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Changeset 14200 for NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles – NEMO

Ignore:
Timestamp:
2020-12-17T15:36:44+01:00 (3 years ago)
Author:
mcastril
Message:

Merging r14117 through r14199 into dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final

Location:
NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles
Files:
8 edited

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Unmodified
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  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r11693 r14200  
    4646 
    4747\begin{listing} 
    48   \nlst{namdom_domcfg} 
     48%  \nlst{namdom_domcfg} 
     49  \begin{forlines} 
     50!----------------------------------------------------------------------- 
     51&namdom        !   space and time domain (bathymetry, mesh, timestep) 
     52!----------------------------------------------------------------------- 
     53   nn_bathy    =    1      !  compute analyticaly (=0) or read (=1) the bathymetry file 
     54                           !  or compute (2) from external bathymetry 
     55   nn_interp   =    1                          ! type of interpolation (nn_bathy =2)                        
     56   cn_topo     =  'bathymetry_ORCA12_V3.3.nc'  ! external topo file (nn_bathy =2) 
     57   cn_bath     =  'Bathymetry'                 ! topo name in file  (nn_bathy =2) 
     58   cn_lon      =  'nav_lon'                    ! lon  name in file  (nn_bathy =2) 
     59   cn_lat      =  'nav_lat'                    ! lat  name in file  (nn_bathy =2) 
     60   rn_scale    = 1 
     61   rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1 
     62   jphgr_msh   =       0               !  type of horizontal mesh 
     63   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1) 
     64   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1) 
     65   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees) 
     66   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees) 
     67   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees) 
     68   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees) 
     69   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients 
     70   ppa0        =     255.58049070440   ! (default coefficients) 
     71   ppa1        =     245.58132232490   ! 
     72   ppkth       =      21.43336197938   ! 
     73   ppacr       =       3.0             ! 
     74   ppdzmin     =  999999.              !  Minimum vertical spacing 
     75   pphmax      =  999999.              !  Maximum depth 
     76   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates 
     77   ppa2        =  999999.              !  Double tanh function parameters 
     78   ppkth2      =  999999.              ! 
     79   ppacr2      =  999999.              ! 
     80/ 
     81  \end{forlines} 
    4982  \caption{\forcode{&namdom_domcfg}} 
    5083  \label{lst:namdom_domcfg} 
    … …  
    383416\subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln_sco}{ln\_sco})} 
    384417\label{sec:DOMCFG_sco} 
     418 
    385419\begin{listing} 
    386   \nlst{namzgr_sco_domcfg} 
     420%  \nlst{namzgr_sco_domcfg} 
    387421  \caption{\forcode{&namzgr_sco_domcfg}} 
    388422  \label{lst:namzgr_sco_domcfg} 
     423  \begin{forlines} 
     424!----------------------------------------------------------------------- 
     425&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate                (default: OFF) 
     426!----------------------------------------------------------------------- 
     427   ln_s_sh94   = .false.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)| 
     428   ln_s_sf12   = .false.   !  Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the NEMO tanh stretching is applied 
     429   ln_sigcrit  = .false.   !  use sigma coordinates below critical depth (T) or Z coordinates (F) for Siddorn & Furner stretch 
     430                           !  stretching coefficients for all functions 
     431   rn_sbot_min =   10.0    !  minimum depth of s-bottom surface (>0) (m) 
     432   rn_sbot_max = 7000.0    !  maximum depth of s-bottom surface (= ocean depth) (>0) (m) 
     433   rn_hc       =  150.0    !  critical depth for transition to stretched coordinates 
     434                        !!!!!!!  Envelop bathymetry 
     435   rn_rmax     =    0.3    !  maximum cut-off r-value allowed (0<r_max<1) 
     436                        !!!!!!!  SH94 stretching coefficients  (ln_s_sh94 = .true.) 
     437   rn_theta    =    6.0    !  surface control parameter (0<=theta<=20) 
     438   rn_bb       =    0.8    !  stretching with SH94 s-sigma 
     439                        !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.) 
     440   rn_alpha    =    4.4    !  stretching with SF12 s-sigma 
     441   rn_efold    =    0.0    !  efold length scale for transition to stretched coord 
     442   rn_zs       =    1.0    !  depth of surface grid box 
     443                           !  bottom cell depth (Zb) is a linear function of water depth Zb = H*a + b 
     444   rn_zb_a     =    0.024  !  bathymetry scaling factor for calculating Zb 
     445   rn_zb_b     =   -0.2    !  offset for calculating Zb 
     446                        !!!!!!!! Other stretching (not SH94 or SF12) [also uses rn_theta above] 
     447   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1) 
     448/ 
     449  \end{forlines} 
    389450\end{listing} 
    390 Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only). 
     451 
     452Options are defined in \forcode{&zgr_sco} (\texttt{DOMAINcfg} only). 
    391453In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from 
    392454the product of a depth field and either a stretching function or its derivative, respectively: 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_DYN.tex

