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gforget |
1.1 |
\section{ECCO: model-data comparisons using gridded data sets} |
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\label{sec:pkg:ecco} |
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\begin{rawhtml} |
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<!-- CMIREDIR:package_ecco: --> |
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\end{rawhtml} |
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\def\mitgcmCheckpointVersion{65x} |
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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 |
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\begin{align} |
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\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} \\ |
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\vec{d}_i &= \mathcal{P}(\vec{m}_i - \vec{o}_i), \label{eq:Jposproc} \\ |
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\vec{m}_i &= \mathcal{S}\mathcal{D}\mathcal{M}(\vec{v}), \label{eq:Jpreproc} \\ |
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\vec{v} &= \mathcal{Q}(\vec{u}), \label{eq:Upreproc} \\ |
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\vec{u} &= \mathcal{R}(\vec{u}') \label{eq:Uprecond} |
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\end{align} |
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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}. |
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\begin{table}[!ht] |
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\centering |
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\begin{tabular}{rl} |
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symbol & definition \\ \hline |
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$\vec{u}$ & vector of nondimensional control variables \\ |
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$\vec{v}$ & vector of dimensional control variables \\ |
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$\alpha_i, \beta_j$ & misfit and control cost function multipliers (1 by default) \\ |
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$R_i$ & data error covariance matrix ($R_i^{-1}$ are weights) \\ |
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$\vec{d}_i$ & a set of model-data differences \\ |
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$\vec{o}_i$ & observational data vector \\ |
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$\vec{m}_i$ & model counterpart to $\vec{o}_i$ \\ |
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$\mathcal{P}$ & post-processing operator (e.g., a smoother) \\ |
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$\mathcal{M}$ & forward model dynamics operator \\ |
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$\mathcal{D}$ & diagnostic computation operator \\ |
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$\mathcal{S}$ & averaging/subsampling operator \\ |
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$\mathcal{Q}$ & Pre-processing operator \\ |
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$\mathcal{R}$ & Pre-conditioning operator |
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\end{tabular} |
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\caption{Symbol definitions for pkg/ecco and pkg/ctrl generic cost functions.} |
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\label{tbl:gencost_symbols} |
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\end{table} |
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\subsection{Generic Cost Function Terms} \label{costgen} |
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gforget |
1.2 |
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: |
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1.1 |
\begin{itemize} |
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\itemsep0em |
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\item MITgcm\_contrib/verification\_other/global\_oce\_cs32/input/data.ecco |
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\item MITgcm\_contrib/verification\_other/global\_oce\_cs32/input\_ad.sens/data.ecco |
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\item MITgcm\_contrib/gael/verification/global\_oce\_llc90/input.ecco\_v4/data.ecco |
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\end{itemize} |
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\noindent |
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1.2 |
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. |
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1.1 |
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gforget |
1.2 |
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}). |
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1.1 |
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1.2 |
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'). |
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gforget |
1.1 |
\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. |
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gforget |
1.2 |
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. |
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gforget |
1.1 |
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gforget |
1.2 |
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}). |
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1.1 |
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\begin{table}[!ht] |
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\centering |
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\begin{tabular}{lll} |
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parameter & type & function \\ \hline |
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%\texttt{using\_gencost} & logical & Turns specified generic cost term on. \\ |
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\texttt{gencost\_name} & character(*) & Name of cost term \\ |
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\texttt{gencost\_barfile} & character(*) & File to receive model counterpart $\vec{m}_i$ (see table~\ref{tbl:gencost_ecco_barfile}) \\ |
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\texttt{gencost\_datafile} & character(*) & File containing observational data $\vec{o}_i$ \\ |
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\texttt{gencost\_avgperiod} & character(5) & Averaging period for $\vec{o}_i$ and $\vec{m}_i$ (see text) \\ |
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\texttt{gencost\_outputlevel} & integer & Greater than 0 will output misfit fields\\ |
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\texttt{gencost\_errfile} & character(*) & File containing diagonal of error matrix $R_i$\\ |
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\texttt{mult\_gencost} & real & Multiplier $\alpha_i$ (default: 1) \\ |
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\hline |
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\texttt{gencost\_preproc} & character(*) & Preprocessor names \\ |
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\texttt{gencost\_preproc\_c} & character(*) & Preprocessor character arguments \\ |
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\texttt{gencost\_preproc\_i} & integer(*) & Preprocessor integer arguments \\ |
