<p><b>kavulich@ucar.edu</b> 2014-07-19 01:59:40 -0600 (Sat, 19 Jul 2014)</p><p>-images<br>
-Adding "images" directory to carry PNGs for eventual LaTeX version<br>
<br>
users_guide_chap6.doc<br>
-Continued fixing typos<br>
<br>
Users_Guide.tex<br>
-Made "GEN_BE" shortcut<br>
<br>
Chapter_6.tex<br>
-Continued transcription/improvement: BE section, Exercises section<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/wrf/UsersGuide/Chapter_6.tex
===================================================================
--- trunk/wrf/UsersGuide/Chapter_6.tex        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/Chapter_6.tex        2014-07-19 07:59:40 UTC (rev 505)
@@ -13,7 +13,7 @@
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}
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/chap6/WRFDA_system_chart}
\vspace*{3mm}
In the above chart, the following symbols are used:
@@ -29,7 +29,7 @@
$\mathbf{y^o}$: 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
+$\mathbf{B_0}$: background error statistics from generic BE data (CV3) or \genbe
$\mathbf{R}$: observational and representative error statistics.
@@ -42,7 +42,7 @@
\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.
+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-genbe]{Running \genbe}'' 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.
@@ -113,7 +113,7 @@
\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/\genbe} & Source code of \genbe, 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 \\
@@ -285,7 +285,7 @@
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}.
+The basic \genbe 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. See the section on \hyperref[wrfda-updatebc]{updating boundary conditions} for details.
@@ -403,7 +403,7 @@
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}
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/chap6/OBSPROC_3DVAR_time_window_diagram}
OBSPROC requires at least 3 files to run successfully:
@@ -468,7 +468,7 @@
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}
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/chap6/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.
@@ -548,7 +548,7 @@
\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) \\
+\hline & & & \genbe 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 \\
@@ -843,7 +843,7 @@
Aside from the log files and namelist.output, there will be many text files containing various diagnostics for your WRFDA run; these will be explained in the section on (\hyperref[wrfda-diagnostic-files]{WRFDA Diagnostics}).
-For more practice running WRFDA, see the section (\hyperref[wrfda-exercises]{WRFDA additional exercises}), which give examples on how to use many other useful namelist options.
+For more practice running WRFDA, see the section (\hyperref[wrfda-exercises]{WRFDA Additional Exercises}), which gives examples on how to use many other useful namelist options.
\subsection{Run tutorial 4DVAR case}
\label{wrfda-4dvar-test-case}
@@ -858,7 +858,7 @@
\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) \\
+\hline & & & \genbe utility (CV5) \\
Background Error & \texttt{be.dat} & Binary & \textit{or} \\
& & & Included in WRFDA package (CV3) \\
\hline & \texttt{GENPARM.TBL} & & \\
@@ -973,7 +973,7 @@
Aside from the log files and namelist.output, there will be many text files containing various diagnostics for your WRFDA run; these will be explained in the section on (\hyperref[wrfda-diagnostic-files]{WRFDA Diagnostics}).
-For more practice running WRFDA, see the section (\hyperref[wrfda-exercises]{WRFDA additional exercises}), which give examples on how to use many other useful namelist options.
+For more practice running WRFDA, see the section (\hyperref[wrfda-exercises]{WRFDA Additional Exercises}), which give examples on how to use many other useful namelist options.
\section{Radiance Data Assimilation in WRFDA}
@@ -1031,7 +1031,7 @@
\subsection{Radiance Data Ingest}
\label{wrfda-radiance-ingest}
-Currently, the ingest interface for NCEP BUFR radiance data is implemented in WRFDA. Some radiance data (AIRS, AMSU-A, AMSU-B, HIRS-3, HIRS-4, IASI, and MHS) are available through NCEP’s public ftp server (\url{ftp://ftp.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gdas.yyyymmddhh}) in near real-time (with a 6-hour delay) and can meet requirements for both research purposes and some real-time applications. The following table summarizes the instruments, file names, and namelist switches (in \texttt{\&wrfvar4}) for each supported radiance observation type.
