/[MITgcm]/manual/s_autodiff/doc_ad_examples.tex

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-revision 1.4 by adcroft,
Wed Apr 24 19:23:58 2002 UTC
+revision 1.5 by adcroft,
Thu May 16 15:54:37 2002 UTC
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  %**********************************************************************
  \section{Sensitivity of Air-Sea Exchange to Tracer Injection Site }
+ \label{www:tutorials}
  \label{sect:eg-simple-tracer-adjoint}
  \label{sec_ad_setup_ex}
  \label{sect:tutorialIII}
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 The AD-relevant hooks in the code are sk
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 The AD-relevant hooks in the code are sk
  \ref{fig:adthemodel}, \ref{fig:adthemain}.
  \subsection{Overview of the experiment}
+ \label{www:tutorials}
  We describe an adjoint sensitivity analysis of out-gassing from
  the ocean into the atmosphere of a carbon-like tracer injected
  into the ocean interior (see \cite{hil-eta:01}).
  \subsubsection{Passive tracer equation}
+ \label{www:tutorials}
  For this work the MITGCM was augmented with a thermodynamically
  inactive tracer, $C$. Tracer residing in the ocean
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 As source we choose a constant in time i
+Line 62 
 As source we choose a constant in time i
  $ S = 1 \,\, {\rm mol / s}$.
  \subsubsection{Model configuration}
+ \label{www:tutorials}
  The model configuration employed has a constant
  $4^\circ \times 4^\circ$ resolution horizontal grid and realistic
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 fresh-water forcing the model reproduces
+Line 74 
 fresh-water forcing the model reproduces
  features of the ocean general circulation.
  \subsubsection{Out-gassing cost function}
+ \label{www:tutorials}
  To quantify and understand out-gassing due to injections of $C$
  in eqn. (\ref{carbon_ddt}),
-Line 96 
 and regions in which $CO_2$ injections w
+Line 101 
 and regions in which $CO_2$ injections w
  sequestered within the ocean.
  \subsection{Code configuration}
+ \label{www:tutorials}
  The model configuration for this experiment resides under the
  directory {\it verification/carbon/}.
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 Below we describe the customizations of
+Line 177 
 Below we describe the customizations of
  specific to this experiment.
  \subsubsection{File {\it .genmakerc}}
+ \label{www:tutorials}
  This file overwrites default settings of {\it genmake}.
  In the present example it is used to switch on the following
  packages which are related to automatic differentiation
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 Other packages which are not needed are
+Line 187 
 Other packages which are not needed are
  \hspace*{4ex} {\tt set DISABLE=( aim obcs zonal\_filt shap\_filt cal exf )}
  \subsubsection{File {\it COST\_CPPOPTIONS.h,  CTRL\_OPTIONS.h}}
+ \label{www:tutorials}
  These files used to contain package-specific CPP-options
  (see Section \ref{???}).
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 To retain the modularity, the files have
+Line 197 
 To retain the modularity, the files have
  the standard include of the {\it CPP\_OPTIONS.h} file.
  \subsubsection{File {\it CPP\_EEOPTIONS.h}}
+ \label{www:tutorials}
  This file contains 'wrapper'-specific CPP options.
  It only needs to be changed if the code is to be run
  in a parallel environment (see Section \ref{???}).
  \subsubsection{File {\it CPP\_OPTIONS.h}}
+ \label{www:tutorials}
  This file contains model-specific CPP options
  (see Section \ref{???}).
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 adjoint-generated gradient.
+Line 236 
 adjoint-generated gradient.
  The gradient check package is further described in Section ???.
  \subsubsection{File {\it ECCO\_OPTIONS.h}}
+ \label{www:tutorials}
  The CPP options of several AD-related packages are grouped
  in this file:
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 isopycnal diffusivity \\
+Line 319 
 isopycnal diffusivity \\
  \end{itemize}
  \subsubsection{File {\it SIZE.h}}
+ \label{www:tutorials}
  The file contains the grid point dimensions of the forward
  model. It is identical to the {\it verification/exp2/}: \\
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 with standard overlap dimensioning
+Line 332 
 with standard overlap dimensioning
  {\tt OLx = OLy = 3}.
  \subsubsection{File {\it adcommon.h}}
+ \label{www:tutorials}
  This file contains common blocks of some adjoint variables
  that are generated by TAMC.
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 The header file is enabled via the CPP-o
+Line 365 
 The header file is enabled via the CPP-o
  {\bf ALLOW\_AUTODIFF\_MONITOR}.
  \subsubsection{File {\it tamc.h}}
+ \label{www:tutorials}
  This routine contains the dimensions for TAMC checkpointing
  and some indices relevant for storing ky computations.
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 The following parameters may be worth de
+Line 409 
 The following parameters may be worth de
  ~
  \subsubsection{File {\it makefile}}
+ \label{www:tutorials}
  This file contains all relevant parameter flags and
  lists to run TAMC or TAF.
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 adjoint routines refer to the TAMC defau
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 adjoint routines refer to the TAMC defau
  \subsubsection{The input parameter files}
+ \label{www:tutorials}
  \paragraph{File {\it data}}
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 surface boundary values (surface wind st
+Line 529 
 surface boundary values (surface wind st
  Contains model state after model spinup.
  \subsection{Compiling the model and its adjoint}
+ \label{www:tutorials}
  The built process of the adjoint model is slightly more
  complex than that of compiling the forward code.

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