Changeset 11591


Ignore:
Timestamp:
2019-09-25T13:52:24+02:00 (12 months ago)
Author:
nicolasmartin
Message:

Cleaning, linking and renaming

Location:
NEMO/trunk/doc/latex
Files:
15 added
2 deleted
10 edited
14 moved

Legend:

Unmodified
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  • NEMO/trunk/doc/latex/NEMO/main/settings.tex

    r11558 r11591  
    77%\def \subheading{} 
    88\def \spacedown{ \vspace*{0.75cm } } 
    9 \def \authorswidth{  0.3\linewidth} 
     9\def \authorswidth{ 0.3\linewidth} 
    1010\def \rulelenght{270pt} 
    1111\def \abstractwidth{0.6\linewidth} 
    1212 
    1313%% Manual color (frontpage banner, links  and chapter boxes) 
    14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} } 
     14\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .4} } 
    1515 
    1616%% IPSL publication number 
  • NEMO/trunk/doc/latex/SI3/main/settings.tex

    r11558 r11591  
    66\def \heading{Sea Ice modelling Integrated Initiative (SI$^3$)} 
    77\def \subheading{The NEMO sea ice engine} 
    8 \def \spacedown{ \vspace*{1cm  } } 
     8\def \spacedown{ \vspace*{  1cm} } 
    99\def \authorswidth{0.2\linewidth} 
    1010\def \rulelenght{230pt} 
  • NEMO/trunk/doc/latex/SI3/subfiles

    • Property svn:ignore deleted
  • NEMO/trunk/doc/latex/TOP/main/chapters.tex

    r11171 r11591  
    1 \subfile{../subfiles/introduction} 
    21\subfile{../subfiles/model_description} 
    32\subfile{../subfiles/model_setup} 
  • NEMO/trunk/doc/latex/TOP/main/introduction.tex

    r11558 r11591  
    1 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} 
    2 \begin{document} 
    31% ================================================================ 
    42% INTRODUCTION 
     
    97TOP (Tracers in the Ocean Paradigm) handles oceanic passive tracers in NEMO. At present, this component provides the physical constraints and boundaries conditions for oceanic tracers transport and represents a generalized, hardwired interface toward biogeochemical models to enable a seamless coupling. 
    108 
    11 It includes three independent components :   
     9It includes three independent components : 
    1210 
    1311\begin{itemize} 
     
    3432\end{itemize} 
    3533 
    36 \begin{figure}[ht]         
     34\begin{figure}[ht] 
    3735\begin{center} 
    3836\vspace{0cm} 
     
    4139\caption{A schematic view of NEMO-TOP component} 
    4240\label{topdesign} 
    43 \end{center}    
     41\end{center} 
    4442\end{figure} 
    45  
    46 \end{document} 
    47  
  • NEMO/trunk/doc/latex/TOP/main/settings.tex

    r11558 r11591  
    44%% Title and cover page settings 
    55\def \spacetop{  \vspace*{1.3cm} } 
    6 \def \heading{Tracers in Ocean Paradigm (TOP) 
     6\def \heading{Tracers in Ocean Paradigm (TOP)} 
    77\def \subheading{The NEMO passive tracers engine} 
    8 \def \spacedown{ \vspace*{1cm  } } 
     8\def \spacedown{ \vspace*{  1cm} } 
    99\def \authorswidth{0.15\linewidth} 
    1010\def \rulelenght{110pt} 
     
    1212 
    1313%% Color for document (frontpage banner, links and chapter boxes) 
    14 \def \setcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, 0.4} } 
     14\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, .4} } 
    1515 
    1616%% IPSL publication number 
  • NEMO/trunk/doc/latex/TOP/subfiles

    • Property svn:ignore deleted
  • NEMO/trunk/doc/latex/TOP/subfiles/miscellaneous.tex

    r10896 r11591  
    1 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} 
     1\documentclass[../main/TOP_manual]{subfiles} 
    22 
    33\begin{document} 
     
    4343\begin{minted}{bash} 
    4444   bld::tool::fppkeys   key_iomput key_mpp_mpi key_top 
    45     
     45 
    4646   src::MYBGC::initialization         <MYBGCPATH>/initialization 
    4747   src::MYBGC::pelagic                <MYBGCPATH>/pelagic 
  • NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex

    r11043 r11591  
    1 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} 
     1\documentclass[../main/TOP_manual]{subfiles} 
    22 
    33\newcommand{\cd}{\mathrm{CO_2}} 
     
