Changeset 9407 for branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
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branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex
r9394 r9407 5 5 % ================================================================ 6 6 \chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} 7 \label{ DIA}7 \label{chap:DIA} 8 8 \minitoc 9 9 … … 15 15 % ================================================================ 16 16 \section{Old model output (default)} 17 \label{ DIA_io_old}17 \label{sec:DIA_io_old} 18 18 19 19 The model outputs are of three types: the restart file, the output listing, … … 56 56 % ================================================================ 57 57 \section{Standard model output (IOM)} 58 \label{ DIA_iom}58 \label{sec:DIA_iom} 59 59 60 60 … … 595 595 596 596 \subsection{XML reference tables} 597 \label{ IOM_xmlref}597 \label{subsec:IOM_xmlref} 598 598 599 599 (1) Simple computation: directly define the computation when refering to the variable in the file definition. … … 998 998 \subsection{CF metadata standard compliance} 999 999 1000 Output from the XIOS-1.0 IO server is compliant with \href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of the CF metadata standard. Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of section \ ref{IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard.1000 Output from the XIOS-1.0 IO server is compliant with \href{http://cfconventions.org/Data/cf-conventions/cf-conventions-1.5/build/cf-conventions.html}{version 1.5} of the CF metadata standard. Therefore while a user may wish to add their own metadata to the output files (as demonstrated in example 4 of section \autoref{subsec:IOM_xmlref}) the metadata should, for the most part, comply with the CF-1.5 standard. 1001 1001 1002 1002 Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by the namelist parameter \np{ln\_cfmeta} in the \ngn{namrun} namelist. This must be set to true if these metadata are to be included in the output files. … … 1007 1007 % ================================================================ 1008 1008 \section{NetCDF4 support (\protect\key{netcdf4})} 1009 \label{ DIA_iom}1009 \label{sec:DIA_iom} 1010 1010 1011 1011 Since version 3.3, support for NetCDF4 chunking and (loss-less) compression has … … 1070 1070 respectively in the mono-processor case (i.e. global domain of {\small\tt 182x149x31}). 1071 1071 An illustration of the potential space savings that NetCDF4 chunking and compression 1072 provides is given in table \ ref{Tab_NC4} which compares the results of two short1072 provides is given in table \autoref{tab:NC4} which compares the results of two short 1073 1073 runs of the ORCA2\_LIM reference configuration with a 4x2 mpi partitioning. Note 1074 1074 the variation in the compression ratio achieved which reflects chiefly the dry to wet … … 1106 1106 ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\%\\ 1107 1107 \end{tabular} 1108 \caption{ \protect\label{ Tab_NC4}1108 \caption{ \protect\label{tab:NC4} 1109 1109 Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression} 1110 1110 \end{table} … … 1126 1126 % ------------------------------------------------------------------------------------------------------------- 1127 1127 \section{Tracer/Dynamics trends (\protect\ngn{namtrd})} 1128 \label{ DIA_trd}1128 \label{sec:DIA_trd} 1129 1129 1130 1130 %------------------------------------------namtrd---------------------------------------------------- … … 1166 1166 % ------------------------------------------------------------------------------------------------------------- 1167 1167 \section{FLO: On-Line Floats trajectories (\protect\key{floats})} 1168 \label{ FLO}1168 \label{sec:FLO} 1169 1169 %--------------------------------------------namflo------------------------------------------------------- 