update to MOM6 main 20230504 updating#113

Merged

jiandewang merged 239 commits into

NOAA-EMC:dev/emcfrom

jiandewang:feature/update-to-main-20230504

May 22, 2023

Commits on Jul 26, 2022

Add missing units

gustavo-marques
authored and
alperaltuntas
committed
Follow MOM6 code style guide

gustavo-marques
authored and
alperaltuntas
committed
Merge branch 'mom-ocean:main' into dev/ncar
alperaltuntas
authored

Commits on Aug 1, 2022

Commits on Aug 5, 2022

Merge pull request #223 from mom-ocean/main
gustavo-marques
authored

Commits on Aug 30, 2022

Commits on Sep 22, 2022

Commits on Oct 7, 2022

Fix string order in regional_section
gustavo-marques
committed

Commits on Oct 28, 2022

+Created remapping_attic.F90

Hallberg-NOAA
authored and
marshallward
committed
+Move interpolate_column to MOM_remapping.F90

Hallberg-NOAA
authored and
marshallward
committed
+Remove missing_value arg to interpolate_column

Hallberg-NOAA
authored and
marshallward
committed
Add check_remapped_values

Hallberg-NOAA
authored and
marshallward
committed

Commits on Oct 30, 2022

gitlab-ci: Adds (command-line) tool to simplify .gitlab-ci.yml

adcroft
authored and
marshallward
committed

Commits on Oct 31, 2022

Bug fix for categorize_axes causing crash

nikizadehgfdl
authored and
marshallward
committed
Bug fix for categorize_axes causing crash

nikizadehgfdl
authored and
marshallward
committed
Avoid an uninitialized string in categorize_axes

Hallberg-NOAA
authored and
marshallward
committed

Commits on Nov 7, 2022

(*)Simplify interpolate_column weight calculations

Hallberg-NOAA
authored and
marshallward
committed
Autoconf: Fortran-netCDF C compatibility test

marshallward
authored and
adcroft
committed

Commits on Nov 9, 2022

Autoconf: Fortran testing of C bindings

marshallward
authored and
adcroft
committed

Commits on Nov 10, 2022

Obc setup plus segment update period (#198)

nikizadehgfdl
and
Hallberg-NOAA
authored

Commits on Nov 11, 2022

Ice dynamics (#228)
OlgaSergienko
authored

Commits on Nov 14, 2022

Commits on Nov 15, 2022

Merge branch 'main' into main_to_dev
marshallward
committed

Commits on Nov 16, 2022

Commits on Nov 21, 2022

Commits on Nov 22, 2022

Remove Python venv setup from GitLab-CI rules

marshallward
authored and
adcroft
committed
+Add mask_edges argument to interpolate_column

Hallberg-NOAA
authored and
marshallward
committed
+Add ALE_remap_interface_vals and ALE_remap_vertex_vals

Hallberg-NOAA
authored and
marshallward
committed
+Add REMAP_AUXILIARY_VARS to remap accelerations

Hallberg-NOAA
authored and
marshallward
committed
Option to read horizontally varying KHTH from file

NoraLoose
authored and
marshallward
committed
Allow KHTH_FILE directory to be set independently

NoraLoose
authored and
marshallward
committed
Add parameter that specifies name of khth variable in file

NoraLoose
authored and
marshallward
committed
Change terminology in comments

NoraLoose
authored and
marshallward
committed

Commits on Nov 23, 2022

+Correct reported units for 4 diagnostics

Hallberg-NOAA
authored and
marshallward
committed
(*)Rescale DENSE_WATER_EAST_SPONGE_SALT

Hallberg-NOAA
authored and
marshallward
committed

Commits on Nov 24, 2022

+Removed 31 meaningless get_param units

Hallberg-NOAA
authored and
marshallward
committed
.testing: Fix concurrency errors in tc4 rules
marshallward
committed

Commits on Nov 25, 2022

Merge pull request #255 from marshallward/tc4_rule_fixes
Hallberg-NOAA
authored
Better document parameter units in 4 user modules

Hallberg-NOAA
authored and
marshallward
committed
(*)Update remap_answer_date set in uninitialized types

