DART-CAM setup

closest · DART/models/cam/work/input.nml

-> mpirun filter executable 
   -> mpirun filter executable 
      -> advance_model.csh
      -> advance_model.csh
         -> trans_time executable
         -> dart_to_cam executable
         -> trans_sv_pv executable
         -> run_pc.csh
         -> run-cam.csh
            -> bld-namelist 
            -> bld-namelist 
            -> advance of CAM
            -> advance of CAM (version dependent)
         -> trans_pv_sv executable
         -> cam_to_dart executable
   -> qsub auto_re2ms.csh
   -> qsub auto_re2hpss.csh
   -> qsub auto_diag2hpss_LSF.csh
      -> analyses2initial.csh
         -> NetCDF operators 
        (-> clm_ens_avg.f90
-          &camexp
-          ncdata         = 'caminput.nc'
-          caseid         = 'whatever_you_want'
-          nsrest         = 0
-          calendar       = 'GREGORIAN'
-          inithist       = 'ENDOFRUN'
-          /
-          &clmexp
-          finidat        = 'clminput.nc'
-          /
-          
-          >  nhtfrq         = 4368
-          >  start_ymd      = 20020901
-          >  start_tod      = 0
-          >  stop_ymd       = 20021201
-          >  stop_tod       = 0
-          
+             CAM 3.1 - 3.5
+                &camexp
+                 ncdata         = 'caminput.nc'
+                 caseid         = 'whatever_you_want'
+                 nsrest         = 0
+                 calendar       = 'GREGORIAN'
+                 inithist       = 'ENDOFRUN'
+                /
+                &clmexp
+                 finidat        = 'clminput.nc'
+                /
+             CAM 3.6 - 4.?
+                &seq_timemgr_inparm
+                 calendar       = 'GREGORIAN'
+                 restart_n      = 12
+                 restart_option = 'nsteps'
+                 stop_option    = 'date'
+                /
+                &cam_inparm
+                 ncdata   = 'caminput.nc'
+                 inithist = 'ENDOFRUN'
+                 div24del2flag = 4,
+                 nhtfrq = -6
+                /
+                &clm_inparm
+                 finidat = 'clminput.nc'
+                /
+                &dom_inparm
+                 bndtvs  = '/your/SST/file/here/resolution/cam_version/sst_HadOIBl_bc_1.9x2.5_1949_2007.nc'
+                 sstcyc  = .false.
+                /
+                
+                >  start_ymd      = 20020901
+                >  start_tod      = 0
+                >  stop_ymd       = 20021201
+                >  stop_tod       = 0
+             
+                   empty_htapes    = .true.,
+                   mfilt           =  1
+                   avgflag_pertape = 'A'
+                   fincl1   = 'A', 'Few', 'Useful', 'CAM' ,'Fields'
+             
+&filter_nml
+   ...
+   start_from_restart       = .false.,
+   restart_in_file_name     = "filter_ic",
+   ...
+/
+&model_nml
+   ...
+   pert_names         = 'T       ','US      ','VS      '
+   pert_sd           = 1.0d0,2.0d0,2.0d0
+   ...
+/
+
       Obsseq_#  
       obs_#  
           DART 
           CICE  
           H##  
+
 A typical pathname for a restart file in my case would be:
-/scratch/cluster/raeder/T21x80/Taper1/01_03/DART/filter_ic#
-                        |      |      |     |    restart file(s)
-                        |      |      |     DART restart file directory
-			|      |      Obs_seq (3rd obs_seq.out of a Jan case)
-                        |      Experiment (reduced influence of obs above 150 hPa)
-                        Central directory (resolution x num_ens_members)
+/scratch/raeder/T21x80/Taper1/obs_0003/DART/filter_ic#
+                |      |      |        |    restart file(s)
+                |      |      |        DART restart file directory
+	        |      |      Obs_seq (3rd obs_seq.out of a series starting at 1)
+                |      Experiment (reduced influence of obs above 150 hPa)
+                Central directory (resolution x num_ens_members)
 
-
+
+


 You may also want to make a subdirectory within Experiment 
 for each set of obs_space postscript and .dat files created by obs_diag and matlab.
+
 
 
 
@@ -445,81 +683,119 @@
 
 HELPFUL HINTS
 
-For async=2 use the ensemble size, available compute nodes, and processors/node  to figure how many
-nodes to request.  Make this request in job_mpi.csh.  For example,  on a machine with
-2 processors/node, and running an assimilation with a 
-typical ensemble of 20 members, it's efficient to request 5 nodes.
-This will advance CAM in 2 batches of 10 (1 CAM/processor).  
 
+In the following, MPI filter uses all of the requested processors.
+There is flexibility in how the ensemble of CAMs uses them.
+The choice of async and number of processors to use 
+will depend on the memory available on each node, 
+as well as the number of processors available.
+See also models/cam/doc/html/filter_async_modes.html in the DART code tree, after registering.
+
 


+For async = 2 use the ensemble size, available compute nodes, processors/node  ,
+and memory/node to figure how many nodes to request.  
+Make this request in job_mpi.csh.  
+For example, on a machine with 8 processors/node, and running an assimilation 
+with an ensemble of 80 members (recommended), it's efficient to request 5 (or 10) nodes.
+This will advance the single-process CAMs in 2 (or 1) batches of 40 (80).  
+That's assuming that each node has the memory to accomodate 8 CAMs.
 
+


+async = 4 runs an ensemble of pure-MPI CAMs 1 at a time and is usually a poor choice for CAM 
+assimilations because the start-up process for CAM is single process
+and takes significant time.  
+So all but one of the processors wait a long time while CAM is setting itself up,
+then they all work for a short time to make the short forecast, 
+and then repeat for the next ensemble member.
+
+


+async = 3 is part way between async = 2 and 4.  
+CAM must be compiled with pure OpenMP parallelism.
+Then the MPI filter can execute multiple CAMs simultaneously on several processors each.
+The start-up for each is still a single process, 
+but a smaller fraction of the processors wait.  
+This mode will make reasonably efficient use of hundreds of processors.
+
+


+
 Each batch of restart data can be saved to a mass store using (a modified) 
-auto_re2ms and retrieved using .../ms2restart.  Execute the
-commands with no arguments to see instructions.  They package files of each ensemble
-member together, and then bundle batches of ensemble members together for efficient

@@ Diff output truncated at 40000 characters. @@

From nancy at ucar.edu  Thu Jun  2 10:58:20 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 02 Jun 2011 10:58:20 -0600
Subject: [Dart-dev] [4939] DART/trunk/models/cam/model_mod.html: Extensive
 revisions by Kevin ( content) and me (formatting).
Message-ID: 

Revision: 4939
Author:   nancy
Date:     2011-06-02 10:58:20 -0600 (Thu, 02 Jun 2011)
Log Message:
-----------
Extensive revisions by Kevin (content) and me (formatting).

Modified Paths:
--------------
    DART/trunk/models/cam/model_mod.html

-------------- next part --------------
Modified: DART/trunk/models/cam/model_mod.html
===================================================================

--- DART/trunk/models/cam/model_mod.html	2011-06-02 16:27:14 UTC (rev 4938)
+++ DART/trunk/models/cam/model_mod.html	2011-06-02 16:58:20 UTC (rev 4939)
@@ -4,6 +4,7 @@
 
 module model_mod (CAM)
 
+
 
 
 
@@ -24,34 +25,49 @@
 
 
 
-NAMELIST /
-INTERFACES /
+
+   
+
+NAMELIST / 
+INTERFACES / 
+PRIVATE COMPONENTS /
 FILES /
 REFERENCES /
 ERRORS /
+BUGS /
 PLANS /
-PRIVATE COMPONENTS /
 TERMS OF USE
 
+
+
+
 
Overview
 
 
-The 17 public interfaces in model_mod
-are standardized for all DART compliant models. These interfaces allow
-DART to advance the model, get the model state and metadata describing 
-this state, find state variables that are close to a given location, 
-and do spatial interpolation for a variety of variables required in
-observational operators.
-
-
-
 This is the DART interface module for the stand-alone CAM model,
 using the either the Eulerian and Finite Volume dynamical core,
+soon the HOMME core on the cubed sphere,
 and possibly the Semi-Lagrangian core. 
-It is designed to work for versions of CAM starting with 2.0.1,
+It is designed to work for versions of CAM from 2.0.1 
+through the currently released version(s)
 by specifying the version number in the model_mod namelist.
-This implementation of DART-CAM uses the CAM (and CLM) initial files for 
+This implementation of DART-CAM uses the CAM initial files for 
 transferring the model state to/from the filter/CAM.  
+The intent of this interface design is to facilitate using any CAM
+version with minimal changes to the model_mod code and accompanying scripts.
+Non-state variables, which are updated by the forecasts, are also 
+carried forward by the CAM and CLM initial files.
+For CAM 3.6 and later the ICE restart files also carry along non-state variables.
+
 
 
 
@@ -60,10 +76,12 @@
 state vector via model_mod namelist entries.   This may include quantities
 the model considers to be parameters, although ongoing research is
 being conducted into the difficulties and meaning of 
-assimilating model parameters of various kinds.
-The CLM incorporated in the stand-alone CAM is currently (4/16/2007)
+tuning  model parameters of various kinds by this method.
+The CLM incorporated in the stand-alone CAM is currently (2011-4)
 treated as a parameterization.  That is, none of its variables
 are incorporated into the DART state vector.
+For each distinct set of fields comprizing a state vector, 
+an ensemble of initial files for the program 'filter' must be created.
 
 
 
@@ -71,77 +89,76 @@
 from model_interpolate.  Surface observations can not yet be interpolated,
 due to the difference between the model surface and the earth's surface
 where the observations are made.  Model_interpolate can be queried for any
-(non-surface) variable in the state vector, which are variables native to
-CAM, plus pressure on height levels.  The default state vector is (PS), T,
-U, V, Q, CLDLIQ, CLDICE.  Other variables can be added, but minor
-modifications to model_mod.f90 will be necessary.  Use the existing code
-for the current state variables as a template.  In particular add the
-TYPE_s in the declarations at the beginning of the module, and see
-subroutines order_state_fields and obs_field_location,
-where those TYPE_s are used.  Modify CAM to write the new fields to the
-initial files, and modify the model_mod_nml 
-(in input.nml) to include the new state vector components.  
-In the namelist the vertical coordinate type of the new fields must also be
-specified.  See which_vert in 
- location_mod 
+(non-surface) variable in the state vector (which are variables native to
+CAM) plus pressure on height levels.  The default state vector is PS, T,
+U, V, Q, CLDLIQ, CLDICE.  
+Variables which are not on the initial file 
+can be added  , 
+but minor modifications to model_mod.f90 (and perhaps CAM) may be necessary.  
 
 
 
-Links to information about 
+The 16 public interfaces in model_mod
+are standardized for all DART compliant models. These interfaces allow
+DART to advance the model, get the model state and metadata describing 
+this state, find state variables that are close to a given location, 
+and do spatial interpolation for a variety of variables required by
+observational operators.
+
+
+
+Help with several aspects of
  setting up assimilation experiments  
-using CAM and parallel architecture computers, including:
-
+using CAM and parallel architecture computers is available:
 
-     script and executable calling tree 
-     file contents and purposes
-     output directory structure for use by obs_diag
-     experiment set-up
-     helpful hints
-     space requirements of various CAM resolutions
+      experiment set-up  
+     creating initial ensembles  
+      script and executable calling tree  
+      output directory structure for use by obs_diag  
+      file contents and purposes  
+      helpful hints  
+      space requirements of various CAM resolutions  
  
+
 
 
-
-
+
 
 
 
 NAMELIST
-We adhere to the F90 standard of starting a namelist with an ampersand
-'&' and terminating with a slash '/' for all our namelist input.
-The declarations have a different syntax, naturally.
-
+We adhere to the F90 standard of starting a namelist with an ampersand 
+'&' and terminating with a slash '/'.
 

 -namelist / model_nml /  &
-     output_state_vector,  model_version,  model_config_file,          &  
-       state_num_0d,   state_num_1d,   state_num_2d,   state_num_3d,   &  
-     state_names_0d, state_names_1d, state_names_2d, state_names_3d,   &
-                      which_vert_1d,  which_vert_2d,  which_vert_3d,   &
-     pert_names, pert_sd, pert_base_vals,                              &
-     highest_obs_pressure_mb, highest_state_pressure_mb,               &
-     max_obs_lat_degree, Time_step_seconds, Time_step_days
+namelist / model_nml /  &
+     output_state_vector,  model_version,  model_config_file,                &  
+       state_num_0d,   state_num_1d,   state_num_2d,   state_num_3d,         &  
+     state_names_0d, state_names_1d, state_names_2d, state_names_3d,         &
+                      which_vert_1d,  which_vert_2d,  which_vert_3d,         &
+     pert_names, pert_sd, pert_base_vals,                                    &
+     highest_obs_pressure_mb, highest_state_pressure_mb ,max_obs_lat_degree, &
+     Time_step_seconds, Time_step_days, impact_only_same_kind, print_details
+    
 
 
+
 
-
-
-
 
-This namelist is read in a file called input.nml
+This namelist is read from a file called input.nml
 The specification of lists of names and numbers for the various dimensions 
 enables the very flexible definition of the state vector.  It can be
 done via the namelist, instead of recompiling DART for each different set.
-One hurdle that still remains is that distinct filter_ics are
-necessary for each separate set of fields which compose the state vector.
+One hurdle that still remains is that distinct filter initial condition files are
+necessary for each distinct set of fields which compose the state vector.
 
 
 
 The dimension of these lists is currently hardwired to size 100. 
-If more variables types need to be assimilated (e.g. many chemical species),
+If more fields need to be assimilated (e.g. many chemical species),
 look for the integer parameter MAX_STATE_NAMES in the source code
 and change it to a long enough value and recompile DART.
-Longer term we intend to investigate using 2 different nameslists
+Longer term we intend to investigate using 2 different namelists
 inside model_mod; one for setting the length of the lists and another
 to actually read in the data which fills the lists.
 
@@ -234,7 +251,7 @@
 highest_obs_pressure_mb       
     real(r8)                      
     Observations higher than this pressure are ignored.
-                       Default  150.0 hPa 
+                       Default  150.0 hPa (Use 100. for GPS) 
 highest_state_pressure_mb     
     real(r8)                      
     Influence of all obs on model points higher than 
@@ -242,73 +259,88 @@
                        Default  150.0 hPa 
 Time_step_seconds          
     real(r8)                   
-    Forecast duration (the part < 1 day)
+    Minimum forecast duration (the part < 1 day)
                        Default  21600 sec 
 Time_step_days             
     real(r8)                   
-    Forecast duration (the part > 24*3600 sec)
+    Minimum forecast duration (the part > 24*3600 sec)
                        Default  0 days 
+impact_only_same_kind             
+    character(len=32)                 
+    Name of one observation kind which can only affect 
+                       state variables of the same kind.
+                       Default ' ' 
+print_details                    
+    logical                          
+    If true, print out detailed information about
+                       the sizes, shapes, offsets, etc of items in the
+                       CAM state vector.  If false, just print out the
+                       names of the fields as they are read into the state
+                       vector.
+                       Default .FALSE. 
 
-
-
 

 
 
-
 
-
+
 
 OTHER MODULES USED
 -       netcdf
-       obs_kind_mod
-       random_nr_mod
-       random_seq_mod
-       threed_sphere/location_mod
-       time_manager_mod
-       types_mod
-       utilities_mod
-       mpi_utilities (or null_mpi_utilities, depending on the calling program)
+obs_kind_mod
+random_nr_mod
+random_seq_mod
+threed_sphere/location_mod
+time_manager_mod
+types_mod
+utilities_mod
+mpi_utilities
 
 
 
-
-
-
-
-
-
 
+
+
 
 
 PUBLIC INTERFACES
 
+FILTER INTERFACE
+
+Here they are listed alphabetically, except for the last 4 interfaces,
+which are only required for low-order models where advancing
+the model can be done by a call to a subroutine. 
+The CAM model only advances by executing the program cam (via script run-pc.csh). 
+Thus the last 4 interfaces only appear as stubs in the CAM module.
+Following this list they are listed in 
+the order in which they appear in model_mod.f90, which is separated into sections
+corresponding to the main functions of model_mod.f90: static_init_model,
+I/O, model_interpolate, vector<->field translations, get_close_obs, and
+utility routines.
+
+
 
-                   
+                   
+
+
+
+
+
-
-
-
-
-
-
+
 use model_mod, only : get_model_size
ens_mean_for_model
  get_close_maxdist_init
  get_close_obs_init
  get_close_obs
  get_model_time_step
  get_model_size
   get_state_meta_data
   model_interpolate
  get_model_time_step
  static_init_model
   nc_write_model_atts
   nc_write_model_vars
   pert_model_state
  get_close_maxdist_init
  get_close_obs_init
  get_close_obs
  ens_mean_for_model
  static_init_model
   adv_1step
   end_model
   init_time
   init_conditions
 
 
+
 
-The last 4 interfaces are only required for low-order models where advancing
-the model can be done by a call to a subroutine. The CAM model only advances by
-executing the program cam (via script run-pc.csh). Thus the last 4 interfaces 
-only appear as stubs in the CAM module.
-


 The interface pert_model_state is provided for CAM, and it allows each
 field of the state vector to be randomly perturbed using a separate
 standard deviation.   Even this may not be flexible enough to handle
@@ -316,57 +348,73 @@
 from the surface to the top of the model.
 
 
+OTHER PUBLIC INTERFACES
 
-Optional namelist interface
-&model_nml
-may be read from file input.nml.
+The list of interfaces above is part of the list of public routines in this module.
+The rest of the public list are used by programs other than filter;
+dart_to_cam, cam_to_dart, etc.
 
 
+
+
+                   
+
+
+
+use model_mod, only : prog_var_to_vector
  read_cam_init
  vector_to_prog_var
  write_cam_init
+
 
-   A note about documentation style.
-   Optional arguments are enclosed in brackets
-   [like this].
+Namelist interface
+ &model_nml 
+is read from file input.nml.
 
 
-
+


+
+
+
+
 
-
-

+
+
+
+
+
 
- model_size = get_model_size( )
+call static_init_model( )
 -integer ::  get_model_size 
-
-
+
-integer,             intent(in)  :: index_in
-type(location_type), intent(out) :: location
-integer, optional,   intent(out) ::  var_type 
-
+ real(r8), dimension(:), intent(in)  :: ens_mean
+ 
-real(r8), dimension(:), intent(in)  :: x
-type(location_type),    intent(in)  :: location
-integer,                intent(in)  :: obs_type
-real(r8),               intent(out) :: interp_val
-integer,                intent(out) :: istatus
-
-type(time_type) :: get_model_time_step
-
+integer,                              ::  nc_write_model_atts 
+integer,                  intent(in)  ::  ncFileId 
+
+integer                               ::  nc_write_model_vars 
+integer,                  intent(in)  ::  ncFileID 
+real(r8), dimension(:),   intent(in)  ::  statevec 
+integer,                  intent(in)  ::  copyindex
+integer,                  intent(in)  ::  timeindex 
+
-type(get_close_type), intent(inout) :: gc
-real(r8),             intent(in)    :: maxdist
-
+ character, intent(in)                     :: file_name
+ type(model_type), allocatable, intent(in) :: var
+ 
-type(get_close_type), intent(inout) :: gc
-integer,              intent(in)    :: num
-type(location_type),  intent(in)    :: obs(num)
-
+ type(model_type), allocatable, intent(in)        :: var
+ real(r8), allocatable, dimension(:), intent(out) :: x
+ 
+ real(r8), allocatable, dimension(:), intent(in) :: x
+ type(model_type), allocatable, intent(out)      :: var
+ 
-real(r8), dimension(:), intent(in)  :: ens_mean
-
-integer             :: nc_write_model_atts
-integer, intent(in) :: ncFileID
-
T
F

+&obs_def_radar_mod_nml
+   convert_to_dbz            =  .true. ,
+   dbz_threshold             =   0.001 ,
+   apply_ref_limit_to_obs    = .false. ,
+   reflectivity_limit_obs    =     0.0 ,
+   lowest_reflectivity_obs   = -888888.0,
+   apply_ref_limit_to_state  = .false. ,
+   reflectivity_limit_state  =     0.0 ,
+   lowest_reflectivity_state = -888888.0 /
+

+&obs_def_radar_mod_nml
+   apply_ref_limit_to_obs     =  .true. ,
+   reflectivity_limit_obs     =     0.0 ,
+   lowest_reflectivity_obs    =     0.0 ,
+   apply_ref_limit_to_fwd_op  =  .true. ,
+   reflectivity_limit_fwd_op  =     0.0 ,
+   lowest_reflectivity_fwd_op =     0.0 ,
+   dielectric_factor          =   0.224 ,
+   n0_rain                    =   8.0e6 ,
+   n0_graupel                 =   4.0e6 ,
+   n0_snow                    =   3.0e6 ,
+   rho_rain                   =  1000.0 ,
+   rho_graupel                =   400.0 ,
+   rho_snow                   =   100.0 ,
+   allow_wet_graupel          = .false.,
+   microphysics_type          =       3 ,
+   allow_dbztowt_conv         = .false. /
+
T
F
+namelist /obs_def_gps_nml/ &
+   max_gpsro_obs  
+
+&obs_def_gps_nml
+   max_gpsro_obs = 100000
+/
+
+types_mod
+utilities_mod
+location_mod (threed_sphere)
+assim_model_mod
+obs_kind_mod
+
+integer,          intent(out)          :: gpskey
+integer,          intent(in)           :: ifile
+character(len=*), intent(in), optional :: fform
+
+integer,          intent(in)           :: gpskey
+integer,          intent(in)           :: ifile
+character(len=*), intent(in), optional :: fform
+
+real(r8),            intent(in)  :: state_vector(:)
+type(location_type), intent(in)  :: location
+integer,             intent(in)  :: gpskey
+real(r8),            intent(out) :: ro_ref
+integer,             intent(out) :: istatus
+
+integer, intent(out) :: gpskey
+
+integer,          intent(out) :: gpskey
+real(r8),         intent(in)  :: nx
+real(r8),         intent(in)  :: ny
+real(r8),         intent(in)  :: nz
+real(r8),         intent(in)  :: rfict0
+real(r8),         intent(in)  :: ds
+real(r8),         intent(in)  :: htop
+character(len=6), intent(in)  :: subset0
+
+integer,          intent(in)  :: gpskey
+real(r8),         intent(out) :: nx
+real(r8),         intent(out) :: ny
+real(r8),         intent(out) :: nz
+real(r8),         intent(out) :: rfict0
+real(r8),         intent(out) :: ds
+real(r8),         intent(out) :: htop
+character(len=6), intent(out) :: subset0
+
 &obs_def_gps_nml

Added: DART/trunk/obs_def/obs_def_gps_mod.nml
===================================================================
--- DART/trunk/obs_def/obs_def_gps_mod.nml	                        (rev 0)
+++ DART/trunk/obs_def/obs_def_gps_mod.nml	2011-06-07 22:11:08 UTC (rev 4955)
@@ -0,0 +1,4 @@
+
+&obs_def_gps_nml
+  max_gpsro_obs = 100000,
+/ 


Property changes on: DART/trunk/obs_def/obs_def_gps_mod.nml
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:eol-style
   + native

Modified: DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml
===================================================================
--- DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml	2011-06-07 22:03:16 UTC (rev 4954)
+++ DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml	2011-06-07 22:11:08 UTC (rev 4955)
@@ -46,6 +46,10 @@
 &obs_kind_nml
    /
 
+&obs_def_gps_nml
+  max_gpsro_obs = 100000,
+  / 
+
 &preprocess_nml
     input_obs_kind_mod_file = '../../../../obs_kind/DEFAULT_obs_kind_mod.F90',
    output_obs_kind_mod_file = '../../../../obs_kind/obs_kind_mod.f90',

Modified: DART/trunk/observations/utilities/threed_sphere/input.nml
===================================================================
--- DART/trunk/observations/utilities/threed_sphere/input.nml	2011-06-07 22:03:16 UTC (rev 4954)
+++ DART/trunk/observations/utilities/threed_sphere/input.nml	2011-06-07 22:11:08 UTC (rev 4955)
@@ -28,6 +28,10 @@
 &location_nml
    /
 
+&obs_def_gps_nml
+   max_gpsro_obs = 100000,
+  / 
+
 &obs_sequence_nml
    write_binary_obs_sequence = .false.  /
 

Modified: DART/trunk/observations/var/work/input.nml
===================================================================
--- DART/trunk/observations/var/work/input.nml	2011-06-07 22:03:16 UTC (rev 4954)
+++ DART/trunk/observations/var/work/input.nml	2011-06-07 22:11:08 UTC (rev 4955)
@@ -25,6 +25,11 @@
  nmlfilename = 'convert.nml'
  /
 
+&obs_def_gps_nml
+ max_gpsro_obs = 100000,
+ / 
+
+
 &obs_sequence_nml
    write_binary_obs_sequence = .false.  /
 

From nancy at ucar.edu  Tue Jun  7 16:12:22 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 07 Jun 2011 16:12:22 -0600
Subject: [Dart-dev] [4956]
 DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml.template: Add
 default GPS namelist to a template input.nml file which is
Message-ID: 

Revision: 4956
Author:   nancy
Date:     2011-06-07 16:12:22 -0600 (Tue, 07 Jun 2011)
Log Message:
-----------
Add default GPS namelist to a template input.nml file which is
used in scripting.

