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.
December 6 2024 :: Developer tests. Tag v11.8.6
Tests for distribution modules: normal, beta, gamma
Removed out-of-date tests for state IO
November 12 2024 :: MPAS bug-fixes. Tag v11.8.5
Fixed 2m and 10m fields not being updated - set istatus for VERTISHEIGHT and VERTISLEVEL for convert_vert_distrib_state.
Fixed vertical location in convert_vertical_obs to use zGridFace.
November 8 2024 :: POP initial ensemble available from GDEX. Tag v11.8.4
Documentation update:
POP initial ensemble available from GDEX.
Bug-fixes:
Removed unnecessary loops around calendar types in time_manager_mod.
Removed unused routine from normal_distribution_mod which case giving compilation warnings.
Replaced broadcast_minmax calls with all_reduce_min_max.
November 7 2024 :: MPI window memory reduction. Tag v11.8.3
Removes unnecessary copy of state into mpi window.
Removes cray pointer version of the mpi window.
- Fortran-testanything included in developer tests.From dennisdjensen: see developer_tests/contrib/fortran-testanything/LICENSE.txt
October 22 2024 :: Bug-fixes: WRF and GOES. Tag v11.8.2
Force THM to be the WRF-DART temperature variable
Remove offset on GOES observation converter
September 27 2024 :: MOM6 mask bug-fix. Tag v11.8.1
Fix for MOM6 CESM3 workhorse 2/3 degree grid TL319_t232 to mask missing geolon|lat|u|v|t values
September 10 2024 :: MARBL_column. Tag v11.8.0
Interface for MARBL_column for DART:
state estimation
state and parameter estimation
parameter estimation only
BATS observation converter, and BATS climatology scripting
contributed by Robin Armstrong
Bugfix:
fix for IO for NetCDF files when only some variables have the unlimited dimension
August 29 2024 :: Bug fixes for shortest_time_between_assimilations and get_close_init. Tag v11.7.1
Bug fixes:
Prevent hang by erroring out if shortest_time_between_assimilations <=0
Catch and error out if max_dist or max_dist_list is <=0 for 3d sphere 3d cartesian get_close_init
Improved defaults for template model input.nml
Doc fixes:
Removed out-of-date info about inflation flavor character strings
Remove out-of-date info on qceff branch checkout
GitHub template for reporting documentation issues
August 26 2024 :: KQCEF. Tag v11.7.0
Adds a Quantile-Conserving Ensemble Filter Based on Kernel-Density Estimation to DART.
New distribution module kde_distribution_mod.
New module rootfinding_mod that provides a different implementation of inv_cdf.
Contributed by Ian Grooms
August 15 2024 :: WRF fwd operator bug fixes. Tag v11.6.1
WRF-DART bug-fixes:
Bug fix for surface temperature observations to use QTY_2M_TEMPERATURE
Bug fix for conversion of vapor mixing ratio to specific humidity
Bug fix for diagnostics_obs.csh
Improved documentation for WRF model_mod and WRF-DART Tutorial
July 26 2024 :: Library build tools for DART. Tag v11.6.0
Buildtools for compiling DART as a shared or a static library.
Bugfix: correct order of arguments in count_state_ens_copies for ‘input’ stages_to_write.
July 11 2024 :: Bgrid documentation and scripting fix. Tag v11.5.1
Updated Bgrid documentation and removed outdated scripts and files
Fixed obs_diag rank histogram documentation links
Improved inflation file documentation
GitHub action for running all quickbuilds in DART
May 16 2024 :: WRF v4. Tag v11.5.0
WRF-DART and WRF-DART Tutorial updated to WRFv4. Note, not backwards compatible with WRFv3.9.
local particle filter default value for pf_enkf_hybrid=.false. contributed by Jon Poterjoy
April 23 2024 :: Bug-fix: WRF hybrid vertical coordinate. Tag v11.4.1
DART now detects whether WRF is using Hybrid Vertical Coordinate (HVC) introduced in WRFv3.9 or terrain following (TF) system. This fix is also compatible with pre WRFv3.9 versions which did not include explicit attribute information for vertical coordinate system.
Improved obs_impact_tool documentation.
