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\subsection*{LPJ-WHy: Modeling peatlands and permafrost in a DGVM (Wania et
  al. 2009a, b)}
\vspace{0.5cm}


Data model citation at ORNL DAAC:

\vspace{0.5cm}

Wania, R., I. Ross and I.C. Prentice. 2009. LPJ-WHy: Modeling
peatlands and permafrost in a DGVM (Wania et al. 2009a, b). Model
product. Available on-line [http://www.daac.ornl.gov] from Oak Ridge
National Laboratory Distributed Active Archive Center, Oak Ridge,
Tennessee, U.S.A.
\vspace{0.5cm}

{\bf Modeling Manuscript Archive Entry for: Wania et al., 2009a
  and b.}
\vspace{0.5cm}

{\bf Model release documentation for LPJ-WHy, Version 1.2.}

\subsection*{Last updated:}
16 October 2009

\subsection*{Scientific point of contact:}
Rita Wania\\
School of Earth and Ocean Sciences\\
University of Victoria\\
PO Box 3065\\
Victoria, BC, V8W 3V6\\
Email: rita@wania.net\\
Phone: (250) 721-6181

\subsection*{Published manuscript reference:} 

Wania, R., I. Ross, and I. C. Prentice (2009a), Integrating peatlands
and permafrost into a dynamic global vegetation model: 1. Evaluation
and sensitivity of physical land surface processes, \emph{Global
  Biogeochemical Cycles}, 23, GB3014, doi:10.1029/2008GB003412.

\vspace{0.25cm}

Wania, R., I. Ross, and I. C. Prentice (2009b), Integrating peatlands
and permafrost into a dynamic global vegetation model: 2. Evaluation
and sensitivity of vegetation and carbon cycle processes, \emph{Global
  Biogeochemical Cycles}, 23, GB3015, doi:10.1029/2008GB003413.

\subsection*{Target compute platform:}

The model can be run on any platform.

\subsection*{Model build environment:}

Fortran 77 and C++. The code can be compiled by using freely available
compilers such as ifort, g77 and gcc.

\subsection*{Additional analysis environment requirements:}

LPJ-WHy produces NetCDF files, which can be viewed and processed in
any suitable environment. To analyse the data, we used the \emph{CDO}
and \emph{NCO} tools and to view and plot the data we used data
visualisation software such as \emph{Ferret} or \emph{NCL}, all of
these are freely available software packages and are just listed as
examples.
\vspace{0.25cm}

\begin{tabular}{ll}
CDO:& \url{http://www.mad.zmaw.de/Pingo/post/post.cdo.home.html}\\
NCO:& \url{http://nco.sourceforge.net/}\\
Ferret:& \url{http://ferret.wrc.noaa.gov/Ferret/}\\
NCL:& \url{http://www.ncl.ucar.edu/}\\
\end{tabular}


\subsection*{Detailed instructions:}

First, we provide a list of all the directories and files.  The
material is split up into five directories, \texttt{utils},
\texttt{src}, \texttt{doc} and \texttt{data}.

\subsubsection*{The \texttt{utils} directory}
The \texttt{utils} directory contains auxiliary code for the use of
the input/output driver (lpjio.cpp), which uses NetCDF files as input
and output.  Written by Ian Ross.

\begin{tabular}{lp{0.8\textwidth}}
\texttt{apply-base.cpp} & C++ auxiliary file. \\
\texttt{Array.cpp} & C++ auxiliary file. \\
\texttt{Array.hh} & C++ header file. \\
\texttt{clamp-value.cpp} & C++ auxiliary file. \\
\texttt{ncminmax.cpp} & C++ auxiliary file. \\
\texttt{Makefile} & File to link and compile the above files.
\end{tabular}

\subsubsection*{The \texttt{src} directory}
The main LPJ-WHyMe source code and driver file are located in this
directory.

