Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#697 closed upgrade (Done)

Important: 4D-Var or EnKF initial/restart file, ROMS depths, Observations

Reported by: arango Owned by: arango
Priority: major Milestone: Release ROMS/TOMS 3.7
Component: Nonlinear Version: 3.7
Keywords: Cc:

Description (last modified by arango)

A new output NetCDF file DAINAME was added to input script, which includes the 4D-Var analysis that can be used as initial conditions for the next data assimilation cycle. Also, it can be used to restart the next run of an Ensemble Kalman Filter (EnKF). For example, this file can be read by the DART (Data Assimilation Research Testbed) software developed at DAReS NCAR.

A new C-preprocessing option ENKF_RESTART is added for using DART or other offline EnKF data assimilation packages. It generates ROMS nonlinear model initial/restart conditions for the ensemble runs.

The DAINAME file contains the usual model state variables needed to initialize ROMS:

       double zeta(ocean_time, eta_rho, xi_rho) ;
               zeta:long_name = "free-surface" ;
               zeta:units = "meter" ;
               zeta:time = "ocean_time" ;
               zeta:water_points = "mask_rho" ;
               zeta:coordinates = "lon_rho lat_rho ocean_time" ;
               zeta:field = "free-surface, scalar, series" ;
               zeta:_FillValue = 1.e+37 ;
       double ubar(ocean_time, eta_u, xi_u) ;
               ubar:long_name = "vertically integrated u-momentum component" ;
               ubar:units = "meter second-1" ;
               ubar:time = "ocean_time" ;
               ubar:coordinates = "lon_u lat_u ocean_time" ;
               ubar:field = "ubar-velocity, scalar, series" ;
               ubar:_FillValue = 1.e+37 ;
       double vbar(ocean_time, eta_v, xi_v) ;
               vbar:long_name = "vertically integrated v-momentum component" ;
               vbar:units = "meter second-1" ;
               vbar:time = "ocean_time" ;
               vbar:coordinates = "lon_v lat_v ocean_time" ;
               vbar:field = "vbar-velocity, scalar, series" ;
               vbar:_FillValue = 1.e+37 ;
       double u(ocean_time, s_rho, eta_u, xi_u) ;
               u:long_name = "u-momentum component" ;
               u:units = "meter second-1" ;
               u:time = "ocean_time" ;
               u:coordinates = "lon_u lat_u s_rho ocean_time" ;
               u:field = "u-velocity, scalar, series" ;
               u:_FillValue = 1.e+37 ;
       double v(ocean_time, s_rho, eta_v, xi_v) ;
               v:long_name = "v-momentum component" ;
               v:units = "meter second-1" ;
               v:time = "ocean_time" ;
               v:coordinates = "lon_v lat_v s_rho ocean_time" ;
               v:field = "v-velocity, scalar, series" ;
               v:_FillValue = 1.e+37 ;
       double temp(ocean_time, s_rho, eta_rho, xi_rho) ;
               temp:long_name = "potential temperature" ;
               temp:units = "Celsius" ;
               temp:time = "ocean_time" ;
               temp:coordinates = "lon_rho lat_rho s_rho ocean_time" ;
               temp:field = "temperature, scalar, series" ;
               temp:_FillValue = 1.e+37 ;
       double salt(ocean_time, s_rho, eta_rho, xi_rho) ;
               salt:long_name = "salinity" ;
               salt:time = "ocean_time" ;
               salt:coordinates = "lon_rho lat_rho s_rho ocean_time" ;
               salt:field = "salinity, scalar, series" ;
               salt:_FillValue = 1.e+37 ;

In addition, this output file also contains the time independent (zeta=0) depths z_rho, z_u, z_v, and z_w that are computed in new routine set_depth0 inside of set_depth.F:

       double z_rho(s_rho, eta_rho, xi_rho) ;
               z_rho:long_name = "time independent depth of RHO-points" ;
               z_rho:units = "meter" ;
               z_rho:negative_value = "downwards" ;
               z_rho:coordinates = "lon_rho lat_rho s_rho" ;
       double z_u(s_rho, eta_u, xi_u) ;
               z_u:long_name = "time independent depth of U-points" ;
               z_u:units = "meter" ;
               z_u:negative_value = "downwards" ;
               z_u:coordinates = "lon_u lat_u s_rho" ;
       double z_v(s_rho, eta_v, xi_v) ;
               z_v:long_name = "time independent depth of V-points" ;
               z_v:units = "meter" ;
               z_v:negative_value = "downwards" ;
               z_v:coordinates = "lon_v lat_v s_rho" ;
       double z_w(s_w, eta_rho, xi_rho) ;
               z_w:long_name = "time independent depth of W-points" ;
               z_w:units = "meter" ;
               z_w:negative_value = "downwards" ;
               z_w:coordinates = "lon_rho lat_rho s_w" ;

These depths and the state variable longitude and latitudes locations are need in EnKF packages for 3D localization and inflation techniques.

