Changes between Version 12 and Version 13 of WorkingGroups/TOP/TOP-UserQuickGuide
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- 2018-01-17T11:52:45+01:00 (6 years ago)
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WorkingGroups/TOP/TOP-UserQuickGuide
v12 v13 83 83 == TOP namelist Walkthrough == 84 84 === namelist_top === 85 Here below are listed the features/options of the TOP interface accessible through the namelist_top_ref and modifiable by means of namelist_top_cfg (as for NEMO physical ones). 85 Here below are listed the features/options of the TOP interface accessible through the namelist_top_ref and modifiable by means of namelist_top_cfg (as for NEMO physical ones). 86 86 87 87 Note that ## is used to refer to a number in an array field. 88 88 89 |||| & namtrc_run !run information ||90 || nn_dttrc || Time step frequency for TOP computation ||89 |||| &'''namtrc_run''' ! run information || 90 || nn_dttrc || Time step frequency for TOP computation (if >1 substepping is used) || 91 91 || ln_top_euler || Use Euler Forward integration instead of leap-frog || 92 92 || ln_rsttr || Start from a restart file (T) or not (F) || 93 || nn_rsttr || Restart control.[[BR]] [[BR]]0 : initial time step is not compared to the restart file value.[[BR]][[BR]]1 : do not use the value in the restart file.[[BR]][[BR]]2 : calendar parameters read in the restart file. ||94 || cn_trcrst_in cn_trcrst_indir || Suffix of tracers INPUT restart file[[BR]][[BR]]Root directory for the location of INPUT restart files ||95 || cn_trcrst_out[[BR]] [[BR]]cn_trcrst_outdir || suffix of tracers OUTPUT restart file[[BR]][[BR]]Root directory for the location of OUTPUT restart files ||96 |||| & namtrc !tracers definition ||93 || nn_rsttr || Restart control.[[BR]]0 : initial time step is not compared to the restart file value.[[BR]]1 : do not use the value in the restart file.[[BR]]2 : calendar parameters read in the restart file. || 94 || cn_trcrst_in [[BR]]cn_trcrst_indir || Suffix of tracers INPUT restart file[[BR]]Root directory for the location of INPUT restart files || 95 || cn_trcrst_out[[BR]]cn_trcrst_outdir || suffix of tracers OUTPUT restart file[[BR]]Root directory for the location of OUTPUT restart files || 96 |||| &'''namtrc''' ! tracers definition || 97 97 || jp_bgc || Number of passive tracers of the BGC model || 98 || ln_pisces / ln_my_trc || Run PISCES or MY_TRC BGC modules. The recannot be run at the same time since they both rely on jp_bgc ||98 || ln_pisces / ln_my_trc || Run PISCES or MY_TRC BGC modules. These modules cannot be run at the same time since they both rely on jp_bgc || 99 99 || ln_age, ln_cfc11, ln_cfc12, ln_sf6, ln_c14 || Activate sub-modules: tracers are automatically defined within each module. These can run along with main BGC modules. || 100 100 || ln_trcdta || Initialisation from data input file (T) or not (F) || 101 || ln_trcdmp , ln_trcdmp_clo || Add a damping term (T) or not (F)[[BR]][[BR]]Add a damping term (T) or not (F) for closed seas ||101 || ln_trcdmp[[BR]]ln_trcdmp_clo || Add a damping term (T) or not (F)[[BR]]Add a damping term (T) or not (F) for closed seas || 102 102 || jp_dia3d, jp_dia2d || Number of 3D/2D diagnostic variables to populate dedicated array beside the direct usage of iom_put calls. || 103 103 || sn_tracer(''##'') || Data