<p><b>kavulich@ucar.edu</b> 2014-03-20 23:20:22 -0600 (Thu, 20 Mar 2014)</p><p>- Fixed a few problems in the current User's Guide Chapter 6 (.doc), since it looks like I won't be able to finish the conversion to LaTeX by release time<br>
<br>
- Continuing conversion of User's Guide to LaTeX. Finished chapter 6 through the section on Radiative Transfer Models (so about 1/3 done)<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/wrf/UsersGuide/Chapter_6.tex
===================================================================
--- trunk/wrf/UsersGuide/Chapter_6.tex        2014-03-13 23:25:47 UTC (rev 467)
+++ trunk/wrf/UsersGuide/Chapter_6.tex        2014-03-21 05:20:22 UTC (rev 468)
@@ -134,31 +134,29 @@
 \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
+Some external libraries (\eg 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}
-&gt; setenv NETCDF your_netcdf_path
+     &gt; setenv NETCDF your_netcdf_path
 \end{verbatim}
 </font>
<font color="red">ormalsize
 
 
-\label{wrfda-rtm}
+\textbf{\textit{Important notes}}
 
-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
+\begin{itemize}
+\item 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.
 
-\small\begin{verbatim}
-&gt; setenv RTTOV /usr/local/rttov11/pgi
-\end{verbatim}
-</font>
<font color="red">ormalsize
+\item If you will eventually want to assimilate radiance data using RTTOV, you will need to set the \texttt{RTTOV} environment variable. See the section on \hyperref[wrfda-rtm]{radiative transfer models} for instructions.
+\end{itemize}
 
-\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}
-&gt; cd WRFDA
-&gt; ./configure wrfda
+     &gt; cd WRFDA
+     &gt; ./configure wrfda
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -168,7 +166,8 @@
 For example, on a Linux machine such as NCAR's Yellowstone, the above steps will look similar to the following: 
 
 \small\begin{verbatim}
-&gt; ./configure wrfda
+     &gt; ./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
@@ -235,14 +234,15 @@
 To compile WRFDA, type
 
 \small\begin{verbatim}
-&gt; ./compile all_wrfvar &gt;\&amp; compile.out}
+     &gt; ./compile all_wrfvar &gt;\&amp; compile.out}
 \end{verbatim}
 </font>
<font color="gray">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}
-&gt;ls -l var/build/*exe var/obsproc/src/obsproc.exe
+     &gt;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
@@ -311,22 +311,22 @@
 
 
 \scriptsize\begin{verbatim}
-&gt; cd WRFPLUSV3 
-&gt; ./configure wrfplus
+     &gt; cd WRFPLUSV3 
+     &gt; ./configure wrfplus
 \end{verbatim}
 </font>
<font color="red">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}
-&gt; ./compile em_real &gt;&amp; compile.out
+     &gt; ./compile em_real &gt;&amp; compile.out
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
 After compilation has finished, you should see the following files:
 
 \scriptsize\begin{verbatim}
-&gt; ls -ls main/*.exe 
+     &gt; 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
@@ -338,20 +338,20 @@
 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}
-&gt;setenv WRFPLUS_DIR ${your_source_code_dir}
+     &gt;setenv WRFPLUS_DIR ${your_source_code_dir}
 \end{verbatim}
 </font>
<font color="red">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.
+If you intend to assimilate satellite radiance data using RTTOV, you should set the RTTOV environment variable as appropriate. See the section on \hyperref[wrfda-rtm]{radiative transfer models} 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}
-&gt;./configure 4dvar
-&gt;./compile all_wrfvar &gt;&amp; compile.out
-&gt;ls -ls var/build/*.exe var/obsproc/*.exe
+     &gt;./configure 4dvar
+     &gt;./compile all_wrfvar &gt;&amp; compile.out
+     &gt;ls -ls var/build/*.exe var/obsproc/*.exe
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -365,14 +365,14 @@
 To remove all object files and executables, type:
 
 \scriptsize\begin{verbatim}
-./clean
+     ./clean
 \end{verbatim}
 </font>
<font color="red">ormalsize
 
 To remove all build files, including \texttt{configure.wrf}, type:
 
 \scriptsize\begin{verbatim}
-./clean -a
+     ./clean -a
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -416,8 +416,8 @@
 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}
-&gt; cd $WRFDA_DIR/var/obsproc
-&gt; cp namelist.obsproc.3dvar.wrfvar-tut namelist.obsproc
+     &gt; cd $WRFDA_DIR/var/obsproc
+     &gt; cp namelist.obsproc.3dvar.wrfvar-tut namelist.obsproc
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -428,7 +428,7 @@
 To run OBSPROC, type
 
 \scriptsize\begin{verbatim}
-&gt; ./obsproc.exe &gt;&amp; obsproc.out
+     &gt; ./obsproc.exe &gt;&amp; obsproc.out
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -461,7 +461,7 @@
 \end{verbatim}
 </font>
<font color="gray">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.
+Before running WRFDA, you may find it useful to learn more about various types of data that will be processed (\eg 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}
@@ -475,8 +475,8 @@
 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}
-&gt; cd $WRFDA_DIR/var/obsproc
-&gt; cp namelist.obsproc.4dvar.wrfvar-tut namelist.obsproc
+     &gt; cd $WRFDA_DIR/var/obsproc
+     &gt; cp namelist.obsproc.4dvar.wrfvar-tut namelist.obsproc
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -489,7 +489,7 @@
 To run OBSPROC, type
 
 \scriptsize\begin{verbatim}
-&gt; ./obsproc.exe &gt;&amp; obsproc.out
+     &gt; ./obsproc.exe &gt;&amp; obsproc.out
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -521,15 +521,15 @@
 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}
-&gt; setenv DAT_DIR your_choice_of_dat_dir
+     &gt; setenv DAT_DIR your_choice_of_dat_dir
 \end{verbatim}
 </font>
<font color="red">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}
-&gt; gunzip WRFDAV3.5-testdata.tar.gz
-&gt; tar -xvf WRFDAV3.5-testdata.tar 
+     &gt; gunzip WRFDAV3.5-testdata.tar.gz
+     &gt; tar -xvf WRFDAV3.5-testdata.tar 
 \end{verbatim}
 </font>
<font color="gray">ormalsize
 
