| Description |
This update includes several enhancements to the BIO_FENNEL ecosystem module. Many thanks to Katja Fennel and Arnaud Laurent for providing the updated fennel.h, fennel_def.h, fennel_inp.h, fennel_mod.h, fennel_var.h, and fennel_wrt.h files.
- If P04 is activated, an additional component is added representing phosphate concentration. With this option, the phytoplankton growth can be limited by either nitrogen or phosphorous (see Laurent et al., 2012).
- RIVER_DON is activated, an additional biological tracer (or two if CARBON is defined) is added, representing the non-sinking dissolved organic matter from rivers described in Yu et al. (2015).
- If the RW14_OXYGEN_SC and or RW14_CO2_SC options are used, the model will use Wanninkhof (2014) air-sea flux parameterization of the Schmidt transfer coefficients. With the TALK_NONCONSERV option, alkalinity is affected by biological fluxes, as described in Laurent et al. (2017).
- With the PCO2AIR_DATA option, atmospheric pCO2 uses Laurent et al. (2017) annual climatory curve. The PCO2AIR_SECULARoption provides an alternative time-dependent atmospheric pCO2 evolution. If none of the two options are defined, atmospheric pCO2 is constant.
- WARNING: The input bio_Fennel.in script was modified to include new parameters. Also, several new variables were added to the varinfo.dat metadata file.
References:
Laurent, A., Fennel, K., Hu, J., Hetland, R. 2012: Simulating the Effects of Phosphorus Limitation in the Mississippi and Atchafalaya River Plumes, Biogeosciences, 9 (11), 4707-4723, doi:10.5194/bg-9-4707-2012.
Yu, L., Fennel, K., Laurent, A., Murrell, M. C., Lehrter, J. C.
2015: Numerical Analysis of the Primary Processes Controlling
Oxygen Dynamics on the Louisiana Shelf, Biogeosciences, 12 (7), 2063-2076, doi:10.5194/bg-12-2063-2015.
Wanninkhof, R. 2014: Relationship between Wind Speed and Gas Exchange over the Ocean Revisited, Limnol. Oceanogr. Methods, 12 (6), 351-362, doi:10.4319/lom.2014.12.351.
Also, included minor updates to few files:
- mp_routines.F: Added Fortran 2003 FLUSH (unit) intrinsic to my_flush subroutine to flush the contents of a unit buffer.
- comp_Jb0.F: Removed CPP conditional around USE mod_scalars to avoid compilation errors.
- Change information format in get_2dfld.F, get_2dfldr.F, get_3dfld.F, and get_3dfldr.F.
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| Description |
The following is a very critical update of ROMS 4D-Var algorithms. Several permanent changes are done on how the surface forcing fields for all the adjoint-based algorithms are specified. Please read the following information carefully.
- WARNING: Due to the complexities of the split 4D-Var, coupled 4dvar, and regular 4D-Var algorithms and their associated analysis tools, the processing logic of how the surface atmospheric forcing, in general, is changed in routines get_data.F and set_data.F and respective TLM, RPM, and ADM versions.
We have incredible convoluted CPP options with BULK_FLUXES on and off, direct atmosphere coupling (FRC_COUPLING) on and off, and forward trajectory forcing of the TLM, RPM, and ADM kernels. Also, we may desire to impose or not the NLM prior surface forcing in subsequent outer-loops (if Nouter>1) and in the analysis 4D-Var phase.
The state variable for the surface (stflx) and bottom (btlfx) tracer fluxes are no longer used for I/O processing. New variables (stflux) and (btflux) are introduced for such tasks. Therefore, we now have:
! Surface tracer fluxes. !
! !
! stflux Forcing surface flux of tracer type variables from !
! data, coupling, bulk flux parameterization, or !
! analytical formulas. !
! !
! stflux(:,:,itemp) surface net heat flux !
! stflux(:,:,isalt) surface net freshwater flux (E-P) !
! !
! stfluxG Latest two-time snapshots of input "stflux" grided !
! data used for interpolation. !
