, and obs_provenance:flag_meanings attributes are totally ignored - those relationships are specified by the global attribute obs_provenance.
Locations only specified by obs_Xgrid, obs_Ygrid, obs_depth are not supported.
filter and perfect_model_obs must also be informed which DART observation types use precomputed
forward operators. This is done by setting the input.nml&obs_kind_nml namelist. An example is shown at the
end of the PROGRAMS section below.Namelist
This namelist is read from the file input.nml. Namelists start with an ampersand ‘&’ and terminate with a slash ‘/’.
Character strings that contain a ‘/’ must be enclosed in quotes to prevent them from prematurely terminating the
namelist.
&convert_roms_obs_nml
ens_size = 1
roms_mod_obs_files = ''
roms_mod_obs_filelist = 'filelist.txt'
dart_output_obs_file = 'obs_seq.out'
append_to_existing = .false.
use_precomputed_values = .true.
add_random_noise = .false.
pert_amplitude = 0.01
verbose = 0
type_translations = 'NULL'
/
Item |
Type |
Description |
|---|---|---|
ens_size |
integer |
Number of ensemble members which are expected to be found when creating the expected obs values. This must match the number of ROMS “mod” files listed in either the ‘roms_mod_obs_files’ or ‘roms_mod_obs_filelist’ namelist items. It is an error if they are not the same length. |
roms_mods_obs_files |
character(len=256), dimension(100) |
List of filenames, one per ensemble member, that contain the observation values for each ensemble member. These are output from the ROMS program. If listing the files explicitly in this list, ‘roms_mod_obs_filelist’ must be ‘ ‘ (null). |
roms_mods_obs_filelist |
character(len=256) |
The name of an ASCII file which contains, one per line, a list of filenames, one per ensemble member, that contain the expected obs values for each ensemble member. The filenames should NOT be quoted. These are output from the ROMS program. If using a filelist, then ‘roms_mod_obs_files’ must be ‘ ‘ (null). |
dart_output_obs_file |
character(len=256) |
The name of the DART obs_seq file to create. If a file already exists with this name, it is either appended to or overwritten depending on the ‘append_to_existing’ setting below. |
append_to_existing |
logical |
If an existing ‘dart_output_obs_file’ is found, this namelist item controls how it is handled. If .true. the new observations are appended to the existing file. If .false. the new observations overwrite the existing file. |
use_precomputed_values |
logical |
flag to indicate that the output DART observation
sequence file should include the verification
observation values from all of the ROMS observation
files. If |
add_random_noise |
logical |
Almost always should be .false. . The exception is
the first cycle of an assimilation if all the ROMS
input files are identical (no ensemble currently
exists). To create differences in the forward
operator values (since they are computed by ROMS),
we can add gaussian noise here to give them
perturbed values. This should be set as well as the
“perturb_from_single_instance = .true.” namelist in
the |
pert_amplitude |
real(r8) |
Ignored unless ‘add_random_noise’ is .true. . Controls the range of random values added to the expected obs values. Sets the width of a gaussian. |
verbose |
integer |
If greater than 0, prints more information during the conversion. |
type_translations |
character(256), dimension(2, 100) |
A set of strings which control the mapping of ROMS
observation types to DART observation types. These
should be specified in pairs. The first column
should be a string that occurs in the global
attribute ‘ |
Data sources
The origin of the input observation files used by ROMS are completely unknown to me.
Programs
convert_roms_obs
Only convert_roms_obs will be discussed here.
