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Changeset 11015 – NEMO

Changeset 11015


Ignore:
Timestamp:
2019-05-20T20:57:09+02:00 (5 years ago)
Author:
nicolasmartin
Message:

Modification of the content to be in line with the NEMO manual
SI3 manual can now be build like the NEMO manual with ./manual_build.sh SI3

  • Mimick the directory organisation with main and subfiles folders.
  • Regarding the particular case of namelists
    • Remove the duplicates already contained in the global namelists folder at 1st level of ./doc
    • Keep the namelists sub-folder only for namdyn_adv & namsbc which already exist in ocean namelists
  • Rewriting of SI3_manual.tex with NEMO_manual.tex as template to easily highlight differences
  • Updating of several paths for figures/namelists inclusion or LaTeX files referencing
  • LaTeX source:
    • Replacement of \forfile command for namelists with pre-configured \nlst alias
    • " "" \bm with \mathbf (save installation of an extra package)
Location:
NEMO/trunk/doc/latex/SI3
Files:
1 added
15 deleted
15 edited
2 moved

Legend:

Unmodified
Added
Removed

  • NEMO/trunk/doc/latex/SI3/main/SI3_manual.tex

    r9995 r11015  
    11%% ============================================================================== 
    2 %% NEMO_book.tex: build the NEMO Reference Manual 
     2%% SI3 Reference Manual 
    33%% ============================================================================== 
    4  
    5  
    6 %% Run ../build_NEMO_manual.sh to generate the PDF version (with pdflatex) 
    7  
    8 %% Document layout 
    9 %% ============================================================================== 
    10  
    11 \documentclass[a4paper, 11pt]{book} 
    124 
    135 
    … …  
    157%% ============================================================================== 
    168 
    17 \usepackage{../../tex_main/NEMO_manual} 
    18 \usepackage{../../tex_sub/NEMO_minted} 
     9%% Document layout 
     10\documentclass{book} 
    1911 
    20 \usepackage{bm} 
     12%% Custom style (.sty) 
     13\usepackage{../../NEMO/main/NEMO_manual} 
     14 
     15%% Include references and index for single subfile compilation 
     16\newcommand{\biblio}{\bibliography{../main/SI3_manual}} 
     17\newcommand{\pindex}{\printindex} 
    2118 
    2219\makeindex 
    2320 
     21%% End of common preamble between main and sub-files 
     22\begin{document} 
    2423 
    25 %%  
    26 %% ============================================================================== 
    27  
    28 \begin{document} 
     24%% Override custom cmds for full manual compilation 
     25\renewcommand{\biblio}{} 
     26\renewcommand{\pindex}{} 
    2927 
    3028 
    … …  
    3230%% ============================================================================== 
    3331 
     32\graphicspath{{../../figures/logos/}} 
     33 
    3434%% Frontpage 
     35\title{ 
     36  \includegraphics[height=0.05\textheight]{CMCC}\hfill 
     37  \includegraphics[height=0.05\textheight]{CNRS}\hfill 
     38  \includegraphics[height=0.05\textheight]{MOI} \hfill 
     39  \includegraphics[height=0.05\textheight]{UKMO}\hfill 
     40  \includegraphics[height=0.05\textheight]{NERC}       \\ 
     41  {\Huge SI$^3$ \\} 
     42  {\Large Sea Ice modelling Integrated Initiative -- The NEMO Sea Ice engine}\\  
     43  {\small \textcolor{red}{First draft documentation. Needs completion and rewriting}.} 
     44} 
     45\author{The NEMO Sea Ice Working Group 
     46%  \thanks{ 
     47% 
     48%  }                                                        \\ 
     49%                                                           \\ 
     50  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\ 
     51  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\ 
     52  \textit{ISSN 1288-1619} 
     53} 
     54\date{\today} 
    3555 
    36 \title{ 
    37 \vspace{1.5cm} 
    38 \rule{400pt}{1.5pt} \\ 
    39 \vspace{0.45cm} 
    40  {\Huge SI$^3$ \\} 
    41  {\Large -- Sea Ice modelling Integrated Initiative --}\\ 
    42  {\Large The NEMO Sea Ice engine}\\  
    43 \date{\today} 
    44 \author{The NEMO Sea Ice Working Group \\ 
    45 \\ 
    46 \small \textit{Note du P\^ole de mod\'elisation de l'Institut Pierre-Simon Laplace No 31} \\ 
    47 \small \textcolor{red}{First draft documentation. Needs completion and rewriting}. \\ 
    48 \\ 
    49 ISSN No 1288-1619\\ 
    50 } 
    51 \rule{400pt}{1.5pt} 
    52 } 
    53  
    54 \maketitle                 % generate the title 
    55  
     56\maketitle 
    5657\frontmatter 
    5758 
     59 
    5860%% ToC i.e. Table of Contents 
    59  
    6061\dominitoc 
    6162\tableofcontents 
    … …  
    6768\mainmatter 
    6869 
    69 \subfile{../tex_sub/todolist} 
     70\graphicspath{{../../figures/SI3/}} 
     71 
     72\subfile{../subfiles/todolist} 
    7073 
    7174%% Abstract - Foreword 
    7275 
    73 \subfile{../tex_sub/abstract_foreword} 
     76\subfile{../subfiles/abstract_foreword} 
    7477 
    7578% Introduction 
    7679 
    77 \subfile{../tex_sub/introduction} 
     80\subfile{../subfiles/introduction} 
    7881 
    7982% Chapters 
    8083 
    81 \subfile{../tex_sub/chap_model_basics} 
     84\subfile{../subfiles/chap_model_basics} 
    8285 
    83 \subfile{../tex_sub/chap_domain} 
     86\subfile{../subfiles/chap_domain} 
    8487 
    85 \subfile{../tex_sub/chap_dynamics} 
     88\subfile{../subfiles/chap_dynamics} 
    8689 
    87 \subfile{../tex_sub/chap_transport} 
     90\subfile{../subfiles/chap_transport} 
    8891 
    89 \subfile{../tex_sub/chap_ridging_rafting} 
     92\subfile{../subfiles/chap_ridging_rafting} 
    9093 
    91 \subfile{../tex_sub/chap_radiative_transfer} 
     94\subfile{../subfiles/chap_radiative_transfer} 
    9295 
    93 \subfile{../tex_sub/chap_thermo} 
     96\subfile{../subfiles/chap_thermo} 
    9497 
    95 \subfile{../tex_sub/chap_interfaces} 
     98\subfile{../subfiles/chap_interfaces} 
    9699 
    97 \subfile{../tex_sub/chap_output_diagnostics} 
     100\subfile{../subfiles/chap_output_diagnostics} 
    98101 
    99 \subfile{../tex_sub/chap_single_category_use} 
     102\subfile{../subfiles/chap_single_category_use} 
    100103 
    101 \subfile{../tex_sub/chap_bdy_agrif} 
     104\subfile{../subfiles/chap_bdy_agrif} 
    102105 
    103 \subfile{../tex_sub/chap_miscellaneous} 
     106\subfile{../subfiles/chap_miscellaneous} 
    104107 
    105108%% Appendix 
    … …  
    117120\addcontentsline{toc}{chapter}{Bibliography} 
    118121 
    119 \bibliography{../tex_main/SI3_manual.bbl} 
     122\bibliography{../main/SI3_manual} 
    120123%\bibliography{/Users/ioulianikolskaia/Boulot/LIBRARY/BIBTEX/Martin_biblio.bib}  
    121124 

