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CHANGELOG
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CHANGELOG
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# DART software - Copyright 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
#
# DART $Id$
SEE THE BOTTOM OF THIS FILE FOR THE MOST RECENT CHANGES!
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Jan 13th 2017 :: rma_fixed_filenames merge changes. Revision: 10902
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Specific namelist changes include:
1. ) Earlier versions of the RMA branch code supported both direct NetCDF
reads/writes and the original binary/ascii DART format restart files.
As of the next update DART format files are no longer supported. All
I/O is NetCDF only. If your model does not use NetCDF you will still
need a model_to_dart and dart_to_model converter; otherwise all DART
programs read the model's NetCDF files directly. The namelist options
related to selecting direct netcdf I/O have been removed.
2. ) Diagnostic and state space data (such as inflation, mean and sd
information) that were previously stored in {Prior,Posterior}_Diag.nc
are now broken up into multiple files and have fixed filenames. This
decreases the IO time for diagnostic output and reduces the number of
namelist options.
3. ) There is no longer support for observation space inflation
(i.e. inf_flavor = 1). Contact us at [email protected] if you have an
interest in using this option.
------------------------------------------------------------------------------
Changes to the filter_nml are :
------------------------------------------------------------------------------
* restart_in_file_name -- has been replaced with input_restart_file_list.
The namelist must contain one or more file names,
each of which is a textfile containing a list of N
NetCDF restart files, one per line for each ensemble member.
For models with multiple domains (e.g. nested WRF or
CLM) you must specify a listfile for each domain.
* restart_out_file_name -- has been replaced with output_restart_file_list.
Same format as input_restart_file_list.
* inf_in_file_name -- REMOVED, now have fixed names of the form
input_{prior,posterior}inf_{mean,sd}.nc
* inf_out_file_name -- REMOVED, now have fixed names of the form
output_{prior,posterior}inf_{mean,sd}.nc.
* inf_diag_filename -- REMOVED
* inf_output_restart -- REMOVED, inflation restarts will be written
out if inflation is turned on
* output_inflation -- REMOVED, inflation diagnostic files will be written
if inflation is turned on
* stages_to_write -- There is more control over what state data
to write. Options are at stages :
'input', 'preassim', postassim', 'output'.
Stages preassim and postassim will output
state data originally contained within the
copies of Prior_Diag.nc and Posterior_Diag.nc.
See rma_doc/rma.html for details on the
filename conventions. For example, running
filter with prior inflation enabled with
stage 'preassim' enabled will produce files
with names:
preassim_member_####.nc
preassim_{mean,sd}.nc
preassim_priorinf_{mean,sd}.nc
* write_all_stages_at_end -- important for large models - all output file
I/O is deferred until the end of filter, but
will use more memory to store the data. More
detailed info is in rma_doc/rma.html
* output_restart_mean -- renamed output_mean
* output_restart -- renamed output_restarts
* direct_netcdf_{read,write} -- REMOVED, always true
* restart_list_file -- renamed input_restart_file_list
* single_restart_file_in -- renamed single_file_in
* single_restart_file_out -- renamed single_file_out
* add_domain_extension -- REMOVED
* use_restart_list -- REMOVED
* overwrite_state_input -- REMOVED, equivalent functionality can be set
with single_restart_file_in = single_restart_file_out
------------------------------------------------------------------------------
Changes to the perfect_model_obs_nml are :
------------------------------------------------------------------------------
* restart_in_filename -- renamed restart_in_file_names takes a NetCDF
file. For multiple domains you can specify a
list.
* direct_netcdf_{read,write} -- REMOVED, always true
------------------------------------------------------------------------------
Changes to the state_space_diag_nml are :
------------------------------------------------------------------------------
* single_file -- REMOVED, diagnostic files are now controlled
in filter_nml with stages_to_write
* make_diagnostic_files -- REMOVED, no longer produce original
Prior_Diag.nc and Posterior_Diag.nc
* netCDF_large_file_support -- REMOVED, always true
------------------------------------------------------------------------------
Changes to the state_vector_io_nml are :
------------------------------------------------------------------------------
* write_binary_restart_files -- REMOVED
------------------------------------------------------------------------------
Changes to the ensemble_manager_nml are :
------------------------------------------------------------------------------
* flag_unneeded_transposes -- REMOVED
------------------------------------------------------------------------------
Changes to the integrate_model_nml are :
------------------------------------------------------------------------------
* advance_restart_format -- REMOVED, only supporting NetCDF format.
