--- manual/s_ecco/text/ecco.tex	2016/09/18 21:19:54	1.2
+++ manual/s_ecco/text/ecco.tex	2016/09/21 01:28:57	1.3
@@ -6,7 +6,7 @@
 
 \def\mitgcmCheckpointVersion{65x}
 
-The functionalities implemented in \texttt{pkg/ecco} are: (1) output time-averaged model fields to compare with gridded data sets; (2) compute normalized model-data distances or cost functions. The former is achieved as the model runs forwards in time whereas the latter occurs after time-integration has completed. Following \cite{for-eta:15} the resulting `cost function' is formulated generically as
+The functionalities implemented in \texttt{pkg/ecco} are: (1) output time-averaged model fields to compare with gridded data sets; (2) compute normalized model-data distances (i.e., cost functions); (3) compute averages and transports (i.e., integrals). The former is achieved as the model runs forwards in time whereas the others occur after time-integration has completed. Following \cite{for-eta:15} the total cost function is formulated generically as
 \begin{align} 
 	\mathcal{J}(\vec{u}) &= \sum_i \alpha_i \left(\vec{d}_i^T R_i^{-1} \vec{d}_i\right) + \sum_j \beta_j \vec{u}^T\vec{u}, \label{eq:Jtotal} \\
 	\vec{d}_i &= \mathcal{P}(\vec{m}_i - \vec{o}_i), \label{eq:Jposproc} \\
@@ -14,7 +14,7 @@
 	\vec{v}	  &= \mathcal{Q}(\vec{u}), \label{eq:Upreproc} \\
 	\vec{u}	  &= \mathcal{R}(\vec{u}') \label{eq:Uprecond}
 \end{align}
-using symbols defined in table~\ref{tbl:gencost_symbols}. Per Eq.~\eqref{eq:Jpreproc} model counterparts ($\vec{m}_i$) to observational data ($\vec{o}_i$) derive from adjustable model parameters ($\vec{v}$) through the model dynamics integration ($\mathcal{M}$), diagnostic calculations ($\mathcal{D}$), and averaging in space and time ($\mathcal{S}$). Alternatively $\mathcal{S}$ stands for subsampling in space and time (section~\ref{sec:pkg:profiles}). Plain model-data misfits ($\vec{m}_i-\vec{o}_i$) can be penalized directly in Eq.~\eqref{eq:Jtotal} but penalized misfits ($\vec{d}_i$) more generally derive from $\vec{m}_i-\vec{o}_i$ through the generic $\mathcal{P}$ post-processor (Eq. \eqref{eq:Jposproc}). Eqs.~\eqref{eq:Upreproc}-\eqref{eq:Uprecond} pertain to model control parameter adjustment capabilities described in section~\ref{sec:pkg:ctrl}.
+using symbols defined in table~\ref{tbl:gencost_symbols}. Per Eq.~\eqref{eq:Jpreproc} model counterparts ($\vec{m}_i$) to observational data ($\vec{o}_i$) derive from adjustable model parameters ($\vec{v}$) through model dynamics integration ($\mathcal{M}$), diagnostic calculations ($\mathcal{D}$), and averaging in space and time ($\mathcal{S}$). Alternatively $\mathcal{S}$ stands for subsampling in space and time (section~\ref{sec:pkg:profiles}). Plain model-data misfits ($\vec{m}_i-\vec{o}_i$) can be penalized directly in Eq.~\eqref{eq:Jtotal} but penalized misfits ($\vec{d}_i$) more generally derive from $\vec{m}_i-\vec{o}_i$ through the generic $\mathcal{P}$ post-processor (Eq. \eqref{eq:Jposproc}). Eqs.~\eqref{eq:Upreproc}-\eqref{eq:Uprecond} pertain to model control parameter adjustment capabilities described in section~\ref{sec:pkg:ctrl}.
 
 \begin{table}[!ht]
 \centering
@@ -38,9 +38,9 @@
 \label{tbl:gencost_symbols}
 \end{table}
 
-\subsection{Generic Cost Function Terms} \label{costgen}
+\subsection{Generic Cost Function} \label{costgen}
 
-The parameters available for configuring generic cost terms in \texttt{data.ecco} are given in table~\ref{tbl:gencost_ecco_params} and examples of possible specifications are available in:
+The parameters available for configuring generic cost function terms in \texttt{data.ecco} are given in table~\ref{tbl:gencost_ecco_params} and examples of possible specifications are available in:
 \begin{itemize}
 \itemsep0em
 \item MITgcm\_contrib/verification\_other/global\_oce\_cs32/input/data.ecco
@@ -49,16 +49,15 @@
 \end{itemize}
  
