/[MITgcm]/manual/s_examples/global_oce_latlon/climatalogical_ogcm.tex

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-revision 1.16 by jmc,
Tue Jan 15 20:04:06 2008 UTC
+revision 1.20 by jmc,
Thu Apr 21 20:05:12 2011 UTC
 Line 1
  % $Header$
  % $Name$
- \section[Global Ocean MITgcm Exmaple]{Global Ocean Simulation at $4^\circ$ Resolution}
+ \section[Global Ocean MITgcm Example]{Global Ocean Simulation at $4^\circ$ Resolution}
- \label{www:tutorials}
+ %\label{www:tutorials}
- \label{sect:eg-global}
+ \label{sec:eg-global}
  \begin{rawhtml}
  <!-- CMIREDIR:eg-global: -->
  \end{rawhtml}
 Line 38 
 can be integrated forward for thousands
  processor desktop computer.
  \\
  \subsection{Overview}
- \label{www:tutorials}
+ %\label{www:tutorials}
  The model is forced with climatological wind stress data and surface
  flux data from DaSilva \cite{DaSilva94}. Climatological data
 Line 52 
 Altogether, this yields the following fo
  in the model surface layer.
  \begin{eqnarray}
- \label{EQ:eg-global-global_forcing}
+ \label{eq:eg-global-global_forcing}
- \label{EQ:eg-global-global_forcing_fu}
+ \label{eq:eg-global-global_forcing_fu}
  {\cal F}_{u} & = & \frac{\tau_{x}}{\rho_{0} \Delta z_{s}}
  \\
- \label{EQ:eg-global-global_forcing_fv}
+ \label{eq:eg-global-global_forcing_fv}
  {\cal F}_{v} & = & \frac{\tau_{y}}{\rho_{0} \Delta z_{s}}
  \\
- \label{EQ:eg-global-global_forcing_ft}
+ \label{eq:eg-global-global_forcing_ft}
  {\cal F}_{\theta} & = & - \lambda_{\theta} ( \theta - \theta^{\ast} )
   - \frac{1}{C_{p} \rho_{0} \Delta z_{s}}{\cal Q}
  \\
- \label{EQ:eg-global-global_forcing_fs}
+ \label{eq:eg-global-global_forcing_fs}
  {\cal F}_{s} & = & - \lambda_{s} ( S - S^{\ast} )
   + \frac{S_{0}}{\Delta z_{s}}({\cal E} - {\cal P} - {\cal R})
  \end{eqnarray}
 Line 92 
 respectively. The salinity forcing field
  $\cal{E}-\cal{P}-\cal{R}$) have units of ${\rm ppt}$ and ${\rm m}~{\rm s}^{-1}$
  respectively. The source files and procedures for ingesting this data into the
  simulation are described in the experiment configuration discussion in section
- \ref{SEC:eg-global-clim_ocn_examp_exp_config}.
+ \ref{sec:eg-global-clim_ocn_examp_exp_config}.
  \subsection{Discrete Numerical Configuration}
- \label{www:tutorials}
+ %\label{www:tutorials}
   The model is configured in hydrostatic form.  The domain is discretised with
 Line 147 
 The implicit free surface form of the pr
  \cite{marshall:97a} is employed. A Laplacian operator, $\nabla^2$, provides viscous
  dissipation. Thermal and haline diffusion is also represented by a Laplacian operator.
- Wind-stress forcing is added to the momentum equations in (\ref{EQ:eg-global-model_equations})
+ Wind-stress forcing is added to the momentum equations in (\ref{eq:eg-global-model_equations})
  for both the zonal flow, $u$ and the meridional flow $v$, according to equations
- (\ref{EQ:eg-global-global_forcing_fu}) and (\ref{EQ:eg-global-global_forcing_fv}).
+ (\ref{eq:eg-global-global_forcing_fu}) and (\ref{eq:eg-global-global_forcing_fv}).
  Thermodynamic forcing inputs are added to the equations
- in (\ref{EQ:eg-global-model_equations}) for
+ in (\ref{eq:eg-global-model_equations}) for
  potential temperature, $\theta$, and salinity, $S$, according to equations
- (\ref{EQ:eg-global-global_forcing_ft}) and (\ref{EQ:eg-global-global_forcing_fs}).
