Changes between Version 11 and Version 12 of Working Groups/TOP/TOP-User Quick Guide


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Timestamp:
2018-01-17T11:47:55+01:00 (3 years ago)
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lovato
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  • Working Groups/TOP/TOP-User Quick Guide

    v11 v12  
    2222Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and all submodules preprocessing macros from previous versions were removed. 
    2323 
    24 [[BR]] 
    25  
    26  
    2724Here below the list of preprocessing keys that applies to the TOP interface (beside key_top): 
    2825 
     
    3734key_trdtrc & key_trdmxl_trc : trend computation for tracers 
    3835 
    39 [[BR]] 
    40  
    4136== TOP synthetic Workflow == 
    4237A synthetic description of the TOP interface workflow is given below to summarize the steps involved in the computation of biogeochemical and physical trends and their time integration and outputs, by reporting also the principal Fortran subroutine herein involved. 
    43  
    44 [[BR]] 
    4538 
    4639'''Model initialization (OPA_SRC/nemogcm.F90)''' 
     
    5952 
    6053  ↳ call trc_sub_ini, setup substepping if nn_dttrc /= 1 
    61  
    62 [[BR]] 
    6354 
    6455'''Time marching procedure (OPA_SRC/stp.F90)''' 
     
    8071  ↳ call trc_adv, compute tracers advection 
    8172 
    82     ↳ call to trc_ldf, compute tracers lateral diffusion 
     73  ↳ call to trc_ldf, compute tracers lateral diffusion 
    8374 
    84     ↳ call to trc_zdf, vertical mixing and after tracer fields 
     75  ↳ call to trc_zdf, vertical mixing and after tracer fields 
    8576 
    86     ↳ call to trc_nxt, tracer fields at next time step 
     77  ↳ call to trc_nxt, tracer fields at next time step 
    8778 
    88     ↳ call to trc_rad, Correct artificial negative concentrations 
     79  ↳ call to trc_rad, Correct artificial negative concentrations 
    8980 
    9081  ↳ call trc_rst_wri, output tracers restart files 
    9182 
    92 [[BR]] 
     83== TOP namelist Walkthrough == 
     84=== namelist_top === 
     85Here 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).  
    9386 
     87Note that ## is used to refer to a number in an array field. 
    9488 
    95 == TOP namelist Walkthrough == 
    96  
    97 === namelist_top === 
    98 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). Note that ## is used to refer to a number in an array field. 
     89|||| &namtrc_run      !   run information || 
     90|| nn_dttrc || Time step frequency for TOP computation || 
     91|| ln_top_euler || Use Euler Forward integration instead of leap-frog || 
     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 || 
     97|| jp_bgc || Number of passive tracers of the BGC model || 
     98|| ln_pisces / ln_my_trc || Run PISCES or MY_TRC BGC modules. There cannot be run at the same time since they both rely on jp_bgc || 
     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|| 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 || 
     102|| jp_dia3d, jp_dia2d || Number of 3D/2D diagnostic variables to populate dedicated array beside the direct usage of iom_put calls. || 
     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 || 
     105|| sn_trcdta(##) || Data structure to read tracers Initial conditions according to sn_tracer%llinit option. See structure description after this table. || 
     106|| rf_trfac(''##'') || Multiplicative factor for initialized tracer. If omitted default is 1.0. || 
     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 || 
     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.) || 
     118|| rn_fact_lap || Multiplicative factor to enhance zonal eddy diffusivity. || 
     119|||| &namtrc_zdf      !   vertical physics || 
     120|| ln_trczdf_exp || Split explicit (T) or implicit (F) time stepping || 
     121|| nn_trczdf_exp || Number of sub-timestep for ln_trczdfexp=T || 
     122|||| &namtrc_rad      !  treatment of negative concentrations || 
     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) || 
     126|| cn_resto_tr || NetCDF filename with input damping coefficients || 
     127|||| &namtrc_ice      !    Representation of sea ice growth & melt effects || 
     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') || 
     130|| nn_trd_trc || Time step frequency and tracers trends || 
     131|| nn_ctls_trc || Control surface type in mixed-layer trends (0,1 or n<jpk) || 
     132|| rn_ucf_trc || Unit conversion factor (=1 -> /seconds ; =86400. -> /day) || 
     133|| ln_trdmld_trc_restart || Use restart (T) or not (F) for ML diagnostics || 
     134|| ln_trdmld_trc_instant || Diagnose trends of instantaneous (T) or mean (F) ML T/S || 
     135|| ln_trdtrc(##) || Compute trend for nth tracer. Array of logical values. || 
     136|||| &namtrc_bc       !   Forcing data for boundary conditions || 
     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|| rn_trsfac(''##''), rn_trcfac(##), rn_trofac(##) || Multiplicative factor for SURFACE (sbc), COASTAL (cbc), and LATERAL (obc) forcing data files || 
     139|| cn_dir_sbc, cn_dir_cbc, cn_dir_obc || Root directory for the location of SURFACE (sbc), COASTAL (cbc), and LATERAL (obc) forcing data files || 
     140|| ln_rnf_ctl || Remove runoff dilution on tracers with absent river load (only without VVL) || 
     141|| rn_bc_time || Time scaling factor for SBC and CBC data (seconds in a day) || 
     142|||| &namtrc_bdy      !   Setup of tracer boundary conditions || 
     143|| cn_trc_dflt || Open Boundary Condition applied by default to all tracers || 
     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 || 
     147|| rn_age_depth || Depth over which age tracer reset to zero || 
     148|| rn_age_kill_rate || Relaxation timescale (s) for age tracer shallower than age depth ||