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Commit 3c14c03d authored by Tomas Lovato's avatar Tomas Lovato
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add new nlstlocal command to read non default namelist from chapter folder

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doc/latex/TOP/namelists/nam_trc_age 0 → 100644
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! Variable setting
ctrcnm (jp_age) = 'Age'
ctrcln (jp_age) = 'Sea water age since surface contact'
ctrcun (jp_age) = 'year'
ln_trc_ini(jp_age) = .false.
ln_trc_sbc(jp_age) = .false.
ln_trc_cbc(jp_age) = .false.
ln_trc_obc(jp_age) = .false.
doc/latex/TOP/namelists/namdta_dyn_linssh 0 → 100644
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!-----------------------------------------------------------------------
&namdta_dyn ! offline ocean input files (OFF_SRC only)
!-----------------------------------------------------------------------
cn_dir = './' ! root directory for the ocean data location
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_tem = 'dyna_grid_T' , 120. , 'votemper' , .true. , .true. , 'yearly'
sn_sal = 'dyna_grid_T' , 120. , 'vosaline' , .true. , .true. , 'yearly'
sn_mld = 'dyna_grid_T' , 120. , 'somixhgt' , .true. , .true. , 'yearly'
sn_emp = 'dyna_grid_T' , 120. , 'sowaflup' , .true. , .true. , 'yearly'
sn_fmf = 'dyna_grid_T' , 120. , 'iowaflup' , .true. , .true. , 'yearly'
sn_ice = 'dyna_grid_T' , 120. , 'soicecov' , .true. , .true. , 'yearly'
sn_qsr = 'dyna_grid_T' , 120. , 'soshfldo' , .true. , .true. , 'yearly'
sn_wnd = 'dyna_grid_T' , 120. , 'sowindsp' , .true. , .true. , 'yearly'
sn_uwd = 'dyna_grid_U' , 120. , 'uocetr_eff', .true. , .true. , 'yearly'
sn_vwd = 'dyna_grid_V' , 120. , 'vocetr_eff', .true. , .true. , 'yearly'
sn_wwd = 'dyna_grid_W' , 120. , 'wocetr_eff', .true. , .true. , 'yearly'
sn_avt = 'dyna_grid_W' , 120. , 'voddmavs' , .true. , .true. , 'yearly'
sn_ubl = 'dyna_grid_U' , 120. , 'sobblcox' , .true. , .true. , 'yearly'
sn_vbl = 'dyna_grid_V' , 120. , 'sobblcoy' , .true. , .true. , 'yearly'
/
doc/latex/TOP/namelists/namdta_dyn_nolinssh 0 → 100644
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!-----------------------------------------------------------------------
&namdta_dyn ! offline ocean input files (OFF_SRC only)
!-----------------------------------------------------------------------
ln_dynrnf = .true. ! runoffs option enabled (T) or not (F)
ln_dynrnf_depth = .false. ! runoffs is spread in vertical (T) or not (F)
!
cn_dir = './' ! root directory for the ocean data location
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_tem = 'dyna_grid_T' , 120. , 'thetao' , .true. , .true. , 'yearly'
sn_sal = 'dyna_grid_T' , 120. , 'so' , .true. , .true. , 'yearly'
sn_div = 'dyna_grid_T' , 120. , 'hdivtr' , .true. , .true. , 'yearly'
sn_mld = 'dyna_grid_T' , 120. , 'mldr10_1' , .true. , .true. , 'yearly'
sn_emp = 'dyna_grid_T' , 120. , 'wfo' , .true. , .true. , 'yearly'
sn_empb = 'dyna_grid_T' , 120. , 'wfob' , .true. , .true. , 'yearly'
sn_fmf = 'dyna_grid_T' , 120. , 'fmmflx' , .true. , .true. , 'yearly'
sn_rnf = 'dyna_grid_T' , 120. , 'runoffs' , .true. , .true. , 'yearly'
sn_ice = 'dyna_grid_T' , 120. , 'siconc' , .true. , .true. , 'yearly'
sn_qsr = 'dyna_grid_T' , 120. , 'rsntds' , .true. , .true. , 'yearly'
sn_wnd = 'dyna_grid_T' , 120. , 'windsp' , .true. , .true. , 'yearly'
sn_uwd = 'dyna_grid_U' , 120. , 'uocetr_eff', .true. , .true. , 'yearly'
sn_vwd = 'dyna_grid_V' , 120. , 'vocetr_eff', .true. , .true. , 'yearly'
sn_wwd = 'dyna_grid_W' , 120. , 'wocetr_eff', .true. , .true. , 'yearly'
sn_avt = 'dyna_grid_W' , 120. , 'difvsolog' , .true. , .true. , 'yearly'
sn_ubl = 'dyna_grid_U' , 120. , 'ahu_bbl' , .true. , .true. , 'yearly'
sn_vbl = 'dyna_grid_V' , 120. , 'ahv_bbl' , .true. , .true. , 'yearly'
/
doc/latex/TOP/namelists/namisf_cfg_eORCA1 0 → 100644
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!-----------------------------------------------------------------------
&namisf ! Top boundary layer (ISF) (default: OFF)
!-----------------------------------------------------------------------
!