The global attribute obs_provenance is used to relate the observation provenance to DART observation TYPES. The
ROMS ‘MODname’ netCDF file(s) must have both the obs_provenance variable and a obs_provenance global
attribute. The exact strings must be repeated in the DART convert_roms_obs_nml:type_translations variable
to be able to convert from the integer value of the obs_provenance to th DART type in the following example:
ncdump -h roms_mod_obs.nc (the output has been pruned for clarity)
netcdf roms_mod_obs {
dimensions:
record = 2 ;
survey = 5376 ;
state_var = 8 ;
datum = 2407217 ;
variables:
{snip}
int obs_provenance(datum) ;
obs_provenance:long_name = "observation origin" ;
obs_provenance:flag_values = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
double obs_time(datum) ;
obs_time:long_name = "time of observation" ;
obs_time:units = "days since 1900-01-01 00:00:00 GMT" ;
obs_time:calendar = "gregorian" ;
double obs_lon(datum) ;
obs_lon:long_name = "observation longitude" ;
obs_lon:units = "degrees_east" ;
double obs_lat(datum) ;
obs_lat:long_name = "observation latitude" ;
obs_lat:units = "degrees_north" ;
double obs_depth(datum) ;
obs_depth:long_name = "ROMS internal depth of observation variable" ;
obs_depth:units = "meters or fractional z-levels" ;
obs_depth:negative_value = "downwards" ;
obs_depth:missing_value = 1.e+37 ;
double obs_error(datum) ;
obs_error:long_name = "observation error covariance" ;
double obs_value(datum) ;
obs_value:long_name = "observation value" ;
double obs_scale(datum) ;
obs_scale:long_name = "observation screening/normalization scale" ;
obs_scale:_FillValue = 0. ;
double NLmodel_value(datum) ;
NLmodel_value:long_name = "nonlinear model at observation locations" ;
NLmodel_value:_FillValue = 1.e+37 ;
{snip}
:obs_provenance = "\n",
"1: gridded AVISO sea level anomaly (zeta)\n",
"2: gridded Aquarius SSS (salinity)\n",
"3: XBT from Met Office (temperature)\n",
"4: CTD from Met Office (temperature)\n",
"5: CTD from Met Office (salinity)\n",
"6: ARGO floats (temperature)\n",
"7: ARGO floats (salinity)\n",
"8: glider UCSD (temperature)\n",
"9: glider UCSD (salinity)\n",
"10: blended satellite SST (temperature)" ;
{snip}
input.nml:&convert_roms_obs_nml
ens_size = 32
roms_mod_obs_filelist = 'precomputed_files.txt'
dart_output_obs_file = 'obs_seq.out'
append_to_existing = .false.
use_precomputed_values = .true.
add_random_noise = .false.
verbose = 1
type_translations = "gridded AVISO sea level anomaly (zeta)", "SATELLITE_SSH",
"gridded Aquarius SSS (salinity)", "SATELLITE_SSS",
"XBT from Met Office (temperature)", "XBT_TEMPERATURE",
"CTD from Met Office (temperature)", "CTD_TEMPERATURE",
"CTD from Met Office (salinity)", "CTD_SALINITY",
"ARGO floats (temperature)", "ARGO_TEMPERATURE",
"ARGO floats (salinity)", "ARGO_SALINITY",
"glider UCSD (temperature)", "GLIDER_TEMPERATURE",
"glider UCSD (salinity)", "GLIDER_SALINITY",
"blended satellite SST (temperature)", "SATELLITE_BLENDED_SST"
/
A complete list of DART observation TYPES for oceans is described in MODULE obs_def_ocean_mod
Any or all of the DART observation types that appear in the second column of type_translations must also be
designated as observations that have precomputed forward operators. This is done by setting the
input.nml&obs_kind_nml namelist as follows:
&obs_kind_nml
assimilate_these_obs_types = 'SATELLITE_SSH',
'SATELLITE_SSS',
'XBT_TEMPERATURE',
'CTD_TEMPERATURE',
'CTD_SALINITY',
'ARGO_TEMPERATURE',
'ARGO_SALINITY',
'GLIDER_TEMPERATURE',
'GLIDER_SALINITY',
'SATELLITE_BLENDED_SST'
use_precomputed_FOs_these_obs_types = 'SATELLITE_SSH',
'SATELLITE_SSS',
'XBT_TEMPERATURE',
'CTD_TEMPERATURE',
'CTD_SALINITY',
'ARGO_TEMPERATURE',
'ARGO_SALINITY',
'GLIDER_TEMPERATURE',
'GLIDER_SALINITY',
'SATELLITE_BLENDED_SST'
/