  • NEMO/trunk/doc/latex/SI3/subfiles/abstract_foreword.tex

    r9974 r11015  
    11 
    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_bdy_agrif.tex

    r9974 r11015  
    1 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     1\documentclass[../main/SI3_manual]{subfiles} 
    22 
    33\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_domain.tex

    r9983 r11015  
    11 
    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 
    … …  
    3232\begin{center} 
    3333\vspace{0cm} 
    34 \includegraphics[height=6cm,angle=-00]{../Figures/time_stepping.png} 
     34\includegraphics[height=6cm,angle=-00]{time_stepping} 
    3535\caption{Schematic representation of time stepping in SI$^3$, assuming $nn\_fsbc=5$.} 
    3636\label{ice_scheme} 
    … …  
    5656\begin{center} 
    5757\vspace{0cm} 
    58 \includegraphics[height=10cm,angle=-00]{../Figures/thermogrid.eps} 
     58\includegraphics[height=10cm,angle=-00]{thermogrid.eps} 
    5959\caption{\footnotesize{Vertical grid of the model, used to resolve vertical temperature and salinity profiles}}\label{fig_dom_icelayers} 
    6060\end{center} 
    … …  
    6969To increase numerical efficiency of the code, the two horizontal dimensions of an array $X(ji,jj,jk,jl)$ are collapsed into one (array $X\_1d(ji,jk,jl)$) for thermodynamic computations, and re-expanded afterwards. 
    7070 
    71 \forfile{../namelists/nampar} 
     71\nlst{nampar} 
    7272 
    7373\section{Thickness space domain} 
    7474 
    75 \forfile{../namelists/namitd} 
     75\nlst{namitd} 
    7676 
    7777Thickness space is discretized using $jl=1, ..., jpl$ thickness categories, with prescribed boundaries $hi\_max(jl-1),hi\_max(jl)$. Following \cite{Lipscomb01}, ice thickness can freely evolve between these boundaries. The number of ice categories $jpl$ can be adjusted from the namelist ($nampar$). 
    … …  
    9191\begin{center} 
    9292\vspace{0cm} 
    93 \includegraphics[height=6cm,angle=-00]{../Figures/ice_cats.eps} 
     93\includegraphics[height=6cm,angle=-00]{ice_cats.eps} 
    9494\caption{\footnotesize{Boundaries of the model ice thickness categories (m) for varying number of categories and prescribed mean thickness ($\overline h$). The formerly used $tanh$ formulation is also depicted.}}\label{fig_dom_icecats} 
    9595\end{center} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_dynamics.tex