  \noindent
-The gridded observation file name is specified by \texttt{gencost\_datafile}. Observational time series may be provided as on big file or split into yearly files finishing in \texttt{`\_1992'}, \texttt{`\_1993'}, etc. The corresponding $\vec{m}_i$ physical variable is specified via the \texttt{gencost\_barfile} root (see table~\ref{tbl:gencost_ecco_barfile}). A file named as specified by \texttt{gencost\_barfile} gets created where averaged fields are written progressively as the model steps forward in time. After the final time step this file is re-read by \texttt{cost\_generic.F} to compute the cost function. If \texttt{gencost\_outputlevel} = 1 then \texttt{cost\_generic.F} outputs model-data misfit fields (i.e., $\vec{d}_i$) to a file which name starts with `misfit\_' for offline analysis and visualization.
+The gridded observation file name is specified by \texttt{gencost\_datafile}. Observational time series may be provided as on big file or split into yearly files finishing in `\_1992', `\_1993', etc. The corresponding $\vec{m}_i$ physical variable is specified via the \texttt{gencost\_barfile} root (see table~\ref{tbl:gencost_ecco_barfile}). A file named as specified by \texttt{gencost\_barfile} gets created where averaged fields are written progressively as the model steps forward in time. After the final time step this file is re-read by \texttt{cost\_generic.F} to compute the corresponding cost function term. If \texttt{gencost\_outputlevel} = 1 and \texttt{gencost\_name}=`foo' then \texttt{cost\_generic.F} outputs model-data misfit fields (i.e., $\vec{d}_i$) to a file named `misfit\_foo.data' for offline analysis and visualization.
 
-In the current implementation, model-data error covariance matrices $R_i$ omit non-diagonal terms. Specifying $R_i$ thus boils down to providing uncertainty fields ($\sigma_i$ such that $R_i=\sigma_i^2$) in a file specified via \texttt{gencost\_errfile}. By default $\sigma_i$ is assumed to be time-invariant but a $\sigma_i$ time series of the same length as $\vec{o}_i$ time series can be provided using the \texttt{variaweight} option (table~\ref{tbl:gencost_ecco_preproc}). By default cost functions are quadratic but $\vec{d}_i^T R_i^{-1} \vec{d}_i$ can be replaced with $R_i^{-1/2} \vec{d}_i$ using the \texttt{nosumsq} option (table~\ref{tbl:gencost_ecco_preproc}). 
+In the current implementation, model-data error covariance matrices $R_i$ omit non-diagonal terms. Specifying $R_i$ thus boils down to providing uncertainty fields ($\sigma_i$ such that $R_i=\sigma_i^2$) in a file specified via \texttt{gencost\_errfile}. By default $\sigma_i$ is assumed to be time-invariant but a $\sigma_i$ time series of the same length as the $\vec{o}_i$ time series can be provided using the \texttt{variaweight} option (table~\ref{tbl:gencost_ecco_preproc}). By default cost functions are quadratic but $\vec{d}_i^T R_i^{-1} \vec{d}_i$ can be replaced with $R_i^{-1/2} \vec{d}_i$ using the \texttt{nosumsq} option (table~\ref{tbl:gencost_ecco_preproc}). 
 
-In principle, any averaging frequency should be possible, but only \texttt{`day'}, \texttt{`month'}, \texttt{`step'}, and \texttt{`const'} are implemented for \texttt{gencost\_avgperiod}. If two different averaging frequencies are needed for the same variable in separate cost function terms (e.g., daily and monthly) then an extension starting with `\_' should be added to \texttt{gencost\_barfile} (such as `\_day' and `\_mon').
-\footnote{ecco\_check may be missing a test for conflicting names.} If two cost function terms use the same variable and periodicity, however, then using a common \texttt{gencost\_barfile} saves disk space. 
+In principle, any averaging frequency should be possible, but only {`day'}, {`month'}, {`step'}, and {`const'} are implemented for \texttt{gencost\_avgperiod}. If two different averaging frequencies are needed for a variable used in multiple cost function terms (e.g., daily and monthly) then an extension starting with `\_' should be added to \texttt{gencost\_barfile} (such as `\_day' and `\_mon'). \footnote{ecco\_check may be missing a test for conflicting names...} If two cost function terms use the same variable and frequency, however, then using a common \texttt{gencost\_barfile} saves disk space. 
 
