1 | \documentclass[../main/TOP_manual]{subfiles} |
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2 | |
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3 | \begin{document} |
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4 | |
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5 | \chapter{ Model Setup} |
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6 | |
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7 | The usage of TOP is activated i) by including in the configuration definition the component TOP and ii) by adding the macro key\_top in the configuration CPP file (see for more details “Learn more about the model”). |
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8 | As an example, the user can refer to already available configurations in the code, ORCA2\_ICE\_PISCES being the NEMO biogeochemical demonstrator and GYRE\_BFM to see the required configuration elements to couple with an external biogeochemical model (see also Section 4).\\ |
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9 | Note 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.\\ |
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10 | |
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11 | Below is the list of preprocessing keys that apply to the TOP interface (beside key\_top): |
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12 | \begin{itemize} |
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13 | \item key\_xios use XIOS I/O |
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14 | \item key\_agrif enables AGRIF coupling |
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15 | \item key\_trdtrc and key\_trdmxl\_trc trend computation for tracers |
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16 | \end{itemize} |
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17 | |
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18 | There are only two entry points in the NEMOGCM model for passive tracers : |
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19 | \begin{itemize} |
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20 | \item initialization (trcini) : general initialization of global variables and parameters of BGCM |
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21 | \item time-stepping (trcstp) : time-evolution of SMS first, then time evolution of tracers by transport |
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22 | \end{itemize} |
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23 | |
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24 | \section{ Setting up a passive tracer configuration} |
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25 | %------------------------------------------namtrc_int---------------------------------------------------- |
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26 | \nlst{namtrc} |
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27 | %------------------------------------------------------------------------------------------------------------- |
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28 | |
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29 | As a reminder, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : |
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30 | |
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31 | \begin{itemize} |
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32 | \item \textbf{PISCES}, default BGC model |
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33 | \item \textbf{MY\_TRC}, template for creation of new modules couplings (maybe run a single passive tracer) |
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34 | \item \textbf{CFC}, inert tracers dynamics (CFC$_{11}$,CFC$_{12}$,SF$_{6}$) updated based on OMIP-BGC guidelines (Orr et al, 2016) |
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35 | \item \textbf{C14}, radiocarbon passive tracer |
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36 | \item \textbf{AGE}, water age tracking |
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37 | \end{itemize} |
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38 | |
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39 | For inert, C14, and Age tracers, all variables settings (\textit{sn\_tracer} definitions) are hard-coded in \textit{trc\_nam\_*} routines. For instance, for Age tracer: |
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40 | %------------------------------------------namtrc_int---------------------------------------------------- |
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41 | \nlst{nam_trc_age} |
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42 | %--------------------------------------------------------------------------------------------------------- |
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43 | |
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44 | The modular approach was also implemented in the definition of the total number of passive tracers (jptra) which is specified by the user in \textit{namtrc} |
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45 | |
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46 | \section{ TOP Tracer Initialization} |
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47 | |
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48 | Two main types of data structure are used within TOP interface to initialize tracer properties and to provide related initial and boundary conditions. |
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49 | In addition to providing name and metadata for tracers, the use of initial and boundary conditions is also defined here (sn\_tracer). |
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50 | The data structure is internally initialized by the code with dummy names and all initialization/forcing logical fields are set to \textit{false} . |
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51 | Below are listed some features/options of the TOP interface accessible through the \textit{namelist\_top\_ref} and modifiable by means of \textit{namelist\_top\_cfg} (as for NEMO physical ones). |
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52 | |
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53 | There are three options to initialize TOP tracers in the \textit{namelist\_top } file: (1) initialization to hard-coded constant values when \textit{ln\_trcdta} at \textit{false}, (2) initialization from files when \textit{ln\_trcdta} at \textit{true}, and (3) initialisation from restart files by setting \textit{ln\_rsttr} to \textit{true} in \textit{namelist}. |
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54 | |
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55 | In the following, an example of the full structure definition is given for four tracers (DIC, Fe, NO$_{3}$, PHY) with initial conditions and different surface boundary and coastal forcings for DIC, Fe, and NO$_{3}$: |
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56 | |
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57 | %------------------------------------------namtrc_int---------------------------------------------------- |
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58 | \nlst{namtrc_cfg} |
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59 | %--------------------------------------------------------------------------------------------------------- |
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60 | |