------------------------------------------------------------------------------
Scripting with CESM
------------------------------------------------------------------------------
See models/cam-fv/scripts_cesm1_5/assimilate.csh for an example of how to
handle the new filename conventions.
(To help find things: input_priorinf_mean output_priorinf_mean )
{in,out}put_{prior,post}inf_{mean,sd}.nc ARE in use;
Search for stage_metadata%filenames turned up
interface set_file_metadata
module procedure set_explicit_file_metadata
module procedure set_stage_file_metadata
! stage_name is {input,preassim,postassim,output}
! base_name is {mean,sd,{prior,post}inf_{mean,sd}} from filter/filter_mod.f90.
write(string1,'(A,''.nc'')') trim(stage_name)//'_'//trim(base_name)
file_info%stage_metadata%filenames(my_copy,1) = trim(string1)
This shows where inflation file names are defined.
> grep -I set_file_metadata */*.f90 | grep inf
filter/filter_mod.f90:
call set_file_metadata(file_info, PRIOR_INF_MEAN, stage, 'priorinf_mean', 'prior inflation mean')
call set_file_metadata(file_info, PRIOR_INF_SD, stage, 'priorinf_sd', 'prior inflation sd')
call set_file_metadata(file_info, POST_INF_MEAN, stage, 'postinf_mean', 'posterior inflation mean')
call set_file_metadata(file_info, POST_INF_SD, stage, 'postinf_sd', 'posterior inflation sd')
subroutine set_member_file_metadata(file_info, ens_size, my_copy_start)
call set_file_metadata(file_info, icopy, stage_name, base_name, desc, offset)
subroutine set_stage_file_metadata(file_info, copy_number, stage, base_name, desc, offset)
write(string1,'(A,''.nc'')') trim(stage_name)//'_'//trim(base_name)
subroutine set_explicit_file_metadata(file_info, cnum, fnames, desc)
file_info%stage_metadata%filenames(cnum,idom) = trim(fnames(idom))
file_info%stage_metadata%file_description(cnum,idom) = trim(string1)
function construct_file_names(file_info, ens_size, copy, domain)
write(construct_file_names, '(A, ''_member_'', I4.4, A, ''.nc'')') &
trim(file_info%root_name), copy, trim(dom_str)
Also see
harnesses/filename_harness/files: ENS_MEAN_COPY PriorDiag_mean.nc
------------------------------------------------------------------------------
ADDITIONAL NOTES :
------------------------------------------------------------------------------
* currently the closest_member_tool is broken but plans on being fixed soon.
* restart_file_tool and most model_to_dart/dart_to_model programs have been
deprecated, since DART formated restarts are no longer supported.
* some programs such as model_mod_check have not been fully tested and need
to be exercised with the new naming conventions.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Feb 15th 2017 :: rma_single_file merge changes. Revision: 11136
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Filter and PMO can now run with multiple cycles for low order models. The output
for this is only supported with single file output (members, inflation, mean, sd
are all in the same file).
Added matlab support for diagnostics format in lower order models.
