/[MITgcm]/manual/s_overview/text/manual.tex

Diff of /manual/s_overview/text/manual.tex

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-revision 1.26 by edhill,
Wed Jun 28 15:22:13 2006 UTC
+revision 1.30 by jmc,
Wed May 11 18:45:43 2016 UTC
 Line 34
  % Section: Overview
- % $Header$
- % $Name$
  This document provides the reader with the information necessary to
  carry out numerical experiments using MITgcm. It gives a comprehensive
  description of the continuous equations on which the model is based, the
-Line 61 
 hydrodynamical kernel is used to drive f
+Line 58 
 hydrodynamical kernel is used to drive f
  models - see fig \ref{fig:onemodel}
  %% CNHbegin
- \input{part1/one_model_figure}
+ \input{s_overview/text/one_model_figure}
  %% CNHend
  \item it has a non-hydrostatic capability and so can be used to study both
  small-scale and large scale processes - see fig \ref{fig:all-scales}
  %% CNHbegin
- \input{part1/all_scales_figure}
+ \input{s_overview/text/all_scales_figure}
  %% CNHend
  \item finite volume techniques are employed yielding an intuitive
-Line 76 
 discretization and support for the treat
+Line 73 
 discretization and support for the treat
  orthogonal curvilinear grids and shaved cells - see fig \ref{fig:finite-volumes}
  %% CNHbegin
- \input{part1/fvol_figure}
+ \input{s_overview/text/fvol_figure}
  %% CNHend
  \item tangent linear and adjoint counterparts are automatically maintained
-Line 87 
 studies.
+Line 84 
 studies.
  computational platforms.
  \end{itemize}
  Key publications reporting on and charting the development of the model are
- \cite{hill:95,marshall:97a,marshall:97b,adcroft:97,marshall:98,adcroft:99,hill:99,maro-eta:99,adcroft:04a,adcroft:04b,marshall:04}:
+ \cite{hill:95,marshall:97a,marshall:97b,adcroft:97,mars-eta:98,adcroft:99,hill:99,maro-eta:99,adcroft:04a,adcroft:04b,marshall:04}
+ (an overview on the model formulation can also be found in \cite{adcroft:04c}):
  \begin{verbatim}
  Hill, C. and J. Marshall, (1995)
-Line 137 
 J. Geophysical Res., 104(C12), 29,529-29
+Line 136 
 J. Geophysical Res., 104(C12), 29,529-29
  We begin by briefly showing some of the results of the model in action to
  give a feel for the wide range of problems that can be addressed using it.
- % $Header$
- % $Name$
  \section{Illustrations of the model in action}
  MITgcm has been designed and used to model a wide range of phenomena,
-Line 175 
 in Held and Suarez; 1994 designed to tes
+Line 171 
 in Held and Suarez; 1994 designed to tes
  there are no mountains or land-sea contrast.
  %% CNHbegin
- \input{part1/cubic_eddies_figure}
+ \input{s_overview/text/cubic_eddies_figure}
  %% CNHend
  As described in Adcroft (2001), a `cubed sphere' is used to discretize the
-Line 191 
 cube-sphere grid and the flow calculated
+Line 187 
 cube-sphere grid and the flow calculated
  latitude-longitude grid. Both grids are supported within the model.
  %% CNHbegin
- \input{part1/hs_zave_u_figure}
+ \input{s_overview/text/hs_zave_u_figure}
  %% CNHend
  \subsection{Ocean gyres}
-Line 222 
 transport of warm water northward by the
+Line 218 
 transport of warm water northward by the
  is also clearly visible.
  %% CNHbegin
- \input{part1/atl6_figure}
+ \input{s_overview/text/atl6_figure}
  %% CNHend
-Line 244 
 Figure \ref{fig:large-scale-circ} (botto
+Line 240 
 Figure \ref{fig:large-scale-circ} (botto
  circulation of the global ocean in Sverdrups.
  %%CNHbegin
- \input{part1/global_circ_figure}
+ \input{s_overview/text/global_circ_figure}
  %%CNHend
  \subsection{Convection and mixing over topography}
-Line 267 
 strong, and replaced by lateral entrainm
+Line 263 
 strong, and replaced by lateral entrainm
  instability of the along-slope current.
  %%CNHbegin
- \input{part1/convect_and_topo}
+ \input{s_overview/text/convect_and_topo}
  %%CNHend
  \subsection{Boundary forced internal waves}
-Line 289 
 using MITgcm's finite volume spatial dis
+Line 285 
 using MITgcm's finite volume spatial dis
  nonhydrostatic dynamics.
  %%CNHbegin
- \input{part1/boundary_forced_waves}
+ \input{s_overview/text/boundary_forced_waves}
  %%CNHend
  \subsection{Parameter sensitivity using the adjoint of MITgcm}
-Line 312 
 deep water for the thermohaline circulat
+Line 308 
 deep water for the thermohaline circulat
  yields sensitivities to all other model parameters.
  %%CNHbegin
- \input{part1/adj_hf_ocean_figure}
+ \input{s_overview/text/adj_hf_ocean_figure}
  %%CNHend
  \subsection{Global state estimation of the ocean}
-Line 333 
 consistency with altimetric and in-situ
+Line 329 
 consistency with altimetric and in-situ
 -1997.
  %% CNHbegin
- \input{part1/assim_figure}
+ \input{s_overview/text/assim_figure}
  %% CNHend
  \subsection{Ocean biogeochemical cycles}
-Line 353 