@@ -556,18 +556,599 @@
 \hline
 \end{longtable}
 
-Now you should find the following files under \texttt{\$DAT\_DIR}:
+If you have already \hyperref[wrfda-test-data]{downloaded the test dataset}, 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 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:
+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 (\ie \texttt{setenv WORK\_DIR \$WRFDA\_DIR/3dvar}). Then follow the steps below:
 
+\scriptsize\begin{verbatim}
+     &gt; cd $WORK_DIR 
+     &gt; cp $WRFDA_DIR/var/test/tutorial/namelist.input .
+     &gt; ln -sf $WRFDA_DIR/run/LANDUSE.TBL .
+     &gt; ln -sf $DAT_DIR/rc/2008020512/wrfinput_d01 ./fg
+     &gt; ln -sf $WRFDA_DIR/var/obsproc/obs_gts_2008-02-05_12:00:00.3DVAR ./ob.ascii (note the different name!)
+     &gt; ln -sf $DAT_DIR/be/be.dat . 
+     &gt; ln -sf $WRFDA_DIR/var/da/da_wrfvar.exe .
+\end{verbatim}
+</font>
<font color="red">ormalsize
 
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+Now open the file \texttt{namelist.input}, which is a very basic namelist for the tutorial test case, and is shown below. 
+
+\scriptsize\begin{verbatim}
+&amp;wrfvar1
+var4d=false,
+print_detail_grad=false,
+/
+&amp;wrfvar2
+/
+&amp;wrfvar3
+ob_format=2,
+/
+&amp;wrfvar4
+/
+&amp;wrfvar5
+/
+&amp;wrfvar6
+max_ext_its=1,
+ntmax=50,
+orthonorm_gradient=true,
+/
+&amp;wrfvar7
+cv_options=5,
+/
+&amp;wrfvar8
+/
+&amp;wrfvar9
+/
+&amp;wrfvar10
+test_transforms=false,
+test_gradient=false,
+/
+&amp;wrfvar11
+/
+&amp;wrfvar12
+/
+&amp;wrfvar13
+/
+&amp;wrfvar14
+/
+&amp;wrfvar15
+/
+&amp;wrfvar16
+/
+&amp;wrfvar17
+/
+&amp;wrfvar18
+analysis_date=&quot;2008-02-05_12:00:00.0000&quot;,
+/
+&amp;wrfvar19
+/
+&amp;wrfvar20
+/
+&amp;wrfvar21
+time_window_min=&quot;2008-02-05_11:00:00.0000&quot;,
+/
+&amp;wrfvar22
+time_window_max=&quot;2008-02-05_13:00:00.0000&quot;,
+/
+&amp;wrfvar23
+/
+&amp;time_control
+start_year=2008,
+start_month=02,
+start_day=05,
+start_hour=12,
+end_year=2008,
+end_month=02,
+end_day=05,
+end_hour=12,
+/
+&amp;fdda
+/
+&amp;domains
+e_we=90,
+e_sn=60,
+e_vert=41,
+dx=60000,
+dy=60000,
+/
+&amp;dfi_control
+/
+&amp;tc
+/
+&amp;physics
+mp_physics=3,
+ra_lw_physics=1,
+ra_sw_physics=1,
+radt=60,
+sf_sfclay_physics=1,
+sf_surface_physics=1,
+bl_pbl_physics=1,
+cu_physics=1,
+cudt=5,
+num_soil_layers=5,
+mp_zero_out=2,
+co2tf=0,
+/
+&amp;scm
+/
+&amp;dynamics
+/
+&amp;bdy_control
+/
+&amp;grib2
+/
+&amp;fire
+/
+&amp;namelist_quilt
+/
+&amp;perturbation
+/
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+No edits should be needed if you are running the tutorial case without radiance data. If you plan to use the PREPBUFR-format observations, change the \texttt{ob\_format=1} in \texttt{\&amp;wrfvar3} in \texttt{namelist.input} and link the \texttt{ob.bufr} file instead: 
+
+\scriptsize\begin{verbatim}
+     &gt; ln -fs $DAT_DIR/ob/2008020512/gds1.t12.prepbufr.nr  ob.bufr
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Once you have changed any other necessary namelist variables, run the WRFDA executable file: 
+
+\scriptsize\begin{verbatim}
+     &gt; da_wrfvar.exe &gt;&amp; wrfda.log
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+After successful completion, \texttt{wrfvar\_output} (the WRFDA analysis file, \ie the new initial condition for WRF) should appear in the working directory, along with a number of other output files. The file \texttt{wrfda.log} (or \texttt{rsl.out.0000}, if run in distributed-memory mode) contains important WRFDA runtime log information. Always check the log after a WRFDA run:
+
+\scriptsize\begin{verbatim}
+***  VARIATIONAL ANALYSIS ***
+ DYNAMICS OPTION: Eulerian Mass Coordinate
+    alloc_space_field: domain            1,              606309816 bytes allocat
+ ed
+ WRF TILE   1 IS      1 IE     89 JS      1 JE     59
+ WRF NUMBER OF TILES =   1
+Set up observations (ob)
+  
+Using ASCII format observation input
+  
+ scan obs ascii
+ end scan obs ascii
+Observation summary
+   ob time  1
+      sound                 86 global,      86 local
+      synop                757 global,     750 local
+      pilot                 85 global,      85 local
+      satem                106 global,     105 local
+      geoamv              2556 global,    2499 local
+      polaramv               0 global,       0 local
+      airep                224 global,     221 local
+      gpspw                187 global,     187 local
+      gpsrf                  3 global,       3 local
+      metar               2416 global,    2408 local
+      ships                145 global,     140 local
+      ssmi_rv                0 global,       0 local
+      ssmi_tb                0 global,       0 local
+      ssmt1                  0 global,       0 local
+      ssmt2                  0 global,       0 local
+      qscat               2190 global,    2126 local
+      profiler              61 global,      61 local
+      buoy                 247 global,     247 local
+      bogus                  0 global,       0 local
+      pseudo                 0 global,       0 local
+      radar                  0 global,       0 local
+      radiance               0 global,       0 local
+      airs retrieval         0 global,       0 local
+      sonde_sfc             86 global,      86 local
+      mtgirs                 0 global,       0 local
+      tamdar                 0 global,       0 local