March 27 2024 :: WRF-Hydro Developments; AIRS converter documentation update; Add citation.cff file. Tag v11.4.0
WRF-Hydro:
Added a new perfect model obs experimental capability to HydroDART
Modified the Streamflow obs converter to allow for better diagnostics: allows DART to compute obs space diagnostics on all gauges from the Routelink
Enhanced performance in the model_mod and noah_hydro_mod when running a full CONUS domain
Improved HydroDART Diagnostics with new capabilities (saves the hydrographs in a high-resolution pdf, handles hybrid DA components, separate plots for the hybrid statistics, allows the openloop to have different ens size and gauges than the DA runs)
AIRS and AMSU-A observation converters:
Updated the documentation to use up-to-date build suggestions for the HDFEOS library
Updated the AIRS converter code to be able to use version 7 of the AIRS data formats
Removed unused and non-functional code: AIRS/BUILD_HDF-EOS.sh, AIRS/L1_AMSUA_to_netcdf.f90, AIRS/shell_scripts/Build_HDF_to_netCDF.sh, AIRS/shell_scripts/Convert_HDF_to_netCDF.csh
Removed the unnecessary entries from obs_def_rttov_nml in the input.nml
Added a citation.cff file to help users correctly cite DART software - creates a link to cite the repository on the landing page sidebar on GitHub.
March 13 2024 :: Update WRF-DART scripts and bug template to Derecho; remove no-op routines in ensemble manager. Tag v11.3.1
Updated the csh scripting templates used to run WRF-DART and WRF-DART tutorial from Cheyenne to Derecho
Updated bug report template to use Derecho instead of Cheyenne
Removed the following no-op routines from ensemble manager: prepare_to_write_to_vars, prepare_to_write_to_copies, prepare_to_read_from_vars, prepare_to_read_from_copies, prepare_to_update_vars, prepare_to_update_copies
March 12 2024 :: MITgcm/N-BLING with Compressed Staggered Grids. Tag v11.3.0
The DART-MITgcm code now supports compressed grids, especially suited for areas like the Red Sea where land occupies more than 90% of the domain. Built upon work contributed by Jiachen Liu.
Allows writing the BGC fields into MITgcm’s pickup files.
Allows different compression for the regular and staggered grids.
March 12 2024 :: Aether lat-lon. Tag v11.2.0
Aether lat-lon interface added to DART.
March 11 2024 :: SEIR model for infectious diseases. Tag v11.1.0
Added SEIR model which simulates the spread of infectious diseases, for example COVID-19.
February 13 2024 :: Fortran Standards. Tag v11.0.3
Replace f2kcli with Fortran intrinsics for command line arguments.
AIRS and quikscat mkmf.templates with appropriate HDF, HDFEOS, RTTOV library flags.
Simplified noah_hydro_mod.f90 number of non-zero element counts.
WRF pert_sounding_module random iseed now integer.
February 1 2024 :: RTTOV13 cloud bug-fix. Tag v11.0.2
Initialize RTTOV13 profile cloud arrays to zero for profiles.
Updated docs with RTTOV13 namelist info.
New obs_def_rttov13_mod.f90 namelist option wfetch_value.
Updated mkmf.templates for RTTOV on Derecho: HDF5 library flags.
GitHub actions changes:
checkout action updated to v4.
January 17 2024 :: CLM bug-fixes. Tag v11.0.1
CLM5-DART SourceMods path variable correction
dart_to_clm:
Resolved compiler error by changing the arrays for number of snow layers (snlsno and clm_SNLSNO) to integer types
Forcing h2oliq_po to be slightly larger than zero to be consistent with h2oice_po and dzsno_po
Adding checks to ensure that the values for h2oliq_po, h2oice_po, dzsno_po, and snowdp_po are never negative
January 11 2024 :: QCEFF. Tag v11.0.0
Nonlinear and Non-Gaussian Data Assimilation Capabilities in DART
Adds a Quantile-Conserving Ensemble Filtering Framework (QCEFF) to DART. Publications: QCEFF part1, QCEFF part 2.
The default QCEFF options are EAKF, normal distribution (no bounds).
User interface changes:
filter_kind is now a per-qty option through QCEFF table.
