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$Id: PostI_diffs_from_I.html 11996 2017-10-17 22:19:25Z nancy@ucar.edu $

DART "POST Iceland release" summary of changes.

$Id: PostI_diffs_from_I.html 11996 2017-10-17 22:19:25Z nancy@ucar.edu $

The DART POST Iceland release (16 June 2006) is an intermediate release designed to provide error fixes required for a number of users and to provide enhanced support for the CAM, WRF, and PBL_1D models. It also provides several new assimilation algorithm options that are already widely used by CAM implementations. The most important are additional methods for doing adaptive inflation. The previously existing observation space inflation is retained and two new options for adaptive state space inflation are introduced. One option has a value of inflation that is constant across all state variables but varies in time. The second has an inflation factor for EACH state variable and these can each vary in time. An initial version of an algorithm to do adaptive localization is also introduced. The local density of observations is measured by computing the number of observations from a set at a given time that is close to the observation being assimilated. If the density is such that more than a given threshold number of observations is close to the current observation, the localization radius is adjusted so that the expected number of observations in the adjusted radius is equal to the threshold value. This will decrease the localization radius in areas with dense observations.

Another important new capability is provided by a merge_obs_sequence program that can combine most existing observation sequences into a single sequence.

The shell scripts used to coordinate the execution of the model advances or regional assimilation have been modified to be more robust and easier to read. Furthermore, each script has been standardized to be much more machine/queueing system independent. Each script should now be able to be used interactively (in a debug scenario), with the LSF queueing system (as a batch job), or with the PBS queueing system. The scripts have a block of logic that converts the system-specific variables to ones commonly used throughout the DART documentation. This has now made it possible to prepare a script that will conditionally execute a series of batch jobs wherein each batch job will process exactly one observation sequence file. Only upon successful completion of the previous batch job with the subsequent batch job be started. Look for information on Qfiller.csh on the DART www page.

merge_obs_sequence program that can combine most existing observation sequences into a single sequence.

An initial version of an ensemble smoother was added to DART and implemented with the low-order models and the bgrid model. The smoother continues to use the OLD inflation options and an old version of the assim_tools_mod module.