------------------------------------------------------------------------------
Changes to the filter_nml are :
------------------------------------------------------------------------------
output_restart -- RENAMED to output_members
restart_in_file_name -- RENAMED to input_state_file_list
restart_out_file_name -- RENAMED to output_state_file_list
single_restart_file_in -- RENAMED to single_file_in
single_restart_file_out -- RENAMED to single_file_out
input_state_files -- ADDED - not currently working
output_state_files -- ADDED - not currently working
has_cycling -- ADDED for low order models
------------------------------------------------------------------------------
Changes to the perfect_model_obs_nml are :
------------------------------------------------------------------------------
start_from_restart -- RENAMED read_input_state_from_file
output_restart -- RENAMED write_output_state_to_file
restart_in_file_name -- RENAMED input_state_files
restart_out_file_name -- RENAMED output_state_files
single_file_in -- ADDED for low order models
single_file_out -- ADDED for low order models
has_cycling -- ADDED for low order models
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Feb 15th 2017 :: filter updates. Revision: 11160
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The postassim diagnostics file was being incorrectly written after
posterior inflation was applied. It is now written immediately after
the assimilation update, and then posterior inflation, if enabled,
is applied.
Sampling Error Correction now reads data from a single netcdf file
for any ensemble size. To add other sizes, a program can generate
any ensemble size and append it to this file. The default file is
currently in system_simulation:
system_simulation/work/sampling_error_correction_table.nc
Filter and PMO no longer need the "has_cycling" flag.
------------------------------------------------------------------------------
Changes to the filter_nml are :
------------------------------------------------------------------------------
has_cycling -- REMOVED for low order models
------------------------------------------------------------------------------
Changes to the perfect_model_obs_nml are :
------------------------------------------------------------------------------
has_cycling -- REMOVED for low order models
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ April 27th 2017 :: diagnostic file changes. Revision: 11545
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Two additional Diagnostic Files (forecast and analysis) in Filter
which can be set with the namelist option (stages_to_write)
input - writes out mean and sd if requested. for low order models
mean and sd are only inserted into restart files with a
single time step.
forecast - contains the forecast and potentially the mean and sd for the,
this is mostly important for lower order models which cycle
preassim - before assimilation
* No Inflation: same as forecast
* Prior Inf: the inflated ensemble and damped prior inf
* Post Inf: same as forecast
* Prior and Post Inf: the inflated ensemble and damped prior inf
postassim - after assimilation (before posterior infation)
* No Inflation: same as analysis
* Prior Inf: same as analysis
* Post Inf: assimilated ensemble and damped posterior inflation
* Prior and Post Inf: assimilated ensemble and damped posterior inflation
analysis - after assimilation and before potentially update posterior inflation ensemble
and updated prior inf
* No Inflation: assimilated ensemble
* Prior Inf: assimilated ensemble and updated prior inf
* Post Inf: post inflated ensemble and updated posterior inflation
* Prior and Post Inf: post inflated ensemble and updated prior inf and posterior
inflation
output - a single time step of the output ensemble and potentially updated prior inf
and posterior inflation
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ May 5th 2017 :: major changes to model_mod interfaces. Revision: 11615
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
A long-awaited overhaul of the model_mod interfaces. All models which are
in our subversion repository and are supported in the Manhattan release
have been updated to match the new interfaces. If you have model_mods with
extensive changes, our recommendation is to diff your changes with the version
you checked out and insert those changes into the new version. The changes for
this update are unfortunately extensive.
The detailed list of changes:
model_mod::get_state_meta_data() is no longer passed an ensemble_handle as the
first argument. it should not do vertical coordinate conversion. that will be
done as a separate step by convert_vertical_state()
model_mod::vert_convert is replaced by convert_vertical_state() and convert_vertical_obs()
Any vertical conversion code that was in get_state_meta_data should be moved
to convert_vertical_state() which has access to the state vector index, so the
code should move easily.
model_mod::query_vert_localization_coord is no longer a required interface
model_mod::get_close_maxdist_init is not longer a required interface
model_mod::get_close_obs_init is not longer a required interface
model_mod::get_close_obs has a different calling convention and is split into
get_close_obs() and get_close_state(). the close obs routine is passed both the
obs types and quantities, and the close state routine is passed both the
state quantities and the state index, for ease in vertical conversion if needed.
model_mod::nc_write_model_vars() is deprecated for now; it may return in a
slightly different form in the future.
model_mod::nc_write_model_atts() is now a subroutine with different arguments.
it should now only write any global attributes wanted, and possibly some grid
information. it should NOT write any of the state variables; those will be
written by DART routines.
model_mod::get_model_size() needs to return an i8 for the size.
