<p><b>kavulich@ucar.edu</b> 2014-03-13 17:25:47 -0600 (Thu, 13 Mar 2014)</p><p>Starting conversion of User's Guide to LaTeX.<br>
</p><hr noshade><pre><font color="gray">Added: trunk/wrf/UsersGuide/Chapter_6.tex
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+\chapter{WRF Data Assimilation}
+\label{WRFDA}
+
+\setcounter{minitocdepth}{3} % List as deep as subsubsections in chapter table of contents
+</font>
<font color="blue">omtcpagenumbers % No page numbers in chapter TOC
+\minitoc % Chapter TOC
+
+
+\section{Introduction}
+\label{wrfda-intro}
+
+Data assimilation is the technique by which \textbf{observations} are combined with an NWP product (the \textbf{first guess} or background forecast) and their respective error statistics to provide an improved estimate (the \textbf{analysis}) of the atmospheric (or oceanic, Jovian, etc.) state. Variational (Var) data assimilation achieves this through the iterative minimization of a prescribed cost (or penalty) function. Differences between the analysis and observations/first guess are penalized (damped) according to their perceived error. The difference between three-dimensional (3DVAR) and four-dimensional (4DVAR) data assimilation is the use of a numerical forecast model in the latter.
+
+The MMM Division of NCAR supports a unified (global/regional, multi-model, 3/4D-Var) model-space data assimilation system (WRFDA) for use by the NCAR staff and collaborators, and is also freely available to the general community, together with further documentation, test results, plans etc., from the WRFDA webpage (\url{http://www.mmm.ucar.edu/wrf/users/wrfda/index.html}).
+
+Various components of the WRFDA system are shown in blue in the sketch below, together with their relationship with the rest of the WRF system.
+
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/WRFDA_system_chart}
+
+\vspace*{3mm}
+In the above chart, the following symbols are used:
+
+\vspace*{3mm}
+$\mathbf{x^b}$: first guess, either from a previous WRF forecast or from WPS/REAL output
+
+$\mathbf{x^{lbc}}$: lateral boundary from WPS/REAL output
+
+$\mathbf{x^a}$: analysis from the WRFDA data assimilation system
+
+$\mathbf{x^f}$: WRF forecast output
+
+$\mathbf{y^o}$: observations processed by OBSPROC (note: PREPBUFR input, radar, radiance, and rainfall data do not go through OBSPROC)
+
+$\mathbf{B_0}$: background error statistics from generic BE data (CV3) or gen\_be
+
+$\mathbf{R}$: observational and representative error statistics.
+
+\vspace*{3mm}
+In this chapter, you will learn how to install and run the various components of the WRFDA system. For training purposes, you are supplied with a test case, including the following input data:
+
+\begin{itemize}
+ \item an observation file (which must be processed through OBSPROC)
+ \item a netCDF background file (WPS/REAL output, the first guess of the analysis)
+ \item background error statistics (estimate of errors in the background)
+\end{itemize}
+
+This tutorial dataset can be downloaded from the WRFDA Users Page (\url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/testdata.html}), and will be described later in more detail. In your own work, however, you will have to create all these input files yourself. See the section "\hyperref[wrfda-obsproc]{Observation Preprocessor (OBSPROC)}" for creating your observation files. See the section "\hyperref[wrfda-gen_be]{Running gen\_be}" for generating your background error statistics file, if you want to use cv\_options=5 or cv\_options=6.
+
+Before using your own data, we suggest that you start by running through the WRFDA-related programs using the supplied test case. This serves two purposes: First, you can learn how to run the programs with data we have tested ourselves, and second you can test whether your computer is capable of running the entire modeling system. After you have done the tutorial, you can try running other, more computationally intensive case studies, and experimenting with some of the many namelist variables.
+
+Hopefully, our test cases will prepare you for the variety of ways in which you may wish to run your own WRFDA experiments. Please inform us about your experiences (wrfhelp@ucar.edu).
+
+As a professional courtesy, we ask that any publications which make use of any part of the WRFDA system cite the appropriate reference(s) from the following list:
+
+\vspace*{3mm}
+\textbf{WRFDA system}
+
+</font>
<font color="blue">i Barker, D., X.-Y. Huang, Z. Liu, T. Auligné, X. Zhang, S. Rugg, R. Ajjaji, A. Bourgeois, J. Bray, Y. Chen, M. Demirtas, Y.-R. Guo, T. Henderson, W. Huang, H.-C. Lin, J. Michalakes, S. Rizvi, and X. Zhang, 2012: \href{http://journals.ametsoc.org/doi/abs/10.1175/BAMS-D-11-00167.1}{The Weather Research and Forecasting Model's Community Variational/Ensemble Data Assimilation System: WRFDA}. \textit{Bull. Amer. Meteor. Soc.}, \textbf{93}, 831--843.
+
+\vspace*{3mm}
+\textbf{3DVAR}
+
+</font>
<font color="blue">i Barker, D. M., W. Huang, Y.-R. Guo, and Q. N. Xiao., 2004: \href{http://journals.ametsoc.org/doi/abs/10.1175/1520-0493(2004)132<0897:ATVDAS>2.0.CO;2}{A Three-Dimensional (3DVAR) Data Assimilation System For Use With MM5: Implementation and Initial Results}. \textit{Mon. Wea. Rev.}, \textbf{132}, 897--914.
+
+\vspace*{3mm}
+\textbf{4DVAR}
+
+Huang, X.-Y., Q. Xiao, D.M. Barker, X. Zhang, J. Michalakes, W. Huang, T. Henderson, J. Bray, Y. Chen, Z. Ma, J. Dudhia, Y. Guo, X. Zhang, D.-J. Won, H.-C. Lin, and Y.H. Kuo, 2009: \href{http://journals.ametsoc.org/doi/abs/10.1175/2008MWR2577.1}{Four-Dimensional Variational Data Assimilation for WRF: Formulation and Preliminary Results}. \textit{Mon. Wea. Rev.}, \textbf{137}, 299--314.
