<p><b>xinzhang</b> 2009-03-30 15:15:11 -0600 (Mon, 30 Mar 2009)</p><p>Save Chapt. 6 changes<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/wrf/UsersGuide/users_guide_chap6.doc
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--- trunk/wrf/UsersGuide/users_guide_chap6.doc 2009-03-30 20:41:10 UTC (rev 158)
+++ trunk/wrf/UsersGuide/users_guide_chap6.doc 2009-03-30 21:15:11 UTC (rev 159)
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HYPERLINK \l "_Installing_WRFNL_and" Installing WRFNL and WRFPLUS
HYPERLINK \l "_Running_Observation_Preprocessor_1" Running Observation Preprocessor (OBSPROC)
HYPERLINK \l "_Running_WRF-Var_1"Running WRF-Var
+ HYPERLINK \l "_Radiance_Data_Assimilations" Radiance Data Assimilations in WRF-Var
HYPERLINK \l "_WRF-Var_Diagnostics_1"WRF-Var Diagnostics
HYPERLINK \l "_Updating_WRF_lateral_1"Updating WRF boundary conditions
HYPERLINK \l "_Running_gen_be_1" Running gen_be
@@ -617,6 +619,216 @@
./da_wrfvar.exe >&! wrfda.log
wrfda.log (or rsl.out.0000 if running in distributed-memory mode) contains important WRF-4DVar runtime log. Always check the log after a WRF-4DVar run.
+Radiance Data Assimilations in WRF-Var
+This section gives brief description for various aspects related to radiance assimilation in WRF-Var. Each aspect is described mainly from the viewpoint of usage rather than more technical and scientific details, which will appear in separated technical report and scientific paper. Namelist parameters controlling different aspects of radiance assimilation will be detailed in the following sections. Note that this section does not cover general aspects of WRF-Var assimilation which can be found in other sections of this users guide chapter 6 or other WRF-Var documentation.
+
+a. Running WRF-Var with radiances
+
+In addition to the basic input files (LANDUSE.TBL, fg, ob.ascii, be.dat) mentioned in HYPERLINK \l "_Running_WRF-Var_1" R
unning WRF-Var section, the following extra files are required for radiances: radiance data in NCEP BUFR format, radiance_info files, VARBC.in, RTM (CRTM or RTTOV) coefficient files.
+
+Edit namelist.input (Pay special attention to &wrfvar4, &wrfvar14, &wrfvar21, and &wrfvar22 for radiance-related options)
+ln -sf ${DAT_DIR}/gdas1.t00z.1bamua.tm00.bufr_d ./amsua.bufr
+ln -sf ${DAT_DIR}/gdas1.t00z.1bamub.tm00.bufr_d ./amsub.bufr
+ln -sf WRFDA/var/run/radiance_info ./radiance_info # (radiance_info is a directory)
+ln -sf WRFDA/var/run/VARBC.in ./VARBC.in
+(CRTM only) ln -sf REL-1.2.JCSDA_CRTM/crtm_coeffs ./crtm_coeffs #(crtm_coeffs is a directory)
+(RTTOV only) ln -sf rttov87/rtcoef_rttov7/* . # (a list of rtcoef* files)
+
+See the following sections for more details on each aspect.
+
+b. Radiance Data Ingest
+
+Currently, the ingest interface for NCEP BUFR radiance data is implemented in WRF-Var. The radiance data are available through NC
EPs public ftp server ftp://ftp.ncep.noaa.gov/pub/data/nccf!
/com/gfs
/prod/gdas.${yyyymmddhh} in near real-time (with 6-hour delay) and can meet requirements both for research purposes and some real-time applications.