Modified Paths:
--------------
    DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml.template

-------------- next part --------------
Modified: DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml.template
===================================================================
--- DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml.template	2011-06-07 22:11:08 UTC (rev 4955)
+++ DART/trunk/observations/NCEP/ascii_to_obs/work/input.nml.template	2011-06-07 22:12:22 UTC (rev 4956)
@@ -45,6 +45,10 @@
 &obs_kind_nml
    /
 
+&obs_def_gps_nml
+   max_gpsro_obs = 100000
+   /
+
 &preprocess_nml
     input_obs_kind_mod_file = '../../../../obs_kind/DEFAULT_obs_kind_mod.F90',
    output_obs_kind_mod_file = '../../../../obs_kind/obs_kind_mod.f90',

From nancy at ucar.edu  Tue Jun  7 16:14:54 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 07 Jun 2011 16:14:54 -0600
Subject: [Dart-dev] [4957]
 DART/trunk/models/wrf/regression/Global-V3/input.nml.2002Dec31: One more
 possible namelist file in the repository that includes
Message-ID: 

Revision: 4957
Author:   nancy
Date:     2011-06-07 16:14:54 -0600 (Tue, 07 Jun 2011)
Log Message:
-----------
One more possible namelist file in the repository that includes
GPS type obs in the preprocess namelist.  add the GPS namelist.

Modified Paths:
--------------
    DART/trunk/models/wrf/regression/Global-V3/input.nml.2002Dec31

-------------- next part --------------
Modified: DART/trunk/models/wrf/regression/Global-V3/input.nml.2002Dec31
===================================================================
--- DART/trunk/models/wrf/regression/Global-V3/input.nml.2002Dec31	2011-06-07 22:12:22 UTC (rev 4956)
+++ DART/trunk/models/wrf/regression/Global-V3/input.nml.2002Dec31	2011-06-07 22:14:54 UTC (rev 4957)
@@ -124,6 +124,9 @@
    reflectivity_limit_state  =     0.0 ,
    lowest_reflectivity_state =     0.0 /
 
+&obs_def_gps_nml
+   max_gpsro_obs = 100000 /
+
 &assim_model_nml
    write_binary_restart_files = .true.  /
 

From nancy at ucar.edu  Tue Jun  7 16:54:21 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 07 Jun 2011 16:54:21 -0600
Subject: [Dart-dev] [4958] DART/trunk/doc/html/Kodiak_release.html: Add an
 item to the ' non-backwards-compatible' list about
Message-ID: 

Revision: 4958
Author:   nancy
Date:     2011-06-07 16:54:21 -0600 (Tue, 07 Jun 2011)
Log Message:
-----------
Add an item to the 'non-backwards-compatible' list about 
requiring a GPS namelist if you use the GPS obs_def module.

Modified Paths:
--------------
    DART/trunk/doc/html/Kodiak_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html	2011-06-07 22:14:54 UTC (rev 4957)
+++ DART/trunk/doc/html/Kodiak_release.html	2011-06-07 22:54:21 UTC (rev 4958)
@@ -248,6 +248,12 @@
 no other compilers.
 
 integer, intent(in)                    :: level
 character(len=*), intent(in)           :: routine
@@ -386,6 +386,8 @@
 character(len=*), intent(in)           :: rev
 character(len=*), intent(in)           :: rdate
 character(len=*), optional, intent(in) :: aut
+character(len=*), optional, intent(in) :: text2
+character(len=*), optional, intent(in) :: text3
 
+&bob_nml
+  bob1 = 2
+  bob3 = 4,
+/
+
+types_mod
+utilities_mod
+random_seq_mod
+time_manager_mod
+ensemble_manager_mod
+
+real(r8),           intent(in) :: arg1
+real(r8), optional, intent(in) :: arg2
+
+logical,                           :: function1
+adaptive_inflate_type, intent(in)  :: arg1
+
+type bob_type
+   private
+   integer :: bob1
+   integer :: bob2
+end type bob_type
+
-doc/html/Jamaica_release
-doc/html/Jamaica_diffs_from_I
-doc/html/mpi_intro
-doc/html/filter_async_modes
-doc/html/ASP_DART_exercise
-doc/html/DART_ASP_Summer2003
-doc/html/Fiji_release
-doc/html/Guam_release
-doc/html/I_diffs_from_workshop
-doc/html/Iceland_release
-doc/html/PostI_diffs_from_I
-doc/html/Post_Iceland_release
-doc/html/boilerplate
-doc/html/hawaii_release
-doc/html/header
-doc/html/pre_guam_release
-doc/html/pre_hawaii_release
-doc/html/pre_j_release
-converters/littler_tf_dart
-mkmf/mkmf
-DART_LAB/DART_LAB
+Kodiak release notes
+Jamaica release notes
+Jamaica differences from Iceland
+MPI intro
+Filter 'async' modes
+ASP DART exercises
+DART ASP Summer 2003 Workshop
+Fiji release notes
+Guam release notes
+I_diffs_from_workshop
+Iceland release notes
+PostI_diffs_from_I
+Post_Iceland_release
+template doc file
+Hawaii release notes
+Pre_guam release notes
+Pre_hawaii release notes
+Pre_J release notes
+mkmf
+DART_LAB
 
T
F
  namelist /mpi_utilities_nml/ 
-       reverse_task_layout, all_tasks_print,    &
-       verbose, async2_verbose, async4_verbose, &
-       shell_name, separate_node_sync,          &
-       create_local_comm  /
+       reverse_task_layout, all_tasks_print,    &
+       verbose, async2_verbose, async4_verbose, &
+       shell_name, separate_node_sync,          &
+       create_local_comm 
 

From nancy at ucar.edu  Mon Jun 13 16:59:20 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 16:59:20 -0600
Subject: [Dart-dev] [4999] DART/trunk/observations/observations.html: Fix
 formatting of the mailto: tag.
Message-ID: 

Revision: 4999
Author:   nancy
Date:     2011-06-13 16:59:20 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Fix formatting of the mailto: tag.

Modified Paths:
--------------
    DART/trunk/observations/observations.html

-------------- next part --------------
Modified: DART/trunk/observations/observations.html
===================================================================
--- DART/trunk/observations/observations.html	2011-06-13 22:56:28 UTC (rev 4998)
+++ DART/trunk/observations/observations.html	2011-06-13 22:59:20 UTC (rev 4999)
@@ -96,7 +96,7 @@
 of collecting information and conversion programs for and which will
 eventually be added to this directory.  In the meantime, if you have
 converters for data or interest in something that is not in the
-repository, please email the DART group.
+repository, please email the DART group.
 
 
 
@@ -284,6 +284,7 @@
 to read various external formats and convert the observations into the
 format requried by DART.  In addition this external program produces
 DART observation sequence files:
+
 
 
      Observation Processing And Wind Synthesis (OPAWS):
@@ -293,7 +294,7 @@
      Vis5d, and/or DART (Data Assimilation Research Testbed) formats.
 
 
-

+

 For generating synthetic observations, see the
 create_obs_sequence 
 program documentation.
@@ -330,7 +331,7 @@
 
FUTURE PLANS
 
 Contact the
-DART development group
+DART development group
 if you have observations in a different format that you want
 to convert.  We can give you advice and pointers on how to
 approach writing the code.

From nancy at ucar.edu  Mon Jun 13 17:00:11 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 17:00:11 -0600
Subject: [Dart-dev] [5000]
 DART/trunk/system_simulation/system_simulation.html: Remove dangling 
Message-ID: 

Revision: 5000
Author:   nancy
Date:     2011-06-13 17:00:10 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Remove dangling 

Modified Paths:
--------------
    DART/trunk/system_simulation/system_simulation.html

-------------- next part --------------
Modified: DART/trunk/system_simulation/system_simulation.html
===================================================================
--- DART/trunk/system_simulation/system_simulation.html	2011-06-13 22:59:20 UTC (rev 4999)
+++ DART/trunk/system_simulation/system_simulation.html	2011-06-13 23:00:10 UTC (rev 5000)
@@ -123,9 +123,6 @@
 
 
 
-
-
-
 
 
 

From nancy at ucar.edu  Mon Jun 13 17:01:20 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 17:01:20 -0600
Subject: [Dart-dev] [5001] DART/trunk/utilities/closest_member_tool.html:
 Fix nesting of   tags.
Message-ID: 

Revision: 5001
Author:   nancy
Date:     2011-06-13 17:01:20 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Fix nesting of 
  tags.

Modified Paths:
--------------
    DART/trunk/utilities/closest_member_tool.html

-------------- next part --------------
Modified: DART/trunk/utilities/closest_member_tool.html
===================================================================
--- DART/trunk/utilities/closest_member_tool.html	2011-06-13 23:00:10 UTC (rev 5000)
+++ DART/trunk/utilities/closest_member_tool.html	2011-06-13 23:01:20 UTC (rev 5001)
@@ -53,6 +53,7 @@
 will contribute to the total difference value.
 

 Available methods are:
+
 
 1 - simple absolute difference:
 
@@ -80,7 +81,7 @@
 vector and the corresponding item in each ensemble member.
 
 
-

+

 This program could be used to select one or more ensemble
 members to run a free model forecast forward in time after
 the assimilation is finished.  Each member is an equally likely
@@ -101,7 +102,7 @@
 member data and convert it to the model input format for a 
 free forecast, for example.
 
-
+
 Namelist interface
 &closest_member_tool_nml 
 is read from file input.nml.

From nancy at ucar.edu  Mon Jun 13 17:02:55 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 17:02:55 -0600
Subject: [Dart-dev] [5002] DART/trunk/utilities/model_mod_check.html: Fix
	
 nesting.
Message-ID: 

Revision: 5002
Author:   nancy
Date:     2011-06-13 17:02:55 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Fix  nesting.

Modified Paths:
--------------
    DART/trunk/utilities/model_mod_check.html

-------------- next part --------------
Modified: DART/trunk/utilities/model_mod_check.html
===================================================================
--- DART/trunk/utilities/model_mod_check.html	2011-06-13 23:01:20 UTC (rev 5001)
+++ DART/trunk/utilities/model_mod_check.html	2011-06-13 23:02:55 UTC (rev 5002)
@@ -195,6 +195,7 @@
 DART, so to be able to build and run model_mod_check,
 you will need to create a path_names_model_mod_check
 file with the following contents:
+
  assim_model/assim_model_mod.f90
 common/types_mod.f90
@@ -221,13 +222,13 @@
 [~/DART/models/yourmodel/work] % ./model_mod_check
 
 
-
 
 
 Unlike other DART components, you are expected
 to modify model_mod_check.f90 to suit your needs as
 you develop your model_mod. The code is roughly 
 divided into the following categories:
+
 Check the geometry information,
     write a trivial restart file,
     read either a restart file,
@@ -235,7 +236,6 @@
     check the metadata, and
     [optionally] run a test of the model interpolation routine.
 
-
 
 Checking the Geometry Information:
 

From nancy at ucar.edu  Mon Jun 13 17:06:26 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 17:06:26 -0600
Subject: [Dart-dev] [5003] DART/trunk/models/cam/cam_to_dart.html: Fix an
 unescaped & and fix a reference to a namelist.
Message-ID: 

Revision: 5003
Author:   nancy
Date:     2011-06-13 17:06:26 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Fix an unescaped & and fix a reference to a namelist.

Modified Paths:
--------------
    DART/trunk/models/cam/cam_to_dart.html

-------------- next part --------------
Modified: DART/trunk/models/cam/cam_to_dart.html
===================================================================
--- DART/trunk/models/cam/cam_to_dart.html	2011-06-13 23:02:55 UTC (rev 5002)
+++ DART/trunk/models/cam/cam_to_dart.html	2011-06-13 23:06:26 UTC (rev 5003)
@@ -90,7 +90,7 @@
 
 
 -namelist / cam_to_dart_nml /  cam_to_dart_input_file, &
+namelist / cam_to_dart_nml /  cam_to_dart_input_file, &
                                        cam_to_dart_output_file
 
 
@@ -151,7 +151,7 @@
 
     DART namelist file; input.nml
     CAM restart file; caminput.nc
-    CAM "phis" file specified in model_nml&cam_phis 
+    
CAM "phis" file specified in &model_nml::cam_phis 
         (normally cam_phis.nc)
 
 

From nancy at ucar.edu  Mon Jun 13 17:07:06 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 17:07:06 -0600
Subject: [Dart-dev] [5004] DART/trunk/models/cam/dart_to_cam.html: Fix a
	namelist reference.
Message-ID: 

Revision: 5004
Author:   nancy
Date:     2011-06-13 17:07:05 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Fix a namelist reference.

Modified Paths:
--------------
    DART/trunk/models/cam/dart_to_cam.html

-------------- next part --------------
Modified: DART/trunk/models/cam/dart_to_cam.html
===================================================================
--- DART/trunk/models/cam/dart_to_cam.html	2011-06-13 23:06:26 UTC (rev 5003)
+++ DART/trunk/models/cam/dart_to_cam.html	2011-06-13 23:07:05 UTC (rev 5004)
@@ -155,7 +155,7 @@
 
     DART namelist file; input.nml
     DART initial conditions/restart file; e.g. dart_ics
-    CAM "phis" file specified in model_nml&cam_phis 
+    
CAM "phis" file specified in &model_nml::cam_phis 
         (normally cam_phis.nc)
 
 

From nancy at ucar.edu  Mon Jun 13 17:21:06 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Mon, 13 Jun 2011 17:21:06 -0600
Subject: [Dart-dev] [5005] DART/trunk/models/NCOMMAS: This is long-overdue
 documentation for NCOMMAS.
Message-ID: 

Revision: 5005
Author:   thoar
Date:     2011-06-13 17:21:06 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
This is long-overdue documentation for NCOMMAS.
The model_mod.html still needs quite a bit of work in the Description
section, but all the interfaces are believed to be accurate.

Modified Paths:
--------------
    DART/trunk/models/NCOMMAS/model_mod.f90
    DART/trunk/models/NCOMMAS/model_mod.nml

Added Paths:
-----------
    DART/trunk/models/NCOMMAS/dart_ncommas_mod.html
    DART/trunk/models/NCOMMAS/dart_to_ncommas.html
    DART/trunk/models/NCOMMAS/model_mod.html
    DART/trunk/models/NCOMMAS/ncommas_to_dart.html

-------------- next part --------------
Added: DART/trunk/models/NCOMMAS/dart_ncommas_mod.html
===================================================================
--- DART/trunk/models/NCOMMAS/dart_ncommas_mod.html	                        (rev 0)
+++ DART/trunk/models/NCOMMAS/dart_ncommas_mod.html	2011-06-13 23:21:06 UTC (rev 5005)
@@ -0,0 +1,907 @@
+
+
+
+
+module dart_ncommas_mod
+
+
+
+
+
+
+namelist /time_manager_nml/  allow_leapyear, stop_count, stop_option
+
+namelist /io_nml/  luse_pointer_files, pointer_filename
+
+namelist /restart_nml/  restart_freq_opt, restart_freq
+
+namelist /init_ts_nml/  init_ts_option, init_ts_file, init_ts_file_fmt
+
+namelist /domain_nml/  ew_boundary_type
+
+namelist /grid_nml/  horiz_grid_opt,  vert_grid_opt,  topography_opt, &
+                               horiz_grid_file, vert_grid_file, topography_file
+
+real(r8), dimension(:,:) :: ULAT,  &! latitude  (radians) of U points
+real(r8), dimension(:,:) :: ULON,  &! longitude (radians) of U points
+real(r8), dimension(:,:) :: HTN ,  &! length (cm) of north edge of T box
+real(r8), dimension(:,:) :: HTE ,  &! length (cm) of east  edge of T box
+real(r8), dimension(:,:) :: HUS ,  &! length (cm) of south edge of U box
+real(r8), dimension(:,:) :: HUW ,  &! length (cm) of west  edge of U box
+real(r8), dimension(:,:) :: ANGLE  &! angle
+
cell thickness(in cm)   cell center(in m)   cell bottom(in m)
+integer, dimension(:,:), :: KMT    &! k index of deepest grid cell on T grid
+
+KMU               k index of deepest grid cell on U grid
+HT                real(r8) value of deepest valid T depth (in cm)
+HU                real(r8) value of deepest valid U depth (in cm)
+
+types_mod
+time_manager_mod
+utilities_mod
+typesizes
+netcdf
+
+character(len=*), intent(out) :: calstring
+
+type(time_type), intent(out) :: ncommastimestep
+
+integer, intent(out) :: Nx, Ny
+
+integer, intent(out) :: Nz
+
+integer,                    intent(in)  :: nx, ny
+real(r8), dimension(nx,ny), intent(out) :: ULAT, ULON, TLAT, TLON
+
+integer,                   intent(in)  :: nx, ny
+integer, dimension(nx,ny), intent(out) :: KMT, KMU
+
+integer,                 intent(in)  :: nz
+real(r8), dimension(nz), intent(out) :: ZC, ZG
+
+type(time_type), intent(in)  :: model_time
+type(time_type), intent(in)  :: adv_to_time
+
+character(len=*), intent(out) :: filename
+
+namelist / dart_to_ncommas_nml /  dart_to_ncommas_input_file, advance_time_present
+
+namelist / model_nml /  ncommas_restart_filename, calendar
+
+namelist / ncommas_vars_nml /  ncommas_state_variables
+
-namelist /time_manager_nml/  allow_leapyear, stop_count, stop_option
-
-namelist /io_nml/  luse_pointer_files, pointer_filename
-
-namelist /restart_nml/  restart_freq_opt, restart_freq
-
-namelist /init_ts_nml/  init_ts_option, init_ts_file, init_ts_file_fmt
-
-namelist /domain_nml/  ew_boundary_type
-
-namelist /grid_nml/  horiz_grid_opt,  vert_grid_opt,  topography_opt, &
-                               horiz_grid_file, vert_grid_file, topography_file
-
-real(r8), dimension(:,:) :: ULAT,  &! latitude  (radians) of U points
-real(r8), dimension(:,:) :: ULON,  &! longitude (radians) of U points
-real(r8), dimension(:,:) :: HTN ,  &! length (cm) of north edge of T box
-real(r8), dimension(:,:) :: HTE ,  &! length (cm) of east  edge of T box
-real(r8), dimension(:,:) :: HUS ,  &! length (cm) of south edge of U box
-real(r8), dimension(:,:) :: HUW ,  &! length (cm) of west  edge of U box
-real(r8), dimension(:,:) :: ANGLE  &! angle
-
cell thickness(in cm)   cell center(in m)   cell bottom(in m)
-integer, dimension(:,:), :: KMT    &! k index of deepest grid cell on T grid
-
-KMU               k index of deepest grid cell on U grid
-HT                real(r8) value of deepest valid T depth (in cm)
-HU                real(r8) value of deepest valid U depth (in cm)
-
-types_mod
-time_manager_mod
-utilities_mod
-typesizes
-netcdf
-
-character(len=*), intent(out) :: calstring
-
-type(time_type), intent(out) :: ncommastimestep
-
-integer, intent(out) :: Nx, Ny
-
-integer, intent(out) :: Nz
-
-integer,                    intent(in)  :: nx, ny
-real(r8), dimension(nx,ny), intent(out) :: ULAT, ULON, TLAT, TLON
-
-integer,                   intent(in)  :: nx, ny
-integer, dimension(nx,ny), intent(out) :: KMT, KMU
-
-integer,                 intent(in)  :: nz
-real(r8), dimension(nz), intent(out) :: ZC, ZG
-
-type(time_type), intent(in)  :: model_time
-type(time_type), intent(in)  :: adv_to_time
-
-character(len=*), intent(out) :: filename
-
 types_mod
@@ -108,7 +121,7 @@
 
 
 
-
+
 NAMELIST
 We adhere to the F90 standard of starting a namelist with an ampersand
 '&' and terminating with a slash '/' for all our namelist input.
@@ -176,12 +189,12 @@
 
 types_mod
@@ -394,7 +394,7 @@
 
 
 
-
+
 FILES
 
      path_names_create_real_obs; the list of modules used in the
@@ -410,7 +410,7 @@
 
 
 
-
+
 REFERENCES
 
 .../DART/observations/NCEP/prep_bufr/docs/* 
@@ -422,7 +422,7 @@
 
 
 
-
+
 ERROR CODES and CONDITIONS
 
 
@@ -445,10 +445,10 @@
 
-
+
FUTURE PLANS

-Further development to get observations directly from original 

+Further development to get observations directly from original 

 (undecoded) NCEP BUFR files.
 