! ---------------- ice shelf melt formulation -------------------------------
!
ln_isf = .true. ! activate ice shelf module
!
! ---------------- cavities opened -------------------------------
!
ln_isfcav_mlt = .false. ! ice shelf melting into the cavity (need ln_isfcav = .true. in domain_cfg.nc)
cn_isfcav_mlt = '3eq' ! ice shelf melting formulation (spe/2eq/3eq/oasis)
! ! spe = fwfisf is read from a forcing field
! ! 2eq = ISOMIP like: 2 equations formulation (Hunter et al., 2006 for a short description)
! ! 3eq = ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2016 for a short description
rn_htbl = 30. ! thickness of the top boundary layer (Losh et al. 2008)
! ! 0 => thickness of the tbl = thickness of the first wet cell
!
!* 'spe' and 'oasis' case
!---------------------------------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_isfcav_fwf = 'isfmlt_cav', -12. , 'fwflisf' , .false. , .true. , 'yearly'
!
! ---------------- cavities parametrised -------------------------------
!
ln_isfpar_mlt = .true. ! ice shelf melting parametrised
cn_isfpar_mlt = 'spe' ! ice shelf melting parametrisation (spe/bg03/oasis)
! ! spe = fwfisf is read from a forcing field
!
!---------------------------------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_isfpar_zmax = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sodepmax_isf' , .false. , .true. , 'yearly'
sn_isfpar_zmin = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sodepmin_isf' , .false. , .true. , 'yearly'
!* 'spe' and 'oasis' case
sn_isfpar_fwf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sornfisf', .false. , .true. , 'yearly'
doc/latex/TOP/namelists/namsbc_rnf_cfg_eORCA1 0 → 100644
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!-----------------------------------------------------------------------
&namsbc_rnf ! runoffs (ln_rnf =T)
!-----------------------------------------------------------------------
ln_rnf_mouth = .false. ! specific treatment at rivers mouths
rn_hrnf = 15.e0 ! depth over which enhanced vertical mixing is used (ln_rnf_mouth=T)
rn_avt_rnf = 1.e-3 ! value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T)
rn_rfact = 1.e0 ! multiplicative factor for runoff
ln_rnf_icb = .true. ! read iceberg flux
cn_dir = './' ! root directory for the location of the runoff files
!---------------------------------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_rnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', -1 , 'sorunoff', .true. , .true. , 'yearly'
sn_i_rnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', -1 , 'Icb_flux', .true. , .true. , 'yearly'
sn_cnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', 0 , 'socoefr' , .false. , .true. , 'yearly'
sn_s_rnf = 'runoffs' , 24. , 'rosaline', .true. , .true. , 'yearly'
sn_t_rnf = 'runoffs' , 24. , 'rotemper', .true. , .true. , 'yearly'
sn_dep_rnf = 'runoffs' , 0. , 'rodepth' , .false. , .true. , 'yearly'
doc/latex/TOP/namelists/namtrc_ais_cfg 0 → 100644
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!-----------------------------------------------------------------------
&namtrc_ais ! Representation of Antarctic Ice Sheet tracers supply
!-----------------------------------------------------------------------
rn_trafac(3) = 4.476e-07 ! ( 0.5e-3 / 55.85 * 0.05 )
!