+
+So far, WRF-Var 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 instrument names (i.e., each file for one type instrument) and each file contains global radiance (generally converted to brightness temperature) within 6-hour assimilation window from multi-platforms. For running WRF-Var, users need to rename NCEP corresponding BUFR files (table 1) to hirs3.bufr (including HIRS data from NOAA-15/16/17), hirs4.bufr (including HIRS data from NOAA-18, METOP-2), amsua.bufr (including AMSU-A data from NOAA-15/16/18, METOP-2), amsub.bufr (including AMSU-B data from NOAA-15/16/17), mhs.bufr (including MHS data from NOAA-18 and METOP-2), airs.bufr (including AIRS and AMSU-A data from EOS-
AQUA) and ssmis.bufr (SSMIS data from DMSP-16, AFWA provided) for WRF-Var filename convention. Note that airs.bufr file contains not only AIRS data but also AMSU-A, which is collocated with AIRS pixels (1 AMSU-A pixels collocated with 9 AIRS pixels). Users also have to place these files in the working directory where WRF-Var executable is located. Should be mentioned that WRF-Var reads directly these BUFR radiance files and no separate pre-processing program is used. All processing of radiance data, such as quality control, thinning and bias correction and so on, is carried out inside WRF-Var. This is different from conventional observation assimilation, which requires a pre-processing package (OBSPROC) to generate WRF-Var readable ASCII files. For reading radiance BUFR files, WRF-Var must be compiled with NCEP BUFR library (see http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB/ ).
+
+Table 1: NCEP and WRF-Var radiance BUFR file naming convention
+NCEP BUFR file namesWRF-Va
r naming conventiongdas1.t00z.1bamua.tm00.bufr_damsua.buf!
rgdas1
.t00z.1bamub.tm00.bufr_damsub.bufrgdas1.t00z.1bhrs3.tm00.bufr_dhirs3.bufrgdas1.t00z.1bhrs4.tm00.bufr_dhirs4.bufrgdas1.t00z.1bmhs.tm00.bufr_dmhs.bufrgdas1.t00z.airsev.tm00.bufr_dairs.bufr
+A few namelist parameters are used to control if reading in corresponding BUFR files into WRF-Var or not. For instance, USE_AMSUAOBS, USE_AMSUBOBS, USE_HIRS3OBS, USE_HIRS4OBS, USE_MHSOBS, USE_AIRSOBS, USE_EOS_AMSUAOBS and USE_SSMISOBS control respectively to read the corresponding files or not. These are logical parameters and are assigned to FALSE by default (means that you must switch them to TRUE for reading in these data). Notice also that these parameters only control whether read in the data or not, but not control whether assimilate the data included in the files, which is controlled by other namelist parameters explained in the next section.
+
+NCEP BUFR files downloaded from NCEPs public ftp server ftp://ftp.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gdas.${yyyymmddhh}
are Fortran-blocked on big-endian machine and can be directly used on big-endian machines (for example, IBM). For most Linux clusters with Intel platforms, users need to first unblock the BUFR files, then block them. The utility for blocking/unblocking is available from http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB/toc/cwordsh
+
+
+c. Radiative Transfer Model
+
+The core component for direct radiance assimilation is to incorporate radiative transfer model (RTM, should be accurate enough yet fast) into WRF-Var system as one part of observation operators. Two widely used RTMs in NWP community, RTTOV8* developed by EUMETSAT in Europe and CRTM developed by the Joint Center for Satellite Data Assimilation (JCSDA) in US, are already implemented in WRF-Var system with flexible and consistent user interface. Which RTM to use is controlled by a simple namelist parameter RTM_OPTION (1 for RTTOV by default, 2 for CRTM). WRF-Var is designed to be able to compile with only one of
two RTM libraries or without RTM libraries (for those not in!
terested
in radiance assimilation) by simple setup of environment variables CRTM and RTTOV (see Installing WRF-Var section).