-Climatologies of $\vec{m}_i$ can be formed from the time series of model averages in order to compare with climatologies of $\vec{o}_i$ by activating the \texttt{`clim'} option via \texttt{gencost\_preproc} and setting the corresponding \texttt{gencost\_preproc\_i}  integer parameter to the number of records (i.e., months, days, or time steps) per climatological cycle. The generic post-processor ($\mathcal{P}$ in Eq.~\eqref{eq:Jposproc}) also allows model-data misfits to be, for example, smoothed in space by setting \texttt{gencost\_posproc} to \texttt{`smooth'}. Other options associated with the computation of Eq.~\eqref{eq:Jtotal} are summarized in table~\ref{tbl:gencost_ecco_preproc} and further discussed below. Multiple \texttt{gencost\_preproc} / \texttt{gencost\_posproc} options may be specified per cost term. 
+Climatologies of $\vec{m}_i$ can be formed from the time series of model averages in order to compare with climatologies of $\vec{o}_i$ by activating the `clim' option via \texttt{gencost\_preproc} and setting the corresponding \texttt{gencost\_preproc\_i}  integer parameter to the number of records (i.e., a \# of months, days, or time steps) per climatological cycle. The generic post-processor ($\mathcal{P}$ in Eq.~\eqref{eq:Jposproc}) also allows model-data misfits to be, for example, smoothed in space by setting \texttt{gencost\_posproc} to {`smooth'} and specifying the smoother parameters via \texttt{gencost\_posproc\_c} and \texttt{gencost\_posproc\_i} (see table~\ref{tbl:gencost_ecco_preproc}). Other options associated with the computation of Eq.~\eqref{eq:Jtotal} are summarized in table~\ref{tbl:gencost_ecco_preproc} and further discussed below. Multiple \texttt{gencost\_preproc} / \texttt{gencost\_posproc} options may be specified per cost term. 
 
-In general the specification of \texttt{gencost\_name} is optional, has no impact on the end-result, and only serves to identify cost function terms in model outputs (STDOUT.0000, STDERR.0000, costfunction000, misfit*.data). Exceptions listed in table~\ref{tbl:gencost_ecco_name} activate alternative cost function codes (in place of \texttt{cost\_generic.F}) described in the following subsections. The specification of \texttt{gencost\_mask} allows the user to specify whether the gridded data input and model counterparts are located at tracer points (`c'; the default) or velocity points (`w' or `s'). However the `c' option (not `w' or `s') should be used when gridded velocity data is provided as zonal/meridional components at tracer points (e.g., for all vector cases listed in table~\ref{tbl:gencost_ecco_barfile}). 
+In general the specification of \texttt{gencost\_name} is optional, has no impact on the end-result, and only serves to distinguish between cost function terms amongst the model output (STDOUT.0000, STDERR.0000, costfunction000, misfit*.data). Exceptions listed in table~\ref{tbl:gencost_ecco_name} however activate alternative cost function codes (in place of \texttt{cost\_generic.F}) described in section~\ref{v4custom}. The specification of \texttt{gencost\_mask}\footnote{This should be renamed \texttt{gencost\_loc} or \texttt{gencost\_point}...} allows the user to specify whether the gridded data input and model counterparts are located at tracer points (`c'; the default) or velocity points (`w' or `s'). However the `c' option (not `w' or `s') should be used when gridded velocity data is provided as zonal/meridional components at tracer points (e.g., for all vector cases listed in table~\ref{tbl:gencost_ecco_barfile}). 
 