nn_ais_tr = 1 ! tracer concentration in iceberg and ice shelf
! = 0 (null concentrations)
! = 1 prescribed concentrations
rn_icbdep = 120. ! Mean underwater depth of iceberg (m)
doc/latex/TOP/namelists/namtrc_bc_cfg 0 → 100644
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!----------------------------------------------------------------------
&namtrc_bc ! data for boundary conditions
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_trcsbc(2) = 'dust.orca.new' , -1 , 'dustfer' , .true. , .true. , 'yearly'
sn_trcsbc(3) = 'ndeposition.orca', -12 , 'ndep' , .false. , .true. , 'yearly'
rn_trsfac(2) = 6.266e-04 ! Multiplicative factor
rn_trsfac(3) = 5.4464e-01 !
!
sn_trccbc(1) = 'river.orca' , -12 , 'riverdic' , .true. , .true. , 'yearly'
sn_trccbc(2) = 'river.orca' , -12 , 'riverdfe' , .true. , .true. , 'yearly'
sn_trccbc(3) = 'river.orca' , -12 , 'riverdin' , .true. , .true. , 'yearly'
rn_trcfac(1) = 1.0 ! Multiplicative factor
rn_trcfac(2) = 1.0 !
rn_trcfac(3) = 1.0 !
rn_cbc_time = 3.1536e+7 ! Time scaling factor for CBC data (seconds in a year)
doc/latex/TOP/namelists/namtrc_cfg 0 → 100644
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!-----------------------------------------------------------------------
&namtrc ! tracers definition
!-----------------------------------------------------------------------
jp_bgc = 24
!
ln_pisces = .true.
ln_my_trc = .false.
ln_age = .false.
ln_cfc11 = .false.
ln_cfc12 = .false.
ln_c14 = .false.
!
!
ln_trcdta = .true. ! Initialisation from data input file (T) or not (F)
ln_trcdmp = .false. ! add a damping termn (T) or not (F)
ln_trcdmp_clo = .false. ! damping term (T) or not (F) on closed seas
ln_trcbc = .true. ! Surface, Lateral or Open Boundaries conditions
ln_trcais = .true. ! Antarctic Ice Sheet nutrient supply
! ! ! ! ! !
! ! name ! title of the field ! units ! init ! sbc ! cbc ! obc ! ais
sn_tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mol-C/L' , .true. , .false., .true. , .false. , .false.
sn_tracer(2) = 'Fer ' , 'Dissolved Iron Concentration ', 'mol-C/L' , .true. , .true. , .true. , .false. , .true.
sn_tracer(3) = 'NO3 ' , 'Nitrates Concentration ', 'mol-C/L' , .true. , .true. , .true. , .false. , .false.
sn_tracer(4) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false.
doc/latex/TOP/namelists/namtrc_dta_cfg 0 → 100644
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!-----------------------------------------------------------------------
&namtrc_dta ! Initialisation from data input file
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
sn_trcdta(1) = 'data_DIC_nomask.nc', -12 , 'PiDIC' , .false. , .true. , 'yearly' ,
sn_trcdta(2) = 'data_FER_nomask.nc', -1 , 'Fer' , .true. , .true. , 'yearly' ,
sn_trcdta(3) = 'data_NO3_nomask.nc', -1 , 'NO3' , .true. , .true. , 'yearly' ,
!
rn_trfac(1) = 1.028e-06 ! multiplicative factor
rn_trfac(2) = 1.0e-06 ! - - - -
rn_trfac(3) = 7.6e-06 ! - - - -
doc/latex/TOP/subfiles/model_description.tex
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......@@ -122,11 +122,11 @@ There are two sets of fields to perform offline simulations :
to transport : the effective ocean transport velocities (eulerian plus the eddy induced plus all others parameterizations), vertical diffusion coefficient and the freshwater flux
.