A new module "default_model_mod" supplies default routines for any required
interfaces that don't need to be specialized for this model.
A new module "netcdf_utilities_mod" can do some simple netcdf functions for
you and we plan to add many more over the next couple months.
model_mod::get_model_time_step has been replaced by shortest_time_between_assimilations()
since in fact it has always controlled the minimum time filter would request a model advance
and never had anything to do with the internal time step of the dynamics of the model.
We have removed 'output_state_vector' from the namelist of all model_mods since
we no longer output a single 1d vector. all i/o is now in netcdf format.
Models now have more control over when vertical conversion happens - on demand
as needed, or all up front before assimilation.
Models that were doing vertical conversion in get_state_meta_data should set:
&assim_tools_nml
convert_all_state_verticals_first = .true.
convert_all_obs_verticals_first = .true.
Models which were not should set:
convert_all_state_verticals_first = .false.
convert_all_obs_verticals_first = .true.
The location_mod::vert_is_xxx() routines have become a single is_vertical(loc, "string") where
string is one of: "PRESSURE", "HEIGHT", "SURFACE", "LEVEL", "UNDEFINED", "SCALE_HEIGHT"
Models doing vertical localization should add a call to set_vertical_localization_coord()
in their static_init_model() routine to tell dart what vertical coordinate system they
are expecting to convert to for vert localization
Most path_names_xxx files have been updated to add additional modules. compare against
what is checked out to see the differences.
Some of the internal changes include pulling common code from the locations
modules into a location_io_mod which contains common functions for creating
and writing 'location' variables for any location type.
QTY_RAW_STATE_VARIABLE is redundant and was shortened to QTY_STATE_VARIABLE
Many utility programs use the template/model_mod.f90 because they don't
depend on any model-specific functions. this file was also updated to
match the new interfaces.
The obs_impact facility is enabled in the assim_tools namelist. you can
use the obs_impact_tool to construct a table which prevents one class of
observations from impacting another class of state.
Sampling Error Correction now reads the values it needs from a single
netcdf file found in assimilation_code/programs/gen_sampling_err_table/work.
copy it to the same directory as where filter is running. all ensemble
sizes which were previously in final_full.XX files are included, and there
is a tool to generate and append to the file any other ensemble size required.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Jun 2nd 2017 :: tutorial, DART_LAB, and various updates. Revision: 11696
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- bring the DART tutorial pdf slides up to date with the current release.
- include new GUIs with adaptive inflation options in DART_LAB:
oned_model_inf.m
run_lorenz_96_inf.m
- added the lorenz_96_2scale model - additional kinds of
QTY_SMALL_SCALE_STATE and QTY_LARGE_SCALE_STATE added as required.
- add useful attributes to the variables in the diagnostic files
- updates and minor bug fixes to the matlab diagnostic scripts
- updates to the default input.nmls for models
- updates to the cam-fv shell scripts to work with the cesm 2.0 framework
- updates to the cam-fv model_mod for support of cam-chem variables
Added more QUANTITIES/KINDS for chemistry species.
Removed support for 'stand-alone' CAM and CAM-SE (cam-se will be a separate 'model').
- major bug fix in the simple_advection model_mod: Fixed an error with
the layout of the state vector.
- obs_def_radar_mod: Fixed a serious bug in the fall velocity forward operator.
If the fall speed field is not in the state the test for a bad istatus from
the interpolate() call was looking at the wrong variable and returning ok
even if interpolate() had set bad values.
- bug fix in the wrf model_mod for fields which have a vertical stagger
- fix to the makefiles for the GSI2DART observation converter
- added additional netcdf and location utility routines
- various fixes to documentation and test code
- renamed QTY_RAW_STATE_VARIABLE to QTY_STATE_VARIABLE (RAW is redundant)
- direct_netcdf_mod: Renamed 'limit_mem' to 'buffer_state_io'.
buffer_state_io is now a logical that states if a variable that tells
DART it it should read and write variables all at once or variable-by-variable.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ June 27rd 2017 :: CICE 5, model_mod_check, tutorial. Revision: 11770
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Updated support for CICE5.