Two new required namelists (add to input.nml files):
probit_transform_nml
algorithm_info_nml
assim_tools_mod namelist:
sort_obs_inc namelist option applied to ENKF only, so default is now .true.
spread_restoration
is not supported in this version
algorithm_info_mod QCEFF options read at runtime from .csv or .txt file
New probability distribution modules:
beta_distribution_mod contributed by Chris Riedel
bnrh_distribution_mod (bounded normal rank histogram)
gamma_distribution_mod
normal_distribution_mod
probit_transform_mod
distribution_params_mod
Update to lorenz_96_tracer_advection:
positive_tracer
more tracer namelist options available and changed defaults
updated perturbation routine
bug-fix: real(r8) rather than real(i8)
Fix: obs_def_1d_state_mod (oned forward operators):
For non-integer powers, fix up values for negative bases
Documentation:
main page section on Nonlinear and Non-Gaussian Data Assimilation Capabilities in DART
QCEFF instructions: Quantile-Conserving Ensemble Filter Framework
Example to work through: QCEFF: Examples with the Lorenz 96 Tracer Model
January 9 2024 :: Derecho CLM-DART. Tag v10.10.1
CLM-DART scripting updated for Derecho.
CLM-DART SourceMods packaged with DART.
Reinstituted both ‘complete’ and ‘single_year’ datm streamlist files in shell scripts due to delays when initializing the CAM reanalysis files through campaign/collections directory.
bug-fixes:
Fixed format statement in assert_mod to conform to Fortran standards.
Fixed debugging output for failed forward operators.
doc-fixes:
Remove broken link for register for dart.
December 13 2023 :: Developer tests and bug fixes. Tag v10.10.0
new developer tests to run all builds for all compilers on NSF NCAR machine Derecho.
removed redundant nc_check routine from utilities_mod in favor of netcdf_utilities_mod::nc_check
Improved default thinning options for AIRS L2 converter.
bug-fixes:
AIRS L2 converter message prints correct number of obs.
MOM6 model_mod .eqv. used for logical comparison to conform to Fortran standard.
December 1 2023 :: Bringing DART documentation in accordance with NSF Policy. Tag v10.9.2
doc-fixes:
Brings DART documentation in accordance with the November 2023, “Official Policy on Brand Standards of the U.S. National Science Foundation.” Changes instances of “NCAR” to “NSF NCAR” and adds NSF logo to the DART logo in the navigation menu.
November 9 2023 :: Github Actions MPIf08 Check. Tag v10.9.1
Adds a new check to the Github Actions workflow that uses the mpif08 module (compiles with ./quickbuild mpif08 and runs filter on 2 mpi tasks with the lorenz_96 model).
November 7 2023 :: MPI f08 quickbuild option. Tag v10.9.0
quickbuild.sh mpif08 option to build using the mpi_f08 module
nvhpc mkmf.template for use on Derecho
bug-fixes:
filter_mod.dopperlerfold in sync with filter_mod
unnecessary loop removed from Mersenne twister developer test
doc-fixes:
rename assim_model_mod.rst to match the module
fix various Sphinx warnings and broken link
November 2 2023 :: QCEFF Input Table. Tag v11.1.0-alpha
The QCEFF input table allows for the specification of QCEFF/probit input options, per QTY, at runtime.
This replaces the functionality of using an algorithm_info_mod specific to the model, which meant editing algorithm_info_mod.f90 to specify which distribution should be used for which quantity.
The algorithm_info_mod files for the lorenz_96_tracer_advection model examples have been replaced with set QCF tables (all_bnrhf_qcf_table.csv, all_eakf_qcf_table.csv, state_eakf_tracer_bnrhf_qcf_table.csv, neg_qcf_table.csv) and can be found in lorenz_96_tracer_advection/work.
Removed the ‘global’ version of filter_kind from assim_tools_mod.f90 and the &assim_tools_nml
October 5 2023 :: WRF-DART tutorial diagnostic section. Tag v10.8.5
Improvements:
Added a more complete diagnostics section to the WRF-DART Tutorial.
Developer test for Mersenne twister random number generator.
Bug-fix:
1D location subsetting fixed for obs_sequence_tool.
contributed by Henry Santer
September 18 2023 :: Fluxnet observation converter and obs_def_rttov13_mod.f90 bug-fixes. Tag v10.8.4
Fluxnet obs converter:
Generates a new observation converter (Fluxnetfull_to_obs) for eddy covariance flux tower data (carbon, water energy fluxes)
Documentation changes made to the older, deprecated ameriflux converter (level4_to_obs) and the broken links have been fixed
New flux tower observation types added to accomodate the forward operator approach for time aggregated fluxes (daily through monthly)
obs_def_rttov13_mod.f90 bug-fixes:
Added public get_channel to obs_def_rttov13_mod.f90 to compile WRF successfully with rttov13.
