--- manual/s_examples/tracer_adjsens/doc_ad_examples.tex	2008/01/15 20:16:44	1.2
+++ manual/s_examples/tracer_adjsens/doc_ad_examples.tex	2010/08/30 23:09:20	1.3
@@ -1,12 +1,12 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/tracer_adjsens/doc_ad_examples.tex,v 1.2 2008/01/15 20:16:44 jmc Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_examples/tracer_adjsens/doc_ad_examples.tex,v 1.3 2010/08/30 23:09:20 jmc Exp $
 % $Name:  $
 
 %**********************************************************************
 \section{Sensitivity of Air-Sea Exchange to Tracer Injection Site }
-\label{www:tutorials}
-\label{sect:eg-simple-tracer-adjoint}
+%\label{www:tutorials}
+\label{sec:eg-simple-tracer-adjoint}
 \label{sec_ad_setup_ex}
-\label{sect:tutorialIII}
+\label{sec:tutorialIII}
 \begin{rawhtml}
 <!-- CMIREDIR:sec_ad_setup_ex: -->
 \end{rawhtml}
@@ -14,6 +14,7 @@
 (in directory: {\it verification/tutorial\_tracer\_adjsens/})
 \end{center}
 %**********************************************************************
+\label{ask_the_author:tracer_adjsens:doc_ad_examples}
 
 MITgcm has been adapted to enable AD using TAMC or TAF.
 The present description, therefore, is specific to the
@@ -26,14 +27,14 @@
 \ref{fig:adthemodel}, \ref{fig:adthemain}.
 
 \subsection{Overview of the experiment}
-\label{www:tutorials}
+%\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}
+%\label{www:tutorials}
 
 For this work MITgcm was augmented with a thermodynamically 
 inactive tracer, $C$. Tracer residing in the ocean 
@@ -68,7 +69,7 @@
 $ S = 1 \,\, {\rm mol / s}$.
 
 \subsubsection{Model configuration}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 The model configuration employed has a constant 
 $4^\circ \times 4^\circ$ resolution horizontal grid and realistic 
@@ -80,7 +81,7 @@
 features of the ocean general circulation. 
 
 \subsubsection{Out-gassing cost function}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 To quantify and understand out-gassing due to injections of $C$
 in eqn. (\ref{carbon_ddt}),
@@ -107,7 +108,7 @@
 sequestered within the ocean.
 
 \subsection{Code configuration}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 The model configuration for this experiment resides under the
 directory {\it verification/carbon/}.
@@ -183,7 +184,7 @@
 specific to this experiment.
 
 \subsubsection{File {\it .genmakerc}}
-\label{www:tutorials}
+%\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
@@ -193,27 +194,27 @@
 \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}
+%\label{www:tutorials}
 
 These files used to contain package-specific CPP-options
-(see Section \ref{???}).
+(see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
 For technical reasons those options have been grouped together
 in the file {\it ECCO\_OPTIONS.h}.
 To retain the modularity, the files have been kept and contain
 the standard include of the {\it CPP\_OPTIONS.h} file.
 
 \subsubsection{File {\it CPP\_EEOPTIONS.h}}
-\label{www:tutorials}
+%\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{???}).
+in a parallel environment (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
 
 \subsubsection{File {\it CPP\_OPTIONS.h}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 This file contains model-specific CPP options
-(see Section \ref{???}).
+(see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
 Most options are related to the forward model setup.
 They are identical to the global steady circulation setup of
 {\it verification/global\_ocean.90x40x15/}.
@@ -242,7 +243,7 @@
 The gradient check package is further described in Section ???.
 
 \subsubsection{File {\it ECCO\_OPTIONS.h}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 The CPP options of several AD-related packages are grouped
 in this file:
@@ -266,7 +267,7 @@
 %
 \hspace*{4ex} {\tt \#define ALLOW\_TAMC\_CHECKPOINTING} \\
 enables the checkpointing feature of TAMC
-(see Section \ref{???}).
+(see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
 In the present example a 3-level checkpointing is implemented.
 The code contains the relevant store directives, common block
 and tape initializations, storing key computation,
@@ -279,16 +280,16 @@
 %
 \hspace*{4ex} {\tt \#define ALLOW\_AUTODIFF\_MONITOOR} \\
 enables the monitoring of intermediate adjoint variables
-(see Section \ref{???}). \\
+(see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}). \\
 %
 \hspace*{4ex} {\tt \#define ALLOW\_DIVIDED\_ADJOINT} \\
 enables adjoint dump and restart
-(see Section \ref{???}).
+(see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
 %
 \item Cost function package: {\it pkg/cost/} \\
 This package contains all relevant routines for
 initializing, accumulating and finalizing the cost function
-(see Section \ref{???}). \\
+(see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}). \\
 \hspace*{4ex} {\tt \#define ALLOW\_COST} \\
 enables all general aspects of the cost function handling,
 in particular the hooks in the forward code for
@@ -325,7 +326,7 @@
 \end{itemize}
 
 \subsubsection{File {\it SIZE.h}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 The file contains the grid point dimensions of the forward
 model. It is identical to the {\it verification/exp2/}: \\
@@ -338,7 +339,7 @@
 {\tt OLx = OLy = 3}.
 
 \subsubsection{File {\it adcommon.h}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 This file contains common blocks of some adjoint variables
 that are generated by TAMC. 
@@ -371,7 +372,7 @@
 {\bf ALLOW\_AUTODIFF\_MONITOR}.
 
 \subsubsection{File {\it tamc.h}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 This routine contains the dimensions for TAMC checkpointing
 and some indices relevant for storing ky computations.
@@ -380,7 +381,7 @@
 %
 \item {\tt \#ifdef ALLOW\_TAMC\_CHECKPOINTING} \\
 3-level checkpointing is enabled, i.e. the timestepping
-is divided into three different levels (see Section \ref{???}).
+is divided into three different levels (see Section \ref{ask_the_author:tracer_adjsens:doc_ad_examples}).
 The model state of the outermost ({\tt nchklev\_3}) and the
 intermediate ({\tt nchklev\_2}) timestepping loop are stored to file
 (handled in {\it the\_main\_loop}).
@@ -415,7 +416,7 @@
 ~
  
 \subsubsection{File {\it makefile}}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 This file contains all relevant parameter flags and
 lists to run TAMC or TAF.
@@ -499,7 +500,7 @@
 
 
 \subsubsection{The input parameter files}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 \paragraph{File {\it data}}
 
@@ -535,7 +536,7 @@
 Contains model state after model spinup.
 
 \subsection{Compiling the model and its adjoint}
-\label{www:tutorials}
+%\label{www:tutorials}
 
 The built process of the adjoint model is slightly more
 complex than that of compiling the forward code.
@@ -657,7 +658,7 @@
 {\small
 \[
 \boxed{
-\begin{split}
+\begin{aligned}
  ~ & \mbox{\tt cd bin} \\
  ~ & \mbox{\tt ln -s ../verification/my\_experiment/code/.genmakerc .} \\
  ~ & \mbox{\tt ln -s ../verification/my\_experiment/code/*.[Fh] .} \\
@@ -669,7 +670,7 @@
  ~ & \hspace*{6ex} \mbox{\tt                 adrestore small\_f allcode admodeltaf/admodeltamc adchange} \\
  ~ & \mbox{\tt cd ../bin} \\
  ~ & \mbox{\tt make} \\
-\end{split}
+\end{aligned}
 }
 \]
 }