+
+Both RTMs can calculate radiances for almost all available instruments aboard various satellite platforms in orbit. An important feature of WRF-Var design is that all data structures related to radiance assimilation are dynamically allocated during running time according to simple namelist setup. The instruments to be assimilated are controlled by 4 integer namelist parameters in running time: RTMINIT_NSENSOR (total number of sensors to be assimilated), RTMINIT_PLATFORM (platforms IDs array to be assimilated with dimension RTMINIT_NSENSOR, e.g., 1 for NOAA, 9 for EOS, 10 for METOP and 2 for DMSP), RTMINIT_SATID (satellite IDs array) and RTMINIT_SENSOR (sensor IDs array, e.g., 0 for HIRS, 3 for AMSU-A, 4 for AMSU-B, 15 for MHS, 10 for SSMIS, 11 for AIRS). For instance, configuration for assimilating 12 sensors from 7 satellites (what WRF-Var can assimilat
ed currently) will be
+
+RTMINIT_NSENSOR = 12 # 5 AMSUA; 3 AMSUB; 2 MHS; 1 AIRS; 1 SSMIS
+RTMINIT_PLATFORM = 1,1,1,9,10, 1,1,1, 1,10, 9, 2
+RTMINIT_SATID = 15,16,18,2,2, 15,16,17, 18,2, 2, 16
+RTMINIT_SENSOR = 3,3,3,3,3, 4,4,4, 15,15, 11, 10
+
+The instrument triplets (platform, satellite and sensor ID) in the namelist can be rank in any order. More detail about the convention of instrument triplet can be found at the tables 2 and 3 in RTTOV8/9 Users Guide (http://www.metoffice.gov.uk/research/interproj/nwpsaf/rtm/rttov8_ug.pdf Or http://www.metoffice.gov.uk/research/interproj/nwpsaf/rtm/rttov9_files/users_guide_91_v1.6.pdf)
+
+CRTM uses different instrument naming method. A convert routine inside WRF-Var is already created to make CRTM use the same instrument triplet as RTTOV such that the user interface remains the same for RTTOV and CRTM.
+
+When running WRF-Var with radiance assimilation switched on (RTTOV or CRTM), a
set of RTM coefficient files need to be loaded. For RTTOV o!
ption, R
TTOV coefficient files are to be directly copied or linked under the working directory; for CRTM option, CRTM coefficient files are to be copied or linked to a sub-directory crtm_coeffs under the working directory. Only coefficients listed in namelist are needed. Potentially WRF-Var can assimilate all sensors as long as the corresponding coefficient files are provided with RTTOV and CRTM. In addition, necessary developments on corresponding data interface, quality control and bias correction are also important to make radiance data assimilated properly. However, a modulized design of radiance relevant routines already facilitates much to add more instruments in WRF-Var.
+
+RTTOV and CRTM packages are not distributed with WRF-Var due to license and support issues. Users are encouraged to contact the corresponding team for obtaining RTMs. See following links for more information.
+http://www.metoffice.gov.uk/research/interproj/nwpsaf/rtm/index.html for RTTOV,
+ftp://ftp.emc.n
cep.noaa.gov/jcsda/CRTM/ for CRTM.
+
+
+d. Channel Selection
+
+Channel selection in WRF-Var is controlled by some radiance info files located in the sub-directory radiance_info under the working directory. These files are separated by satellites and sensors, e.g., noaa-15-amsua.info, noaa-16-amsub.info, dmsp-16-ssmis.info and so on. An example for 5 channels from noaa-15-amsub.info is shown below. The fourth column is used by WRF-Var to control if assimilating corresponding channel. Channels with the value -1 indicates not assimilated (channels 1, 2 and 4 in this case), with the value 1 means assimilated (channels 3 and 5). The sixth column is used by WRF-Var to set the observation error for each channel. Other columns are not used by WRF-Var. It should be mentioned that these error values are not necessarily optimal for your applications, it is users responsibility to obtain the optimal error statistics for your own applications.
+
+ sensor channel IR/MW use
idum varch polarisation(0:vertical;1:horizontal)
+ 415 !
1 1
-1 0 0.5500000000E+01 0.0000000000E+00
+ 415 2 1 -1 0 0.3750000000E+01 0.0000000000E+00
+ 415 3 1 1 0 0.3500000000E+01 0.0000000000E+00
+ 415 4 1 -1 0 0.3200000000E+01 0.0000000000E+00
+ 415 5 1 1 0 0.2500000000E+01 0.0000000000E+00
+
+
+e. Bias Correction
+
+Satellite radiance is generally considered biased with respect to a reference (e.g., background or analysis field in NWP assimilation) due to system error of observation itself, reference field and RTM. Bias correction is a necessary step prior to assimilating radiance data. In WRF-Var, there are two ways of performing bias correction. One is based on Harris and Kelly (1992) method and is carried out using a set of coefficient files pre-calculated with an off-line statistics package, which will apply to a training dataset for a month-long period. The other is Variational Bias Correction (VarBC). Only VarBC is introduced here and recommended for users
because of its relative simplicity in usage.
