s_examples/global_oce_latlon/inp_data.templ

% $Header: /u/gcmpack/manual/s_examples/global_oce_latlon/inp_data.templ,v 1.4 2011/05/08 15:17:07 jmc Exp $
% $Name:  $

%\subsubsection{File {\it input/data}}
%\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 PUT_LINE_NB:tRef=--PUT_LINE_NB:sRef=
\begin{verbatim}
tRef= 15*20.,
sRef= 15*35.,
\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}) \\
{\it S/R INI\_SALT}({\it ini\_salt.F})
\end{minipage}
}

\item Line PUT_LINE_NB:viscAr=,
\begin{verbatim}
viscAr=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.

\fbox{
\begin{minipage}{5.0in}
{\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
\end{minipage}
}

\item Line PUT_LINE_NB:viscAh=,
\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 PUT_LINE_NB:diffKhT= and PUT_LINE_NB:diffKhS=,
\begin{verbatim}
diffKhT=0.,
diffKhS=0.,
\end{verbatim}
set the horizontal diffusion coefficient for temperature and salinity
to 0, since package GMREDI is used.

\item Lines PUT_LINE_NB:diffKrT= and PUT_LINE_NB:diffKrS=,
\begin{verbatim}
diffKrT=3.E-5,
diffKrS=3.E-5,
\end{verbatim}
set the vertical diffusion coefficient for temperature and 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 PUT_LINE_NB:rhonil=--PUT_LINE_NB:eosType=
\begin{verbatim}
rhonil=1035.,
rhoConstFresh=1000.,
eosType = 'JMD95Z',
\end{verbatim}
set the reference densities for sea water and fresh water, and selects
the equation of state \citep{jackett95}
\fbox{
\begin{minipage}{5.0in}
{\it S/R FIND\_RHO}~({\it find\_rho.F})\\
{\it S/R FIND\_ALPHA}~({\it find\_alpha.F}) \\
{\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 Lines PUT_LINE_NB:ivdc_kappa=--PUT_LINE_NB:implicitDiffusion=,
\begin{verbatim}
 ivdc_kappa=100.,
 implicitDiffusion=.TRUE.,
\end{verbatim}
specify an ``implicit diffusion'' scheme with increased vertical
diffusivity of 100~m$^2$/s in case of instable stratification.
\fbox{
\begin{minipage}{5.0in}
\end{minipage}
}

\item \ldots

\item Line PUT_LINE_NB:readBinaryPrec=,
\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 PUT_LINE_NB:cg2dMaxIters=,
\begin{verbatim}
cg2dMaxIters=500,
\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 PUT_LINE_NB:cg2dTargetResidual=,
\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
%- note: Description of Conjugate gradient method (& related params) is missing
%  in the mean time, substitute this eq ref:
\ref{eq:elliptic-backward-free-surface} %\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 PUT_LINE_NB:nIter0=,
\begin{verbatim}
nIter0=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 step value \verb+nIter0+.
The internal time counter works in seconds. Alternatively,
\verb+startTime+ can be set.

\item Line PUT_LINE_NB:nTimeSteps=,
\begin{verbatim}
nTimeSteps=20,
\end{verbatim}
Sets the time step number 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. Alternatively \verb+endTime+ can be set.

\item Line PUT_LINE_NB:deltaTmom=,
\begin{verbatim}
deltaTmom=1800.,
\end{verbatim}
Sets the timestep $\Delta t_{v}$ used in the momentum equations to
$30~{\rm mins}$.
%- note: Distord Physics (using different time-steps) is not described
%  in the mean time, put this section ref:
See section \ref{sec:time_stepping}. %\ref{sec:mom_time_stepping}.

\fbox{
\begin{minipage}{5.0in}
{\it S/R TIMESTEP}({\it timestep.F})
\end{minipage}
}

\item Line PUT_LINE_NB:tauCD=,
\begin{verbatim}
tauCD=321428.,
\end{verbatim}
Sets the D-grid to C-grid coupling time scale $\tau_{CD}$
used in the momentum equations.
%- note: description of CD-scheme pkg (and related params) is missing;
%  in the mean time, comment out this ref.
%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 Lines PUT_LINE_NB:deltaTtracer=--PUT_LINE_NB:deltaTfreesurf=,
\begin{verbatim}
deltaTtracer=86400.,
deltaTClock = 86400.,
deltaTfreesurf= 86400.,
\end{verbatim}
Sets the default timestep, $\Delta t_{\theta}$, for tracer equations
and implicit free surface equations to
$24~{\rm hours}$.
% - note: Distord Physics (using different time-steps) is not
% described in the mean time, put this section ref:
See section \ref{sec:time_stepping}. %\ref{sec:tracer_time_stepping}.