Removed cloud_overlap (integer) from the function: get_rttov_option_logical
August 21 2023 :: CAM-FV shell scripts. Tag v10.8.3
Performance improvements for CAM-FV shell scripts:
Avoid listing files if the CAM_PHIS file already exists.
Avoid using /var/tmp
RUNDIR defined after CIME_OUTPUT_ROOT change.
Warn if no inflation files found.
August 8 2023 :: MPAS-ATM constants and readthedocs fix. Tag v10.8.2
MPAS-ATM constants updated to MPAS v5+
readthedocs build info updated.
July 27 2023 :: Bug-fixes for MOM6 and WRF. Tag v10.8.1
bug-fixes:
MOM6 read_model_time converts to dart time to match observation sequences.
MOM6 salinity units converted to MSU during model_interpolate.
WRF get_dist calculation fixed for observations with VERTISUNDEF.
doc-fixes:
WOD and GTSPP converter documentation notes about salinity units.
MOM6 documentation for setting the Gregorian calendar in CESM.
comment fix in filter_mod.f90
June 27 2023 :: CAM-DART observation preprocessor. Tag v10.8.0
Tool to remove observations above a given CAM level from an obs sequence file
bug-fixes:
MOM6 added check for too deep observations
test_interpolate_range write format corrected
removed unused code from mpas_atm directory
doc: removed outdated references to prep_buf.html
June 1 2023 :: Smoother removal. Tag v10.7.3
Dead smoother code removed.
Documentation fix for quality control.
Cray Compiler Environment mkmf.template
May 10 2023 :: Doc-fix. Tag v10.7.2
conf.py changes for latest readthedocs. Fixes search and flyout menu.
May 8 2023 :: CLM-DART: CAM reanalysis site-level bias correction tool. Tag v10.7.1
Initial version of bias correction for CAM reanalysis forcing for site-level assimilation with CLM-DART.
mkmf change: make clean removes .mod files.
bug-fix: readthedocs yaml file for online documentation build.
April 21 2023 :: MOM6. Tag v10.7.0
CESM-MOM6 interface added to DART.
April 11 2023 :: Bug-fixes for WRF Tutorial and developer test quickbuilds. Tag v10.6.5
Fixes the developer_tests quickbuild.sh files
Fixes the broken link to WRF DART tutorial input.nml.template
February 22 2023 :: Bug-fix release. Tag v10.6.4
Removes unused and uninitialized argument to adaptive_inflate_init.
Fixes HDF5_utilities_mod i4 i8 mismatch.
Removes HDF tutorial code which is not part of DART.
Fixes misleading comment in filter_mod.f90
February 9 2023 :: Bug-fix for vertical conversion QC 8. Tag v10.6.3
QC 8 values now correctly recorded. Previously this info was lost if the posterior FO was skipped.
Fixes QC overwrite for forward operators when running distributed_state = .false.
WRF tutorial bug fix for setting paramfile.
January 27 2023 :: Documentation update for porting new models. Tag v10.6.2
Improved ‘porting new models to DART’ documentation.
Removed outdated references to previous build system.
December 21 2022 :: Documentation update for CLM and the DART Tutorial. Tag v10.6.1
Improved instructions for the CLM-DART tutorial.
Fixes link within the documentation to a section describing how to configure MATLAB’s path to use DART MATLAB functions.
December 12 2022 :: Automated testing of pull requests. Tag v10.6.0
GitHub actions for pull requests which checkout, compile and run a given model. Current workflow: lorenz_96 (mpi) and lorenz_63 (no mpi)
contributed by Anderson Chauphan
December 2 2022 :: Bug-fix cam-fv. Tag v10.5.6
Fix for assimilate.csh purge of restart files when the interval for restart saves is given as a string rather than an integer.
Fix for setting ptype when no_normalization_of_scale_heights = .false.
November 8 2022 :: Improved clean_nml and CLM quickbuild.sh. Tag v10.5.5
clean_nml tool for comparing input.nmls given optional arguments to keep the original order of nmls and/or entries, and optionally keep namelist comments.
fill_inflation_restart now a default build for CLM.