+Set up background errors for regional application for cv_options =   5
+
+   Using the averaged regression coefficients for unbalanced part
+  
+   WRF-Var dry control variables are:psi, chi_u, t_u and ps_u
+   Humidity control variable is rh
+  
+Vertical truncation for psi    =  15(  99.00%)

+Vertical truncation for chi_u  =  20(  99.00%)

+Vertical truncation for t_u    =  29(  99.00%)

+Vertical truncation for rh     =  22(  99.00%)

+  
+   Scaling: var, len, ds:   0.100000E+01   0.100000E+01   0.600000E+05
+   Scaling: var, len, ds:   0.100000E+01   0.100000E+01   0.600000E+05
+   Scaling: var, len, ds:   0.100000E+01   0.100000E+01   0.600000E+05
+   Scaling: var, len, ds:   0.100000E+01   0.100000E+01   0.600000E+05
+   Scaling: var, len, ds:   0.100000E+01   0.100000E+01   0.600000E+05
+Calculate innovation vector(iv)
+  
+Minimize cost function using CG method
+  
+Starting outer iteration :   1
+Starting cost function:  2.53214888D+04, Gradient=  2.90675545D+02
+For this outer iteration gradient target is:        2.90675545D+00
+----------------------------------------------------------
+Iter    Cost Function         Gradient             Step
+  1      2.32498037D+04      2.55571188D+02      4.90384516D-02
+  2      2.14988144D+04      2.22354203D+02      5.36154186D-02
+  3      2.01389088D+04      1.62537907D+02      5.50108123D-02
+  4      1.93433827D+04      1.26984567D+02      6.02247687D-02
+  5      1.88877194D+04      9.84565874D+01      5.65160951D-02
+  6      1.86297777D+04      7.49071361D+01      5.32184146D-02
+  7      1.84886755D+04      5.41516421D+01      5.02941363D-02
+  8      1.84118462D+04      4.68329312D+01      5.24003071D-02
+  9      1.83485166D+04      3.53595537D+01      5.77476335D-02
+ 10      1.83191278D+04      2.64947070D+01      4.70109040D-02
+ 11      1.82984221D+04      2.06996271D+01      5.89930206D-02
+ 12      1.82875693D+04      1.56426527D+01      5.06578447D-02
+ 13      1.82807224D+04      1.15892153D+01      5.59631997D-02
+ 14      1.82773339D+04      8.74778514D+00      5.04582959D-02
+ 15      1.82751663D+04      7.22150257D+00      5.66521675D-02
+ 16      1.82736284D+04      4.81374868D+00      5.89786400D-02
+ 17      1.82728636D+04      3.82286871D+00      6.60104384D-02
+ 18      1.82724306D+04      3.16737517D+00      5.92526480D-02
+ 19      1.82721735D+04      2.23392283D+00      5.12604438D-02
+----------------------------------------------------------

