<p><b>kavulich@ucar.edu</b> 2014-04-10 15:42:00 -0600 (Thu, 10 Apr 2014)</p><p>- Updated .doc User Guide section on wind speed/direction assimilation<br>
<br>
- Continuing conversion of User's Guide to LaTeX. Finished chapter 6 through the section on Precipitation assimilation<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/wrf/UsersGuide/Chapter_6.tex
===================================================================
--- trunk/wrf/UsersGuide/Chapter_6.tex        2014-04-10 18:24:17 UTC (rev 473)
+++ trunk/wrf/UsersGuide/Chapter_6.tex        2014-04-10 21:42:00 UTC (rev 474)
@@ -1240,32 +1240,197 @@
\subsection{Other namelist options for radiance assimilation}
\label{wrfda-radiance-other}
+\small\begin{longtable}[h]{|l|l|l|l|l|}
+\hline Variable & Type & Size & Default & Description \\
+\hline \multicolumn{5}{|l|}{\texttt{\&wrfvar14}} \\
+\hline rad\_monitoring & integer & \texttt{rtminit\_sensor} & 0 & 0 for assimilating mode, 1 for monitoring\\
+ & & & & mode (only calculates innovation)\\
+\hline thinning & logical & 1 & .true. & Controls thinning on radiance data (highly \\
+ & & & & recommended) \\
+\hline thinning\_mesh & real & \texttt{rtminit\_sensor} & 60 & Thinning mesh (in km) for each sensor \\
+\hline thinning & logical & 1 & .true. & Controls if quality control is performed \\
+ & & & & (highly recommended) \\
+\hline write\_iv\_rad\_ascii & logical & 1 & .false. & Controls whether to output observation minus \\
+ & & & & background (O$-$B) files, which are in ASCII \\
+ & & & & format and separated by sensor and processor used \\
+\hline write\_oa\_rad\_ascii & logical & 1 & .false. & Controls whether to output observation minus \\
+ & & & & analysis(O$-$A) files (including also O$-$B \\
+ & & & & information), which are in ASCII format and \\
+ & & & & separated for each sensor and processor used \\
+\hline use\_error\_factor\_rad & logical & 1 & .false. & use of a radiance error tuning factor file \\
+ & & & & (radiance\_error.factor) which is created with \\
+ & & & & empirical values, or generated using a variational \\
+ & & & & tuning method (Desroziers and Ivanov, 2001) \\
+\hline only\_sea\_rad & logical & 1 & .false. & Controls whether only assimilating radiance over \\
+ & & & & water \\
+\hline use\_antcorr &logical&\texttt{rtminit\_sensor}&.false.& Controls the use of Antenna Correction in CRTM \\
+\hline use\_clddet\_mmr & logical & 1 & .false. & Controls whether to use the MMR scheme for cloud \\
+ & & & & detection for infrared radiance \\
+\hline use\_clddet\_ecmwf & logical & 1 & .false. & Controls whether to use the ECMWF scheme for \\
+ & & & & cloud detection for infrared radiance. This option \\
+ & & & & requires downloading and installing the ECMWF \\
+ & & & & cloud detection code separately. \\
+\hline airs\_warmest\_fov & logical & 1 & .false. & Controls whether to use the observation brightness \\
+ & & & & temperature for AIRS Window channel \#914 as \\
+ & & & & criterion for GSI thinning \\
+\hline use\_crtm\_kmatrix & logical & 1 & .true. & Controls whether to use the the CRTM K matrix \\
+ & & & & rather than calling CRTM TL and AD routines for \\
+ & & & & gradient calculation \\
+\hline use\_rttov\_kmatrix & logical & 1 & .false. & Controls whether to use the the RTTOV K matrix \\
+ & & & & rather than calling RTTOV TL and AD routines for \\
+ & & & & gradient calculation \\
+\hline rttov\_emis\_atlas\_ir & integer & 1 & 0 & Controls the use of the IR emissivity atlas. \\
+ & & & & Emissivity atlas data (should be downloaded \\
+ & & & & separately from the RTTOV web site) needs to \\
+ & & & & be copied or linked under a sub-directory of the \\
+ & & & & working directory (\texttt{emis\_data}) if \\
+ & & & & \texttt{rttov\_emis\_atlas\_ir} is set to 1. \\
+\hline rttov\_emis\_atlas\_ir & integer & 1 & 0 & Controls the use of the MW emissivity atlas. \\
+ & & & & Emissivity atlas data (should be downloaded \\
+ & & & & separately from the RTTOV web site) needs to \\
+ & & & & be copied or linked under a sub-directory of the \\
+ & & & & working directory (\texttt{emis\_data}) if \\
+ & & & & \texttt{rttov\_emis\_atlas\_mw} is set to 1 or 2. \\
+\hline
+\end{longtable}
+</font>
<font color="red">ormalsize
+
+
+\subsection{Diagnostics and monitoring}
+\label{wrfda-radiance-diagnostics-monitoring}
+
+\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:
+
\begin{itemize}
-\item \texttt{rad\_monitoring}: Integer array of dimension \texttt{rtminit\_sensor}, 0 for assimilating mode, 1 for monitoring mode (only calculates innovation).
