Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Elizabeth Hunke <[email protected]>

* Add .readthedocs.yaml

Copy CICE's readthedocs configuration as of
CICE-Consortium/CICE@06282a53 (Update version to 6.4.2 (#864),
2023-09-08).

* doc: mention code variables relating to 'calc_dragio'

At the end of the "Ocean" section, we mention that 'dragio' can be
computed from 'iceruf_ocn' and 'thickness_ocn_layer1', but do not
mention these code variables, nor the 'calc_dragio' setting used to
activate that computation. Mention the code variables next to their
mathematical symbol, for more clarity.

…ters (#465)

All parameters of icepack_parameters::icepack_query_parameters are
intent(out), so it does not make sense to recompute constants at the end
of that subroutine since no constants are changed. This superfluous call
dates back to the introduction of icepack_query_parameters (then called
icepack_query_constants) in 7646f2a (Migrate icepack_constants out of
the columnphysics/constants directory..., 2017-10-04).

Remove that call.

* Remove older "_old" tfrz_options, added for backwards compatibility

Modify tfrz_option logic in icepack_sea_freezing_temperature to trap unsupported values

* Update Icepack set_nml settings, remove _old from tfrz_option

* Clarify documentation associated with namelist inputs

Alphabetize cpl_frazil namelist documentation

* Update documentation

* Update 5-band dEdd to support test data

Add an interpolation method in icepack_shortwave.F90 for rsnw

Refactor portions of icepack_shortwave to improve robustness

Add snicar and snicartest test cases

* Update the 5-band snicar shortwave rsnw_snicar_tab interpolation

This changes answers but QC tests pass.  The new implementation checks
whether the rsnw_snicar_tab is an array of integer values with deltas
of value 1 (and sets the rsnw_snicar_chk variable).  If so, it uses a
shortcut to find the rsnw_snicar_tab bounds for interpolation, otherwise
it calls the shortwave_search routine.  In testing, the shortcut did not
change performance much, but that could change in the future.

* Clean up debug output

* Refactor the logic to control rsnw table interpolation in the shortwave.
Set a character string, rsnw_datatype, at initialization.

…ation (#476)

* correct ks units, clean up comments, big fix for BL99 enthalpy calculation

* make it pretty

…ompiler (#477)

Update pull request template to ask for additional information about the PR. This information can and will be used during the squash merge process to produce more useful commit logs.

Update Macros.conda_macos to remove ffpe-trap=invalid from debug flags.
This flag causes nf90_create to fail with the latest version of
the conda environment. This happens when debug flags are on
and a test with netcdf is turned on. I believe this is a compiler error.

* Add gnuplot to the conda environment

This fix allows the timeseries.csh script to be used for Icepack standalone runs.

* add tutorial documentation

* add tutorial

* add tutorial

* add tutorial

* add tutorial

* add tutorial

* Minor clarifications and grammatical updates.

---------

Co-authored-by: Elizabeth Hunke <[email protected]>

Update Copyright to 2024 in code and LICENSE file

Add run_testoutput script to generate release plots for Icepack

Documentation is being update based on the Consortium workshop in 2024. The "adding a tracer" section has been updated as has the tutorial section related to adding a fluff tracer. An example set of code diffs for the tutorial is also includes as reference.

Port to NCAR's cluster, casper using the HTC nodes using standard cpus. This will support testing and development on another piece of hardware other than derecho and izumi and provides a good option for smaller test cases. Added intel, inteloneapi, and gnu compiler options.

The -check debug option is very sensitive in this version of Inteloneapi, so it has been turned off.

Add congel_freeze namelist and add 'one-step' option to the default 'two-step' option.

Namelist flag congel_freeze chooses which formulation to use. The original is ‘two-step’, since only the mushy boundary moves in the first step and the phase change happens in the next step. Plante et al. (‘one-step’) moves the boundary and performs the phase change in a single time step.  Maintain 'two-step' as default for now.

This is a significant update in the BGC including refactoring Icepack interfaces.

Deprecate skl BGC but leave code alone for now hoping we get help from the community to validate the latest code.

Add BGC parameters to icepack_parameters.F90

Update BGC physics, consistent with E3SM-Project/E3SM#6457.  Remove redundant arguments in BGC interfaces.

    icepack_aerosol.F90
        revised subroutine update_snow_bgc
    icepack_algae.F90
        revised subroutine zbio
        revised subroutine z_biogeochemistry
        revised subroutine algal_dyn
        add subroutine bgc_carbon_sum
    icepack_brine.F90
        revise subroutine prepare_hbrine
        revise subroutine update_hbrine
    icepack_mechred.F90
        add mbio calculation to subroutine ridge_shift
        add flux_bio calculation to subroutine ridge_ice
    icepack_therm_itd.F90
        update calculation of dvssl and dvint in subroutine lateral_melt
    icepack_zbgc.F90
        lots of stuff
    icepack_zbgc_shared.F90
        lots of stuff

Remove redundant arguments in non-BGC interfaces.

    icepack_atmo.F90
    icepack_fsd.F90
    icepack_isotope.F90
    icepack_itd.F90
    icepack_meltpond_topo.F90
    icepack_mushy_physics.F90
    icepack_snow.F90
    icepack_therm_bl99.F90
    icepack_therm_mushy.F90
    icepack_therm_shared.F90
    icepack_therm_vertical.F90
    icepack_tracers.F90
    icepack_wavefracspec.F90

Generalize merge_fluxes to make all arguments optional

Fix bug in subroutine snow_redist computation of hsn_new when nslyr=1

Update the Icepack driver consistent with Icepack interface changes

Update zbgc initialization in the Icepack driver, move bgc parameter intiialization to icepack_init_parameters, update icepack_init_zbgc call.

Update some calls to icepack_warnings_setabort to add file and line number.

Update warning package to improve OpenMP robustness. Fixes potential race conditions that show up when lots of output is produced.

Modified congel implementation in subroutine thickness_changes in icepack_therm_vertical.F90 to recover bit-for-bit results. New congel and new bgc implementation were bit-for-bit independently, but when combining the changes, the intel compiler (with -O2) introduces non bit-for-bit changes (roundoff).

Update bgc namelist defaults and settings in icepack_in

Update bgc tracer sizing in set_env files

Update testing, remove skl tests, add zaero tests.

---------

Co-authored-by: Elizabeth Hunke <[email protected]>
Co-authored-by: David Bailey <[email protected]>
Co-authored-by: Nicole Jeffery <[email protected]>

Update inteloneapi, cray, intel, nvhpc modules/compiler. Changes answers for inteloneapi and cray.

Switch default Derecho queue from main to develop to support quicker turn around and lower costs. Develop is a shared queue.

Error in the snow physics with the cray compiler needs further assessment, but suggest we merge this now as is. That error does not present itself in CICE with snow physics with the same cray compiler.