Changelog

This file documents the most user-visible changes to the DART code. It is not intended to document every change, but instead is intended to inform people what features are now available or have been removed. Detailed changes are always available through the version control framework.

DART now uses Git for version control but has preserved the revision history from when subversion (and CVS before that) was used. The previous revision numbers can be related to git hashes by searching the output of git log

0[1011] machine:DART % git log > full_git_log.txt

A reminder that since many files were moved or renamed, the best way to get the complete log is to use git log --follow for information on individual files.

The changes are now listed with the most recent at the top.

May 4 2021 :: issue and pull request templates. Tag: v9.10.2

Github changes

  • Templates for pull requests, bug reports and feature requests

Documenation updates

  • Removed outdated instructions for checking out a tag

April 29 2021 :: change default GitHub branch. Tag: v9.10.1

  • Replaced the default branch (“Manhattan”) with “main”. “main” is now the latest and stable version. The HEAD of “main” will be the source of releases using the vX.Y.Z format.

April 27 2021 :: preprocess, inflation options, external FO output, wrf-hydro, AMSU-A, DART_LAB. Tag: v9.10.0

New features

  • Updated preprocess:

    • Integers for quantities (kinds) are created and managed by preprocess instead of through a list of integers in DEFAULT_obs_kind_mod.F90.

    • Quantities are defined by name in files: xxx_quantities_mod.f90.

    • preprocess is backwards compatible with existing (v9.9.0) DEFAULT_obs_kind_mod.F90 files and corresponding &preprocess_nml options.

  • Inflation algorithm options in &filter_nml can be given as strings.

  • External forward operators can be selectively written out by observation type in obs_sequence_tool.

  • Updated wrf-hydro interface from James McCreight.

  • Added AIRS/convert_amsu_L1.f90 and amsua_bt_mod.f90 to support converting AMSUA brightness temperatures to obs_seq.

  • AIRS/airs_JPL_mod.f90 strictly supports HDF-EOS2 (not HDF-EOS5) and is only used for Level 2 (i.e. retrievals of) temperature and humidity observations.

  • POP CESM2.1 scripts use the unzipped CAM reanalysis files available on the Research Data Archive (RDA).

  • Enhanced adaptive inflation added to DART_LAB.

  • Improved support for RTPS: output posterior inflation files now contain posterior inflation values when using RTPS.

  • Improved support for RTTOV in MPAS:

    • loc_sea variable used to create sfc, 2m, 10m locations relative to model surface elevation.

    • new error code for pressure not monotonically decreasing with level.

    • QTY_CLOUD_FRACTION added.

  • E_CONTINUE added to allow programs continue after throwing an error. Used in developer tests.

  • Support for more Flux Tower observations (obs_def_tower_mod.f90)

  • Expanded support for netcdf in netcdf_utilities_mod.

  • Documentation converted to reStructuredText and available online. Reorganization of directories to support this: docs -> guide, docs/tutorial -> theory.

Bug fixes

  • Check for monotonically decreasing pressure from TOA down to surface in obs_def_rttov_mod.f90 now checks for greater than or equal to previous level.

  • External forward operators now use the correct ensemble members when distributed_state=false.

  • The obs_sequence_tool now writes out external forward operator values. Thanks to Chris Riedel for reporting this and providing the original bug-fix.

  • obs_def_radar_mod.f90 now correctly applies apply_ref_limit_to_fwd_op when QTY_RADAR_REFLECTIVITY is in the state. Thanks to Craig Schwartz for providing the bug-fix.

  • quality_control_mod.f90 now correctly handles enable_special_outlier = .true. Thanks to Craig Schwartz for providing the bug-fix.

Removed

  • Doxygen directory.

  • Removed svn logging variables and register_module for cleaner log messages. The svn info has not been used since DART moved to Git.

Oct 29 2020 :: radiance support, MPAS, obs converters Tag: v9.9.0

  • Use RTTOV (Radiative Transfer for TOVS) routines to support radiance assimilation.

  • NOTE: The build_templates/mkmf.template file has been removed from version control. You must now explicitly copy the best example mkmf.template into place before compiling. If there is no mkmf.template when you try to build, an error message is displayed.

  • MPAS regional configurations now supported.

  • Converted CHANGELOG to a markdown document, put newest content at top.

  • Converted many HTML documents to markdown

    • renamed observations/obs_converters/observations.html to observations/obs_converters/README.md for example.

  • Updated Publications

  • declare hexadecimal constants according to the Fortran standard.

  • GSI2DART converter updated - Thanks to Craig Schwartz & Jamie Bresch.

  • The WRF-DART tutorial has been rewritten as models/wrf/tutorial/README.md

  • Hydro-DART (AKA wrf-hydro/DART) has been updated to be Manhattan-compliant.

    • also support masked bucket

    • added perturbed forcing capability

  • The support for POP and CESM2 has been implemented and documented.

  • obs_diag now correctly handles the special case when the observation is properly assimilated or evaluated but the posterior forward operator fails. The posterior DART QC in the obs_diag_output.nc should be a ‘2’, not a ‘4’. The prior DART QC value in obs_diag_output.nc can still be a 7 if need be.