+
+\vspace*{3mm}
+\textbf{WRFPLUS}
+
+</font>
<font color="blue">i Zhang, X., X.-Y. Huang, and N. Pan, 2013: \href{http://journals.ametsoc.org/doi/abs/10.1175/JTECH-D-12-00213.1}{Development of the Upgraded Tangent Linear and Adjoint of the Weather Research and Forecasting (WRF) Model}. \textit{J. Atmos. Oceanic Technol.}, \textbf{30}, 1180--1188.
+
+\vspace*{3mm}
+\textbf{Hybrid/ETKF}
+
+</font>
<font color="blue">i Wang, X., D. M. Barker, C. Snyder, and T. M. Hamill, 2008: \href{http://journals.ametsoc.org/doi/abs/10.1175/2008MWR2444.1}{A hybrid ETKF--3DVAR data assimilation scheme for the WRF model. Part I: Observing system simulation experiment}. \textit{Mon. Wea. Rev.}, \textbf{136}, 5116--5131.
+
+</font>
<font color="blue">i Wang, X., D. M. Barker, C. Snyder, and T. M. Hamill, 2008: \href{http://journals.ametsoc.org/doi/abs/10.1175/2008MWR2445.1}{A Hybrid ETKF--3DVAR Data Assimilation Scheme for the WRF Model. Part II: Real Observation Experiments}. \textit{Mon. Wea. Rev.}, \textbf{136}, 5132--5147.
+
+\vspace*{3mm}
+You can find more helpful publications on the WRFDA system, as well as publications making use of the WRFDA system, on the website (\url{http://www.mmm.ucar.edu/wrf/users/wrfda/publications.html}).
+
+\subsection{Important notes}
+\label{wrfda-intro-notes}
+
+\begin{itemize}
+\item \textbf{It is impossible to test every permutation of computer, compiler, number of processors, case, namelist option, etc. for every WRFDA release. The namelist options that are supported are indicated in the ``\texttt{WRFDA/var/README.namelist}'', and these are the default options.}
+
+\item \textbf{Running WRFDA requires a Fortran 90 compiler. The most recent WRFDA release has been tested on the following platforms: PC/Linux (INTEL, GFORTRAN, PGI), and Macintosh (G95/PGI). Previous releases have been tested on IBM (XLF) and SGI Altix (INTEL) platforms. Please contact us (wrfhelp@ucar.edu) if this does not meet your requirements, and we will attempt to add other machines to our list of supported architectures, as resources allow.}
+
+\item \textbf{This chapter assumes the user is using \texttt{csh} or some other derivative shell. When using \texttt{bash} or certain other shells, some commands (particularly \texttt{setenv}) will be different.}
+\end{itemize}
+
+
+\section{Installing WRFDA}
+\label{install-wrfda}
+
+\subsection{Obtaining WRFDA source code}
+\label{wrfda-source}
+
+Users can download the WRFDA source code from \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/get_source.html}.
+
+\textbf{Note: WRF compiles with the –r4 option while WRFDA compiles with –r8.} For this reason, WRF and WRFDA cannot reside or be compiled in the same directory.
+
+After the tar file is unzipped (\texttt{gunzip WRFDAV3.5.TAR.gz}) and untarred (\texttt{tar -xf WRFDAV3.5.TAR}), the directory \texttt{WRFDA} should be created. This directory contains the WRFDA source, external libraries, and other required files. The following is a list of the system components and content for each subdirectory:
+
+
+\begin{table}[h]
+\begin{center}
+\vspace*{3mm}
+\begin{tabular}{|l|l|}
+\hline \textbf{Directory} & \textbf{Content} \\
+\hline \texttt{var/build} & Where the WRFDA executables will be built \\
+\hline \texttt{var/da} & WRFDA source code \\
+\hline \texttt{var/external} & Libraries needed by WRFDA, including CRTM, BUFR, LAPACK, and BLAS \\
+\hline \texttt{var/gen\_be} & Source code of gen\_be, the utility to create background error statistics files \\
+\hline \texttt{var/obsproc} & OBSPROC source code, namelist, and observation error files \\
+\hline \texttt{var/run} & Fixed input files required by WRFDA, such as background error covariance, \\
+ & radiance-related files, CRTM coefficients and VARBC.in \\
+\hline \texttt{var/test} & Several WRFDA test cases and README files \\
+\hline
+\end{tabular}
+\end{center}
+\vspace*{-5mm}
+\end{table}
+
+\subsection{Obtaining WRFPLUS source code}
+\label{wrfplus-source}
+
+If compiling for 4DVAR, it is also necessary to download WRFPLUS (the WRF tangent-linear and adjoint model), which can be found at \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/wrfplus.html}. After the tar file is unzipped (\texttt{gunzip WRFPLUS\_V3.5.tar.gz}) and untarred (\texttt{tar -xf WRFPLUS\_V3.5.tar}), the directory \texttt{WRFPLUSV3} should be created. This directory contains the WRFPLUS source code.