+Currently, the ingest interface for NCEP BUFR radiance data is implemented in WRFDA. Some radiance data (AIRS, AMSU-A, AMSU-B, HIRS-3, HIRS-4, IASI, MHS, and SEVIRI) are available through NCEP’s public ftp server (\url{ftp://ftp.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gdas.yyyymmddhh}) in near real-time (with a 6-hour delay) and can meet requirements for both research purposes and some real-time applications. The following table summarizes the instruments, file names, and namelist switches (in \texttt{\&wrfvar4}) for each supported radiance observation type.
\begin{longtable}[h]{|l|l|l|l|}
\hline \textbf{Instrument} & \textbf{Satellite} & \textbf{File name} & \textbf{Namelist switch} \\
@@ -1217,7 +1217,7 @@
\subsubsection{Offline bias correction with VarBC}
\label{wrfda-varbc-offline}
-The analysis of the VarBC parameters can be performed "offline" ; \ie independent of the main WRFDA analysis. This can be achieved simply by setting the following \texttt{max\_vert\_var*} namelist variables to be 0, which will disable the standard control variables and only keep the VarBC control variables:
+The analysis of the VarBC parameters can be performed ``offline''; \ie independent of the main WRFDA analysis. This can be achieved simply by setting the following \texttt{max\_vert\_var*} namelist variables to be 0, which will disable the standard control variables and only keep the VarBC control variables:
\small\begin{verbatim}
max_vert_var1=0.0
@@ -1234,7 +1234,7 @@
\subsubsection{Other useful namelist options}
\label{wrfda-varbc-other}
-In certain circumstances, it is useful to keep the VarBC bias parameters constant in time ("frozen"). In this case, the bias correction parameters will be read from the \texttt{VARBC.in} file and applied to the innovations, but will not be updated during the minimization. This can be achieved by setting the namelist option \texttt{freeze\_varbc = .true.}
+In certain circumstances, it is useful to keep the VarBC bias parameters constant in time (``frozen''). In this case, the bias correction parameters will be read from the \texttt{VARBC.in} file and applied to the innovations, but will not be updated during the minimization. This can be achieved by setting the namelist option \texttt{freeze\_varbc = .true.}
VarBC uses specific preconditioning, which can be scaled through the namelist option \texttt{varbc\_factor} (default = 1.0). A higher value for \texttt{varbc\_factor} will result in a greater impact from preconditioning, and vice versa.
@@ -1305,7 +1305,7 @@
\subsubsection{WRFDA radiance monitoring capability}
\label{wrfda-radiance-monitoring}
-WRFDA can run in "monitoring mode" for radiance assimilation, where innovations will be calculated for diagnostics but will not be used for minimisation. This mode is controlled by the \texttt{rad\_monitoring} parameter in record \&wrfvar14 of \texttt{namelist.input}. This mode can be controlled on a by-instrument basis, so \texttt{rad\_monitoring} is a vector of length \texttt{rtminit\_nsensor}, where each set value controls the corresponding instrument triplet as follows:
+WRFDA can run in ``monitoring mode'' for radiance assimilation, where innovations will be calculated for diagnostics but will not be used for minimisation. This mode is controlled by the \texttt{rad\_monitoring} parameter in record \&wrfvar14 of \texttt{namelist.input}. This mode can be controlled on a by-instrument basis, so \texttt{rad\_monitoring} is a vector of length \texttt{rtminit\_nsensor}, where each set value controls the corresponding instrument triplet as follows:
\begin{itemize}
@@ -1344,7 +1344,7 @@
\4DVAR can assimilate NCEP Stage IV radar and gauge precipitation data. NCEP Stage IV archived data are available on the NCAR CODIAC web page: \url{http://data.eol.ucar.edu/codiac/dss/id=21.093} (for more information, please see the NCEP Stage IV Q\&A Web page at \url{http://www.emc.ncep.noaa.gov/mmb/ylin/pcpanl/QandA/}). The original precipitation data are at 4-km resolution on a polar-stereographic grid. Hourly, 6-hourly and 24-hourly analyses are available. The following image shows the accumulated 6-h precipitation (in mm) for the tutorial case.