Hallberg-NOAA
authored and
marshallward
committed

Commits on Nov 28, 2022

+Rossby_front_2d_init and BFB_init cleanup

Hallberg-NOAA
authored and
marshallward
committed
GitLab: Fix nolib build directories

marshallward
authored and
adcroft
committed

Commits on Nov 29, 2022

Document units in 9 vertical param modules

Hallberg-NOAA
authored and
adcroft
committed

Commits on Dec 3, 2022

Use small minimum ustar in mixed layer restratification

angus-g
authored and
Hallberg-NOAA
committed

Commits on Dec 7, 2022

Switch from mpich to openmpi

adcroft
authored and
marshallward
committed

Commits on Dec 8, 2022

Merge branch 'dev/ncar' into main_08Dec22
gustavo-marques
committed

Commits on Dec 9, 2022

Switch from mpich to openmpi

adcroft
authored and
gustavo-marques
committed
makedep PEP8 cleanup
marshallward
committed
makedep: Include C derived object files in list of "externals"

adcroft
authored and
marshallward
committed
makedep: PEP8 cleanup

adcroft
authored and
marshallward
committed

Commits on Dec 12, 2022

Commits on Dec 13, 2022

Commits on Dec 14, 2022

Merge pull request #229 from gustavo-marques/merge_main_08Dec22
alperaltuntas
authored
Make sure EBT structure is computed when desired

NoraLoose
authored and
marshallward
committed
+Add units to 11 log_param calls

Hallberg-NOAA
authored and
marshallward
committed

Commits on Dec 15, 2022

+Rescaled time variables in all MOM6 drivers

Hallberg-NOAA
authored and
marshallward
committed
+Rescaled real time arguments to step_MOM

Hallberg-NOAA
authored and
marshallward
committed
+Specify CVMix parameter units and rescale CVMix

Hallberg-NOAA
authored and
marshallward
committed

Commits on Dec 16, 2022

Only add runoff tracer flux to surface flux if it has not already been added

andrew-c-ross
authored and
Hallberg-NOAA
committed

Commits on Dec 18, 2022

*Fix new scaling bug in ML restrat minimum ustar

Hallberg-NOAA
authored and
marshallward
committed

Commits on Dec 19, 2022

+Add runtime params KV_RESTRAT & RESTRAT_USTAR_MIN

Hallberg-NOAA
authored and
marshallward
committed
(*)Correct two rescaling bugs in MOM_EOS

Hallberg-NOAA
authored and
marshallward
committed
+(*)Fix numerous issues with MOM_stoch_eos

Hallberg-NOAA
authored and
marshallward
committed
(*)Correct USE_STANLEY domain extents in EOS calls

Hallberg-NOAA
authored and
marshallward
committed
(*)Correct scaling of USE_STANLEY_PGF diagnostics

Hallberg-NOAA
authored and
marshallward
committed
(*)Test for inconsistent USE_STANLEY flags

Hallberg-NOAA
authored and
marshallward
committed
(*)Correct scaling of DT_OBC_SEG_UPDATE_OBGC

Hallberg-NOAA
authored and
marshallward
committed
Rescale interface heights for MOM_IC

Hallberg-NOAA
authored and
marshallward
committed
Unit descriptions in MOM_spherical_harmonics

Hallberg-NOAA
authored and
marshallward
committed
Correct scattered unit description syntax

Hallberg-NOAA
authored and
marshallward
committed
+Correct MOM_wave_interface unit descriptions

Hallberg-NOAA
authored and
marshallward
committed

Commits on Dec 20, 2022

(+)Correct units of INTERNAL_TIDE_SOURCE_X params

Hallberg-NOAA
authored and
marshallward
committed
+Standardize user module axis unit documentation

Hallberg-NOAA
authored and
marshallward
committed
+Document and rescale ISOMIP parameters

Hallberg-NOAA
authored and
marshallward
committed
+Standard seamount_initialization axis unit docs

Hallberg-NOAA
authored and
marshallward
committed
+Document units in Neverworld_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Document units in RGC_initialization & RGC_tracer

