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Merge changes from GFDL to main (2023-04-06) #249

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merged 197 commits into from
Jul 7, 2023
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2ba1af1
+Created remapping_attic.F90
Hallberg-NOAA Oct 23, 2022
f937288
+Move interpolate_column to MOM_remapping.F90
Hallberg-NOAA Oct 23, 2022
1faf2a8
+Remove missing_value arg to interpolate_column
Hallberg-NOAA Oct 23, 2022
b525932
Add check_remapped_values
Hallberg-NOAA Oct 23, 2022
bc01d95
gitlab-ci: Adds (command-line) tool to simplify .gitlab-ci.yml
adcroft Aug 31, 2022
f95a5ff
Bug fix for categorize_axes causing crash
nikizadehgfdl Oct 17, 2022
7d9bf03
Bug fix for categorize_axes causing crash
nikizadehgfdl Oct 18, 2022
e26d8da
Avoid an uninitialized string in categorize_axes
Hallberg-NOAA Oct 28, 2022
82cbb09
(*)Simplify interpolate_column weight calculations
Hallberg-NOAA Oct 25, 2022
d46de87
Autoconf: Fortran-netCDF C compatibility test
marshallward Nov 3, 2022
522e7aa
Autoconf: Fortran testing of C bindings
marshallward Nov 9, 2022
9d5a320
Obc setup plus segment update period (#198)
nikizadehgfdl Nov 10, 2022
f92a4ab
Ice dynamics (#228)
OlgaSergienko Nov 11, 2022
2623242
Merge branch 'main' into main_to_dev
marshallward Nov 15, 2022
f1fe63d
Merge pull request #242 from NOAA-GFDL/main_to_dev
Hallberg-NOAA Nov 16, 2022
2b03f95
+Set input file variable names via runtime params
Hallberg-NOAA Nov 7, 2022
530cd58
+Set more input file variable names at runtime
Hallberg-NOAA Nov 14, 2022
08c9aa1
*Fix bug with TIDAL_ENERGY_TYPE = "ER03"
Hallberg-NOAA Nov 7, 2022
2ef7ba1
.testing: Use Fortran to generate tc inputs
marshallward Nov 17, 2022
56cf125
Remove Python venv setup from GitLab-CI rules
marshallward Nov 21, 2022
b918b2a
+Add mask_edges argument to interpolate_column
Hallberg-NOAA Oct 25, 2022
14f9482
+Add ALE_remap_interface_vals and ALE_remap_vertex_vals
Hallberg-NOAA Oct 26, 2022
aa44c32
+Add REMAP_AUXILIARY_VARS to remap accelerations
Hallberg-NOAA Nov 18, 2022
f162e6f
Option to read horizontally varying KHTH from file
NoraLoose Nov 11, 2022
ca44692
Allow KHTH_FILE directory to be set independently
NoraLoose Nov 14, 2022
ca7207e
Add parameter that specifies name of khth variable in file
NoraLoose Nov 14, 2022
2070175
Change terminology in comments
NoraLoose Nov 14, 2022
6eab2b6
+Correct reported units for 4 diagnostics
Hallberg-NOAA Nov 14, 2022
6765e27
(*)Rescale DENSE_WATER_EAST_SPONGE_SALT
Hallberg-NOAA Nov 15, 2022
321e0eb
+Removed 31 meaningless get_param units
Hallberg-NOAA Nov 15, 2022
7a962e5
.testing: Fix concurrency errors in tc4 rules
marshallward Nov 23, 2022
571ddd9
Merge pull request #255 from marshallward/tc4_rule_fixes
Hallberg-NOAA Nov 25, 2022
6bf43d6
Better document parameter units in 4 user modules
Hallberg-NOAA Nov 15, 2022
2fa9f3a
(*)Update remap_answer_date set in uninitialized types
Hallberg-NOAA Nov 16, 2022
5431682
+Rossby_front_2d_init and BFB_init cleanup
Hallberg-NOAA Nov 18, 2022
798ba7a
GitLab: Fix nolib build directories
marshallward Nov 25, 2022
7055b7c
Document units in 9 vertical param modules