    r14113 r14200  
    763763which imposes a very small time step when an explicit time stepping is used. 
    764764Two methods are proposed to allow a longer time step for the three-dimensional equations: 
    765 the filtered free surface, which is a modification of the continuous equations (see \autoref{eq:MB_flt?}), 
     765the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi 
    766766and the split-explicit free surface described below. 
    767767The extra term introduced in the filtered method is calculated implicitly, 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_LBC.tex

    r14113 r14200  
    372372The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 
    373373Each boundary set can be either defined as a series of straight line segments directly in the namelist 
    374 (\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
     374(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
    375375The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 
    376376In the example above, there are two boundary sets, the first of which is defined via a file and 
    … …  
    569569\autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary. 
    570570 
    571 The boundary geometry for each set may be defined in a namelist nambdy\_index or 
     571The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or 
    572572by reading in a ``\ifile{coordinates.bdy}'' file. 
    573 The nambdy\_index namelist defines a series of straight-line segments for north, east, south and west boundaries. 
    574 One nambdy\_index namelist block is needed for each boundary condition defined by indexes. 
     573The \texttt{nambdy\_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 
     574One \texttt{nambdy\_index} namelist block is needed for each boundary condition defined by indexes. 
    575575For the northern boundary, \texttt{nbdysegn} gives the number of segments, 
    576576\jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11708 r14200  
    892892\subsubsection{Running} 
    893893 
    894 The simplest way to use the executable is to edit and append the \textbf{sao.nml} namelist to 
     894The simplest way to use the executable is to edit and append the \nam{sao}{sao} namelist to 
    895895a full \NEMO\ namelist and then to run the executable as if it were nemo.exe. 
    896896 
    … …  
    914914For example, to read the second time counter from a single file the namelist would be. 
    915915 
    916 \begin{forlines} 
     916\begin{listing} 
     917%  \nlst{namsao} 
     918  \begin{forlines} 
    917919!---------------------------------------------------------------------- 
    918920!       namsao Standalone obs_oper namelist 
    … …  
    924926   nn_sao_idx = 2 
    925927/ 
    926 \end{forlines} 
     928  \end{forlines} 
     929  \caption{\forcode{&namsao}} 
     930  \label{lst:namsao} 
     931\end{listing} 
    927932 
    928933%% ================================================================================================= 
    … …  
    11191124To plot some data run IDL and then: 
    11201125 
    1121 \begin{minted}{idl} 
     1126\begin{verbatim} 
    11221127IDL> dataplot, "filename" 
    1123 \end{minted} 
     1128\end{verbatim} 
    11241129 
    11251130To read multiple files into dataplot, 
    … …  
    11271132the easiest method is to use the spawn command to generate a list of files which can then be passed to dataplot. 
    11281133 
    1129 \begin{minted}{idl} 
     1134\begin{verbatim} 
    11301135IDL> spawn, 'ls profb*.nc', files 
    11311136IDL> dataplot, files 
    1132 \end{minted} 
     1137\end{verbatim} 
    11331138 
    11341139\autoref{fig:OBS_dataplotmain} shows the main window which is launched when dataplot starts. 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_SBC.tex