\begin{tabular}{lp{0.8\textwidth}}
\texttt{lpjmain.f} & Main LPJ-WHy code (Fortran 77).  Contains all
subroutines and changes described in Wania \emph{et al.} 2009a and
b. \\
\texttt{params.cb} & Common block containing parameter values. \\
\texttt{inputvars.cb} & Common block containing definition of climate
input variables. \\
\texttt{soilvars.cb} & Common block containing definition of soil
relevant variables. \\
\texttt{vegvars.cb} & Common block containing definition of vegetation
relevant variables. \\
\texttt{ch4vars.cb} & Common block containing definition of methane
relevant variables. \\
\texttt{lpjio.cpp} & C++ driver for LPJ-WHyMe, used to handle input
and output files.  (Written by Ian Ross.) \\
\texttt{Makefile} & File to link and compile the code.
\end{tabular}

\subsubsection*{The \texttt{data} directory}
In the subdirectory \texttt{global}, we provide the land mask and soil
type data on a $1^\circ \times 1^\circ$ resolution for the region
$60^\circ$S to $90^\circ$N.  The soil type map is based on the FAO
data set, but is overlain by soil organic carbon data from the
IGBP-DIS data set @citep(IGBP-map).  As climate input data, we used
either a climatology or a time series data set provided by the Climate
Research Unit (CRU) at the University of East Anglia, United Kingdom
@citep(New-cru, Mitchell-cru).  Here, we provide data only for one
example grid cell as we cannot distribute the global data sets. The
global data are on a $0.5^\circ \times 0.5^\circ$ resolution and can
be downloaded at \url{http://www.cru.uea.ac.uk/cru/data/hrg.htm}.
\vspace{0.5cm}

The subdirectory \texttt{example-site} contains data from the
Deger\"{o} site in Sweden.

\begin{tabular}{lp{0.7\textwidth}}
\texttt{pftin.dat} & Plant functional type parameter file, read by
\texttt{lpjmain.f}. \\
\texttt{lpj.cfg} & Configuration file giving names of input files and
output variables.  Description of \texttt{lpj.cfg} file format and 
  \texttt{lpjio.cpp} driver can be found in
  \texttt{doc/USING-The-netCDF-Driver.txt}. \\
\texttt{lpj\_land\_mask.nc} & Land/ocean mask. \\
\texttt{lpj\_soil\_type.nc} & Soil type map. \\
\end{tabular}

\begin{tabular}{lp{0.7\textwidth}}
\texttt{tas.nc} & Monthly mean temperature ($^\circ$C) from the CRU CL
1.0 climatology @citep(New-cru). \\

\texttt{pr.nc} & Monthly mean precipitation (mm per month) from the
CRU CL 1.0 climatology @citep(New-cru). \\

\texttt{clt.nc} & Monthly mean cloud cover (\%) from the CRU CL 1.0 climatology
  @citep(New-cru). \\
\texttt{wetdays.nc} & Monthly mean wet days from the CRU CL 1.0
climatology @citep(New-cru).
\end{tabular}

\subsection*{Running LPJ-WHyMe}

To run LPJ-WHyMe using the provided test data:

\begin{enumerate}
  \item[1.]{In the \texttt{utils} directory, ensure that all paths are
    set correctly in the \texttt{Makefile}.  Then type \texttt{make}.}
  \item[2.]{In the \texttt{src} directory, ensure that all paths are set
    correctly in the \texttt{Makefile}.  Then type \texttt{make}.}
  \item[3.]{Copy the pftin.dat and lpj.cfg files into the
    \texttt{data} directory.  Run the \texttt{lpj-whyme} executable
    produced in step 2 in the \texttt{data} directory.}
  \item[4.]{An output file called \texttt{out\_280-1001.nc} will be
    produced in the \texttt{data} directory.}
\end{enumerate}


@bibliography(Readme)
@ref(IGBP-map AU=Task Group, TI=gridded surfaces, YR=2000)
@ref(Mitchell-cru AU=Mitchell, TI=observations, YR=2005)
@ref(New-cru AU=New, TI=climatology, YR=1999)


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