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61 | You have to activate which tracers (\textit{sn\_tracer}) you want to initialize by setting them to \texttt{true} in the column. |
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62 | |
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63 | \nlst{namtrc_dta_cfg} |
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64 | |
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65 | In \textit{namtrc\_dta}, you prescribe from which files the tracer are initialized (\textit{sn\_trcdta}). |
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66 | A multiplicative factor can also be set for each tracer (\textit{rn\_trfac}). |
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67 | |
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68 | |
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69 | \section{ TOP Boundaries Conditions} |
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70 | |
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71 | \subsection{Surface and lateral boundaries} |
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72 | |
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73 | Lateral and surface boundary conditions for passive tracers are prescribed in \textit{namtrc\_bc} as well as whether temporal interpolation of these files is enabled. Here we show the cases of Fe and NO$_{3}$ from dust and rivers with different output frequencies. |
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74 | |
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75 | %------------------------------------------namtrc_bc---------------------------------------------------- |
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76 | \nlst{namtrc_bc_cfg} |
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77 | %--------------------------------------------------------------------------------------------------------- |
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78 | |
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79 | \subsection{Antartic Ice Sheet tracer supply} |
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80 | |
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81 | As a reminder, the supply of passive tracers from the AIS is currently implemented only for dissolved Fe. The activation of this Fe source is done by setting \textit{ln\_trcais} to \textit{true} and by adding the Fe tracer (\textit{sn\_tracer(2) = .true.}) in the 'ais' column in \textit{\&namtrc} (see section 2.2). \\ |
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82 | |
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83 | As the external source of Fe from the AIS is represented by associating a sedimentary Fe content (with a solubility fraction) to the freshwater fluxes of icebergs and ice shelves, these fluxes have to be activated in \textit{namelist\_cfg}. The reading of the freshwater flux file from ice shelves is activated in \textit{namisf} with the namelist parameter \textit{ln\_isf} set to \textit{true}. |
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84 | |
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85 | You have to choose between two options depending whether the cavities under ice shelves are open or not in your grid configuration: |
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86 | \begin{itemize} |
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87 | \item ln\_isfcav\_mlt = .false. (resolved cavities) |
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88 | \item ln\_isfpar\_mlt = .true. (parameterized distribution for unopened cavities) |
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89 | \end{itemize} |
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90 | |
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91 | %------------------------------------------namisf---------------------------------------------------- |
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92 | \nlst{namisf_cfg_eORCA1} |
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93 | %----------------------------------------------------------------------------------------------------- |
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94 | |
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95 | Runoff from icebergs is activated by setting \textit{ln\_rnf\_icb} to \textit{true} in the \textit{\&namsbc\_rnf} section of \textit{namelist\_cfg}. |
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96 | |
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97 | %------------------------------------------namsbc_rnf-------------------------------------------------- |
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98 | \nlst{namsbc_rnf_cfg_eORCA1} |
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99 | %--------------------------------------------------------------------------------------------------------- |
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100 | |
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101 | The freshwater flux from ice shelves and icebergs is based on observations and modeled climatologies and is available for eORCA1 and eORCA025 grids : |
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102 | \begin{itemize} |
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103 | \item runoff-icb\_DaiTrenberth\_Depoorter\_eORCA1\_JD.nc |
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104 | \item runoff-icb\_DaiTrenberth\_Depoorter\_eORCA025\_JD.nc |
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105 | \end{itemize} |
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106 | |
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107 | %------------------------------------------namtrc_ais---------------------------------------------------- |
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108 | \nlst{namtrc_ais_cfg} |
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109 | %--------------------------------------------------------------------------------------------------------- |
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110 | |
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111 | Two options for tracer concentrations in iceberg and ice shelf can be set with the namelist parameter \textit{nn\_ais\_tr}: |
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112 | \begin{itemize} |
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113 | \item 0 : null concentrations corresponding to dilution of BGC tracers due to freshwater fluxes from icebergs and ice shelves |
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114 | \item 1 : prescribed concentrations set with the \textit{rn\_trafac} factor |
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115 | \end{itemize} |
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116 | |
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117 | The depth until which Fe from melting iceberg is delivered can be set with the namelist parameter \textit{rn\_icbdep}. The value of 120 m is the average underwater depth of the different iceberg size classes modeled by the NEMO iceberg module, which was used to produce the freshwater flux climatology of icebergs. |
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118 | |
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119 | |
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120 | \end{document} |
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