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%\label{www:tutorials} |
%\label{www:tutorials} |
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This file, reproduced completely below, specifies the main parameters |
This file, reproduced completely below, specifies the main parameters |
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for the experiment. The parameters that are significant for this configuration |
for the experiment. The parameters that are significant for this configuration |
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are |
are |
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\begin{itemize} |
\begin{itemize} |
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\item Lines 7-10 and 11-14 |
\item Lines 7--8 |
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\begin{verbatim} tRef= 16.0 , 15.2 , 14.5 , 13.9 , 13.3 , \end{verbatim} |
\begin{verbatim} |
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$\cdots$ \\ |
tRef= 15*20., |
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sRef= 15*35., |
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\end{verbatim} |
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%$\cdots$ |
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\\ |
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set reference values for potential |
set reference values for potential |
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temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and |
temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and |
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${\rm ppt}$. The entries are ordered from surface to depth. |
${\rm ppt}$. The entries are ordered from surface to depth. |
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Density is calculated from anomalies at each level evaluated |
Density is calculated from anomalies at each level evaluated |
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with respect to the reference values set here.\\ |
with respect to the reference values set here.\\ |
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\fbox{ |
\fbox{ |
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\begin{minipage}{5.0in} |
\begin{minipage}{5.0in} |
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{\it S/R INI\_THETA}({\it ini\_theta.F}) |
{\it S/R INI\_THETA}({\it ini\_theta.F}) \\ |
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{\it S/R INI\_SALT}({\it ini\_salt.F}) |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 9, |
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\item Line 15, |
\begin{verbatim} |
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\begin{verbatim} viscAz=1.E-3, \end{verbatim} |
viscAr=1.E-3, |
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\end{verbatim} |
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this line sets the vertical Laplacian dissipation coefficient to |
this line sets the vertical Laplacian dissipation coefficient to |
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$1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions |
$1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions |
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for this operator are specified later. This variable is copied into |
for this operator are specified later. |
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model general vertical coordinate variable {\bf viscAr}. |
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\fbox{ |
\fbox{ |
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\begin{minipage}{5.0in} |
\begin{minipage}{5.0in} |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 16, |
\item Line 10, |
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\begin{verbatim} |
\begin{verbatim} |
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viscAh=5.E5, |
viscAh=5.E5, |
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\end{verbatim} |
\end{verbatim} |
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$5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions |
$5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions |
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for this operator are specified later. |
for this operator are specified later. |
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\item Lines 17, |
\item Lines 11 and 13, |
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\begin{verbatim} |
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no_slip_sides=.FALSE. |
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\end{verbatim} |
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this line selects a free-slip lateral boundary condition for |
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the horizontal Laplacian friction operator |
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e.g. $\frac{\partial u}{\partial y}$=0 along boundaries in $y$ and |
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$\frac{\partial v}{\partial x}$=0 along boundaries in $x$. |
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\item Lines 9, |
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\begin{verbatim} |
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no_slip_bottom=.TRUE. |
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\end{verbatim} |
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this line selects a no-slip boundary condition for bottom |
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boundary condition in the vertical Laplacian friction operator |
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e.g. $u=v=0$ at $z=-H$, where $H$ is the local depth of the domain. |
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\item Line 19, |
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\begin{verbatim} |
\begin{verbatim} |
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diffKhT=1.E3, |
diffKhT=0.0, |
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diffKhS=0.0, |
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\end{verbatim} |
\end{verbatim} |
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this line sets the horizontal diffusion coefficient for temperature |
set the horizontal diffusion coefficient for temperature and salinity |
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to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this |
to 0, since package GMREDI is used. |
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operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on |
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all boundaries. |
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\item Line 20, |
\item Lines 12 and 14, |
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\begin{verbatim} |
\begin{verbatim} |
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diffKzT=3.E-5, |
diffKrT=3.E-5, |
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diffKrS=3.E-5, |
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\end{verbatim} |
\end{verbatim} |
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this line sets the vertical diffusion coefficient for temperature |
set the vertical diffusion coefficient for temperature and salinity |
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to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary |
to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary |
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condition on this operator is $\frac{\partial}{\partial z}=0$ at both |
condition on this operator is $\frac{\partial}{\partial z}=0$ at both |
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the upper and lower boundaries. |
the upper and lower boundaries. |
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\item Line 21, |
\item Lines 15--17 |
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\begin{verbatim} |
\begin{verbatim} |
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diffKhS=1.E3, |
rhonil=1035., |
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\end{verbatim} |
rhoConstFresh=1000., |
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this line sets the horizontal diffusion coefficient for salinity |
eosType = 'JMD95Z', |