  • obs_def_tower_mod.f90 was refactored into obs_def_tower_mod.f90 and obs_def_land_mod.f90.

  • WRF-Chem/DART documentation and datasets have been updated for Manhattan. Dr. Arthur Mizzi is the father of the WRF-Chem/DART project. If you’d like to use WRF-Chem/DART, please email Dr. Mizzi.

  • Fixed bug in obs_seq_to_netcdf to correctly append to existing netCDF files.

  • Support absolute humidity observations - Thanks to Michael Ying.

  • DEFAULT_obs_kind_mod.F90 has many added quantities.

  • new observation converters including (but not limited to):

    • absolute humidity

    • streamflow observations from the Mexican water agency

    • streamflow observations from the USGS

    • total water storage observations from GRACE

    • radiance observations from GOES

  • the following forward operator modules are either new or modified:

      1. observations/forward_operators/DEFAULT_obs_def_mod.F90

      1. observations/forward_operators/obs_def_GRACE_mod.f90

      1. observations/forward_operators/obs_def_abs_humidity_mod.f90

      1. observations/forward_operators/obs_def_altimeter_mod.f90

      1. observations/forward_operators/obs_def_land_mod.f90

      1. observations/forward_operators/obs_def_mesonet_mod.f90

      1. observations/forward_operators/obs_def_oxygen_ion_density_mod.f90

      1. observations/forward_operators/obs_def_reanalysis_bufr_mod.f90

      1. observations/forward_operators/obs_def_rel_humidity_mod.f90

      1. observations/forward_operators/obs_def_rttov_mod.f90

      1. observations/forward_operators/obs_def_streamflow_mod.f90

      1. observations/forward_operators/obs_def_tower_mod.f90

      1. observations/forward_operators/obs_def_upper_atm_mod.f90

      1. observations/forward_operators/rttov_sensor_db.csv

  • fill_inflation_restart now correctly creates inflation values for all variables in the DART state, regardless of the setting of the no update metadata.

  • GITM is now fully Manhattan compliant.

  • fix bug in madis rawin converter

  • avoid computing posterior inflation if using the ‘relaxation to prior spread’ inflation option – Thanks to Craig Schwartz.

  • add additional reporting options to the obs_assim_count utility

Nov 20 2019 :: FESOM,NOAH-MP model support, better testing Tag: v9.8.0

  • first release entirely from GIT

  • 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.

  • Removing the clamping messages in clamp_variable() of clamped values

  • changed argument names using reserved keywords.

    • state_vector_io_mod:read_state() 'time' to 'model_time'

    • random_seq_mod:random_gamma() 'shape' to 'rshape', 'scale' to 'rscale'

    • random_seq_mod:random_inverse_gamma() 'shape' to 'rshape', 'scale' to 'rscale'

    • obs_def_mod:init_obs_def() 'kind' to 'obkind', 'time' to 'obtime'

    • obs_utilities_mod: 'start' to 'varstart', 'count' to 'varcount'

  • The FESOM model is now Manhattan-ready. Thanks to Ali Aydogdu

  • The noah model is now Manhattan-ready and may be used with NOAH-MP.

  • bugfixed references to the documentation directory that was renamed docs to comply with GitHub Pages.

  • improved test_dart.csh functionality.

Apr 30 2019 :: cam-fv refactor, posteriors optional, QC 8 Revision: 13138

  • 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.

Aug 03 2018 :: performance fix for distributed mean Revision: 12758

  • 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.

Jun 18 2018 :: CAM/CESM 2.0, DART QC 8, closest_member_tool Revision: 12682

  • 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

May 21 2018 :: enhanced inflation option, scripting Revision: 12591

  • 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.

Mar 01 2018 :: ROMS, MMC, PMO, mpas_atm debug, etc Revision: 12419

  • 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 dart@ucar.edu 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.

Dec 01 2017 :: ROMS scripting, debugging aids Revision: 12166

  • 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.

Nov 22 2017 :: minor updates for DA challenge files Revision: 12144

  • added obs_seq.in.power to the Lorenz 96 directory

  • added new obs types to the workshop version of the input.nml assimilation list

Nov 21 2017 :: 1D obs_diag fix, 1D power forward operator Revision: 12138

  • 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.

Oct 17 2017 :: mpas_atm bug fix, various other updates. Revision: 12002

  • 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

Aug 2 2017 :: single filenames, random distributions, bug fixes. Revision: 11864

  • 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

July 18 2017 :: bug fixes, documentation updates. Revision: 11830

  • 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 = .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.

July 7th 2017 :: cam-fv, mpas_atm scripts, single file i/o. Revision: 11807

  • 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.)

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 immediately.

  • 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 immediately.

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 CESM2.0 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.

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 (a long integer) 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 do not 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.

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

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

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

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 dart@ucar.edu 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 :

  1. currently the closest_member_tool is broken but plans on being fixed soon.

  2. restart_file_tool and most model_to_dart/dart_to_model programs have been deprecated, since DART formatted restarts are no longer supported.

  3. some programs such as model_mod_check have not been fully tested and need to be exercised with the new naming conventions.

ancient history

To see previous history, it is probably best to use

  • git log --follow

  • git diff --name-status XXXX YYYY where XXXX and YYYY are commits, branches, …

or something along those lines.