structure to specify tracer name and metadata for the chosen BGC module. Here set initialization and Boundary conditions. See structure description after this table. || 104 |||| & namtrc_dta !Initialisation from data input file ||104 |||| &'''namtrc_dta''' ! Initialisation from data input file || 105 105 || sn_trcdta(##) || Data structure to read tracers Initial conditions according to sn_tracer%llinit option. See structure description after this table. || 106 106 || rf_trfac(''##'') || Multiplicative factor for initialized tracer. If omitted default is 1.0. || 107 107 || cn_dir || Root directory for the location of INPUT data files || 108 |||| & namtrc_adv !advection scheme for passive tracer ||109 || ln_trcadv_cen[[BR]] [[BR]]nn_cen_h[[BR]][[BR]]nn_cen_v || 2nd order centered scheme[[BR]][[BR]]=2 or 4, horizontal 2nd / 4th order[[BR]][[BR]]=2 or 4, vertical 2nd / 4th order ||110 || ln_trcadv_fct[[BR]] [[BR]]nn_fct_h[[BR]][[BR]]nn_fct_v[[BR]][[BR]]nn_fct_zts || FCT scheme[[BR]][[BR]]=2 or 4, horizontal 2nd / 4th order[[BR]][[BR]]=2 or 4, vertical 2nd / 4th order[[BR]][[BR]]>=1,number of sub-timestep for 2nd order vertical scheme ||111 || ln_trcadv_mus[[BR]] [[BR]]ln_mus_ups || MUSCL scheme[[BR]][[BR]]use (T) or not (F) upstream scheme near river mouths ||112 || ln_trcadv_ubs[[BR]] [[BR]]nn_ubs_v || UBS scheme[[BR]][[BR]]= 2 , vertical 2nd order FCT ||108 |||| &'''namtrc_adv''' ! advection scheme for passive tracer || 109 || ln_trcadv_cen[[BR]]nn_cen_h[[BR]]nn_cen_v || 2nd order centered scheme[[BR]]=2 or 4, horizontal 2nd / 4th order[[BR]]=2 or 4, vertical 2nd / 4th order || 110 || ln_trcadv_fct[[BR]]nn_fct_h[[BR]]nn_fct_v[[BR]]nn_fct_zts || FCT scheme[[BR]]=2 or 4, horizontal 2nd / 4th order[[BR]]=2 or 4, vertical 2nd / 4th order[[BR]]>=1, number of sub-timestep for 2nd order vertical scheme || 111 || ln_trcadv_mus[[BR]]ln_mus_ups || MUSCL scheme[[BR]]use (T) or not (F) upstream scheme near river mouths || 112 || ln_trcadv_ubs[[BR]]nn_ubs_v || UBS scheme[[BR]]= 2 , vertical 2nd order FCT || 113 113 || ln_trcadv_qck || QUICKEST scheme || 114 |||| & namtrc_ldf !lateral diffusion scheme for passive tracer ||115 || ln_trcldf_lap[[BR]] [[BR]]rn_ahtrc_0 || Laplacian operator (use .T. or not .F.)[[BR]][[BR]]Lateral eddy diffusivity coefficient [m2/s] ||116 || ln_trcldf_bilap[[BR]] [[BR]]rn_bhtrc_0 || Bilaplacian operator (use .T. or not .F.)[[BR]][[BR]]Lateral eddy diffusivity coefficient [m2/s] ||117 || ln_trcldf_lev[[BR]] [[BR]]ln_trcldf_hor[[BR]][[BR]]ln_trcldf_iso[[BR]][[BR]]ln_trcldf_triad || Iso-level direction (use .T. or not .F.)[[BR]][[BR]]horizontal (geopotential) direction (use .T. or not .F.)[[BR]][[BR]]iso-neutral (standard operator) direction (use .T. or not .F.)[[BR]][[BR]]iso-neutral (triad operator) direction (use .T. or not .F.) ||114 |||| &'''namtrc_ldf''' ! lateral diffusion scheme for passive tracer || 115 || ln_trcldf_lap[[BR]]rn_ahtrc_0 || Laplacian operator (use .T. or not .F.)[[BR]]Lateral eddy diffusivity coefficient [m2/s] || 116 || ln_trcldf_bilap[[BR]]rn_bhtrc_0 || Bilaplacian operator (use .T. or not .F.)[[BR]]Lateral eddy diffusivity coefficient [m2/s] || 117 || ln_trcldf_lev[[BR]]ln_trcldf_hor[[BR]]ln_trcldf_iso[[BR]]ln_trcldf_triad || Iso-level direction (use .T. or not .F.)[[BR]]Horizontal (geopotential) direction (use .T. or not .F.)