! !
! stflx ROMS state surface flux of tracer type variables !
! (TracerUnits m/s) at horizontal RHO-points, as used !
! in the governing equations. ! !
! !
! Bottom tracer fluxes. !
! !
! btflux Forcing bottom flux of tracer type variables from !
! data or analytical formulas. Usually, the bottom !
! flux of tracer is zero. !
! !
! btflux(:,:,itemp) bottom heat flux !
! btflux(:,:,isalt) bottom freshwater flux !
! !
! btfluxG Latest two-time snapshots of input "vtflux" grided !
! data used for interpolation. !
! !
! btflx ROMS state bottom flux of tracer type variables !
! (TracerUnits m/s) at horizontal RHO-points, as used !
! in the governing equations. !
Recall that stflx and btflx are the surface and bottom boundary conditions for the vertical tracer diffusion term. The new strategy removes the issues we were having when manipulating such fluxes in set_vbc.F, like surface heat and freshwater corrections. In particular, the scaling of freshwater flux (E-P)/ρ, which needs to be multiplied by the surface salinity, was problematic. This issue was addressed earlier in src:ticket:806, but it is further reworked here.
This change simplified the logic in all the get_data and set_data routines. It is a generic solution to all combinations of options and algorithms. For example, in tl_set_data we have:
# ifdef SALINITY
# ifdef ANA_SSFLUX
!
! Surface freshwater (E-P) flux (m/s) from analytical function.
!
CALL ana_stflux (ng, tile, iNLM, isalt)
# else
# if !(defined BULK_FLUXES || defined EMINUSP || \
defined FRC_COUPLING || defined SRELAXATION)
!
! Surface freshwater (E-P) flux (m/s) from NetCDF variable "swflux".
!
CALL set_2dfld_tile (ng, tile, iNLM, idsfwf, &
& LBi, UBi, LBj, UBj, &
& FORCES(ng)%stfluxG(:,:,:,isalt), &
& FORCES(ng)%stflux (:,:,isalt), &
& update)
IF (FoundError(exit_flag, NoError, __LINE__, &
& __FILE__)) RETURN
# elif defined BULK_FLUXES && !defined EMINUSP
!
! Surface freshwater (E-P) flux (m/s) from NetCDF variable "EminusP".
!
IF (Lprocess) THEN
CALL set_2dfld_tile (ng, tile, iNLM, idEmPf, &
& LBi, UBi, LBj, UBj, &
& FORCES(ng)%stfluxG(:,:,:,isalt), &
& FORCES(ng)%stflux (:,:,isalt), &
& update)
IF (FoundError(exit_flag, NoError, __LINE__, &
& __FILE__)) RETURN
END IF
# endif
# endif
...
# endif
Again, the important difference is that data processing is done with variables stflux and stfluxG and not with state variable stflx.
- WARNING: The CPP option NL_BULK_FLUXES is deprecated and replaced with FORWARD_FLUXES and PRIOR_BULK_FLUXES.
- The option FORWARD_FLUXES indicates that the surface forcing fields for the TLM, RPM, and ADM kernels is from the background nonlinear model trajectory (BLK file structure) instead of input atmosphere forcing files (FRC file structure). Such fields are now stored in the quicksave (QCK) output NetCDF instead of history (FWD) files. It allows saving the surface forcing frequently (say every 1, 2, or 3 hours) without increasing the history file size. Currently, we have the following statement in mosty all the adjoint-based drivers:
# ifdef FORWARD_FLUXES
!
! Set the BLK structure to contain the nonlinear model surface fluxes
! needed by the tangent linear and adjoint models. Also, set switches
! to process that structure in routine "check_multifile". Notice that
! it is possible to split the solution into multiple NetCDF files to
! reduce their size.
!
! The switch LreadFRC is deactivated because all the atmospheric
! forcing, including shortwave radiation, is read from the NLM
! surface fluxes or is assigned during ESM coupling. Such fluxes
! are available from the QCK structure. There is no need for reading
! and processing from the FRC structure input forcing-files.