\begin{center}
-\includegraphics[width=4in, keepaspectratio=true]{images/rainfall_tutorial_case}
+\includegraphics[width=4in, keepaspectratio=true]{images/chap6/rainfall_tutorial_case}
\end{center}
It should be mentioned that the NCEP Stage IV archived data is in GRIB1 format and it cannot be ingested into the WRFDA directly. A tool ``\texttt{precip\_converter}'' is provided to reformat GRIB1 observations into the WRFDA-readable ASCII format. It can be downloaded from the WRFDA users page at \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/precip_converter.tar.gz}. The NCEP GRIB libraries ``w3'' and ``g2'' are required to compile \texttt{precip\_converter}. These libraries are available for download from NCEP at \url{http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/}. The output files from the converter utility are named in the format \texttt{ob.rain.yyyymmddhh.xxh}; The ``\texttt{yyyymmddhh}'' in the file name is the ending hour of the accumulation period, and ``xx'' (= 01, 06, or 24) is the accumulating time period.
@@ -1500,35 +1500,242 @@
</font>
<font color="red">ormalsize
These settings will direct UPDATE\_BC to update the lateral boundary conditions (\texttt{wrf\_bdy\_file} will be overwritten with lateral boundary conditions from \texttt{da\_file}).
+
As mentioned in \hyperref[wrfda-lateral-bc]{the previous section}, lateral boundary conditions for child domains (\texttt{wrfinput\_02}, \texttt{wrfinput\_03}, etc.) come from their respective parent domains, so running UPDATE\_BC is not necessary after running WRFDA in these cases. However, in a cycling procedure, the lower boundaries in each of the nested domains' WRFDA analysis files still need to be updated. In these cases, you must set the namelist variable \texttt{domain\_id} > 1 (default is 1 for domain 1), and provide the appropriate wrfinput file (\texttt{wrf\_input = './wrfinput\_d02'} for domain 2, for example).
+\subsection{\4DVAR with lateral boundary conditions as control variables}
+\label{wrfda-update-bc-4dvar-lbc}
+If you activate the \texttt{var4d\_lbc} option in a \4DVAR run, in addition to the above-mentioned files you will also need the \texttt{ana02} file from the WRFDA working directory. In \texttt{parame.in}, set \texttt{var4d\_lbc} to \texttt{.true} and use \texttt{da\_file\_02} to point to the location of the \texttt{ana02} file.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\scriptsize\begin{verbatim}
+ da_file_02 = './ana02'
+ var4d_lbc = .true.
+\end{verbatim}
+</font>
<font color="red">ormalsize
-\section{WRFDA Diagnostics}
-\label{wrfda-diagnostic-files}
+\section{Background error}
+\label{wrfda-be}
-\section{WRFDA additional exercises}
+%%%%%%%%%%%%
+%CHECK THE VARIABLES USED IN THIS SECTION!!!!
+%%%%%%%%%%%%
+
+Users have three choices for background error covariance (BE) to use with WRFDA. We call them CV3, CV5, and CV6. With CV3 and CV5, the background errors are applied to the same set of the control variables: stream function ($\psi'$), unbalanced potential velocity ($\chi'$), unbalanced temperature ($T'$), unbalanced surface pressure ($ps'$), and pseudo-relative-humidity ($q'$). However, for CV6 the moisture control variable is the unbalanced part of pseudo-relative-humidity. With CV3, the control variables are in physical space, while with CV5 and CV6, the control variables are in eigenvector space. The major difference between these two categories of BE is the vertical covariance: CV3 uses a vertical recursive filter to model the vertical covariance while CV5 and CV6 use an empirical orthogonal function (EOF) to represent the vertical covariance. The recursive filters to model the horizontal covariance are also different between the three BE methods. We have not conducted a
systematic comparison of analyses based on these BE methods. However, CV3 (a BE file provided with our WRFDA system) is a global BE and can be used for any regional domain, while CV5 and CV6 BE’s are domain-dependent, which should be generated based on the forecast data from that particular domain. We can not give a recommendation of any BE method being the \textit{best}; the impact on analysis will likely vary on a case-by-case basis.