+
+\subsection{WRFDA--3DVAR}
+\label{install-wrfda-3dvar}
+
+Some external libraries (e.g., LAPACK, BLAS, and NCEP BUFR) are included in the WRFDA tar file. To compile the WRFDA code, the only mandatory library is the netCDF library. You should set an environment variable NETCDF to point to the directory where your netCDF library is installed
+
+\small\begin{verbatim}
+> setenv NETCDF your_netcdf_path
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+
+\label{wrfda-rtm}
+
+If satellite radiance data are to be used, a Radiative Transfer Model (RTM) is required. The current RTM versions that WRFDA supports are CRTM V2.1.3 and RTTOV V11.1. CRTM V2.1.3 is included in the WRFDA tar file, and is automatically compiled. If the user wishes to use RTTOV, download and install the RTTOV v11 library before compiling WRFDA. This library can be downloaded from \url{http://research.metoffice.gov.uk/research/interproj/nwpsaf/rtm}. \textbf{The RTTOV libraries must be compiled with the ``emis\_atlas'' option in order to work with WRFDA}. After compiling RTTOV (see the RTTOV documentation for detailed instructions), set the ``RTTOV'' environment variable to the path where the lib directory resides. For example, if the library files can be found in \texttt{/usr/local/rttov11/pgi/lib/librttov11.1.0\_*.a}, you should set RTTOV as
+
+\small\begin{verbatim}
+> setenv RTTOV /usr/local/rttov11/pgi
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+\textbf{\textit{Note}: Make sure the required libraries were all compiled using the same compiler that will be used to build WRFDA}, since the libraries produced by one compiler may not be compatible with code compiled with another.
+Assuming all required libraries are available and the WRFDA source code is ready, you can start to build WRFDA using the following steps:
+
+Enter the WRFDA directory and run the configure script:
+
+\small\begin{verbatim}
+> cd WRFDA
+> ./configure wrfda
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+</font>
<font color="blue">i A list of configuration options should appear. Each option combines an operating system, a compiler type, and a parallelism option. Since the configuration script doesn't check which compilers are \textit{actually} installed on your system, be sure to select only among the options that you have available to you. The available parallelism options are single-processor (serial), shared-memory parallel (smpar), distributed-memory parallel (dmpar), and distributed-memory with shared-memory parallel (sm+dm). \textbf{However, shared-memory (smpar and sm+dm) options are not supported as of WRFDA Version 3.5, so we do not recommend selecting any of these options.}
+
+
+For example, on a Linux machine such as NCAR's Yellowstone, the above steps will look similar to the following:
+
+\small\begin{verbatim}
+> ./configure wrfda
+checking for perl5... no
+checking for perl... found /usr/bin/perl (perl)
+Will use NETCDF in dir: /glade/apps/opt/netcdf/4.2/intel/default
+PHDF5 not set in environment. Will configure WRF for use without.
+$JASPERLIB or $JASPERINC not found in environment, configuring to build without grib2 I/O...
+------------------------------------------------------------------------
+Please select from among the following supported platforms.
+
+ 1. Linux x86_64 i486 i586 i686, PGI compiler with gcc (serial)
+ 2. Linux x86_64 i486 i586 i686, PGI compiler with gcc (smpar)
+ 3. Linux x86_64 i486 i586 i686, PGI compiler with gcc (dmpar)
+ 4. Linux x86_64 i486 i586 i686, PGI compiler with gcc (dm+sm)
+ 5. Linux x86_64 i486 i586 i686 PGI compiler with pgcc YELLOWSTONE (serial)
+ 6. Linux x86_64 i486 i586 i686 PGI compiler with pgcc YELLOWSTONE (smpar)
+ 7. Linux x86_64 i486 i586 i686 PGI compiler with pgcc YELLOWSTONE (dmpar)
+ 8. Linux x86_64 i486 i586 i686 PGI compiler with pgcc YELLOWSTONE (dm+sm)
+ 9. Linux x86_64, PGI compiler with pgcc, SGI MPT (serial)
+ 10. Linux x86_64, PGI compiler with pgcc, SGI MPT (smpar)
+ 11. Linux x86_64, PGI compiler with pgcc, SGI MPT (dmpar)
+ 12. Linux x86_64, PGI compiler with pgcc, SGI MPT (dm+sm)
+ 13. Linux x86_64, PGI accelerator compiler with gcc (serial)
+ 14. Linux x86_64, PGI accelerator compiler with gcc (smpar)
+ 15. Linux x86_64, PGI accelerator compiler with gcc (dmpar)
+ 16. Linux x86_64, PGI accelerator compiler with gcc (dm+sm)
+ 17. Linux x86_64 i486 i586 i686, ifort compiler with icc (serial)
+ 18. Linux x86_64 i486 i586 i686, ifort compiler with icc (smpar)
+ 19. Linux x86_64 i486 i586 i686, ifort compiler with icc (dmpar)
+ 20. Linux x86_64 i486 i586 i686, ifort compiler with icc (dm+sm)
+ 21. Linux x86_64 i486 i586 i686, Xeon Phi (MIC architecture) ifort compiler with icc (dm+sm)
+ 22. Linux x86_64 i486 i586 i686, Xeon (SNB with AVX mods) ifort compiler with icc (serial)
+ 23. Linux x86_64 i486 i586 i686, Xeon (SNB with AVX mods) ifort compiler with icc (smpar)
+ 24. Linux x86_64 i486 i586 i686, Xeon (SNB with AVX mods) ifort compiler with icc (dmpar)
+ 25. Linux x86_64 i486 i586 i686, Xeon (SNB with AVX mods) ifort compiler with icc (dm+sm)
+ 26. Linux x86_64 i486 i586 i686, ifort compiler with icc YELLOWSTONE (serial)
+ 27. Linux x86_64 i486 i586 i686, ifort compiler with icc YELLOWSTONE (smpar)
+ 28. Linux x86_64 i486 i586 i686, ifort compiler with icc YELLOWSTONE (dmpar)
+ 29. Linux x86_64 i486 i586 i686, ifort compiler with icc YELLOWSTONE (dm+sm)
+ 30. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (serial)
+ 31. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (smpar)
+ 32. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (dmpar)
+ 33. Linux x86_64 i486 i586 i686, ifort compiler with icc, SGI MPT (dm+sm)
+ 34. Linux x86_64 i486 i586 i686, ifort compiler with icc, IBM POE (serial)
+ 35. Linux x86_64 i486 i586 i686, ifort compiler with icc, IBM POE (smpar)
+ 36. Linux x86_64 i486 i586 i686, ifort compiler with icc, IBM POE (dmpar)
+ 37. Linux x86_64 i486 i586 i686, ifort compiler with icc, IBM POE (dm+sm)
+ 38. Linux i486 i586 i686 x86_64, PathScale compiler with pathcc (serial)
+ 39. Linux i486 i586 i686 x86_64, PathScale compiler with pathcc (dmpar)
+ 40. x86_64 Linux, gfortran compiler with gcc (serial)
+ 41. x86_64 Linux, gfortran compiler with gcc (smpar)
+ 42. x86_64 Linux, gfortran compiler with gcc (dmpar)
+ 43. x86_64 Linux, gfortran compiler with gcc (dm+sm)
+
+Enter selection [1-43] : 28
+------------------------------------------------------------------------
+Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:
+Configuration successful. To build the model type compile .