+ (\ref{eq:eg-global-global_forcing_ft}) and (\ref{eq:eg-global-global_forcing_fs}).
  This produces a set of equations solved in this configuration as follows:
  \begin{eqnarray}
- \label{EQ:eg-global-model_equations}
+ \label{eq:eg-global-model_equations}
  \frac{Du}{Dt} - fv +
    \frac{1}{\rho}\frac{\partial p^{'}}{\partial x} -
    \nabla_{h}\cdot A_{h}\nabla_{h}u -
 Line 214 
 elevation $\eta$ and the hydrostatic pre
  \\
  \subsubsection{Numerical Stability Criteria}
- \label{www:tutorials}
+ %\label{www:tutorials}
  The Laplacian dissipation coefficient, $A_{h}$, is set to $5 \times 10^5 m s^{-1}$.
  This value is chosen to yield a Munk layer width \cite{adcroft:95},
  \begin{eqnarray}
- \label{EQ:eg-global-munk_layer}
+ \label{eq:eg-global-munk_layer}
  && M_{w} = \pi ( \frac { A_{h} }{ \beta } )^{\frac{1}{3}}
  \end{eqnarray}
 Line 233 
 time step $\delta t_{\theta}=30~{\rm hou
  $\delta t_{v}=40~{\rm minutes}$ for momentum terms. With this time step, the stability
  parameter to the horizontal Laplacian friction \cite{adcroft:95}
  \begin{eqnarray}
- \label{EQ:eg-global-laplacian_stability}
+ \label{eq:eg-global-laplacian_stability}
  && S_{l} = 4 \frac{A_{h} \delta t_{v}}{{\Delta x}^2}
  \end{eqnarray}
 Line 245 
 $\phi=80^{\circ}$ where $\Delta x=r\cos(
  \noindent The vertical dissipation coefficient, $A_{z}$, is set to
  $1\times10^{-3} {\rm m}^2{\rm s}^{-1}$. The associated stability limit
  \begin{eqnarray}
- \label{EQ:eg-global-laplacian_stability_z}
+ \label{eq:eg-global-laplacian_stability_z}
  S_{l} = 4 \frac{A_{z} \delta t_{v}}{{\Delta z}^2}
  \end{eqnarray}
 Line 260 
 and $3 \times 10^{-5}~{\rm m}^{2}{\rm s}
  related to $K_{h}$ will be at $\phi=80^{\circ}$ where $\Delta x \approx 77 {\rm km}$.
  Here the stability parameter
  \begin{eqnarray}
- \label{EQ:eg-global-laplacian_stability_xtheta}
+ \label{eq:eg-global-laplacian_stability_xtheta}
  S_{l} = \frac{4 K_{h} \delta t_{\theta}}{{\Delta x}^2}
  \end{eqnarray}
  evaluates to $0.07$, well below the stability limit of $S_{l} \approx 0.5$. The
  stability parameter related to $K_{z}$
  \begin{eqnarray}
- \label{EQ:eg-global-laplacian_stability_ztheta}
+ \label{eq:eg-global-laplacian_stability_ztheta}
  S_{l} = \frac{4 K_{z} \delta t_{\theta}}{{\Delta z}^2}
  \end{eqnarray}
  evaluates to $0.005$ for $\min(\Delta z)=50{\rm m}$, well below the stability limit
 Line 277 
 of $S_{l} \approx 0.5$.
  \cite{adcroft:95}
  \begin{eqnarray}
- \label{EQ:eg-global-inertial_stability}
+ \label{eq:eg-global-inertial_stability}
  S_{i} = f^{2} {\delta t_v}^2
  \end{eqnarray}
 Line 290 
 horizontal flow
  speed of $ | \vec{u} | = 2 ms^{-1}$
  \begin{eqnarray}
- \label{EQ:eg-global-cfl_stability}
+ \label{eq:eg-global-cfl_stability}
  S_{a} = \frac{| \vec{u} | \delta t_{v}}{ \Delta x}
  \end{eqnarray}
 Line 303 
 with a maximum speed of $c_{g}=10~{\rm m
  \cite{adcroft:95}
  \begin{eqnarray}
- \label{EQ:eg-global-gfl_stability}
+ \label{eq:eg-global-gfl_stability}
  S_{c} = \frac{c_{g} \delta t_{v}}{ \Delta x}
  \end{eqnarray}
 Line 311 
 S_{c} = \frac{c_{g} \delta t_{v}}{ \Delt
  stability limit of 0.5.