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to $1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this |
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operator is $\frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on |
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all boundaries. |
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\item Line 22, |
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\begin{verbatim} |
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diffKzS=3.E-5, |
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\end{verbatim} |
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this line sets the vertical diffusion coefficient for salinity |
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to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary |
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condition on this operator is $\frac{\partial}{\partial z}=0$ at both |
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the upper and lower boundaries. |
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\item Lines 23-26 |
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\begin{verbatim} |
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beta=1.E-11, |
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\end{verbatim} |
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\vspace{-5mm}$\cdots$\\ |
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These settings do not apply for this experiment. |
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\item Line 27, |
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\begin{verbatim} |
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gravity=9.81, |
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\end{verbatim} |
\end{verbatim} |
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Sets the gravitational acceleration coefficient to $9.81{\rm m}{\rm s}^{-1}$.\\ |
set the reference densities for sea water and fresh water, and selects |
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the equation of state \citep{jackett95} |
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\fbox{ |
\fbox{ |
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\begin{minipage}{5.0in} |
\begin{minipage}{5.0in} |
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{\it S/R FIND\_RHO}~({\it find\_rho.F})\\ |
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{\it S/R FIND\_ALPHA}~({\it find\_alpha.F}) \\ |
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{\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\ |
{\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\ |
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{\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\ |
{\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\ |
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{\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\ |
{\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\ |
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} |
} |
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\item Line 28-29, |
\item Lines 18--19, |
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\begin{verbatim} |
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rigidLid=.FALSE., |
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implicitFreeSurface=.TRUE., |
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\end{verbatim} |
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Selects the barotropic pressure equation to be the implicit free surface |
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formulation. |
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\item Line 30, |
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\begin{verbatim} |
\begin{verbatim} |
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eosType='POLY3', |
ivdc_kappa=100., |
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implicitDiffusion=.TRUE., |
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\end{verbatim} |
\end{verbatim} |
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Selects the third order polynomial form of the equation of state.\\ |
specify an ``implicit diffusion'' scheme with increased vertical |
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diffusivity of 100~m$^2$/s in case of instable stratification. |
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\fbox{ |
\fbox{ |
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\begin{minipage}{5.0in} |
\begin{minipage}{5.0in} |
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{\it S/R FIND\_RHO}~({\it find\_rho.F})\\ |
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{\it S/R FIND\_ALPHA}~({\it find\_alpha.F}) |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 31, |
\item \ldots |
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\item Line 28, |
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\begin{verbatim} |
\begin{verbatim} |
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readBinaryPrec=32, |
readBinaryPrec=32, |
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\end{verbatim} |
\end{verbatim} |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 36, |
\item Line 33, |
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\begin{verbatim} |
\begin{verbatim} |
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cg2dMaxIters=1000, |
cg2dMaxIters=500, |
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\end{verbatim} |
\end{verbatim} |
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Sets maximum number of iterations the two-dimensional, conjugate |
Sets maximum number of iterations the two-dimensional, conjugate |
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gradient solver will use, {\bf irrespective of convergence |
gradient solver will use, {\bf irrespective of convergence |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 37, |
\item Line 34, |
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\begin{verbatim} |
\begin{verbatim} |
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cg2dTargetResidual=1.E-13, |
cg2dTargetResidual=1.E-13, |
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\end{verbatim} |
\end{verbatim} |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 42, |
\item Line 39, |
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\begin{verbatim} |
\begin{verbatim} |
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startTime=0, |
nIter0=0, |
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\end{verbatim} |
\end{verbatim} |
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Sets the starting time for the model internal time counter. |
Sets the starting time for the model internal time counter. |
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When set to non-zero this option implicitly requests a |
When set to non-zero this option implicitly requests a |
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checkpoint file be read for initial state. |
checkpoint file be read for initial state. |
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By default the checkpoint file is named according to |
By default the checkpoint file is named according to |
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the integer number of time steps in the {\bf startTime} value. |
the integer number of time step value \verb+nIter0+. |
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The internal time counter works in seconds. |
The internal time counter works in seconds. Alternatively, |
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\verb+startTime+ can be set. |
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\item Line 43, |
\item Line 40, |
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\begin{verbatim} |
\begin{verbatim} |
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endTime=2808000., |
nTimesteps=20, |
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\end{verbatim} |
\end{verbatim} |
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Sets the time (in seconds) at which this simulation will terminate. |
Sets the time step number at which this simulation will terminate. |
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At the end of a simulation a checkpoint file is automatically |