Hallberg-NOAA
authored and
marshallward
committed
+Document units in adjustment_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Rescale default salinity in dumbbell_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Document variable units in shelfwave_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Document units in dye_example

Hallberg-NOAA
authored and
marshallward
committed
Reorder i- and j-loops to be stride-1 in memory

Hallberg-NOAA
authored and
marshallward
committed

Commits on Dec 21, 2022

Made STANLEY_COEFF<0 warnings be fatal

adcroft
authored and
marshallward
committed
State-dependent options for diag coordinates

ashao
authored and
adcroft
committed
Ensure ref_pressure propagates to RHO/HYCOM CS

ashao
authored and
adcroft
committed
Update diagnostic P_REF description

ashao
authored and
adcroft
committed

Commits on Dec 22, 2022

POSIX: siglongjmp and sigsetjmp_missing fixes
marshallward
committed

Commits on Dec 23, 2022

Add GL90 parameterization for stacked shallow water (#268)
NoraLoose
authored
Rescale internal vars in reset_face_lengths_list

Hallberg-NOAA
authored and
marshallward
committed
Merge pull request #233 from marshallward/siglongjmp_name_fix
alperaltuntas
authored
(+)Better units documentation in tracer_hordiff

Hallberg-NOAA
authored and
marshallward
committed
Rescale input fields in MOM_tidal_mixing

Hallberg-NOAA
authored and
marshallward
committed
Rescale diagnostics from MOM_CVMix_KPP

Hallberg-NOAA
authored and
marshallward
committed
Avoid using the unscaled argument to MOM_get_param

Hallberg-NOAA
authored and
marshallward
committed

Commits on Dec 29, 2022

Commits on Dec 30, 2022

makedep: Include object file dependencies

marshallward
authored and
Hallberg-NOAA
committed

Commits on Jan 3, 2023

Commits on Jan 4, 2023

+Pass ocean_grid_type to call_tracer_register

Hallberg-NOAA
authored and
marshallward
committed

Commits on Jan 5, 2023

+Add runtime parameters for benchmark_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameters for DOME2d_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameters for sloshing_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameters for DOME_initialization

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter MIN_DZ_FOR_SLOPE_N2

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter EN_CHECK_TOLERANCE

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter MEKE_LSCALE_MAX_VAL

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter MEKE_MIN_DEPTH_DIFF

Hallberg-NOAA
authored and
marshallward
committed
(*)Require dz_subML to calculate the sub-ML N2

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter KD_SEED_KAPPA_SHEAR

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter ENTRAIN_DIFFUSIVE_MAX_ENT

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter KPP_LT_MLD_GUESS_MIN

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter REG_SFC_SUFFICIENT_ADJ

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter SALT_EXTRACTION_LIMIT

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter MECH_TKE_FLOOR

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter VARYING_SPONGE_MASK_THICKNESS

Hallberg-NOAA
authored and
marshallward
committed

Commits on Jan 7, 2023

Standardize the output of tiny real values

Hallberg-NOAA
authored and
marshallward
committed
*+Use runtime params in adjustment_initialization

Hallberg-NOAA
authored and
marshallward
committed

Commits on Jan 9, 2023

Remove La_SL from wave_parameters_CS

Hallberg-NOAA
authored and
marshallward
committed
+Add 3 Charnock coefficient runtime parameters

Hallberg-NOAA
authored and
marshallward
committed
+Add LANGMUIR_STOKES_BACKGROUND runtime parameter

Hallberg-NOAA
authored and
marshallward
committed
+Add WAVE_INTERFACE_ANSWER_DATE runtime parameter

Hallberg-NOAA
authored and
marshallward
committed
+Make get_StokesSL_LiFoxKemper more robust

Hallberg-NOAA
authored and
marshallward
committed
+Make Update_Stokes_Drift more robust

Hallberg-NOAA
authored and
marshallward
committed
+Eliminate wave_parameters_CS%StkLevelMode

