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Ticket | Owner | Reporter | Resolution | Summary |
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#700 | Done | Important: Changes to Bed Bottom Sediment Output Switches | ||
Description |
The bed bottom sediment output switches in ROMS ocean.in standard input file: ! Logical switches (TRUE/FALSE) to activate writing of exposed sediment ! layer properties into HISTORY output file. Currently, MBOTP properties ! are expected for the bottom boundary layer and/or sediment models: ! ! idBott( 1=isd50) grain_diameter mean grain diameter ! idBott( 2=idens) grain_density mean grain density ! idBott( 3=iwsed) settling_vel mean settling velocity ! idBott( 4=itauc) erosion_stress critical erosion stress ! idBott( 5=irlen) ripple_length ripple length ! idBott( 6=irhgt) ripple_height ripple height ! idBott( 7=ibwav) bed_wave_amp wave excursion amplitude ! idBott( 8=izdef) Zo_def default bottom roughness ! idBott( 9=izapp) Zo_app apparent bottom roughness ! idBott(10=izNik) Zo_Nik Nikuradse bottom roughness ! idBott(11=izbio) Zo_bio biological bottom roughness ! idBott(12=izbfm) Zo_bedform bed form bottom roughness ! idBott(13=izbld) Zo_bedload bed load bottom roughness ! idBott(14=izwbl) Zo_wbl wave bottom roughness ! idBott(15=iactv) active_layer_thickness active layer thickness ! idBott(16=ishgt) saltation saltation height ! ! 1 1 1 1 1 1 1 ! 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 Hout(idBott) == T T T T T T T T T F F F F F F F were moved to input script sediment.in and reformatted for easy use: ! Logical switches (TRUE/FALSE) to activate writing of bed bottom sediment ! parameters, [1:Ngrids] values expected. Hout(isd50) == T ! grain_diameter mean grain diameter Hout(idens) == T ! grain_density mean grain density Hout(iwsed) == T ! settling_vel mean settling velocity Hout(itauc) == T ! erosion_stress critical erosion stress Hout(irlen) == T ! ripple_length ripple length Hout(irhgt) == T ! ripple_height ripple height Hout(ibwav) == T ! bed_wave_amp wave excursion amplitude Hout(izdef) == T ! Zo_def default bottom roughness Hout(izapp) == T ! Zo_app apparent bottom roughness Hout(izNik) == F ! Zo_Nik Nikuradse bottom roughness Hout(izbio) == F ! Zo_bio biological bottom roughness Hout(izbfm) == F ! Zo_bedform bed form bottom roughness Hout(izbld) == F ! Zo_bedload bed load bottom roughness Hout(izwbl) == F ! Zo_wbl wave bottom roughness Hout(iactv) == F ! active_layer_thickness active layer thickness Hout(ishgt) == F ! saltation saltation height In addition, the script sediment.in was reordered to more logical distribution of the sediment standard input parameters. However, ROMS can read the parameters in input scripts in any arbitrary order except dimension parameters at the top of ocean.in. Similarly, the switches in input script station.in: ! Logical switches (TRUE/FALSE) to activate writing of exposed sediment ! layer properties into STATIONS output file. Currently, MBOTP properties ! are expected for the bottom boundary layer and/or sediment models: ! ! idBott( 1=isd50) grain_diameter mean grain diameter ! idBott( 2=idens) grain_density mean grain density ! idBott( 3=iwsed) settling_vel mean settling velocity ! idBott( 4=itauc) erosion_stress critical erosion stress ! idBott( 5=irlen) ripple_length ripple length ! idBott( 6=irhgt) ripple_height ripple height ! idBott( 7=ibwav) bed_wave_amp wave excursion amplitude ! idBott( 8=izdef) Zo_def default bottom roughness ! idBott( 9=izapp) Zo_app apparent bottom roughness ! idBott(10=izNik) Zo_Nik Nikuradse bottom roughness ! idBott(11=izbio) Zo_bio biological bottom roughness ! idBott(12=izbfm) Zo_bedform bed form bottom roughness ! idBott(13=izbld) Zo_bedload bed load bottom roughness ! idBott(14=izwbl) Zo_wbl wave bottom roughness ! idBott(15=iactv) active_layer_thickness active layer thickness ! idBott(16=ishgt) saltation saltation height ! ! 1 1 1 1 1 1 1 ! 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 Sout(idBott) == T T T T T T T T T T T T T T T T were reformatted as: ! Logical switches (TRUE/FALSE) to activate writing of exposed sediment ! layer properties into STATIONS output file. Sout(isd50) == T ! grain_diameter mean grain diameter Sout(idens) == T ! grain_density mean grain density Sout(iwsed) == T ! settling_vel mean settling velocity Sout(itauc) == T ! erosion_stress critical erosion stress Sout(irlen) == T ! ripple_length ripple length Sout(irhgt) == T ! ripple_height ripple height Sout(ibwav) == T ! bed_wave_amp wave excursion amplitude Sout(izdef) == T ! Zo_def default bottom roughness Sout(izapp) == T ! Zo_app apparent bottom roughness Sout(izNik) == T ! Zo_Nik Nikuradse bottom roughness Sout(izbio) == T ! Zo_bio biological bottom roughness Sout(izbfm) == T ! Zo_bedform bed form bottom roughness Sout(izbld) == T ! Zo_bedload bed load bottom roughness Sout(izwbl) == T ! Zo_wbl wave bottom roughness Sout(iactv) == T ! active_layer_t... active layer thickness Sout(ishgt) == T ! saltation saltation height for easy use. Many thanks to John Warner to suggesting this change. It makes more sense to have these output logical switches in the sediment.in input script. WARNING: All the ocean.in, sediment.in, and station.in input scripts in the trunk and test repositories were changed. The old format for these switches will ignored in ROMS. However, if any of these variables are desired in the output NetCDF files users need the new format for these switches. |