    2626\end{equation} 
    2727 
    28 where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{nemo_manual}  
     28where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{nemo_manual} 
    2929 
    3030{S(C)} , the first term on the right hand side of \ref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer.  In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. In the case of a tracer comprising carbon,  {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. 
    3131 
    32 The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$  
    33  
    34 The third term  represents the change due to lateral diffusion.  
     32The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 
     33 
     34The third term  represents the change due to lateral diffusion. 
    3535 
    3636The fourth term is change due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes : 
     
    6868 
    6969The passive tracer transport component  shares the same advection/diffusion routines with the dynamics, with specific treatment of some features like the surface boundary conditions, or the positivity of passive tracers concentrations. 
    70   
     70 
    7171 \subsection{ Advection} 
    7272%------------------------------------------namtrc_adv---------------------------------------------------- 
     
    8080\nlst{namtrc_ldf} 
    8181%------------------------------------------------------------------------------------------------------------- 
    82 In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}.  
     82In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 
    8383 
    8484 
    8585%-----------------We also offers the possibility to increase zonal equatorial diffusion for passive tracers by introducing an enhanced zonal diffusivity coefficent in the equatorial domain which can be defined by the equation below : 
    8686%-----------------\begin{equation} \label{eq:traqsr_iradiance} 
    87 %-----------------Aht  = Aht *  rn_fact_lap * \exp( - \max( 0., z -1000  ) / 1000}  \quad \text{for $L=1$ to $N$}   
     87%-----------------Aht  = Aht *  rn_fact_lap * \exp( - \max( 0., z -1000  ) / 1000}  \quad \text{for $L=1$ to $N$} 
    8888%-----------------\end{equation} 
    8989 
    9090 \subsection{ Tracer damping} 
    91   
     91 
    9292%------------------------------------------namtrc_dmp---------------------------------------------------- 
    9393\nlst{namtrc_dmp} 
     
    9898 
    9999 \subsection{ Tracer positivity} 
    100   
     100 
    101101%------------------------------------------namtrc_rad---------------------------------------------------- 
    102102\nlst{namtrc_rad} 
     
    160160As can be seen in the figure, while the concentration of SF6 continues to rise to the present  day, the concentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s. 
    161161These declines have been driven by the Montreal Protocol (effective since August 1989), which has banned the production of CFC-11 and CFC-12 (as well as other CFCs) because of their role in the depletion of 
    162 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases  
     162stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 
    163163than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\ 
    164164 
     
    168168% concentrations increased until around the late 1990s afterwhich they began to decline in 
    169169% response to the Montreal Protocol. 
    170 % In the case of SF6, release began in the 1950s  
     170% In the case of SF6, release began in the 1950s 
    171171% This release began in the 1930s for CFC-11 and CFC-12, and the 1950s for SF6, and 
    172 % regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12,  
     172% regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, 
    173173% and is still increasing, and SF6 (see Figure \ref{img_cfcatm}).  \\ 
    174174 
     
    177177Because they only enter the ocean via surface air-sea exchange, and are almost completely chemically and biologically inert, their distribution within the ocean interior reveals its ventilation via transport and mixing. 
    178178Measuring the dissolved concentrations of the gases -- as well as the mixing ratios between them -- shows circulation pathways within the ocean as well as water mass ages (i.e. the time since last contact with the 
    179 atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and  
     179atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 
    180180ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ 
    181181 
     
    183183 
    184184Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA, 
    185 whereas sources and sinks are done by the CFC module within TOP.  
    186 The only source for CFCs in the ocean is via air-sea gas exchange at its surface, and since CFCs are generally  
    187 stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior.  
     185whereas sources and sinks are done by the CFC module within TOP. 
     186The only source for CFCs in the ocean is via air-sea gas exchange at its surface, and since CFCs are generally 
     187stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. 
    188188Consequently, the sinks-minus-sources term for CFCs consists only of their air-sea fluxes, $F_{cfc}$, as 
    189189described in the Ocean Model Inter-comparison Project (OMIP) protocol \citep{orr_2017}: 
     
    196196F_{cfc} = K_{w} \, \cdot \, (C_{sat} - C_{surf}) \, \cdot  \, (1 - f_{i}) 
    197197\label{equ_CFC_flux} 
    198 \end{eqnarray}   
    199  
    200 Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ref{equ_Kw};  
    201 $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat};  
    202 $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$);  
     198\end{eqnarray} 
     199 
     200Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ref{equ_Kw}; 
     201$C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; 
     202$C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); 
    203203and $f_{i}$ is the fractional sea-ice cover of the local ocean (ranging between 0.0 for ice-free ocean, 
    204204through to 1.0 for completely ice-covered ocean with no air-sea exchange). 
     