+
+f. Variational Bias Correction
+
+Getting started with VarBC
+To use VarBC, set namelist option USE_VARBC to TRUE and have a VARBC.in file in the working directory. VARBC.in is a VarBC setup file in ASCII format. A template is provided with the WRF-Var package (WRFDA/var/run/VARBC.in).
+
+Input and Output files
+All VarBC input is passed through one single ASCII file called VARBC.in file. Once WRF-Var has run with the VarBC option switched on, it will produce a VARBC.out file file which looks very much like the VARBC.in file you provided. This output file will then be used as input file for the next assimilation cycle.
+
+Coldstart
+Coldstarting means starting the VarBC from scratch... i.e. when you do not know the values of the bias parameters.
+
+The Coldstart is a routine in WRF-Var. The bias predictor statistics (mean and standard deviation) are computed automatically and will be used to normalize the bias parameters. All
coldstarted bias parameters are set to zero, except the firs!
t bias p
arameter (= simple offset), which is set to the mode (=peak) of the distribution of the (uncorrected) innovations for the given channel.
+
+A threshold of number of observations can be set through a namelist option VARBC_NOBSMIN (default = 10), under which it is considered that not enough observations are present to keep the Coldstart values (i.e. bias predictor statistics and bias parameter values) for the next cycle. In this case, the next cycle will do another Coldstart.
+
+Background Constraint for the bias parameters
+The background Constraint controls the inertia you want to impose on the predictors (i.e. the smoothing in the predictor time series). It corresponds to an extra term in the WRF-Var cost function.
+
+It is defined through an integer number in the VARBC.in file. This number is related to a number of observations: the bigger the number, the more inertia constraint. If these numbers are set to zero, the predictors can evolve without any constraint.
+
+Scaling
factor
+The VarBC uses a specific preconditioning, which can be scale through a namelist option VARBC_FACTOR (default = 1.0).
+
+Offline bias correction
+The analysis of the VarBC parameters can be performed "offline", i.e. independently from the main WRF-Var analysis. No extra code is needed, just set the following MAX_VERT_VAR* namelist variables to be 0, which will disable the standard control variable and only keep the VarBC control variable.
+
+MAX_VERT_VAR1=0.0
+MAX_VERT_VAR2=0.0
+MAX_VERT_VAR3=0.0
+MAX_VERT_VAR4=0.0
+MAX_VERT_VAR5=0.0
+
+Freeze VarBC
+In certain circumstances, you might want to keep the VarBC bias parameters constant in time (="frozen"). In this case, the bias correction is read and applied to the innovations, but it is not updated during the minimization. This can easily be achieved by setting the namelist options:
+
+USE_VARBC=false
+FREEZE_VARBC=true
+
+Passive observations
+Some observations are useful for preprocessing (e.g. Q
uality Control, Cloud detection) but you might not want to a!
ssimilat
e them. If you still need to estimate their bias correction, these observations need to go through the VarBC code in the minimization. For this purpose, the VarBC uses a separate threshold on the QC values, called "qc_varbc_bad". This threshold is currently set to the same value as "qc_bad", but can easily be changed to any ad hoc value.
+
+g. Other namelist variables to control radiance assimilation
+
+RAD_MONITORING (30)
+Integer array with dimension RTMINIT_NSENSER, where 0 for assimilating mode, 1 for monitoring mode (only calculate innovation).
+
+THINNING
+Logical, TRUE will perform thinning on radiance data.
+
+THINNING_MESH (30)
+Real array with dimension RTMINIT_NSENSOR, values indicate thinning mesh (in KM) for different sensors.
+
+QC_RAD
+Logical, control if perform quality control, always set to TRUE.
+
+WRITE_IV_RAD_ASCII
+Logical, control if output Observation minus Background files which are in ASCII format and separated by sensors and
processors.