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+After running the configuration script and choosing a compilation option, a \texttt{configure.wrf} file will be created. Because of the variety of ways that a computer can be configured, if the WRFDA build ultimately fails, there is a chance that minor modifications to the \texttt{configure.wrf} file may be needed.
+
+\textit{\textbf{Hint}}: It is helpful to start with something simple, such as the serial build. If it is successful, move on to build dmpar code. Remember to type '\texttt{clean –a}' between each build to remove the old settings and executable files.
+
+To compile WRFDA, type
+
+\small\begin{verbatim}
+> ./compile all_wrfvar >\& compile.out}
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Successful compilation will produce 44 executables: 43 of which are in the \texttt{var/build} directory and linked in the \texttt{var/da} directory, with the 44th, \texttt{obsproc.exe}, found in the \texttt{var/obsproc/src} directory. You can list these executables by issuing the command:
+
+\scriptsize \begin{verbatim}
+>ls -l var/build/*exe var/obsproc/src/obsproc.exe
+-rwxr-xr-x 1 user 885143 Apr 4 17:22 var/build/da_advance_time.exe
+-rwxr-xr-x 1 user 1162003 Apr 4 17:24 var/build/da_bias_airmass.exe
+-rwxr-xr-x 1 user 1143027 Apr 4 17:23 var/build/da_bias_scan.exe
+-rwxr-xr-x 1 user 1116933 Apr 4 17:23 var/build/da_bias_sele.exe
+-rwxr-xr-x 1 user 1126173 Apr 4 17:23 var/build/da_bias_verif.exe
+-rwxr-xr-x 1 user 1407973 Apr 4 17:23 var/build/da_rad_diags.exe
+-rwxr-xr-x 1 user 1249431 Apr 4 17:22 var/build/da_tune_obs_desroziers.exe
+-rwxr-xr-x 1 user 1186368 Apr 4 17:24 var/build/da_tune_obs_hollingsworth1.exe
+-rwxr-xr-x 1 user 1083862 Apr 4 17:24 var/build/da_tune_obs_hollingsworth2.exe
+-rwxr-xr-x 1 user 1193390 Apr 4 17:24 var/build/da_update_bc_ad.exe
+-rwxr-xr-x 1 user 1245842 Apr 4 17:23 var/build/da_update_bc.exe
+-rwxr-xr-x 1 user 1492394 Apr 4 17:24 var/build/da_verif_grid.exe
+-rwxr-xr-x 1 user 1327002 Apr 4 17:24 var/build/da_verif_obs.exe
+-rwxr-xr-x 1 user 26031927 Apr 4 17:31 var/build/da_wrfvar.exe
+-rwxr-xr-x 1 user 1933571 Apr 4 17:23 var/build/gen_be_addmean.exe
+-rwxr-xr-x 1 user 1944047 Apr 4 17:24 var/build/gen_be_cov2d3d_contrib.exe
+-rwxr-xr-x 1 user 1927988 Apr 4 17:24 var/build/gen_be_cov2d.exe
+-rwxr-xr-x 1 user 1945213 Apr 4 17:24 var/build/gen_be_cov3d2d_contrib.exe
+-rwxr-xr-x 1 user 1941439 Apr 4 17:24 var/build/gen_be_cov3d3d_bin3d_contrib.exe
+-rwxr-xr-x 1 user 1947331 Apr 4 17:24 var/build/gen_be_cov3d3d_contrib.exe
+-rwxr-xr-x 1 user 1931820 Apr 4 17:24 var/build/gen_be_cov3d.exe
+-rwxr-xr-x 1 user 1915177 Apr 4 17:24 var/build/gen_be_diags.exe
+-rwxr-xr-x 1 user 1947942 Apr 4 17:24 var/build/gen_be_diags_read.exe
+-rwxr-xr-x 1 user 1930465 Apr 4 17:24 var/build/gen_be_ensmean.exe
+-rwxr-xr-x 1 user 1951511 Apr 4 17:24 var/build/gen_be_ensrf.exe
+-rwxr-xr-x 1 user 1994167 Apr 4 17:24 var/build/gen_be_ep1.exe
+-rwxr-xr-x 1 user 1996438 Apr 4 17:24 var/build/gen_be_ep2.exe
+-rwxr-xr-x 1 user 2001400 Apr 4 17:24 var/build/gen_be_etkf.exe
+-rwxr-xr-x 1 user 1942988 Apr 4 17:24 var/build/gen_be_hist.exe
+-rwxr-xr-x 1 user 2021659 Apr 4 17:24 var/build/gen_be_stage0_gsi.exe
+-rwxr-xr-x 1 user 2012035 Apr 4 17:24 var/build/gen_be_stage0_wrf.exe
+-rwxr-xr-x 1 user 1973193 Apr 4 17:24 var/build/gen_be_stage1_1dvar.exe
+-rwxr-xr-x 1 user 1956835 Apr 4 17:24 var/build/gen_be_stage1.exe
+-rwxr-xr-x 1 user 1963314 Apr 4 17:24 var/build/gen_be_stage1_gsi.exe
+-rwxr-xr-x 1 user 1975042 Apr 4 17:24 var/build/gen_be_stage2_1dvar.exe
+-rwxr-xr-x 1 user 1938468 Apr 4 17:24 var/build/gen_be_stage2a.exe
+-rwxr-xr-x 1 user 1952538 Apr 4 17:24 var/build/gen_be_stage2.exe
+-rwxr-xr-x 1 user 1202392 Apr 4 17:22 var/build/gen_be_stage2_gsi.exe
+-rwxr-xr-x 1 user 1947836 Apr 4 17:24 var/build/gen_be_stage3.exe
+-rwxr-xr-x 1 user 1928353 Apr 4 17:24 var/build/gen_be_stage4_global.exe
+-rwxr-xr-x 1 user 1955622 Apr 4 17:24 var/build/gen_be_stage4_regional.exe
+-rwxr-xr-x 1 user 1924416 Apr 4 17:24 var/build/gen_be_vertloc.exe
+-rwxr-xr-x 1 user 2057673 Apr 4 17:24 var/build/gen_mbe_stage2.exe
+-rwxr-xr-x 1 user 2110993 Apr 4 17:32 var/obsproc/src/obsproc.exe
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+The main executable for running WRFDA is \texttt{da\_wrfvar.exe}. Make sure it has been created after the compilation: it is common that all the executables will be successfully compiled except this main executable. If this occurs, please check the compilation log file carefully for any errors.