 \begin{table}[!ht]
 \centering
@@ -90,14 +89,8 @@
 \texttt{gencost\_startdate2} 	&	integer			&	Start date of observations (HHMMSS)				\\
 \texttt{gencost\_is3d}		&	logical 		&	Needs to be true for 3D fields \\
 \hline
-\texttt{gencost\_smooth2Ddiffnbt} &integer		&	Smoother \# of time steps (sec.~\ref{v4custom} only)
-\\
-\texttt{gencost\_scalefile}	&	character(*)	&	Smoothing scale file (sec.~\ref{v4custom} only)
-\\
-\texttt{gencost\_nrecperiod} 	&	integer		&	Deprecated	\\
-\texttt{gencost\_timevaryweight}&	logical 		&	Deprecated	\\
-\texttt{gencost\_enddate1} 		&	integer	&	Not fully implemented \\
-\texttt{gencost\_enddate2} 		&	integer	&	Not fully implemented \\
+\texttt{gencost\_enddate1} 		&	integer	&	Not fully implemented (sec.~\ref{v4custom} only)\\
+\texttt{gencost\_enddate2} 		&	integer	&	Not fully implemented (sec.~\ref{v4custom} only)\\
 \end{tabular}
 \caption{Parameters in \texttt{ecco\_gencost\_nml} namelist in \texttt{data.ecco}. All parameters are vectors of length \texttt{NGENCOST} (the \# of available cost terms) except for \texttt{gencost\_*proc*} are arrays of size \texttt{NGENPPROC}$\times$\texttt{NGENCOST}. Notes: \texttt{gencost\_is3d} will automatically be reset to true in cases listed as 3D in table~\ref{tbl:gencost_ecco_barfile}; the last group of parameters should be disregarded except for the section~\ref{v4custom} special cases.}
 \label{tbl:gencost_ecco_params}
@@ -134,7 +127,7 @@
 \texttt{m\_geothermalflux}		&	geothermal heat flux			& constant \\ 
 \texttt{m\_bottomdrag}		&	bottom drag				& constant \\
 \end{tabular}
-\caption{Implemented \texttt{gencost\_barfile} options (as of checkpoint \mitgcmCheckpointVersion) that can be used via \texttt{cost\_generic.F} as explained in section~\ref{costgen}. An extension starting with `\_' can be appended at the end of the variable name to distinguish between separate cost function terms. Notes: here `zonal' / `meridional' are to be taken literally (unlike in other parts of the manual) and these components are computed on tracer points (not on the C-grid vector points); the `m\_eta' formula depends on the \texttt{ATMOSPHERIC\_LOADING} and \texttt{ALLOW\_PSBAR\_STERIC} compile time options and `useRealFreshWaterFlux' run time parameter.}
+\caption{Implemented \texttt{gencost\_barfile} options (as of checkpoint \mitgcmCheckpointVersion) that can be used via \texttt{cost\_generic.F} (section~\ref{costgen}). An extension starting with `\_' can be appended at the end of the variable name to distinguish between separate cost function terms. Notes: here `zonal' / `meridional' are to be taken literally (unlike in other parts of the manual) and these components are centered (i.e., not at the staggered C-grid velocity points); the `m\_eta' formula depends on the \texttt{ATMOSPHERIC\_LOADING} and \texttt{ALLOW\_PSBAR\_STERIC} compile time options and `useRealFreshWaterFlux' run time parameter.}
 \label{tbl:gencost_ecco_barfile}
 \end{table}
 
@@ -159,22 +152,37 @@
 
 \clearpage
 
-\subsection{Custom Cost Function Terms} \label{v4custom}
+\subsection{Generic Integral Function} \label{intgen}
 
-This section pertains to the special cases of \texttt{cost\_gencost\_bpv4.F}, \texttt{cost\_gencost\_seaicev4.F}, \texttt{cost\_gencost\_sshv4.F}, and \texttt{cost\_gencost\_sstv4.F}. It is very much a work in progress. If \texttt{gencost\_name} is either `sshv4-mdt' or `sshv4-lsc' then additional smoothing arguments can be specified via \texttt{gencost\_scalefile} (file containing the smoothing scale field) and \texttt{gencost\_smooth2Ddiffnbt} (number of smoothing time steps).\footnote{These parameters are otherwise not used and \texttt{gencost\_posproc*} will eventually be used instead.}
+The functionality described in this section is operated by \texttt{cost\_gencost\_boxmean.F}. It is primarily aimed at obtaining a mechanistic understanding of a chosen physical variable via adjoint sensitivity computations (see Chapter~\ref{chap:autodiff}) as done for example in \cite{maro-eta:99,heim-eta:11,fuku-etal:14}. Thus the quadratic term in Eq.~\ref{eq:Jtotal} ($\vec{d}_i^T R_i^{-1} \vec{d}_i$) is by default replaced with a $d_i$ scalar\footnote{The quadratic option in fact does not yet exist in \texttt{cost\_gencost\_boxmean.F}...} that derives from model fields through a generic integral formula (Eq.~\ref{eq:Jpreproc}). The specification of \texttt{gencost\_barfile} again selects the physical variable type. Current valid options to use \texttt{cost\_gencost\_boxmean.F} are reported in table~\ref{tbl:genint_ecco_barfile}. A suffix starting with \texttt{`\_'} can again be appended to \texttt{gencost\_barfile}.
+% and the basic averaging  frequency is specified via \texttt{gencost\_avgperiod}. 
 