+Inner iteration stopped after   19 iterations

+Final:  19 iter, J= 1.98187399D+04, g= 2.23392283D+00
+----------------------------------------------------------
+  
+Diagnostics
+   Final cost function J       =     19818.74
+  
+   Total number of obs.        =    39800
+   Final value of J            =     19818.73988
+   Final value of Jo           =     16859.85861
+   Final value of Jb           =      2958.88127
+   Final value of Jc           =         0.00000
+   Final value of Je           =         0.00000
+   Final value of Jp           =         0.00000
+   Final value of Jl           =         0.00000
+   Final J / total num_obs     =         0.49796
+   Jb factor used(1)           =         1.00000        1.00000        1.00000        1.00000        1.00000
+        1.00000        1.00000        1.00000        1.00000        1.00000
+   Jb factor used(2)           =         1.00000        1.00000        1.00000        1.00000        1.00000
+        1.00000        1.00000        1.00000        1.00000        1.00000
+   Jb factor used(3)           =         1.00000        1.00000        1.00000        1.00000        1.00000
+        1.00000        1.00000        1.00000        1.00000        1.00000
+   Jb factor used(4)           =         1.00000        1.00000        1.00000        1.00000        1.00000
+        1.00000        1.00000        1.00000        1.00000        1.00000
+   Jb factor used(5)           =         1.00000        1.00000        1.00000        1.00000        1.00000
+        1.00000        1.00000        1.00000        1.00000        1.00000
+   Jb factor used              =         1.00000
+   Je factor used              =         1.00000
+   VarBC factor used           =         1.00000
+  
+ *** WRF-Var completed successfully ***
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+</font>
<font color="blue">i If the line ``\texttt{*** WRF-Var completed successfully ***}'' does not appear, something has likely gone wrong: check the \texttt{rsl.error.*} files for error messages.
+
+The file \texttt{namelist.output.da} (which contains the complete namelist settings) will be generated after a successful run of \texttt{da\_wrfvar.exe}. The settings appearing in \texttt{namelist.output.da}, but not specified in your \texttt{namelist.input}, are the default values from \texttt{\$WRFDA\_DIR/Registry/registry.var}.
+
+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.
+
+\subsection{Run tutorial 4DVAR case}
+\label{wrfda-4dvar-test-case}
+
+While \WRFDA3DVAR required at least five input files, the \4DVAR 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}  &amp; \textbf{File name}      &amp; \textbf{Format}  &amp; \textbf{Source} \\
+\hline First Guess          &amp; \texttt{fg}             &amp; netCDF           &amp; WRF Preprocessing System (WPS) and \\
+                            &amp;                         &amp;                  &amp; \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.}
+                            &amp; \texttt{ob.ascii*}      &amp; LITTLE\_R (ASCII)&amp; OBSPROC \\
+                            &amp; \texttt{ob.bufr*}       &amp; PREPBUFR         &amp; 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                      &amp;                         &amp;                  &amp; WRFDA--GEN\_BE utility (CV5) \\
+       Background Error     &amp; \texttt{be.dat}         &amp; Binary           &amp; \textit{or} \\
+                            &amp;                         &amp;                  &amp; Included in WRFDA package (CV3) \\
+\hline                      &amp; \texttt{GENPARM.TBL}    &amp;                  &amp; \\
+       WRF Data tables      &amp; \texttt{LANDUSE.TBL}    &amp; ASCII            &amp; Included in WRFDA package \\
+       (for WRFPLUS)        &amp; \texttt{SOILPARM.TBL}   &amp;                  &amp; \\
+                            &amp; \texttt{VEGPARM.TBL}    &amp;                  &amp; \\
+\hline WRFDA namelist       &amp; \texttt{namelist.input} &amp; ASCII            &amp; Included in WRFDA package \\
+\hline
+\end{longtable}
+
+If you have already \hyperref[wrfda-test-data]{downloaded the test dataset}, you should find the following files under \texttt{\$DAT\_DIR}:
+
+
+\begin{itemize}
+\item This case uses the standard seven time windows, for each of which there is an observation file:
+\scriptsize\begin{verbatim}
+     ob/2008020512/ob.ascii+
+     ob/2008020513/ob.ascii
+     ob/2008020514/ob.ascii
+     ob/2008020515/ob.ascii
+     ob/2008020516/ob.ascii
+     ob/2008020517/ob.ascii
+     ob/2008020518/ob.ascii-
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+\item The first guess file (\texttt{rc/2008020512/wrfinput\_d01})
+\item The background error file (\texttt{be/be.dat})
+\end{itemize}
+
+To run {\4DVAR}, first create and enter a working directory, (for example, \texttt{\$WRFDA\_DIR/4dvar}), and set the environment variable \texttt{\$WORK\_DIR} to this directory (\ie \texttt{setenv WORK\_DIR \$WRFDA\_DIR/4dvar}). Then enter the working directory and copy and link the files as shown:
+
+\scriptsize\begin{verbatim}
+     &gt; cd $WORK_DIR
+     &gt; ln -fs $WRFDA_DIR/var/da/da_wrfvar.exe .
+     &gt; ln -fs $DAT_DIR/ob/2008020512/ob.ascii+ ob01.ascii
+     &gt; ln -fs $DAT_DIR/ob/2008020513/ob.ascii  ob02.ascii
+     &gt; ln -fs $DAT_DIR/ob/2008020514/ob.ascii  ob03.ascii
+     &gt; ln -fs $DAT_DIR/ob/2008020515/ob.ascii  ob04.ascii
+     &gt; ln -fs $DAT_DIR/ob/2008020516/ob.ascii  ob05.ascii
+     &gt; ln -fs $DAT_DIR/ob/2008020517/ob.ascii  ob06.ascii
+     &gt; ln -fs $DAT_DIR/ob/2008020518/ob.ascii- ob07.ascii
+     &gt; ln -fs $DAT_DIR/rc/2008020512/wrfinput_d01 .
+     &gt; ln -fs wrfinput_d01 fg
+     &gt; ln -fs $DAT_DIR/be/be.dat .
+     &gt; ln -fs $WRFDA_DIR/run/LANDUSE.TBL .
+     &gt; ln -fs $WRFDA_DIR/run/GENPARM.TBL .
+     &gt; ln -fs $WRFDA_DIR/run/SOILPARM.TBL .
+     &gt; ln -fs $WRFDA_DIR/run/VEGPARM.TBL .
+     &gt; ln –fs $WRFDA_DIR/run/RRTM_DATA_DBL RRTM_DATA
+     &gt; cp $WRFDA_DIR/var/test/4dvar/namelist.input .
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+Open \texttt{namelist.input}. The most important namelist variables related to 4DVAR are listed below. Please refer to \texttt{README.namelist} under the \texttt{\$WRFDA\_DIR/var} directory. Common mistakes users make are in the time information settings. The general rules are: \texttt{analysis\_date}, \texttt{time\_window\_min} and \texttt{start\_xxx} in \texttt{\&amp;time\_control} should always be equal to each other; \texttt{time\_window\_max} and \texttt{end\_xxx} should always be equal to each other; and \texttt{run\_hours} is the difference between \texttt{start\_xxx} and \texttt{end\_xxx}, which is the length of the 4DVAR time window.
+
+\scriptsize\begin{verbatim}
+&amp;wrfvar1
+var4d=true,
+var4d_lbc=false,
+var4d_bin=3600,
+/
+……
+&amp;wrfvar18
+analysis_date=&quot;2008-02-05_12:00:00.0000&quot;,
+/
+……
+&amp;wrfvar21
+time_window_min=&quot;2008-02-05_12:00:00.0000&quot;,
+/
+……
+&amp;wrfvar22
+time_window_max=&quot;2008-02-05_18:00:00.0000&quot;,
+/
+……
+&amp;time_control
+run_hours=6,
+start_year=2008,
+start_month=02,
+start_day=05,
+start_hour=12,
+end_year=2008,
+end_month=02,
+end_day=05,
+end_hour=18,
+interval_seconds=21600,
+debug_level=0,
+/
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+If you want to use PREPBUFR format observation data instead of ASCII, set \texttt{ob\_format=1} in \texttt{\&amp;wrfvar3} in \texttt{namelist.input}. Because NCEP PREPBUFR data only includes the data from 3 hours before and after the main observation hours (for 12UTC, this is 9UTC to 15UTC), for 4DVAR you should include both 12UTC and 18UTC PREPBUFR data:
+
+\scriptsize\begin{verbatim}
+&gt; ln -fs $DAT_DIR/ob/2008020512/gds1.t12.prepbufr.nr  ob01.bufr
+&gt; ln -fs $DAT_DIR/ob/2008020518/gds1.t18.prepbufr.nr  ob02.bufr
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+
+Now run WRFDA:
+\scriptsize\begin{verbatim}
+&gt; ./da_wrfvar.exe &gt;&amp; wrfda.log
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+After successful completion, \texttt{wrfvar\_output} (the WRFDA analysis file, \ie the new initial condition for WRF) should appear in the working directory, along with a number of other output files. The file \texttt{wrfda.log} (or \texttt{rsl.out.0000}, if run in distributed-memory mode) contains important WRFDA runtime log information. Always check the log after a WRFDA run. If the line ``\texttt{*** WRF-Var completed successfully ***}'' does not appear at the end, something has likely gone wrong: check the \texttt{rsl.error.*} files for error messages.