+
+The basic \texttt{gen\_be} utility for the regional model consists of \texttt{gen\_be\_stage0\_wrf.exe}, \texttt{gen\_be\_stage1.exe}, \texttt{gen\_be\_stage2.exe}, \texttt{gen\_be\_stage2a.exe}, \texttt{gen\_be\_stage3.exe}, \texttt{gen\_be\_stage4\_regional.exe}, and \texttt{gen\_be\_diags.exe}.
+
+\texttt{da\_update\_bc.exe} is used for updating the WRF lower and lateral boundary conditions before and after a new WRFDA analysis is generated.
+
+\texttt{da\_advance\_time.exe} is a very handy and useful tool for date/time manipulation. Type \texttt{var/build/da\_advance\_time.exe} to see its usage instructions.
+
+\texttt{obsproc.exe} is the executable for preparing conventional observations for assimilation by WRFDA.
+
+If you specified that BUFR or CRTM libraries were needed, check \texttt{\$WRFDA\_DIR/var/external/bufr} and \texttt{\$WRFDA\_DIR/var/external/crtm/libsrc} to ensure \texttt{libbufr.a} and \texttt{libCRTM.a} were generated.
+
+\subsection{Installing WRFPLUS and WRFDA for 4D-Var Run}
+\label{install-wrfda-4dvar}
+
+If you intend to run WRFDA 4DVAR, it is necessary to install WRFPLUS first. WRFPLUS contains the adjoint and tangent linear models based on a version of the WRF model with simplified physics parameterizations such as surface drag, large scale condensation and precipitation, and cumulus parameterization.
+
+To begin the installation process, \hyperref[wrfda-source]{download the source code} if you have not yet done so. Then enter the \texttt{WRFPLUSV3} directory, then run the configure script:
+
+
+\scriptsize\begin{verbatim}
+> cd WRFPLUSV3
+> ./configure wrfplus
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+As with 3DVAR, ``serial'' means single-processor, and ``dmpar'' means Distributed Memory Parallel (MPI). Be sure to select the same option for WRFPLUS as you will use for WRFDA. If configuration is successful, run the compile script:
+
+\scriptsize\begin{verbatim}
+> ./compile em_real >& compile.out
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+After compilation has finished, you should see the following files:
+
+\scriptsize\begin{verbatim}
+> ls -ls main/*.exe
+-rwxr-xr-x 1 user users 23179920 Apr 3 15:22 main/ndown.exe
+-rwxr-xr-x 1 user users 22947466 Apr 3 15:22 main/nup.exe
+-rwxr-xr-x 1 user users 23113961 Apr 3 15:22 main/real.exe
+-rwxr-xr-x 1 user users 22991725 Apr 3 15:22 main/tc.exe
+-rwxr-xr-x 1 user users 32785447 Apr 3 15:20 main/wrf.exe
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+If WRFPLUS was compiled successfully, you can now install WRFDA. Prior to running the WRFDA configure script, set the environment variable WRFPLUS\_DIR to the appropriate directory:
+
+\scriptsize\begin{verbatim}
+>setenv WRFPLUS_DIR ${your_source_code_dir}
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+In other words, if you compiled WRFPLUS in the /home/user/WRFPLUSV3 directory, enter the command \texttt{setenv WRFPLUS\_DIR /home/user/WRFPLUSV3}.
+
+If you intend to assimilate satellite radiance data using RTTOV, you should set the RTTOV environment variable as appropriate. See \hyperref[wrfda-rtm]{the previous section} for instructions.
+
+Now run the WRFDA configure script for 4DVAR, select the appropriate option (``dmpar'' is \textbf{highly} recommended due to the large memory requirements for 4DVAR):
+
+\scriptsize\begin{verbatim}
+>./configure 4dvar
+>./compile all_wrfvar >& compile.out
+>ls -ls var/build/*.exe var/obsproc/*.exe
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+You should see the same 44 executables as are listed in the above 3DVAR section, including \texttt{da\_wrfvar.exe}.
+
+
+
+\subsection{Clean Compilation}
+\label{wrfda-clean}
+
+To remove all object files and executables, type:
+
+\scriptsize\begin{verbatim}
+./clean
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+To remove all build files, including \texttt{configure.wrf}, type:
+
+\scriptsize\begin{verbatim}
+./clean -a
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+The \texttt{clean -a} command is recommended if your compilation fails, or if the configuration file has been changed and you wish to restore the default settings.