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\texttt{gencost\_preproc\_r} & real(*) & Preprocessor real arguments \\ |
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\texttt{gencost\_posproc} & character(*) & Post-processor names \\ |
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\texttt{gencost\_posproc\_c} & character(*) & Post-processor character arguments \\ |
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\texttt{gencost\_posproc\_i} & integer(*) & Post-processor integer arguments \\ |
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\texttt{gencost\_posproc\_r} & real(*) & Post-processor real arguments \\ |
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\hline |
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\texttt{gencost\_mask} & character(1) & Location of $\vec{m}_i$\\ |
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\texttt{gencost\_spmin} & real & Data less than this value will be omitted \\ |
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\texttt{gencost\_spmax} & real & Data greater than this value will be omitted \\ |
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\texttt{gencost\_spzero} & real & Data points equal to this value will be omitted \\ |
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\texttt{gencost\_startdate1} & integer & Start date of observations (YYYMMDD) \\ |
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\texttt{gencost\_startdate2} & integer & Start date of observations (HHMMSS) \\ |
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\texttt{gencost\_is3d} & logical & Needs to be true for 3D fields \\ |
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\hline |
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\texttt{gencost\_smooth2Ddiffnbt} &integer & Smoother \# of time steps (sec.~\ref{v4custom} only) |
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\\ |
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\texttt{gencost\_scalefile} & character(*) & Smoothing scale file (sec.~\ref{v4custom} only) |
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\\ |
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\texttt{gencost\_nrecperiod} & integer & Deprecated \\ |
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\texttt{gencost\_timevaryweight}& logical & Deprecated \\ |
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\texttt{gencost\_enddate1} & integer & Not fully implemented \\ |
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\texttt{gencost\_enddate2} & integer & Not fully implemented \\ |
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\end{tabular} |
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\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.} |
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\label{tbl:gencost_ecco_params} |
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\end{table} |
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\begin{table}[!ht] |
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\centering |
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\begin{tabular}{lll} |
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1.2 |
variable name & description & remarks \\ \hline\hline |
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\texttt{m\_eta} & sea surface height & free surface + ice + global steric correction \\ |
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\texttt{m\_sst} & sea surface temperature & first level potential temperature \\ |
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\texttt{m\_sss} & sea surface salinity & first level salinity \\ |
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\texttt{m\_bp} & bottom pressure & phiHydLow\\ |
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\texttt{m\_siarea} & sea-ice area & from pkg/seaice \\ |
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\texttt{m\_siheff} & sea-ice effective thickness & from pkg/seaice \\ |
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\texttt{m\_sihsnow} & snow effective thickness & from pkg/seaice \\ \hline |
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\texttt{m\_theta} & potential temperature & three-dimensional \\ |
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\texttt{m\_salt} & salinity & three-dimensional \\ |
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\texttt{m\_UE} & zonal velocity & three-dimensional \\ |
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\texttt{m\_VN} & meridional velocity & three-dimensional \\ \hline |
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\texttt{m\_ustress} & zonal wind stress & from pkg/exf \\ |
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\texttt{m\_vstress} & meridional wind stress & from pkg/exf\\ |
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\texttt{m\_uwind} & zonal wind & from pkg/exf\\ |
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\texttt{m\_vwind} & meridional wind & from pkg/exf\\ |
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\texttt{m\_atemp} & atmospheric temperature & from pkg/exf\\ |
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\texttt{m\_aqh} & atmospheric specific humidity & from pkg/exf\\ |
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\texttt{m\_precip} & precipitation & from pkg/exf\\ |
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\texttt{m\_swdown} & downward shortwave & from pkg/exf\\ |
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\texttt{m\_lwdown} & downward longwave & from pkg/exf\\ |
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\texttt{m\_wspeed} & wind speed & from pkg/exf\\ \hline |
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\texttt{m\_diffkr} & vertical/diapycnal diffusivity & three-dimensional, constant \\ |
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\texttt{m\_kapgm} & GM diffusivity & three-dimensional, constant \\ |
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\texttt{m\_kapredi} & isopycnal diffusivity & three-dimensional, constant \\ |
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gforget |
1.2 |
\texttt{m\_geothermalflux} & geothermal heat flux & constant \\ |
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\texttt{m\_bottomdrag} & bottom drag & constant \\ |
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gforget |
1.1 |
\end{tabular} |
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gforget |
1.2 |
\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.} |
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gforget |
1.1 |
\label{tbl:gencost_ecco_barfile} |
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\end{table} |
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\begin{table}[!ht] |
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\centering |
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\begin{tabular}{lll} |
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name & description & specs needed via \texttt{gencost\_preproc\_i}, \texttt{\_r}, or \texttt{\_c} \\ \hline\hline |
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\texttt{gencost\_preproc} \\ \hline |
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\texttt{clim} & Use climatological misfits & integer: no.\ of records per climatological cycle \\ |