\fbox{
\begin{minipage}{5.0in}
{\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
\end{minipage}
}

\item Line PUT_LINE_NB:bathyFile=,
\begin{verbatim}
bathyFile='bathymetry.bin'
\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 32-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 $<0m$ indicates open ocean.


\item Lines PUT_LINE_NB:zonalWindFile=--PUT_LINE_NB:meridWindFile=,
\begin{verbatim}
zonalWindFile='trenberth_taux.bin'
meridWindFile='trenberth_tauy.bin'
\end{verbatim}
  These lines specify the names of the files from which the x- and y-
  direction surface wind stress is read. These files are also
  three-dimensional ($x,y,time$) maps and are enumerated and formatted
  in the same manner as the bathymetry file.
\end{itemize}

\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{s_examples/global_oce_latlon/input/data}
\end{small}

1	jmc	1.5	% $Header: /u/gcmpack/manual/s_examples/global_oce_latlon/inp_data.templ,v 1.4 2011/05/08 15:17:07 jmc Exp $
2	jmc	1.1	% $Name: $
3
4			%\subsubsection{File {\it input/data}}
5			%\label{www:tutorials}
6
7	jmc	1.4	This file, reproduced completely below, specifies the main parameters
8			for the experiment. The parameters that are significant for this configuration
9	jmc	1.1	are
10
11			\begin{itemize}
12
13	jmc	1.4	\item Lines PUT_LINE_NB:tRef=--PUT_LINE_NB:sRef=
14			\begin{verbatim}
15	mlosch	1.2	tRef= 15*20.,
16			sRef= 15*35.,
17	jmc	1.4	\end{verbatim}
18			%$\cdots$
19	jmc	1.3	%\\
20	jmc	1.1	set reference values for potential
21	jmc	1.4	temperature and salinity at each model level in units of $^{\circ}\mathrm{C}$ and
22	jmc	1.1	${\rm ppt}$. The entries are ordered from surface to depth.
23			Density is calculated from anomalies at each level evaluated
24			with respect to the reference values set here.\\
25			\fbox{
26			\begin{minipage}{5.0in}
27	mlosch	1.2	{\it S/R INI\_THETA}({\it ini\_theta.F}) \\
28			{\it S/R INI\_SALT}({\it ini\_salt.F})
29	jmc	1.1	\end{minipage}
30			}
31
32	jmc	1.4	\item Line PUT_LINE_NB:viscAr=,
33			\begin{verbatim}
34	mlosch	1.2	viscAr=1.E-3,
35			\end{verbatim}
36	jmc	1.1	this line sets the vertical Laplacian dissipation coefficient to
37			$1 \times 10^{-3} {\rm m^{2}s^{-1}}$. Boundary conditions
38	mlosch	1.2	for this operator are specified later.
39	jmc	1.1
40			\fbox{
41			\begin{minipage}{5.0in}
42			{\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F})
43			\end{minipage}
44			}
45
46	jmc	1.4	\item Line PUT_LINE_NB:viscAh=,
47	jmc	1.1	\begin{verbatim}
48			viscAh=5.E5,
49	jmc	1.4	\end{verbatim}
50	jmc	1.1	this line sets the horizontal Laplacian frictional dissipation coefficient to
51			$5 \times 10^{5} {\rm m^{2}s^{-1}}$. Boundary conditions
52			for this operator are specified later.
53
54	jmc	1.4	\item Lines PUT_LINE_NB:diffKhT= and PUT_LINE_NB:diffKhS=,
55	jmc	1.1	\begin{verbatim}
56	jmc	1.4	diffKhT=0.,
57			diffKhS=0.,
58	jmc	1.1	\end{verbatim}
59	mlosch	1.2	set the horizontal diffusion coefficient for temperature and salinity
60			to 0, since package GMREDI is used.
61	jmc	1.1
62	jmc	1.4	\item Lines PUT_LINE_NB:diffKrT= and PUT_LINE_NB:diffKrS=,
63	jmc	1.1	\begin{verbatim}
64	mlosch	1.2	diffKrT=3.E-5,
65			diffKrS=3.E-5,
66	jmc	1.1	\end{verbatim}
67	mlosch	1.2	set the vertical diffusion coefficient for temperature and salinity
68	jmc	1.4	to $3 \times 10^{-5}\,{\rm m^{2}s^{-1}}$. The boundary
69	jmc	1.1	condition on this operator is $\frac{\partial}{\partial z}=0$ at both
70			the upper and lower boundaries.
71
72	jmc	1.4	\item Lines PUT_LINE_NB:rhonil=--PUT_LINE_NB:eosType=
73			\begin{verbatim}
74	mlosch	1.2	rhonil=1035.,
75			rhoConstFresh=1000.,