Hallberg-NOAA Nov 23, 2022
d01c42a
Use small minimum ustar in mixed layer restratification
angus-g Nov 21, 2022
e2ef845
Switch from mpich to openmpi
adcroft Dec 7, 2022
01242a7
makedep PEP8 cleanup
marshallward Sep 12, 2022
8f7b1fb
makedep: Include C derived object files in list of "externals"
adcroft Dec 9, 2022
9bc8772
makedep: PEP8 cleanup
adcroft Dec 9, 2022
3327037
Document units in 8 lat_param or diag modules
Hallberg-NOAA Nov 24, 2022
c933460
+Add 10 units arguments to get_param calls
Hallberg-NOAA Nov 29, 2022
0111d45
+Add x_ax_unit_short to ocean_grid_type
Hallberg-NOAA Nov 30, 2022
490bfca
Scale default parameters
Hallberg-NOAA Dec 3, 2022
c80db67
Make sure EBT structure is computed when desired
NoraLoose Dec 2, 2022
c6c84c8
+Add units to 11 log_param calls
Hallberg-NOAA Dec 2, 2022
74c0de6
+Rescaled time variables in all MOM6 drivers
Hallberg-NOAA Nov 30, 2022
60c1d7b
+Rescaled real time arguments to step_MOM
Hallberg-NOAA Nov 30, 2022
8ddd854
+Specify CVMix parameter units and rescale CVMix
Hallberg-NOAA Dec 2, 2022
5ef380c
Only add runoff tracer flux to surface flux if it has not already bee…
andrew-c-ross Nov 16, 2022
7173432
*Fix new scaling bug in ML restrat minimum ustar
Hallberg-NOAA Dec 4, 2022
8de33f9
+Add runtime params KV_RESTRAT & RESTRAT_USTAR_MIN
Hallberg-NOAA Dec 4, 2022
b2ba9d9
(*)Correct two rescaling bugs in MOM_EOS
Hallberg-NOAA Dec 7, 2022
5db4d0c
+(*)Fix numerous issues with MOM_stoch_eos
Hallberg-NOAA Dec 8, 2022
73add03
(*)Correct USE_STANLEY domain extents in EOS calls
Hallberg-NOAA Dec 8, 2022
50a2278
(*)Correct scaling of USE_STANLEY_PGF diagnostics
Hallberg-NOAA Dec 8, 2022
73b4ff9
(*)Test for inconsistent USE_STANLEY flags
Hallberg-NOAA Dec 8, 2022
5a8c333
(*)Correct scaling of DT_OBC_SEG_UPDATE_OBGC
Hallberg-NOAA Dec 8, 2022
674687c
Rescale interface heights for MOM_IC
Hallberg-NOAA Dec 8, 2022
52e0152
Unit descriptions in MOM_spherical_harmonics
Hallberg-NOAA Dec 9, 2022
bc28a13
Correct scattered unit description syntax
Hallberg-NOAA Dec 9, 2022
46a6159
+Correct MOM_wave_interface unit descriptions
Hallberg-NOAA Dec 9, 2022
92a1c3c
(+)Correct units of INTERNAL_TIDE_SOURCE_X params
Hallberg-NOAA Dec 2, 2022
92af13f
+Standardize user module axis unit documentation
Hallberg-NOAA Dec 15, 2022
e410a93
+Document and rescale ISOMIP parameters
Hallberg-NOAA Dec 15, 2022
12fba70
+Standard seamount_initialization axis unit docs
Hallberg-NOAA Dec 15, 2022
595c8b0
+Document units in Neverworld_initialization
Hallberg-NOAA Dec 15, 2022
17def80
+Document units in RGC_initialization & RGC_tracer
Hallberg-NOAA Dec 15, 2022
1b00485
+Document units in adjustment_initialization
Hallberg-NOAA Dec 15, 2022
09d2adf
+Rescale default salinity in dumbbell_initialization
Hallberg-NOAA Dec 15, 2022
e306cbb
+Document variable units in shelfwave_initialization
Hallberg-NOAA Dec 15, 2022
dba12c1
+Document units in dye_example
Hallberg-NOAA Dec 15, 2022
022531c
Reorder i- and j-loops to be stride-1 in memory
Hallberg-NOAA Dec 17, 2022
43fd2e1
Made STANLEY_COEFF<0 warnings be fatal
adcroft Dec 19, 2022
8e603a1
State-dependent options for diag coordinates
ashao Oct 22, 2022
ced34c5