At the end of a simulation a checkpoint file is automatically |
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written so that a numerical experiment can consist of multiple |
written so that a numerical experiment can consist of multiple |
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stages. |
stages. Alternatively \verb+endTime+ can be set. |
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\item Line 44, |
\item Line 44, |
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\begin{verbatim} |
\begin{verbatim} |
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#endTime=62208000000, |
deltaTmom=1800.0, |
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\end{verbatim} |
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A commented out setting for endTime for a 2000 year simulation. |
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\item Line 45, |
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\begin{verbatim} |
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deltaTmom=2400.0, |
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\end{verbatim} |
\end{verbatim} |
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Sets the timestep $\delta t_{v}$ used in the momentum equations to |
Sets the timestep $\delta t_{v}$ used in the momentum equations to |
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$20~{\rm mins}$. |
$30~{\rm mins}$. |
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%- note: Distord Physics (using different time-steps) is not described |
%- note: Distord Physics (using different time-steps) is not described |
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% in the mean time, put this section ref: |
% in the mean time, put this section ref: |
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See section \ref{sec:time_stepping}. %\ref{sec:mom_time_stepping}. |
See section \ref{sec:time_stepping}. %\ref{sec:mom_time_stepping}. |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 46, |
\item Line 45, |
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\begin{verbatim} |
\begin{verbatim} |
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tauCD=321428., |
tauCD=321428., |
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\end{verbatim} |
\end{verbatim} |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 47, |
\item Lines 46--48, |
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\begin{verbatim} |
\begin{verbatim} |
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deltaTtracer=108000., |
deltaTtracer=86400., |
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\end{verbatim} |
deltaTClock = 86400., |
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Sets the default timestep, $\delta t_{\theta}$, for tracer equations to |
deltaTfreesurf= 86400., |
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$30~{\rm hours}$. |
\end{verbatim} |
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%- note: Distord Physics (using different time-steps) is not described |
Sets the default timestep, $\delta t_{\theta}$, for tracer equations |
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% in the mean time, put this section ref: |
and implicit free surface equations to |
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$24~{\rm hours}$. |
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% - note: Distord Physics (using different time-steps) is not |
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% described in the mean time, put this section ref: |
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See section \ref{sec:time_stepping}. %\ref{sec:tracer_time_stepping}. |
See section \ref{sec:time_stepping}. %\ref{sec:tracer_time_stepping}. |
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\fbox{ |
\fbox{ |
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\end{minipage} |
\end{minipage} |
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} |
} |
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\item Line 47, |
\item Line 76, |
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\begin{verbatim} |
\begin{verbatim} |
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bathyFile='topog.box' |
bathyFile='bathymetry.bin' |
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\end{verbatim} |
\end{verbatim} |
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This line specifies the name of the file from which the domain |
This line specifies the name of the file from which the domain |
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bathymetry is read. This file is a two-dimensional ($x,y$) map of |
bathymetry is read. This file is a two-dimensional ($x,y$) map of |
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depths. This file is assumed to contain 64-bit binary numbers |
depths. This file is assumed to contain 32-bit binary numbers |
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giving the depth of the model at each grid cell, ordered with the x |
giving the depth of the model at each grid cell, ordered with the x |
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coordinate varying fastest. The points are ordered from low coordinate |
coordinate varying fastest. The points are ordered from low coordinate |
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to high coordinate for both axes. The units and orientation of the |
to high coordinate for both axes. The units and orientation of the |
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depths in this file are the same as used in the MITgcm code. In this |
depths in this file are the same as used in the MITgcm code. In this |
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experiment, a depth of $0m$ indicates a solid wall and a depth |
experiment, a depth of $0m$ indicates a solid wall and a depth |
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of $-2000m$ indicates open ocean. The matlab program |
of $<0m$ indicates open ocean. |
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{\it input/gendata.m} shows an example of how to generate a |
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bathymetry file. |
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\item Line 50, |
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\begin{verbatim} |
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zonalWindFile='windx.sin_y' |
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\end{verbatim} |
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This line specifies the name of the file from which the x-direction |
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surface wind stress is read. This file is also a two-dimensional |
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($x,y$) map and is enumerated and formatted in the same manner as the |
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bathymetry file. The matlab program {\it input/gendata.m} includes example |
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code to generate a valid |
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{\bf zonalWindFile} |
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file. |
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\item Line 79--80, |
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\begin{verbatim} |
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zonalWindFile='trenberth_taux.bin' |
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meridWindFile='trenberth_tauy.bin' |
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\end{verbatim} |
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These lines specify the names of the files from which the x- and y- |
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direction surface wind stress is read. These files are also |
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three-dimensional ($x,y,time$) maps and are enumerated and formatted |
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in the same manner as the bathymetry file. |
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\end{itemize} |
\end{itemize} |
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\noindent other lines in the file {\it input/data} are standard values |
\noindent other lines in the file {\it input/data} are standard values |