+
+The file \texttt{namelist.output.da} (which contains the complete namelist settings) will be generated after a successful run of \texttt{da\_wrfvar.exe}. The settings appearing in \texttt{namelist.output.da}, but not specified in your \texttt{namelist.input}, are the default values from \texttt{\$WRFDA\_DIR/Registry/registry.var}. For 4DVAR, there will also be a \texttt{namelist.output} file generated by WRFPLUS.
+
+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.
+
+
+\section{Radiance Data Assimilation in WRFDA}
+\label{wrfda-radiance}
+
+%%%%%% In addition to more conventional observations, WRFDA has the ability to assimilate raw radiance observations from over a dozen satellite instruments. Radiance observations can be ingested in any mode of assimilation in WRFDA (3DVAR, 4DVAR, Hybrid), and there are two radiative transfer models available: CRTM and RTTOV.
+This section gives a brief description for various aspects related to radiance assimilation in WRFDA. Each aspect is described mainly from the viewpoint of usage, rather than more technical and scientific details, which will appear in a separate technical report and scientific paper. Namelist parameters controlling different aspects of radiance assimilation will be detailed in the following sections. It should be noted that this section does not cover general aspects of the assimilation process with WRFDA; these can be found in other sections of chapter 6 of this user’s guide, or other WRFDA documentation.
+
+%\subsection{Radiative Transfer Model (RTM)}
+%\label{wrfda-rtm}
+
+\subsection{Running WRFDA with radiance observations}
+\label{wrfda-radiance-run}
+
+In addition to the basic input files (LANDUSE.TBL, fg, ob.ascii, be.dat) mentioned in the “Running WRFDA” section, the following additional files are required for the assimilation radiances: 
+
+\begin{longtable}[h]{|l|l|l|l|}
+\hline \textbf{Input file}   &amp; \textbf{File name}      &amp; \textbf{Format}  &amp; \textbf{Source} \\
+\hline Observations          &amp; \texttt{*.bufr}         &amp; BUFR             &amp; Online \footnote{WRFDA can assimilate all radiance data from the Global Data Assimilation System (GDAS), found at the UCAR RDA website: \url{http://rda.ucar.edu/datasets/ds735.0/}. Data from other supported platforms can be found at various other websites}\\
+\hline Instrument info       &amp; \texttt{radiance\_info} &amp; Binary files     &amp; Included in WRFDA package \\
+\hline Variational Bias      &amp;                         &amp;                  &amp; \\
+       Correction statistics &amp; \texttt{VARBC.in}       &amp; ASCII            &amp; Included in WRFDA package \\
+\hline RTM coefficient files &amp; \texttt{crtm\_coeffs}   &amp;                  &amp; Included in WRFDA package (CRTM)\\
+       (CRTM or RTTOV)       &amp; \textit{or}             &amp; Binary files     &amp; \textit{or} \\
+                             &amp; \texttt{rttov\_coeffs}  &amp;                  &amp; Download from UK Met Office/EUMETSAT\footnote{\url{http://research.metoffice.gov.uk/research/interproj/nwpsaf/rtm/}} (RTTOV)\\
+\hline
+\end{longtable}
+
+
+Edit \texttt{namelist.input} (Pay special attention to \texttt{\&amp;wrfvar4}, \texttt{\&amp;wrfvar14}, \texttt{\&amp;wrfvar21}, and \texttt{\&amp;wrfvar22} for radiance-related options. A very basic \texttt{namelist.input} for running the radiance test case is provided in \texttt{WRFDA/var/test/radiance/namelist.input})
+
+For the tutorial case provided (see the \hyperref[wrfda-test-data]{test data section} for details), you will need to link the following additional files (and \texttt{radiance\_info}, a directory) to your working directory before running WRFDA:
+
+\scriptsize\begin{verbatim}
+&gt; ln -sf $DAT_DIR/gdas1.t00z.1bamua.tm00.bufr_d   ./amsua.bufr
+&gt; ln -sf $DAT_DIR/gdas1.t00z.1bamub.tm00.bufr_d   ./amsub.bufr
+&gt; ln -sf $WRFDA_DIR/var/run/radiance_info  ./radiance_info
+&gt; ln -sf $WRFDA_DIR/var/run/VARBC.in  ./VARBC.in
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+</font>
<font color="blue">i You will also need to link the directory which contains the binary coefficient files for the RTM of your choice. For CRTM this directory is included; for RTTOV you must download and compile the code separately.
+
+For CRTM:
+\scriptsize\begin{verbatim}
+&gt; ln -sf WRFDA/var/run/crtm_coeffs ./crtm_coeffs
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+For RTTOV:
+\scriptsize\begin{verbatim}
+&gt; ln -sf your_RTTOV_path/rtcoef_rttov10/rttov7pred51L  ./rttov_coeffs
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+\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{\&amp;wrfvar4}) for each supported radiance observation type.
+
+\begin{longtable}[h]{|l|l|l|l|}
+\hline \textbf{Instrument} &amp; \textbf{Satellite}  &amp; \textbf{File name}    &amp; \textbf{Namelist switch} \\
+\hline AIRS                &amp; EOS-Aqua            &amp; \texttt{airs.bufr}    &amp; \texttt{use\_airsobs} \\
+\hline AMSU-A              &amp; EOS-Aqua            &amp; \texttt{amsua.bufr}   &amp; \texttt{use\_eos\_amsuaobs} \\
+\hline AMSU-A              &amp; METOP-A             &amp; \texttt{amsua.bufr}   &amp; \texttt{use\_amsuaobs} \\
+                           &amp; NOAA 15{</font>
<font color="blue">d}19      &amp;                       &amp; \\
+\hline AMSU-B              &amp; NOAA 15{</font>
<font color="blue">d}17      &amp; \texttt{amsub.bufr}   &amp; \texttt{use\_amsubobs} \\
+\hline ATMS                &amp; Suomi-NPP           &amp; \texttt{atms.bufr}    &amp; \texttt{use\_atmsobs} \\
+\hline HIRS-3              &amp; NOAA 15{</font>
<font color="blue">d}17      &amp; \texttt{hirs3.bufr}   &amp; \texttt{use\_hirs3obs} \\
+\hline HIRS-4              &amp; METOP-A             &amp; \texttt{hirs4.bufr}   &amp; \texttt{use\_hirs4obs} \\
+                           &amp; NOAA 18{</font>
<font color="blue">d}19      &amp;                       &amp; \\
+\hline IASI                &amp; METOP-A             &amp; \texttt{iasi.bufr}    &amp; \texttt{use\_iasiobs} \\
+\hline MHS                 &amp; METOP-A             &amp; \texttt{mhs.bufr}     &amp; \texttt{use\_mhsobs} \\
+                           &amp; NOAA 18{</font>
<font color="blue">d}19      &amp;                       &amp; \\
+\hline MWHS                &amp; FY-3A               &amp; \texttt{mwhsa.dat}$^{*}$&amp; \texttt{use\_mwhsobs} \\
+\hline MWHS                &amp; FY-3B               &amp; \texttt{mwhsb.dat}$^{*}$&amp; \texttt{use\_mwhsobs} \\
+\hline MWTS                &amp; FY-3A               &amp; \texttt{mwtsa.dat}$^{*}$&amp; \texttt{use\_mwtsobs} \\
+\hline MWTS                &amp; FY-3B               &amp; \texttt{mwtsb.dat}$^{*}$&amp; \texttt{use\_mwtsobs} \\
+\hline SEVIRI              &amp; Meteosat 8{</font>
<font color="blue">d}10   &amp; \texttt{seviri.bufr}  &amp; \texttt{use\_seviriobs} \\
+\hline SSMIS               &amp; DMSP 16{</font>
<font color="blue">d}18      &amp; \texttt{ssmis.bufr}   &amp; \texttt{use\_ssmisobs} \\
+\hline
+\end{longtable}
+
+</font>
<font color="blue">i$^*$Data from FY-3 series satellites is not in BUFR format, but another binary format
+
+%As of Version 3.4, WRFDA can read data from the NOAA ATOVS instruments (HIRS, AMSU-A, AMSU-B and MHS), the EOS Aqua instruments (AIRS, AMSU-A) and DMSP instruments (SSMIS). Note that NCEP radiance BUFR files are separated by in-strument names (i.e., one file for each type of instrument), and each file contains global radiance (generally converted to brightness temperature) within a 6-hour assimilation window, from multi-platforms. For running WRFDA, users need to rename NCEP corre-sponding BUFR files (table 1) to hirs3.bufr (including HIRS data from NOAA-15/16/17), hirs4.bufr (including HIRS data from NOAA-18/19, METOP-2), amsua.bufr (including AMSU-A data from NOAA-15/16/18/19, METOP-2), amsub.bufr (including AMSU-B data from NOAA-15/16/17), mhs.bufr (including MHS data from NOAA-18/19 and METOP-2), airs.bufr (including AIRS and AMSU-A data from EOS-AQUA) ssmis.bufr (SSMIS data from DMSP-16, AFWA provided) and iasi.bufr (IASI data from Metop-2) for WRFDA filename conventio
