Changeset 14200 for NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc
- Timestamp:
- 2020-12-17T15:36:44+01:00 (4 years ago)
- Location:
- NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc
- Files:
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- 8 deleted
- 10 edited
- 10 copied
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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 46 46 47 47 \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} 49 82 \caption{\forcode{&namdom_domcfg}} 50 83 \label{lst:namdom_domcfg} … … 383 416 \subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln_sco}{ln\_sco})} 384 417 \label{sec:DOMCFG_sco} 418 385 419 \begin{listing} 386 \nlst{namzgr_sco_domcfg}420 % \nlst{namzgr_sco_domcfg} 387 421 \caption{\forcode{&namzgr_sco_domcfg}} 388 422 \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} 389 450 \end{listing} 390 Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only). 451 452 Options are defined in \forcode{&zgr_sco} (\texttt{DOMAINcfg} only). 391 453 In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from 392 454 the 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 763 763 which imposes a very small time step when an explicit time stepping is used. 764 764 Two 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?}),765 the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi 766 766 and the split-explicit free surface described below. 767 767 The 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 372 372 The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 373 373 Each 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). 375 375 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 376 376 In the example above, there are two boundary sets, the first of which is defined via a file and … … 569 569 \autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary. 570 570 571 The boundary geometry for each set may be defined in a namelist nambdy\_indexor571 The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or 572 572 by reading in a ``\ifile{coordinates.bdy}'' file. 573 The nambdy\_indexnamelist defines a series of straight-line segments for north, east, south and west boundaries.574 One nambdy\_indexnamelist block is needed for each boundary condition defined by indexes.573 The \texttt{nambdy\_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 574 One \texttt{nambdy\_index} namelist block is needed for each boundary condition defined by indexes. 575 575 For the northern boundary, \texttt{nbdysegn} gives the number of segments, 576 576 \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 892 892 \subsubsection{Running} 893 893 894 The simplest way to use the executable is to edit and append the \ textbf{sao.nml} namelist to894 The simplest way to use the executable is to edit and append the \nam{sao}{sao} namelist to 895 895 a full \NEMO\ namelist and then to run the executable as if it were nemo.exe. 896 896 … … 914 914 For example, to read the second time counter from a single file the namelist would be. 915 915 916 \begin{forlines} 916 \begin{listing} 917 % \nlst{namsao} 918 \begin{forlines} 917 919 !---------------------------------------------------------------------- 918 920 ! namsao Standalone obs_oper namelist … … 924 926 nn_sao_idx = 2 925 927 / 926 \end{forlines} 928 \end{forlines} 929 \caption{\forcode{&namsao}} 930 \label{lst:namsao} 931 \end{listing} 927 932 928 933 %% ================================================================================================= … … 1119 1124 To plot some data run IDL and then: 1120 1125 1121 \begin{ minted}{idl}1126 \begin{verbatim} 1122 1127 IDL> dataplot, "filename" 1123 \end{ minted}1128 \end{verbatim} 1124 1129 1125 1130 To read multiple files into dataplot, … … 1127 1132 the easiest method is to use the spawn command to generate a list of files which can then be passed to dataplot. 1128 1133 1129 \begin{ minted}{idl}1134 \begin{verbatim} 1130 1135 IDL> spawn, 'ls profb*.nc', files 1131 1136 IDL> dataplot, files 1132 \end{ minted}1137 \end{verbatim} 1133 1138 1134 1139 \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 16 16 Release & Author(s) & Modifications \\ 17 17 \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] 19 19 {\em 4.0} & {\em ...} & {\em ...} \\ 20 20 {\em 3.6} & {\em ...} & {\em ...} \\ … … 664 664 For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 665 665 basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based 666 on \citet{zeng.beljaars_GRL05} for ECMWF , and \citet{fairall.ea_19} for COARE666 on \citet{zeng.beljaars_GRL05} for ECMWF \iffalse, and \citet{fairall.ea_19?} for COARE \fi 667 667 3.6. 668 668 … … 671 671 turbulence input from Langmuir circulation). 672 672 673 Importantly, COARE warm-layer scheme \ citep{fairall.ea_19}includes a prognostic673 Importantly, COARE warm-layer scheme \iffalse \citep{fairall.ea_19?