76	jmc	1.4	eosType = 'JMD95Z',
77	jmc	1.1	\end{verbatim}
78	mlosch	1.2	set the reference densities for sea water and fresh water, and selects
79			the equation of state \citep{jackett95}
80	jmc	1.1	\fbox{
81			\begin{minipage}{5.0in}
82	mlosch	1.2	{\it S/R FIND\_RHO}~({\it find\_rho.F})\\
83			{\it S/R FIND\_ALPHA}~({\it find\_alpha.F}) \\
84	jmc	1.1	{\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})\\
85			{\it S/R INI\_CG2D}~({\it ini\_cg2d.F})\\
86			{\it S/R INI\_CG3D}~({\it ini\_cg3d.F})\\
87			{\it S/R INI\_PARMS}~({\it ini\_parms.F})\\
88			{\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F})
89			\end{minipage}
90			}
91
92
93	jmc	1.4	\item Lines PUT_LINE_NB:ivdc_kappa=--PUT_LINE_NB:implicitDiffusion=,
94	jmc	1.1	\begin{verbatim}
95	mlosch	1.2	ivdc_kappa=100.,
96			implicitDiffusion=.TRUE.,
97	jmc	1.1	\end{verbatim}
98	mlosch	1.2	specify an ``implicit diffusion'' scheme with increased vertical
99			diffusivity of 100~m$^2$/s in case of instable stratification.
100	jmc	1.1	\fbox{
101			\begin{minipage}{5.0in}
102			\end{minipage}
103			}
104
105	mlosch	1.2	\item \ldots
106
107	jmc	1.4	\item Line PUT_LINE_NB:readBinaryPrec=,
108	jmc	1.1	\begin{verbatim}
109			readBinaryPrec=32,
110			\end{verbatim}
111			Sets format for reading binary input datasets holding model fields to
112			use 32-bit representation for floating-point numbers.\\
113			\fbox{
114			\begin{minipage}{5.0in}
115			{\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\
116			{\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F})
117			\end{minipage}
118			}
119
120	jmc	1.4	\item Line PUT_LINE_NB:cg2dMaxIters=,
121	jmc	1.1	\begin{verbatim}
122	mlosch	1.2	cg2dMaxIters=500,
123	jmc	1.1	\end{verbatim}
124			Sets maximum number of iterations the two-dimensional, conjugate
125	jmc	1.4	gradient solver will use, {\bf irrespective of convergence
126	jmc	1.1	criteria being met}.\\
127			\fbox{
128			\begin{minipage}{5.0in}
129			{\it S/R CG2D}~({\it cg2d.F})
130			\end{minipage}
131			}
132
133	jmc	1.4	\item Line PUT_LINE_NB:cg2dTargetResidual=,
134	jmc	1.1	\begin{verbatim}
135			cg2dTargetResidual=1.E-13,
136			\end{verbatim}
137			Sets the tolerance which the two-dimensional, conjugate
138	jmc	1.4	gradient solver will use to test for convergence in equation
139	jmc	1.1	%- note: Description of Conjugate gradient method (& related params) is missing
140			% in the mean time, substitute this eq ref:
141	jmc	1.4	\ref{eq:elliptic-backward-free-surface} %\ref{eq:congrad_2d_resid}
142	jmc	1.1	to $1 \times 10^{-13}$.
143	jmc	1.4	Solver will iterate until tolerance falls below this value or until the
144	jmc	1.1	maximum number of solver iterations is reached.\\
145			\fbox{
146			\begin{minipage}{5.0in}
147			{\it S/R CG2D}~({\it cg2d.F})
148			\end{minipage}
149			}
150
151	jmc	1.4	\item Line PUT_LINE_NB:nIter0=,
152	jmc	1.1	\begin{verbatim}
153	mlosch	1.2	nIter0=0,
154	jmc	1.1	\end{verbatim}
155			Sets the starting time for the model internal time counter.
156	jmc	1.4	When set to non-zero this option implicitly requests a
157	jmc	1.1	checkpoint file be read for initial state.
158			By default the checkpoint file is named according to
159	mlosch	1.2	the integer number of time step value \verb+nIter0+.
160			The internal time counter works in seconds. Alternatively,
161			\verb+startTime+ can be set.
162	jmc	1.1
163	jmc	1.4	\item Line PUT_LINE_NB:nTimeSteps=,
164	jmc	1.1	\begin{verbatim}
165	jmc	1.4	nTimeSteps=20,
166	jmc	1.1	\end{verbatim}
167	mlosch	1.2	Sets the time step number at which this simulation will terminate.
168	jmc	1.1	At the end of a simulation a checkpoint file is automatically
