Changes between Version 17 and Version 18 of Working Groups/TOP/TOP-User Quick Guide


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Timestamp:
2018-01-17T12:20:35+01:00 (3 years ago)
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lovato
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  • Working Groups/TOP/TOP-User Quick Guide

    v17 v18  
    11= TOP interface User Quick Guide (NEMO 4.0+) = 
    22=  = 
     3 
     4[[BR]] 
     5 
    36== TOP interface structure == 
    47TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers.  It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules.  TOP interfaces has the following location in the code repository 
     
    3437key_trdtrc & key_trdmxl_trc : trend computation for tracers 
    3538 
     39[[BR]] 
     40 
    3641== TOP synthetic Workflow == 
    3742A 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. 
     
    5156  ↳ call trc_ini_state, read passive tracers from a restart or input data 
    5257 
    53   ↳ call trc_sub_ini, setup substepping if nn_dttrc /= 1 
     58  ↳ call trc_sub_ini, setup substepping if {{{nn_dttrc /= 1}}} 
    5459 
    5560'''Time marching procedure (OPA_SRC/stp.F90)''' 
     
    6772  ↳ call trc_trp (TRP/trctrp.F90), compute physical trends 
    6873 
    69   ↳ call trc_sbc, get trend due to surface concentration/dilution 
    70  
    71   ↳ call trc_adv, compute tracers advection 
    72  
    73   ↳ call to trc_ldf, compute tracers lateral diffusion 
    74  
    75   ↳ call to trc_zdf, vertical mixing and after tracer fields 
    76  
    77   ↳ call to trc_nxt, tracer fields at next time step 
    78  
    79   ↳ call to trc_rad, Correct artificial negative concentrations 
     74    ↳ call trc_sbc, get trend due to surface concentration/dilution 
     75 
     76    ↳ call trc_adv, compute tracers advection 
     77 
     78    ↳ call to trc_ldf, compute tracers lateral diffusion 
     79 
     80    ↳ call to trc_zdf, vertical mixing and after tracer fields 
     81 
     82    ↳ call to trc_nxt, tracer fields at next time step 
     83 
     84    ↳ call to trc_rad, Correct artificial negative concentrations 
    8085 
    8186  ↳ call trc_rst_wri, output tracers restart files 
     87 
     88[[BR]] 
    8289 
    8390== TOP namelist Walkthrough == 
     
    8693 
    8794Note that ## is used to refer to a number in an array field. 
     95 
     96[[BR]] 
    8897 
    8998|||| &'''namtrc_run'''      !   run information || 
     
    152161'''1. TOP tracers initialization''' : sn_tracer (namtrc) 
    153162 
    154 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. 
     163Beside 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. 
    155164 
    156165In 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: 
     
    179188This 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). 
    180189 
    181 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 in namelist filename), with a doubled initial value, and located in the usr/work/model/inputdata/ folder: 
     190The following example illustrates 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 in namelist filename), with a doubled initial value, and located in the usr/work/model/inputdata/ folder: 
    182191 
    183192{{{ 
     
    188197  cn_dir = “usr/work/model/inputdata/” 
    189198}}} 
    190 The Lateral Open Boundaries conditions are applied to the segments defined for the physical core of NEMO (see BDY description in the User Manual). 
     199Note that, the Lateral Open Boundaries conditions are applied on the segments defined for the physical core of NEMO (see BDY description in the User Manual). 
     200 
     201[[BR]] 
    191202 
    192203=== namelist_trc ===