} \fi includes a prognostic 674 674 equation for the thickness of the warm-layer, while it is considered as constant 675 675 in the ECWMF algorithm. … … 971 971 and tidal analysis in the model framework. This includes the computation of the gravitational 972 972 surface forcing, as well as support for lateral forcing at open boundaries (see 973 \autoref{subsec:LBC_bdy_tides}) and tidal harmonic analysis (see974 \autoref{subsec:DIA_diamlr } and \autoref{subsec:DIA_diadetide}). The module is973 \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 975 975 activated with \np[=.true.]{ln_tide}{ln\_tide} in namelist 976 976 \nam{_tide}{\_tide}. It provides the same 34 tidal constituents that are … … 1777 1777 \label{subsec:SBC_fwb} 1778 1778 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 1785 For global ocean simulations, it can be useful to introduce a control of the 1786 mean sea level in order to prevent unrealistic drifting of the sea surface 1787 height due to unbalanced freshwater fluxes. In \NEMO, two options for 1788 controlling the freshwater budget are proposed. 1782 1789 1783 1790 \begin{description} 1784 \item [{\np[=0]{nn_fwb}{nn\_fwb}} ] no control at all.1785 The mean sea level isfree 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. 1787 1794 %GS: comment below still relevant ? 1788 1795 %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}. 1793 1803 \end{description} 1794 1804 -
NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_ZDF.tex
r14113 r14200 731 731 \subsubsection{Evolution of the boundary layer depth} 732 732 733 The prognostic equation for the depth of the neutral/unstable boundary layer is given by \ citep{grant+etal18},733 The prognostic equation for the depth of the neutral/unstable boundary layer is given by \iffalse \citep{grant+etal18?}, \fi 734 734 735 735 \begin{equation} … … 747 747 equation for the case when the pycnocline has a finite thickness, 748 748 based on the potential energy budget of the OSBL, is the leading term 749 \ citep{grant+etal18}of a generalization of that used in mixed-layer749 \iffalse \citep{grant+etal18?} \fi of a generalization of that used in mixed-layer 750 750 models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero. 751 751 -
NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/NEMO/subfiles/chap_cfgs.tex
r14113 r14200 243 243 Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in 244 244 the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 245 analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgrroutines.245 analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines. 246 246 Its 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 \\247 setting \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*} 252 252 253 253 Obviously, the namelist parameters have to be adjusted to the chosen resolution, 254 254 see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). 255 255 In 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} 256 270 257 271 The 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 95 95 which imposes a very small time step when an explicit time stepping is used. 96 96 Two 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?}),97 the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi , 98 98 and the split-explicit free surface described below. 99 99 The extra term introduced in the filtered method is calculated implicitly, -
NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/SI3/namelists/namdyn_adv
r11703 r14200 2 2 &namdyn_adv ! Ice advection 3 3 !------------------------------------------------------------------------------ 4 ln_adv_Pra = .true. ! Advection scheme (Prather)5 ln_adv_UMx = .false. 4 ln_adv_Pra = .true. ! Advection scheme (Prather) 5 ln_adv_UMx = .false. ! Advection scheme (Ultimate-Macho) 6 6 nn_UMx = 5 ! order of the scheme for UMx (1-5 ; 20=centered 2nd order) 7 7 / -
NEMO/branches/2020/dev_r14116_HPC-04_mcastril_Mixed_Precision_implementation_final/doc/latex/SI3/namelists/namsbc
r11026 r14200 3 3 !------------------------------------------------------------------------------ 4 4 rn_cio = 5.0e-03 ! ice-ocean drag coefficient (-) 5 rn_blow_s = 0.66 ! mesure of snow blowing into the leads 5 nn_snwfra = 2 ! calculate the fraction of ice covered by snow (for zdf and albedo) 6 ! = 0 fraction = 1 (if snow) or 0 (if no snow) 7 ! = 1 fraction = 1-exp(-0.2*rhos*hsnw) [MetO formulation] 8 ! = 2 fraction = hsnw / (hsnw+0.02) [CICE formulation] 9 rn_snwblow = 0.66 ! mesure of snow blowing into the leads 6 10 ! = 1 => no snow blowing, < 1 => some snow blowing 7 11 nn_flxdist = -1 ! Redistribute heat flux over ice categories … … 12 16 ln_cndflx = .false. ! Use conduction flux as surface boundary conditions (i.e. for Jules coupling) 13 17 ln_cndemulate = .false. ! emulate conduction flux (if not provided in the inputs) 18 nn_qtrice = 1 ! Solar flux transmitted thru the surface scattering layer: 19 ! = 0 Grenfell and Maykut 1977 (depends on cloudiness and is 0 when there is snow) 20 ! = 1 Lebrun 2019 (equals 0.3 anytime with different melting/dry snw conductivities) 14 21 /
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