+
+\subsection{CV3}
+\label{wrfda-be-cv3}
+
+CV3 is the NCEP background error covariance. It is estimated in grid space by what has become known as the NMC method (Parrish and Derber 1992\footnote{CORRECT THIS DAMN CITATION Ban, J., X. Zhang, and X.-Y. Huang,2014: The impact of assimilating NCEP Stage IV Precipitation on analyses and short-range forecasts in WRFDA 4D-Var. \textit{Wea. Forecasting}, under revision.}) . The statistics are estimated with the differences between 24- and 48-hour GFS forecasts with T170 resolution (POSSIBLY INCLUDE FOOTNOTE ABOUT T-NUMBER HERE), valid at the same time of day for 357 consecutive cases over a period of one year. Both the amplitudes and the scales of the background error have to be tuned to represent the forecast error in the estimated fields. The statistics that project multivariate relations among variables are also derived from the NMC method.
+
+The variance of each variable, and the variance of its second derivative, are used to estimate its horizontal scales. For example, the horizontal scales of the stream function can be estimated from the variance of the vorticity and stream function.
+
+The vertical scales are estimated with the vertical correlation of each variable. A table is built to cover the range of vertical scales for the variables. The table is then used to find the scales in vertical grid units. The filter profile and the vertical correlation are fitted locally. The scale of the best fit from the table is assigned as the scale of the variable at that vertical level for each latitude. Note that the vertical scales are locally defined so that negative correlation at higher and/or lower levels is not included.
+
+CV3 is a generic background error statistics method, which can be used for any case. It is quite straightforward to use CV3 in your own case: set \texttt{cv\_options=3} in \texttt{\&wrfvar7} in \texttt{namelist.input}, and link or copy the CV3 BE file provided at \texttt{WRFDA/var/run/be.dat.cv3} into your working directory as \texttt{be.dat}.
+
+\subsection{CV5 and CV6}
+\label{wrfda-be-cv5-cv6}
+
+\subsection{\genbe}
+\label{wrfda-genbe}
+
+To use CV5 or CV6 background error covariance, it is necessary to generate your own domain-specific background error statistics with the \genbe utility. The background error statistics file, supplied with the tutorial test case, can NOT be used for these applications.
+
+The source code for \genbe can be found in \texttt{WRFDA/var/gen\_be}. The executables of \genbe should have been created when you compiled the WRFDA code (\hyperref[install-wrfda]{as described earlier}). The scripts which should be used to run these codes can be found in \texttt{WRFDA/var/scripts/gen\_be}.
+
+The input data for \genbe are netCDF WRF forecast output (``wrfout'') files at specified forecast ranges, which are used to generate model perturbations, used as a proxy for estimates of forecast error. For the NMC-method, the model perturbations are differences between forecasts valid at the same time (\eg T+24 minus T+12 is typical for regional applications, T+48 minus T+24 for global). Climatological estimates of background error may then be obtained by averaging these forecast differences over a period of time (\eg one month). Given input from an ensemble prediction system (EPS), the inputs are ensemble forecasts, and the model perturbations created are the transformed ensemble perturbations. The \genbe code has been designed to work with either forecast difference or ensemble-based perturbations. The former is illustrated in this tutorial example.
+
+It is advisable to use forecasts initialized at various times to remove the influence of the diurnal cycle (\ie do not run \genbe using just 00Z or 12Z model perturbations alone).