-\subsection{Boxmean Generic Cost Function} \label{genboxmean}
+The integral formula is defined by masks provided via binary files which names are specified via \texttt{gencost\_errfile}. There are two cases: (1) if \texttt{gencost\_errfile = `foo\_mask'} and \texttt{gencost\_barfile} is of the `m\_boxmean*' type then the model will search for horizontal, vertical, and temporal mask files  named \texttt{foo\_maskC}, \texttt{foo\_maskK}, and \texttt{foo\_maskT}; (2) if instead \texttt{gencost\_barfile} is of the `m\_horflux\_*' type then the model will search for \texttt{foo\_maskW}, \texttt{foo\_maskS}, \texttt{foo\_maskK}, and \texttt{foo\_maskT}. 
 
-This section pertains to the special case of cost\_gencost\_boxmean.F and is very much a work in progress. The boxmean generic cost function penalizes the mean of a model field over a ``box" (non quadratic cost function). To use this cost function, set \texttt{gencost\_name} to `boxmean' followed by a suffix starting with \texttt{`\_'}. The model field of interest is specified by \texttt{gencost\_barfile}. Currently valid options are \texttt{m\_boxmean\_theta}, \texttt{m\_boxmean\_salt}, and \texttt{m\_boxmean\_eta}. The ``box'' is defined by a mask of ones and zeros read from files whose root is given by the string \texttt{gencost\_errfile}. Different files contain the horizontal, vertical, and temporal masks; these files are distinguished by the suffixes \texttt{`C'}, \texttt{`K'}, and \texttt{`T'}, respectively. For example, if \texttt{gencost\_errfile = `foo\_mask'}, then the horizontal, vertical, and temporal mask files are named \texttt{foo\_maskC}, \texttt{foo\_maskK}, and \texttt{foo\_maskT}. Note that the horizontal mask can have an arbitrary shape; the ``box'' is not necessarily rectangular.
+The `C' mask or the `W' / `S' masks are expected to be two-dimensional fields. The `K' and T masks (both optional; all 1 by default) are expected to be one-dimensional vectors. The`K' vector length should match Nr. The `T' vector length should match the \# of records that the specification of \texttt{gencost\_avgperiod} implies but there is no restriction on its values. In case \#1 (`m\_boxmean*') the `C' and `K' masks should consists of +1 and 0 values and a volume average will be computed accordingly. In case \#2 (`m\_horflux*') the `W', `S', and `K' masks should consists of +1, -1, and 0 values and an integrated horizontal transport (or overturn) will be computed accordingly. 
 
-\subsection{Transport Generic Cost Function} \label{gentrsp}
+\begin{table}[!ht]
+\centering
+\begin{tabular}{lll}
+variable name				&	description						&	remarks \\ \hline\hline
+\texttt{m\_boxmean\_theta}	&	mean of theta over box			& specify box \\
+\texttt{m\_boxmean\_salt}		&	mean of salt over box			& specify box \\
+\texttt{m\_boxmean\_eta}		&	mean of SSH over box			& specify box \\
+\hline
+\texttt{m\_horflux\_vol}		&	volume transport through section	& specify transect \\ 
+\end{tabular}
+\caption{Implemented \texttt{gencost\_barfile} options (as of checkpoint \mitgcmCheckpointVersion) that can be used via \texttt{cost\_gencost\_boxmean.F} (section~\ref{intgen}).}
+\label{tbl:genint_ecco_barfile}
+\end{table}
 
-This section pertains to the special case of cost\_gencost\_transp.F and is very much a work in progress. The transport generic cost function penalizes a transport of volume, heat, or salt through a specified section (non quadratic cost function). To use this cost function, set \texttt{gencost\_name = `transp*'}, where \texttt{*} is an optional suffix starting with \texttt{`\_'}, and set \texttt{gencost\_barfile} to one of \texttt{m\_trVol}, \texttt{m\_trHeat}, and \texttt{m\_trSalt}. The section is specified via masks of +1, -1, and 0 values at `w' and `s' velocity points. The mask files name root is given by the string \texttt{gencost\_errfile}, with the suffixes \texttt{`W'} and \texttt{`S'} denoting the ``w'' and ``s'' points, respectively. Temporal and vertical masks remain to be implemented, although temporal masking can already be achieved using the \texttt{variaweight} post-processor.
+\subsection{Custom Cost Functions} \label{v4custom}
+
+This section (very much a work in progress...) pertains to the special cases of \texttt{cost\_gencost\_bpv4.F}, \texttt{cost\_gencost\_seaicev4.F}, \texttt{cost\_gencost\_sshv4.F}, \texttt{cost\_gencost\_sstv4.F}, and \texttt{cost\_gencost\_transp.F}. The cost\_gencost\_transp.F function can be used to compute a transport of volume, heat, or salt through a specified section (non quadratic cost function). To this end one sets \texttt{gencost\_name = `transp*'}, where \texttt{*} is an optional suffix starting with \texttt{`\_'}, and set \texttt{gencost\_barfile} to one of \texttt{m\_trVol}, \texttt{m\_trHeat}, and \texttt{m\_trSalt}. 
 