+
+
+\section{Running the Observation Preprocessor (OBSPROC)}
+\label{wrfda-obsproc}
+The OBSPROC program reads observations in LITTLE\_R format (a text-based format, in use since the MM5 era). We have provided observations for the tutorial case, but for your own applications, you will have to prepare your own observation files. Please see \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/free\_data.html} for the sources of some freely-available observations. Because the raw observation data files have many possible formats, such as ASCII, BUFR, PREPBUFR, MADIS, and HDF, the free data site also contains instructions for converting the observations to LITTLE\_R format. To make the WRFDA system as general as possible, the LITTLE\_R format was adopted as an intermediate observation data format for the WRFDA system, however, the conversion of the user-specific source data to LITTLE\_R format is the user's task. A more complete description of the LITTLE\_R format, as well as conventional observation data sources for WRFDA, can be found by reading the “Observ
ation Pre-processing” tutorial found at \url{http://www.mmm.ucar.edu/wrf/users/wrfda/Tutorials/2013_July/tutorial_presentation_summer_2013.html}, or by referencing Chapter 7 of this User's Guide.
+
+The purpose of OBSPROC is to:
+
+\begin{itemize}
+\item Remove observations outside the specified temporal and spatial domains
+\item Re-order and merge duplicate (in time and location) data reports
+\item Retrieve pressure or height based on observed information using the hydrostatic assumption
+\item Check multi-level observations for vertical consistency and superadiabatic conditions
+\item Assign observation errors based on a pre-specified error file
+\item Write out the observation file to be used by WRFDA in ASCII or BUFR format
+\end{itemize}
+
+The OBSPROC program (obsproc.exe) should be found under the directory WRFDA/var/obsproc/src if ``\texttt{compile all\_wrfvar}'' completed successfully.
+If you haven't already, you should download the tutorial case, which contains example files for all the exercises in this User's Guide. The case can be found at the WRFDA website (\url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/testdata.html}).
+
+
+\subsection{Prepare observational data for 3DVAR}
+\label{wrfda-obsproc-3dvar}
+
+As an example, to prepare the observation file at the analysis time, all the observations in the range ±1h will be processed, which means that (in the example case) the observations between 23h and 1h are treated as the observations at 0h. This is illustrated in the following figure:
+
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/OBSPROC_3DVAR_time_window_diagram}
+
+OBSPROC requires at least 3 files to run successfully:
+
+\begin{itemize}
+\item A namelist file (\texttt{namelist.obsproc})
+\item An observation error file (\texttt{obserr.txt})
+\item One or more observation files
+\end{itemize}
+
+To create the required namelist file, we have provided an example file (\texttt{namelist.obsproc.3dvar.wrfvar-tut} in the \texttt{var/obsproc} directory. Thus, proceed as follows.
+
+\scriptsize\begin{verbatim}
+> cd $WRFDA_DIR/var/obsproc
+> cp namelist.obsproc.3dvar.wrfvar-tut namelist.obsproc
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Next, edit the namelist file, namelist.obsproc, to accommodate your experiments. You will likely only need to change variables listed under records 1, 2, 6, 7, and 8. See \texttt{WRFDA/var/obsproc/README.namelist}, or the section \hyperref[wrfda-namelist]{Description of Namelist Variables} for details; you should pay special attention to \texttt{NESTIX} and \texttt{NESTJX}.
+
+If you are running the tutorial case, you should copy or link the sample observation file (\texttt{ob/2008020512/obs.2008020512}) to the \texttt{obsproc} directory. Alternatively, you can edit the namelist variable \texttt{obs\_gts\_filename} to point to the observation file's full path.
+
+To run OBSPROC, type
+
+\scriptsize\begin{verbatim}
+> ./obsproc.exe >& obsproc.out
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Once \texttt{obsproc.exe} has completed successfully, you will see an observation data file, with the name formatted \texttt{obs\_gts\_YYYY-MM-DD\_HH:NN:SS.3DVAR}, in the \texttt{obsproc} directory. For the tutorial case, this will be \texttt{obs\_gts\_2008-02-05\_12:00:00.3DVAR}. This is the input observation file for WRFDA. It is an ASCII file that contains a header section (listed below) followed by observations. The meanings and format of observations in the file are described in the last six lines of the header section.
+
+\scriptsize\begin{verbatim}
+TOTAL = 9066, MISS. =-888888.,
+SYNOP = 757, METAR = 2416, SHIP = 145, BUOY = 250, BOGUS = 0, TEMP = 86,
+AMDAR = 19, AIREP = 205, TAMDAR= 0, PILOT = 85, SATEM = 106, SATOB = 2556,
+GPSPW = 187, GPSZD = 0, GPSRF = 3, GPSEP = 0, SSMT1 = 0, SSMT2 = 0,
+TOVS = 0, QSCAT = 2190, PROFL = 61, AIRSR = 0, OTHER = 0,
+PHIC = 40.00, XLONC = -95.00, TRUE1 = 30.00, TRUE2 = 60.00, XIM11 = 1.00, XJM11 = 1.00,
+base_temp= 290.00, base_lapse= 50.00, PTOP = 1000., base_pres=100000., base_tropo_pres= 20000., base_strat_temp= 215.,
+IXC = 60, JXC = 90, IPROJ = 1, IDD = 1, MAXNES= 1,
+NESTIX= 60,
+NESTJX= 90,
+NUMC = 1,
+DIS = 60.00,
+NESTI = 1,
+NESTJ = 1,
+INFO = PLATFORM, DATE, NAME, LEVELS, LATITUDE, LONGITUDE, ELEVATION, ID.
+SRFC = SLP, PW (DATA,QC,ERROR).
+EACH = PRES, SPEED, DIR, HEIGHT, TEMP, DEW PT, HUMID (DATA,QC,ERROR)*LEVELS.