November 3 2022 :: Bug-fix release. Tag v10.5.4
Perfect_model_obs (pmo) fixed for running with MPI and advancing the model inside pmo.
MPAS_ATM xtime string padded with blanks for easier bitwise comparison.
lorenz_96_tracer_advection quickbuild.sh fixed.
October 13 2022 :: Bug-fix for read variables. Tag v10.5.3
Per-file check for unlimited dimension before variable read. Netcdf dimension counts adjusted accordingly. Fixes problems when reading from DART created netcdf files, for example, from fill_inflation_restart
Bug-fix for verbose printing of state_structure info
October 10 2022 :: Bug-fix for obs_converter builds. Tag v10.5.2
Bug fix for converter builds using the template model_mod.f90
Performance fix for MPAS_ATM
September 23 2022 :: Bug-fix for pertub_single_instance. Tag v10.5.1
Program perturb_single_instance was running without perturbing when interf_provided = .false. (silent fail). Model specific pert_model_copies is now required to run perturb_single_instance
September 22 2022 :: CAM-SE. Tag: v10.5.0
CAM-SE interface for Manhattan
Shared code for CAM-SE and CAM-FV model_mods in cam-common-code
September 21 2022 :: ROMS model_mod perturbation routine Tag: v10.4.0
Adds a pert_model_copies subroutine to the ROMS model_mod to enable proper functioning of perturb_single_instance for ROMS.
Updates ROMS documentation with an explanation of how to generate an initial ensemble of history files.
September 16 2022 :: Bug-fix for CLM shell scripts. Tag: v10.3.2
Fixes dtlimit bug in cesm2.2 CLM shell scripts. Loads all CAM reanalysis files within datm data stream file regardless if it is single year or multi-year run.
Fixes single instance bug in cems2.2 CLM shell scripts. Allows for freerun scripts to generate single instance simulations.
September 14 2022 :: Bug-fix for POP shell scripts. Tag: v10.3.1
Fixes bug in POP CESM2.1 shell scripts in which inflation files were not being propagated properly due to link destination already existing.
August 19 2022 :: Automated setup of new model interfaces. Tag: v10.3.0
Automated initial setup of new model interfaces to aid users developing model_mod code and documentation.
contributed by Benjamin Gunn
August 18 2022 :: Bug-fixes for obs_utilities build and mpas_atm. Tag: v10.2.1
obs_utilities_mod no longer included by default for model/work builds because these utilities are for threed_sphere and threed_cartesian location_mods only.
mpas_atm model_mod check for required quantities changed to handle multiple variables of the same quantity.
August 3 2022 :: TIEGCM. Tag v10.2.0
TIEGCM model_mod updated to Manhattan
Added hyperslice subroutine to state_structure_mod to read only part of a netcdf variable into the state.
Replaced stub get_expected_vtec with COMMON_CODE.
August 2 2022 :: RTTOV v13. Tag v10.1.0
Support for RTTOV v13
Contributed by Lukas Kugler
July 27 2022 :: Bug-fix for WRF model_mod nc_write_model_atts. Tag: v10.0.5
Removes obsolete domain dimension from nc_write_model_atts for WRF model_mod. This code was left over from when multiple domains could be written to a single NetCDF file in DART.
July 21 2022 :: Bug-fixes for DART_LAB rank histograms and get_close caching. Tag: v10.0.4
Fixes DART_LAB prior and posterior rank histogram calculation.
Fix for intent(inout) for get_close_X_caching routines.
Obsolete GitHub workflow removed.
July 14 2022 :: Performance improvement - removal of redundant caching. Tag: v10.0.3
Reduces the runtime by removing redundant caching in the get_close_obs_cached and get_close_state_cached subroutines in assim_tools_mod.f90
June 24 2022 :: Bug-fixes for MITgcm_ocean and Var obs converter. Tag: v10.0.2
MITgcm_ocean pert_model_copies routine fixed to use the correct variable clamping value and indices for each element of the copies array.
Var obs converter quicklbuild.sh fixed to correctly locate the required 3DVAR_OBSPROC code.
Documentation for Var obs converter updated with information for where to get the latest WRF 3DVAR_OBSPROC code.
