--- manual/s_overview/text/manual.tex 2001/11/13 20:13:07 1.9 +++ manual/s_overview/text/manual.tex 2004/03/23 16:47:04 1.19 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ %tci%\documentclass[12pt]{book} @@ -34,12 +34,10 @@ % Section: Overview -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ -\section{Introduction} - -This documentation provides the reader with the information necessary to +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 numerical algorithms the model employs and a description of the associated @@ -49,6 +47,12 @@ both process and general circulation studies of the atmosphere and ocean are also presented. +\section{Introduction} +\begin{rawhtml} + +\end{rawhtml} + + MITgcm has a number of novel aspects: \begin{itemize} @@ -84,12 +88,56 @@ \end{itemize} Key publications reporting on and charting the development of the model are -listed in an Appendix. +\cite{hill:95,marshall:97a,marshall:97b,adcroft:97,marshall:98,adcroft:99,hill:99,maro-eta:99}: + +\begin{verbatim} +Hill, C. and J. Marshall, (1995) +Application of a Parallel Navier-Stokes Model to Ocean Circulation in +Parallel Computational Fluid Dynamics +In Proceedings of Parallel Computational Fluid Dynamics: Implementations +and Results Using Parallel Computers, 545-552. +Elsevier Science B.V.: New York + +Marshall, J., C. Hill, L. Perelman, and A. Adcroft, (1997) +Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling +J. Geophysical Res., 102(C3), 5733-5752. + +Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heisey, (1997) +A finite-volume, incompressible Navier Stokes model for studies of the ocean +on parallel computers, +J. Geophysical Res., 102(C3), 5753-5766. + +Adcroft, A.J., Hill, C.N. and J. Marshall, (1997) +Representation of topography by shaved cells in a height coordinate ocean +model +Mon Wea Rev, vol 125, 2293-2315 + +Marshall, J., Jones, H. and C. Hill, (1998) +Efficient ocean modeling using non-hydrostatic algorithms +Journal of Marine Systems, 18, 115-134 + +Adcroft, A., Hill C. and J. Marshall: (1999) +A new treatment of the Coriolis terms in C-grid models at both high and low +resolutions, +Mon. Wea. Rev. Vol 127, pages 1928-1936 + +Hill, C, Adcroft,A., Jamous,D., and J. Marshall, (1999) +A Strategy for Terascale Climate Modeling. +In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors +in Meteorology, pages 406-425 +World Scientific Publishing Co: UK + +Marotzke, J, Giering,R., Zhang, K.Q., Stammer,D., Hill,C., and T.Lee, (1999) +Construction of the adjoint MIT ocean general circulation model and +application to Atlantic heat transport variability +J. Geophysical Res., 104(C12), 29,529-29,547. + +\end{verbatim} 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: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ \section{Illustrations of the model in action} @@ -102,10 +150,15 @@ numerical algorithm and implementation that lie behind these calculations is given later. Indeed many of the illustrative examples shown below can be easily reproduced: simply download the model (the minimum you need is a PC -running linux, together with a FORTRAN\ 77 compiler) and follow the examples +running Linux, together with a FORTRAN\ 77 compiler) and follow the examples described in detail in the documentation. \subsection{Global atmosphere: `Held-Suarez' benchmark} +\begin{rawhtml} + +\end{rawhtml} + + A novel feature of MITgcm is its ability to simulate, using one basic algorithm, both atmospheric and oceanographic flows at both small and large scales. @@ -126,7 +179,7 @@ %% CNHend As described in Adcroft (2001), a `cubed sphere' is used to discretize the -globe permitting a uniform gridding and obviated the need to Fourier filter. +globe permitting a uniform griding and obviated the need to Fourier filter. The `vector-invariant' form of MITgcm supports any orthogonal curvilinear grid, of which the cubed sphere is just one of many choices. @@ -142,6 +195,12 @@ %% CNHend \subsection{Ocean gyres} +\begin{rawhtml} + +\end{rawhtml} +\begin{rawhtml} + +\end{rawhtml} Baroclinic instability is a ubiquitous process in the ocean, as well as the atmosphere. Ocean eddies play an important role in modifying the @@ -163,11 +222,14 @@ visible. %% CNHbegin -\input{part1/ocean_gyres_figure} +\input{part1/atl6_figure} %% CNHend \subsection{Global ocean circulation} +\begin{rawhtml} + +\end{rawhtml} Figure \ref{fig:large-scale-circ} (top) shows the pattern of ocean currents at the surface of a 4$^{\circ }$ @@ -186,6 +248,10 @@ %%CNHend \subsection{Convection and mixing over topography} +\begin{rawhtml} + +\end{rawhtml} + Dense plumes generated by localized cooling on the continental shelf of the ocean may be influenced by rotation when the deformation radius is smaller @@ -205,6 +271,9 @@ %%CNHend \subsection{Boundary forced internal waves} +\begin{rawhtml} + +\end{rawhtml} The unique ability of MITgcm to treat non-hydrostatic dynamics in the presence of complex geometry makes it an ideal tool to study internal wave @@ -224,6 +293,9 @@ %%CNHend \subsection{Parameter sensitivity using the adjoint of MITgcm} +\begin{rawhtml} + +\end{rawhtml} Forward and tangent linear counterparts of MITgcm are supported using an `automatic adjoint compiler'. These can be used in parameter sensitivity and @@ -231,7 +303,7 @@ As one example of application of the MITgcm adjoint, Figure \ref{fig:hf-sensitivity} maps the gradient $\frac{\partial J}{\partial \mathcal{H}}$where $J$ is the magnitude -of the overturning streamfunction shown in figure \ref{fig:large-scale-circ} +of the overturning stream-function shown in figure \ref{fig:large-scale-circ} at 60$^{\circ }$N and $ \mathcal{H}(\lambda,\varphi)$ is the mean, local air-sea heat flux over a 100 year period. We see that $J$ is @@ -244,22 +316,30 @@ %%CNHend \subsection{Global state estimation of the ocean} +\begin{rawhtml} + +\end{rawhtml} + An important application of MITgcm is in state estimation of the global ocean circulation. An appropriately defined `cost function', which measures the departure of the model from observations (both remotely sensed and -insitu) over an interval of time, is minimized by adjusting `control +in-situ) over an interval of time, is minimized by adjusting `control parameters' such as air-sea fluxes, the wind field, the initial conditions -etc. Figure \ref{fig:assimilated-globes} shows an estimate of the time-mean -surface elevation of the ocean obtained by bringing the model in to +etc. Figure \ref{fig:assimilated-globes} shows the large scale planetary +circulation and a Hopf-Muller plot of Equatorial sea-surface height. +Both are obtained from assimilation bringing the model in to consistency with altimetric and in-situ observations over the period -1992-1997. {\bf CHANGE THIS TEXT - FIG FROM PATRICK/CARL/DETLEF} +1992-1997. %% CNHbegin -\input{part1/globes_figure} +\input{part1/assim_figure} %% CNHend \subsection{Ocean biogeochemical cycles} +\begin{rawhtml} + +\end{rawhtml} MITgcm is being used to study global biogeochemical cycles in the ocean. For example one can study the effects of interannual changes in meteorological @@ -275,9 +355,12 @@ %%CNHend \subsection{Simulations of laboratory experiments} +\begin{rawhtml} + +\end{rawhtml} Figure \ref{fig:lab-simulation} shows MITgcm being used to simulate a -laboratory experiment enquiring in to the dynamics of the Antarctic Circumpolar Current (ACC). An +laboratory experiment inquiring into the dynamics of the Antarctic Circumpolar Current (ACC). An initially homogeneous tank of water ($1m$ in diameter) is driven from its free surface by a rotating heated disk. The combined action of mechanical and thermal forcing creates a lens of fluid which becomes baroclinically @@ -289,10 +372,13 @@ \input{part1/lab_figure} %%CNHend -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ \section{Continuous equations in `r' coordinates} +\begin{rawhtml} + +\end{rawhtml} To render atmosphere and ocean models from one dynamical core we exploit `isomorphisms' between equation sets that govern the evolution of the @@ -301,8 +387,8 @@ and encoded. The model variables have different interpretations depending on whether the atmosphere or ocean is being studied. Thus, for example, the vertical coordinate `$r$' is interpreted as pressure, $p$, if we are -modeling the atmosphere (left hand side of figure \ref{fig:isomorphic-equations}) -and height, $z$, if we are modeling the ocean (right hand side of figure +modeling the atmosphere (right hand side of figure \ref{fig:isomorphic-equations}) +and height, $z$, if we are modeling the ocean (left hand side of figure \ref{fig:isomorphic-equations}). %%CNHbegin @@ -426,13 +512,13 @@ at fixed and moving $r$ surfaces we set (see figure \ref{fig:zandp-vert-coord}): \begin{equation} -\dot{r}=0atr=R_{fixed}(x,y)\text{ (ocean bottom, top of the atmosphere)} +\dot{r}=0 \text{\ at\ } r=R_{fixed}(x,y)\text{ (ocean bottom, top of the atmosphere)} \label{eq:fixedbc} \end{equation} \begin{equation} -\dot{r}=\frac{Dr}{Dt}atr=R_{moving}\text{ \ -(oceansurface,bottomoftheatmosphere)} \label{eq:movingbc} +\dot{r}=\frac{Dr}{Dt} \text{\ at\ } r=R_{moving}\text{ \ +(ocean surface,bottom of the atmosphere)} \label{eq:movingbc} \end{equation} Here @@ -569,6 +655,10 @@ \subsection{Hydrostatic, Quasi-hydrostatic, Quasi-nonhydrostatic and Non-hydrostatic forms} +\begin{rawhtml} + +\end{rawhtml} + Let us separate $\phi $ in to surface, hydrostatic and non-hydrostatic terms: @@ -1028,7 +1118,7 @@ Tangent linear and adjoint counterparts of the forward model are described in Chapter 5. -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ \section{Appendix ATMOSPHERE} @@ -1155,7 +1245,7 @@ \frac{D\theta }{Dt} &=&\frac{\mathcal{Q}}{\Pi } \end{eqnarray} -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ \section{Appendix OCEAN} @@ -1178,7 +1268,7 @@ \label{eq:non-boussinesq} \end{eqnarray} These equations permit acoustics modes, inertia-gravity waves, -non-hydrostatic motions, a geostrophic (Rossby) mode and a thermo-haline +non-hydrostatic motions, a geostrophic (Rossby) mode and a thermohaline mode. As written, they cannot be integrated forward consistently - if we step $\rho $ forward in (\ref{eq-zns-cont}), the answer will not be consistent with that obtained by stepping (\ref{eq-zns-heat}) and (\ref @@ -1371,7 +1461,7 @@ _{nh}=0$ form of these equations that are used throughout the ocean modeling community and referred to as the primitive equations (HPE). -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.9 2001/11/13 20:13:07 adcroft Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_overview/text/manual.tex,v 1.19 2004/03/23 16:47:04 afe Exp $ % $Name: $ \section{Appendix:OPERATORS}