  \subsection{Experiment Configuration}
- \label{www:tutorials}
+ %\label{www:tutorials}
- \label{SEC:eg-global-clim_ocn_examp_exp_config}
+ \label{sec:eg-global-clim_ocn_examp_exp_config}
  The model configuration for this experiment resides under the
  directory {\it tutorial\_examples/global\_ocean\_circulation/}.
 Line 338 
 experiments. Below we describe the custo
  to these files associated with this experiment.
  \subsubsection{Driving Datasets}
- \label{www:tutorials}
+ %\label{www:tutorials}
- Figures (\ref{FIG:sim_config_tclim}-\ref{FIG:sim_config_empmr}) show the
+ Figures ({\it --- missing figures ---})
- relaxation temperature ($\theta^{\ast}$) and salinity ($S^{\ast}$) fields,
+ %(\ref{fig:sim_config_tclim}-\ref{fig:sim_config_empmr})
- the wind stress components ($\tau_x$ and $\tau_y$), the heat flux ($Q$)
+ show the relaxation temperature ($\theta^{\ast}$) and salinity ($S^{\ast}$)
+ fields, the wind stress components ($\tau_x$ and $\tau_y$), the heat flux ($Q$)
  and the net fresh water flux (${\cal E} - {\cal P} - {\cal R}$) used
- in equations \ref{EQ:global_forcing_fu}-\ref{EQ:global_forcing_fs}. The figures
+ in equations
- also indicate the lateral extent and coastline used in the experiment.
+ (\ref{eq:eg-global-global_forcing_fu}-\ref{eq:eg-global-global_forcing_fs}).
- Figure ({\ref{FIG:model_bathymetry}) shows the depth contours of the model
+ The figures also indicate the lateral extent and coastline used in the
- domain.
+ experiment. Figure ({\it --- missing figure --- }) %ref{fig:model_bathymetry})
+ shows the depth contours of the model domain.
  \subsubsection{File {\it input/data}}
- \label{www:tutorials}
+ %\label{www:tutorials}
- This file, reproduced completely below, specifies the main parameters
- for the experiment. The parameters that are significant for this configuration
- are
- \begin{itemize}
- \item Lines 7-10 and 11-14
- \begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 ,  \end{verbatim}
- $\cdots$ \\
- set reference values for potential
- temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and
- ${\rm ppt}$. The entries are ordered from surface to depth.
- Density is calculated from anomalies at each level evaluated
- with respect to the reference values set here.\\
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R INI\_THETA}({\it ini\_theta.F})
- \end{minipage}
- }
- \item Line 15,
- \begin{verbatim} viscAz=1.E-3, \end{verbatim}
- this line sets the vertical Laplacian dissipation coefficient to
- $1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
- for this operator are specified later. This variable is copied into
- model general vertical coordinate variable {\bf viscAr}.
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
- \end{minipage}
- }
- \item Line 16,
- \begin{verbatim}
- viscAh=5.E5,
- \end{verbatim}
- this line sets the horizontal Laplacian frictional dissipation coefficient to
- $5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
- for this operator are specified later.
- \item Lines 17,
- \begin{verbatim}
- no_slip_sides=.FALSE.
- \end{verbatim}
- this line selects a free-slip lateral boundary condition for
- the horizontal Laplacian friction operator
- e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and
- $\frac{\partial v}{\partial x}$=0 along boundaries in $x$.
- \item Lines 9,
- \begin{verbatim}
- no_slip_bottom=.TRUE.
- \end{verbatim}
- this line selects a no-slip boundary condition for bottom
- boundary condition in the vertical Laplacian friction operator
- e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain.