+INFO_FMT = (A12,1X,A19,1X,A40,1X,I6,3(F12.3,11X),6X,A40)
+SRFC_FMT = (F12.3,I4,F7.2,F12.3,I4,F7.3)
+EACH_FMT = (3(F12.3,I4,F7.2),11X,3(F12.3,I4,F7.2),11X,3(F12.3,I4,F7.2))
+#------------------------------------------------------------------------------#
+…… observations ………
+
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Before running WRFDA, you may find it useful to learn more about various types of data that will be processed (e.g., their geographical distribution). The observation file that you have created is in ASCII format and so you can easily view it. For a graphical view of the file's content, there is an NCL script available in the WRFDA Tools package (can be downloaded at \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/tools.html}); this script is located at \texttt{\$TOOLS\_DIR/var/graphics/ncl/plot\_ob\_ascii\_loc.ncl} (for more information on NCL, the NCAR Command Language, see \url{http://www.ncl.ucar.edu/}). To use this script, you need to provide the WRFDA first guess file to the NCL script, and have NCL installed in your system.
+
+\subsection{Prepare observational data for 4DVAR}
+\label{wrfda-obsproc-4dvar}
+
+To prepare the observation file for a 4DVAR run, at the analysis time (0h in this example), all observations from 0h to 6h will be processed and grouped in 7 sub-windows (slot1 through slot7) as illustrated in the following figure:
+
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/OBSPROC_4DVAR_time_window_diagram}
+
+\textbf{NOTE}: The ``analysis time'' in the above figure is not the actual analysis time. It indicates the \texttt{time\_analysis} setting in the namelist file, which in this example is three hours later than the actual analysis time. The actual analysis time (the time at which the analysis will be valid) is 0h in this example.
+
+An example file (\texttt{namelist.obsproc.3dvar.wrfvar-tut} has already been provided in the \texttt{var/obsproc} directory. Thus, proceed as follows.
+
+\scriptsize\begin{verbatim}
+> cd $WRFDA_DIR/var/obsproc
+> cp namelist.obsproc.4dvar.wrfvar-tut namelist.obsproc
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+In the namelist file, you need to change the following variables to accommodate your experiments. In this tutorial case, as mentioned above, the actual analysis time is 2008-02-05\_12:00:00, but in the namelist, \texttt{time\_analysis} should be set to 3 hours later. The different values of \texttt{time\_analysis}, \texttt{num\_slots\_past}, and \texttt{time\_slots\_ahead} contribute to the actual times analyzed. For example, if you set \texttt{time\_analysis = 2008-02-05\_16:00:00}, and set the \texttt{num\_slots\_past = 4} and \texttt{time\_slots\_ahead=2}, the final results will be the same as before.
+
+Edit all the domain settings according to your own experiment. You should pay special attention to \texttt{NESTIX} and \texttt{NESTJX}; these and other namelist settings are described in the \hyperref[wrfda-namelist]{Description of Namelist Variables} section.
+
+If you are running the tutorial case, you should copy or link the sample observation file (\texttt{ob/2008020512/obs.2008020512}) to the \texttt{obsproc} directory. Alternatively, you can edit the namelist variable \texttt{obs\_gts\_filename} to point to the observation file's full path.
+
+To run OBSPROC, type
+
+\scriptsize\begin{verbatim}
+> ./obsproc.exe >& obsproc.out
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Once \texttt{obsproc.exe} has completed successfully, you will see 7 observation data files, which for the tutorial case are named
+
+\scriptsize\begin{verbatim}
+obs_gts_2008-02-05_12:00:00.4DVAR
+obs_gts_2008-02-05_13:00:00.4DVAR
+obs_gts_2008-02-05_14:00:00.4DVAR
+obs_gts_2008-02-05_15:00:00.4DVAR
+obs_gts_2008-02-05_16:00:00.4DVAR
+obs_gts_2008-02-05_17:00:00.4DVAR
+obs_gts_2008-02-05_18:00:00.4DVAR
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+They are the input observation files to WRFDA for 4DVAR.
+
+
+\section{Running WRFDA}
+\label{wrfda-run}
+
+\subsection{Download test data}
+\label{wrfda-test-data}
+
+
+If you have not already done so, download the example data for the tutorial case from \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/testdata.html}. The the tutorial case is for a Continental US domain, valid at 12 UTC 5 February 2008: the day of a major tornado outbreak over the central and eastern United States. The first guess comes from the NCEP FNL (Final) Operational Global Analysis data, passed through the WRF-WPS and real programs. There is data for both 3DVAR and 4DVAR test cases included.
+
+You should download the data for the tutorial case in a directory defined by the environment variable \texttt{\$DAT\_DIR}. This directory can be in any location, and it should have read access. Type
+
+\scriptsize\begin{verbatim}
+> setenv DAT_DIR your_choice_of_dat_dir
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Here, \texttt{your\_choice\_of\_dat\_dir} is the directory where the WRFDA input data will be unpacked. Once you have downloaded the \texttt{WRFDAV3.5-testdata.tar.gz} file to \texttt{\$DAT\_DIR}, extract it by typing
+
+\scriptsize\begin{verbatim}
+> gunzip WRFDAV3.5-testdata.tar.gz
+> tar -xvf WRFDAV3.5-testdata.tar
+\end{verbatim}
+</font>
<font color="gray">ormalsize
+
+At this point you should have successfully downloaded and compiled the WRFDA code, and have the necessary input files for the provided tutorial case. If this is correct, you are ready to learn how to run WRFDA.