+
+\subsection{\genbe input data}
+\label{wrfda-genbe-input}
+
+The inputs to \genbe are netCDF WRF forecast output (``wrfout'') files at specified forecast ranges. To avoid unnecessary large single data files, it is assumed that all forecast ranges are output to separate files. For example, if we wish to calculate BE statistics using the NMC-method with (T+24)$-$(T+12) forecast differences, setting the WRF \texttt{namelist.input} options \texttt{history\_interval=720}, and \texttt{frames\_per\_outfile=1} (the latter being necessary to ensure that a separate file will be created for each output time) we get the necessary output datasets. Then the forecast output files should be arranged in directory trees, with each forecast (including all output files for that individual forecast) in a separate directory. The directory name should be the initial time for each individual forecast, \eg file named \texttt{2008020512/wrfout\_d01\_2008-02-06\_00:00:00} means a 12-hour forecast valid at 2008020600, initialized at 2008020512.
+
+%%%%% PERHAPS INCLUDE SCRIPT IN SOURCE CODE, ALONG WITH README?????
+
+A small example dataset consisting of only three forecasts can be found at \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/testdata.html}. When you untar the \texttt{gen\_be\_forecasts\_20080205.tar.gz} file you will find three directories:
+
+\scriptsize\begin{verbatim}
+ >ls -al
+
+THIS PART NEEDS TO BE FIXED WHEN YOU GET BACK TO WORK
+
+-rw-r--r-- 1 users 11556492 2008020512/wrfout_d01_2008-02-06_00:00:00
+-rw-r--r-- 1 users 11556492 2008020600/wrfout_d01_2008-02-06_12:00:00
+-rw-r--r-- 1 users 11556492 2008020612/wrfout_d01_2008-02-07_00:00:00
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+In the above example, only a 24-hour period (12Z 05 Feb to 12Z 06 Feb 2008) of forecasts, initialized every 12 hours, is supplied to estimate forecast error covariance. It is only for demonstration; it should not be used for actual research applications. The minimum number of forecasts required depends on the application, number of grid points, etc., but should almost always be more than a 3-week period of forecasts. Four weeks or more of forecasts are typically recommended for the NMC method.
+
+Describe gen\_be\_wrapper.ksh in this paragraph. Perhaps reference a readme file.
+
+\subsection{Running \genbe}
+\label{wrfda-genbe-run}
+
+The \genbe utility consists of a number of executables. These should typically not be run individually; a wrapper script (\texttt{gen\_be\_wrapper.ksh}) is provided in \texttt{WRFDA/var/scripts/gen\_be} to generate the BE data file. The following variables need to be set at the beginning of the wrapper script to fit your case:
+
+\scriptsize\begin{verbatim}
+export WRFVAR_DIR=/users/noname/work/code/WRFDA
+export START_DATE=2008020612 # the first perturbation valid date
+export END_DATE=2008020700 # the last perturbation valid date
+export NUM_LEVELS=40 # e_vert - 1
+export BIN_TYPE=5 # 5 for CV5, 6 for CV6
+export FC_DIR=/users/noname/work/exps/expt/fc # where wrf forecasts are
+export RUN_DIR=/users/noname/work/exps/gen_be${BIN_TYPE}
+
+CHANGE ALL THIS TO MATCH THE ACTUAL EXAMPLE DATA
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+\textbf{Note:} \texttt{START\_DATE} and \texttt{END\_DATE} are the valid dates for the \emph{perturbations}, not the forecast start dates. In other words, and as shown in the example above, when you have 24-hour and 12-hour forecasts initialized at 2008020512, through 2008020612, the first and final forecast difference valid dates are 2008020612 and 2008020700, respectively.
+
+%%%%%%%%%%%
+%VERIFY ALL OF THIS!!! I think the dates are wrong!!!
+%%%%%%%%%%%
+
+The directories containing the forecasts should be located in \texttt{FC\_DIR}
+
+Once all of the above variables have been properly set, run the wrapper script:
+
+\scriptsize\begin{verbatim}
+ >./gen_be_wrapper.ksh
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Once the script has finished running (step 4 can take quite some time), the \texttt{be.dat} file containing the necessary background error statistics can be found under the \texttt{RUN\_DIR} directory.