    209209C_{sat} = Sol \, \cdot \, P_{cfc} 
    210210\label{equ_C_sat} 
    211 \end{eqnarray}   
    212  
    213 Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ref{equ_Sol_CFC};  
     211\end{eqnarray} 
     212 
     213Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ref{equ_Sol_CFC}; 
    214214and $P_{cfc}$ is the atmosphere concentration of the CFC (in parts per trillion by volume, pptv). 
    215215This latter concentration is provided to the model by the historical time-series of \citet{bullister_2017}. 
    216 This includes bulk atmospheric concentrations of the CFCs for both hemispheres -- this is necessary because of  
    217 the geographical asymmetry in the production and release of CFCs to the atmosphere.  
    218 Within the model, hemispheric concentrations are uniform, with the exception of the region between  
     216This includes bulk atmospheric concentrations of the CFCs for both hemispheres -- this is necessary because of 
     217the geographical asymmetry in the production and release of CFCs to the atmosphere. 
     218Within the model, hemispheric concentrations are uniform, with the exception of the region between 
    21921910$^{\circ}$N and 10$^{\circ}$ in which they are linearly interpolated. 
    220220 
    221 The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{-1}$) and sea surface temperature,  
     221The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{-1}$) and sea surface temperature, 
    222222$T$ (in $^{\circ}$C), and is calculated here following \citet{wanninkhof_1992}: 
    223223 
     
    225225K_{w} = X_{conv} \, \cdot \, a \, \cdot \, u^2 \, \cdot \, \sqrt{ \frac{Sc(T)}{660} } 
    226226\label{equ_Kw} 
    227 \end{eqnarray}  
    228  
    229 Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity  
    230 from cm~h$^{-1}$ to m~s$^{-1}$;  
     227\end{eqnarray} 
     228 
     229Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity 
     230from cm~h$^{-1}$ to m~s$^{-1}$; 
    231231$a$ is a constant re-estimated by \citet{wanninkhof_2014} to 0.251 (in $\frac{cm~h^{-1}}{(m~s^{-1})^{2}}$); 
    232232and $u$ is the 10~m wind speed in m~s$^{-1}$ from either an atmosphere model or reanalysis atmospheric forcing. 
     
    236236Sc =  a0 + (a1 \, \cdot \, T) + (a2  \, \cdot \, T^2) + (a3 \, \cdot \, T^3) + (a4 \, \cdot \, T^4) 
    237237\label{equ_Sc} 
    238 \end{eqnarray}  
    239  
    240 The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$,  
    241 and is specific for each gas.  
    242 It has been experimentally estimated by \citet{warner_1985} as a function of temperature  
     238\end{eqnarray} 
     239 
     240The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, 
     241and is specific for each gas. 
     242It has been experimentally estimated by \citet{warner_1985} as a function of temperature 
    243243and salinity: 
    244244 
     
    246246% code version that I have to hand, although this might be out of date; in any case, I'dag 
    247247% strongly suggest avoiding the use of the \frac{}{100}, and instead substitute a term that is 
    248 % "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius  
     248% "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius 
    249249% so that you're not using T twice in different ways 
    250250 
     
    252252\ln{(Sol)} = a_1 + \frac{a_2}{ T_{X}} + a_3 \, \cdot \, \ln{ T_{X} } + a_4 \, \cdot \, T_{X}^2 + S \, \cdot \, ( b_1 + b_2 \, \cdot \, T_{X} + b_3 \, \cdot \, T_{X}^2 ) 
    253253\label{equ_Sol_CFC} 
    254 \end{eqnarray}   
     254\end{eqnarray} 
    255255 
    256256% \begin{eqnarray} 
    257257% \ln{(Sol)} = a1 + a2 \, \frac{100}{T} + a3 \, \ln{ (\frac{T}{100}) } + a4 \, \frac{T}{100}^2 + S \, ( b1 + b2 \, \frac{T}{100} + b3 \, \frac{T}{100}^2 ) 
    258258% \label{equ_Sol_CFC} 
    259 % \end{eqnarray}   
    260  
    261 Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature;  
     259% \end{eqnarray} 
     260 
     261Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; 
    262262and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \ref{tab_ref_CFC}). 
    263263This is then converted to mol~m$^{-3}$~pptv$^{-1}$ assuming a constant atmospheric surface pressure of 1~atm. 
    264 The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes.  
     264The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. 
    265265Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \ref{img_cfcsol}). 
    266266 
     
    289289\centering 
    290290\begin{tabular}{l l l l l l l l l} 
    291 \hline  
    292 Gas   & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\           
     291\hline 
     292Gas   & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\ 
    293293\hline 
    294294CFC-11 & & -218.0971 & 298.9702 & 113.8049 & -1.39165 & -0.143566  & 0.091015   & -0.0153924 \\ 
     