Hallberg-NOAA
authored and
marshallward
committed
+Renamed internal Cd variables

Hallberg-NOAA
authored and
marshallward
committed
Add GL90 diagnostics (#293)
NoraLoose
authored
fix gnu restart issue by removing leading spaces in restartfiles list
alperaltuntas
committed

Commits on Jan 10, 2023

Merge pull request #234 from alperaltuntas/fix_gnu_restart
gustavo-marques
authored

Commits on Jan 12, 2023

Commits on Jan 13, 2023

+Add DOME_tracer and tracer_example runtime params

Hallberg-NOAA
authored and
marshallward
committed

Commits on Jan 16, 2023

update more write units to stdout in mom6 nuopc cap and let only rootpe write logs.
alperaltuntas
committed

Commits on Jan 18, 2023

Named argument assignment white-space clean-up

Hallberg-NOAA
authored and
marshallward
committed
Merge pull request #231 from jedwards4b/cesm_logging_improvements
alperaltuntas
authored
+Make z_tol arg non-optional to cut_off_column_top

Hallberg-NOAA
authored and
marshallward
committed
Revise tc4/MOM_input with updated parameter names

Hallberg-NOAA
authored and
marshallward
committed
+Obsoleted the runtime parameter NEW_SPONGES

Hallberg-NOAA
authored and
marshallward
committed
Updated comments in MOM_initialize_topography

Hallberg-NOAA
authored and
marshallward
committed
Added units to comments in MOM_grid_initialization

Hallberg-NOAA
authored and
marshallward
committed
Document units of variables in MOM_wave_speed

Hallberg-NOAA
authored and
marshallward
committed
+Add runtime parameter INTERNAL_WAVE_CG1_THRESH

Hallberg-NOAA
authored and
marshallward
committed

Commits on Jan 22, 2023

Add KE_visc_gl90 diagnostic (#305)
NoraLoose
authored

Commits on Jan 27, 2023

Generic I/O layer for infra and netCDF

marshallward
authored and
Hallberg-NOAA
committed

Commits on Jan 28, 2023

pipeline: compile preproc executables on login nodes

adcroft
authored and
marshallward
committed
.testing: Add WORKSPACE cpp macro to control scratch space

adcroft
authored and
marshallward
committed
pipeline: Show list of PASSes

adcroft
authored and
marshallward
committed
+(*)Use reproducing sums to homogenize fields

Hallberg-NOAA
authored and
marshallward
committed

Commits on Jan 31, 2023

(*)Corrected the units of VarMix_CS%slope_x

Hallberg-NOAA
authored and
marshallward
committed
Cancel out rescaling factors in wave_speed

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 1, 2023

Use rescaled variables for global mean T & S diags

Hallberg-NOAA
authored and
marshallward
committed
+Add optional unscale argument to check_redundant

Hallberg-NOAA
authored and
marshallward
committed
Use unscale args to check_redundant calls

Hallberg-NOAA
authored and
marshallward
committed
Document units of variables in MOM_spatial_means

Hallberg-NOAA
authored and
marshallward
committed
Document units of variables in MOM_checksums

Hallberg-NOAA
authored and
marshallward
committed
Document units of arguments in MOM_io

Hallberg-NOAA
authored and
marshallward
committed
Document units of arguments in MOM_restart

Hallberg-NOAA
authored and
marshallward
committed
Document units of arguments in MOM_array_transform

Hallberg-NOAA
authored and
marshallward
committed
Revise argument units in MOM_horizontal_regridding

Hallberg-NOAA
authored and
marshallward
committed
Document units of invcosh and its argument

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 2, 2023

Document units of variables in MOM_energetic_PBL

Hallberg-NOAA
authored and
marshallward
committed
Document units of variables in MOM_diapyc_energy_req

Hallberg-NOAA
authored and
marshallward
committed
Document units of 16 variables in MOM_opacity

Hallberg-NOAA
authored and
marshallward
committed
Document units of 21 variables in MOM_bulk_mixed_layer

Hallberg-NOAA
authored and
marshallward
committed
Clean up of a get_param call in vertvisc_init

Hallberg-NOAA
authored and
marshallward
committed
Document units of 14 variables in MOM_tidal_mixing