 
@@ -457,13 +457,13 @@
 
-
+
Terms of Use

-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is",

+without charge, subject to all terms of use at

 
 http://www.image.ucar.edu/DAReS/DART/DART_download
 

Modified: DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -3,24 +3,36 @@
 program prepbufr
-
+
 
-
-INSTRUCTIONS / 
-NAMELIST / 
-FILES /
-REFERENCES /
+PROGRAM prepbufr
+
+
 
 
 
 
 
 
 
 
 
 
 
 
 
 
+
+    
+    
+
+
+    
+    
+       Jump to DART Documentation Main Index

+          version information for this file: 

+          
+          $Id$
+       
+
+DATA SOURCES /
+PROGRAMS / 
+MODULES /
+NAMELIST /
 ERRORS /
-PLANS /
-PRIVATE COMPONENTS /
+FUTURE PLANS /
 TERMS OF USE
-
 
-PROGRAM prepbufr
-$Id$
+Overview
 
 
 Translating NCEP BUFR files into DART obs_seq.out files (input
@@ -35,7 +47,7 @@
 
 
 
-

+
 INSTRUCTIONS
 
 The prep_bufr package is free-standing and has not been completely
@@ -282,25 +294,27 @@
 

 Change directories into the prep_bufr/data subdirectory.
 From a machine with access to the MSS use
-

-msrcp mss:/DSS/A##### data.tar
or

-msrcp mss:/DSS/A#####.blk data.tar

+

+msrcp mss:/DSS/A##### data.tar
or

+msrcp mss:/DSS/A#####.blk data.tar

 where ##### is the data set number, to read the NCEP BUFR data tar files.
 The files which include ACARS data have a read
 password; to specify that to the 'msrcp' command, add the '-rpwd pass' 
 argument (where pass is a 1-8 character password).
-


+


 You must then run the 'cosconvert' program to convert the file into a
 readable tar file. 
+
 
 On bluefire: /contrib/bin/cosconvert -b data.tar 
 
On other platforms, download the appropriate version from: 
 http://www.dss.ucar.edu/libraries/io/cos_blocking/utils/
 
+
 Then 
-


+


 tar -xvf data.tar 
-


+


 will yield individual 6-hourly
 NCEP BUFR data files for the observations in the +/- 3-hour time windows
 of 00Z,  06Z, 12Z, and 18Z of each day.  Note that DART obs_seq files are
@@ -357,7 +371,7 @@
 
 
 
-

+
 OTHER MODULES USED
 
 This is a piece of code that is intended to be 'close' to the original,
@@ -371,7 +385,7 @@
 
 
 
-

+
 NAMELIST
 We adhere to the F90 standard of starting a namelist with an ampersand
 '&' and terminating with a slash '/' for all our namelist input.
@@ -437,14 +451,14 @@
 
 
 
-

+

 
 
 
 
 
 
-
+
 FILES
 input file(s); NCEP BUFR  observation files named using ObsBase 
         with the  "yymmddhh" date tag on the end.  Input to grabbufr if big- to 
@@ -460,7 +474,7 @@
 
 
 
-
+
 REFERENCES
 DART/observations/NCEP/prep_bufr/docs/*  (NCEP text files describing the BUFR files)
 
@@ -469,7 +483,7 @@
 
 
 
-
+
 ERROR CODES and CONDITIONS
 
 this space intentionally left blank
@@ -485,7 +499,7 @@
 
 
 
-

+
 FUTURE PLANS
 
 Further development to get observations directly from original
@@ -497,13 +511,13 @@
 
 
 
-

+
 Terms of Use
 
 
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is", 

-without charge, subject to all terms of use at 

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is", 

+without charge, subject to all terms of use at 

 
 http://www.image.ucar.edu/DAReS/DART/DART_download
 

Modified: DART/trunk/observations/SSEC/SSEC.html
===================================================================
--- DART/trunk/observations/SSEC/SSEC.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/SSEC/SSEC.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -3,24 +3,38 @@
 
 
 SSEC Data Center
-
+
 
 
 
 
-
-OVERVIEW /
+SSEC Data Center
+
+
+
+    
+    
+
+
+    
+    
+       Jump to DART Documentation Main Index

+          version information for this file: 

+          
+          $Id$
+       
+
 DATA SOURCES /
-PROGRAMS /
-REFERENCES /
-KNOWN BUGS /
+PROGRAMS / 
+MODULES /
+NAMELIST /
+ERRORS /
 FUTURE PLANS /
 TERMS OF USE
-
 
-SSEC Data Center
-$Id$
+Overview
 
+
 
 The program in this directory takes satellite wind data from the
 University of Wisconsin-Madison Space Science and Engineering
@@ -31,7 +45,7 @@
 
 
 
-

+
 DATA SOURCES
 
 
@@ -58,7 +72,7 @@
 
 
 
-

+
 PROGRAMS
 
 
@@ -67,8 +81,8 @@
 Go into the work directory and run 
 the quickbuild.csh script to
 compile the necessary files.
-

-

+

+

 The program reads standard input for the data time range,
 which types of observations to convert, and then, if quality control
 information is found in the input file, what type of quality
@@ -81,7 +95,7 @@
 
 
 
-

+
 REFERENCES
 
 
@@ -102,7 +116,7 @@
 
 
 
-
+
 KNOWN BUGS
 
 none
@@ -113,7 +127,7 @@
 
 
 
-

+
 FUTURE PLANS
 
 none
@@ -124,13 +138,13 @@
 
 
 
-

+
 Terms of Use
 
 
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is",

+without charge, subject to all terms of use at

 
 http://www.image.ucar.edu/DAReS/DART/DART_download
 

Modified: DART/trunk/observations/WOD/WOD.html
===================================================================
--- DART/trunk/observations/WOD/WOD.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/WOD/WOD.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -3,12 +3,27 @@
 
 
 WOD Observations
-
+
 
 
 
 
-
+WOD Observations
+
+
+
+    
+    
+
+
+    
+    
+       Jump to DART Documentation Main Index

+          version information for this file: 

+          
+          $Id$
+       
+
 DATA SOURCES /
 PROGRAMS /
 MODULES /
@@ -16,13 +31,10 @@
 ERRORS /
 FUTURE PLANS /
 TERMS OF USE
-
 
-WOD Observations
-Last subversion update of this doc file:
-$Id$
-
+Overview
 
+
 
 The WOD (World Ocean Database) data is a collection of data from various
 sources, combined into a single format with uniform treatment.

Modified: DART/trunk/observations/gps/gps.html
===================================================================
--- DART/trunk/observations/gps/gps.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/gps/gps.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -3,38 +3,38 @@
 
 
 GPS Observations
-
+
 
 
 
 
-

-
-DART Project Documentation 

-
+GPS Observations
+
+
-
-
-
+    
+    
-
 
-DART Documentation Main Index 
- 
-Subversion info for this html file: 

-$Id$  
+    
+    
+       Jump to DART Documentation Main Index

+          version information for this file: 

+          
+          $Id$
+       
 
 

-OVERVIEW /
+
+
 DATA SOURCES /
-PROGRAMS /
+PROGRAMS / 
+MODULES /
 NAMELIST /
-MODULES USES /
-KNOWN BUGS /
+ERRORS /
 FUTURE PLANS /
 TERMS OF USE
-
-
 
-GPS Observations
+Overview
 
+
 
 GPS Radio Occultation data are being returned
 from a series of satellites as part of the
@@ -43,8 +43,8 @@
 The programs in this directory extract the
 data from the distribution files and put them into
 DART observation sequence (obs_seq) file format.
-

-

+
+
 The COSMIC satellites measure the phase delay caused
 by deviation of the
 straight-line path of the GPS satellite signal as
@@ -66,7 +66,7 @@
 
 
 
-

+
 DATA SOURCES
 
 
@@ -94,7 +94,7 @@
 
 
 
-

+
 PROGRAMS
 
 
@@ -105,8 +105,8 @@
 The files in this directory (a combination
 of C shell scripts and a Fortran source executable)
 do this data conversion.
-

-

+
+
 The shell_scripts directory contains several example scripts, including one 
 which downloads the raw data files a day at a time (download_script.csh), 
 and one which executes the conversion program (convert_script.csh).  
@@ -117,14 +117,14 @@
 and do not use the script options to automatically delete the input files.
 Keep the files around until you are sure you are satisified with the
 output files and then delete them by hand.
-

-

+
+
 The conversion executable convert_cosmic_gps_cdf, 
 reads the namelist
  &convert_cosmic_gps_nml 
 from the file input.nml.
-

-

+
+
 The namelist lets you select from one of two different forward
 operators.  The 'local' forward operator computes the expected
 observation value at a single point: the requested height at the
@@ -137,8 +137,8 @@
 the conversion, and the type of operator is stored in the observation,
 so at runtime the corresponding forward operator will be used to
 compute the expected observation value.
-

-

+
+
 The namelist also lets you specify at what heights you want
 observations to be extracted.  The raw data is very dense in
 the vertical; using all values would not results in a set of
@@ -153,7 +153,7 @@
 
 
 
-

+
 NAMELIST
 We adhere to the F90 standard of starting a namelist with an ampersand
 '&' and terminating with a slash '/' for all our namelist input.
@@ -237,12 +237,12 @@
 
 
 
-

+

 
 
 
 
-

+
 MODULES USED
  types_mod
@@ -260,7 +260,7 @@
 
 
 
-
+
 KNOWN BUGS
 
 Some COSMIC files seem to have internal times which differ from the
@@ -277,7 +277,7 @@
 
 
 
-

+
 FUTURE PLANS
 
 The current code bins the data into 200 vertical bins as a first step,
@@ -293,13 +293,13 @@
 
 
 
-

+
 Terms of Use
 
 
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is",

+without charge, subject to all terms of use at

 
 http://www.image.ucar.edu/DAReS/DART/DART_download
 

Modified: DART/trunk/observations/quikscat/QuikSCAT.html
===================================================================
--- DART/trunk/observations/quikscat/QuikSCAT.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/quikscat/QuikSCAT.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -3,23 +3,36 @@
 
 
 QuikSCAT SeaWinds Data
-
+
 
 
 
 
-
-OVERVIEW /
+QuikSCAT SeaWinds Data
+
+
+
+    
+    
+
+
+    
+    
+       Jump to DART Documentation Main Index

+          version information for this file: 

+          
+          $Id$
+       
+
 DATA SOURCES /
-PROGRAMS /
+PROGRAMS / 
+MODULES /
 NAMELIST /
-KNOWN BUGS /
+ERRORS /
 FUTURE PLANS /
 TERMS OF USE
-
 
-QuikSCAT SeaWinds Data
-$Id$
+Overview
 
 
 NASA's QuikSCAT mission is described in 
@@ -41,8 +54,8 @@
 error characteristics of the retrieved wind speeds and directions,
 as does rain, interference of land in the radar footprint, and very
 low wind speeds.  Hence, not all wind retrievals are created equal.
-

-

+
+
 The algorithm that converts the 'sigma naughts' (the measure of radar
 backscatter) into wind speeds and directions has multiple solutions.
 Each candidate solution is called an 'ambiguity', and there are several
@@ -71,7 +84,7 @@
 
 
 
-

+
 DATA SOURCES
 
 
@@ -84,8 +97,8 @@
 libraries (which can be downloaded from 
 http://www.hdfgroup.org/products/hdf4/)
-

-

+
+
 If you go to the official JPL data distribution site
 http://podaac.jpl.nasa.gov/DATA_CATALOG/quikscatinfo.html, 
@@ -101,7 +114,7 @@
 
 
 
-

+
 PROGRAMS
 
 There are several programs that are distributed from the JPL www-site,
@@ -151,8 +164,8 @@
 obs_sequence_nml:write_binary_obs_sequence = .true.)
 will result in observation sequence files that are about half
 the size of the ASCII format.
-

-

+
+
 Since there are about 14 QuikSCAT orbits per day, it may be useful to
 convert individual orbits to an observation sequence file and then
 concatenate multiple observation sequence files into one file per day.
@@ -178,7 +191,7 @@
 
 
 
-

+
 NAMELIST
 We adhere to the F90 standard of starting a namelist with an ampersand
 '&' and terminating with a slash '/' for all our namelist input.
@@ -198,8 +211,8 @@
 
 

 This namelist is read in a file called input.nml.
-

-

+
+
 It is possible to restrict the output observation sequence to contain
 data from a region of interest throught the use of the namelist
 parameters. If you need a region that spans the Prime Meridian,
@@ -266,14 +279,14 @@
 
 
 
-

+

 
 
 
 
 
 
-

+
 KNOWN BUGS
 
 There are no known bugs at this time.
@@ -284,7 +297,7 @@
 
 
 
-

+
 FUTURE PLANS
 
    There is one bit of error-checking that I did not survive the
@@ -307,13 +320,13 @@
 
 
 
-
+
 Terms of Use
 
 
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is",

+without charge, subject to all terms of use at

 
 http://www.image.ucar.edu/DAReS/DART/DART_download
 

Modified: DART/trunk/observations/radar/radar.html
===================================================================
--- DART/trunk/observations/radar/radar.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/radar/radar.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -3,22 +3,36 @@
 
 
 Radar Observations
-
+
 
 
 
 
-
-OVERVIEW /
+Radar Observations
+
+
+
+    
+    
+
+
+    
+    
+       Jump to DART Documentation Main Index

+          version information for this file: 

+          
+          $Id$
+       
+
 DATA SOURCES /
-PROGRAMS /
-KNOWN BUGS /
+PROGRAMS / 
+MODULES /
+NAMELIST /
+ERRORS /
 FUTURE PLANS /
 TERMS OF USE
-
 
-Radar Observations
-$Id$
+Overview
 
 
 Several programs for converting radar observations into DART obs_seq format
@@ -45,7 +59,7 @@
 
 
 
-

+
 DATA SOURCES
 
 
@@ -55,7 +69,7 @@
 
 
 
-

+
 PROGRAMS
 
 
@@ -70,7 +84,7 @@
 
 
 
-

+
 KNOWN BUGS
 
 none
@@ -81,7 +95,7 @@
 
 
 
-

+
 FUTURE PLANS
 
 none
@@ -92,13 +106,13 @@
 
 
 
-

+
 Terms of Use
 
 
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is",

+without charge, subject to all terms of use at

 
 http://www.image.ucar.edu/DAReS/DART/DART_download
 

Modified: DART/trunk/observations/text/text_to_obs.html
===================================================================
--- DART/trunk/observations/text/text_to_obs.html	2011-06-14 16:53:02 UTC (rev 5008)
+++ DART/trunk/observations/text/text_to_obs.html	2011-06-14 17:30:28 UTC (rev 5009)
@@ -45,6 +45,7 @@
 
 
 The workflow is usually: 
+
 
 read in the needed information about each
 observation - location, time, data value, observation type - from 
@@ -57,6 +58,7 @@
 
finally, call a write subroutine that writes out the entire series to a file in 
 a format that DART can read in
 
+
 It is not recommended that you try to mimic the ascii file format
 by other means; the format is subject to change and the library routines
 will continue to be supported even if the physical format changes.
@@ -71,7 +73,7 @@
 
 
 
-

+
 DATA SOURCES
 
 
@@ -86,7 +88,7 @@
 
 
 
-

+
 PROGRAMS
 
 The text_to_obs.f90 file is the source
@@ -131,7 +133,7 @@
 
 
 
-

+
 DECISIONS YOU MIGHT NEED TO MAKE
 
 
@@ -147,7 +149,7 @@
 
 
 
-

+
 KNOWN BUGS
 
 none
@@ -158,7 +160,7 @@
 
 
 
-

+
 FUTURE PLANS
 
 none
@@ -169,13 +171,13 @@
 
 
 
-

+
 Terms of Use
 
 
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

+DART software - Copyright 2004 - 2011 UCAR.

+This open source software is provided by UCAR, "as is",

+without charge, subject to all terms of use at

 
 http://www.image.ucar.edu/DAReS/DART/DART_download

@@ Diff output truncated at 40000 characters. @@

From nancy at ucar.edu  Tue Jun 14 11:45:41 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 14 Jun 2011 11:45:41 -0600
Subject: [Dart-dev] [5010] DART/trunk: Various fixes for html files,
	including:
Message-ID: 

Revision: 5010
Author:   nancy
Date:     2011-06-14 11:45:41 -0600 (Tue, 14 Jun 2011)
Log Message:
-----------
Various fixes for html files, including:
- No spaces in link names (e.g. )
- all & changed to &
- misspelled table attribute 'celpadding' -> 'cellpadding'
- list items with tables or embedded lists need to have
  the tags be:  
stuff 
                    or another 
                
    and not:    stuff 
                  other stuff outside any  sections
- not sure if this is because of the standard or not, but
  the validators don't like tables or lists inside paragraph
  tags.  so close the pending paragraph before other tags.

Modified Paths:
--------------
    DART/trunk/diagnostics/threed_sphere/obs_diag.html
    DART/trunk/doc/html/template.html
    DART/trunk/location/threed_sphere/location_mod.html
    DART/trunk/models/cam/doc/cam_guidelines.html
    DART/trunk/models/cam/model_mod.html
    DART/trunk/models/lorenz_63/model_mod.html
    DART/trunk/models/wrf/WRF_DART_utilities/dart_to_wrf.html
    DART/trunk/models/wrf/WRF_DART_utilities/replace_wrf_fields.html
    DART/trunk/obs_def/obs_def_mod.html
    DART/trunk/utilities/model_mod_check.html

-------------- next part --------------
Modified: DART/trunk/diagnostics/threed_sphere/obs_diag.html
===================================================================
--- DART/trunk/diagnostics/threed_sphere/obs_diag.html	2011-06-14 17:30:28 UTC (rev 5009)
+++ DART/trunk/diagnostics/threed_sphere/obs_diag.html	2011-06-14 17:45:41 UTC (rev 5010)
@@ -42,8 +42,8 @@
    to the observation and several quantities are calculated. These quantities
    are then saved in a netCDF file that has all the metadata to create
    meaningful figures.
-   

-   

+
+
    Each obs_seq.final file contains an observation 
    sequence that has multiple 'copies' of the observation. One copy is
    the actual observation, another copy is the prior ensemble mean estimate 
@@ -57,16 +57,16 @@
    'observation'. It may, in some instances be useful to compare against
    the 'truth', in which case you will have to hand-edit the code and 
    recompile. Caveat emptor.
-   

-   

+
+
    Each ensemble member applies a forward operator to the state to compute
    the "expected" value of an observation. Given multiple estimates of 
    the observation, several quantities can be calculated. It is possible to
    compute the expected observations from the state vector before 
    assimilating (the "guess", "forecast", or "prior") or after the
    assimilation (the "analysis", or "posterior"). 
-   

-   

+
+
    Even with input.nml:filter_nml:num_output_obs_members 
    set to 0; the full [prior,posterior] ensemble mean and
    [prior,posterior] ensemble spread are preserved in the 
@@ -80,6 +80,7 @@
    In this case, the obs_seq.final file contains enough 
    information to calculate a rank histograms, verify forecasts, etc. 
    The ensemble means are still used for many other calculations.
+
    

    
    
@@ -88,7 +89,8 @@
    

    
    
-   

+
+
    There are two versions of this program, one for high-order models that have
    real observations and another for low-order models. Since this program
    is fundamentally interested in the response as a function of region, the 
@@ -98,13 +100,13 @@
    to investigate. The low-order models output simple text files instead of
    netCDF files - the intent is to move these toward netCDF files in the near
    future.
-   

-   

+
+
    Identity observations (only possible from "perfect model experiments") 
    are already explored with state-space diagnostics,
    so obs_diag simply skips them.
-   

-   

+
+
    obs_diag is designed to explore the effect of 
    the assimilation in three ways; 1) as a function of time for a particular 
    variable and level (this is the figure on the left), 2) as a 
@@ -124,15 +126,15 @@
    The rank histogram information can easily be plotted with ncview,
    a free third-party piece of software or with 
    plot_rank_histogram.m.
-   

-   

+
+
    obs_diag
    is not explicitly designed to explore OSSE's.  In general, it is 
    used for 'real' observations and looks through the metadata for
    the observation sequence to identify which 'copy' is labeled 'observation'.
    It is THAT copy that is used as the noisy estimate of the truth.
-   

-   

+
+
    The observation sequence files contain only the time of the observation, 
    nothing of the assimilation interval, etc. - so it requires user guidance 
    to declare what sort of temporal binning for the temporal evolution 
@@ -141,8 +143,8 @@
    the observation sequence. The actual algorithm is that the user input for
    the start date and bin width set up a sequence that ends in one of two ways ...
    the last time is reached or the number of bins has been reached. 
-   

-   

+
+
    obs_diag reads obs_seq.final
    files and calculates the following quantities (in no particular order) 
    for an arbitrary number of regions and levels. It is necessary to query
@@ -808,7 +810,7 @@
    explore the assimilation. By way of an example, we will NOT be using 
    outlier observations in the rank histogram. Lets presume that all your 
    obs_seq.final files are in alphabetically-nice directories:
-     
+     
 
 
 
@@ -901,7 +903,8 @@
   
 Example: plotting locations deprecated
 
-please convert your observation sequence file to netCDF format with obs_seq_to_netcdf and use 
+please convert your observation sequence file to netCDF format with obs_seq_to_netcdf
+and use 
 plot_obs_netcdf.m.
 
 

Modified: DART/trunk/doc/html/template.html
===================================================================
--- DART/trunk/doc/html/template.html	2011-06-14 17:30:28 UTC (rev 5009)
+++ DART/trunk/doc/html/template.html	2011-06-14 17:45:41 UTC (rev 5010)
@@ -96,6 +96,7 @@
 
 
 
+
 
 
 
@@ -264,8 +265,8 @@
 volume, pages.

 
-doi: nn.yyyy/rest_of_number 
-

+doi: nn.yyyy/rest_of_number 

+
 
 
 

Modified: DART/trunk/location/threed_sphere/location_mod.html
===================================================================
--- DART/trunk/location/threed_sphere/location_mod.html	2011-06-14 17:30:28 UTC (rev 5009)
+++ DART/trunk/location/threed_sphere/location_mod.html	2011-06-14 17:45:41 UTC (rev 5010)
@@ -103,6 +103,7 @@
 
 
 The expected calling sequence of the get_close routines 
 is as follows:
+
  
 call get_close_maxdist_init()  ! is called before get_close_obs_init()
@@ -113,6 +114,7 @@
 call get_close_obs_destroy()
 
 
+
 In the threed_sphere implementation the
 first routine initializes some data structures, the second one
 bins up the list of locations, and then the third one is called
@@ -154,13 +156,15 @@
 a common case is for the model_mod to want to supply additions to
 the get_close_obs() routine only.  At the top of the model_mod code
 it would declare:
+
  
-use location_mod, only :: location_get_close_obs => get_close_obs,    &
-                          get_close_maxdist_init, get_close_obs_init, &
+use location_mod, only :: location_get_close_obs => get_close_obs,    &
+                          get_close_maxdist_init, get_close_obs_init, &
                           get_close_obs_destroy
 
 
+
 That makes calls to the maxdist_init, init, and destroy routines simply pass
 through to the code in the location_mod, but the model_mod must supply
 a get_close_obs() subroutine.  When it wants to call the code in the 

Modified: DART/trunk/models/cam/doc/cam_guidelines.html
===================================================================
--- DART/trunk/models/cam/doc/cam_guidelines.html	2011-06-14 17:30:28 UTC (rev 5009)
+++ DART/trunk/models/cam/doc/cam_guidelines.html	2011-06-14 17:45:41 UTC (rev 5010)
@@ -57,11 +57,11 @@
 !!
 -->
 
-CALLING TREE /
-SET-UP /
-INITIAL ENSEMBLE /
-FILE CONTENTS /
-OUTPUT DIRECTORY /
+CALLING TREE /
+SET-UP /
+INITIAL ENSEMBLE /
+FILE CONTENTS /
+OUTPUT DIRECTORY /
 HINTS /
 SPACE
 
@@ -130,19 +130,19 @@
 The sequence of operations for assimilating a single obs_seq.out file follows.
 The functionality of each operation has been restricted to one "domain".
 A script/program is specific to:
+
 
     a machine where the experiment is run (e.g. NCARS IBM Power6 'bluefire'); 
     a model version used in the assimilation (e.g. CAM 4.0.1); 
     the filter version; 
     or the experiment being conducted using the choices for the previous 3.
 
-
 
 
 Go to cam/model_mod page  
  
 
-
+
 
 CALLING TREE
 
@@ -190,7 +190,7 @@
      Central/Experiment/obs_####. Archives diagnostic output. 
       -> analyses2initial.csh
      machine 
-     Central/Experiment/obs_####/H##  Generates analyses in CAM,CLM,CICE initial files.  May also save CAM .h0. history files (but  make them small !) 
+     Central/Experiment/obs_####/H##  Generates analyses in CAM,CLM,CICE initial files.  May also save CAM .h0. history files (but  make them small !) 
          -> NetCDF operators 
      machine 
      Central/Experiment/obs_####/H##  Averaging of CAM,CLM,CICE fields. 
@@ -201,7 +201,7 @@
 
 
 
-
-
+
 
 EXPERIMENT SET-UP
 
@@ -222,25 +222,28 @@
 Instructions for setting up a DART/CAM in "stand-alone" mode assimilation.
 This section does not describe setting up assimilations within the CESM
 framework (available in late 2011?).
+
 
 

 
-   
+   
    
-   DART
-      
+   DART
+      
          Register and check out DART from the 
-             download site.  

+             download site.  
          In .../DART/mkmf link mkmf.template to 
              the mkmf.template.xxxx which is appropriate for your computer 
              (or make one of your own).  
           cd to .../DART/models/cam/work and edit input.nml:preprocess_nml:input_files 
              to choose obs_def source code files to load via the preprocessor.  
 