    r14116 r14200  
    1616    Release & Author(s) & Modifications \\ 
    1717    \hline 
    18     {\em  next} & {\em Simon M{\" u}ller} & {\em Update of \autoref{sec:SBC_TDE}}\\[2mm] 
     18    {\em  next} & {\em Simon M{\" u}ller} & {\em Update of \autoref{sec:SBC_TDE}; revision of \autoref{subsec:SBC_fwb}}\\[2mm] 
    1919    {\em   4.0} & {\em ...} & {\em ...} \\ 
    2020    {\em   3.6} & {\em ...} & {\em ...} \\ 
    … …  
    664664For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 
    665665basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based 
    666 on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE 
     666on \citet{zeng.beljaars_GRL05} for ECMWF \iffalse, and \citet{fairall.ea_19?} for COARE \fi 
    6676673.6. 
    668668 
    … …  
    671671turbulence input from Langmuir circulation). 
    672672 
    673 Importantly, COARE warm-layer scheme \citep{fairall.ea_19} includes a prognostic 
     673Importantly, COARE warm-layer scheme \iffalse \citep{fairall.ea_19?} \fi includes a prognostic 
    674674equation for the thickness of the warm-layer, while it is considered as constant 
    675675in the ECWMF algorithm. 
    … …  
    971971and tidal analysis in the model framework. This includes the computation of the gravitational 
    972972surface forcing, as well as support for lateral forcing at open boundaries (see 
    973 \autoref{subsec:LBC_bdy_tides}) and tidal harmonic analysis (see 
    974 \autoref{subsec:DIA_diamlr} and \autoref{subsec:DIA_diadetide}). The module is 
     973\autoref{subsec:LBC_bdy_tides}) and tidal harmonic analysis \iffalse (see 
     974\autoref{subsec:DIA_diamlr?} and \autoref{subsec:DIA_diadetide?}) \fi . The module is 
    975975activated with \np[=.true.]{ln_tide}{ln\_tide} in namelist 
    976976\nam{_tide}{\_tide}. It provides the same 34 tidal constituents that are 
    … …  
    17771777\label{subsec:SBC_fwb} 
    17781778 
    1779 For global ocean simulation, it can be useful to introduce a control of the mean sea level in order to 
    1780 prevent unrealistic drift of the sea surface height due to inaccuracy in the freshwater fluxes. 
    1781 In \NEMO, two way of controlling the freshwater budget are proposed: 
     1779\begin{listing} 
     1780  \nlst{namsbc_fwb} 
     1781  \caption{\forcode{&namsbc_fwb}} 
     1782  \label{lst:namsbc_fwb} 
     1783\end{listing} 
     1784 
     1785For global ocean simulations, it can be useful to introduce a control of the 
     1786mean sea level in order to prevent unrealistic drifting of the sea surface 
     1787height due to unbalanced freshwater fluxes. In \NEMO, two options for 
     1788controlling the freshwater budget are proposed. 
    17821789 
    17831790\begin{description} 
    1784 \item [{\np[=0]{nn_fwb}{nn\_fwb}}] no control at all. 
    1785   The mean sea level is free to drift, and will certainly do so. 
    1786 \item [{\np[=1]{nn_fwb}{nn\_fwb}}] global mean \textit{emp} set to zero at each model time step. 
     1791\item [{\np[=0]{nn_fwb}{nn\_fwb}}:] No control at all; the mean sea level is 
     1792  free to drift, and will certainly do so. 
     1793\item [{\np[=1]{nn_fwb}{nn\_fwb}}:] The global mean \textit{emp} is set to zero at each model time step. 
    17871794  %GS: comment below still relevant ? 
    17881795  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
    1789 \item [{\np[=2]{nn_fwb}{nn\_fwb}}] freshwater budget is adjusted from the previous year annual mean budget which 
    1790   is read in the \textit{EMPave\_old.dat} file. 
    1791   As the model uses the Boussinesq approximation, the annual mean fresh water budget is simply evaluated from 
    1792   the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file. 
     1796\item [{\np[=2]{nn_fwb}{nn\_fwb}}:] \textit{emp} is adjusted by adding a 
     1797  spatially uniform, annual-mean freshwater flux that balances the freshwater 
     1798  budget at the end of the previous year; as the model uses the Boussinesq 
     1799  approximation, the freshwater budget can be evaluated from the change in the 
     1800  mean sea level and in the ice and snow mass after the end of each simulation 
     1801  year; at the start of the model run, an initial adjustment flux can be set 
     1802  using parameter \np{rn_rwb0}{rn\_fwb0} in namelist \nam{sbc_fwb}{sbc\_fwb}. 
    17931803\end{description} 
    17941804 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r14113 r14200  
    731731\subsubsection{Evolution of the boundary layer depth} 
    732732 
    733 The prognostic equation for the depth of the neutral/unstable boundary layer is given by \citep{grant+etal18}, 
     733The prognostic equation for the depth of the neutral/unstable boundary layer is given by \iffalse \citep{grant+etal18?}, \fi 
    734734 
    735735\begin{equation} 
    … …  
    747747equation for the case when the pycnocline has a finite thickness, 
    748748based on the potential energy budget of the OSBL, is the leading term 
    749 \citep{grant+etal18} of a generalization of that used in mixed-layer 
     749\iffalse \citep{grant+etal18?} \fi of a generalization of that used in mixed-layer 
    750750models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero. 
    751751 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r14113 r14200  
    243243Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in 
    244244the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 
    245 analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
     245analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines. 
    246246Its horizontal resolution (and thus the size of the domain) is determined by 
    247 setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: \\ 
    248  
    249 \jp{jpiglo} $= 30 \times$ \np{nn_GYRE}{nn\_GYRE} + 2  \\ 
    250  
    251 \jp{jpjglo} $= 20 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\ 
     247setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: 
     248\begin{align*} 
     249  \jp{jpiglo} = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\ 
     250  \jp{jpjglo} = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} 
     251\end{align*} 
    252252 
    253253Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
    254254see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). 
    255255In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}). 
     256 
     257\begin{listing} 
     258  \begin{forlines} 
     259!----------------------------------------------------------------------- 
     260&namusr_def    !   GYRE user defined namelist   
     261!----------------------------------------------------------------------- 
     262   nn_GYRE     =     1     !  GYRE resolution [1/degrees] 
     263   ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant 
     264   jpkglo      =    31     !  number of model levels 
     265/ 
     266  \end{forlines} 
     267  \caption{\forcode{&namusr_def}} 
     268  \label{lst:namusr_def} 
     269\end{listing} 
    256270 
    257271The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and 

  • NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r14113 r14200  
    9595which imposes a very small time step when an explicit time stepping is used. 
    9696Two methods are proposed to allow a longer time step for the three-dimensional equations: 
    97 the filtered free surface, which is a modification of the continuous equations %(see \autoref{eq:MB_flt?}), 
     97the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi , 
    9898and the split-explicit free surface described below. 
    9999The extra term introduced in the filtered method is calculated implicitly, 
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