Updated support for model_mod_check - now compatible with netCDF input files,
input is through [input,output]_state_files namelist variable
(variables renamed).
Ensured consistency between low-order namelists and the updated DART tutorial.
Updated documentation of many namelists. More to come.
location_mod: namelist variable 'maintain_original_vert' was deprecated,
it is now removed. You must remove it from your existing namelists or
DART will error out right away.
obs_diag: namelist variables 'rat_cri' and 'input_qc_threshold' have been
deprecated for years, they have been removed. You must remove them from
your existing namelists or obs_diag will error out right away.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ July 7th 2017 :: cam-fv, MPAS-ATM scripts, single file i/o. Revision: 11807
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
models/mpas_atm: scripts completely revised for the Manhattan release.
Many thanks to Soyoung Ha and Ryan Torn for the contributed code.
cam-fv: scripts and model_mod.f90 updated for cesm2_0_beta05.
Single File I/O:
Now we are able to run 'single_file_in' and 'single_file_out' with MPI.
single_file_io_mod.f90 has been removed and its functionality has been moved
to direct_netcdf_mod.f90.
single_file_io_mod.f90 has been removed from all of the path_names_* files
in the repository. (Remove it from any private path_names_* files.)
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+ July 18 2017 :: bug fixes, documentation updates. Revision: 11830
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- fixed bug in obs_impact_tool when generating the run-time table. specifying
a generic quantity resulted in selecting the wrong specific obs types.
- fixed a bug that would not allow filter to start from a single ensemble member
if single_file_in was true.
- updates to HTML documentation especially for types/quantities (replacing kinds)
- updates to input.nml namelists, code comments, and shell scripts where
names changed from 'restart' to 'state' for input and output files.
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+ Aug 2 2017 :: single filenames, random distributions, bug fixes. Revision: 11864
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- added code to support listing input and output filenames directly in the
namelist instead of having to go through an indirect text file. most useful
for programs that take a single input and output file, but works for all cases.
- bug fix in location_io_mod.f90 that affected obs_seq_to_netcdf (error in adding
vertical location types to output file).
- fix to convert_gpsro_bufr.f90 converter (GPS obs from BUFR files) that failed
if r8 defined to be r4.
- added draws from gamma, inverse gamma, and exponential distributions to the
random sequence module.
- various updates to the CAM scripts to work more smoothly with the most
recent CIME changes and DART Manhattan updates.
- added QTY_CWP_PATH and QTY_CWP_PATH_ZERO to the default quantities list for
the obs_def_cwp_mod.f90 forward operator.
- improved some error messages in the diagnostic matlab scripts
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+ Oct 17 2017 :: MPAS ATM bug fix, various other updates. Revision: 12002
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- Fixed a bug in the MPAS-ATM model_mod that affected surface observations,
in particular altimeter obs. also fixed a bug in the vertical conversion
if using 'scale height' as the vertical localization type.
- Fixed a bug in the CAM-FV model_mod which might have excluded observations
with a vertical coordinate of height (meters) which were in fact below the
equivalent highest_obs_pressure_Pa namelist setting. also fixed a possible
memory leak.
- Added two new modules: options_mod.f90 and obs_def_utilities_mod.f90
this was required so we didn't have circular dependencies in our modules
as we reused common code in more places.
We have updated all the path_names* files which are in the repository.
if you have your own path_names files you may need to add these new modules
to your path lists.
assimilation_code/modules/utilities/options_mod.f90
observations/forward_operators/obs_def_utilities_mod.f90
- Removed QTY_SURFACE_TEMPERATURE from the default obs quantities list
and added QTY_2M_SPECIFIC_HUMIDITY. QTY_2M_TEMPERATURE exists for
atmospheric models, and QTY_SKIN_TEMPERATURE and QTY_SOIL_TEMPERATURE
exist for other models. if you were using QTY_SURFACE_TEMPERATURE
please replace it with the corresponding other temperature quantity.