 \begin{table}[!ht]
 \centering
 \begin{tabular}{lll}
-name						&	description					&	remarks \\ \hline\hline
+name					&	description				&	remarks \\ \hline\hline
 \texttt{sshv4-mdt}			&	sea surface height			&	mean dynamic topography (SSH - geod) \\
 \texttt{sshv4-tp}				&	sea surface height			&	Along-Track Topex/Jason SLA (level 3) \\
 \texttt{sshv4-ers}			&	sea surface height			&	Along-Track ERS/Envisat SLA (level 3)\\
@@ -187,33 +195,17 @@
 \texttt{si4-cons}				&	sea ice concentration		& 	needs sea-ice adjoint (level 4)\\
 \texttt{si4-deconc}			&	model sea ice deficiency		& 	proxy penalty (from the above)\\
 \texttt{si4-exconc}			&	model sea ice excess		& 	proxy penalty (from the above)\\ \hline
-\texttt{boxmean}			&	mean over a box			&	see section~\ref{genboxmean}  \\
-\texttt{transp}				&	transport across section		&	see section~\ref{gentrsp} \\ 
+\texttt{transp\_trVol}			&	volume transport			& specify section as in section~\ref{intgen}\\ 
+\texttt{transp\_trHeat}		&	heat transport				& specify section as in section~\ref{intgen} \\ 
+\texttt{transp\_trSalt}			&	salt transport				& specify section as in section~\ref{intgen} \\ 
 \end{tabular}
-\caption{Pre-defined \texttt{gencost\_name} special cases (sections~\ref{v4custom}, \ref{genboxmean}, \ref{gentrsp}).}
+\caption{Pre-defined \texttt{gencost\_name} special cases (as of checkpoint \mitgcmCheckpointVersion; section~\ref{v4custom}).}
 \label{tbl:gencost_ecco_name}
 \end{table}
 
-\begin{table}[!ht]
-\centering
-\begin{tabular}{lll}
-variable name				&	description						&	remarks \\ \hline\hline
-\texttt{m\_trVol}			&	volume transport				& three-dimensional, specify section \\ 
-\texttt{m\_trHeat}			&	heat transport					& three-dimensional, specify section \\ 
-\texttt{m\_trSalt}			&	salt transport					& three-dimensional, specify section \\ 
-\texttt{m\_boxmean\_theta}	&	mean of theta over box			& specify box \\
-\texttt{m\_boxmean\_salt}	&	mean of salt over box			& specify box \\
-\texttt{m\_boxmean\_eta}	&	mean of SSH over box			& specify box 
-\end{tabular}
-\caption{Implemented \texttt{gencost\_barfile} options (as of checkpoint \mitgcmCheckpointVersion) that can be used via \texttt{cost\_gencost\_boxmean.F} or \texttt{cost\_gencost\_transp.F} (see sections~\ref{genboxmean} and ~\ref{gentrsp}.}
-\label{tbl:gencost_ecco_barfile_custom}
-\end{table}
-
-
-
 \subsection{Key Routines}
 
-TBA... \texttt{cost\_generic.F}, \texttt{ecco\_check.F}, \texttt{ecco\_phys.F}, \texttt{ecco\_summary.F}, \texttt{ecco\_readparms.F}, ...
+TBA... \texttt{cost\_generic.F}, \texttt{cost\_gencost\_boxmean.F}, \texttt{ecco\_phys.F}, \texttt{cost\_gencost\_customize.F}, \texttt{cost\_averagesfields.F} ... \texttt{ecco\_readparms.F}, \texttt{ecco\_check.F}, \texttt{ecco\_summary.F}, ...
 
 \subsection{Compile Options}
 