    r9974 r11015  
    11 
    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_interfaces.tex

    r9974 r11015  
    1 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     1\documentclass[../main/SI3_manual]{subfiles} 
    22 
    33\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_miscellaneous.tex

    r9974 r11015  
    1 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     1\documentclass[../main/SI3_manual]{subfiles} 
    22 
    33\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_model_basics.tex

    r9974 r11015  
    11 
    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 
    … …  
    4141\begin{center} 
    4242\vspace{0cm} 
    43 \includegraphics[height=10cm,angle=-00]{../Figures/ice_scheme.png} 
    44 \caption{Representation of the ice pack, using multiple categories with specific ice concentration ($a_l, l=1, 2, ..., L$), thickness ($h^i_l$), snow depth ($h^s_l$), vertical temperature and salinity profiles ($T^i_{kl}$, $S^{*}_{kl}$) and a single ice velocity vector ($\bm{u}$).} 
     43\includegraphics[height=10cm,angle=-00]{ice_scheme} 
     44\caption{Representation of the ice pack, using multiple categories with specific ice concentration ($a_l, l=1, 2, ..., L$), thickness ($h^i_l$), snow depth ($h^s_l$), vertical temperature and salinity profiles ($T^i_{kl}$, $S^{*}_{kl}$) and a single ice velocity vector ($\mathbf{u}$).} 
    4545\label{ice_scheme} 
    4646\end{center} 
    … …  
    162162%------------------------------------------------------------------------------------------------------------------------- 
    163163 
    164 We first present the essentials of the thickness distribution framework \citep{Thorndikeetal75}. Consider a given region of area $R$ centered at spatial coordinates $(\bm{x})$ at a given time $t$. $R$ could be e.g. a model grid cell. The ice thickness distribution $g(\mathbf{x},t, h)$ is introduced as follows: 
     164We first present the essentials of the thickness distribution framework \citep{Thorndikeetal75}. Consider a given region of area $R$ centered at spatial coordinates $(\mathbf{x})$ at a given time $t$. $R$ could be e.g. a model grid cell. The ice thickness distribution $g(\mathbf{x},t, h)$ is introduced as follows: 
    165165\begin{linenomath} 
    166166\begin{align} 
    … …  
    184184\begin{center} 
    185185\vspace{0cm} 
    186 \includegraphics[height=6cm,angle=-00]{../Figures/g_h.png} 
     186\includegraphics[height=6cm,angle=-00]{g_h} 
    187187\caption{Representation of the relation between real thickness profiles and the ice thickness distribution function $g(h)$} 
    188188\label{fig_g_h} 
    … …  
    202202\begin{linenomath} 
    203203\begin{align} 
    204 \frac{\partial a_l}{\partial t} = - \bm{\nabla} \cdot (a_l \mathbf{u}) + \Theta^a_l + \int_{H^*_{l-1}}^{H^*_l} dh \psi. 
     204\frac{\partial a_l}{\partial t} = - \mathbf{\nabla} \cdot (a_l \mathbf{u}) + \Theta^a_l + \int_{H^*_{l-1}}^{H^*_l} dh \psi. 
    205205\label{eq:gt} 
    206206\end{align} 
    … …  
    211211\begin{linenomath} 
    212212\begin{align} 
    213  A(\bm{x},t) &=\int_{0^+}^{\infty} dh \cdot g(h,\bm{x},t) \sim A_{ij} = \sum_{l=1}^L a_{ijl}, & \\ 
    214  V_i(\bm{x},t)&=\int_{0}^{\infty} dh \cdot g(h,\bm{x},t) \cdot h \sim V^i_{ij} = \sum_{l=1}^L v^i_{ijl}. & \\ 
     213 A(\mathbf{x},t) &=\int_{0^+}^{\infty} dh \cdot g(h,\mathbf{x},t) \sim A_{ij} = \sum_{l=1}^L a_{ijl}, & \\ 
     214 V_i(\mathbf{x},t)&=\int_{0}^{\infty} dh \cdot g(h,\mathbf{x},t) \cdot h \sim V^i_{ij} = \sum_{l=1}^L v^i_{ijl}. & \\ 
    215215\end{align} 
    216216\end{linenomath} 