-             The default file (obs_def_reanalysis_bufr_mod.f90) will handle 
-	     observations from NCEP reanalysis BUFR files.  (Warning; assimilating the
+             The default file 
+             
+             obs_def/obs_def_reanalysis_bufr_mod.f90 will handle 
+	     observations from NCEP reanalysis BUFR files.  (Warning: assimilating the
 	     obs in the example GPS obs_seq.out file available from the 
-             DART Obs_sets site
+             DART Obs_sets site
 	     requires loading more than just the obs_def_gps_mod.f90.)
          Script DART/models/cam/work/quick_build.csh is recommended for compiling 
              the package.  
@@ -254,9 +257,10 @@
              to fit in the memory of a single processor, so this is only suitable
              for low resolution, small ensemble testing.
      
+     
 
-    CAM 
-      
+    CAM 
+      
    
           Put the DART modifications 
              (.../DART/models/cam/Cam[version#]_DART_mods.tar),
@@ -282,33 +286,33 @@
 
                            CAM 3.1 - 3.5
-                &camexp
+                &camexp
                  ncdata         = 'caminput.nc'
                  caseid         = 'whatever_you_want'
                  nsrest         = 0
                  calendar       = 'GREGORIAN'
                  inithist       = 'ENDOFRUN'
                 /
-                &clmexp
+                &clmexp
                  finidat        = 'clminput.nc'
                 /
              CAM 3.6 - 4.?
-                &seq_timemgr_inparm
+                &seq_timemgr_inparm
                  calendar       = 'GREGORIAN'
                  restart_n      = 12
                  restart_option = 'nsteps'
                  stop_option    = 'date'
                 /
-                &cam_inparm
+                &cam_inparm
                  ncdata   = 'caminput.nc'
                  inithist = 'ENDOFRUN'
                  div24del2flag = 4,
                  nhtfrq = -6
                 /
-                &clm_inparm
+                &clm_inparm
                  finidat = 'clminput.nc'
                 /
-                &dom_inparm
+                &dom_inparm
                  bndtvs  = '/your/SST/file/here/resolution/cam_version/sst_HadOIBl_bc_1.9x2.5_1949_2007.nc'
                  sstcyc  = .false.
                 /
@@ -320,9 +324,9 @@
                 >  stop_ymd       = 20021201
                 >  stop_tod       = 0
              
-             
+             
              If you want to make the .h0. history files small and focused, for archiving:
-                add to &cam_inparm
+                add to &cam_inparm
                                  empty_htapes    = .true.,
                    mfilt           =  1
@@ -362,28 +366,28 @@
              (Matching is important; CAM checks that the CLM initial file has the expected
               grid parameters.)
              Only the grid information is used from these files, so their dates don't matter.
+      
+      
+
    
-      
-    Set up an experiment central directory ("Central" here) where there's 
-   enough space  for output.  
-         Copy the DART namelist file (DART/models/cam/work/input.nml)
+       
 Set up an experiment central directory ("Central" here) where there's 
+              enough space  for output.  
+       Copy the DART namelist file (DART/models/cam/work/input.nml)
              into one called "input_1.nml" in Central.
-   
-         Copy DART/models/cam/shell_scripts/job_mpi.csh  to Central 
+       
Copy DART/models/cam/shell_scripts/job_mpi.csh  to Central 
 
-   EXPERIMENT
+   EXPERIMENT
    
-       
+       
 
           If you need to make up synthetic observations get create_obs_sequence, 
              create_fixed_network_seq and perfect_model_obs and learn how to use them.  
-
-             Otherwise, use the obs_seq.out files provided 
-             here
+             Otherwise, use the obs_seq.out files provided  
+             here
              or similar 'real observations' files.
           
           Edit job_mpi.csh.  It has more detailed instructions about how to:
-              
+              
                  define experiment output directory names
                  tell it whether CAM is MPI or OpenMP
 
@@ -394,9 +398,9 @@
                       here.
                  find and provide the path name of the obs_seq.out files
 		 find and provide the path name of the filter_ic[.#] files.
-		     Such an ensemble can be created from CAM initial files
+		     Such an ensemble can be created from CAM initial files
                      using 
-		     .../DART/models/cam/cam_to_dart.f90. 
+		     cam_to_dart. 
                  define which CAM and CLM initial files to use.  
                      Some initial and filter_ic files are available from 
                      the NCAR Mass Store:/RAEDER/DAI/CAM_init/[Resol]_[model_version] and more from
@@ -409,7 +413,7 @@
    
           
Edit input_1.nml to configure the assimilation of the first obs_seq.out.
               Be sure that 
-              
+              
                  filenames listed in it agree with what's required by job_mpi.csh
                      and what is or will be available in the Central directory. 
                  start from restart is .true. if you have an initial ensemble,
@@ -423,19 +427,21 @@
               
           
           Copy input_1.nml to input_n.nml and edit input_n.nml. 
-
+
               Set start_from_restart to .true.  
               Change init_time_days = -1, init_time_seconds = -1.
 	   Run the experiment by executing job_mpi.csh, 
 	       either through the batch queue or interactively. 
 
        
+       
 
-
 
+
 
-
+
 
 CAM INITIAL ENSEMBLES
 
@@ -446,10 +452,10 @@
 All of these strategies require converting CAM initial file(s) into 
       filter_ic.#### files, which is done by the 
        same method.  
-

+
  MINIMAL WORK; Get an ensemble of filter and CAM/CLM[/CICE] initial files
      from someone else (DART has a few dates for a few model cores and resolutions
-     here.
+     here.
      This limits the investigations you can undertake,
      but is the fastest and cheapest way to start assimilating.
 
@@ -466,13 +472,13 @@
      This will make the ensemble advance long enough to balance the fields,
      without being perturbed by the assimilation of any observations.
 -&filter_nml
+&filter_nml
    ...
    start_from_restart       = .false.,
    restart_in_file_name     = "filter_ic",
    ...
 /
-&model_nml
+&model_nml
    ...
    pert_names         = 'T       ','US      ','VS      '
    pert_sd           = 1.0d0,2.0d0,2.0d0
@@ -526,7 +532,7 @@
 
 
 
-
+
 
 FILE CONTENTS
 
@@ -537,6 +543,7 @@
 
 The contents of some of the files which appear there are listed here.
 # refers to the list of ensemble members.
+
 
 
@@ -602,15 +609,14 @@
    are derived.  
 FILE   
 
 
-
 
 
-
+
 
 OUTPUT DIRECTORY 
 
-
 Organization of output directories: 
+
 
 
@@ -662,7 +668,8 @@
      to be averaged for analyses archiving by auto_diag2hpss_LSF.csh.
 DIRECTORY   
 
 
-
+

+ A typical pathname for a restart file in my case would be:
 /scratch/raeder/T21x80/Taper1/obs_0003/DART/filter_ic#
                 |      |      |        |    restart file(s)
@@ -672,26 +679,26 @@
                 Central directory (resolution x num_ens_members)
 
 
-


+
 You may also want to make a subdirectory within Experiment 
 for each set of obs_space postscript and .dat files created by obs_diag and matlab.
-
 
 
 
 
 
 HELPFUL HINTS
+
 
-
 In the following, MPI filter uses all of the requested processors.
 There is flexibility in how the ensemble of CAMs uses them.
 The choice of async and number of processors to use 
 will depend on the memory available on each node, 
 as well as the number of processors available.
 See also models/cam/doc/html/filter_async_modes.html in the DART code tree, after registering.
+
 
-


+
 For async = 2 use the ensemble size, available compute nodes, processors/node  ,
 and memory/node to figure how many nodes to request.  
 Make this request in job_mpi.csh.  
@@ -699,51 +706,51 @@
 with an ensemble of 80 members (recommended), it's efficient to request 5 (or 10) nodes.
 This will advance the single-process CAMs in 2 (or 1) batches of 40 (80).  
 That's assuming that each node has the memory to accomodate 8 CAMs.
+
 
-


+
 async = 4 runs an ensemble of pure-MPI CAMs 1 at a time and is usually a poor choice for CAM 
 assimilations because the start-up process for CAM is single process
 and takes significant time.  
 So all but one of the processors wait a long time while CAM is setting itself up,
 then they all work for a short time to make the short forecast, 
 and then repeat for the next ensemble member.
+
 
-


+
 async = 3 is part way between async = 2 and 4.  
 CAM must be compiled with pure OpenMP parallelism.
 Then the MPI filter can execute multiple CAMs simultaneously on several processors each.
 The start-up for each is still a single process, 
 but a smaller fraction of the processors wait.  
 This mode will make reasonably efficient use of hundreds of processors.
+
 
-


-
+
 Each batch of restart data can be saved to a mass store using (a modified) 
 auto_re2hpss and retrieved using models/cam/full_experiment/hpss2restart.  
 Execute the commands with no arguments to see instructions.  
 Then package files of each ensemble member together, and then bundle batches 
 of ensemble members together for efficient storage in a directory named 
 similarly to the one where they exist on the main computer.
+
 
-
-


-
 
 
-


-
+
 Modify and use alias 'rmtemp' to remove the temporary files from
 the central directory where the experiment is run, after a run bombs and
 before running another experiment.
+
  alias rmtemp 'rm *_ud* *_ic[0-9]* cam_*_temp* c[al]minput_[1-9]*.nc  \
               *control filter_ic_old* obs_seq.out times'
 
+
 Needless to say, be careful that you don't name files you want to keep in such a way that
 they'll be deleted by this.
-
 
 
 
@@ -751,9 +758,10 @@
 
 
 SPACE REQUIREMENTS
+
 
-
 Space requirements (Mb per ensemble member) for several CAM resolutions.
+
 
 


 
@@ -772,9 +780,10 @@
 FV0.9x1.25 CAM5 trop_mam3 80. 500.  205.  ???  + " 
 
 
-obs_seq.final typically ranges from 50-150 Mb, independent of model resolution.
-Compression can meaningfully reduce the size of the NetCDF and obs_seq.final files for archiving.
-
+
+obs_seq.final typically ranges from 50-150 Mb, independent of model
+resolution.  Compression can meaningfully reduce the size of the NetCDF and
+obs_seq.final files for archiving.  
 
 
 

Modified: DART/trunk/models/cam/model_mod.html
===================================================================
--- DART/trunk/models/cam/model_mod.html	2011-06-14 17:30:28 UTC (rev 5009)
+++ DART/trunk/models/cam/model_mod.html	2011-06-14 17:45:41 UTC (rev 5010)
@@ -110,16 +110,16 @@
 Help with several aspects of
  setting up assimilation experiments  
 using CAM and parallel architecture computers is available:
+
 
-      experiment set-up  
-     creating initial ensembles  
-      script and executable calling tree  
-      output directory structure for use by obs_diag  
-      file contents and purposes  
+      experiment set-up  
+     creating initial ensembles  
+      script and executable calling tree  
+      output directory structure for use by obs_diag  
+      file contents and purposes  
       helpful hints  
       space requirements of various CAM resolutions  
  
-
 
 
 
@@ -128,21 +128,21 @@
 
 NAMELIST
 We adhere to the F90 standard of starting a namelist with an ampersand 
-'&' and terminating with a slash '/'.
+'&' and terminating with a slash '/'.
+
 
 -namelist / model_nml /  &
-     output_state_vector,  model_version,  model_config_file,                &  
-       state_num_0d,   state_num_1d,   state_num_2d,   state_num_3d,         &  
-     state_names_0d, state_names_1d, state_names_2d, state_names_3d,         &
-                      which_vert_1d,  which_vert_2d,  which_vert_3d,         &
-     pert_names, pert_sd, pert_base_vals,                                    &
-     highest_obs_pressure_mb, highest_state_pressure_mb ,max_obs_lat_degree, &
+namelist / model_nml /  &
+     output_state_vector,  model_version,  model_config_file,                &  
+       state_num_0d,   state_num_1d,   state_num_2d,   state_num_3d,         &  
+     state_names_0d, state_names_1d, state_names_2d, state_names_3d,         &
+                      which_vert_1d,  which_vert_2d,  which_vert_3d,         &
+     pert_names, pert_sd, pert_base_vals,                                    &
+     highest_obs_pressure_mb, highest_state_pressure_mb ,max_obs_lat_degree, &
      Time_step_seconds, Time_step_days, impact_only_same_kind, print_details
     
 
 
-
 
 
 This namelist is read from a file called input.nml
@@ -259,11 +259,11 @@
                        Default  150.0 hPa 
 Time_step_seconds          
     real(r8)                   
-    Minimum forecast duration (the part < 1 day)
+    Minimum forecast duration (the part < 1 day)
                        Default  21600 sec 
 Time_step_days             
     real(r8)                   
-    Minimum forecast duration (the part > 24*3600 sec)
+    Minimum forecast duration (the part > 24*3600 sec)
                        Default  0 days 
 impact_only_same_kind             
     character(len=32)                 
@@ -283,7 +283,7 @@
 
 
 
-
+
 

 OTHER MODULES USED
 @@ -382,8 +382,7 @@
 
 
 call static_init_model( )
--
+
 
 
 
@@ -454,7 +453,7 @@
 saves a local copy of the ensemble means which can be used for 
 computing vertical heights, for example.
  
- 
+ 

  ens_mean    
      Ensemble mean state vector
  
@@ -495,7 +494,7 @@
 assimilation from using "time steps" which are too small.  This is because
 CAM uses a leapfrog time scheme, but the initial files store only a 
 single timestep.  The initial forecast step is a simple forward step, so if 
-repeated short forecasts (< ~9 model time steps) are made, the model 
+repeated short forecasts (< ~9 model time steps) are made, the model 
 becomes unstable.
 In the long run, a more general extended interface may be required that specifies 
 the models range of time stepping possibilities.
@@ -590,7 +589,7 @@
 
 Reads state vector fields from a CAM initial file.  Fields are specified in model_mod.nml.
 
-
+
@@ -613,7 +612,7 @@
  
  Write fields that have been updated by assimilation to the CAM 'initial' file.
  
- 
 file_name    
     CAM initial file name.
 var    
+ 
@@ -694,7 +693,7 @@
  
  Insert CAM fields (N-D) into DART state vector array (1-D)
  
- 
  file_name    
      Name of CAM initial file to which var will be written.
  var    
+ 
@@ -717,7 +716,7 @@
  
  Extract CAM fields (N-D) from state vector (1-D).
  
- 
  var    
      Structure containing all the fields of the state vector.
  x    
+ 
@@ -766,9 +765,9 @@
 Currently namelist variables highest_obs_pressure_mb and
 highest_state_pressure_mb control this.
 All observations on height and level are handled automatically, using the 
-ensemble mean for calculations. The influence declines 
+ensemble mean for calculations. For CAM with 26 vertical levels, the influence declines 
 to 0 above model level 6 for highest_obs_pressure_mb = 150
-( ~ model level 12).
+( ~ model level 12).
 
 
@@ -912,8 +911,7 @@
 
 call end_model( )
--
+
 
@@ -1040,7 +1038,7 @@
  

  Gets the number of lons, lats and levels from a netcdf CAM initial file
  
- 

  x    
      DART state vector.
  var    
 
 
 
 
+ 
@@ -1070,7 +1068,7 @@
  # = 1,2,3 for the numbers of dimensions of the variables.
  
 
- 
  file_name    
      CAM initial file.
  num_lons    
+ 

  ncfileid    
      The file ID number of the caminput.nc file.
  
@@ -1100,7 +1098,7 @@
  Reads the grid size from the cam_phis.nc file, which contains the surface
  elevation data.
  
- 
+ 
@@ -1129,7 +1127,7 @@
  Read a 2-D field from a NetCDF file, so far just surface height (phis)
  from cam_phis.nc.
  
- 
  ncfileid    
      The file ID number of the cam_phis.nc file.
  num_nlons    
+ 
@@ -1159,7 +1157,7 @@
  
  Reads the value of an attribute for each of the fields in cflds.
  
- 
  ncfileid    
      The file ID number of the caminput.nc file.
  var    
+ 
@@ -1186,7 +1184,7 @@
  
  Reads a coordinate array and metadata from a CAM initial file.
  
- 
  att    
      The name of an attribute of the fields on a CAM initial file.
  att_vals    
+ 
@@ -1217,7 +1215,7 @@
  one structure.  The rest of var is filled 
  in read_cam_coord.
  
- 
  var    
      A coordinate array from a CAM initial file.
  idim    
+ 
@@ -1254,7 +1252,7 @@
  
  Deallocate the array components of the variable of defined type grid_1d_type.
  
- 
  var    
      The coordinate variable to read from caminput.nc.
  length    
+ 

  var    
      Coordinate variable and metadata.
  
@@ -1277,7 +1275,7 @@
  Also assigns field TYPE_ variables for use by get_state_meta_data,
  and other routines.
  
- 
+ 
@@ -1329,7 +1327,7 @@
   Define a coordinate variable on the P[oste]rior_Diag.nc file
   and write some of it's attributes there.
  
- 
  cflds    
      Master list of CAM fields to be incorporated in the DART state vector.
  nflds    
+ 
@@ -1368,7 +1366,7 @@
  above the lower of highest_obs_level and the models highest level,
  and below the lowest model level are excluded.  So are PS and Q observations.
  
- 
  c_name    
       Coordinate name.
  ncFileID    
+ 
@@ -1412,7 +1410,7 @@
  above the lower of highest_obs_pressure_mb and the model's highest level,
  and below the lowest model level are excluded.  
  
- 
  val    
      The value of the obs_kind variable interpolated from state vector x.
  x    
+ 
@@ -1456,7 +1454,7 @@
  above the lower of highest_obs_height_m and the model's highest level,
  and below the lowest model level are excluded.  So are PS and Q observations.
  
- 
  val    
      The value of the obs_kind variable interpolated from state vector x.
  x    
+ 
@@ -1495,7 +1493,7 @@
  
  Extracts the value of a field at a specified location from the DART state vector.
  
- 
  val    
      The value of the obs_kind variable interpolated from state vector x.
  x    
+ 
@@ -1533,7 +1531,7 @@
   Uses model information and subroutines to convert the vertical location of an ob
   (prior, model state variable, or actual ob) into the standard vertical coordinate (pressure).
  
- 
  val    
      The value of the obs_kind variable at a grid point, from state vector x.
  x    
+ 
@@ -1569,7 +1567,7 @@
   Function to generate the state vector index corresponding to the grid location
   and variable given.
  
- 
  old_array    
      The location array of the incoming ob.
  old_which    
+ 
@@ -1600,7 +1598,7 @@
   Function to return the index of a character string as found within a list
   of character strings, typically variable or dimension names.
  
- 
  lev_ind    
      Level of the desired variable.
  lon_ind    
+ 
@@ -1627,7 +1625,7 @@
   Given the name of the coordinate to be searched and the index into that array,

@@ Diff output truncated at 40000 characters. @@

From nancy at ucar.edu  Tue Jun 14 16:03:21 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 14 Jun 2011 16:03:21 -0600
Subject: [Dart-dev] [5011] DART/trunk/doc/html/Kodiak_release.html: Updated
 section on New Diagnostics and Documentation as well as
Message-ID: 

Revision: 5011
Author:   thoar
Date:     2011-06-14 16:03:21 -0600 (Tue, 14 Jun 2011)
Log Message:
-----------
Updated section on New Diagnostics and Documentation as well as
New Utilities.

Modified Paths:
--------------
    DART/trunk/doc/html/Kodiak_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html	2011-06-14 17:45:41 UTC (rev 5010)
+++ DART/trunk/doc/html/Kodiak_release.html	2011-06-14 22:03:21 UTC (rev 5011)
@@ -31,7 +31,7 @@
 New Models /
 Changed Models /
 New Observations /
-New Diagnostics and Documentation /
+New Diagnostics and Documentation /
 New Utilities /
 Terms of Use
 
@@ -632,31 +632,178 @@
 
 New Diagnostics and Documentation
 
+
+Better Web Pages.
+We've put a lot of effort into expanding
+our documentation, but there's always room for more. For example, please check out the Matlab 
+diagnostics section: http://www.image.ucar.edu/DAReS/DART/DART_Documentation.php#mat_obs or the pages
+outlining the observation sequence file contents: http://www.image.ucar.edu/DAReS/DART/DART_Observations.php#obs_seq_overview.
+

+

+Please let us know where we are lacking.
+
+
 
+There is now a 
+    DART/index.html
+    in the DART distribution to quickly guide you to any of the documentation for the 
+    routines or modules.
+
+
 DART_LAB

 Matlab GUI presentation of fundamental assimilation concepts
-linkobs
-rank histograms
-two (or more) experiment comparisons
-native netcdf support in matlab

-Does not depend on CSIRO and netcdf_toolbox; now uses snctools
-matlab support for wrf
+
+link_obs.m

+    allows one to view multiple observation attributes simultaneously and dynamically 
+    select subsets of observations in one view and have those same obs highlighted 
+    in the other views. Commonly called 'data brushing'.
+
+obs_diag
+    has undergone extensive revision. User-defined levels for all coordinate (height/pressure/etc), arbitrary
+    number of regions, the inclusion of separate copies for all DART QC values, can 
+    creates rank histograms from the obs_seq.final files, if possible, and more.
+
+Comparing two (or more) experiments

+    two_experiments_profile.m and 
+    two_experiments_evolution.m
+    compare multiple (not just two) obs_diag_output.nc
+    files on the same graphic to allow for easy examination of experiment attributes
+    (rmse, biase, etc.). Some new utilities for subsetting observation sequence files in order to 
+    make fair comparisons are described below.
+
+Simpler netCDF support in Matlab.

+    The DART Matlab routines no longer depend on 4 third-party toolboxes, we are down to just
+    mexnc and 
+    snctools. Soon, we may just use snctools!
+
+Matlab support for CAM.

+    CAM is now fully supported for all the Matlab interfaces that are used in the demos -
+    this includes the state-space tools in DART/matlab that allow for 
+    determining correlations among state variables, among other things. 
+    
+
+Matlab support for WRF.