 $\frac{1}{3}^{\circ}\times\frac{1}{3}^{\
+Line 349 
 $\frac{1}{3}^{\circ}\times\frac{1}{3}^{\
  shown).
  %%CNHbegin
- \input{part1/biogeo_figure}
+ \input{s_overview/text/biogeo_figure}
  %%CNHend
  \subsection{Simulations of laboratory experiments}
-Line 371 
 arrested by its instability in a process
+Line 367 
 arrested by its instability in a process
  stratification of the ACC.
  %%CNHbegin
- \input{part1/lab_figure}
+ \input{s_overview/text/lab_figure}
  %%CNHend
- % $Header$
- % $Name$
  \section{Continuous equations in `r' coordinates}
  \begin{rawhtml}
  <!-- CMIREDIR:z-p_isomorphism: -->
-Line 394 
 and height, $z$, if we are modeling the
+Line 387 
 and height, $z$, if we are modeling the
  \ref{fig:isomorphic-equations}).
  %%CNHbegin
- \input{part1/zandpcoord_figure.tex}
+ \input{s_overview/text/zandpcoord_figure.tex}
  %%CNHend
  The state of the fluid at any time is characterized by the distribution of
-Line 408 
 kinematic boundary conditions can be app
+Line 401 
 kinematic boundary conditions can be app
  see figure \ref{fig:zandp-vert-coord}.
  %%CNHbegin
- \input{part1/vertcoord_figure.tex}
+ \input{s_overview/text/vertcoord_figure.tex}
  %%CNHend
  \begin{equation}
-Line 659 
 which, for convenience, are written out
+Line 652 
 which, for convenience, are written out
  \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and
  Non-hydrostatic forms}
+ \label{sec:all_hydrostatic_forms}
  \begin{rawhtml}
  <!-- CMIREDIR:non_hydrostatic: -->
  \end{rawhtml}
-Line 767 
 Grad and div operators in spherical coor
+Line 761 
 Grad and div operators in spherical coor
  OPERATORS.
  %%CNHbegin
- \input{part1/sphere_coord_figure.tex}
+ \input{s_overview/text/sphere_coord_figure.tex}
  %%CNHend
  \subsubsection{Shallow atmosphere approximation}
-Line 888 
 stepping forward the horizontal momentum
+Line 882 
 stepping forward the horizontal momentum
  stepping forward the vertical momentum equation.
  %%CNHbegin
- \input{part1/solution_strategy_figure.tex}
+ \input{s_overview/text/solution_strategy_figure.tex}
  %%CNHend
  There is no penalty in implementing \textbf{QH} over \textbf{HPE} except, of
-Line 1126 
 to discretize the model.
+Line 1120 
 to discretize the model.
  Tangent linear and adjoint counterparts of the forward model are described
  in Chapter 5.
- % $Header$
- % $Name$
  \section{Appendix ATMOSPHERE}
  \subsection{Hydrostatic Primitive Equations for the Atmosphere in pressure
-Line 1148 
 p\alpha &=&RT  \label{eq:atmos-eos} \\
+Line 1139 
 p\alpha &=&RT  \label{eq:atmos-eos} \\
  c_{v}\frac{DT}{Dt}+p\frac{D\alpha }{Dt} &=&\mathcal{Q}  \label{eq:atmos-heat}
  \end{eqnarray}
  where $\vec{\mathbf{v}}_{h}=(u,v,0)$ is the `horizontal' (on pressure
- surfaces) component of velocity,$\frac{D}{Dt}=\vec{\mathbf{v}}_{h}\cdot
+ surfaces) component of velocity, $\frac{D}{Dt}=\frac{\partial}{\partial t}
- \mathbf{\nabla }_{p}+\omega \frac{\partial }{\partial p}$ is the total
+ +\vec{\mathbf{v}}_{h}\cdot \mathbf{\nabla }_{p}+\omega \frac{\partial }{\partial p}$
- derivative, $f=2\Omega \sin \varphi$ is the Coriolis parameter, $\phi =gz$ is
+ is the total derivative, $f=2\Omega \sin \varphi$ is the Coriolis parameter,
- the geopotential, $\alpha =1/\rho $ is the specific volume, $\omega =\frac{Dp
+ $\phi =gz$ is the geopotential, $\alpha =1/\rho $ is the specific volume,
- }{Dt}$ is the vertical velocity in the $p-$coordinate. Equation(\ref
+ $\omega =\frac{Dp }{Dt}$ is the vertical velocity in the $p-$coordinate.
- {eq:atmos-heat}) is the first law of thermodynamics where internal energy $
+ Equation(\ref {eq:atmos-heat}) is the first law of thermodynamics where internal
- e=c_{v}T$, $T$ is temperature, $Q$ is the rate of heating per unit mass and $
+ energy $e=c_{v}T$, $T$ is temperature, $Q$ is the rate of heating per unit mass
- p\frac{D\alpha }{Dt}$ is the work done by the fluid in compressing.
+ and $p\frac{D\alpha }{Dt}$ is the work done by the fluid in compressing.
  It is convenient to cast the heat equation in terms of potential temperature
  $\theta $ so that it looks more like a generic conservation law.
-Line 1255 
 _{h}+\mathbf{\nabla }_{p}\phi ^{\prime }
+Line 1246 
 _{h}+\mathbf{\nabla }_{p}\phi ^{\prime }
  \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi }
  \end{eqnarray}
- % $Header$
- % $Name$
  \section{Appendix OCEAN}
  \subsection{Equations of motion for the ocean}
-Line 1472 
 the perturbation density. Nevertheless,
+Line 1460 
 the perturbation density. Nevertheless,
  _{nh}=0$ form of these equations that are used throughout the ocean modeling
  community and referred to as the primitive equations (HPE).
- % $Header$
- % $Name$
  \section{Appendix:OPERATORS}
  \subsection{Coordinate systems}

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