169			written so that a numerical experiment can consist of multiple
170	mlosch	1.2	stages. Alternatively \verb+endTime+ can be set.
171	jmc	1.1
172	jmc	1.4	\item Line PUT_LINE_NB:deltaTmom=,
173	jmc	1.1	\begin{verbatim}
174	jmc	1.4	deltaTmom=1800.,
175	jmc	1.1	\end{verbatim}
176	jmc	1.5	Sets the timestep $\Delta t_{v}$ used in the momentum equations to
177	mlosch	1.2	$30~{\rm mins}$.
178	jmc	1.1	%- note: Distord Physics (using different time-steps) is not described
179			% in the mean time, put this section ref:
180			See section \ref{sec:time_stepping}. %\ref{sec:mom_time_stepping}.
181
182			\fbox{
183			\begin{minipage}{5.0in}
184			{\it S/R TIMESTEP}({\it timestep.F})
185			\end{minipage}
186			}
187
188	jmc	1.4	\item Line PUT_LINE_NB:tauCD=,
189	jmc	1.1	\begin{verbatim}
190			tauCD=321428.,
191			\end{verbatim}
192	jmc	1.4	Sets the D-grid to C-grid coupling time scale $\tau_{CD}$
193	jmc	1.1	used in the momentum equations.
194			%- note: description of CD-scheme pkg (and related params) is missing;
195			% in the mean time, comment out this ref.
196			%See section \ref{sec:cd_scheme}.
197
198			\fbox{
199			\begin{minipage}{5.0in}
200			{\it S/R INI\_PARMS}({\it ini\_parms.F})\\
201			{\it S/R MOM\_FLUXFORM}({\it mom\_fluxform.F})
202			\end{minipage}
203			}
204
205	jmc	1.4	\item Lines PUT_LINE_NB:deltaTtracer=--PUT_LINE_NB:deltaTfreesurf=,
206	jmc	1.1	\begin{verbatim}
207	mlosch	1.2	deltaTtracer=86400.,
208			deltaTClock = 86400.,
209			deltaTfreesurf= 86400.,
210			\end{verbatim}
211	jmc	1.5	Sets the default timestep, $\Delta t_{\theta}$, for tracer equations
212	mlosch	1.2	and implicit free surface equations to
213			$24~{\rm hours}$.
214			% - note: Distord Physics (using different time-steps) is not
215			% described in the mean time, put this section ref:
216	jmc	1.1	See section \ref{sec:time_stepping}. %\ref{sec:tracer_time_stepping}.
217
218			\fbox{
219			\begin{minipage}{5.0in}
220			{\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F})
221			\end{minipage}
222			}
223
224	jmc	1.4	\item Line PUT_LINE_NB:bathyFile=,
225	jmc	1.1	\begin{verbatim}
226	mlosch	1.2	bathyFile='bathymetry.bin'
227	jmc	1.1	\end{verbatim}
228			This line specifies the name of the file from which the domain
229			bathymetry is read. This file is a two-dimensional ($x,y$) map of
230	jmc	1.4	depths. This file is assumed to contain 32-bit binary numbers
231			giving the depth of the model at each grid cell, ordered with the x
232	jmc	1.1	coordinate varying fastest. The points are ordered from low coordinate
233			to high coordinate for both axes. The units and orientation of the
234			depths in this file are the same as used in the MITgcm code. In this
235			experiment, a depth of $0m$ indicates a solid wall and a depth
236	mlosch	1.2	of $<0m$ indicates open ocean.
237
238	jmc	1.1
239	jmc	1.4	\item Lines PUT_LINE_NB:zonalWindFile=--PUT_LINE_NB:meridWindFile=,
240	mlosch	1.2	\begin{verbatim}
241			zonalWindFile='trenberth_taux.bin'
242			meridWindFile='trenberth_tauy.bin'
243			\end{verbatim}
244			These lines specify the names of the files from which the x- and y-
245			direction surface wind stress is read. These files are also
246			three-dimensional ($x,y,time$) maps and are enumerated and formatted
247	jmc	1.4	in the same manner as the bathymetry file.
248	jmc	1.1	\end{itemize}
249
250			\noindent other lines in the file {\it input/data} are standard values
251			that are described in the MITgcm Getting Started and MITgcm Parameters
252			notes.
253
254			\begin{small}
255			\input{s_examples/global_oce_latlon/input/data}
256			\end{small}
257