+    WRF is now fully supported for all the Matlab interfaces that are used in the demos -
+    this predominanty includes the state-space tools in DART/matlab
+    like plot_total_err.
+    The map_wrf.m function can finally plot WRF fields now that the required metadata is part of the
+    Posterior_Diag.nc,
+    Prior_Diag.nc, and (not required)
+    True_State.nc files. It's a small step to augment this routine to make
+    publication-quality figures of WRF fields.
+    
+
 regression tests for wrf
-other new model support
-better web pages
-plot wind vectors from netcdf obs files
-plot correlations
-top level index page in distribution
-optional detailed execution trace messages from filter
-input.nml contents written out to diag netCDF files
-better error checking in obs_sequence creation to avoid out-of-time-order
-    observations being inserted by incorrect programs
-better error checking in the open_file() routine
-individual html pages have links back to the index page, have the
-namelists moved up to be the first thing in the page after the
-Overview, and other minor formatting improvements
+
+other new model support

+    The simple_advection and MITgcm_ocean are fully
+    supported in the Matlab diagnostics.
+
+
+Optional detailed execution trace messages from
+    filter by setting
+    the namelist variable trace_execution.
+
+input.nml contents preserved in True_State.nc, 
+    Prior_Diag.nc, and Posterior_Diag.nc as 
+    variable inputnml.
+
+Better error checking in obs_sequence creation to avoid out-of-time-order
+    observations being inserted by incorrect programs.
+
+Better error checking in the utilities_mod
+    open_file() routine.
+
+In the DART code tree, individual html pages have links back to the index page, 
+    the namelists are moved up to be more prominent, and have other minor 
+    formatting improvements.
+
+The following Matlab observation-space diagnostic routines have been removed:
+    
  nam    
      The string to be found within list.
  list    
+    
+        
+    
+        
+    
+        
+    
+        
+    
+        
+    
+        
+    
+        
+    fit_ens_mean_time.m    plotted the temporal evolution of the ensemble mean of some quantity.
fit_ens_spread_time.m  plotted the temporal evolution of the ensemble spread of some quantity.
fit_mean_spread_time.m plotted the temporal evolution of the mean and spread of some quantity.
obs_num_time.m         plotted the temporal evolution of the observation density. 
fit_ens_mean_vertical.m plotted the vertical profile of the ensemble mean of some quantity.
fit_ens_bias_vertical.m plotted the vertical profile of the bias of the ensemble mean of some quantity.
obs_num_vertical.m     plotted the vertical profile of the observation density.
+
+
+The following Matlab observation-space diagnostic routines have been added:
+    
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+
+    
+        
+    plot_profile.m plots the vertical profile of any quantity for any copy with an overlay of 
+            the observation density and number of observations assimilated.
plot_rmse_xxx_profile.m plots the vertical profile of the rmse and any quantity for any copy with an
+            overlay of the observation density and number of observations assimilated.
plot_bias_xxx_profile.m plots the vertical profile of the bias and any quantity for any copy with an 
+            overlay of the observation density and number of observations assimilated.
two_experiments_profile.m plots the vertical profile of any quantity for any copy for multiple experiments 
+            with an overlay of the observation density and number of observations assimilated 
+            in each experiment.
plot_evolution.m plots the temporal evolution of any quantity for any copy with an overlay of 
+            the observation density and number of observations assimilated.
plot_rmse_xxx_evolution.m plots the temporal evolution of the rmse and any quantity for any copy with an 
+            overlay of the observation density and number of observations assimilated.
two_experiments_evolution.m plots the temporal evolution for any quantity for any copy for multiple 
+            experiements with an overlay of the observation density and number of 
+            observations assimilated in each experiment.
read_obs_netcdf.m reads a netCDF format observation sequence file. Simply need a single copy 
+            and a single qc - no actual observation required. 
plot_obs_netcdf.m reads and plots the locations and values of any copy of the observations in 
+            a DART netCDF format observation sequence file.
plot_obs_netcdf_diffs.m reads and plots the locations and the difference of any two copies of the 
+            observations in a DART netCDF format observation sequence file.
plot_wind_vectors.m reads and plots the wind vectors of the observations in a DART netCDF format 
+            observation sequence file (created by 
+            obs_seq_to_netcdf.f90)
link_obs.m data brushing tool. Explores many facets of the observations simultaneously. 
plot_rank_histogram.m If the ensemble members were preserved in the obs_seq.final 
+            file, obs_diag will create rank histogram information 
+            and store it in the obs_diag_output.nc file. 
+            plot_rank_histogram.m will plot it.
+            There are instructions on how to view the results with ncview 
+            or plot_rank_histogram.m 
+            on the 
+            DART Observation-space Diagnostics 
+            page.
+
 
 
+
 
 
 
@@ -664,23 +811,42 @@
 New Utilities
 
 
-convert obs_seq files to netCDF

+
obs_seq_to_netcdf

+    Almost any DART observation sequences may be converted to a netCDF format file. I still haven't figured out how to succinctly store
+    some of the radar observation metadata, but the observation values, locations, QC values etc. will be converted. This allows for variety
+    of new diagnostics.  
 
-observation coverage

+
+
obs_seq_coverage

+    is a step towards determining what locations and quantities are repeatedly observed during a specific time interval. This
+    may be used to determine a network of observations that will be used to verify forecasts. 
 
-observation selection

+
+
obs_selection

+    is an optional companion routine to obs_seq_coverage. This thins the observation sequence files to contain
+    just the desired set of observations to use in the forecast step. There's no point evaluating all the observations that
+    will not be used in the verification ...
 
-observation verification

+
+
obs_seq_verify

+    is a companion routine to obs_seq_coverage. This creates a netCDF file with variables that should
+    make the calculation of skill scores, etc. easy. Variables like:
+    METAR_U_10_METER_WIND(analysisT, stations, levels, copy, nmembers, forecast_lead)
 
-
-select common observation subsets

+
+
select common observation subsets

 A tool that operates on two (will be extended to more) obs_seq.final 
 files which were output from two different runs of filter.  Assumes the same 
 obs_seq.out input file was used in both cases.  Outputs two new
 obs_seq.final.new files containing only the observations which were
-assimilated in both experiments.  It makes a comparision with the diagnostic tools easier
-to interpret.
+assimilated in both experiments.  It allows for a fair comparision with the diagnostic tools.
 
+
 restart file tool

 Generic tool that works on any DART restart file.  It is compiled with
 the corresponding model_mod which tells it how large the state vector is.
@@ -718,7 +884,8 @@
 first job step can start from a restart file as all subsequent job steps do and
 allows the use of a single input.nml file.
 
-replace WRF fields tool

+
replace WRF fields tool

 WRF-specific tool that moves netCDF variables from one
 file to another.  Field names to be moved can be specified
 directly in the namelist or can be listed in a separate file.

From nancy at ucar.edu  Tue Jun 14 16:15:54 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 14 Jun 2011 16:15:54 -0600
Subject: [Dart-dev] [5012] DART/trunk/models/wrf/regression: WRF V3 has a
 regression case - add it to the readmes.
Message-ID: 

Revision: 5012
Author:   nancy
Date:     2011-06-14 16:15:54 -0600 (Tue, 14 Jun 2011)
Log Message:
-----------
WRF V3 has a regression case - add it to the readmes.

Modified Paths:
--------------
    DART/trunk/models/wrf/regression/README
    DART/trunk/models/wrf/regression/README.website

-------------- next part --------------
Modified: DART/trunk/models/wrf/regression/README
===================================================================
--- DART/trunk/models/wrf/regression/README	2011-06-14 22:03:21 UTC (rev 5011)
+++ DART/trunk/models/wrf/regression/README	2011-06-14 22:15:54 UTC (rev 5012)
@@ -18,6 +18,7 @@
 The current contents are:
 
 CONUS-V2: WRF Version 2, continental US.
+CONUS-V3: WRF Version 3, continental US.
 Global-V3: WRF Version 3, Global 
 Radar: WRF Version 2, surface radar obs
 

Modified: DART/trunk/models/wrf/regression/README.website
===================================================================
--- DART/trunk/models/wrf/regression/README.website	2011-06-14 22:03:21 UTC (rev 5011)
+++ DART/trunk/models/wrf/regression/README.website	2011-06-14 22:15:54 UTC (rev 5012)
@@ -17,6 +17,7 @@
 The current contents are:
 
 CONUS-V2: WRF Version 2, continental US.
+CONUS-V3: WRF Version 3, continental US.
 Global-V3: WRF Version 3, Global 
 Radar: WRF Version 2, surface radar obs
 

From nancy at ucar.edu  Tue Jun 14 16:27:31 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 14 Jun 2011 16:27:31 -0600
Subject: [Dart-dev] [5013] DART/trunk/doc/html/Kodiak_release.html: Add info
 about the WRF regression directory, and a disclaimer
Message-ID: 

Revision: 5013
Author:   nancy
Date:     2011-06-14 16:27:31 -0600 (Tue, 14 Jun 2011)
Log Message:
-----------
Add info about the WRF regression directory, and a disclaimer
about the obs diagnostic routines not supporting scale height
for observation vertical coordinates.

Modified Paths:
--------------
    DART/trunk/doc/html/Kodiak_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html	2011-06-14 22:15:54 UTC (rev 5012)
+++ DART/trunk/doc/html/Kodiak_release.html	2011-06-14 22:27:31 UTC (rev 5013)
@@ -289,9 +289,11 @@
 
 Scale height vertical localization option in 3d models
     See here
-         for a discussion of specifying vertical localization in term of
+         for a discussion of specifying vertical localization in terms of
          scale height, and here
-         for a Wikipedia discussion of how Scale Height is defined.
+         for a Wikipedia discussion of how scale height is defined.  Note that 
+         there is no support in the diagnostic Matlab routines for observations
+         using scale height as the vertical coordinate.
 
 CAM supports FV code, PBS scripting
     See here for details
@@ -693,8 +695,14 @@
     publication-quality figures of WRF fields.
     
 
-regression tests for wrf
+Regression tests for WRF

+   WRF test cases for WRF V2 and V3 for CONUS (Continental or Contiguous
+   United States), a Global WRF case, and a Radar test case.  The data files
+   are on a web server because they are too large to add to the repository.
+   The README files in each directory gives instructions on how to download them.
+
 
+
 other new model support

     The simple_advection and MITgcm_ocean are fully
     supported in the Matlab diagnostics.

From nancy at ucar.edu  Wed Jun 15 11:55:59 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 15 Jun 2011 11:55:59 -0600
Subject: [Dart-dev] [5015] DART/trunk/doc/html/Kodiak_release.html: Added a
 'Known Problems' section, and added an item about
Message-ID: 

Revision: 5015
Author:   nancy
Date:     2011-06-15 11:55:59 -0600 (Wed, 15 Jun 2011)
Log Message:
-----------
Added a 'Known Problems' section, and added an item about
getting an internal compiler error with gfortran 4.1.2 on
linux machines when building obs_diag for the bgrid model.

Modified Paths:
--------------
    DART/trunk/doc/html/Kodiak_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html	2011-06-15 16:34:20 UTC (rev 5014)
+++ DART/trunk/doc/html/Kodiak_release.html	2011-06-15 17:55:59 UTC (rev 5015)
@@ -33,6 +33,7 @@
 New Observations /
 New Diagnostics and Documentation /
 New Utilities /
+Known Problems /
 Terms of Use
 
 
@@ -65,8 +66,8 @@
 
 
 
+
[top]
 
-
 Non-backwards Compatible Changes
 
 
@@ -263,8 +264,8 @@
 
 
 
+
[top]
 
-
 New Features
 
 
@@ -395,8 +396,8 @@
 
 
 
+
[top]
 
-
 New Models
 
 
@@ -449,8 +450,8 @@
 
 
 
+
[top]
 
-
 Changed Models
 
 
@@ -536,8 +537,8 @@
 
 
 
+
[top]
 
-
 New Observation Types/Sources
 
 
@@ -630,8 +631,8 @@
 
 
 
+
[top]
 
-
 New Diagnostics and Documentation
 
 
@@ -814,8 +815,8 @@
 
 
 
+
[top]
 
-
 New Utilities
 
 
@@ -919,13 +920,27 @@
 programs contributed by users.
 
 
+
 
+
[top]
+
+Known Problems
+
+
+We get an internal compiler error when
+compiling the obs_diag program for the B-grid
+model on a Linux machine using the gfortran compiler version 4.1.2.
+If you get this error try a newer version of the Gnu compiler tools.
+We have used 4.3 and 4.4 successfully.
+
+
+
 
 
 
 
+
[top]
 
-
 Terms of Use
 
 

From nancy at ucar.edu  Wed Jun 15 13:30:28 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 15 Jun 2011 13:30:28 -0600
Subject: [Dart-dev] [5016] DART/trunk/doc/html/Kodiak_release.html: remove
 the reference to a particular model for the obs_diag/ compiler problem
Message-ID: 

Revision: 5016
Author:   nancy
Date:     2011-06-15 13:30:28 -0600 (Wed, 15 Jun 2011)
Log Message:
-----------
remove the reference to a particular model for the obs_diag/compiler problem

Modified Paths:
--------------
    DART/trunk/doc/html/Kodiak_release.html

-------------- next part --------------
Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html	2011-06-15 17:55:59 UTC (rev 5015)
+++ DART/trunk/doc/html/Kodiak_release.html	2011-06-15 19:30:28 UTC (rev 5016)
@@ -928,8 +928,8 @@
 
 

 We get an internal compiler error when
-compiling the obs_diag program for the B-grid
-model on a Linux machine using the gfortran compiler version 4.1.2.
+compiling the obs_diag program 
+on a Linux machine using the gfortran compiler version 4.1.2.
 If you get this error try a newer version of the Gnu compiler tools.
 We have used 4.3 and 4.4 successfully.
 

From thoar at ucar.edu  Thu Jun 16 11:14:13 2011
From: thoar at ucar.edu (Tim Hoar)
Date: Thu, 16 Jun 2011 11:14:13 -0600
Subject: [Dart-dev] Kodiak is on the loose ...
Message-ID: <0113B77D-6748-43AB-BAE0-AE3B0AA5C9E4@ucar.edu>

We've pretty much released Kodiak (all but the advertising)

If you go to the DART downloads page and fill in the registration
form, there are instructions on how to get kodiak ... and more.

Please do this and let me know what you think ...

I also updated the DART wiki:

https://wiki.ucar.edu/display/DARTdev/Home

Cheers -- Tim

Tim Hoar, Associate Scientist
National Center for Atmospheric Research
thoar at ucar.edu
303 497 1708

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From nancy at ucar.edu  Fri Jun 24 14:00:46 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Fri, 24 Jun 2011 14:00:46 -0600
Subject: [Dart-dev] [5030]
 DART/trunk/observations/NCEP/prep_bufr/data/198901: change mime-type
 property
Message-ID: 

Revision: 5030
Author:   nancy
Date:     2011-06-24 14:00:45 -0600 (Fri, 24 Jun 2011)
Log Message:
-----------
change mime-type property

Property Changed:
----------------
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010106.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010112.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010118.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010200.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010206.gz

-------------- next part --------------

Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010106.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/octet-stream
   + application/x-gzip


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010112.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/octet-stream
   + application/x-gzip


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010118.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/octet-stream
   + application/x-gzip


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010200.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/octet-stream
   + application/x-gzip


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010206.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/octet-stream
   + application/x-gzip

From nancy at ucar.edu  Tue Jun 28 09:21:46 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Tue, 28 Jun 2011 09:21:46 -0600
Subject: [Dart-dev] [5031]
 DART/trunk/observations/NCEP/prep_bufr/data/198901: unzip, zip,
 trying to get a new checksum
Message-ID: 

Revision: 5031
Author:   thoar
Date:     2011-06-28 09:21:46 -0600 (Tue, 28 Jun 2011)
Log Message:
-----------
unzip, zip, trying to get a new checksum

Modified Paths:
--------------
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010106.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010112.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010118.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010200.gz
    DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010206.gz

-------------- next part --------------
Modified: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010106.gz
===================================================================
(Binary files differ)

Modified: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010112.gz
===================================================================
(Binary files differ)

Modified: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010118.gz
===================================================================
(Binary files differ)

Modified: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010200.gz
===================================================================
(Binary files differ)

Modified: DART/trunk/observations/NCEP/prep_bufr/data/198901/prepqm89010206.gz
===================================================================
(Binary files differ)

From nancy at ucar.edu  Wed Jun 29 09:45:49 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 09:45:49 -0600
Subject: [Dart-dev] [5035] DART/trunk/observations/NCEP/prep_bufr/data:
 different set of example data files
Message-ID: 

Revision: 5035
Author:   nancy
Date:     2011-06-29 09:45:49 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
different set of example data files

Added Paths:
-----------
    DART/trunk/observations/NCEP/prep_bufr/data/201011/
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110406.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110412.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110418.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110500.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz

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===================================================================
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Added: svn:mime-type
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===================================================================
(Binary files differ)


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===================================================================
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Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz
___________________________________________________________________
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   + application/x-gzip

From nancy at ucar.edu  Wed Jun 29 09:46:26 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 09:46:26 -0600
Subject: [Dart-dev] [5036]
 DART/trunk/observations/NCEP/prep_bufr/data/198901/: remove old example
 files
Message-ID: 

Revision: 5036
Author:   nancy
Date:     2011-06-29 09:46:26 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
remove old example files

Removed Paths:
-------------
    DART/trunk/observations/NCEP/prep_bufr/data/198901/

-------------- next part --------------


From nancy at ucar.edu  Wed Jun 29 09:47:02 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 09:47:02 -0600
Subject: [Dart-dev] [5037]
	DART/trunk/observations/NCEP/prep_bufr/data/README: update comment
Message-ID: 

Revision: 5037
Author:   nancy
Date:     2011-06-29 09:47:02 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
update comment

Modified Paths:
--------------
    DART/trunk/observations/NCEP/prep_bufr/data/README

-------------- next part --------------
Modified: DART/trunk/observations/NCEP/prep_bufr/data/README
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/data/README	2011-06-29 15:46:26 UTC (rev 5036)
+++ DART/trunk/observations/NCEP/prep_bufr/data/README	2011-06-29 15:47:02 UTC (rev 5037)
@@ -1,3 +1,4 @@
 # DART $Id$
 
-This directory needs to exist (but can be empty) 
+This directory contains example data files for input
+to the converter.

From thoar at ucar.edu  Wed Jun 29 09:49:13 2011
From: thoar at ucar.edu (Tim Hoar)
Date: Wed, 29 Jun 2011 09:49:13 -0600
Subject: [Dart-dev] [5036]
	DART/trunk/observations/NCEP/prep_bufr/data/198901/: remove
	old example files
In-Reply-To: 
References: 
Message-ID: <225989F9-FC51-41AE-9F9E-D28C2C6B1158@ucar.edu>

OH HAPPY DAY!!!!!!!


0[1022] nolton:~/svn/DART/kodiak % svn merge --force --accept theirs-full https://proxy.subversion.ucar.edu/DAReS/DART/trunk
--- Merging r5020 through r5037 into '.':
A    observations/NCEP/prep_bufr/data/201011
A    observations/NCEP/prep_bufr/data/201011/prepqm10110406.gz
A    observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz
A    observations/NCEP/prep_bufr/data/201011/prepqm10110418.gz
A    observations/NCEP/prep_bufr/data/201011/prepqm10110500.gz
A    observations/NCEP/prep_bufr/data/201011/prepqm10110412.gz
U    observations/NCEP/prep_bufr/data/README
D    observations/NCEP/prep_bufr/data/198901
0[1023] nolton:~/svn/DART/kodiak % 



And the choir of heavenly angels SING! Divine trumpets BLARE!

Oh, the rapture!!!!

On Jun 29, 2011, at 9:46 AM, nancy at ucar.edu wrote:

> Revision: 5036
> Author:   nancy
> Date:     2011-06-29 09:46:26 -0600 (Wed, 29 Jun 2011)
> Log Message:
> -----------
> remove old example files
> 
> Removed Paths:
> -------------
>    DART/trunk/observations/NCEP/prep_bufr/data/198901/
> 
> _______________________________________________
> Dart-dev mailing list
> Dart-dev at mailman.ucar.edu
> http://mailman.ucar.edu/mailman/listinfo/dart-dev

Tim Hoar, Associate Scientist
National Center for Atmospheric Research
thoar at ucar.edu
303 497 1708

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From nancy at ucar.edu  Wed Jun 29 09:51:14 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 09:51:14 -0600
Subject: [Dart-dev] [5039] DART/trunk/observations/NCEP/prep_bufr/work: make
 scripts match examples
Message-ID: 

Revision: 5039
Author:   nancy
Date:     2011-06-29 09:51:14 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
make scripts match examples

Modified Paths:
--------------
    DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh
    DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh
    DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh

-------------- next part --------------
Modified: DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh	2011-06-29 15:50:39 UTC (rev 5038)
+++ DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh	2011-06-29 15:51:14 UTC (rev 5039)
@@ -69,8 +69,8 @@
 # files will be located in subdirectories by month, with the names following
 # the pattern YYYYMM, and then inside the subdirectories, the files are
 # named by the pattern 'prepqmYYMMDDHH'.  for example, if the dir below
-# is the default ../data, then the 6Z file for jan 1st, 1989 would be:
-#  ../data/198901/prepqm89010106
+# is the default ../data, then the 6Z file for nov 4th, 2010 would be:
+#  ../data/201011/prepqm10110406
 # but the conventions for names of prepqm files have changed over the years,
 # so if the prepqm files do *not* follow this pattern, you will have to edit
 # the BUFR_in variable in the script below to match the filenames you have.

Modified: DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh	2011-06-29 15:50:39 UTC (rev 5038)
+++ DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh	2011-06-29 15:51:14 UTC (rev 5039)
@@ -29,10 +29,10 @@
 # USER SETTINGS HERE
 
 # Set year, month, days for to pass as args to prepbufr.csh
-set year     = 2002
-set month    =   10
-set startday =   21
-set endday   =   31
+set year     = 2010
+set month    =   11
+set startday =    1
+set endday   =   30
 
 # Subdirectory base name.  If running multiple months at the
 # same time, must have different base names.  (could add month

Modified: DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh	2011-06-29 15:50:39 UTC (rev 5038)
+++ DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh	2011-06-29 15:51:14 UTC (rev 5039)
@@ -86,8 +86,8 @@
   set beginday = $argv[3]
   set endday   = $argv[4]
 else
-  set year     = 2003
-  set month    = 1
+  set year     = 2010
+  set month    = 11
   set beginday = 10
   set endday   = 20
 endif
@@ -96,8 +96,8 @@
 # files will be located in subdirectories by month, with the names following
 # the pattern YYYYMM, and then inside the subdirectories, the files are
 # named by the pattern 'prepqmYYMMDDHH'.  for example, if the dir below
-# is the default ../data, then the 6Z file for jan 1st, 1989 would be:
-#  ../data/198901/prepqm89010106
+# is the default ../data, then the 6Z file for nov 4th, 2010 would be:
+#  ../data/201011/prepqm10110406
 # but the conventions for names of prepqm files have changed over the years,
 # so if the prepqm files do *not* follow this pattern, you will have to edit
 # the BUFR_in variable in the script below to match the filenames you have.

From nancy at ucar.edu  Wed Jun 29 10:22:55 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 10:22:55 -0600
Subject: [Dart-dev] [5040] DART/trunk/models/cam: Minor updates -
 incorporate the cgd-cam information in the model_mod.html
Message-ID: 

Revision: 5040
Author:   nancy
Date:     2011-06-29 10:22:55 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
Minor updates - incorporate the cgd-cam information in the model_mod.html
page, and add a bit more intro stuff to the cam_guidelines.  so far the
async3 option is NOT part of the distribution so remove references to it
in the cam doc for now.

Modified Paths:
--------------
    DART/trunk/models/cam/doc/cam_guidelines.html
    DART/trunk/models/cam/model_mod.html

-------------- next part --------------
Modified: DART/trunk/models/cam/doc/cam_guidelines.html
===================================================================
--- DART/trunk/models/cam/doc/cam_guidelines.html	2011-06-29 15:51:14 UTC (rev 5039)
+++ DART/trunk/models/cam/doc/cam_guidelines.html	2011-06-29 16:22:55 UTC (rev 5040)
@@ -69,26 +69,48 @@
 
 
 
-DART-CAM OVERVIEW
+DART-CAM Setup Overview
 
 
-The up-to-date overview will always be available at 
-
-http://www.image.ucar.edu/DAReS/DART/cgd_cam.shtml
+This document gives specific help in setting up a
+DART-CAM experiment for the first time.
+Unless you just came from there, also see the
+model_mod documentation
+on the code-level interfaces and namelist values for DART-CAM.
 
 
+
+Usually a run of DART-CAM involves executing multiple sequential
+batch job steps, each step consisting of a day's worth
+of assimilation.  Between job steps the output from the
+previous job step must be saved or moved to be used as
+input for the next job step.  Files may need to be archived
+or postprocessed.  And finally, DART is a parallel MPI program
+and CAM can be compiled as a serial job, an OpenMP parallel job,
+or an MPI parallel job.  On some systems an MPI parallel job
+cannot start another MPI parallel job, so running both a
+parallel DART and parallel CAM as a single job can be hard.
+
 
 
-For the  Kodiak_release 
-and beyond, the async=3 (.../input.nml:filter_nml) option 
-has been given a new functionality; advancing several purely OpenMP CAMs at once.
-This contrasts with async = 4, which runs each purely MPI CAM on all available processors
-in sequence.
+The DART distribution comes with some scripts which will probably
+have to be customizes for other users.  The shell_scripts
+directory contains simple example scripts.  The 
+full_experiment directory contains scripts which do a full-up
+experiment with multiple days and automatic archiving.
+
 
-Async=2 also runs an MPI filter, but a single-threaded CAM.
-This will advance 1 ensemble member on each processor 
-(up to the lesser of the number of ensemble members or the number of processors).  
+
+For parallelism options it is fastest to run a serial (single-threaded)
+or OpenMP CAM with a parallel DART.  This is selected by compiling
+CAM with the proper options, and then setting the async
+namelist variable in the &filter_nml
+namelist to 2.   If there is not enough memory to run CAM as a serial
+job CAM can be compiled as a parallel program using MPI and then the
+async value is set to 4 instead.
+
 
+
 For the short forecasts (6 hours) typically needed for assimilation,
 and on machines with at least as many processors as ensemble members,
 async=4 is usually much less efficient than async=2.
@@ -98,11 +120,10 @@
 async=2 lets all the start-up phases run at the same time on all of the processors.
 The drawback of async=2 is that there may not be enough memory on a single
 processor to handle a whole CAM.
-Async = 3 will be between 2 and 4, and depend on the distribution of processors.
 