-\item \texttt{thinning}: Logical, \texttt{.true.} will perform thinning on radiance data (highly recommended).
-\item \texttt{thinning\_mesh}: Real array with dimension \texttt{rtminit\_sensor}, values indicate thinning mesh (in km) for different sensors.
-\item \texttt{qc\_rad}: Logical, controls if quality control is performed, should almost always be set to \texttt{.true.}
-\item \texttt{write\_iv\_rad\_ascii}: Logical, controls whether to output observation minus background (O$-$B) files, which are in ASCII format and separated for each sensor and processor used.
-\item \texttt{write\_oa\_rad\_ascii}: Logical, controls whether to output observation minus analysis (O$-$A) files (including also O$-$B information), which are in ASCII format and separated for each sensor and processor used.
-\item \texttt{use\_error\_factor\_rad}: Logical, controls use of a radiance error tuning factor file
-(radiance\_error.factor) which is created with empirical values, or generated using a variational tuning method (Desroziers and Ivanov, 2001).
-\item \texttt{only\_sea\_rad}: Logical, controls whether only assimilating radiance over water.        
-\item \texttt{use\_antcorr}: Logical array with dimension \texttt{rtminit\_sensor}, controls the use of Antenna Correction in CRTM.
-\item \texttt{use\_clddet\_mmr}: Logical, controls whether to use the MMR scheme to conduct cloud detection for infrared radiance.
-\item \texttt{use\_clddet\_ecmwf}: Logical, controls whether to use the ECMWF scheme to conduct cloud detection for infrared radiance. This option requires downloading and installing the ECMWF cloud detection code separately.
-\item \texttt{airs\_warmest\_fov}: Logical, controls whether to use the observation brightness temperature for AIRS Window channel \#914 as criterion for GSI thinning.
-\item \texttt{use\_crtm\_kmatrix}: Logical, controls whether to use the CRTM K matrix rather than calling CRTM TL and AD routines for gradient calculation.
-\item \texttt{use\_rttov\_kmatrix}: Logical, controls whether to use the RTTOV K matrix rather than calling RTTOV TL and AD routines for gradient calculation.
-\item \texttt{rttov\_emis\_atlas\_ir}: Integer, controls the use of the IR emissivity atlas. Emissivity atlas data (should be downloaded separately from the RTTOV web site) needs to be copied or linked under a sub-directory of the working directory (\texttt{emis\_data}) if \texttt{rttov\_emis\_atlas\_ir} is set to 1.
-\item \texttt{rttov\_emis\_atlas\_mw}: Integer, controls the use of the MW emissivity atlas. Emissivity atlas data (should be downloaded separately from the RTTOV web site) need to be copied or linked under a sub-directory of the working directory (\texttt{emis\_data}) if \texttt{rttov\_emis\_atlas\_mw} is set to 1 or 2.
+
+\item 0 is assimilating mode. Innovations (O minus B) are calculated and data are used in minimization.
+1 is monitoring mode: innovations are calculated for diagnostics and monitoring. Data are not used in minimization.
+\end{itemize}
+
+</font>
<font color="red">i If \texttt{rad\_monitoring} is not set, then the default value of 0 will be used for all sensors.
+
+\subsubsection{Outputting and plotting radiance diagnostics}
+\label{wrfda-radiance-diagnostics}
+
+WRFDA has the ability to output a number of different diagnostics files for radiance assimilation by utilizing the following namelist options in record \texttt{\&wrfvar14} in \texttt{namelist.input}:
+
+\begin{itemize}
+\item \texttt{write\_iv\_rad\_ascii}: Logical, \texttt{.true.} instructs WRFDA to write out diagnostics information (\eg observation-background) in plain-text files with the prefix ``\texttt{inv}'', followed by the instrument name and the processor id. For example, \texttt{01\_inv\_noaa-17-amsub.0000} (01 is the outerloop index, 0000 is the processor index)
+\item \texttt{write\_oa\_rad\_ascii}: Logical, \texttt{.true.} instructs WRFDA to write out diagnostics information (\eg observation-background, observation-analysis) in plain-text files with the prefix ``\texttt{oma}'', followed by the instrument name and the processor id. For example, \texttt{01\_oma\_noaa-18-mhs.0001}
\end{itemize}
-\subsection{Diagnostics and monitoring}
-\label{wrfda-radiation-diagnostic}
+Each processor writes out the information for one instrument in one file in the WRFDA working directory.