!
CALL edit_multifile ('QCK2BLK')
IF (FoundError(exit_flag, NoError, __LINE__, &
& __FILE__)) RETURN
DO ng=1,Ngrids
LreadBLK(ng)=.TRUE.
LreadFRC(ng)=.FALSE.
LreadQCK(ng)=.FALSE.
END DO
# endif
The User needs to provide a reasonable value for NQCK in roms.in to correctly sample the daily cycle. Please avoid activating the Qout switches for lots of fields written in the quicksave file, so it is relatively small. Avoid activating switches for 3D variables. Optimally, we need to activate the following switches:
Qout(idsurT) == T T ! temp_sur, salt_sur surface temperature and salinity
Qout(idUsms) == T ! sustr surface U-stress
Qout(idVsms) == T ! svstr surface V-stress
Qout(idPair) == T ! Pair surface air pressure
Qout(idTair) == T ! Tair surface air temperature
Qout(idUair) == T ! Uair surface U-wind component
Qout(idVair) == T ! Vair surface V-wind component
Qout(idTsur) == T T ! shflux, ssflux surface net heat and salt flux
Qout(idLhea) == T ! latent latent heat flux
Qout(idShea) == T ! sensible sensible heat flux
Qout(idLrad) == T ! lwrad longwave radiation flux
Qout(idSrad) == T ! swrad shortwave radiation flux
Qout(idEmPf) == T ! EminusP E-P flux
Qout(idevap) == T ! evaporation evaporation rate
Qout(idrain) == T ! rain precipitation rate
Some of these fields depend on the activated CPP options. The appropriate fields are written to the quicksave NetCDF file.
Previously, the time snapshots of the background trajectory used to linearize the TLM and ADM were incompatible with the direct forcing from atmospheric input files if SOLAR_SOURCE and DIURNAL_SRFLUX are activated. The shortwave contribution to the net surface heat flux is not the same. The new strategy removes the inconsistency.
- The option PRIOR_BULK_FLUXES is used to impose the initial background trajectory (prior) surface forcing fields stored in QCK in subsequent outer-loops (Nouter>1) and the analysis phase. In main3d.F, the call to bulk_flux is avoided in such cases:
DO ig=1,GridsInLayer(nl)
ng=GridNumber(ig,nl)
DO tile=first_tile(ng),last_tile(ng),+1
# ifdef BULK_FLUXES
# if defined FOUR_DVAR && defined PRIOR_BULK_FLUXES
IF (Nrun.eq.1) CALL bulk_flux (ng, tile)
# else
CALL bulk_flux (ng, tile)
# endif
# endif
...
END DO
END DO
Notice that get_data.F will read the required surface forcing fields from the QCK NetCDF file.
- The observation operator was updated to include new variables in the output MOD NetCDF file:
double NLmodel_unvetted(datum) ;
NLmodel_unvetted:long_name = "initial nonlinear model at observation locations unvetted by quality control" ;
NLmodel_unvetted:units = "state variable units" ;
double NLmodel_value_unvetted(Nouter, datum) ;
NLmodel_value_unvetted:long_name = "nonlinear model at observation locations unvetted by quality control per outer-loop" ;
NLmodel_value_unvetted:units = "state variable units" ;
The values rejected during background quality control (BGQC) are saved before multiplying by obs_scale screening. It facilitates analyzing and comparing the observation vector. If BGQC is activated, NLmodel_unvetted will have values for all the observations bounded in space and time for the 4D-Var cycle, whereas NLmodel_initial will have only the values after the quality control screening.
All the _FillValue attributes for output variables in the MOD NetCDF file were removed. Many thanks to John Wilkin for his suggestions to improve the output MOD NetCDF file.
- Added option REGRID_SHPIRO to apply a Shapiro filter in routine regrid.F called by nf_fread2d to remove spikes and noise due to the bilinear interpolation of very coarse 2D input data.