+
+WRITE_OA_RAD_ASCII
+Logical, control if output Observation minus Analysis files (including also O minus B) which are ASCII format and separated by sensors and processors.
+
+USE_ERROR_FACTOR_RAD
+Logical, control if use a radiance error tuning factor file radiance_error.factor, which is created with empirical values or generated using variational tunning method (Desroziers and Ivanov, 2001)
+
+ONLY_SEA_RAD
+Logical, control if only assimilating radiance over water.
+
+TIME_WINDOW_MIN
+String, e.g., "2007-08-15_03:00:00.0000", start time of assimilation time window
+
+TIME_WINDOW_MAX
+String, e.g., "2007-08-15_09:00:00.0000", end time of assimilation time window
+
+CRTM_ATMOSPHERE
+Integer, used by CRTM to choose climatology reference profile used above model top (up to 0.01hPa).
+0: Invalid (default, use U.S. Standard Atmosphere)
+1: Tropical
+2: Midlatitude summer
+3: Midlatitude winter
+4: Subarctic summer
+5: Subarctic winter
+6:
U.S. Standard Atmosphere
+
+USE_ANTCORR (30)
+Logical array!
with di
mension RTMINIT_NSENSER, control if performing Antenna Correction in CRTM.
+
+AIRS_WARMEST_FOV
+Logical, control if using the observation brightness temperature for AIRS Window channel #914 as criterium for GSI thinning.
+
+
+h. Diagnostics and Monitoring
+
+(1) Monitoring capability within WRF-Var.
+
+Run WRF-Var with the rad_monitoring namelist parameter in record wrfvar14 in namelist.input.
+
+0 means assimilating mode, innovations (O minus B) are calculated and data are used in minimization.
+1 means monitoring mode: innovations are calculated for diagnostics and monitoring. Data are not used in minimization.
+
+Numbers of rad_monitoring should correspond to number of rtminit_nsensor. If rad_monitoring is not set, then default value of 0 will be used for all sensors.
+
+(2) Outputing radiance diagnostics from WRF-Var
+
+Run WRF-Var with the following namelist variables in record wrfvar14 in namelist.input.
+
+write_iv_rad_ascii=.true.
+to write out (observation-backgro
und) and other diagnostics information in plain-text files with prefix inv followed by instrument name and processor id. For example, inv_noaa-17-amsub.0000
+
+write_oa_rad_ascii=.true.
+to write out (observation-background), (observation-analysis) and other diagnostics information in plain-text files with prefix oma followed by instrument name and processor id. For example, oma_noaa-18-mhs.0001
+
+Each processor writes out information of one instrument in one file in the WRF-var working directory.
+
+(3) Radiance diagnostics data processing
+
+A Fortran90 program is used to collect the inv* or oma* files and write out in netCDF format (one instrument in one file with prefix diags followed by instrument name, analysis date, and suffix .nc)) for easier data viewing, handling and plotting with netCDF utilities and NCL scripts.
+
+(4) Radiance diagnostics plotting
+
+NCL scripts (WRFDA/var/graphics/ncl/plot_rad_diags.ncl and WRFDA/var/graphics/ncl/advance_cymdh.ncl) are used f
or plotting. The NCL script can be run from a shell script, !
or run s
tand-alone with interactive ncl command (need to edit the NCL script and set the plot options. Also the path of advance_cymdh.ncl, a date advancing script loaded in the main NCL plotting script, may need to be modified).
+
+Step (3) and (4) can be done by running a single ksh (WRFDA/var/scripts/da_rad_diags.ksh) with proper settings. In addition to the settings of directories and what instruments to plot, there are some useful plotting options, explained below.
+export OUT_TYPE=ncgmncgm or pdf
+pdf will be much slower than ncgm and generate huge output if plots are not splitted. But pdf has higher resolution than ncgm.export PLOT_STATS_ONLY=falsetrue or false
+true: only statistics of OMB/OMA vs channels and OMB/OMA vs dates will be plotted.