+
+\subsection{Run tutorial 3DVAR case}
+\label{wrfda-3dvar-test-case}
+
+The \WRFDA3DVAR system requires, at a minimum, five input files to run, as summarized in the following table:
+
+%\begin{longtable}[t]{llllp{5cm}}
+\begin{longtable}[h]{|l|l|l|l|}
+\hline \textbf{Input file} & \textbf{File name} & \textbf{Format} & \textbf{Source} \\
+\hline First Guess & \texttt{fg} & netCDF & WRF Preprocessing System (WPS) and \\
+ & & & \texttt{real.exe} \textit{or} WRF Forecast \\
+\hline Observations\footnote{Other observation types with separate input files are supported, such as satellite radiance, radar, and accumulated rainfall. These will be detailed in later sections.}
+ & \texttt{ob.ascii} & LITTLE\_R (ASCII)& OBSPROC \\
+ & \texttt{ob.bufr} & PREPBUFR & OBSPROC \textit{or} online\footnote{Some PREPBUFR-formatted data sets can be downloaded directly from the UCAR RDA website, for example: \url{http://rda.ucar.edu/datasets/ds337.0/}} \\
+\hline & & & WRFDA--GEN\_BE utility (CV5) \\
+ Background Error & \texttt{be.dat} & Binary & \textit{or} \\
+ & & & Included in WRFDA package (CV3) \\
+\hline Land Use Table & \texttt{LANDUSE.TBL} & ASCII & Included in WRFDA package \\
+\hline WRFDA namelist & \texttt{namelist.input} & ASCII & Included in WRFDA package \\
+\hline
+\end{longtable}
+
+Now you should find the following files under \texttt{\$DAT\_DIR}:
+
+\begin{itemize}
+\item This is the observation data (\texttt{ob/2008020512/ob.2008020512})
+\item The first guess file (\texttt{rc/2008020512/wrfinput\_d01})
+\item The background error file (\texttt{be/be.dat})
+\end{itemize}
+
+To run {\WRFDA3DVAR}, first create and enter a working directory (for example, \texttt{\$WRFDA\_DIR/3dvar}), and set the environment variable \texttt{\$WORK\_DIR} to this directory (e.g., \texttt{setenv WORK\_DIR \$WRFDA\_DIR/3dvar}). Then follow the steps below:
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Description of Namelist Variables}
+\label{wrfda-namelist}
Added: trunk/wrf/UsersGuide/Users_Guide.tex
===================================================================
--- trunk/wrf/UsersGuide/Users_Guide.tex (rev 0)
+++ trunk/wrf/UsersGuide/Users_Guide.tex 2014-03-13 23:25:47 UTC (rev 467)
@@ -0,0 +1,97 @@
+\documentclass[11pt]{book}
+%
+% Use graphicsx package for including epsi figures
+\usepackage{graphicx}
+% Use espfig package and wrapfig for less-than column
+% width figures
+\usepackage{epsfig,wrapfig}
+%
+% Use the ams packages for equations
+\usepackage{amsmath}
+\usepackage{amssymb}
+%
+% Use bibtex package for the citations
+%\usepackage{natbib}
+%\usepackage[square]{natbib}
+%
+%
+% Use fancyhdr package for headers and footers
+\usepackage{fancyhdr}
+% Use appendix package
+\usepackage[page]{appendix}
+
+% Use packages longtable, pdflscape, endnotes, and color for namelist appendix, define gray
+\usepackage{longtable}
+\usepackage{pdflscape}
+\usepackage{endnotes}
+\usepackage{color, colortbl}
+\definecolor{light-gray}{gray}{0.95}
+\definecolor{gray}{gray}{0.5}
+%
+% Use package "comment" for large comments
+\usepackage{comment}
+%
+% Use "chngcntr" for table numbering
+\usepackage{chngcntr}
+\counterwithin{table}{chapter}
+
+% Set up page layout
+\setlength{\textwidth}{6.75in}
+\setlength{\oddsidemargin}{-0.0in}
+\setlength{\evensidemargin}{-0.25in}
+\setlength{\textheight}{9.0in}
+\setlength{\topmargin}{-0.5in}
+\setlength{\headheight}{0.0in}
+\setlength{\headsep}{0.5in}
+\setlength{\topskip}{0.0in}
+\setlength{\footskip}{0.5in}
+\setlength{\tabcolsep}{0.1in}
+%
+
+% Include some coding shortcuts
+\def \eg{{\emph{e.g.} }}
+\def \ie{{\emph{i.e.} }}
+\def \WRFDA3DVAR{{\emph{WRFDA\textendash 3DVAR} }}
+\def </font>
<font color="black">i{</font>
<font color="blue">oindent}
+\def \wrf{ARW}
+</font>
<font color="blue">ewcommand{\xbmf}[1]{\hbox{\sffamily\slshape #1}}
+</font>
<font color="blue">ewcommand{\xmathbf}{\boldsymbol}
+
+\usepackage{minitoc}
+
+% Use hyperref to insert links in pdf documents SHOULD ALWAYS BE LAST
+%\usepackage[colorlinks,citecolor=black,linkcolor=black,urlcolor=black]{hyperref}
+\usepackage[colorlinks,citecolor=red,linkcolor=blue,urlcolor=cyan]{hyperref}
+
+\begin{document}
+\pagestyle{plain}
+%\pagestyle{fancy}
+
+% preliminary pages
+\include{cover}
+\dominitoc% Initialization
+\setcounter{tocdepth}{1}
+\tableofcontents
+% acknowledgments
+\include{acknow}
+\cleardoublepage
+% chapters
+\pagenumbering{arabic}
+\setcounter{page}{1}
+\include{Chapter_1}
+\include{Chapter_2}
+\include{Chapter_3}
+\include{Chapter_4}
+\include{Chapter_5}
+\include{Chapter_6}
+\include{Chapter_7}
+\include{Chapter_8}
+\include{Chapter_9}
+\include{Chapter_10}
+
+% appendices
+\begin{appendices}
+\include{constants}
+\end{appendices}
+
+\end{document}
</font>
</pre>