- Updated and improved the observation converter for ionospheric observations
from the COSMIC GPS satellite.
- Updated the CAM-FV scripts for cesm2_0_beta05.
- Updated the Matlab diagnostics documentation. 'help DART' or 'doc DART'
will give an overview of the available Matlab diagnostics shipped with the
dart distribution.
- Added the observation type COSMIC_ELECTRON_DENSITY to the obs_def_upper_atm_mod
- dart_to_clm and clm_to_dart were resurrected to correctly handle conversions
for the SWE (snow water equivalent) field.
- Updated the channel and column location modules to be compatible with
the current required interfaces.
- Updated the model_mod_check.f90 program (most often used when porting
DART to a new model). there is now more control over exactly which
tests are being run. updated the nml and html documentation files to
match the current code and describe the tests in more detail.
- Fixed a misleading status message in the obs_sequence_tool when all obs
are excluded by the min/max lon/lat box namelist items. the incorrect
message blamed it on observation height instead of the bounding box.
- Added some additional debugging options to the mpi utilities module.
if you have problems that appear to be MPI related, contact us for
more help in enabling them.
- Improved some error messages in location_io_mod and state_structure_mod
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+ Nov 21 2017 :: 1D obs_diag fix, 1D power forward operator Revision: 12138
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- fixed a bad URL reference in tutorial section 18
- fixed a crash with the 1D version of the observation diagnostics program
when including identity observations.
- all models with a workshop_setup.csh now build the same set of programs.
(some/most did not build obs_diag - which is used in the tutorial)
- added a 1D obs-to-a-power forward operator.
- updates to the matlab plotting routines for NetCDF observation formats
- World Ocean Database (WOD) converter supports partial year conversions
and 2013 file formats.
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+ Nov 22 2017 :: minor updates for DA challenge files Revision: 12144
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- added obs_seq.in.power to the Lorenz 96 directory
- added new obs types to the workshop version of the input.nml assimilation list
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+ Dec 01 2017 :: ROMS scripting, debugging aids Revision: 12166
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- Added an option to the ROMS model scripting to advance the model ensemble
members in parallel using a job array.
- Updated the DART_LAB Matlab GUIs to log a history of the settings and
results.
- Added a debug option to the filter namelist, 'write_obs_every_cycle',
to output the full obs_seq.final during each cycle of filter.
(Very slow - use only when debugging a filter crash.)
- Allow the test grid in model_mod_check to cross the prime meridian for testing
longitude interpolation in grids that cross the 360/0 line.
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+ Mar 01 2018 :: ROMS, MMC, PMO, MPAS_ATM debug, etc Revision: 12419
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- Fix a debug message in the MPAS ATM model which might have caused a buffer
overflow crash when formatting a message for a larger ensemble size.
- Update the ROMS shell scripts to support PBS, SLURM, as well as LSF.
Update the ROMS model_mod html documentation.
- Update the default CAM-FV input.nml to have more realistic values
for the highest observation assimilated, and for where the ramp starts
that decreases the increments at the model top. If running with a higher
model top than the default check these items carefully.
- Fixed variable type for 'time' variables we create in diagnostic files
- Miscellaneous minor Bug fixes:
- Print format wider for fractional levels in threed_sphere locations
- Fixed a deallocate call at program shutdown time
- Fixed an indexing problem computing cam-fv U_WIND observations if the
observation used HEIGHT as the vertical coordinate (very unusual).
- Fixed grid creation bug in a test program used with model_mod_check.
Now uses correct spacing for grids in the x,y coordinates.
- Fixed an allocate problem in a test interpolate routine.
- Add surface pressure to the default state list in the wrf work/input.nml
- developer_tests/test_dart.csh can run PMO for more models. required
updates to the work/input.nml in several directories (wrf, cm1, POP,
mpas_atm) to match the current namelist.