 
 
-async=2, 3, and 4 allow users to control the assimilation through a single script,
+async=2 and 4 allow users to control the assimilation through a single script,
 'job_mpi.csh'.
 job_mpi.csh has a section of user set parameters which define many aspects of
 the assimilation.  
@@ -116,12 +137,6 @@
 
 
 
-These options have been tested for DART-CAM in batch submission environments 
-PBS and LSF on Linux clusters and IBM AIX.
-
-
-
-
 There are, no doubt, things missing from these lists, so don't struggle too long
 before contacting raeder'at'ucar.edu.
 
@@ -144,11 +159,11 @@
 
 
 
-CALLING TREE
+Calling Tree
 
 
 The calling tree for the scripts and fortran executables when running under
-async=2, 3, or 4 is:
+async=2 or 4 is:
 
 
 
@@ -203,7 +218,7 @@
 
 
-EXPERIMENT SET-UP
+Experiment Set-Up

 
 Instructions for setting up a DART/CAM in "stand-alone" mode assimilation.
@@ -248,7 +263,7 @@
          
Script DART/models/cam/work/quick_build.csh is recommended for compiling 
              the package.  
 	     It is set up to compile and run the preprocessor, 
-	     compile filter and wakeup_filter as MPI processes (async=2, 3, and 4),
+	     compile filter and wakeup_filter as MPI processes (async=2 and 4),
              and compile all other executables (but not CAM) as single process programs.  
              If you want a single-process filter, quick_build.csh can take -nompi 
              as an argument, which will build filter and wakeup_filter that way.
@@ -443,7 +458,7 @@
 
 
 
-CAM INITIAL ENSEMBLES
+CAM Initial Ensembles
 
 
 Strategies for generating an initial ensemble from which DART can start.
@@ -534,7 +549,7 @@
 
 
 

-FILE CONTENTS
+File Contents
 
 
 See the  Kodiak release notes 
@@ -613,7 +628,7 @@
 
 
 

-OUTPUT DIRECTORY 
+Output Directory 
 
 Organization of output directories: 
 
@@ -687,7 +702,7 @@
 
 
 
-HELPFUL HINTS
+Helpful Hints
 
 
 In the following, MPI filter uses all of the requested processors.
@@ -719,6 +734,8 @@
 
 

 async = 3 is part way between async = 2 and 4.  
+It is part of an experimental version of the code which is in 
+the general release yet.
 CAM must be compiled with pure OpenMP parallelism.
 Then the MPI filter can execute multiple CAMs simultaneously on several processors each.
 The start-up for each is still a single process, 
@@ -757,7 +774,7 @@
 
 
 

-SPACE REQUIREMENTS
+Space Requirements
 
 
 Space requirements (Mb per ensemble member) for several CAM resolutions.

Modified: DART/trunk/models/cam/model_mod.html
===================================================================
--- DART/trunk/models/cam/model_mod.html	2011-06-29 15:51:14 UTC (rev 5039)
+++ DART/trunk/models/cam/model_mod.html	2011-06-29 16:22:55 UTC (rev 5040)
@@ -53,7 +53,65 @@
 
Overview
 
 
-This is the DART interface module for the stand-alone CAM model,
+DAReS has successfully incorporated CAM -- The Community Atmosphere Model --
+into the DART framework. It is being actively used by graduate students,
+post-graduates, and scientists at universities and research labs. Others are
+only using analyses for their time period and resolution of interest,
+produced here at NCAR using DART-CAM. In addition to the standard DART
+features described elsewhere, current capabilities (Jamaica-release) include
+the abilities to:
+
+
+
+Use either the Eulerian or finite-volume core.
+Use any resolution of CAM without recompiling DART. The standard resolutions of 
+T21, T42, T85, FV 2x2.5 and 4x5 have been tested.
+Assimilate a variety of observations; to date the observations 
+successfully assimilated include the NCEP reanalysis BUFR obs (T,U,V), 
+Global Positioning System radio occultation obs, and MOPITT carbon monoxide 
+(when a chemistry model is incorporated into FV CAM). Research is under way to 
+assimilate surface observations, specific humidity, cloud liquid water, and aerosols.
+Specify, via namelist entries, the CAM (initial file) variables which will be 
+directly affected by the observations. This allows users to change the model state 
+without recompiling.
+Generate analyses on the CAM grid which are of comparable quality to those 
+produced by operational centers, but which have only CAM model error in them, 
+rather than the model error of the models used at the centers.
+Generate such analyses with as few as 20 ensemble members.
+
+
+
+In addition to the standard DART package there is a collection of initial
+condition files at the large file website
+http://www.image.ucar.edu/pub/DART/CAM that are helpful for interfacing CAM
+with DART. More information and instructions for setting up assimilation
+experiments are available in the DART/models/cam/model_mod.html documentation
+and links.
+
+
+
+Sample sets of observations, which can be used with DART-CAM assimilations,
+can be found at http://www.image.ucar.edu/pub/DART/Obs_sets/ of which the
+NCEP BUFR observations are the most widely used. More information and
+instructions for setting up assimilation experiments are available in the
+DART/models/cam/model_mod.html documentation and links.
+
+
+
+Experience on a variety of machines has shown that it is a very good idea to
+make sure your run-time environment has the following:
+
+
++limit stacksize unlimited
+
+limit datasize unlimited
+
+
+
+
+This page contains the documentation for 
+the DART interface module for the separate-executable CAM model,
 using the either the Eulerian and Finite Volume dynamical core,
 soon the HOMME core on the cubed sphere,
 and possibly the Semi-Lagrangian core. 
@@ -68,6 +126,7 @@
 carried forward by the CAM and CLM initial files.
 For CAM 3.6 and later the ICE restart files also carry along non-state variables.
 
+We anticipate integrating DART with the full CESM of CAM in the near future.
 
 
 
@@ -77,7 +136,7 @@
 the model considers to be parameters, although ongoing research is
 being conducted into the difficulties and meaning of 
 tuning  model parameters of various kinds by this method.
-The CLM incorporated in the stand-alone CAM is currently (2011-4)
+The CLM incorporated in the separate-executable CAM is currently (as of 6/2011)
 treated as a parameterization.  That is, none of its variables
 are incorporated into the DART state vector.
 For each distinct set of fields comprizing a state vector, 
@@ -92,7 +151,7 @@
 (non-surface) variable in the state vector (which are variables native to
 CAM) plus pressure on height levels.  The default state vector is PS, T,
 U, V, Q, CLDLIQ, CLDICE.  
-Variables which are not on the initial file 
+Variables which are not in the initial file 
 can be added  , 
 but minor modifications to model_mod.f90 (and perhaps CAM) may be necessary.  
 

From nancy at ucar.edu  Wed Jun 29 10:40:34 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 10:40:34 -0600
Subject: [Dart-dev] [5041] DART/trunk/doc/html/cgd_cam.shtml: all content
 moved to either cam_guidelines.html or model_mod.html
Message-ID: 

Revision: 5041
Author:   thoar
Date:     2011-06-29 10:40:34 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
all content moved to either cam_guidelines.html or model_mod.html

Removed Paths:
-------------
    DART/trunk/doc/html/cgd_cam.shtml

-------------- next part --------------
Deleted: DART/trunk/doc/html/cgd_cam.shtml
===================================================================
--- DART/trunk/doc/html/cgd_cam.shtml	2011-06-29 16:22:55 UTC (rev 5040)
+++ DART/trunk/doc/html/cgd_cam.shtml	2011-06-29 16:40:34 UTC (rev 5041)
@@ -1,134 +0,0 @@
-
-
-
-      
-      
-      Data Assimilation Research Testbed -- DART
-      
-      
-      
-
-
-
-
-
-
-

 
 
 
-   
-
-   
-
-   
-
-   
-   
-
-       
-       
-     
-
-      
-      TERMS OF USE
-      
-
-      An overview of DART and CAM
-      $Id$
-
-       
-       DAReS has successfully incorporated CAM --
-       The Community Atmosphere Model -- into the DART framework.  
-       It is being actively used by graduate students, post-graduates, and scientists
-       at universities and research labs.  Others are only using analyses for their time 
-       period and resolution of interest, produced here at NCAR using DART-CAM.
-       In addition to the standard DART features described elsewhere, current capabilities 
-       (Jamaica-release) include the abilities to:
-       
-           Use either the Eulerian or finite-volume core.
-           Use any resolution of CAM without recompiling DART.
-               The standard resolutions of T21, T42, T85, 
-               FV 2x2.5 and 4x5 have been tested.
-           Assimilate a variety of observations; to date the observations
-	       successfully assimilated include the NCEP reanalysis BUFR obs 
-               (T,U,V), Global Positioning System radio occultation obs, and 
-	       MOPITT carbon monoxide (when a chemistry model is incorporated 
-	       into FV CAM).  Research is under way to assimilate surface 
-	       observations, specific humidity, cloud liquid water, and aerosols.
-           Specify, via namelist entries, the CAM (initial file) variables 
-	       which will be directly affected by the observations.  This allows 
-	       users to change the model state without recompiling.
-           Generate analyses on the CAM grid which are of comparable quality 
-	       to those produced by operational centers, but which have only CAM 
-	       model error in them, rather than the model error of the models 
-	       used at the centers.
-           Generate such analyses with as few as 20 ensemble members.
-       
-
-       
-       In addition to the standard DART package there is a collection 
-       of initial condition files at the large file website
-       
-                http://www.image.ucar.edu/pub/DART/CAM  
-       that are helpful for interfacing CAM with DART. More information 
-       and instructions for setting up assimilation experiments are 
-       available in the DART/models/cam/model_mod.html 
-       documentation and links.
-       


-       Sample sets of observations, which can be used with DART-CAM 
-       assimilations, can be found at 
-        
-                http://www.image.ucar.edu/pub/DART/Obs_sets/  
-       of which the 
-       
-          NCEP BUFR observations  
-       are the most widely used. More information and instructions for 
-       setting up assimilation experiments are available in the 
-       DART/models/cam/model_mod.html documentation and links.
-       

-       

-       Experience on a variety of machines has shown that it is a very good idea 
-       to make sure your run-time environment has the following:
-       
-
-       limit stacksize unlimited
-       limit datasize unlimited 
-
-
-       
-       
-
-   
-
-
-
-
-
-
-Terms of Use
-
-
-DART software - Copyright 2004 - 2011 UCAR.

-This open source software is provided by UCAR, "as is",

-without charge, subject to all terms of use at

-
-http://www.image.ucar.edu/DAReS/DART/DART_download
-
-
-
-
-
-
-
-
-Contact:        Kevin Raeder    
Revision:       $Revision$ 
Source:         $URL$ 
Change Date:    $Date$ 
Change history:   try "svn log" or "svn diff" 
-
-
-
-
-

From nancy at ucar.edu  Wed Jun 29 10:47:28 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 10:47:28 -0600
Subject: [Dart-dev] [5042]
 DART/trunk/observations/MADIS/convert_madis_rawin.f90: In the infrequent
 case of a file without the mandatory levels
Message-ID: 

Revision: 5042
Author:   nancy
Date:     2011-06-29 10:47:28 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
In the infrequent case of a file without the mandatory levels
but with supplementary levels, go ahead and process the data
that is there.

Modified Paths:
--------------
    DART/trunk/observations/MADIS/convert_madis_rawin.f90

-------------- next part --------------
Modified: DART/trunk/observations/MADIS/convert_madis_rawin.f90
===================================================================
--- DART/trunk/observations/MADIS/convert_madis_rawin.f90	2011-06-29 16:40:34 UTC (rev 5041)
+++ DART/trunk/observations/MADIS/convert_madis_rawin.f90	2011-06-29 16:47:28 UTC (rev 5042)
@@ -203,7 +203,7 @@
   ! the original code had a line to get the fill value here but it
   ! was commented out.  is there one?  do we need it?
 
-  if (nman <= 0 .or. nman > nmaxml) cycle sondeloop
+  if (nman < 0 .or. nman > nmaxml) cycle sondeloop
 
   if ( otime < 0.0_r8 ) cycle sondeloop
 
@@ -227,153 +227,155 @@
   ! extract actual time of observation in file into oday, osec.
   call get_time(time_obs, osec, oday)
 
-  allocate(pres(nman))  ;  allocate(tair(nman))  ;  allocate(tdew(nman))
-  allocate(wdir(nman))  ;  allocate(wspd(nman))
-
-  allocate(qc_pres(nman))  ;  allocate(qc_tair(nman))  ;  allocate(qc_tdew(nman))
-  allocate(qc_wdir(nman))  ;  allocate(qc_wspd(nman))
-
-  call getvar_real_2d(ncid, "prMan", n, nman, pres, pres_miss)
-  call getvar_real_2d(ncid, "tpMan", n, nman, tair, tair_miss)
-  call getvar_real_2d(ncid, "tdMan", n, nman, tdew, tdew_miss)
-  call getvar_real_2d(ncid, "wdMan", n, nman, wdir, wdir_miss)
-  call getvar_real_2d(ncid, "wsMan", n, nman, wspd, wspd_miss)
-
-  ! if user says to use QC, read them in or fill if not there
-  if (use_input_qc) then
-     call get_or_fill_QC_2d(ncid, "prManQCR", n, nman, qc_pres)
-     call get_or_fill_QC_2d(ncid, "tpManQCR", n, nman, qc_tair)
-     call get_or_fill_QC_2d(ncid, "tdManQCR", n, nman, qc_tdew)
-     call get_or_fill_QC_2d(ncid, "wdManQCR", n, nman, qc_wdir)
-     call get_or_fill_QC_2d(ncid, "wsManQCR", n, nman, qc_wspd)
-  else
-     qc_pres = 0
-     qc_tair = 0 ;  qc_tdew = 0
-     qc_wdir = 0 ;  qc_wspd = 0
-  endif
-
-  if ( pres(1) /= pres_miss .and. qc_pres(1) == 0 ) then
-
-    altim = compute_altimeter(pres(1), elev)
-    oerr  = rawin_pres_error(pres_alt_to_pres(elev) * 0.01_r8)
-    if ( altim >= 890.0_r8 .and. altim <= 1100.0_r8 .and. oerr /= missing_r8 ) then
-
-      call create_3d_obs(lat, lon, elev, VERTISSURFACE, altim, &
-                         RADIOSONDE_SURFACE_ALTIMETER, oerr, oday, osec, qc, obs)
-      call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
-
+  if (nman > 0) then
+    allocate(pres(nman))  ;  allocate(tair(nman))  ;  allocate(tdew(nman))
+    allocate(wdir(nman))  ;  allocate(wspd(nman))
+  
+    allocate(qc_pres(nman))  ;  allocate(qc_tair(nman))  ;  allocate(qc_tdew(nman))
+    allocate(qc_wdir(nman))  ;  allocate(qc_wspd(nman))
+  
+    call getvar_real_2d(ncid, "prMan", n, nman, pres, pres_miss)
+    call getvar_real_2d(ncid, "tpMan", n, nman, tair, tair_miss)
+    call getvar_real_2d(ncid, "tdMan", n, nman, tdew, tdew_miss)
+    call getvar_real_2d(ncid, "wdMan", n, nman, wdir, wdir_miss)
+    call getvar_real_2d(ncid, "wsMan", n, nman, wspd, wspd_miss)
+  
+    ! if user says to use QC, read them in or fill if not there
+    if (use_input_qc) then
+       call get_or_fill_QC_2d(ncid, "prManQCR", n, nman, qc_pres)
+       call get_or_fill_QC_2d(ncid, "tpManQCR", n, nman, qc_tair)
+       call get_or_fill_QC_2d(ncid, "tdManQCR", n, nman, qc_tdew)
+       call get_or_fill_QC_2d(ncid, "wdManQCR", n, nman, qc_wdir)
+       call get_or_fill_QC_2d(ncid, "wsManQCR", n, nman, qc_wspd)
+    else
+       qc_pres = 0
+       qc_tair = 0 ;  qc_tdew = 0
+       qc_wdir = 0 ;  qc_wspd = 0
     endif
-
-  endif
-
-  do k = 2, nman   ! obtain the mandatory level data
-
-    prespa = pres(k) * 100.0_r8
-
-    if ( wdir(k) /= wdir_miss .and. qc_wdir(k) == 0 .and. &
-         wspd(k) /= wspd_miss .and. qc_wspd(k) == 0  ) then
-
-      call wind_dirspd_to_uv(wdir(k), wspd(k), uwnd, vwnd)
-      oerr = rawin_wind_error(pres(k))
-      if ( abs(uwnd) <= 150.0_r8 .and. & 
-           abs(vwnd) <= 150.0_r8 .and. oerr /= missing_r8 ) then
-
-        call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, uwnd, &
-                           RADIOSONDE_U_WIND_COMPONENT, oerr, oday, osec, qc, obs)
+  
+    if ( pres(1) /= pres_miss .and. qc_pres(1) == 0 ) then
+  
+      altim = compute_altimeter(pres(1), elev)
+      oerr  = rawin_pres_error(pres_alt_to_pres(elev) * 0.01_r8)
+      if ( altim >= 890.0_r8 .and. altim <= 1100.0_r8 .and. oerr /= missing_r8 ) then
+  
+        call create_3d_obs(lat, lon, elev, VERTISSURFACE, altim, &
+                           RADIOSONDE_SURFACE_ALTIMETER, oerr, oday, osec, qc, obs)
         call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
- 
-        call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, vwnd, &
-                           RADIOSONDE_V_WIND_COMPONENT, oerr, oday, osec, qc, obs)
-        call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
-
+  
       endif
-
+  
     endif
-
-    if ( tair(k) /= tair_miss .and. qc_tair(k) == 0 ) then
-
-      oerr = rawin_temp_error(pres(k))
-      if ( tair(k) >= 180.0_r8 .and. &
-           tair(k) <= 330.0_r8 .and. oerr /= missing_r8 ) then
-
-        call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, tair(k), &
-                           RADIOSONDE_TEMPERATURE, oerr, oday, osec, qc, obs)
-        call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
-
-      endif
-
-    endif
   
-    ! if the air and dewpoint obs are both ok, then see which of the possible
-    ! three types of moisture obs to generate.
-    if ( tair(k) /= tair_miss .and. qc_tair(k) == 0 .and. &
-         tdew(k) /= tdew_miss .and. qc_tdew(k) == 0  ) then
-
-      ! tdew is the dewpoint depression
-      dptk = tair(k) - tdew(k)
-
-      if ( include_specific_humidity ) then
-
-        qobs = specific_humidity(sat_vapor_pressure(dptk),    prespa)
-        qsat = specific_humidity(sat_vapor_pressure(tair(k)), prespa)
-        if ( LH_err ) then
-          qerr = rh_error_from_dewpt_and_temp(tair(k), dptk)
-        else
-          qerr = rawin_rel_hum_error(pres(k), tair(k), qobs / qsat)
-        endif
-        oerr = max(qerr * qsat, 0.0001_r8)
+    do k = 2, nman   ! obtain the mandatory level data
   
-        if ( qobs >  0.0_r8  .and. &
-             qobs <= 0.07_r8 .and. qerr /= missing_r8 ) then
+      prespa = pres(k) * 100.0_r8
   
-          call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, qobs, &
-                             RADIOSONDE_SPECIFIC_HUMIDITY, oerr, oday, osec, qc, obs)
+      if ( wdir(k) /= wdir_miss .and. qc_wdir(k) == 0 .and. &
+           wspd(k) /= wspd_miss .and. qc_wspd(k) == 0  ) then
+  
+        call wind_dirspd_to_uv(wdir(k), wspd(k), uwnd, vwnd)
+        oerr = rawin_wind_error(pres(k))
+        if ( abs(uwnd) <= 150.0_r8 .and. & 
+             abs(vwnd) <= 150.0_r8 .and. oerr /= missing_r8 ) then
+  
+          call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, uwnd, &
+                             RADIOSONDE_U_WIND_COMPONENT, oerr, oday, osec, qc, obs)
           call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
+   
+          call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, vwnd, &
+                             RADIOSONDE_V_WIND_COMPONENT, oerr, oday, osec, qc, obs)
+          call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
   
         endif
   
       endif
   
-      if ( include_relative_humidity ) then
+      if ( tair(k) /= tair_miss .and. qc_tair(k) == 0 ) then
   
-        rh = temp_and_dewpoint_to_rh(tair(k), dptk)
-        if ( LH_err ) then
-          oerr = rh_error_from_dewpt_and_temp(tair(k), dptk)
-        else
-          oerr = rawin_rel_hum_error(pres(k), tair(k), rh)
-        endif
+        oerr = rawin_temp_error(pres(k))
+        if ( tair(k) >= 180.0_r8 .and. &
+             tair(k) <= 330.0_r8 .and. oerr /= missing_r8 ) then
   
-        if ( rh >  0.0_r8 .and. &
-             rh <= 1.5_r8 .and. oerr /= missing_r8 ) then
-
-          call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, rh, &
-                             RADIOSONDE_RELATIVE_HUMIDITY, oerr, oday, osec, qc, obs)
+          call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, tair(k), &
+                             RADIOSONDE_TEMPERATURE, oerr, oday, osec, qc, obs)
           call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
+  
         endif
-
+  
       endif
+    
+      ! if the air and dewpoint obs are both ok, then see which of the possible
+      ! three types of moisture obs to generate.
+      if ( tair(k) /= tair_miss .and. qc_tair(k) == 0 .and. &
+           tdew(k) /= tdew_miss .and. qc_tdew(k) == 0  ) then
   
-      if ( include_dewpoint ) then
-
-        rh = temp_and_dewpoint_to_rh(tair(k), dptk)
-        oerr = dewpt_error_from_rh_and_temp(tair(k), rh)
+        ! tdew is the dewpoint depression
+        dptk = tair(k) - tdew(k)
   