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\texttt{mean} & Use time mean of misfits & --- \\ |
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\texttt{anom} & Use anomalies from time mean & --- \\ |
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\texttt{variaweight} & Use time-varying weight $W_i$& --- \\ |
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\texttt{nosumsq} & Use linear misfits & --- \\ |
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\texttt{factor} & Multiply $\vec{m}_i$ by a scaling factor & real: the scaling factor \\ \hline \hline |
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\texttt{gencost\_posproc} \\ \hline |
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\texttt{smooth} & Smooth misfits & character: smoothing scale file\\ |
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& & integer: smoother \# of time steps \\ |
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\end{tabular} |
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gforget |
1.2 |
\caption{\texttt{gencost\_preproc} and \texttt{gencost\_posproc} options implemented as of checkpoint \mitgcmCheckpointVersion. Note: the distinction between \texttt{gencost\_preproc} and \texttt{gencost\_posproc} may be revisited in the future.} |
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gforget |
1.1 |
\label{tbl:gencost_ecco_preproc} |
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\end{table} |
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\clearpage |
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\subsection{Custom Cost Function Terms} \label{v4custom} |
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gforget |
1.2 |
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.} |
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1.1 |
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\subsection{Boxmean Generic Cost Function} \label{genboxmean} |
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| 168 |
gforget |
1.2 |
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. |
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gforget |
1.1 |
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\subsection{Transport Generic Cost Function} \label{gentrsp} |
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gforget |
1.2 |
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. |
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gforget |
1.1 |
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\begin{table}[!ht] |
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\centering |
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\begin{tabular}{lll} |
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name & description & remarks \\ \hline\hline |
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gforget |
1.2 |
\texttt{sshv4-mdt} & sea surface height & mean dynamic topography (SSH - geod) \\ |
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\texttt{sshv4-tp} & sea surface height & Along-Track Topex/Jason SLA (level 3) \\ |
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\texttt{sshv4-ers} & sea surface height & Along-Track ERS/Envisat SLA (level 3)\\ |
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\texttt{sshv4-gfo} & sea surface height & Along-Track GFO class SLA (level 3)\\ |
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\texttt{sshv4-lsc} & sea surface height & Large-Scale SLA (from the above)\\ |
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\texttt{sshv4-gmsl} & sea surface height & Global-Mean SLA (from the above)\\ \hline |
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\texttt{bpv4-grace} & bottom pressure & GRACE maps (level 4) \\ \hline |
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\texttt{sstv4-amsre} & sea surface temperature & Along-Swath SST (level 3)\\ |
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\texttt{sstv4-amsre-lsc} & sea surface temperature & Large-Scale SST (from the above)\\ \hline |
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\texttt{si4-cons} & sea ice concentration & needs sea-ice adjoint (level 4)\\ |
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\texttt{si4-deconc} & model sea ice deficiency & proxy penalty (from the above)\\ |
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\texttt{si4-exconc} & model sea ice excess & proxy penalty (from the above)\\ \hline |
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\texttt{boxmean} & mean over a box & see section~\ref{genboxmean} \\ |
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\texttt{transp} & transport across section & see section~\ref{gentrsp} \\ |
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gforget |
1.1 |
\end{tabular} |
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gforget |
1.2 |
\caption{Pre-defined \texttt{gencost\_name} special cases (sections~\ref{v4custom}, \ref{genboxmean}, \ref{gentrsp}).} |
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gforget |
1.1 |
\label{tbl:gencost_ecco_name} |
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\end{table} |
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\begin{table}[!ht] |
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\centering |
| 199 |
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\begin{tabular}{lll} |
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variable name & description & remarks \\ \hline\hline |
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\texttt{m\_trVol} & volume transport & three-dimensional, specify section \\ |
| 202 |
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\texttt{m\_trHeat} & heat transport & three-dimensional, specify section \\ |
| 203 |
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\texttt{m\_trSalt} & salt transport & three-dimensional, specify section \\ |
| 204 |
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\texttt{m\_boxmean\_theta} & mean of theta over box & specify box \\ |
| 205 |
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\texttt{m\_boxmean\_salt} & mean of salt over box & specify box \\ |
| 206 |
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\texttt{m\_boxmean\_eta} & mean of SSH over box & specify box |
| 207 |
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\end{tabular} |
| 208 |
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\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}.} |
| 209 |
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\label{tbl:gencost_ecco_barfile_custom} |
| 210 |
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\end{table} |
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| 212 |
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\subsection{Key Routines} |
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| 216 |
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TBA... \texttt{cost\_generic.F}, \texttt{ecco\_check.F}, \texttt{ecco\_phys.F}, \texttt{ecco\_summary.F}, \texttt{ecco\_readparms.F}, ... |
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\subsection{Compile Options} |
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TBA... ALLOW\_GENCOST3D, ALLOW\_PSBAR\_STERIC, ECCO\_CTRL\_DEPRECATED, ... |
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