 n. Note that the airs.bufr file contains not only AIRS data but also AMSU-A, which is collocated with AIRS pixels (1 AMSU-A pixel collocated with 9 AIRS pixels). Users must place these files in the working directory where the WRFDA executable is run. It should also be mentioned that WRFDA reads these BUFR radiance files directly without the use of any separate pre-processing program. All processing of radiance data, such as quality control, thinning, bias correction, etc., is carried out within WRFDA. This is different from conventional observation assimilation, which requires a pre-processing package (OBSPROC) to generate WRFDA readable ASCII files. For reading the radiance BUFR files, WRFDA must be compiled with the NCEP BUFR library (see http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB/).
+
+</font>
<font color="blue">i The namelist variables listed in the rightmost column are the namelist switches which should be set to \texttt{.true.} (in your namelist file under in \texttt{\&amp;wrfvar4}) if you wish to read the specified data. The file names listed in the third column are the file names where WRFDA will assume the data is. These parameters only control whether the data is read, not whether the data included in the files will be assimilated: that is controlled by other namelist parameters explained in the next section.
+
+
+\subsection{Radiative Transfer Model (RTM)}
+\label{wrfda-rtm}
+
+The core component for direct radiance assimilation is to incorporate a radiative transfer model (RTM) into the WRFDA system as one part of observation operators. Two widely used RTMs in the NWP community, RTTOV (developed by ECMWF and UKMET in Europe), and CRTM (developed by the Joint Center for Satellite Data Assimilation (JCSDA) in the United States), are implemented in the WRFDA system with a flexible and consistent user interface. The CRTM source code is included with the WRFDA package, and it is automatically compiled when the main WRFDA code is compiled. The RTTOV package is not distributed with WRFDA due to licensing issues. Users need to follow the instructions at \url{http://research.metoffice.gov.uk/research/interproj/nwpsaf/rtm} to download the RTTOV source code, supplemental coefficient files, and the emissivity atlas dataset. In WRFDA Version 3.6, only RTTOV Version 11 can be used.
+
+WRFDA is designed to be able to run with either of these RTMs at runtime, provided the appropriate settings were chosen at compile time. the user must select one of the two or neither, via the namelist parameter \texttt{rtm\_option} under \texttt{\&amp;wrfvar14} (1 for RTTOV, the default, and 2 for CRTM).
+
+Both RTMs can calculate radiances for almost all available instruments aboard the various satellite platforms in orbit. An important feature of the WRFDA design is that all data structures related to radiance assimilation are dynamically allocated during running time, according to a simple namelist setup. The instruments to be assimilated are controlled at run-time by four integer namelist parameters, also under \texttt{\&amp;wrfvar14}: \texttt{rtminit\_nsensor} (the total number of sensors to be assimilated), \texttt{rtminit\_platform} (an array of dimension \texttt{rtminit\_nsensor} containing the platform IDs for each sensor to be assimilated, \eg 1 for NOAA, 9 for EOS, 10 for METOP and 2 for DMSP), \texttt{rtminit\_satid} (satellite IDs array) and \texttt{rtminit\_sensor} (sensor IDs array, \eg 0 for HIRS, 3 for AMSU-A, 4 for AMSU-B, 15 for MHS, 10 for SSMIS, 11 for AIRS, 16 for IASI). The full list of instrument triplets can be found in the list below:
+
+\begin{longtable}[h]{|l|l|l|l|}
+\hline \textbf{Instrument} &amp; \textbf{Satellite}  &amp; \textbf{(PLATFORM, SATID, SENSOR)}\\
+\hline AIRS                &amp; EOS-Aqua            &amp; (9,2,11) \\
+\hline AMSU-A              &amp; EOS-Aqua            &amp; (9,2,3) \\
+\hline AMSU-A              &amp; METOP-A             &amp; (10,2,3) \\
+\hline AMSU-A              &amp; NOAA 15{</font>
<font color="black">d}19      &amp; (1,15{</font>
<font color="blue">d}19,3) \\
+\hline AMSU-B              &amp; NOAA 15{</font>
<font color="black">d}17      &amp; (1,15{</font>
<font color="blue">d}17,4) \\
+\hline ATMS                &amp; Suomi-NPP           &amp; (17,0,19) \\
+\hline HIRS-3              &amp; NOAA 15{</font>
<font color="black">d}17      &amp; (1,15{</font>
<font color="blue">d}17,0) \\
+\hline HIRS-4              &amp; METOP-A             &amp; (10,2,0) \\
+\hline HIRS-4              &amp; NOAA 18{</font>
<font color="black">d}19      &amp; (1,18{</font>
<font color="blue">d}19,0) \\
+\hline IASI                &amp; METOP-A             &amp; (10,2,16) \\
+\hline MHS                 &amp; METOP-A             &amp; (10,2,15) \\
+\hline MHS                 &amp; NOAA 18{</font>
<font color="black">d}19      &amp; (1,18{</font>
<font color="blue">d}19,15) \\
+\hline MWHS                &amp; FY-3A{</font>
<font color="black">d}FY-3B     &amp; (23,1{</font>
<font color="blue">d}2,41) \\
+\hline MWTS                &amp; FY-3A{</font>
<font color="black">d}FY-3B     &amp; (23,1{</font>
<font color="blue">d}2,40) \\
+\hline SEVIRI              &amp; Meteosat 8{</font>
<font color="black">d}10   &amp; (3,8{</font>
<font color="black">d}10,21)\footnote{As of V3.6 the CRTM triplet shown here will be used (since RTTOV is not yet supported). In future versions this triplet will likely be changed to the RTTOV triplet (12,1{</font>
<font color="blue">d}3,21) for consistency purposes}\\
+\hline SSMIS               &amp; DMSP 16{</font>
<font color="black">d}18      &amp; (2,16{</font>
<font color="blue">d}18,10) \\
+\hline
+\end{longtable}
+
+Here's an example of this section of the namelist for a user assimilating AMSU-A from NOAA 18{</font>
<font color="black">d}19 and EOS-Aqua, MHS from NOAA 18{</font>
<font color="blue">d}19, and AIRS from EOS-Aqua, utilizing CRTM as their RTM:
+
+\scriptsize\begin{verbatim}
+&amp;wrfvar14
+ rtminit_nsensor = 6
+ rtminit_platform = 1,  1, 9,  1,  1,  9
+ rtminit_satid =   18, 19, 2, 18, 19,  2
+ rtminit_sensor =   3,  3, 3, 15, 15, 11
+ rtm_option = 2,
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+The instrument triplets (platform, satellite, and sensor ID) in the namelist can be ranked in any order, as long as the first sensor listed also corresponds to the first platform and satid, the second sensor listed corresponds to the second platform and satid, etc. More detail about the convention of instrument triplets can be found on the RTTOV web page (\url{http://research.metoffice.gov.uk/research/interproj/nwpsaf/rtm/rttov_description.html})
+or in tables 2 and 3 in the RTTOV v11 User's Guide (\url{http://research.metoffice.gov.uk/research/interproj/nwpsaf/rtm/docs_rttov11/users_guide_11_v1.2.pdf})
+
+CRTM uses a different instrument-naming method, however, a conversion routine inside WRFDA is implemented such that the user interface remains the same for RTTOV and CRTM, using the same instrument triplet for both. 
+
+When running WRFDA with radiance assimilation switched on, a set of RTM coefficient files needs to be loaded. For the RTTOV option, RTTOV coefficient files are to be copied or linked to a sub-directory \texttt{rttov\_coeffs} under the working directory. For the CRTM option, CRTM coefficient files are to be copied or linked to a sub-directory \texttt{crtm\_coeffs} under the working directory. Only coefficients listed in the namelist are needed. WRFDA has the potential to assimilate all sensors as long as the corresponding coefficient files are provided, however, it may require some coding by the user (specifically the data interface, quality control, and bias correction) in order to assimilate sensors not listed above. However, the modular design of the radiance routines (found in \texttt{WRFDA/var/da/da\_radiance}) makes the addition of new sensors relatively painless.
+
+\subsubsection{Compiling for radiance assimilation}
+\label{wrfda-rtm-compile}
+
+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}
+     &gt; setenv RTTOV /usr/local/rttov11/pgi
+\end{verbatim}
+</font>
<font color="blue">ormalsize
+
+
+
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section{WRFDA Diagnostics}
+\label{wrfda-diagnostic-files}
+
+
+\section{WRFDA additional exercises}
+\label{wrfda-exercises}
+
+
+%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 &quot;EPS=0.0001&quot; in the namelist.input record &amp;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.
+
+\scriptsize\begin{verbatim}
+&gt; 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 (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{Description of Namelist Variables}
 \label{wrfda-namelist}