1170 1170 \forfile{../namelists/namflo} … … 1274 1274 % ------------------------------------------------------------------------------------------------------------- 1275 1275 \section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) } 1276 \label{ DIA_diag_harm}1276 \label{sec:DIA_diag_harm} 1277 1277 1278 1278 %------------------------------------------namdia_harm---------------------------------------------------- … … 1316 1316 % ------------------------------------------------------------------------------------------------------------- 1317 1317 \section{Transports across sections (\protect\key{diadct}) } 1318 \label{ DIA_diag_dct}1318 \label{sec:DIA_diag_dct} 1319 1319 1320 1320 %------------------------------------------namdct---------------------------------------------------- … … 1467 1467 % ================================================================ 1468 1468 \section{Diagnosing the steric effect in sea surface height} 1469 \label{ DIA_steric}1469 \label{sec:DIA_steric} 1470 1470 1471 1471 … … 1500 1500 1501 1501 A non-Boussinesq fluid conserves mass. It satisfies the following relations: 1502 \begin{equation} \label{ Eq_MV_nBq}1502 \begin{equation} \label{eq:MV_nBq} 1503 1503 \begin{split} 1504 1504 \mathcal{M} &= \mathcal{V} \;\bar{\rho} \\ … … 1507 1507 \end{equation} 1508 1508 Temporal changes in total mass is obtained from the density conservation equation : 1509 \begin{equation} \label{ Eq_Co_nBq}1509 \begin{equation} \label{eq:Co_nBq} 1510 1510 \frac{1}{e_3} \partial_t ( e_3\,\rho) + \nabla( \rho \, \textbf{U} ) = \left. \frac{\textit{emp}}{e_3}\right|_\textit{surface} 1511 1511 \end{equation} … … 1513 1513 exchanges with the other media of the Earth system (atmosphere, sea-ice, land). 1514 1514 Its global averaged leads to the total mass change 1515 \begin{equation} \label{ Eq_Mass_nBq}1515 \begin{equation} \label{eq:Mass_nBq} 1516 1516 \partial_t \mathcal{M} = \mathcal{A} \;\overline{\textit{emp}} 1517 1517 \end{equation} 1518 1518 where $\overline{\textit{emp}}=\int_S \textit{emp}\,ds$ is the net mass flux 1519 1519 through the ocean surface. 1520 Bringing \ eqref{Eq_Mass_nBq} and the time derivative of \eqref{Eq_MV_nBq}1520 Bringing \autoref{eq:Mass_nBq} and the time derivative of \autoref{eq:MV_nBq} 1521 1521 together leads to the evolution equation of the mean sea level 1522 \begin{equation} \label{ Eq_ssh_nBq}1522 \begin{equation} \label{eq:ssh_nBq} 1523 1523 \partial_t \bar{\eta} = \frac{\overline{\textit{emp}}}{ \bar{\rho}} 1524 1524 - \frac{\mathcal{V}}{\mathcal{A}} \;\frac{\partial_t \bar{\rho} }{\bar{\rho}} 1525 1525 \end{equation} 1526 The first term in equation \ eqref{Eq_ssh_nBq} alters sea level by adding or1526 The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or 1527 1527 subtracting mass from the ocean. 1528 1528 The second term arises from temporal changes in the global mean … … 1531 1531 In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ 1532 1532 appears multiplied by the gravity ($i.e.$ in the hydrostatic balance of the primitive Equations). 1533 In particular, the mass conservation equation, \ eqref{Eq_Co_nBq}, degenerates into1533 In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into 1534 1534 the incompressibility equation: 1535 \begin{equation} \label{ Eq_Co_Bq}1535 \begin{equation} \label{eq:Co_Bq} 1536 1536 \frac{1}{e_3} \partial_t ( e_3 ) + \nabla( \textbf{U} ) = \left. \frac{\textit{emp}}{\rho_o \,e_3}\right|_ \textit{surface} 1537 1537 \end{equation} 1538 1538 and the global average of this equation now gives the temporal change of the total volume, 1539 \begin{equation} \label{ Eq_V_Bq}1539 \begin{equation} \label{eq:V_Bq} 1540 1540 \partial_t \mathcal{V} = \mathcal{A} \;\frac{\overline{\textit{emp}}}{\rho_o} 1541 1541 \end{equation} … … 1553 1553 by the Boussinesq model, via the steric