June 2 2022 :: Bug-fixes for ps_rand_local in the Bgrid Model. Tag: v10.0.1
performs the missing call for initialize_utilities()
fixes improper formatting when writing into ps_rand.out
May 24 2022 :: New build tools for DART. Tag: v10.0.0
mkmf_ and path_names_ files replaced with buildfunctions to collect source code.
quickbuild.csh replaced with quickbuild.sh
developer_tests/build_everything for simultaneous runs of every quickbuild.sh
Several build/compilation related bug fixes
May 23 2022 :: Bug-fix for RTPS inflation flavor. Tag: v9.16.4
Order of operations changed to avoid inadvertent changes to ens when using RTPS.
May 16 2022 :: Installation documentation update. Tag: v9.16.3
Improved installation documentation.
April 5 2022 :: Bug-fix for NetCDF variables with NaN attributes. Tag: v9.16.2
Fix for checking attributes of NetCDF variables that have a NaN as the missing or _FillValue.
April 1 2022 :: Per-obs-type localization for 3D Cartesian location_mod. Tag: v9.16.1
Optional per-obs-type localization for 3D Cartesian location
Contributed by Jon Labriola for use with CM1
March 31 2022 :: MiTgcm-ocean NBLING. Tag: v9.16.0
MITgcm-ocean interface updated to Manhattan.
Support for NBLING (ocean biogeochemistry) for MITgcm-ocean.
New observation converter for ocean color.
March 22 2022 :: CLM5-DART Tutorial. Tag: v9.15.0
New CLM5-DART tutorial providing new users with 13 steps for download, setup, execution, and diagnosis of a simple global assimilation run.
Stage_cesm_files script corrected to re-stage prior inflation files correctly and provide reproducibility
March 10 2022 :: Tracer advection model. Tag v9.14.0
New model for tracer advection based on Lorenz_96 using a Semi-Lagrangian scheme.
Forward operator documentation updated to Manhattan
lorenz_96_tracer_advection contributed by Fairuz Ishraque (SIParCS)
February 11 2022 :: Bug-fix for nag compiler. Tag v9.13.2
Bug-fix for fixsystem preprocessing for NAG compiler
February 7 2022 :: CM1 and 3D Cartesian location_mod updates. Tag v9.13.1
Contributed by Jon Labriola
Updated CM1 model_mod to use mixed-case boundary conditions, for example periodic in the x-direction but non-periodic in the y-direction.
Added capability to CM1 model_mod to interpolate 3D fields such as reflectivity.
Added capability to use multiple localization radii to threed_cartisian location_mod.
Bug-fix for threed_cartesian location_mod for periodic boundaries.
February 3 2022 :: CLM with SWE repartitioning. Tag: v9.13.0
Updated Community Land Model (CLM) model_mod, scripting, and diagnostics.
New capability to repartition snow layer mass and dimension variables. The repartitioning ensures that the adjustments applied to the snow layers are consistent (mass and dimensions are conserved) with the adjustment of the total snow water equivalent.
New observation converters for NASA_Earthdata and NSIDC
Support for netcdf _FillValue
Bug-fix for clm nc_write_model_atts lon vs nlon
January 11 2022 :: Bug fix for inflation namelist options. Tag: v9.12.1
reverted inf_flavor namelist option to be integer only to conform to Fortran standards.
December 7 2021 :: Refactored filter_assim. Tag: v9.12.0
Filter_assim refactored so each process calcuates increments
Code readability changes
November 22 2021 :: Bug fix for groups with posterior spatially-varying adaptive inflation. Tag: v9.11.13
Removed the additional outlier threshold test for each group when using posterior spatially-varying adaptive inflation. The outlier test is done for the entire ensemble when the posterior forward operators are computed.
October 27 2021 :: Observation converter documentation update. Tag: v9.11.12
Improved documentation for radar observation converters
September 30 2021 :: Bug fix for very large models. Tag v9.11.11
mpi_utilties_mod using correct check for message length > SNDRCV_MAXSIZE
new developers test for large message sizes
State vector IO updated to use i8 for state indexing
WRF model_mod now using i8
September 21 2021 :: Bug fix for perfect_model_obs. Tag v9.11.10
perfect_model_obs now exits cleanly when no filenames are given for the input_state_files or output_state_files namelist options.