%------------------------------------------namtrc_sms----------------------------------------------------
\nlst{namdta_dyn_linssh}
\nlstlocal{namdta_dyn_linssh}
%-----------------------------------------------------------------------------------------------------------
\item non linear free surface ( ln\_linssh = .false. or key\_qco ): the same fields than the ones in the linear free surface case. In addition, the horizontal divergence transport is needed to recompute the time evolution of the sea surface heigth and the vertical scale factor and depth, and thus the time evolution of the vertical transport velocity.
%------------------------------------------namtrc_sms----------------------------------------------------
\nlst{namdta_dyn_nolinssh}
\nlstlocal{namdta_dyn_nolinssh}
%-----------------------------------------------------------------------------------------------------------
\end{itemize}
......
doc/latex/TOP/subfiles/model_setup.tex
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......@@ -24,7 +24,7 @@ There are only two entry points in the NEMOGCM model for passive tracers :
\section{ Setting up a passive tracer configuration}
%------------------------------------------namtrc_int----------------------------------------------------
\nlst{namtrc}
%-------------------------------------------------------------------------------------------------------------
%--------------------------------------------------------------------------------------------------------
As a reminder, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top :
......@@ -38,10 +38,10 @@ As a reminder, the revisited structure of TOP interface now counts for five diff
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:
%------------------------------------------namtrc_int----------------------------------------------------
\nlst{nam_trc_age}
%---------------------------------------------------------------------------------------------------------
\nlstlocal{nam_trc_age}
%--------------------------------------------------------------------------------------------------------
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}
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}.
\section{ TOP Tracer Initialization}
......@@ -55,12 +55,12 @@ There are three options to initialize TOP tracers in the \textit{namelist\_top }
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$_{3}$:
%------------------------------------------namtrc_int----------------------------------------------------
\nlst{namtrc_cfg}
%---------------------------------------------------------------------------------------------------------
\nlstlocal{namtrc_cfg}
%--------------------------------------------------------------------------------------------------------
You have to activate which tracers (\textit{sn\_tracer}) you want to initialize by setting them to \texttt{true} in the column.
\nlst{namtrc_dta_cfg}
\nlstlocal{namtrc_dta_cfg}
In \textit{namtrc\_dta}, you prescribe from which files the tracer are initialized (\textit{sn\_trcdta}).
A multiplicative factor can also be set for each tracer (\textit{rn\_trfac}).
......@@ -73,7 +73,7 @@ A multiplicative factor can also be set for each tracer (\textit{rn\_trfac}).
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.
%------------------------------------------namtrc_bc----------------------------------------------------
\nlst{namtrc_bc_cfg}
\nlstlocal{namtrc_bc_cfg}
%---------------------------------------------------------------------------------------------------------
\subsection{Antarctic Ice Sheet tracer supply}
......@@ -89,13 +89,13 @@ You have to choose between two options depending whether the cavities under ice
\end{itemize}
%------------------------------------------namisf----------------------------------------------------
\nlst{namisf_cfg_eORCA1}
\nlstlocal{namisf_cfg_eORCA1}
%-----------------------------------------------------------------------------------------------------
Runoff from icebergs is activated by setting \textit{ln\_rnf\_icb} to \textit{true} in the \textit{\&namsbc\_rnf} section of \textit{namelist\_cfg}.
%------------------------------------------namsbc_rnf--------------------------------------------------
\nlst{namsbc_rnf_cfg_eORCA1}
\nlstlocal{namsbc_rnf_cfg_eORCA1}
%---------------------------------------------------------------------------------------------------------
The freshwater flux from ice shelves and icebergs is based on observations and modeled climatologies and is available for eORCA1 and eORCA025 grids :
......@@ -105,7 +105,7 @@ The freshwater flux from ice shelves and icebergs is based on observations and m
\end{itemize}
%------------------------------------------namtrc_ais----------------------------------------------------
\nlst{namtrc_ais_cfg}
\nlstlocal{namtrc_ais_cfg}
%---------------------------------------------------------------------------------------------------------
Two options for tracer concentrations in iceberg and ice shelf can be set with the namelist parameter \textit{nn\_ais\_tr}:
......
doc/latex/global/highlighting.tex
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......@@ -29,4 +29,5 @@
%% Namelists inclusion
\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}}
\newcommand{\nlstlocal}[1]{\forfile{../namelists/#1}}
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