The primary drivers to the split 4D-Var algorithms are released:
- split_i4dvar_ocean.h: Split I4D-Var algorithm. It uses submit_split_i4dvar.sh to run the driver.
- split_r4dvar_ocean.h: Split R4D-Var algorithm. It uses submit_split_r4dvar.sh to run the driver.
- split_rbl4dvar_ocean.h: Split RBL4D-Var algorithm. It uses submit_split_rbl4dvar.sh to run the driver.
The bash scripts in ROMS/Bin are complex and well documented. Several test cases were added to the test repository for the WC13 application. It took me several months to code and to test these new drivers. We will add documentation to wikiROMS about the new 4D-Var drivers soon.
More complexity is being added and tested for these drivers like coarser grid resolution in the increment phase during the inner-loops. The increment phase may be run at a lower precision.
I am currently testing the coupled 4D-Var that allows the background phase to be part of a coupling system. The coupling between ROMS and the atmosphere model is done with the ESMF/NUOPC library. Such capabilities will be released in the future.
WARNING: The metadata file varinfo.dat was modified to include additional variables.
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| Description |
Several changes were introduced in src:ticket:869 about how to process the surface/bottom tracer fluxes that are used as top/bottom boundary conditions to the vertical diffusion terms. A couple of additional changes are made here to remove any ambiguity about the surface freshwater flux needed for ROMS.
Notice that ROMS has the following vertical surface/bottom boundary condition for temperature and salinity:
In particular, the blue square shows what ROMS needs as a freshwater flux. Usually, E-P is in units of kilogram meter-2 second-1. Then, the flux is divided by freshwater density, which converts to meter second-1. In routine set_vbc.F such flux is multiplied by the surface salinity. Since the salinity does not have physical units, the vertical boundary condition is still in meter second-1.
I cleaned the metadata in varinfo.dat, now we have:
'ssflux' ! Output
'kinematic surface net salt flux, SALT*(E-P)/rhow'
'meter second-1' ! [PSS m/s]
'surface net salt flux, scalar, series'
'ssf_time'
'idTsur(isalt)'
'r2dvar'
1.0d0
'swflux' ! Input
'data surface net freshwater flux, (E-P)/rhow'
'meter second-1' ! Input: [m/s]
'surface net freshwater flux, scalar, series' ! [PSS m/s]
'swf_time'
'idsfwf'
'r2dvar'
1.0d0
'EminusP' ! Input/Output
'modeled surface net freshwater flux, (E-P)/rhow'
'meter second-1' ! computed by NLM ROMS
'EminusP, scalar, series' ! bulk_flux.F or coupling
'ocean_time'
'idEmPf'
'r2dvar'
1.0d0
As specified in the preamble of varinfo.dat, the PSS information is added to indicate that the Practical Salinity Scale was used to determine conductivity, but it is not a physical unit. We are not using the latest UNESCO equation of state.
We have two different variables for input freshwater flux: swflux and EminusP. Historically, swflux has been used for available datasets while EminusP has been used when derived from parameterizations (BULK_FLUXES and atmospheric coupling). To avoid any confusion, the units and scale for swflux were changed to meter second-1 and 1.0d0, respectively. It is the standard unit for freshwater flux. If such field is in centimeter day-1, I recomend to add the scale_factor attribute to the NetCDF, so the conversion is done during reading in ROMS:
float swflux(swf_time, eta_rho, xi_rho) ;
swflux:long_name = "surface freshwater flux, (E-P)/rhow" ;
swflux:units = "meter second-1" ;
swflux:negative = "net evaporation" ;
swflux:positive = "net precipitation" ;
swflux:time = "swf_time" ;
swflux:coordinates = "lon_rho lat_rho swf_time" ;
swflux:scale_factor = 1.157407e-07f ;
We could use the Matlab script to adjust the NetCDF file:
nc_attadd('my_file.nc','scale_factor',0.01/86400,'swflux')
- Corrected get_data.F and set_data.F processing of the freshwater flux when the SCORRECTION is activated.
- Corrected compiling issue in regrid.F. It was missing the MASKING conditional.
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