+
+\textbf{Note:} It is possible for a step to run to completion, but the data produced is invalid (\eg all zeros, NaNs, etc.). Even if the \texttt{be.dat} file is successfully created, it may not contain valid data! Be sure to check the log files for any errors if you suspect your BE file was not created properly.
+
+To get a clear idea of what data are included in \texttt{be.dat}, the script \texttt{gen\_be\_plot\_wrapper.ksh} in the same directory (\texttt{WRFDA/var/scripts/gen\_be}) may be used. This plots various data contained in \texttt{be.dat}; for an example, see the plots below:
+
+\includegraphics[width=\textwidth, keepaspectratio=true]{images/chap6/gen_be_plots}
+
+
+
+\section{WRFDA Additional Exercises}
\label{wrfda-exercises}
+\subsection{Single pseudo-observation test}
+\label{wrfda-exercises-pseudo}
+With the single observation test, you may get some ideas of how the background and observation error statistics work in the model variable space. A single observation test is done in WRFDA by setting \texttt{num\_pseudo=1}, along with other pre-specified values in \texttt{\&wrfvar15} and \texttt{\&wrfvar19} of \texttt{namelist.input}. An example of these settings is shown here:
+
+\scriptsize\begin{verbatim}
+&wrfvar15
+ num_pseudo = 1,
+ pseudo_x = 23.0, CAN THESE BE NON-INTEGER VALUES????
+ pseudo_y = 23.0,
+ pseudo_z = 14.0,
+ pseudo_err = 1.0,
+ pseudo_val = 1.0,
+/
+&wrfvar19
+ pseudo_var = 'u',
+/
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+
+When \texttt{num\_pseudo = 1}, WRFDA will not read in normal observations, but will instead generate a single pseudo-observation with a pre-specified innovation (Observation$-$First Guess) value at the desired location in your domain's grid space. In the above example, it will be a ``u'' observation of innovation = 1.0 $m/s$ at i,j = 23,23 and vertical level 14. The variables which can be used for \texttt{pseudo\_var} are ``u'' (zonal wind, units of $m/s$), ``v'' (meridional wind, $m/s$), ``t'' (temperature, $K$), ``p'' (pressure, \textbf{SHOULD THIS BE hPa or Pa??????}), and ``q''. If \texttt{pseudo\_var} is q, then the reasonable values of \texttt{pseudo\_err} and \texttt{pseudo\_val} are 0.001 rather than 1.0 as in the above example.
+
+\textbf{Extra credit:} Try all the possible values for \texttt{pseudo\_var} and see how the response varies among the different variables.
+
+\subsection{Changing the background error length and variance scales}
+\label{wrfda-exercises-length-scales}
+
+b. Response of BE length scaling parameter:
+Run the single observation test with the following additional parameters in record \texttt{\&wrfvar7} of \texttt{namelist.input}.
+
+%CAN THESE SETTINGS BE USED WITH REAL DATA AS WELL?????
+
+\scriptsize\begin{verbatim}
+&wrfvar7
+ len_scaling1 = 0.5, # reduce psi length scale by 50%
+ len_scaling2 = 0.5, # reduce chi_u length scale by 50%
+ len_scaling3 = 0.5, # reduce T length scale by 50%
+ len_scaling4 = 0.5, # reduce q length scale by 50%
+ len_scaling5 = 0.5, # reduce Ps length scale by 50% IS THIS SURFACE PRESSURE????
+/
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Next, run the single observation test with the following additional parameters in record \texttt{\&wrfvar7} of \texttt{namelist.input}.
+
+%CAN THESE SETTINGS BE USED WITH REAL DATA AS WELL?????