Hallberg-NOAA
authored and
marshallward
committed
Document units of a variable in MOM_ALE_sponge

Hallberg-NOAA
authored and
marshallward
committed
Document units of a variable in MOM_kappa_shear

Hallberg-NOAA
authored and
marshallward
committed
Document units of an argument to find_maxF_kb

Hallberg-NOAA
authored and
marshallward
committed
Document units of 2 variables in MOM_CVMix_KPP

Hallberg-NOAA
authored and
marshallward
committed
Document units of 3 variables in MOM_CVMix_conv

Hallberg-NOAA
authored and
marshallward
committed
Document units of a variable in MOM_bkgnd_mixing

Hallberg-NOAA
authored and
marshallward
committed
Document units of a variable in MOM_regularize_layers

Hallberg-NOAA
authored and
marshallward
committed
Document units of a variable in MOM_set_viscosity

Hallberg-NOAA
authored and
marshallward
committed
Document units of 7 variables in MOM_sponge

Hallberg-NOAA
authored and
marshallward
committed
Document units of variables in MOM_internal_tides

Hallberg-NOAA
authored and
marshallward
committed
Document units of variables in MOM_tidal_forcing

Hallberg-NOAA
authored and
marshallward
committed
Better terminology in thickness_diffuse module

Hallberg-NOAA
authored and
marshallward
committed
(*)Fix MEKE scaling issues with SmartRedis options

Hallberg-NOAA
authored and
marshallward
committed
Document units of 75 scattered variables

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 3, 2023

Document units of about 250 EOS variables

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 8, 2023

Merge branch 'main' into dev/gfdl
marshallward
committed

Commits on Feb 10, 2023

Fixes build failure in gitlab pipeline

adcroft
authored and
marshallward
committed

Commits on Feb 11, 2023

+Make output reproduce across layout if DEBUG=True

Hallberg-NOAA
authored and
marshallward
committed
Document units of 30 driver variables

Hallberg-NOAA
authored and
marshallward
committed
Document units of 172 MOM_EOS_NEMO variables

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 13, 2023

+Add optional unscale argument to log_param_real

Hallberg-NOAA
authored and
marshallward
committed
Use unscale argument in 10 log_param calls

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 15, 2023

(*)Fix bug in CVMix_shear_is_used if USE_PP81=True

Hallberg-NOAA
authored and
marshallward
committed

Commits on Feb 19, 2023

Direct netCDF data reads

marshallward
authored and
Hallberg-NOAA
committed

Commits on Feb 24, 2023

Autoconf configuration of Python

marshallward
authored and
Hallberg-NOAA
committed

Commits on Feb 28, 2023

reopen_MOM_file explicitly runs on root PE

marshallward
authored and
adcroft
committed
GitLab: Extend run test timeouts
marshallward
committed

Commits on Mar 1, 2023

Commits on Mar 2, 2023

Commits on Mar 3, 2023

(*)Fix a bug with BULKMIXEDLAYER & ML_MIX_FIRST>0

Hallberg-NOAA
authored and
marshallward
committed
Only root_PE makes write_energy netcdf file calls

Hallberg-NOAA
authored and
marshallward
committed

Commits on Mar 6, 2023

Commits on Mar 17, 2023

remove inadvertent reassignment of layer_frac
alperaltuntas
committed

Commits on Mar 26, 2023

Fix indexing bugs in get_field_nc (#334)

Hallberg-NOAA
and
marshallward
authored

Commits on Mar 30, 2023

Add PPM_CM and HYCOM1_ONLY_IMPROVES

awallcraft
authored and
marshallward
committed

Commits on Apr 1, 2023

+Update check_MOM6_scaling_factors with C and S

Hallberg-NOAA
authored and
marshallward
committed

Commits on Apr 3, 2023

Commits on Apr 5, 2023

Commits on Apr 29, 2023

Reversion of MOM_mixed_layer_restrat growth_time

marshallward
authored and
Hallberg-NOAA
committed

Commits on May 4, 2023

Merge pull request #1599 from NOAA-GFDL/dev-gfdl-main-candidate-2023-04-06
marshallward
authored