-        if ( rh >  0.0_r8 .and. &
-             rh <= 1.5_r8 .and. oerr /= missing_r8 ) then
-
-          call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, dptk, &
-                             RADIOSONDE_DEWPOINT, oerr, oday, osec, qc, obs)
-          call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
-
+        if ( include_specific_humidity ) then
+  
+          qobs = specific_humidity(sat_vapor_pressure(dptk),    prespa)
+          qsat = specific_humidity(sat_vapor_pressure(tair(k)), prespa)
+          if ( LH_err ) then
+            qerr = rh_error_from_dewpt_and_temp(tair(k), dptk)
+          else
+            qerr = rawin_rel_hum_error(pres(k), tair(k), qobs / qsat)
+          endif
+          oerr = max(qerr * qsat, 0.0001_r8)
+    
+          if ( qobs >  0.0_r8  .and. &
+               qobs <= 0.07_r8 .and. qerr /= missing_r8 ) then
+    
+            call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, qobs, &
+                               RADIOSONDE_SPECIFIC_HUMIDITY, oerr, oday, osec, qc, obs)
+            call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
+    
+          endif
+    
         endif
+    
+        if ( include_relative_humidity ) then
+    
+          rh = temp_and_dewpoint_to_rh(tair(k), dptk)
+          if ( LH_err ) then
+            oerr = rh_error_from_dewpt_and_temp(tair(k), dptk)
+          else
+            oerr = rawin_rel_hum_error(pres(k), tair(k), rh)
+          endif
+    
+          if ( rh >  0.0_r8 .and. &
+               rh <= 1.5_r8 .and. oerr /= missing_r8 ) then
+  
+            call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, rh, &
+                               RADIOSONDE_RELATIVE_HUMIDITY, oerr, oday, osec, qc, obs)
+            call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
+          endif
+  
+        endif
+    
+        if ( include_dewpoint ) then
+  
+          rh = temp_and_dewpoint_to_rh(tair(k), dptk)
+          oerr = dewpt_error_from_rh_and_temp(tair(k), rh)
+    
+          if ( rh >  0.0_r8 .and. &
+               rh <= 1.5_r8 .and. oerr /= missing_r8 ) then
+  
+            call create_3d_obs(lat, lon, prespa, VERTISPRESSURE, dptk, &
+                               RADIOSONDE_DEWPOINT, oerr, oday, osec, qc, obs)
+            call add_obs_to_seq(obs_seq, obs, time_obs, prev_obs, prev_time, first_obs)
+  
+          endif
+  
+        endif
+  
+      endif  ! quality control/missing check on tair, tdew
+  
+    end do
+    deallocate(pres, wdir, wspd, tair, tdew, qc_pres, qc_wdir, qc_wspd, qc_tair, qc_tdew)
+  endif
 
-      endif
-
-    endif  ! quality control/missing check on tair, tdew
-
-  end do
-  deallocate(pres, wdir, wspd, tair, tdew, qc_pres, qc_wdir, qc_wspd, qc_tair, qc_tdew)
-
   !  If desired, read the significant-level temperature data, write to obs_seq
   call getvar_int_1d_1val(ncid, "numSigT", n, nsig )
 

From nancy at ucar.edu  Wed Jun 29 11:58:02 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 11:58:02 -0600
Subject: [Dart-dev] [5043] DART/trunk: Using one consistent DART logo
Message-ID: 

Revision: 5043
Author:   thoar
Date:     2011-06-29 11:58:02 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
Using one consistent DART logo

Modified Paths:
--------------
    DART/trunk/DART_LAB/DART_LAB.html
    DART/trunk/adaptive_inflate/adaptive_inflate_mod.html
    DART/trunk/adaptive_inflate/fill_inflation_restart.html
    DART/trunk/assim_model/assim_model_mod.html
    DART/trunk/assim_tools/assim_tools_mod.html
    DART/trunk/common/types_mod.html
    DART/trunk/cov_cutoff/cov_cutoff_mod.html
    DART/trunk/diagnostics/threed_sphere/obs_diag.html
    DART/trunk/doc/html/Kodiak_release.html
    DART/trunk/doc/html/boilerplate.html
    DART/trunk/doc/html/template.html
    DART/trunk/ensemble_manager/ensemble_manager_mod.html
    DART/trunk/filter/filter.html
    DART/trunk/filter/wakeup_filter.html
    DART/trunk/index.html
    DART/trunk/integrate_model/integrate_model.html
    DART/trunk/location/oned/location_mod.html
    DART/trunk/location/threed_sphere/location_mod.html
    DART/trunk/models/NCOMMAS/dart_to_ncommas.html
    DART/trunk/models/NCOMMAS/model_mod.html
    DART/trunk/models/NCOMMAS/ncommas_to_dart.html
    DART/trunk/models/POP/dart_pop_mod.html
    DART/trunk/models/POP/dart_to_pop.html
    DART/trunk/models/POP/model_mod.html
    DART/trunk/models/POP/pop_to_dart.html
    DART/trunk/models/cam/cam_to_dart.html
    DART/trunk/models/cam/dart_to_cam.html
    DART/trunk/models/cam/deprecated/trans_date_to_dart.html
    DART/trunk/models/cam/deprecated/trans_pv_sv_time0.html
    DART/trunk/models/cam/doc/cam_guidelines.html
    DART/trunk/models/cam/model_mod.html
    DART/trunk/models/lorenz_63/model_mod.html
    DART/trunk/models/model_mod.html
    DART/trunk/models/wrf/WRF_DART_utilities/dart_to_wrf.html
    DART/trunk/models/wrf/model_mod.html
    DART/trunk/mpi_utilities/mpi_utilities_mod.html
    DART/trunk/obs_def/DEFAULT_obs_def_mod.html
    DART/trunk/obs_def/obs_def_1d_state_mod.html
    DART/trunk/obs_def/obs_def_dew_point_mod.html
    DART/trunk/obs_def/obs_def_gps_mod.html
    DART/trunk/obs_def/obs_def_mod.html
    DART/trunk/obs_def/obs_def_ocean_mod.html
    DART/trunk/obs_def/obs_def_radar_mod.html
    DART/trunk/obs_kind/DEFAULT_obs_kind_mod.html
    DART/trunk/obs_kind/obs_kind_mod.html
    DART/trunk/obs_model/obs_model_mod.html
    DART/trunk/obs_sequence/create_fixed_network_seq.html
    DART/trunk/obs_sequence/create_obs_sequence.html
    DART/trunk/obs_sequence/obs_common_subset.html
    DART/trunk/obs_sequence/obs_selection.html
    DART/trunk/obs_sequence/obs_seq_coverage.html
    DART/trunk/obs_sequence/obs_seq_to_netcdf.html
    DART/trunk/obs_sequence/obs_seq_verify.html
    DART/trunk/obs_sequence/obs_sequence_mod.html
    DART/trunk/obs_sequence/obs_sequence_tool.html
    DART/trunk/observations/AIRS/AIRS.html
    DART/trunk/observations/GTSPP/GTSPP.html
    DART/trunk/observations/MADIS/MADIS.html
    DART/trunk/observations/NCEP/ascii_to_obs/create_real_obs.html
    DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html
    DART/trunk/observations/SSEC/SSEC.html
    DART/trunk/observations/WOD/WOD.html
    DART/trunk/observations/gps/gps.html
    DART/trunk/observations/observations.html
    DART/trunk/observations/quikscat/QuikSCAT.html
    DART/trunk/observations/radar/radar.html
    DART/trunk/observations/text/text_to_obs.html
    DART/trunk/observations/var/littler_tf_dart.html
    DART/trunk/observations/var/rad_3dvar_to_dart.html
    DART/trunk/observations/var/var.html
    DART/trunk/perfect_model_obs/perfect_model_obs.html
    DART/trunk/preprocess/preprocess.html
    DART/trunk/random_nr/random_nr_mod.html
    DART/trunk/random_seq/random_seq_mod.html
    DART/trunk/reg_factor/reg_factor_mod.html
    DART/trunk/smoother/smoother_mod.html
    DART/trunk/system_simulation/system_simulation.html
    DART/trunk/time_manager/advance_time.html
    DART/trunk/time_manager/schedule_mod.html
    DART/trunk/time_manager/time_manager_mod.html
    DART/trunk/utilities/PrecisionCheck.html
    DART/trunk/utilities/closest_member_tool.html
    DART/trunk/utilities/model_mod_check.html
    DART/trunk/utilities/restart_file_tool.html
    DART/trunk/utilities/utilities_mod.html

Removed Paths:
-------------
    DART/trunk/doc/html/Dartboard9.png

Property Changed:
----------------
    DART/trunk/doc/html/Dartboard7.png

-------------- next part --------------
Modified: DART/trunk/DART_LAB/DART_LAB.html
===================================================================
--- DART/trunk/DART_LAB/DART_LAB.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/DART_LAB/DART_LAB.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/adaptive_inflate/adaptive_inflate_mod.html
===================================================================
--- DART/trunk/adaptive_inflate/adaptive_inflate_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/adaptive_inflate/adaptive_inflate_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/adaptive_inflate/fill_inflation_restart.html
===================================================================
--- DART/trunk/adaptive_inflate/fill_inflation_restart.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/adaptive_inflate/fill_inflation_restart.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/assim_model/assim_model_mod.html
===================================================================
--- DART/trunk/assim_model/assim_model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/assim_model/assim_model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/assim_tools/assim_tools_mod.html
===================================================================
--- DART/trunk/assim_tools/assim_tools_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/assim_tools/assim_tools_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/common/types_mod.html
===================================================================
--- DART/trunk/common/types_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/common/types_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/cov_cutoff/cov_cutoff_mod.html
===================================================================
--- DART/trunk/cov_cutoff/cov_cutoff_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/cov_cutoff/cov_cutoff_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/diagnostics/threed_sphere/obs_diag.html
===================================================================
--- DART/trunk/diagnostics/threed_sphere/obs_diag.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/diagnostics/threed_sphere/obs_diag.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index



Property changes on: DART/trunk/doc/html/Dartboard7.png
___________________________________________________________________
Deleted: svn:executable
   - *
Modified: svn:mime-type
   - application/octet-stream
   + image/png

Deleted: DART/trunk/doc/html/Dartboard9.png
===================================================================
(Binary files differ)

Modified: DART/trunk/doc/html/Kodiak_release.html
===================================================================
--- DART/trunk/doc/html/Kodiak_release.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/doc/html/Kodiak_release.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/doc/html/boilerplate.html
===================================================================
--- DART/trunk/doc/html/boilerplate.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/doc/html/boilerplate.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/doc/html/template.html
===================================================================
--- DART/trunk/doc/html/template.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/doc/html/template.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -21,7 +21,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/ensemble_manager/ensemble_manager_mod.html
===================================================================
--- DART/trunk/ensemble_manager/ensemble_manager_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/ensemble_manager/ensemble_manager_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/filter/filter.html
===================================================================
--- DART/trunk/filter/filter.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/filter/filter.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/filter/wakeup_filter.html
===================================================================
--- DART/trunk/filter/wakeup_filter.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/filter/wakeup_filter.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/index.html
===================================================================
--- DART/trunk/index.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/index.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        


Modified: DART/trunk/integrate_model/integrate_model.html
===================================================================
--- DART/trunk/integrate_model/integrate_model.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/integrate_model/integrate_model.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/location/oned/location_mod.html
===================================================================
--- DART/trunk/location/oned/location_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/location/oned/location_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/location/threed_sphere/location_mod.html
===================================================================
--- DART/trunk/location/threed_sphere/location_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/location/threed_sphere/location_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/NCOMMAS/dart_to_ncommas.html
===================================================================
--- DART/trunk/models/NCOMMAS/dart_to_ncommas.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/NCOMMAS/dart_to_ncommas.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -12,7 +12,7 @@
 
 
     
-    
+    
     
     
        DART Documentation Main Index


Modified: DART/trunk/models/NCOMMAS/model_mod.html
===================================================================
--- DART/trunk/models/NCOMMAS/model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/NCOMMAS/model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -12,7 +12,7 @@
 
 
     
-    
+    
     
     
        DART Documentation Main Index


Modified: DART/trunk/models/NCOMMAS/ncommas_to_dart.html
===================================================================
--- DART/trunk/models/NCOMMAS/ncommas_to_dart.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/NCOMMAS/ncommas_to_dart.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -12,7 +12,7 @@
 
 
     
-    
+    
     
     
        DART Documentation Main Index


Modified: DART/trunk/models/POP/dart_pop_mod.html
===================================================================
--- DART/trunk/models/POP/dart_pop_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/POP/dart_pop_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/POP/dart_to_pop.html
===================================================================
--- DART/trunk/models/POP/dart_to_pop.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/POP/dart_to_pop.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/POP/model_mod.html
===================================================================
--- DART/trunk/models/POP/model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/POP/model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/POP/pop_to_dart.html
===================================================================
--- DART/trunk/models/POP/pop_to_dart.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/POP/pop_to_dart.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/cam/cam_to_dart.html
===================================================================
--- DART/trunk/models/cam/cam_to_dart.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/cam/cam_to_dart.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/cam/dart_to_cam.html
===================================================================
--- DART/trunk/models/cam/dart_to_cam.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/cam/dart_to_cam.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/cam/deprecated/trans_date_to_dart.html
===================================================================
--- DART/trunk/models/cam/deprecated/trans_date_to_dart.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/cam/deprecated/trans_date_to_dart.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/cam/deprecated/trans_pv_sv_time0.html
===================================================================
--- DART/trunk/models/cam/deprecated/trans_pv_sv_time0.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/cam/deprecated/trans_pv_sv_time0.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/cam/doc/cam_guidelines.html
===================================================================
--- DART/trunk/models/cam/doc/cam_guidelines.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/cam/doc/cam_guidelines.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/cam/model_mod.html
===================================================================
--- DART/trunk/models/cam/model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/cam/model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/lorenz_63/model_mod.html
===================================================================
--- DART/trunk/models/lorenz_63/model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/lorenz_63/model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/model_mod.html
===================================================================
--- DART/trunk/models/model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/wrf/WRF_DART_utilities/dart_to_wrf.html
===================================================================
--- DART/trunk/models/wrf/WRF_DART_utilities/dart_to_wrf.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/wrf/WRF_DART_utilities/dart_to_wrf.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/models/wrf/model_mod.html
===================================================================
--- DART/trunk/models/wrf/model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/models/wrf/model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/mpi_utilities/mpi_utilities_mod.html
===================================================================
--- DART/trunk/mpi_utilities/mpi_utilities_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/mpi_utilities/mpi_utilities_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/DEFAULT_obs_def_mod.html
===================================================================
--- DART/trunk/obs_def/DEFAULT_obs_def_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/DEFAULT_obs_def_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/obs_def_1d_state_mod.html
===================================================================
--- DART/trunk/obs_def/obs_def_1d_state_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/obs_def_1d_state_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/obs_def_dew_point_mod.html
===================================================================
--- DART/trunk/obs_def/obs_def_dew_point_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/obs_def_dew_point_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/obs_def_gps_mod.html
===================================================================
--- DART/trunk/obs_def/obs_def_gps_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/obs_def_gps_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/obs_def_mod.html
===================================================================
--- DART/trunk/obs_def/obs_def_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/obs_def_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/obs_def_ocean_mod.html
===================================================================
--- DART/trunk/obs_def/obs_def_ocean_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/obs_def_ocean_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_def/obs_def_radar_mod.html
===================================================================
--- DART/trunk/obs_def/obs_def_radar_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_def/obs_def_radar_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_kind/DEFAULT_obs_kind_mod.html
===================================================================
--- DART/trunk/obs_kind/DEFAULT_obs_kind_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_kind/DEFAULT_obs_kind_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_kind/obs_kind_mod.html
===================================================================
--- DART/trunk/obs_kind/obs_kind_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_kind/obs_kind_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_model/obs_model_mod.html
===================================================================
--- DART/trunk/obs_model/obs_model_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_model/obs_model_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/create_fixed_network_seq.html
===================================================================
--- DART/trunk/obs_sequence/create_fixed_network_seq.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/create_fixed_network_seq.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/create_obs_sequence.html
===================================================================
--- DART/trunk/obs_sequence/create_obs_sequence.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/create_obs_sequence.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/obs_common_subset.html
===================================================================
--- DART/trunk/obs_sequence/obs_common_subset.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_common_subset.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/obs_selection.html
===================================================================
--- DART/trunk/obs_sequence/obs_selection.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_selection.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/obs_seq_coverage.html
===================================================================
--- DART/trunk/obs_sequence/obs_seq_coverage.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_seq_coverage.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/obs_seq_to_netcdf.html
===================================================================
--- DART/trunk/obs_sequence/obs_seq_to_netcdf.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_seq_to_netcdf.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/obs_seq_verify.html
===================================================================
--- DART/trunk/obs_sequence/obs_seq_verify.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_seq_verify.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/obs_sequence/obs_sequence_mod.html
===================================================================
--- DART/trunk/obs_sequence/obs_sequence_mod.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_sequence_mod.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
     
     
-    
+    
     
     
        Jump to DART Documentation Main Index
          

Modified: DART/trunk/obs_sequence/obs_sequence_tool.html
===================================================================
--- DART/trunk/obs_sequence/obs_sequence_tool.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/obs_sequence/obs_sequence_tool.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -14,7 +14,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/AIRS/AIRS.html
===================================================================
--- DART/trunk/observations/AIRS/AIRS.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/AIRS/AIRS.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/GTSPP/GTSPP.html
===================================================================
--- DART/trunk/observations/GTSPP/GTSPP.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/GTSPP/GTSPP.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/MADIS/MADIS.html
===================================================================
--- DART/trunk/observations/MADIS/MADIS.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/MADIS/MADIS.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/NCEP/ascii_to_obs/create_real_obs.html
===================================================================
--- DART/trunk/observations/NCEP/ascii_to_obs/create_real_obs.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/NCEP/ascii_to_obs/create_real_obs.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/NCEP/prep_bufr/prep_bufr.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/SSEC/SSEC.html
===================================================================
--- DART/trunk/observations/SSEC/SSEC.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/SSEC/SSEC.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/WOD/WOD.html
===================================================================
--- DART/trunk/observations/WOD/WOD.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/WOD/WOD.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     
-    
+    
     
     
        Jump to DART Documentation Main Index


Modified: DART/trunk/observations/gps/gps.html
===================================================================
--- DART/trunk/observations/gps/gps.html	2011-06-29 16:47:28 UTC (rev 5042)
+++ DART/trunk/observations/gps/gps.html	2011-06-29 17:58:02 UTC (rev 5043)
@@ -13,7 +13,7 @@
 
 
     

@@ Diff output truncated at 40000 characters. @@

From nancy at ucar.edu  Wed Jun 29 13:12:34 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 13:12:34 -0600
Subject: [Dart-dev] [5044]
 DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90: Fix an error in the
 interpolation code if the profile crosses crosses the
Message-ID: 

Revision: 5044
Author:   nancy
Date:     2011-06-29 13:12:34 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
Fix an error in the interpolation code if the profile crosses crosses the
dateline (-180/180 longitude) and the user has requested an observation at 
a height exactly between the two levels where the longitude changes sign.  
(in the input file the longitude is between -180 and 180.  we convert it to 
be between 0 and 360 after computing the interpolated longitude.) while this 
is an actual bug, from the amount of work it was to find a test case to
reproduce it i'm going to say that it had very little impact on the
observation files we have already generated.
Also make the test for a requested observation at the lowest level in the
file have an epsilon when testing for equality.  Otherwise in some cases
an observation at the lowest level is mistakenly deemed to be below the
lowest data level and a fatal error is thrown.
Thanks to xingqin for pointing these two things out.

Modified Paths:
--------------
    DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90

-------------- next part --------------
Modified: DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90
===================================================================
--- DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90	2011-06-29 17:58:02 UTC (rev 5043)
+++ DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90	2011-06-29 19:12:34 UTC (rev 5044)
@@ -252,9 +252,10 @@
      call interp_height_wght(hght, obs_levels(k), nobs, zloc, wght)
      if ( zloc < 1 )  cycle obsloop2
    
+     ! lon(zloc) and lon(zloc+1) range from -180 to +180
+     ! call a subroutine to handle the wrap point.
+     lono = compute_lon_wrap(lon(zloc), lon(zloc+1), wght)
      lato  = wght * lat(zloc)  + (1.0_r8 - wght) * lat(zloc+1)
-     lono  = wght * lon(zloc)  + (1.0_r8 - wght) * lon(zloc+1)
-     if ( lono < 0.0_r8 )  lono = lono + 360.0_r8
      hghto = wght * hght(zloc) + (1.0_r8 - wght) * hght(zloc+1)
      hghto = hghto * 1000.0_r8
      refro = wght * refr(zloc) + (1.0_r8 - wght) * refr(zloc+1)
@@ -852,4 +853,63 @@
 return
 end subroutine vprod
 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!
+!   compute_lon_wrap - interpolate between 2 longitude values taking
+!                      into account the wrap at -180 degrees
+!
+!    lon1, lon2 - longitude in degrees between -180 and +180
+!    weight - interpolation weight between lon1 and lon2 (0 to 1)
+! 
+!    returns interpolated longitude between 0 and 360 degrees.
+!
+! if the longitudes are the same sign (both negative or both positive)
+! then do the interpolation with the original values.  if the signs
+! are different then we need to decide if they are crossing 0 (where we
+! still use the original values) or if they are crossing the -180/180 line
+! and we have to wrap the negative value.
+
+! to decide between the 0 and 180 cases, take the positive value and subtract 
+! the negative value (which adds it on) and see if the sum is > 180.  if not, 
+! we're at the 0 crossing and we do nothing.  if yes, then we add 360 to the 
+! negative value and interpolate between two positive values.   in either case
+! once we have the result, if it's < 0 add 360 so the longitude returned is
+! between 0 and 360 in longitude.
+!
+! this does not try to do anything special if the profile is tracking directly
+! over one of the poles.  this is because at the exact poles all longitudes are
+! identical, so being off in the longitude in any direction won't be a large
+! difference in real distance.
+!
+!     created nancy collins NCAR/IMAGe
+!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+function compute_lon_wrap(lon1, lon2, weight)
+
+real(r8), intent(in) :: lon1, lon2, weight
+real(r8) :: compute_lon_wrap
+
+real(r8) :: lon1a, lon2a, lono
+
+! r/w temporaries in case we have to change the value.  
+lon1a = lon1
+lon2a = lon2
+
+
+! if different signs and crossing the -180/180 boundary, add 360
+! to the negative value.
+if (lon1 <= 0.0_r8 .and. lon2 >= 0.0_r8) then
+   if (lon2 - lon1 > 180.0_r8) lon1a = lon1a + 360.0_r8
+else if (lon1 >= 0.0_r8 .and. lon2 <= 0.0_r8) then
+   if (lon1 - lon2 > 180.0_r8) lon2a = lon2a + 360.0_r8
+endif
+
+! linear interpolation, and make return value between 0 and 360.
+lono  = weight * lon1a  + (1.0_r8 - weight) * lon2a
+if (lono < 0.0_r8) lono = lono + 360.0_r8
+
+compute_lon_wrap = lono
+
+end function compute_lon_wrap
+
 end program

From nancy at ucar.edu  Wed Jun 29 13:14:31 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Wed, 29 Jun 2011 13:14:31 -0600
Subject: [Dart-dev] [5045]
 DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90: drat. check in
Message-ID: 

Revision: 5045
Author:   nancy
Date:     2011-06-29 13:14:31 -0600 (Wed, 29 Jun 2011)
Log Message:
-----------
drat.  check in the version of the code which actually has the
second fix in it.

Modified Paths:
--------------
    DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90

-------------- next part --------------
Modified: DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90
===================================================================
--- DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90	2011-06-29 19:12:34 UTC (rev 5044)
+++ DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90	2011-06-29 19:14:31 UTC (rev 5045)
@@ -661,6 +661,9 @@
 integer  :: bot_lev, k
 real(r8) :: fract
 
+bot_lev = -1
+fract = 0.0_r8
+
 !  Search down through height levels
 do k = 2, nobs
   if ( height >= hghtp(k) ) then
@@ -670,6 +673,22 @@
   endif
 end do
 
+! the hghtp() array is currently an interpolated list of levels
+! and on at least 1 PGI compiler version computing the lowest value 
+! rounds enough that a height exactly equal to the lowest level 
+! compares as less than instead of equal.  so test and if it's very very 
+! close to the lowest level then return it as equal; otherwise it's 
+! an internally inconsistent input file.
+if (bot_lev < 0) then
+  if (abs(height - hghtp(nobs)) < 0.00001) then
+     bot_lev = nobs
+     fract = 0.0_r8
+  else
+     call error_handler(E_ERR, 'bad level, below lowest in file', &
+                       source, revision, revdate)
+  endif
+endif
+
 lref = (1.0_r8 - fract) * refp(bot_lev) + fract * refp(bot_lev-1)
 
 return

From nancy at ucar.edu  Thu Jun 30 10:01:06 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 10:01:06 -0600
Subject: [Dart-dev] [5046]
 DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90: Use the original
 profile when computing the line integral
Message-ID: 

Revision: 5046
Author:   nancy
Date:     2011-06-30 10:01:06 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
Use the original profile when computing the line integral
for the non-local operator.  This code was mistakenly using
only the requested output observation heights as the profile.