August 30 2021 :: Repository clean-up and DART registration form. Tag: v9.11.9
removed obsolete code:
cam-old
restart_file_tool
html boilerplate from pre-readthedocs documentation
null versions of clamp_mod and vert_convert_mod
io test harnesses
jekyll website
removed experimental code:
pnetcdf (for restart files)
filter.separate_seq (split obs_seq across cores)
August 26 2021 :: NAG compiler fixes and updates to developer tests Tag: v9.11.8
bug fix for fixsytem for the NAG compiler
new developer test for mpi one-sided communication
removed obsolete async 4 developer tests
August 19 2021 :: WRF-Hydro diagnostics Tag: v9.11.7
Improved DART diagnostic routines for WRF-Hydro
August 10 2021 :: Documentation and GitHub template update Tag: v9.11.6
External forward operator documentation
Typo fixes for GitHub templates
August 5 2021 :: bug fix for obs_seq_to_netcdf and grabbufr.x Tag: v9.11.5
obs_seq_to_netcdf now works correctly with mulitple obs_seq per epoch.
grabbufr.x STAT function returns correctly for long filenames when using PGI
July 23 2021 :: bug fix for wrf non-initialized unique levels. Tag: v9.11.4
The array uniquek is now initialized to an invalid level to prevent random reasonable level values in the array.
June 24 2021 :: bug fix for cam-fv model_interpolate. Tag: v.9.11.3
cam-fv model_interpolate now passes the correct array slice of quad_vals to quad_lon_lat_evaluate
June 24 2021 :: latest version of local particle filter. Tag: v9.11.2
latest version of particle filter from Jon Potterjoy
new mpi routine get_global_max
June 18 2021 :: build fixes for PGI compiler and intel compiler osx. Tag: v9.11.1
mkmf.templates fixes for intel.osx and pgi
input.nml fix for obs_total_error
path_names fix for test_quad_*_interp
June 8 2021 :: New observation converter for Solar Induced Fluorescence (SIF). Tag: v9.11.0
Converter for harmonized SIF retrievals
Jun 7 2021 :: fix typos in POP documentation Tag: v9.10.6
fix some spelling mistakes, does not change meaning.
May 18 2021 :: updated process to generate obs on a sphere. Tag: v9.10.5
Matlab scripts and new scripts for cam-fv make it simpler to generate synthetic observations evenly spaced around the sphere.
Moved create_sphere_obs into the even_sphere directory.
May 10 2021 :: obs_info support for identity obs Tag: v9.10.4
programs/obs_utils/obs_info.f90 now supports reporting identity obs
May 6 2021 :: fix AMSUA converter bug. Tag: v9.10.3
AIRS/convert_amsu_L1.f90 correctly handles multiple input files
separated AIRS/README, convert_amsu_L1, and convert_airs_L2 documentation
May 4 2021 :: issue and pull request templates. Tag: v9.10.2
Github changes
Templates for pull requests, bug reports and feature requests
Documentation 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
andamsua_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 appliesapply_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 handlesenable_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.
WRF, MPAS, and CAM-FV model interfaces now support radiance assimilation.
Added GOES 16-19 ABI converter
NOTE: The
build_templates/mkmf.template
file has been removed from version control. You must now explicitly copy the best examplemkmf.template
into place before compiling. If there is nomkmf.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
toobservations/obs_converters/README.md
for example.