    … …  
    228228\begin{linenomath} 
    229229\begin{align} 
    230 m \frac{\partial \bm{u}} {\partial t} & = \bm{\nabla}\cdot\bm{\sigma} +A \left(\bm{\tau}_{a}+\bm{\tau}_{w}\right) - m f \bm{k} \times \bm{u} - m g \bm{\nabla}{\eta}, 
     230m \frac{\partial \mathbf{u}} {\partial t} & = \mathbf{\nabla}\cdot\mathbf{\sigma} +A \left(\mathbf{\tau}_{a}+\mathbf{\tau}_{w}\right) - m f \mathbf{k} \times \mathbf{u} - m g \mathbf{\nabla}{\eta}, 
    231231\label{a} 
    232232\end{align} 
    233233\end{linenomath} 
    234 where $m=\rho_i V_i + \rho_s V_s $ is the ice and snow mass per unit area, $\bm{u}$ is the ice velocity, $\bm{\sigma}$ is the internal stress tensor, $\bm{\tau}_a$ and $\bm{\tau}_w$ are the air and ocean stresses, respectively, $f$ is the Coriolis parameter, $\bm{k}$ is a unit vector pointing upwards, $g$ is the gravity acceleration and $\eta$ is the ocean surface elevation. The EVP approach used in LIM \citep{Bouillonetal13} gives the stress tensor as a function of the strain rate tensor $\dot{\bm{\epsilon}}$ and some of the sea ice state variables: 
    235 \begin{linenomath} 
    236 \begin{align} 
    237 \bm{\sigma} & = \bm{\sigma} (\dot{ \bm{\epsilon}}, \text{ice state}). 
     234where $m=\rho_i V_i + \rho_s V_s $ is the ice and snow mass per unit area, $\mathbf{u}$ is the ice velocity, $\mathbf{\sigma}$ is the internal stress tensor, $\mathbf{\tau}_a$ and $\mathbf{\tau}_w$ are the air and ocean stresses, respectively, $f$ is the Coriolis parameter, $\mathbf{k}$ is a unit vector pointing upwards, $g$ is the gravity acceleration and $\eta$ is the ocean surface elevation. The EVP approach used in LIM \citep{Bouillonetal13} gives the stress tensor as a function of the strain rate tensor $\dot{\mathbf{\epsilon}}$ and some of the sea ice state variables: 
     235\begin{linenomath} 
     236\begin{align} 
     237\mathbf{\sigma} & = \mathbf{\sigma} (\dot{ \mathbf{\epsilon}}, \text{ice state}). 
    238238\end{align} 
    239239\end{linenomath} 
    … …  
    245245\end{align} 
    246246\end{linenomath} 
    247 including the effets of transport, thermodynamics ($\Theta^X$) and mechanical redistribution ($\Psi^X$). Solving these $jpl.(4+2.jpk)$ equations gives the temporal evolution of $\bm{u}$, $\bm{\sigma}$ and the rest of the global (extensive) variables listed in Table \ref{GVariables_table}. 
     247including the effets of transport, thermodynamics ($\Theta^X$) and mechanical redistribution ($\Psi^X$). Solving these $jpl.(4+2.jpk)$ equations gives the temporal evolution of $\mathbf{u}$, $\mathbf{\sigma}$ and the rest of the global (extensive) variables listed in Table \ref{GVariables_table}. 
    248248 
    249249\section{Ice Dynamics} 
    … …  
    272272\begin{center} 
    273273\vspace{0cm} 
    274 \includegraphics[height=6cm,angle=-00]{../Figures/yield_curve.png} 
     274\includegraphics[height=6cm,angle=-00]{yield_curve} 
    275275\caption{Elliptical yield curve used in the VP rheologies, drawn in the space of the principal components of the stress tensor ($\sigma_1$ and $\sigma_2$).} 
    276276\label{fig_yield} 
    … …  
    383383\begin{center} 
    384384\vspace{0cm} 
    385 \includegraphics[height=8cm,angle=-00]{../Figures/Thermal_properties.png} 
     385\includegraphics[height=8cm,angle=-00]{Thermal_properties} 
    386386\caption{Thermal properties of sea ice vs temperature for different bulk salinities: brine fraction, specific enthalpy, thermal conductivity, and effective specific heat.} 
    387387\label{fig_thermal_properties} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_output_diagnostics.tex