Modified: trunk/wrf/UsersGuide/Users_Guide.tex
===================================================================
--- trunk/wrf/UsersGuide/Users_Guide.tex        2014-03-13 23:25:47 UTC (rev 467)
+++ trunk/wrf/UsersGuide/Users_Guide.tex        2014-03-21 05:20:22 UTC (rev 468)
@@ -36,7 +36,7 @@
 \counterwithin{table}{chapter}
 
 % Set up page layout
-\setlength{\textwidth}{6.75in}
+\setlength{\textwidth}{7.0in}
 \setlength{\oddsidemargin}{-0.0in}
 \setlength{\evensidemargin}{-0.25in}
 \setlength{\textheight}{9.0in}
@@ -52,8 +52,11 @@
 \def \eg{{\emph{e.g.} }}
 \def \ie{{\emph{i.e.} }}
 \def \WRFDA3DVAR{{\emph{WRFDA\textendash 3DVAR} }}
+\def \4DVAR{{\emph{WRFDA\textendash 4DVAR} }}
 \def </font>
<font color="black">i{</font>
<font color="red">oindent}
-\def \wrf{ARW}
+\def </font>
<font color="blue">d{\textendash}
+\def \md{\textemdash}
+\def \wrf{WRF\textendash ARW}
 </font>
<font color="black">ewcommand{\xbmf}[1]{\hbox{\sffamily\slshape #1}}
 </font>
<font color="gray">ewcommand{\xmathbf}{\boldsymbol}
 