    296296SF6    & & -80.0343  & 117.232  & 29.5817  & 0.0      & 0.0335183  & -0.0373942 & 0.00774862 \\ 
    297297\hline 
    298 \end{tabular}  
     298\end{tabular} 
    299299\label{tab_ref_CFC} 
    300300\end{table} 
     
    306306\centering 
    307307\begin{tabular}{l l l l l l l } 
    308 \hline  
    309 Gas  & & a0 & a1 & a2 & a3 & a4 \\           
     308\hline 
     309Gas  & & a0 & a1 & a2 & a3 & a4 \\ 
    310310\hline 
    311311CFC-11 & & 3579.2  & -222.63 & 7.5749 & -0.14595 & 0.0011874   \\ 
     
    313313SF6    & & 3177.5  & -200.57 & 6.8865 & -0.13335 & 0.0010877   \\ 
    314314\hline 
    315 \end{tabular}  
     315\end{tabular} 
    316316\label{tab_Sc} 
    317317\end{table} 
     
    353353%---------------------------------------------------------------------------------------------------------- 
    354354 
    355 The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions.  
     355The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. 
    356356 
    357357\subsubsection{Method} 
     
    368368 
    369369This simplified approach also neglects the effects of fractionation (e.g.,  air-sea exchange) and of biological processes. Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. 
    370 Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations.  
     370Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations. 
    371371 
    372372Therefore the simplified approach is justified for the purpose of assessing the circulation and ventilation of OGCMs. 
     
    425425%The sensitivity to this parametrization is discussed in section \ref{sec:result}. 
    426426% 
    427 \item Chemical enhancement (term $b$  in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}.  
     427\item Chemical enhancement (term $b$  in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. 
    428428\end{itemize} 
    429429 
     
    464464\end{figure} 
    465465 
    466 Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}).  
     466Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). 
    467467 
    468468An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. It is still possible to easily set-up that type of transient experiment for which no previous run is needed.  In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period). 
     
    476476\begin{itemize} 
    477477\item Specify the starting date of the experiment: \CODE{nn\_date0} in \texttt{namelist}.  \CODE{nn\_date0} is written as Year0101 where Year may take any positive value (AD). 
    478 \item Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year).  
     478\item Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year). 
    479479\item These two parameters (\CODE{nn\_rstctl} and \CODE{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file). 
    480480\end{itemize} 
     
    497497 
    498498The file \texttt{intcal13.14c} \citep{reimer_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}. 
    499 The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on  the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP.  
     499The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on  the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. 
    500500 
    501501To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully. 
     
    519519Field & Type & Dim & Units & Description \\ \hline 
    520520RC14 & ptrc & 3-D & -        & Radiocarbon ratio \\ 
    521 DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\  
     521DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\ 
    522522C14Age & diad & 3-D & yr &   Radiocarbon age \\ 
    523523RAge & diad & 2-D & yr & Reservoir age\\ 
    524524qtr\_c14 &  diad & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux\\ 
    525525qint\_c14 & diad & 2-D &   m$^{-2}$ &  Cumulative air-to-sea $\Rq$ flux \\ 
    526 AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\  
    527 AtmC14 & scalar & 0-D & \textperthousand  & Global atmospheric $\Dcq$\\  
    528 K\_CO2 & scalar & 0-D & cm h$^{-1}$  & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\  
    529 K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity  ($ \overline{\kappa_R}$)\\  
     526AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\ 
     527AtmC14 & scalar & 0-D & \textperthousand  & Global atmospheric $\Dcq$\\ 
     528K\_CO2 & scalar & 0-D & cm h$^{-1}$  & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 
     529K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity  ($ \overline{\kappa_R}$)\\ 
    530530C14Inv & scalar & 0-D & $10^{26}$ atoms & Ocean radiocarbon inventory \\ \hline 
    531531\end{tabular} 
     
    534534\end{table} 
    535535%!   Standard ratio: 1.176E-12 ; Avogadro's nbr = 6.022E+23 at/mol ; bomb C14 traditionally reported as 1.E+26 atoms 
    536 %   REAL(wp), PARAMETER            :: atomc14=1.176*6.022E-15   ! conversion factor  
     536%   REAL(wp), PARAMETER            :: atomc14=1.176*6.022E-15   ! conversion factor 
    537537% atomc14 * xdicsur * zdum 
    538538 
    539 The radiocarbon age is computed as  $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$.  
     539The radiocarbon age is computed as  $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 
    540540 
    541541The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} 
     
    561561\subsection{PISCES biogeochemical model} 
    562562 
    563 PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses.  
     563PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. 
    564564Two versions of PISCES are available in NEMO v4.0 : 
    565565 
    566 PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials.  
     566PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 
    567567 
    568568PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. PISCES-QUOTA has thirty-nine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus,  iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted  by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled. 
     