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 theobs_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 intoobs_def_tower_mod.f90
andobs_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:
observations/forward_operators/DEFAULT_obs_def_mod.F90
observations/forward_operators/obs_def_GRACE_mod.f90
observations/forward_operators/obs_def_abs_humidity_mod.f90
observations/forward_operators/obs_def_altimeter_mod.f90
observations/forward_operators/obs_def_land_mod.f90
observations/forward_operators/obs_def_mesonet_mod.f90
observations/forward_operators/obs_def_oxygen_ion_density_mod.f90
observations/forward_operators/obs_def_reanalysis_bufr_mod.f90
observations/forward_operators/obs_def_rel_humidity_mod.f90
observations/forward_operators/obs_def_rttov_mod.f90
observations/forward_operators/obs_def_streamflow_mod.f90
observations/forward_operators/obs_def_tower_mod.f90
observations/forward_operators/obs_def_upper_atm_mod.f90
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 theno 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 valueschanged 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 renameddocs
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 targetsCOSMIC_ELECTRON_DENSITY
has been moved fromobs_def_gps_mod.f90
toobs_def_upper_atm_mod.f90
, which has new quantities forION_O_MIXING_RATIO
andATOMIC_H_MIXING_RATIO
obs_converters/gps/convert_cosmic_ionosphere.f90
has a test datasetsupport for NAG compiler
fixed Intel compiler bug in
lorenz_96
comparing long integers to integer loop indicesget_maxdist()
now a required routine all location modulesDefault 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 supportobs_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, thenconvert_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 conversionUpdates to fix minor problems with the new WRF scripts
Added the
inf_sd_max_change
namelist item to allinput.nml
files for the enhanced inflation optionRevival 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. Usingncap2
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 withfilter_mod.f90
, andassim_tools_mod.pf.f90
in sync withassim_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 filesMiscellaneous minor Bug fixes:
Print format wider for fractional levels in
threed_sphere
locationsFixed 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 thework/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.nmlmodels/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_mod
s.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 fullobs_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 directoryadded 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
andobs_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 thepath_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 addedQTY_2M_SPECIFIC_HUMIDITY
.QTY_2M_TEMPERATURE
exists for atmospheric models, andQTY_SKIN_TEMPERATURE
andQTY_SOIL_TEMPERATURE
exist for other models. if you were usingQTY_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 theobs_def_upper_atm_mod
dart_to_clm
andclm_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
andstate_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 affectedobs_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
andQTY_CWP_PATH_ZERO
to the default quantities list for theobs_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 fromrestart
tostate
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
andsingle_file_out
with MPI.single_file_io_mod.f90
has been removed and its functionality has been moved todirect_netcdf_mod.f90
.single_file_io_mod.f90
has been removed from all of thepath_names_*
files in the repository. (Remove it from any privatepath_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 variablemaintain_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 variablesrat_cri
andinput_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
andQTY_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 ofcam-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
toQTY_STATE_VARIABLE
(RAW is redundant)direct_netcdf_mod
: Renamedlimit_mem
tobuffer_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 tooutput_members
restart_in_file_name
RENAMED toinput_state_file_list
restart_out_file_name
RENAMED tooutput_state_file_list
single_restart_file_in
RENAMED tosingle_file_in
single_restart_file_out
RENAMED tosingle_file_out
input_state_files
ADDED - not currently workingoutput_state_files
ADDED - not currently workinghas_cycling
ADDED for low order models
Changes to the perfect_model_obs_nml are :
start_from_restart
RENAMEDread_input_state_from_file
output_restart
RENAMEDwrite_output_state_to_file
restart_in_file_name
RENAMEDinput_state_files
restart_out_file_name
RENAMEDoutput_state_files
single_file_in
ADDED for low order modelssingle_file_out
ADDED for low order modelshas_cycling
ADDED for low order models
Jan 13th 2017 :: rma_fixed_filenames merge changes. Revision: 10902
Specific namelist changes include:
- 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.
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.
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 withinput_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 withoutput_restart_file_list
. Same format asinput_restart_file_list
.inf_in_file_name
REMOVED, now have fixed names of the form input_{prior,posterior}inf_{mean,sd}.ncinf_out_file_name
REMOVED, now have fixed names of the form output_{prior,posterior}inf_{mean,sd}.nc.inf_diag_filename
REMOVEDinf_output_restart
REMOVED, inflation restarts will be written out if inflation is turned onoutput_inflation
REMOVED, inflation diagnostic files will be written if inflation is turned onstages_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 ofPrior_Diag.nc
andPosterior_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.htmloutput_restart_mean
renamed output_meanoutput_restart
renamed output_restartsdirect_netcdf_{read,write}
REMOVED, always truerestart_list_file
renamed input_restart_file_listsingle_restart_file_in
renamed single_file_insingle_restart_file_out
renamed single_file_outadd_domain_extension
REMOVEDuse_restart_list
REMOVEDoverwrite_state_input
REMOVED, equivalent functionality can be set withsingle_restart_file_in = single_restart_file_out
Changes to the perfect_model_obs_nml are :
restart_in_filename
renamedrestart_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 infilter_nml
withstages_to_write
make_diagnostic_files
REMOVED, no longer produce originalPrior_Diag.nc
andPosterior_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 formatted 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.
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.