- several model_mod_check programs were combined into a single version
that allows for selection of individual tests. many of the input.nml
models/xxx/work/input.nml files have either had a &model_mod_check_nml
section added or updated to match the updated interface.
- the DART QTYs are now available via the state structure in the wrf
and clm model_mods.
- support the NAG compiler better. (contact [email protected] for more
help if you want to use this compiler. some hand work is still needed.)
- streamlined the debug output from the state_structure_info() call to
avoid replicating information that was the same for all variables.
- minor formatting change to the dart log file output for the list of
observation types being assimilated, evaluated, and using precomputed
forward operators.
- fixed an uninitialized variable in the BGRID model code in a routine
that isn't normally used.
- Updated the threed_sphere location module documentation with some usage
notes about issues commonly encountered.
- Fixed an incorrect test when printing out a log message describing if the
inflation would be variance-adaptive or not.
- Change the location of the POP MDT reference file to be relative to the
current run directory and not an absolute file location on cheyenne.
- Make the ROMS, CM1, and POP model_mod log namelist information to the
namelist log file and not the main DART log file.
- Updated several html documentation files, including the template/model_mod.html
which describes the current model_mod required interfaces.
- Updated the instructions for the GSI to DART obs converter to suggest some
needed compiler flags in certain cases.
- Updated the location module test programs.
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+ May 21 2018 :: enhanced inflation option, scripting Revision: 12591
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- Enhanced inflation algorithm added. See the filter_mod.html for new
documentation on this option.
- Updated WRF scripts for the Manhattan release.
- Obs_diag reports statistics on DART QC 8, observation failed vertical
conversion. Matlab scripts also updated to support QC 8.
- New parallel conversion scripts for GPS Radio Occultation observations and
NCEP prepbufr conversions.
- Further updates to documentation files to change KIND to QTY or Quantity.
- Documented required changes when moving from the Lanai/Classic release to
Manhattan in documentation/html/Manhattan_diffs_from_Lanai.html
- Expanded the routines in the netcdf_utilities_mod.f90
- Add an ensemble handle parameter to the 6 ensemble manager routines
where it was missing.
- The advance_time program can read/generate CESM format time strings
(YYYY-MM-DD-SSSSS).
- Fixed a bug in the netcdf read routines that under certain circumstances
could report an array was using the unlimited dimension incorrectly.
- Removed the option to try to bitwise reproduce Lanai results; due to the
number of changes this is no longer possible.
- Minor bug fixes to the (seldom used) perturb routines in the WRF
and MPAS_ATM model_mod.f90 files. (used to add gaussian noise to a
single model state to generate an ensemble; this is never the recommended
method of starting a new experiment but the code remains for testing
purposes.)
- Several remaining model-specific model_mod_check programs were
removed in favor of a single common program source file.
- Keep filter_mod.dopplerfold.f90 in sync with filter_mod.f90,
and assim_tools_mod.pf.f90 in sync with assim_tools_mod.f90.
- Removed makefiles for the obsolete trans_time program.
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+ Jun 18 2018 :: CAM/CESM 2.0, DART QC 8, closest_member_tool Revision: 12682
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- Support for CAM-FV assimilations in the CESM 2.0 release. See
documentation in models/cam-fv/doc/README_cam-fv for details.
- obs_diag and matlab scripts updated to report statistics on DART QC 8,
observation failed vertical conversion
- Updates to fix minor problems with the new WRF scripts
- Added the 'inf_sd_max_change' namelist item to all input.nml files for
the enhanced inflation option
- Revival of the closest_member_tool, which now runs in parallel on
all ensemble members at one time. This tool can be used as a template
for any other tools which need to process something for all ensemble
members in parallel.
- Revival of the fill_inflation_restart tool as a Fortran 90 program.
Using ncap2 is still possible, but if the correct version is not
installed or available this tool can be used.
- Added more functions to the netcdf_utilities_mod.f90
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+ Aug 03 2018 :: performance fix for distributed mean Revision: 12758
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- Important performance fix if model does vertical conversion for localization.
Results were not wrong but performance was poor if 'distribute_mean = .true.'
was selected in the &assim_tools_nml namelist.