+
+\scriptsize\begin{verbatim}
+&wrfvar7
+ var_scaling1 = 0.25, # reduce psi variance by 75%
+ var_scaling2 = 0.25, # reduce chi_u variance by 75%
+ var_scaling3 = 0.25, # reduce T variance by 75%
+ var_scaling4 = 0.25, # reduce q variance by 75%
+ var_scaling5 = 0.25, # reduce Ps variance by 75%
+/
+\end{verbatim}
+</font>
<font color="red">ormalsize
+
+\textbf{Extra credit:} Compare the response of individual variables by only setting one parameter at a time. Note the spread of analysis increment.
+
+
+\subsection{Changing minimization criteria}
+\label{wrfda-exercises-minim}
+
+There are a number of namelist options you can alter to change the criteria at which WRFDA will stop the minimization of the cost function and produce an analysis. By default, eps=0.01, ntmax=200, and max\_external\_its=1.
+
+
%For example, try making the WRFDA convergence criterion more stringent. This is achieved by reducing the value of “EPS” to \eg 0.0001 by adding "EPS=0.0001" in the namelist.input record &wrfvar6.
-\subsubsection{lateral boundary condition CV}
-\4DVAR has the capability to consider lateral boundary conditions as control variables as well during minimization. The namelist variable var4d\_lbc=true turns on this capability. To enable this option, \4DVAR needs not only the first guess at the beginning of the time window, but also the first guess at the end of the time window.
+Run the tutorial case (or another case of your choosing) with the following namelist setting:
+
\scriptsize\begin{verbatim}
+&wrfvar6
+max_ext_its = 2,
+/
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+With this setting, the ``outer loop'' procedure for the minimization will be activated. You may wish to compare various diagnostics with an earlier run.
+
+
+\subsection{Suppressing different data types}
+\label{wrfda-exercises-data-denial}
+
+The types of observations that WRFDA uses in the minimization process depend on what is included in the observation file (obviously), but can also be controlled by the namelist settings. For example, if you have SYNOP data in the observation file, you can suppress its usage in WRFDA by setting \texttt{use\_synopobs=.false.} in record \texttt{\&wrfvar4} of \texttt{namelist.input}. Every observation type can be controlled in this way, but be wary: only some are assimilated by default. For a full list, see the ``use\_*'' settings in record \texttt{\&wrfvar4} in the section ``\hyperref[wrfda-namelist]{Description of Namelist Variables}'' at the end of this chapter.
+
+Turning on and off certain types of observations is widely used for assessing the impact of observations on data assimilation, so you may find these settings very useful.
+
+\subsection{Wind speed/direction assimilation}
+\label{wrfda-exercises-wind-sd}
+
+
+
+
+\subsection{Lateral boundary condition CV}
+\label{wrfda-exercises-4dvar-lbc}
+\4DVAR has the capability to consider lateral boundary conditions as control variables as well during minimization. The namelist variable \texttt{var4d\_lbc=true} turns on this capability. To enable this option, \4DVAR needs not only the first guess at the beginning of the time window, but also the first guess at the end of the time window.
+
+\scriptsize\begin{verbatim}
> ln -fs $DAT_DIR/rc/2008020518/wrfinput_d01 fg02
\end{verbatim}
</font>
<font color="gray">ormalsize
-Please note: For WRFDA beginner, please don’t use this option before you have a good understanding of the 4D-Var lateral boundary conditions control. To disable this feature, make sure var4d\_lbc in namelist.input is set to false.
+Please note: If you utilize the lateral boundary conditions option (\texttt{var4d\_lbc=true}), in addition to the analysis at the beginning of the time window (\texttt{wrfvar\_output}), the analysis at the end of the time window will also be generated as a file named \texttt{ana02}, which will be used in subsequent updating of boundary conditions before the forecast.
-Please note: If you utilize the lateral boundary conditions option (var4d\_lbc=true), in addition to the analysis at the beginning of the time window (wrfvar\_output), the analysis at the end of the time window will also be generated as ana02, which will be used in subsequent updating of boundary conditions before the forecast.