    570570There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. 
    571571 
    572   
     572 
    573573\subsection{MY\_TRC interface for coupling external BGC models} 
    574574\label{Mytrc} 
     
    597597 
    598598Coupling passive tracers offline with NEMO requires precomputed  physical fields from OGCM. Those fields are read from files and interpolated on-the-fly at each model time step 
    599 At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress).  
     599At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress). 
    600600The so-called offline mode is useful since it has lower computational costs for example to perform very longer simulations - about 3000 years - to reach equilibrium of CO2 sinks for climate-carbon studies. 
    601601 
     
    603603 
    604604\begin{itemize} 
    605    \item \textit{dtadyn.F90} :  this module allows to read and compute the dynamical fields at each model time-step  
     605   \item \textit{dtadyn.F90} :  this module allows to read and compute the dynamical fields at each model time-step 
    606606   \item \textit{nemogcm.F90} :  a degraded version of the main nemogcm.F90 code of NEMO to manage the time-stepping 
    607607\end{itemize} 
  • NEMO/trunk/doc/latex/TOP/subfiles/model_setup.tex

    r11019 r11591  
    1 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} 
     1\documentclass[../main/TOP_manual]{subfiles} 
    22 
    33\begin{document} 
     
    1010%------------------------------------------------------------------------------------------------------------- 
    1111 
    12 The usage of TOP is activated  
     12The usage of TOP is activated 
    1313 
    1414\begin{itemize} 
     
    1919As an example, the user can refer to already available configurations in the code, GYRE\_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 \S\ref{SMS_models}) . 
    2020 
    21 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.  
     21Note 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. 
    2222 
    2323There are only three specific keys remaining in TOP 
     
    2828\end{itemize} 
    2929 
    30 For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top :  
     30For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : 
    3131 
    3232\begin{itemize} 
  • NEMO/trunk/doc/latex/global

    • Property svn:ignore deleted
  • NEMO/trunk/doc/latex/global/document.tex

    r11584 r11591  
    1111 
    1212%% Document layout 
    13 \documentclass[fontsize = 10pt, twoside, abstract, draft]{scrreprt} 
     13\documentclass[fontsize = 10pt, twoside, abstract]{scrreprt} 
    1414 
    1515%% Load manual configuration 
  • NEMO/trunk/doc/latex/global/frontpage.tex

    r11563 r11591  
    4040  \begin{minipage}{\authorswidth} 
    4141    \raggedleft 
    42     \input{thanks} 
     42    \input{authors} 
    4343  \end{minipage}\hspace{15pt}\begin{minipage}{0.02\linewidth} 
    4444    \rule{1pt}{\rulelenght} 
    4545  \end{minipage}\hspace{ 5pt}\begin{minipage}{\abstractwidth} 
    4646    \begin{abstract} 
    47       \input{foreword} 
     47      \input{abstract} 
    4848    \end{abstract} 
    4949  \end{minipage} 
  • NEMO/trunk/doc/latex/global/latexmk.pl

    r11584 r11591  
    11 
    22## Defaults 
    3 $silent   = 1; 
    4 $pdf_mode = 1; 
     3$do_cd    = 1;   ## Change to the directory of the main source file 
     4$silent   = 1;   ## Less verbosity 
    55 
    6 ## Using relative paths 
     6## Use of 'build' relative directory 
    77$ENV{'openout_any'}='a'; 
    88$out_dir = '../build'; 
    99 
    10 ## Custom cmds 
    11 $makeindex = 'makeindex -s ../../global/index.ist %O -o %D %S'; 
    12 $pdflatex  = 'xelatex -shell-escape %O %S'; 
     10## Global option 
     11set_tex_cmds( '-shell-escape' ); 
     12 
     13$makeindex = "makeindex %O -s ../../global/index -o $out_dir/%D $out_dir/%S"; 
  • NEMO/trunk/doc/latex/global/prologue.tex

    r11584 r11591  
    11 
    22%% Specific configuration 
    3 \input{../main/definitions} 
     3\input{../main/settings} 
    44 
    55%% Global configuration 
    66\input{../../global/packages} 
    77\input{../../global/highlighting} 
    8 \input{../../global/indexes} 
     8\input{../../global/index} 
    99\input{../../global/styles} 
    1010\input{../../global/new_cmds} 
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