- \item Line 19,
- \begin{verbatim}
- diffKhT=1.E3,
- \end{verbatim}
- this line sets the horizontal diffusion coefficient for temperature
- to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
- operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
- all boundaries.
- \item Line 20,
- \begin{verbatim}
- diffKzT=3.E-5,
- \end{verbatim}
- this line sets the vertical diffusion coefficient for temperature
- to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
- condition on this operator is $\frac{\partial}{\partial z}=0$ at both
- the upper and lower boundaries.
- \item Line 21,
- \begin{verbatim}
- diffKhS=1.E3,
- \end{verbatim}
- this line sets the horizontal diffusion coefficient for salinity
- to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this
- operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on
- all boundaries.
- \item Line 22,
- \begin{verbatim}
- diffKzS=3.E-5,
- \end{verbatim}
- this line sets the vertical diffusion coefficient for salinity
- to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
- condition on this operator is $\frac{\partial}{\partial z}=0$ at both
- the upper and lower boundaries.
- \item Lines 23-26
- \begin{verbatim}
- beta=1.E-11,
- \end{verbatim}
- \vspace{-5mm}$\cdots$\\
- These settings do not apply for this experiment.
- \item Line 27,
- \begin{verbatim}
- gravity=9.81,
- \end{verbatim}
- Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
- {\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
- {\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
- {\it S/R INI\_PARMS}~({\it ini\_parms.F})\\
- {\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F})
- \end{minipage}
- }
- \item Line 28-29,
- \begin{verbatim}
- rigidLid=.FALSE.,
- implicitFreeSurface=.TRUE.,
- \end{verbatim}
- Selects the barotropic pressure equation to be the implicit free surface
- formulation.
- \item Line 30,
- \begin{verbatim}
- eosType='POLY3',
- \end{verbatim}
- Selects the third order polynomial form of the equation of state.\\
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R FIND\_RHO}~({\it find\_rho.F})\\
- {\it S/R FIND\_ALPHA}~({\it find\_alpha.F})
- \end{minipage}
- }
- \item Line 31,
- \begin{verbatim}
- readBinaryPrec=32,
- \end{verbatim}
- Sets format for reading binary input datasets holding model fields to
- use 32-bit representation for floating-point numbers.\\
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\
- {\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F})
- \end{minipage}
- }
- \item Line 36,
- \begin{verbatim}
- cg2dMaxIters=1000,
- \end{verbatim}
- Sets maximum number of iterations the two-dimensional, conjugate
- gradient solver will use, {\bf irrespective of convergence
- criteria being met}.\\
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R CG2D}~({\it cg2d.F})
- \end{minipage}
- }
- \item Line 37,
- \begin{verbatim}
- cg2dTargetResidual=1.E-13,
- \end{verbatim}
- Sets the tolerance which the two-dimensional, conjugate
- gradient solver will use to test for convergence in equation
- \ref{EQ:congrad_2d_resid} to $1 \times 10^{-13}$.
- Solver will iterate until
- tolerance falls below this value or until the maximum number of
- solver iterations is reached.\\
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R CG2D}~({\it cg2d.F})
- \end{minipage}
- }
- \item Line 42,
- \begin{verbatim}
- startTime=0,
- \end{verbatim}
- Sets the starting time for the model internal time counter.
- When set to non-zero this option implicitly requests a
- checkpoint file be read for initial state.
- By default the checkpoint file is named according to
- the integer number of time steps in the {\bf startTime} value.
- The internal time counter works in seconds.
- \item Line 43,
- \begin{verbatim}
- endTime=2808000.,
- \end{verbatim}
- Sets the time (in seconds) at which this simulation will terminate.
- At the end of a simulation a checkpoint file is automatically
- written so that a numerical experiment can consist of multiple
- stages.
- \item Line 44,
- \begin{verbatim}
- #endTime=62208000000,
- \end{verbatim}
- A commented out setting for endTime for a 2000 year simulation.
- \item Line 45,
- \begin{verbatim}
- deltaTmom=2400.0,
- \end{verbatim}
- Sets the timestep $\delta t_{v}$ used in the momentum equations to
- $20~{\rm mins}$.
- See section \ref{SEC:mom_time_stepping}.