Modified: trunk/wrf/UsersGuide/users_guide_chap6.doc
===================================================================
--- trunk/wrf/UsersGuide/users_guide_chap6.doc        2014-03-13 23:25:47 UTC (rev 467)
+++ trunk/wrf/UsersGuide/users_guide_chap6.doc        2014-03-21 05:20:22 UTC (rev 468)
@@ -1,6 +1,6 @@
-ࡱ&gt;        .VWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~        bjbj        dd&quot;.]22v@v@v@v@v@T@@@bA^D\@LPpPPPRZ\,st9v@]
 RR]]v@v@PP&quot;%f]
-'v@Pv@P]NlkK:p`*T&quot;v@]]]]]]]]]]]]]
 ]]2 &lt;?:  -         +ࡱ&gt;        -uxHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrst
         bjbjWW        55.]22?????T0@0@0@@C\0@[
+ LOp`P`P`PQ(Z \6888888$eb\9?]QQ]]\??`P`P&quot;f]&quot;'?`P?`P6]6lH`PL?&quot;
+&quot;p&quot;`[y,yTH&quot;y?j]]]\\]]][]]]]y]]]]]]]]]2  &gt;:        
   Chapter 6: WRF Data Assimilation    Table of Contents @@ -590,7 +590,7 @@
 ob/2008020518  rc/2008020512  be -Note: WRFDA 4D-Var is able to assimilate conventional observational data, satellite radiance BUFR data, radar data, and precipitation data. The input data format can be PREPBUFR format data or observation data, processed by OBSPROC. +Note: WRFDA 4D-Var is able to assimilate conventional observational data, satellite radiance BUFR data, and precipitation data. The input data format can be PREPBUFR format data or ASCII observation data, processed by OBSPROC.  Now follow the steps below:  1) Link the executable file  &gt; cd $WORK_DIR @@ -1508,7 +1508,7 @@
 2: ob_format_ascii (output from obsproc), read in data from ob.ascii (default)  3: ob_format_madis (not tested)  num_fgat_time11: 3DVar -&gt; 1: number of time slots for FGAT and 4DVAR &amp;wrfvar4thin_convtruefor ob_format=1 (NCEP PREPBUFR) only. thinning is mandatory for ob_format=1, as time-duplicate data are &quot;thinned&quot; within the thinning routine; however, thin_conv can be set to .false. for debugging purpose.thin_mesh_conv 20. (max_instruments)for ob_format=1 (NCEP PREPBUFR) only. +&gt; 1: number of time slots for 4DVAR &amp;wrfvar4thin_convtruefor ob_format=1 (NCEP PREPBUFR) only. thinning is mandatory for ob_format=1, as time-duplicate data are &quot;thinned&quot; within the thinning routine; however, thin_conv can be set to .false. for debugging purpose.thin_mesh_conv 20. (max_instruments)for ob_format=1 (NCEP PREPBUFR) only.  km, each observation type can set its thinning mesh and the index/order follows the definition in  WRFDA/var/
 da/da_control/da_control.f90thin_rainobstrue.true.: perform thinning on precipitation datause_synopobstrueuse_xxxobs - .true.: assimilate xxx obs if available  .false.: do not assimilate xxx obs even available @@ -1632,10 +1632,10 @@
      -WRF-ARW V3: Users Guide        6- PAGE 26 +WRF-ARW V3: Users Guide        6- PAGE 20     -WRF-ARW V3: Users Guide        6- PAGE 27 +WRF-ARW V3: Users Guide        6- PAGE 21       @@ -1656,10 +1656,10 @@
      -WRF-ARW V3: Users Guide        6- PAGE 44 +WRF-ARW V3: Users Guide        6- PAGE 42     -&quot;#56VWXdefg                         !        U        V        W                                                                                                                        
+WRF-ARW V3: Users Guide        6-&quot;#56VWXdefg                         !        U        V        W                                                                                                                        
 
 
 
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\ No newline at end of file

</font>
</pre>