Modified Paths:
--------------
    DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90

-------------- next part --------------
Modified: DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90
===================================================================
--- DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90	2011-06-29 19:14:31 UTC (rev 5045)
+++ DART/trunk/observations/gps/convert_cosmic_gps_cdf.f90	2011-06-30 16:01:06 UTC (rev 5046)
@@ -169,7 +169,7 @@
 
 end if
 
-allocate(hghtp(nlevels))  ;  allocate(refrp(nlevels))
+
 did_obs = .false.
 
 ! main loop that does either a single file or a list of files
@@ -206,6 +206,7 @@
    call nc_check( nf90_get_att(ncid,nf90_global,'rfict',rfict),'get_att rfict')
    rfict = rfict * 1000.0_r8
    
+   allocate(hghtp(nobs)) ;  allocate(refrp(nobs))
    allocate( lat(nobs))  ;  allocate( lon(nobs))
    allocate(hght(nobs))  ;  allocate(refr(nobs))
    allocate(azim(nobs))
@@ -235,16 +236,10 @@
    
    call nc_check( nf90_close(ncid) , 'close file')
    
-   obsloop: do k = 1, nlevels
-   
-     call interp_height_wght(hght, obs_levels(k), nobs, zloc, wght)
-     if ( zloc < 1 )  cycle obsloop
-     hghtp(nlevels-k+1) = obs_levels(k) * 1000.0_r8
-     refrp(nlevels-k+1) = exp( wght * log(refr(zloc)) + & 
-                       (1.0_r8 - wght) * log(refr(zloc+1)) ) * 1.0e-6_r8
-   
-   end do obsloop
-   
+   ! convert units here.
+   hghtp(:) = hght(:) * 1000.0_r8
+   refrp(:) = refr(:) * 1.0e-6_r8
+    
    first_obs = .true.
    
    obsloop2: do k = 1, nlevels
@@ -281,7 +276,7 @@
    
        !  compute the excess phase
        call excess(refrp, hghtp, lono, lato, hghto, nx, & 
-                   ny, nz, rfict, ray_ds, ray_htop, phs, nlevels)
+                   ny, nz, rfict, ray_ds, ray_htop, phs, nobs)
    
        !  if too high, phs will return as 0.  cycle loop here.
        if (phs <= 0) cycle obsloop2
@@ -316,7 +311,7 @@
    end do obsloop2
 
   ! clean up and loop if there is another input file
-  deallocate( lat, lon, hght, refr, azim )
+  deallocate( lat, lon, hght, refr, azim, hghtp, refrp)
 
   filenum = filenum + 1
 
@@ -664,14 +659,21 @@
 bot_lev = -1
 fract = 0.0_r8
 
+! make sure it's not higher than the highest available level.
+if (height > hghtp(1)) then
+   write(msgstring, *) 'requested height is ', height, '; highest available is ', hghtp(1)
+   call error_handler(E_ERR, 'bad level, above highest in file', &
+                      source, revision, revdate, text2=msgstring)
+endif
+
 !  Search down through height levels
-do k = 2, nobs
+heights: do k = 2, nobs
   if ( height >= hghtp(k) ) then
     bot_lev = k
     fract = (hghtp(k) - height) / (hghtp(k) - hghtp(k-1))
-    exit
+    exit heights
   endif
-end do
+end do heights
 
 ! the hghtp() array is currently an interpolated list of levels
 ! and on at least 1 PGI compiler version computing the lowest value 
@@ -680,12 +682,13 @@
 ! close to the lowest level then return it as equal; otherwise it's 
 ! an internally inconsistent input file.
 if (bot_lev < 0) then
-  if (abs(height - hghtp(nobs)) < 0.00001) then
+  if (abs(height - hghtp(nobs)) < 0.00001_r8) then
      bot_lev = nobs
      fract = 0.0_r8
   else
+     write(msgstring, *) 'requested height is ', height, '; lowest available is ', hghtp(nobs)
      call error_handler(E_ERR, 'bad level, below lowest in file', &
-                       source, revision, revdate)
+                       source, revision, revdate, text2=msgstring)
   endif
 endif
 

From nancy at ucar.edu  Thu Jun 30 14:20:48 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 14:20:48 -0600
Subject: [Dart-dev] [5047] DART/trunk: Fix the documentation to show the
 seed is an integer and not
Message-ID: 

Revision: 5047
Author:   nancy
Date:     2011-06-30 14:20:48 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
Fix the documentation to show the seed is an integer and not
a derived type. Add a test when initializing with a seed so
large seeds are avoided; the init code succeeds but you get
a fatal error when subsequenctly retrieving a random number.

Modified Paths:
--------------
    DART/trunk/random_nr/random_nr_mod.f90
    DART/trunk/random_seq/random_seq_mod.html

-------------- next part --------------
Modified: DART/trunk/random_nr/random_nr_mod.f90
===================================================================
--- DART/trunk/random_nr/random_nr_mod.f90	2011-06-30 16:01:06 UTC (rev 5046)
+++ DART/trunk/random_nr/random_nr_mod.f90	2011-06-30 20:20:48 UTC (rev 5047)
@@ -65,6 +65,10 @@
 
 if ( .not. module_initialized ) call initialize_module
 
+if (temp >= ic1) then
+    call error_handler(E_ERR,' ran1', 'Use negative seed or seed smaller than 54000', source, revision, revdate)
+endif
+
 ! Initialize the generator for use with
 ! repeatable sequences
 
@@ -105,7 +109,7 @@
 s%ix3 = mod(ia3*s%ix3 + ic3, m3)
 j = 1 + (97*s%ix3) / m3
 if(j > 97 .or. j < 1) then
-      call error_handler(E_ERR,' ran1', 'Fatal error in random_nr_mod', source, revision, revdate)
+    call error_handler(E_ERR,' ran1', 'Fatal error in random_nr_mod', source, revision, revdate)
 endif
 ran1 = s%r(j)
 s%r(j) = (s%ix1 + s%ix2*rm2)*rm1

Modified: DART/trunk/random_seq/random_seq_mod.html
===================================================================
--- DART/trunk/random_seq/random_seq_mod.html	2011-06-30 16:01:06 UTC (rev 5046)
+++ DART/trunk/random_seq/random_seq_mod.html	2011-06-30 20:20:48 UTC (rev 5047)
@@ -119,7 +119,7 @@
  call init_random_seq(r, [,  seed]) 
  type(random_seq_type),           intent(inout) :: r
-type(random_seq_type), optional, intent(in)    :: seed
+integer,               optional, intent(in)    :: seed
 
 
 
@@ -132,6 +132,7 @@
 of independent, reproducible random sequences can be generated by
 having multiple instances of a random_seq_type. A specified integer
 seed, optional, can produce a specific 'random' sequence.
+Seed must be a negative number.
 
 
 

From nancy at ucar.edu  Thu Jun 30 16:27:29 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 16:27:29 -0600
Subject: [Dart-dev] [5049]
 DART/trunk/observations/NCEP/prep_bufr/data/201011: try octet-stream as
 mime-type instead of x-gzip
Message-ID: 

Revision: 5049
Author:   nancy
Date:     2011-06-30 16:27:28 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
try octet-stream as mime-type instead of x-gzip

Property Changed:
----------------
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110406.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110412.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110418.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110500.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz

-------------- next part --------------

Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110406.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/x-gzip
   + application/octet-stream


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110412.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/x-gzip
   + application/octet-stream


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110418.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/x-gzip
   + application/octet-stream


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110500.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/x-gzip
   + application/octet-stream


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz
___________________________________________________________________
Modified: svn:mime-type
   - application/x-gzip
   + application/octet-stream

From nancy at ucar.edu  Thu Jun 30 16:54:46 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 16:54:46 -0600
Subject: [Dart-dev] [5050]
 DART/trunk/observations/NCEP/prep_bufr/data/201011: problems with the mime
 types; pick a different day and try again
Message-ID: 

Revision: 5050
Author:   nancy
Date:     2011-06-30 16:54:46 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
problems with the mime types; pick a different day and try again

Added Paths:
-----------
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112706.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112712.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112718.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112800.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112806.gz

Removed Paths:
-------------
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110406.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110412.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110418.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110500.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz

-------------- next part --------------
Deleted: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110406.gz
===================================================================
(Binary files differ)

Deleted: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110412.gz
===================================================================
(Binary files differ)

Deleted: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110418.gz
===================================================================
(Binary files differ)

Deleted: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110500.gz
===================================================================
(Binary files differ)

Deleted: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10110506.gz
===================================================================
(Binary files differ)

Added: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112706.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112706.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112712.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112712.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112718.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112718.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112800.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112800.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112806.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201011/prepqm10112806.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

From nancy at ucar.edu  Thu Jun 30 16:56:14 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 16:56:14 -0600
Subject: [Dart-dev] [5051] DART/trunk/observations/NCEP/prep_bufr/work: make
 examples in scripts consistent with data files
Message-ID: 

Revision: 5051
Author:   nancy
Date:     2011-06-30 16:56:14 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
make examples in scripts consistent with data files

Modified Paths:
--------------
    DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh
    DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh

-------------- next part --------------
Modified: DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh	2011-06-30 22:54:46 UTC (rev 5050)
+++ DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh	2011-06-30 22:56:14 UTC (rev 5051)
@@ -69,8 +69,8 @@
 # files will be located in subdirectories by month, with the names following
 # the pattern YYYYMM, and then inside the subdirectories, the files are
 # named by the pattern 'prepqmYYMMDDHH'.  for example, if the dir below
-# is the default ../data, then the 6Z file for nov 4th, 2010 would be:
-#  ../data/201011/prepqm10110406
+# is the default ../data, then the 6Z file for nov 27th, 2010 would be:
+#  ../data/201011/prepqm10112706
 # but the conventions for names of prepqm files have changed over the years,
 # so if the prepqm files do *not* follow this pattern, you will have to edit
 # the BUFR_in variable in the script below to match the filenames you have.

Modified: DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh	2011-06-30 22:54:46 UTC (rev 5050)
+++ DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh	2011-06-30 22:56:14 UTC (rev 5051)
@@ -88,16 +88,16 @@
 else
   set year     = 2010
   set month    = 11
-  set beginday = 10
-  set endday   = 20
+  set beginday = 20
+  set endday   = 30
 endif
 
 # directory where the BUFR files are located.  the script assumes the
 # files will be located in subdirectories by month, with the names following
 # the pattern YYYYMM, and then inside the subdirectories, the files are
 # named by the pattern 'prepqmYYMMDDHH'.  for example, if the dir below
-# is the default ../data, then the 6Z file for nov 4th, 2010 would be:
-#  ../data/201011/prepqm10110406
+# is the default ../data, then the 6Z file for nov 27th, 2010 would be:
+#  ../data/201011/prepqm10112706
 # but the conventions for names of prepqm files have changed over the years,
 # so if the prepqm files do *not* follow this pattern, you will have to edit
 # the BUFR_in variable in the script below to match the filenames you have.

From nancy at ucar.edu  Thu Jun 30 17:19:36 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 17:19:36 -0600
Subject: [Dart-dev] [5055] DART/trunk/observations/NCEP/prep_bufr/work: try
	yet another month
Message-ID: 

Revision: 5055
Author:   nancy
Date:     2011-06-30 17:19:36 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
try yet another month

Modified Paths:
--------------
    DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh
    DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh
    DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh

-------------- next part --------------
Modified: DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh	2011-06-30 23:09:56 UTC (rev 5054)
+++ DART/trunk/observations/NCEP/prep_bufr/work/multi_body.csh	2011-06-30 23:19:36 UTC (rev 5055)
@@ -69,8 +69,8 @@
 # files will be located in subdirectories by month, with the names following
 # the pattern YYYYMM, and then inside the subdirectories, the files are
 # named by the pattern 'prepqmYYMMDDHH'.  for example, if the dir below
-# is the default ../data, then the 6Z file for nov 27th, 2010 would be:
-#  ../data/201011/prepqm10112706
+# is the default ../data, then the 6Z file for dec 27th, 2010 would be:
+#  ../data/201012/prepqm10122706
 # but the conventions for names of prepqm files have changed over the years,
 # so if the prepqm files do *not* follow this pattern, you will have to edit
 # the BUFR_in variable in the script below to match the filenames you have.

Modified: DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh	2011-06-30 23:09:56 UTC (rev 5054)
+++ DART/trunk/observations/NCEP/prep_bufr/work/multi_prep.csh	2011-06-30 23:19:36 UTC (rev 5055)
@@ -30,7 +30,7 @@
 
 # Set year, month, days for to pass as args to prepbufr.csh
 set year     = 2010
-set month    =   11
+set month    =   12
 set startday =    1
 set endday   =   30
 

Modified: DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh
===================================================================
--- DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh	2011-06-30 23:09:56 UTC (rev 5054)
+++ DART/trunk/observations/NCEP/prep_bufr/work/prepbufr.csh	2011-06-30 23:19:36 UTC (rev 5055)
@@ -87,7 +87,7 @@
   set endday   = $argv[4]
 else
   set year     = 2010
-  set month    = 11
+  set month    = 12
   set beginday = 20
   set endday   = 30
 endif

From nancy at ucar.edu  Thu Jun 30 17:20:17 2011
From: nancy at ucar.edu (nancy at ucar.edu)
Date: Thu, 30 Jun 2011 17:20:17 -0600
Subject: [Dart-dev] [5056] DART/trunk/observations/NCEP/prep_bufr/data:
 still getting conflicts . try a wh
Message-ID: 

Revision: 5056
Author:   nancy
Date:     2011-06-30 17:20:17 -0600 (Thu, 30 Jun 2011)
Log Message:
-----------
still getting conflicts.  try a whole new month

Added Paths:
-----------
    DART/trunk/observations/NCEP/prep_bufr/data/201012/
    DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122206.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122212.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122218.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122300.gz
    DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122306.gz

Removed Paths:
-------------
    DART/trunk/observations/NCEP/prep_bufr/data/201011/

-------------- next part --------------
Added: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122206.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122206.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122212.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122212.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122218.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122218.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122300.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122300.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122306.gz
===================================================================
(Binary files differ)


Property changes on: DART/trunk/observations/NCEP/prep_bufr/data/201012/prepqm10122306.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream



DIRECTORY	Location of subdirectories of output and some diagnostics files. Typically where the obs-space diagnostics are calculated using obs_diag.
Obsseq_#
obs_#	Exper_obsseq#.script	Each holds the obs-space and model-space output from assimilating one obs_seq.out file. It should be named according to the need for - obs_diag to see a name with the 2 digit month, underscore, and the - number within the series of obs_seq.out files, - i.e. 01_02 for the second obs_seq.final of a January case.
DART	Exper_obsseq#.script	@@ -424,20 +651,31 @@	Exper_obsseq#.script	Same as CAM, but for Community Land Model initial files.
CICE	Exper_obsseq#.script	+ Same as CAM, but for CICE model restart files, tarred by ensemble member.
H##	advance_model.csh	+ Temporary storage for ensembles of CAM, CLM, CICE files + to be averaged for analyses archiving by auto_diag2hpss_LSF.csh.

index_in	Index of state vector element about which information is requested.
index_in	Index into the long state vector.
location	Returns location of indexed state variable. The location should use a location_mod that is appropriate for the model domain. For realistic atmospheric models, for instance, a three-dimensional spherical location module that can represent height in a variety of ways is provided.
var_type	Returns the type of the indexed state variable as an optional argument.

x	A model state vector.
location	Location to which to interpolate.
obs_type	Integer indexing which type of observation is to be interpolated.
interp_val	The interpolated value from the model.
istatus	Integer flag indicating the success of the interpolation.

var	Smallest time step of model.
ncFileId	Integer file descriptor opened to NetCDF file.
ierr	Returned error code.

file_name	CAM initial file name.
var	Structure to hold the state vector fields read from file_name.

Exper_obsseq#.script	experiment	experiment central directory where I/O and execution are organized.
-> mpirun filter executable
-> mpirun filter executable	filter version	local disc on a compute node/processor, or a work directory in the central directory.
-> advance_model.csh
-> advance_model.csh	model	pre-existing work subdirectory of the central directory.
-> trans_time executable
-> dart_to_cam executable	model	Translates DART time format into CAM time format
-> trans_sv_pv executable	model	Inserts DART state vector into CAM initial file
-> run_pc.csh	Translates DART time format into CAM time format and + inserts DART state vector into CAM initial file
-> run-cam.csh	model	Modified form of run script from CAM, now in DART
-> bld-namelist
-> bld-namelist	model	uses namelistin and results of trans_time to make CAM namelist
-> advance of CAM	uses namelistin and results of dart_to_cam to make CAM namelist
-> advance of CAM (version dependent)	model	Single threaded or MPI CAM
-> trans_pv_sv executable
-> cam_to_dart executable		Translates CAM fields in to DART state vector
-> qsub auto_re2ms.csh
-> qsub auto_re2hpss.csh	machine	Central/Experiment/obs_seq_output_directory(i.e. 01_01)
Central/Experiment/obs_####. Archives restart data sets.
-> qsub auto_diag2hpss_LSF.csh	machine	Central/Experiment/obs_####. Archives diagnostic output.
-> analyses2initial.csh	machine	Central/Experiment/obs_####/H## Generates analyses in CAM,CLM,CICE initial files. May also save CAM .h0. history files (but make them small !)
-> NetCDF operators	machine	Central/Experiment/obs_####/H## Averaging of CAM,CLM,CICE fields.
(-> clm_ens_avg.f90	machine	Central/Experiment/obs_####/H## Complicated snow averaging. + Not usable (yet) for CAM 4.0.1 and later.)

use model_mod, only :	get_model_size
ens_mean_for_model
	get_close_maxdist_init
	get_close_obs_init
	get_close_obs
	get_model_time_step
	get_model_size
	get_state_meta_data
	model_interpolate
	get_model_time_step
	static_init_model
	nc_write_model_atts
	nc_write_model_vars
	pert_model_state
	get_close_maxdist_init
	get_close_obs_init
	get_close_obs
	ens_mean_for_model
	static_init_model
	adv_1step
	end_model
	init_time
	init_conditions

use model_mod, only :	prog_var_to_vector
	read_cam_init
	vector_to_prog_var
	write_cam_init

file_name	Name of CAM initial file to which var will be written.
var	Structure containing all the fields of the state vector.

x	Model state vector.
location	Location to which to interpolate.
obs_type	Integer indexing which type of observation is to be interpolated.
interp_val	Value interpolated to location.
istatus	Integer flag indicating the success of the interpolation.

var	Structure containing all the fields of the state vector.
x	DART state vector.

Contact:	DART core group
Revision:	$Revision$
Source:	$URL$
Change Date:	$Date$
Change history:	try "svn log" or "svn diff"

ncfileid	The file ID number of the cam_phis.nc file.
num_nlons

att	The name of an attribute of the fields on a CAM initial file.
att_vals

var	The coordinate variable to read from caminput.nc.
length

cflds	Master list of CAM fields to be incorporated in the DART state vector.
nflds

val	The value of the obs_kind variable interpolated from state vector x.
x

val	The value of the obs_kind variable at a grid point, from state vector x.
x

old_array	The location array of the incoming ob.
old_which

fit_ens_mean_time.m	plotted the temporal evolution of the ensemble mean of some quantity.
fit_ens_spread_time.m	plotted the temporal evolution of the ensemble spread of some quantity.
fit_mean_spread_time.m	plotted the temporal evolution of the mean and spread of some quantity.
obs_num_time.m	plotted the temporal evolution of the observation density.
fit_ens_mean_vertical.m	plotted the vertical profile of the ensemble mean of some quantity.
fit_ens_bias_vertical.m	plotted the vertical profile of the bias of the ensemble mean of some quantity.
obs_num_vertical.m	plotted the vertical profile of the observation density.

plot_profile.m	plots the vertical profile of any quantity for any copy with an overlay of + the observation density and number of observations assimilated.
plot_rmse_xxx_profile.m	plots the vertical profile of the rmse and any quantity for any copy with an + overlay of the observation density and number of observations assimilated.
plot_bias_xxx_profile.m	plots the vertical profile of the bias and any quantity for any copy with an + overlay of the observation density and number of observations assimilated.
two_experiments_profile.m	plots the vertical profile of any quantity for any copy for multiple experiments + with an overlay of the observation density and number of observations assimilated + in each experiment.
plot_evolution.m	plots the temporal evolution of any quantity for any copy with an overlay of + the observation density and number of observations assimilated.
plot_rmse_xxx_evolution.m	plots the temporal evolution of the rmse and any quantity for any copy with an + overlay of the observation density and number of observations assimilated.
two_experiments_evolution.m	plots the temporal evolution for any quantity for any copy for multiple + experiements with an overlay of the observation density and number of + observations assimilated in each experiment.
read_obs_netcdf.m	reads a netCDF format observation sequence file. Simply need a single copy + and a single qc - no actual observation required.
plot_obs_netcdf.m	reads and plots the locations and values of any copy of the observations in + a DART netCDF format observation sequence file.
plot_obs_netcdf_diffs.m	reads and plots the locations and the difference of any two copies of the + observations in a DART netCDF format observation sequence file.
plot_wind_vectors.m	reads and plots the wind vectors of the observations in a DART netCDF format + observation sequence file (created by + obs_seq_to_netcdf.f90)
link_obs.m	data brushing tool. Explores many facets of the observations simultaneously.
plot_rank_histogram.m	If the ensemble members were preserved in the obs_seq.final + file, obs_diag will create rank histogram information + and store it in the obs_diag_output.nc file. + plot_rank_histogram.m will plot it. + There are instructions on how to view the results with ncview + or plot_rank_histogram.m + on the + DART Observation-space Diagnostics + page.

Contact:	Kevin Raeder
Revision:	$Revision$
Source:	$URL$
Change Date:	$Date$
Change history:	try "svn log" or "svn diff"

DART-CAM setup

DART-CAM OVERVIEW

CALLING TREE

EXPERIMENT SET-UP

CAM INITIAL ENSEMBLES

FILE CONTENTS

OUTPUT DIRECTORY

HELPFUL HINTS

Overview

NAMELIST

OTHER MODULES USED

PUBLIC INTERFACES

FILTER INTERFACE

OTHER PUBLIC INTERFACES

DART Kodiak Release Notes

Overview

Non-backwards Compatible Changes

New Features

New Models

Changed Models

New Observations

New Diagnostics and Documentation

New Utilities

Terms of Use

MODULE obs_def_gps_mod

Overview

NAMELIST

OTHER MODULES USED

PUBLIC INTERFACES

FILES

REFERENCES

ERROR CODES and CONDITIONS

KNOWN BUGS

FUTURE PLANS

Terms of Use

New Observations

New Observation Types/Sources

NAMELIST

PROGRM OR MODULE name_of_thing

Overview

NAMELIST

MODULES USED

PUBLIC INTERFACES

FILES

REFERENCES

ERROR CODES and CONDITIONS

KNOWN BUGS

FUTURE PLANS

PRIVATE COMPONENTS

Terms of Use

New Features

New Models

Changed Models

New Observation Types/Sources

New Diagnostics and Documentation

New Utilities

Filter Types

Matlab Hands-On Exercises

Overview of Program Flow

Free run/Forecast After Assimilation

Detailed Program Execution Flow

FILES

Discussion

REFERENCES

FILES

Discussion

REFERENCES

FUTURE PLANS

Checking the Geometry Information:

MODULE dart_ncommas_mod (ncommas)

NAMELIST

OTHER MODULES USED

PUBLIC INTERFACES

Interface Routines

Required Interface Routines

FILES

REFERENCES

ERROR CODES and CONDITIONS

KNOWN BUGS

FUTURE PLANS