+false: data coverage, scatter plots (before and after bias correction), histograms (before and after bias correction), and statistics will be plotted.export PLOT_OPT=sea_onlyall, sea_only, land_onlyexport PLOT_QCED=false
+true
or false
+true: plot only quality-controlled data
+false: plot all dataexport PLOT_HISTO=falsetrue or false: switch for histogram plotsexport PLOT_SCATT=truetrue or false: switch for scatter plotsexport PLOT_EMISS=falsetrue or false: switch for emissivity plotsexport PLOT_SPLIT=falsetrue or false
+true: one frame in each file
+false: all frames in one fileexport PLOT_CLOUDY=false
+true or false
+true: plot cloudy data. Cloudy data to be plotted are defined by PLOT_CLOUDY_OPT (si or clwp), CLWP_VALUE, SI_VALUE settings.export PLOT_CLOUDY_OPT=sisi or clwp
+clwp: cloud liquid water path from model
+si: scatter index from obs, for amsua, amsub and mhs onlyexport CLWP_VALUE=0.2only plot points with
+clwp >= clwp_value (when clwp_value > 0)
+clwp > clwp_value (when clwp_value = 0)export SI_VALUE=3.0
+
+(5) evolution of VarBC parameters
+
+NCL scripts (WRFDA/var/graphics/ncl/plot_rad_varbc_param.ncl and WRFDA/var/graphics/ncl/advance_cymdh.ncl) a
re used for plotting evolutions of VarBC parameters.
+
WRF-!
Var Diag
nostics
WRF-Var produces a number of diagnostic files that contain useful information on how the data assimilation has performed. This section will introduce you to some of these files, and what to look for.
Having run WRF-Var, it is important to check a number of output files to see if the assimilation appears sensible. Please download a complimentary WRF-Var package which includes lots of useful scripts from HYPERLINK "http://www.mmm.ucar.edu/wrf/src/data/WRFV3.1-Var-testdata.tar.gz" http://www.mmm.ucar.edu/wrf/src/data/WRFV3.1-Var-testdata.tar.gz
@@ -863,6 +1075,8 @@
'FGAT ' obs files for FGAT
'4DVAR' obs files for 4DVARnum_slots_pastthe number of time slots before time_analysisnum_slots_aheadthe number of time slots after time_analysiswrite_synopIf keep synop obs in obs_gts (ASCII) files.write_shipIf keep ship obs in obs_gts (ASCII) files.write_metarIf keep metar obs in obs_gts (ASCII) files.write_buoyIf keep buoy obs in obs_gts (ASCII) files.write_pilotIf keep pilot obs in obs_gts (ASCII) files.write_soundIf keep sound obs in obs_gts (ASCII) files.write_amdarIf keep amdar obs in obs_gts (ASCII) files.write_satemIf keep satem obs in obs_gts (ASCII) files.write_satobIf keep satob obs in obs_gts (ASCII) files.write_airepIf keep airep obs in obs_gts (ASCII) files.write_gpspwIf keep gpspw obs in obs_gts (ASCII) files.write_gpsztdIf keep gpsztd obs in obs_gts (ASCII) files.write_gpsrefIf keep gpsref obs in obs_gts (ASCII) files.write_gpsephIf keep gpseph obs in obs_gts (ASCII) files.write_ss
mt1If keep ssmt1 obs in obs_gts (ASCII) files.write_ssmt2If keep ssmt2 obs in obs_gts (ASCII) files.write_ssmiIf keep ssmi obs in obs_gts (ASCII) files.write_tovsIf keep tovs obs in obs_gts (ASCII) files.write_qscatIf keep qscat obs in obs_gts (ASCII) files.write_proflIf keep profile obs in obs_gts (ASCII) files.write_bogusIf keep bogus obs in obs_gts (ASCII) files.write_airsIf keep airs obs in obs_gts (ASCII) files.
+* Current release is RTTOV9, while there is no plan to incorporate RTTOV9 into WRF-Var.
+
@@ -878,10 +1092,10 @@
-WRF-ARW V3: Users Guide 6- PAGE 28
+WRF-ARW V3: Users Guide 6- PAGE 26
-WRF-ARW V3: Users Guide 6- PAGE 29
+WRF-ARW V3: Users Guide 6- PAGE 25
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</font>
</pre>