    r9974 r11015  
    1 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     1\documentclass[../main/SI3_manual]{subfiles} 
    22 
    33\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_radiative_transfer.tex

    r9995 r11015  
    11 
    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 
    … …  
    2828\begin{center} 
    2929\vspace{0cm} 
    30 \includegraphics[height=6cm,angle=-00]{../Figures/radiative_transfer.png} 
     30\includegraphics[height=6cm,angle=-00]{radiative_transfer} 
    3131\caption{Partitionning of solar radiation in the snow-ice system, as represented in SI$^3$.} 
    3232\label{fig_radiative_transfer} 
    … …  
    5454The user has control on 5 reference namelist values, which describe the asymptotic values of albedo of snow and ice for dry and wet conditions, as well as the deep ponded-ice albedo. Observational surveys, in particular during SHEBA in the Arctic \citep{Perovichetal02alb} and further additional experiments \citep{GrenfellPerovich04}, as well as by \cite{Brandtetal05} in the Antarctic, have provided relatively strong constraints on the surface albedo. In this context, the albedo can hardly be used as the main model tuning parameter, at least outside of these observation-based bounds (see namalb for reference values). 
    5555 
    56 \forfile{../namelists/namalb} 
     56\nlst{namalb} 
    5757 
    5858%-------------------------------------------------------------------------------------------------------------------- 
    … …  
    6363\begin{center} 
    6464\vspace{0cm} 
    65 \includegraphics[height=10cm,angle=-00]{../Figures/albedo_cloud_correction.png} 
     65\includegraphics[height=10cm,angle=-00]{albedo_cloud_correction} 
    6666\caption{Albedo correction $\Delta \alpha$ as a function of overcast sky (diffuse light) albedo $\alpha_os$, from field observations \cite[][their Table 3]{GrenfellPerovich04} (squares) and 2nd-order fit (Eq. \ref{eq_albedo_cloud_correction}). Red squares represent the irrelevant data points excluded from the fit. For indication, the amplitude of the correction used in the ocean component is also depicted (blue circle).} 
    6767% ocean uses 0.06 for overcast sky (Payne 74) and Briegleb and Ramanathan parameterization 
    … …  
    9494\begin{center} 
    9595\vspace{0cm} 
    96 \includegraphics[height=4cm,angle=-00]{../Figures/albedo_dependencies.png} 
     96\includegraphics[height=4cm,angle=-00]{albedo_dependencies} 
    9797\caption{Example albedo dependencies on ice thickness, snow depth and pond depth, as parameterized in SI$^3$.} 
    9898\label{fig_albedo_dependencies} 
    … …  
    183183\begin{center} 
    184184\vspace{0cm} 
    185 \includegraphics[height=8cm,angle=-00]{../Figures/radiation_atm_ice_oce.png} 
     185\includegraphics[height=8cm,angle=-00]{radiation_atm_ice_oce} 
    186186\caption{Framing solar radiation transfer through sea ice into the atmosphere-ice-ocean context.} 
    187187% ocean uses 0.06 for overcast sky (Payne 74) and Briegleb and Ramanathan parameterization 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_ridging_rafting.tex

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    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_single_category_use.tex

    r9974 r11015  
    11 
    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_thermo.tex

    r9974 r11015  
    1 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     1\documentclass[../main/SI3_manual]{subfiles} 
    22 
    33\begin{document} 
    … …  
    3434\begin{center} 
    3535\vspace{0cm} 
    36 \includegraphics[height=10cm,angle=-00]{../Figures/Openwater_eb.png} 
     36\includegraphics[height=10cm,angle=-00]{Openwater_eb} 
    3737\caption{Scheme of the estimate of the heat budget of the first ocean level.} 
    3838\label{fig_yield} 

  • NEMO/trunk/doc/latex/SI3/subfiles/chap_transport.tex

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    2 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     2\documentclass[../main/SI3_manual]{subfiles} 
    33 
    44\begin{document} 

  • NEMO/trunk/doc/latex/SI3/subfiles/todolist.tex

    r9995 r11015  
    1 \documentclass[../../tex_main/NEMO_manual]{subfiles} 
     1\documentclass[../main/SI3_manual]{subfiles} 
    22 
    33\begin{document} 
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