For completeness, the time dependent depths (varying zeta) can also be written to the history (HISNAME) output NetCDF file. The user just need to activate the appropriate new switches in

Hout(idpthR) == T       ! z_rho              time-varying depths of RHO-points
Hout(idpthU) == T       ! z_u                time-varying depths of U-points
Hout(idpthV) == T       ! z_v                time-varying depths of V-points
Hout(idpthW) == T       ! z_w                time-varying depths of W-points

In this case, we get the following variables in the history NetCDF file:

       double z_rho(ocean_time, s_rho, eta_rho, xi_rho) ;
               z_rho:long_name = "time dependent depth of RHO-points" ;
               z_rho:units = "meter" ;
               z_rho:time = "ocean_time" ;
               z_rho:coordinates = "lon_rho lat_rho s_rho ocean_time" ;
               z_rho:field = "z_rho, scalar, series" ;
       double z_u(ocean_time, s_rho, eta_u, xi_u) ;
               z_u:long_name = "time dependent depth of U-points" ;
               z_u:units = "meter" ;
               z_u:time = "ocean_time" ;
               z_u:coordinates = "lon_u lat_u s_rho ocean_time" ;
               z_u:field = "z_u, scalar, series" ;
       double z_v(ocean_time, s_rho, eta_v, xi_v) ;
               z_v:long_name = "time dependent depth of V-points" ;
               z_v:units = "meter" ;
               z_v:time = "ocean_time" ;
               z_v:coordinates = "lon_v lat_v s_rho ocean_time" ;
               z_v:field = "z_v, scalar, series" ;
       double z_w(ocean_time, s_w, eta_rho, xi_rho) ;
               z_w:long_name = "time dependent depth of W-points" ;
               z_w:units = "meter" ;
               z_w:time = "ocean_time" ;
               z_w:coordinates = "lon_rho lat_rho s_w ocean_time" ;
               z_w:field = "z_w, scalar, series" ;

Notice that these time varying depths are not needed in various third party software applications because ROMS output files are CF compliant and the NetCDF-Java interface is used to compute these depths automatically using the registered metadata standard_name ocean_s_coordinate_g1 or ocean_s_coordinate_g2. See WikiROMS for more information. Anyway, having these depths in the history NetCDF file has been requested by several users that want to use the R Project for Statistical Computing, for example.

The ROMS observation operator was enhanced so the output file MODNAME contains a complete input observations data in addition the model sampled at the observations locations in space and time:

       double survey_time(survey) ;
               survey_time:long_name = "survey time" ;
               survey_time:units = "days since 1968-05-23 00:00:00 GMT" ;
               survey_time:calendar = "gregorian" ;
       int obs_type(datum) ;
               obs_type:long_name = "model state variable associated with observation" ;
       int obs_provenance(datum) ;
               obs_provenance:long_name = "observation origin" ;
               obs_provenance:flag_values = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 ;
               obs_provenance:flag_meanings = "gridded_AVISO_SLA blended_SST XBT_Met_Office CTD_temperature_Met_Office CTD_salinity_Met_Office ARGO_temperature_Met_Office ARGO_salinity_Met_Office CTD_temperature_CalCOFI CTD_salinity_CalCOFI CTD_temperature_GLOBEC CTD_salinity_GLOBEC" ;
       double obs_time(datum) ;
               obs_time:long_name = "time of observation" ;
               obs_time:units = "days since 1968-05-23 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 = "depth of observation" ;
               obs_depth:units = "meter" ;
               obs_depth:negative_value = "downwards" ;
               obs_depth:missing_value = 1.e+37 ;
       double obs_Xgrid(datum) ;
               obs_Xgrid:long_name = "observation fractional x-grid location" ;
       double obs_Ygrid(datum) ;
               obs_Ygrid:long_name = "observation fractional y-grid location" ;
       double obs_Zgrid(datum) ;
               obs_Zgrid:long_name = "observation fractional z-grid location" ;
       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" ;
       double NLmodel_value(datum) ;
               NLmodel_value:long_name = "nonlinear model at observation locations" ;

A new routine obs_k2z.F was added to convert from factional vertical coordinates to actual depths.

This is done to facilitate offline EnKF packages to perform 3D-FGAT (First Guess at Appropriate Time) data assimilation. This capability will be available in DART EnKF in the near future. It is similar to the 3D-Var using variational approaches. For example, it facilitates assimilating very frequent ocean observation (say, gliders) without the need to restart the EnKF at every ROMS time-step, but at a finite user-defined time window.

Notice that we are using the same observation operators for 4D-Var and offline EnKF. The updated output MODNAME NetCDF file is now self contained and can be use by offline EnKF packages directly since it contains all the necessary information for localization and inflation. Also, it can be use by third party OpenDAP severs like the NOAA's ERDDAP tools to browse and plot its variables.


All the ROMS input scripts including test repository were modified to add the new output DAINAME NetCDF file and the switches to write out depths to the output history NetCDF file Hout(idpthR), Hout(idpthU), Hout(idpthV), and Hout(idpthW).

Also, varinfo.dat was modified to include the depths metadata.

Change History (2)

comment:1 Changed 5 years ago by arango

  • Description modified (diff)
  • Resolution set to Done
  • Status changed from new to closed

comment:2 Changed 5 years ago by arango

By accident I loaded the following files:


These are part of the next big 4D-Var update and need special instructions to the user. I reverted to previous version.

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