Now distributing the mean runs in close to the non-distributed time and uses
much less memory for large models. This only impacts models which do a vertical
conversion of either the observation or state vertical coordinate for localization
AND which set &assim_tools_nml :: distribute_mean = .true. to use less memory.
When using a distributed mean "convert_all_obs_verticals_first = .true." should
be set. If your observations will impact most of the model state, then
"convert_all_state_verticals_first = .true.' can also be set.
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+ Apr 30 2019 :: cam-fv refactor, posteriors optional, QC 8 Revision: 13138
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- The CAM Finite Volume (cam-fv) model_mod.f90 has undergone substantial
refactoring to improve simplicity and remove code for unsupported CAM variants
while also supporting WACCM and WACCM-X. Namelist changes will be required.
- CAM-FV setup and scripting support added for CESM 2.1, including advanced
archiving and compression
- fix for WRF's wind direction vectors when using the Polar Stereographic
map projection. Thanks to Kevin Manning for the fix.
- Add filter namelist option to avoid calling the posterior forward operators
and to not create those copies in the obs_seq.final file.
- Use less memory if writing ensemble member values into the obs_seq.final file.
- added a DART QC of 8 for failed vertical conversions
- updated Matlab scripts support QC=8 and no posterior in obs sequence files.
- sampling error correction table now has all ensemble sizes between 3 and 200
- closest_member_tool can be compiled with other MPI targets
- COSMIC_ELECTRON_DENSITY has been moved from obs_def_gps_mod.f90 to
obs_def_upper_atm_mod.f90, which has new quantities for
ION_O_MIXING_RATIO and ATOMIC_H_MIXING_RATIO
- obs_converters/gps/convert_cosmic_ionosphere.f90 has a test dataset
- support for NAG compiler
- fixed Intel compiler bug in lorenz_96 comparing long integers to integer loop indices
- get_maxdist() now a required routine all location modules
- Default routines now create a time variable as time(time) to allow multiple
files to be concatenated along the unlimited dimension more easily. Also
conforms to the netCDF convention for coordinate dimensions.
- obs_impact_tool handles a continuum of values, not just discrete 0 or 1.
- fill_inflation_restart now produces files with names consistent with filter defaults.
- expanded functionality in xyz_location_mod.f90
- Removed 'slow' sorting routines from sort_mod.f90
- replacing some repeated native netCDF library calls with routines from
the netcdf_utilities_mod.f90
- Updated dewpoint equation to avoid dividing by zero given a very unlikely
scenario (r12832)
- More efficient implementation of adaptive inflation
- Yongfei Zhang and Cecilia Bitz added improvements to the CICE model and
observation converters and forward operators. These changes also use the
locations of the 'new' glade filesystem. They used CESM tag: cesm2_0_alpha06n
- Worked with Yongfei Zhang to remove prototype codes and more completely
document observation converters and data sources for cice assimilation.
- removed 'allow_missing_in_clm' flag from the &assim_tools_nml namelist in
the CICE work directory. The flag moved to a different namelist and the
CICE model doesn't care about it.
- increased the maximum number of input files to obs_diag from 100 to 10000.
- Updated the developer_tests to include more cases.
- Updated oned/obs_diag.f90 to support 'obs_seq.out' files.
- Better error and informational messages in various routines.
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+ MMM DD YYYY :: summary of changes in next Manhattan update hash: NNNNNNN
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- first GIT release
- fixed bug in fill_inflation_restart tool which used the prior inflation mean
and sd for both prior and posterior inflation files. now correctly uses the
posterior mean/sd if requested.
- fixed a typo in the location test script that prevented it from running
- additional functionality in the quad interpolation code, now supports grids
which start at 90 (north) and end at -90 (south).
- if possible, send shorter MPI messages. improves performance on some platforms
and MPI implementations.
- add explicit call to initalize_utilities() where it was missing in a couple of
the WRF utility routines.
- added an example of how to use a namelist to the text_to_obs.f90 observation
converter program.