+All of these separate files can be inconvenient to work with, so WRFDA offers a solution. One of the 44 executables compiled as part of the WRFDA system is the program \texttt{da\_rad\_diags.exe}. This program can be used to collect the \texttt{01\_inv*} or \texttt{01\_oma*} files and write them out in netCDF format (one instrument in one file with prefix ``\texttt{diags}'' followed by the instrument name, analysis date, and the suffix \texttt{.nc}) for easier data viewing, handling and plotting with netCDF utilities and NCL scripts. See \texttt{WRFDA/var/da/da\_monitor/README} for information on how to use this helpful program.
+Several useful plotting utilities can be found in the WRFDA Tools package (see the \hyperref[wrfda-tools]{WRFDA Tools section} for more information). A Korn Shell script (\texttt{\$TOOLS\_DIR/var/scripts/da\_rad\_diags.ksh}) is available to perform a number of useful functions. It can be used to call the above-mentioned \texttt{da\_rad\_diags.exe} to consolidate the diagnostics files, as well as calling several NCL scripts for plotting, such as \texttt{\$TOOLS\_DIR/var/graphics/ncl/plot\_rad\_diags.ncl} and \texttt{\$TOOLS\_DIR/var/graphics/ncl/advance\_cymdh.ncl}. The options for plotting and manipulating the diagnostic data are described in the comments of the main script.
+
+\section{Precipitation Data Assimilation in \4DVAR}
+\label{wrfda-precip}
+
+The assimilation of precipitation observations in \4DVAR is described in this section. Currently, WRFPLUS includes the adjoint and tangent linear codes of large-scale condensation and cumulus scheme, which allows precipitation data can be assimilated directly in 4DVAR. Users who are interested in the scientific detail of 4D-Var assimilation of precipitation should refer to Ban et al., 2014\footnote{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.}, as this section is only a basic guide to running WRFDA Precipitation Assimilation. This section instructs users on data processing, namelist variable settings, and how to run \4DVAR with precipitation observations.
+
+\subsection{Preparing precipitation observations}
+\label{wrfda-precip-obs}
+
+\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}
+\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.
+
+For users wishing to use their own observations instead of NCEP Stage IV, it is the user's own responsibility to write a Fortran main program and call the subroutine \texttt{writerainobs} (in \texttt{write\_rainobs.f90}) to generate their own precipitation data. For more information please refer to the \texttt{README} file in the \texttt{precip\_converter} directory.
+
+\subsection{Running WRFDA for precipitation assimilation}
+\label{wrfda-precip-run}
+
+\4DVAR is able to assimilate hourly, 3-hourly and 6-hourly precipitation data. According to experiments, 6-hour precipitation accumulations are the ideal observations to be assimilated, as this leads to better results than directly assimilating hourly data, though the user is welcome to experiment with their own cases.
+
+The tutorial example is for assimilating 6-hour accumulated precipitation. In your working directory, link all the necessary files as follows,
+
+\scriptsize\begin{verbatim}
+ > ln -fs $WRFDA_DIR/var/da/da_wrfvar.exe .
+ > ln -fs $DAT_DIR/rc/2008020512/wrfinput_d01 .
+ > ln -fs $DAT_DIR/rc/2008020512/wrfbdy_d01 .
+ > ln -fs wrfinput_d01 fg
+ > ln -fs $DAT_DIR/be/be.dat .
+ > ln -fs $WRFDA_DIR/run/LANDUSE.TBL ./LANDUSE.TBL
+ > ln -fs $DAT_DIR/ob/2008020518/ob.rain.2008020518.06h ob07.rain
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+</font>
<font color="blue">i The reason why the observation \texttt{ob.rain.2008020518.06h} is linked as \texttt{ob07.rain} will be explained \hyperref[wrfda-precip-link-obs]{the next section}.
+
+Edit \texttt{namelist.input} and pay special attention to \texttt{\&wrfvar1} and \texttt{\&wrfvar4} for precipitation-related options, as detailed below:
+
+\begin{longtable}[h]{|l|l|l|l|l|}
+\hline Variable & Type & Size & Default & Description \\
+\hline \multicolumn{5}{|l|}{\texttt{\&wrfvar1}} \\
+\hline var4d\_bin\_rain & integer & 1 & 3600 & Precipitation observation sub-window length for 4D-Var. \\
+ & & & & Can be different from \texttt{var4d\_bin}!\\
+\hline print\_detail\_rain & logical & 1 & .false. & Controls additional rainfall-assimilation-related output. \\
+\hline \multicolumn{5}{|l|}{\texttt{\&wrfvar4}} \\
+\hline use\_rainobs & logical & 1 & .false. & Controls whether rainfall will be assimilated \\
+\hline thin\_rainobs & logical & 1 & .true. & Controls whether rainfall data will be thinned \\
+\hline thin\_mesh\_conv & real & 30 & 20. & Controls the thinning mesh for each type of conventional\\
+ & & & & observations; rainfall is index 28 \\
+\hline max\_error\_rain & real & 1 & 5.0 & Sets the maximum allowable innovation (O minus B) \\
+ & & & & for rainfall (in mm); if the innovation for this \\
+ & & & & observation will be higher than \texttt{max\_error\_rain} \\
+ & & & & it will be rejected \\
+\hline max\_rain\_input & integer & 1 & 10000000& Sets the maximum number of rainfall observations to be \\
+ & & & & assimilated \\
+\hline
+\end{longtable}
+
+Now run 4DVAR (for detailed instructions on running 4DVAR, see the section ``\hyperref[wrfda-4dvar-test-case]{Run tutorial 4DVAR case}'').