Changes

A summary list of changes occurring in each DART directory/file follows:
test_dart.csh This testing script in the main DART directory has been updated to test the new inflation options with the new scripts. An attempt has been made to preserve the input environment such that if you wanted to run it twice in a row, you could. It now stores all the run-time output of the lorenz_96 tests in the lorenz_96/work/xxxx directory, where xxx is now an argument to test_dart.csh. Simply typing the file name will now echo usage notes.
adaptive_inflate.f90 This new module now handles all the computations for the adaptive inflation computations. It has the code that was previously in assim_tools to do the Bayesian update of observation space inflation. It also provides the additional algorithms required to do state space inflation. Documentation is provided in the module and in several papers on the DART home page.
assim_tools_mod.f90 Uses adaptive_inflation module. Namelist modified (see below). Storage for observation space inflation for regions no longer needed. No longer an assim_restart file; all restart info is now stored in adaptive_inflate. Routine update_inflation replaces bayes_cov_inflate which has been moved to adaptive_inflate_mod. Correlation is now passed out of update_from_obs_inc for use with adaptive inflation updates. Ability to do sampling_error_correction from a file using correl_error.f90 in system_simulation. This is turned on by namelist parameter sampling_error_correction and requires appropriate error correction files for a given ensemble size (this is still in preliminary testing phase). The inflation values are now passed into filter_assim_region. The mean and variance of the observation space priors are computed up front in filter_assim_region for use with adaptive inflation algorithm. Observational density thinning controlled by namelist parameter num_close_threshold implemented. If number of observations close to a given observation is larger than the cutoff, the localization cutoff is adjusted to try to make the number close the same as the cutoff. This is a fundamentally two-d algorithm in this naive implementation. Update computations for spatial inflation are included in filter_assim_region. Routine filter_assim also gets the inflation values as arguments. Copying of these inflation values for the shell driven files is added. Previously commented print_regional_results is deleted (produced errors with absoft compilers). Routine comp_correl added to compute correlations. Routine get_correction_from_file added to support sampling_error_correction. No longer need routine assim_tools_end since there is no longer a restart requirement. An error in the correlation computation for assimilation was removed. If all prior values of an observation were identical, a NaN could result from the old correlation computation. The assim_tools_nml was modified as follows: Removed cov_inflate, cov_inflate_sd, sd_lower_bound, deterministic_cov_inflate, start_from_assim_restart, assim_restart_in_file_name, assim_restart_out_file_name, cov_inflate_upper_bound. Added sampling_error_correction and num_close_threshold.
assim_tools_smoother.f90 The smoother is still using the previous version of inflation and the corresponding assim_tools module which has been renamed as assim_tools_smoother. Additional routines have been added to support the updates required to do smoothing (see documentation in smoother directory).
diagnostics Observation space diagnostics obs_diag were modified to support observations on model levels. This is particularly useful for "perfect model" experiments. Direct observations of model variables (identity observations) are not supported, as this is an exploration of state-space, not observation-space. However, since the advent of merge_obs_sequence (see below) an observation sequence file may contain synthetic and real observations. Any identity observations are skipped. All other observations may be considered.
ensemble_manager_mod.f90 Modified to be able to handle multiple ensembles at one time to support the smoother which has an ensemble for each lag-time in the smoothing.
filter.f90 The adaptive_inflate module is now used and the namelist entry cov_inflate has been removed from filter_nml. Inflation is now done with filter_ensemble_inflate only if constant or varying spatial inflation is selected in the adaptive_inflate namelist. Information about state space inflation is passed to filter_assim as arguments. The call to assim_tools_end has been replace by adaptive_inflate_end which creates restarts for adaptive inflation. For spatially varying state inflation, two extra fields are tacked onto the state space diagnostic netcdf files to record the inflation mean and standard deviation. At present, inflation is done for the whole state at once; this may be very inefficient and should be examined. The entry cov_inflate was removed from the namelist.
merge_obs_seq.f90 This is a fundamentally new program to DART. This routine can combine any two observation sequence files that are compatible. The files are deemed compatible if the 'copies' of the observations and the QC fields are identical between the two sequences. If one observation sequence file has only an ensemble mean and spread, the other observation sequence file can have only an ensemble mean and spread -- it cannot additionally have the N ensemble member estimates of the observation. Most of the time, this routine is envisioned to be used to combine obs_seq.out files (as opposed to obs_seq.final files). If the two sequences temporally overlap, it is faster to put the shorter sequence as filenam_seq2, the insertion sort can get tedious. A new namelist merge_obs_seq_nml has been added.
mkmf New templates provided to support corral and lightning at NCAR.
models All models work with merge_obs_seq and adaptive inflation options.
PBL_1d The PBL_1d model has undergone extensive revisions as per the author's instructions. The DART portion of the code (i.e. those modules not directly imported from WRF) now compile cleanly with a variety of compilers. Note that because of the WRF convention of naming modules with a .F extension (instead of .F90 or .f90) several compilers try to interpret this code as fixed-format code when it is, in fact, free-format. This necessitates setting the compiler flags to force the free-format interpretation. See your compiler for details.
models/cam-fv is a new model ... the finite-volume core version of CAM.
models/cam Now able to handle observations with height as a vertical coordinate. Can return interpolated values of pressure for use with GPS observation forward operators.
cam/shell_scripts/job.simple.csh is a new script that demonstrates the simplest possible (I think) way to assimilate ONE observation sequence file with CAM. It requires CAM restart files and the like, so it WILL need to be modified to work for you. Hopefully, you can just change a couple of the directories referenced in the script and be off ... This is likely to be the underpinnings of the next generation script that will flood the queue with conditionally executed batch jobs. If the observation sequence file for 06Z completes normally, the batch job for 12Z will start ... that sort of thing.
doc/html/cgd_cam.shtml New, more general information about using CAM and DART is available in cgd_cam.shtml.
models/wrf A new namelist variable, assimilation_period_seconds, allows the specification of the desired assimilation period, which was previously hardwired in the code. The assimilation_period_seconds is guaranteed to be an integer multiple of the underlying wrf model timestep. Added support for gps observations and observations of vortex position.
ncep_obs Made changes to improve translation from prep_bufr. Data from up to 3:00 UTC of the next day is included in the file with the current days' date.
obs_def_gps_mod.f90 Modified to allow merging of two gps observation sequences.
obs_def_radar_mod.f90 Added ability to merge multiple observation sequences.
obs_def_vortex_mod.f90 Provides observation types for position of vortex center.
obs_model_mod.f90 Modified to be compatible with smoother use of multiple ensemble handles.
obs_sequence_mod.f90 Added initialization for observation sequence in init_obs_sequence; prevents possible access to uninitialized pointer.
preprocess.f90 Changed defaults for input and output files to standard values rather than null.
DART/shell_scripts (the machine-specific ones) filter_server.csh, assim_filter.csh, and advance_ens.csh have been modified to use 'standard' language and can be used with multiple queuing systems as well as interactively. Extensive commenting has been added to help explain the semaphore files. All the other scripts in this directory should be considered 'deprecated'.
model/xxx/shell_scripts (the model-specific ones) advance_model.csh, and assim_region.csh have been modified to use 'standard' language and can be used with multiple queuing systems as well as interactively. Extensive commenting has been added to help explain the semaphore files. All the other scripts in this directory should be considered 'deprecated'.
smoother A main program (smoother.f90) to do fixed-lag ensemble smoothing has been added and is documented in the smoother directory. This program still uses the previous version of the inflation and assim_tools, which are available as assim_tools/assim_tools_smoother_mod.f90.
time_manager_mod.f90 Corrected problems with module initialization and modified print format to strictly comply such that it now compiles with gfortran.
tutorial Modified section 12 to give accurate discussion of new implementation of observation space inflation and a brief overview of the state space inflation options.

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Contact: DART core group
Revision: $Revision: 11996 $
Source: $URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Manhattan/documentation/html/history/PostI_diffs_from_I.html $
Change Date: $Date: 2017-10-17 16:19:25 -0600 (Tue, 17 Oct 2017) $
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