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{WRFDA Diagnostics}
+\label{wrfda-diagnostic-files}
+
+
\section{WRFDA Tools}
\label{wrfda-tools}
Modified: trunk/wrf/UsersGuide/Users_Guide.tex
===================================================================
--- trunk/wrf/UsersGuide/Users_Guide.tex        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/Users_Guide.tex        2014-07-19 07:59:40 UTC (rev 505)
@@ -57,6 +57,7 @@
\def </font>
<font color="blue">d{\textendash}
\def \md{\textemdash}
\def \wrf{WRF\textendash ARW}
+\def \genbe{\emph{GEN\_BE}}
</font>
<font color="black">ewcommand{\xbmf}[1]{\hbox{\sffamily\slshape #1}}
</font>
<font color="gray">ewcommand{\xmathbf}{\boldsymbol}
Added: trunk/wrf/UsersGuide/images/chap6/OBSPROC_3DVAR_time_window_diagram.png
===================================================================
(Binary files differ)
Index: trunk/wrf/UsersGuide/images/chap6/OBSPROC_3DVAR_time_window_diagram.png
===================================================================
--- trunk/wrf/UsersGuide/images/chap6/OBSPROC_3DVAR_time_window_diagram.png        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/images/chap6/OBSPROC_3DVAR_time_window_diagram.png        2014-07-19 07:59:40 UTC (rev 505)
Property changes on: trunk/wrf/UsersGuide/images/chap6/OBSPROC_3DVAR_time_window_diagram.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/wrf/UsersGuide/images/chap6/OBSPROC_4DVAR_time_window_diagram.png
===================================================================
(Binary files differ)
Index: trunk/wrf/UsersGuide/images/chap6/OBSPROC_4DVAR_time_window_diagram.png
===================================================================
--- trunk/wrf/UsersGuide/images/chap6/OBSPROC_4DVAR_time_window_diagram.png        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/images/chap6/OBSPROC_4DVAR_time_window_diagram.png        2014-07-19 07:59:40 UTC (rev 505)
Property changes on: trunk/wrf/UsersGuide/images/chap6/OBSPROC_4DVAR_time_window_diagram.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/wrf/UsersGuide/images/chap6/WRFDA_system_chart.png
===================================================================
(Binary files differ)
Index: trunk/wrf/UsersGuide/images/chap6/WRFDA_system_chart.png
===================================================================
--- trunk/wrf/UsersGuide/images/chap6/WRFDA_system_chart.png        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/images/chap6/WRFDA_system_chart.png        2014-07-19 07:59:40 UTC (rev 505)
Property changes on: trunk/wrf/UsersGuide/images/chap6/WRFDA_system_chart.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/wrf/UsersGuide/images/chap6/gen_be_plots.png
===================================================================
(Binary files differ)
Index: trunk/wrf/UsersGuide/images/chap6/gen_be_plots.png
===================================================================
--- trunk/wrf/UsersGuide/images/chap6/gen_be_plots.png        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/images/chap6/gen_be_plots.png        2014-07-19 07:59:40 UTC (rev 505)
Property changes on: trunk/wrf/UsersGuide/images/chap6/gen_be_plots.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/wrf/UsersGuide/images/chap6/rainfall_tutorial_case.png
===================================================================
(Binary files differ)
Index: trunk/wrf/UsersGuide/images/chap6/rainfall_tutorial_case.png
===================================================================
--- trunk/wrf/UsersGuide/images/chap6/rainfall_tutorial_case.png        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/images/chap6/rainfall_tutorial_case.png        2014-07-19 07:59:40 UTC (rev 505)
Property changes on: trunk/wrf/UsersGuide/images/chap6/rainfall_tutorial_case.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/wrf/UsersGuide/users_guide_chap6.doc
===================================================================
--- trunk/wrf/UsersGuide/users_guide_chap6.doc        2014-07-08 22:57:48 UTC (rev 504)
+++ trunk/wrf/UsersGuide/users_guide_chap6.doc        2014-07-19 07:59:40 UTC (rev 505)
@@ -1,4 +1,4 @@
-ࡱ >