+
+\scriptsize\begin{verbatim}
+ >./da_wrfvar.exe >& wrfda.log
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+\subsection{Properly linking observation files}
+\label{wrfda-precip-link-obs}
+
+In the rainfall tutorial case, \texttt{ob.rain.2008020518.06h} is linked as \texttt{ob07.rain}. The number 07 is assigned according to the following rule:
+
+\begin{equation}
+ x = i \times \left( \frac{var4d\_bin\_rain}{var4d\_bin} \right) + 1
+\end{equation}
+
+</font>
<font color="blue">i Here, $i$ is the sequence number of the observation. For $ x < 10$, the observation file should be linked as \texttt{ob0x.rain}, and for $ x \geq 10$, it should be renamed as \texttt{obx.rain}.
+
+In the tutorial example, 6-hour accumulated precipitation data is assimilated in 6-hour time window. In the namelist, values should be set at \texttt{var4d\_bin=3600} and \texttt{var4d\_bin\_rain=21600}, and there is one observation file (i.e., $i=1$) in the time window, thus the value of $x$ is 7, and therefore the file \texttt{ob.rain.2008020518.06h} should be linked as \texttt{ob07.rain}.
+
+Let's look at another example for how to rename observation files, this time for 3-hourly precipitation data in 6-hour time window. The \texttt{\&wrfvar1} namelist record in such a case would be as follows:
+
+\scriptsize\begin{verbatim}
+&wrfvar1
+var4d=true,
+var4d_lbc=true,
+var4d_bin=3600,
+var4d_bin_rain=10800,
+……
+/
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+</font>
<font color="gray">i In this case, WRFDA will expect two observation files, \texttt{ob.rain.2008020515.03h} and \texttt{ob.rain.2008020518.03h}. According to the formula given, the first file ($i=1$) should be linked as \texttt{ob04.rain}, and the second file ($i=2$) linked as \texttt{ob07.rain}.
+
+
+\section{Updating WRF Boundary Conditions}
+\label{wrfda-updatebc}
+
+
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{WRFDA Diagnostics}
@@ -1282,7 +1447,7 @@
\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.
\scriptsize\begin{verbatim}
-> ln -fs $DAT_DIR/rc/2008020518/wrfinput_d01 fg02
+ > ln -fs $DAT_DIR/rc/2008020518/wrfinput_d01 fg02
\end{verbatim}
</font>
<font color="gray">ormalsize
@@ -1291,5 +1456,13 @@
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 Tools}
+\label{wrfda-tools}
+
+The WRFDA Tools package (can be downloaded at \url{http://www.mmm.ucar.edu/wrf/users/wrfda/download/tools.html}) contains a large number of potentially useful shell and NCL scripts (for more information on NCL, the NCAR Command Language, see \url{http://www.ncl.ucar.edu/}) for the convenience of our users. These scripts are used for functions from setting up and running various parts of the WRFDA system to manipulating and displaying diagnostics information. \textbf{These scripts are not supported through wrfhelp; they are offered as-is}, but we hope that users will find them useful.
+
+NCL scripts (also in the WRFDA Tools package: \texttt{\$TOOLS\_DIR/var/graphics/ncl/plot\_rad\_varbc\_param.ncl} and \texttt{\$TOOLS\_DIR/var/graphics/ncl/advance\_cymdh.ncl}) are used for plotting the evolution of VarBC parameters.
+
+
\section{Description of Namelist Variables}
\label{wrfda-namelist}
Modified: trunk/wrf/UsersGuide/users_guide_chap6.doc
===================================================================
--- trunk/wrf/UsersGuide/users_guide_chap6.doc        2014-04-10 18:24:17 UTC (rev 473)
+++ trunk/wrf/UsersGuide/users_guide_chap6.doc        2014-04-10 21:42:00 UTC (rev 474)
@@ -1,6 +1,5 @@
-ࡱ >