contribution to the sea level, $\eta_s$, a spatially 1554 1554 uniform variable, as follows: 1555 \begin{equation} \label{ Eq_M_Bq}1555 \begin{equation} \label{eq:M_Bq} 1556 1556 \mathcal{M}_o = \mathcal{M} + \rho_o \,\eta_s \,\mathcal{A} 1557 1557 \end{equation} … … 1559 1559 the ocean surface is converted into a mean change in sea level. Introducing the total density 1560 1560 anomaly, $\mathcal{D}= \int_D d_a \,dv$, where $d_a= (\rho -\rho_o ) / \rho_o$ 1561 is the density anomaly used in \NEMO (cf. \ S\ref{TRA_eos}) in \eqref{Eq_M_Bq}1561 is the density anomaly used in \NEMO (cf. \autoref{subsec:TRA_eos}) in \autoref{eq:M_Bq} 1562 1562 leads to a very simple form for the steric height: 1563 \begin{equation} \label{ Eq_steric_Bq}1563 \begin{equation} \label{eq:steric_Bq} 1564 1564 \eta_s = - \frac{1}{\mathcal{A}} \mathcal{D} 1565 1565 \end{equation} … … 1581 1581 (wetting and drying of grid point is not allowed). 1582 1582 1583 Third, the discretisation of \ eqref{Eq_steric_Bq} depends on the type of free surface1583 Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface 1584 1584 which is considered. In the non linear free surface case, $i.e.$ \key{vvl} defined, it is 1585 1585 given by 1586 \begin{equation} \label{ Eq_discrete_steric_Bq}1586 \begin{equation} \label{eq:discrete_steric_Bq} 1587 1587 \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t} e_{2t} e_{3t} } 1588 1588 { \sum_{i,\,j,\,k} e_{1t} e_{2t} e_{3t} } … … 1590 1590 whereas in the linear free surface, the volume above the \textit{z=0} surface must be explicitly taken 1591 1591 into account to better approximate the total ocean mass and thus the steric sea level: 1592 \begin{equation} \label{ Eq_discrete_steric_Bq}1592 \begin{equation} \label{eq:discrete_steric_Bq} 1593 1593 \eta_s = - \frac{ \sum_{i,\,j,\,k} d_a\; e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} d_a\; e_{1t}e_{2t} \eta } 1594 1594 {\sum_{i,\,j,\,k} e_{1t}e_{2t}e_{3t} + \sum_{i,\,j} e_{1t}e_{2t} \eta } … … 1608 1608 In AR5 outputs, the thermosteric sea level is demanded. It is steric sea level due to 1609 1609 changes in ocean density arising just from changes in temperature. It is given by: 1610 \begin{equation} \label{ Eq_thermosteric_Bq}1610 \begin{equation} \label{eq:thermosteric_Bq} 1611 1611 \eta_s = - \frac{1}{\mathcal{A}} \int_D d_a(T,S_o,p_o) \,dv 1612 1612 \end{equation} … … 1622 1622 % ------------------------------------------------------------------------------------------------------------- 1623 1623 \section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 1624 \label{ DIA_diag_others}1624 \label{sec:DIA_diag_others} 1625 1625 1626 1626 … … 1658 1658 as well as for the World Ocean. The sub-basin decomposition requires an input file 1659 1659 (\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask 1660 been deduced from the sum of the Indian and Pacific mask ( Fig~\ref{Fig_mask_subasins}).1660 been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}). 1661 1661 1662 1662 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1663 1663 \begin{figure}[!t] \begin{center} 1664 1664 \includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 1665 \caption{ \protect\label{ Fig_mask_subasins}1665 \caption{ \protect\label{fig:mask_subasins} 1666 1666 Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 1667 1667 the heat and salt transports as well as the meridional stream-function: Atlantic basin (red), … … 1681 1681 A series of diagnostics has been added in the \mdl{diaar5}. 1682 1682 They corresponds to outputs that are required for AR5 simulations (CMIP5) 1683 (see also Section \ref{DIA_steric} for one of them).1683 (see also \autoref{sec:DIA_steric} for one of them). 1684 1684 Activating those outputs requires to define the \key{diaar5} CPP key. 1685 1685
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