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#701 | Done | SGRID conventions in ROMS output NetCDF files | ||
Description |
Added Staggered Grid data model (SGRID) conventions to ROMS output NetCDF files for third party post-processing tools. Check the following link for more information about SGRID conventions. If you read the information, you will notice that a new integer variable is defined in ROMS in spherical applications: int grid ; grid:cf_role = "grid_topology" ; grid:topology_dimension = 2 ; grid:node_dimensions = "xi_psi eta_psi" ; grid:face_dimensions = "xi_rho: xi_psi (padding: both) eta_rho: eta_psi (padding: both)" ; grid:edge1_dimensions = "xi_u: xi_psi eta_u: eta_psi (padding: both)" ; grid:edge2_dimensions = "xi_v: xi_psi (padding: both) eta_v: eta_psi" ; grid:node_coordinates = "lon_psi lat_psi" ; grid:face_coordinates = "lon_rho lat_rho" ; grid:edge1_coordinates = "lon_u lat_u" ; grid:edge2_coordinates = "lon_v lat_v" ; grid:vertical_dimensions = "s_rho: s_w (padding: none)" ; or in Cartesian applications: int grid ; grid:cf_role = "grid_topology" ; grid:topology_dimension = 2 ; grid:node_dimensions = "xi_psi eta_psi" ; grid:face_dimensions = "xi_rho: xi_psi (padding: both) eta_rho: eta_psi (padding: both)" ; grid:edge1_dimensions = "xi_u: xi_psi eta_u: eta_psi (padding: both)" ; grid:edge2_dimensions = "xi_v: xi_psi (padding: both) eta_v: eta_psi" ; grid:node_coordinates = "x_psi y_psi" ; grid:face_coordinates = "x_rho y_rho" ; grid:edge1_coordinates = "x_u y_u" ; grid:edge2_coordinates = "x_v y_v" ; grid:vertical_dimensions = "s_rho: s_w (padding: none)" ; Currently, the integer value for the grid variable is arbitrary since it is not used. It is set to unity in ROMS so it can be used as a logical in some post-processing programs. Only the attributes for grid are relevant. Two variable attributes grid and location are added to each state 2D or 3D variable. For example: double zeta(ocean_time, eta_rho, xi_rho) ; zeta:long_name = "free-surface" ; zeta:units = "meter" ; zeta:time = "ocean_time" ; zeta:grid = "grid" ; zeta:location = "face" ; zeta:coordinates = "lon_rho lat_rho ocean_time" ; zeta:field = "free-surface, scalar, series" ; zeta:_FillValue = 1.e+37f ; 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:grid = "grid" ; u:location = "edge1" ; u:coordinates = "lon_u lat_u s_rho ocean_time" ; u:field = "u-velocity, scalar, series" ; u:_FillValue = 1.e+37f ; 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:grid = "grid" ; v:location = "edge2" ; v:coordinates = "lon_v lat_v s_rho ocean_time" ; v:field = "v-velocity, scalar, series" ; v:_FillValue = 1.e+37f ; double temp(ocean_time, s_rho, eta_rho, xi_rho) ; temp:long_name = "potential temperature" ; temp:units = "Celsius" ; temp:time = "ocean_time" ; temp:grid = "grid" ; temp:location = "face" ; temp:coordinates = "lon_rho lat_rho s_rho ocean_time" ; temp:field = "temperature, scalar, series" ; temp:_FillValue = 1.e+37f ; The global Conventions attribute is updated as: :Conventions = "CF-1.4, SGRID-0.3" ; Many thanks to Rich Signell for bringing this to our attention and for his leading role in the standardization conventions used in post-processing tools.
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#702 | Done | IMPORTANT: Big update to 4D-Var Data Assimilation Algorithms | ||
Description |
This is a very important update to the ROMS 4D-Var algorithms. It includes new options and several bug corrections. We have been working and refining these algorithms for the last couple of years. WARNING: If you update to this version, you need to recompute the error covariance normalization coefficients for your 4D-Var application. This is extremely important since several bugs were corrected in the computation of the normalization coefficients. It is the user responsibility to make sure that this takes place in order to have the correct 4D-Var solution with this ROMS update. What is New:
Many thanks to Andy Moore for his help in coding and testing all these algorithms. We have been talking about this update for the last couple of years and have so many research versions of the code that were becoming unmanageable. |