[[BR]]Iso-neutral (standard operator) direction (use .T. or not .F.)[[BR]]Iso-neutral (triad operator) direction (use .T. or not .F.) || 118 118 || rn_fact_lap || Multiplicative factor to enhance zonal eddy diffusivity. || 119 |||| & namtrc_zdf !vertical physics ||119 |||| &'''namtrc_zdf''' ! vertical physics || 120 120 || ln_trczdf_exp || Split explicit (T) or implicit (F) time stepping || 121 121 || nn_trczdf_exp || Number of sub-timestep for ln_trczdfexp=T || 122 |||| & namtrc_rad !treatment of negative concentrations ||122 |||| &'''namtrc_rad''' ! treatment of negative concentrations || 123 123 || ln_trcrad || Artificially correct negative concentrations (T) or not (F) || 124 |||| & namtrc_dmp !passive tracer newtonian damping ||125 || nn_zdmp_tr || Vertical shape of damping term[[BR]] [[BR]]0 : damping throughout the water column[[BR]][[BR]]1 : no damping in the mixing layer (kz criteria)[[BR]][[BR]]2 : no damping in the mixed layer (rho crieria) ||124 |||| &'''namtrc_dmp''' ! passive tracer newtonian damping || 125 || nn_zdmp_tr || Vertical shape of damping term[[BR]]0 : damping throughout the water column[[BR]]1 : no damping in the mixing layer (kz criteria)[[BR]]2 : no damping in the mixed layer (rho crieria) || 126 126 || cn_resto_tr || NetCDF filename with input damping coefficients || 127 |||| &namtrc_ice !Representation of sea ice growth & melt effects ||127 |||| &namtrc_ice ! Representation of sea ice growth & melt effects || 128 128 || nn_ice_tr || Tracer concentration in sea ice. Available options[[BR]][[BR]]-1 (no vvl: identical cc in ice and ocean / vvl: cc_ice = 0)[[BR]][[BR]]0 (no vvl: cc_ice = zero / vvl: cc_ice = )[[BR]][[BR]]1 prescribed to a namelist value (implemented in pisces or through user definition in trcice_my_trc) || 129 |||| & namtrc_trd ! diagnostics on tracer trends('key_trdtrc') ||129 |||| &'''namtrc_trd''' ! diagnostics on tracer trends ('key_trdtrc') || 130 130 || nn_trd_trc || Time step frequency and tracers trends || 131 131 || nn_ctls_trc || Control surface type in mixed-layer trends (0,1 or n<jpk) || … … 134 134 || ln_trdmld_trc_instant || Diagnose trends of instantaneous (T) or mean (F) ML T/S || 135 135 || ln_trdtrc(##) || Compute trend for nth tracer. Array of logical values. || 136 |||| & namtrc_bc !Forcing data for boundary conditions ||136 |||| &'''namtrc_bc''' ! Forcing data for boundary conditions || 137 137 || sn_trcsbc(''##''), sn_trccbc(##), sn_trcobc(##) || Data structure to read tracers boundary conditions according to sn_tracer%llsbc,sn_tracer%llcbc, sn_tracer%llobc options. See structure description after this table. || 138 138 || rn_trsfac(''##''), rn_trcfac(##), rn_trofac(##) || Multiplicative factor for SURFACE (sbc), COASTAL (cbc), and LATERAL (obc) forcing data files || … … 140 140 || ln_rnf_ctl || Remove runoff dilution on tracers with absent river load (only without VVL) || 141 141 || rn_bc_time || Time scaling factor for SBC and CBC data (seconds in a day) || 142 |||| & namtrc_bdy !Setup of tracer boundary conditions ||142 |||| &'''namtrc_bdy''' ! Setup of tracer boundary conditions || 143 143 || cn_trc_dflt || Open Boundary Condition applied by default to all tracers || 144 144 || cn_trc || Boundary conditions used for tracers with data files (selected in namtrc using sn_tracer%llobc) || 