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R TIMESTEP}({\it timestep.F})
- \end{minipage}
- }
- \item Line 46,
- \begin{verbatim}
- tauCD=321428.,
- \end{verbatim}
- Sets the D-grid to C-grid coupling time scale $\tau_{CD}$ used in the momentum equations.
- See section \ref{SEC:cd_scheme}.
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R INI\_PARMS}({\it ini\_parms.F})\\
- {\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
- \end{minipage}
- }
- \item Line 47,
- \begin{verbatim}
- deltaTtracer=108000.,
- \end{verbatim}
- Sets the default timestep, $\delta t_{\theta}$, for tracer equations to
- $30~{\rm hours}$.
- See section \ref{SEC:tracer_time_stepping}.
- \fbox{
- \begin{minipage}{5.0in}
- {\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
- \end{minipage}
- }
- \item Line 47,
- \begin{verbatim}
- bathyFile='topog.box'
- \end{verbatim}
- This line specifies the name of the file from which the domain
- bathymetry is read. This file is a two-dimensional ($x,y$) map of
- depths. This file is assumed to contain 64-bit binary numbers
- giving the depth of the model at each grid cell, ordered with the x
- coordinate varying fastest. The points are ordered from low coordinate
- to high coordinate for both axes. The units and orientation of the
- depths in this file are the same as used in the MITgcm code. In this
- experiment, a depth of $0m$ indicates a solid wall and a depth
- of $-2000m$ indicates open ocean. The matlab program
- {\it input/gendata.m} shows an example of how to generate a
- bathymetry file.
- \item Line 50,
- \begin{verbatim}
- zonalWindFile='windx.sin_y'
- \end{verbatim}
- This line specifies the name of the file from which the x-direction
- surface wind stress is read. This file is also a two-dimensional
- ($x,y$) map and is enumerated and formatted in the same manner as the
- bathymetry file. The matlab program {\it input/gendata.m} includes example
- code to generate a valid
- {\bf zonalWindFile}
- file.
- \end{itemize}
+ \input{s_examples/global_oce_latlon/inp_data}
- \noindent other lines in the file {\it input/data} are standard values
- that are described in the MITgcm Getting Started and MITgcm Parameters
- notes.
- \begin{small}
- \input{part3/case_studies/climatalogical_ogcm/input/data}
- \end{small}
  \subsubsection{File {\it input/data.pkg}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  This file uses standard default values and does not contain
  customisations for this experiment.
  \subsubsection{File {\it input/eedata}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  This file uses standard default values and does not contain
  customisations for this experiment.
  \subsubsection{File {\it input/windx.sin\_y}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  The {\it input/windx.sin\_y} file specifies a two-dimensional ($x,y$)
  map of wind stress ,$\tau_{x}$, values. The units used are $Nm^{-2}$.
-Line 664 
 in MITgcm. The included matlab program {
+Line 380 
 in MITgcm. The included matlab program {
  code for creating the {\it input/windx.sin\_y} file.
  \subsubsection{File {\it input/topog.box}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  The {\it input/topog.box} file specifies a two-dimensional ($x,y$)
-Line 676 
 The included matlab program {\it input/g
+Line 392 
 The included matlab program {\it input/g
  code for creating the {\it input/topog.box} file.
  \subsubsection{File {\it code/SIZE.h}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  Two lines are customized in this file for the current experiment
-Line 699 
 the vertical domain extent in grid point
+Line 415 
 the vertical domain extent in grid point
  \end{itemize}
  \begin{small}
- \input{part3/case_studies/climatalogical_ogcm/code/SIZE.h}
+ \input{s_examples/global_oce_latlon/code/SIZE.h}
  \end{small}
  \subsubsection{File {\it code/CPP\_OPTIONS.h}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  This file uses standard default values and does not contain
  customisations for this experiment.
  \subsubsection{File {\it code/CPP\_EEOPTIONS.h}}
- \label{www:tutorials}
+ %\label{www:tutorials}
  This file uses standard default values and does not contain
  customisations for this experiment.
  \subsubsection{Other Files }
- \label{www:tutorials}
+ %\label{www:tutorials}
  Other files relevant to this experiment are
  \begin{itemize}

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