145 || nn_trcdmp_bdy || Use damping timescales defined in nambdy of namelist[[BR]] [[BR]]0 : NO damping of tracers at open boundaries[[BR]][[BR]]1 : Only for tracers forced with external data[[BR]][[BR]]2 : Damping applied to all tracers ||146 |||| & namage !Water Age module ||145 || nn_trcdmp_bdy || Use damping timescales defined in nambdy of namelist[[BR]]0 : NO damping of tracers at open boundaries[[BR]]1 : Only for tracers forced with external data[[BR]]2 : Damping applied to all tracers || 146 |||| &'''namage''' ! Water Age module || 147 147 || rn_age_depth || Depth over which age tracer reset to zero || 148 148 || rn_age_kill_rate || Relaxation timescale (s) for age tracer shallower than age depth || 149 150 151 152 Two main types of data structure are used within TOP interface to initialize tracer properties (1) and to provide related initial and boundary conditions (2). 153 154 1. TOP tracers initialization : sn_tracer (namtrc) 155 156 157 158 Beside providing name and metadata for tracers, here are also defined the use of initial (sn_tracer%llinit) and boundary (sn_tracer%llsbc,sn_tracer%llcbc, sn_tracer%llobc) conditions. 159 160 In the following, an example of the full structure definition is given for two idealized tracer both with initial conditions given and the first with surface boundary forcing prescribes, while the second has surface and coastal forcing: 161 162 ! ! name ! title of the field ! units ! initial data ! sbc ! cbc ! obc ! 163 164 sn_tracer(1) = 'TRC1' , 'Tracer 1 Concentration ', ' - ' , .true., .true., .false., .true. 165 166 sn_tracer(2) = 'TRC2 ' , 'Tracer 2 Concentration ', ' - ' , .true., .true., .true., .false. 167 168 As tracers in BGC models are increasingly growing, the same structure can be written also in a more compact and readable way: 169 170 ! ! name ! title of the field ! units ! initial data ! 171 172 sn_tracer(1) = 'TRC1' , 'Tracer 1 Concentration ', ' - ' , .true. 173 174 sn_tracer(2) = 'TRC2 ' , 'Tracer 2 Concentration ', ' - ' , .true. 175 176 ! sbc 177 178 sn_tracer(1)%llsbc = .true. 179 180 sn_tracer(2)%llsbc = .true. 181 182 ! cbc 183 184 sn_tracer(2)%llcbc = .true. 185 186 The data structure is internally initialized by code with dummy names and all initialization/forcing logical fields set to .false. . 187 188 2. SBC structure to read input fields : sn_trcdta (namtrc_dta), sn_trcsbc sn_trccbc sn_trcobc (namtrc_bc) 189 190 191 192 This data structure is based on the general one defined for NEMO core in the SBC component (see details in User Manual SBC Chapter on Input Data specification). 193 194 The following example show the data structure in the case of a single tracer with initial conditions contained in the file named tracer_1_data.nc (.nc is implicitly assumed), with a doublef intial value, and located in the usr/work/model/inputdata/ folder: 195 196 ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! 197 198 ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! 199 200 sn_trcdta(1) = !''tracer_1_data' , -12 , 'TRC1' , .false. , .true. , 'yearly' , !'' , !'' , !'' 201 202 rf_trfac(1) = 2.0 203 204 cn_dir = “usr/work/model/inputdata/” 205 206 The Lateral Open Boundaries conditions are applied to the segments defined for the physical core of NEMO (see BDY description in the User Manual).