Ensure ref_pressure propagates to RHO/HYCOM CS
ashao Nov 23, 2022
053752d
Update diagnostic P_REF description
ashao Dec 20, 2022
7869030
Add GL90 parameterization for stacked shallow water (#268)
NoraLoose Dec 23, 2022
747eeff
Rescale internal vars in reset_face_lengths_list
Hallberg-NOAA Dec 16, 2022
3794b83
(+)Better units documentation in tracer_hordiff
Hallberg-NOAA Dec 16, 2022
5a80ec8
Rescale input fields in MOM_tidal_mixing
Hallberg-NOAA Dec 12, 2022
ab68e60
Rescale diagnostics from MOM_CVMix_KPP
Hallberg-NOAA Dec 12, 2022
3310ee3
Avoid using the unscaled argument to MOM_get_param
Hallberg-NOAA Dec 18, 2022
ec7a57f
+Add runtime parameters for MOM_wave_interface
Hallberg-NOAA Dec 21, 2022
775050b
+Add runtime parameter for dumbbell_initialization
Hallberg-NOAA Dec 28, 2022
bd0cd8a
+Add runtime parameters for Kelvin_initialization
Hallberg-NOAA Dec 28, 2022
40c24c5
+Add runtime parameters for tidal_bay_initialization
Hallberg-NOAA Dec 28, 2022
47fa47e
makedep: Include object file dependencies
marshallward Dec 20, 2022
5f1572f
+Revise interfaces to horiz_interp_and_extract
Hallberg-NOAA Dec 19, 2022
31cb517
+Add 7 runtime variables for hard-coded tolerances
Hallberg-NOAA Dec 19, 2022
39f45f0
Document the units of variables in MOM_ALE_sponge
Hallberg-NOAA Dec 19, 2022
19e268d
+Add 11 runtime params for determine_temperature
Hallberg-NOAA Dec 20, 2022
e198296
+Add 2 runtime params for ice shelf temperatures
Hallberg-NOAA Dec 20, 2022
f86d762
+Pass ocean_grid_type to call_tracer_register
Hallberg-NOAA Dec 16, 2022
78da778
+Add runtime parameters for benchmark_initialization
Hallberg-NOAA Dec 23, 2022
9fd2bd0
+Add runtime parameters for DOME2d_initialization
Hallberg-NOAA Dec 23, 2022
f1aed77
+Add runtime parameters for sloshing_initialization
Hallberg-NOAA Dec 23, 2022
8fa8f31
+Add runtime parameters for DOME_initialization
Hallberg-NOAA Dec 23, 2022
9102dbe
+Add runtime parameter MIN_DZ_FOR_SLOPE_N2
Hallberg-NOAA Dec 28, 2022
9045712
+Add runtime parameter EN_CHECK_TOLERANCE
Hallberg-NOAA Dec 28, 2022
ecfe8e5
+Add runtime parameter MEKE_LSCALE_MAX_VAL
Hallberg-NOAA Dec 28, 2022
17ae97b
+Add runtime parameter MEKE_MIN_DEPTH_DIFF
Hallberg-NOAA Dec 28, 2022
f4c0bc1
(*)Require dz_subML to calculate the sub-ML N2
Hallberg-NOAA Dec 28, 2022
391ddba
+Add runtime parameter KD_SEED_KAPPA_SHEAR
Hallberg-NOAA Dec 28, 2022
1db93d3
+Add runtime parameter ENTRAIN_DIFFUSIVE_MAX_ENT
Hallberg-NOAA Dec 28, 2022
42051fc
+Add runtime parameter KPP_LT_MLD_GUESS_MIN
Hallberg-NOAA Dec 29, 2022
4e5f740
+Add runtime parameter REG_SFC_SUFFICIENT_ADJ
Hallberg-NOAA Jan 3, 2023
44f4be4
+Add runtime parameter SALT_EXTRACTION_LIMIT
Hallberg-NOAA Jan 3, 2023
7e2c427
+Add runtime parameter MECH_TKE_FLOOR
Hallberg-NOAA Jan 3, 2023
3cecac4
+Add runtime parameter VARYING_SPONGE_MASK_THICKNESS
Hallberg-NOAA Jan 3, 2023
d7d1351
Standardize the output of tiny real values
Hallberg-NOAA Jan 6, 2023
ca72fcc
*+Use runtime params in adjustment_initialization
Hallberg-NOAA Dec 23, 2022
b3633f5
Remove La_SL from wave_parameters_CS
Hallberg-NOAA Jan 1, 2023
8201db4
+Add 3 Charnock coefficient runtime parameters
Hallberg-NOAA Jan 1, 2023
cfc2ed9
+Add LANGMUIR_STOKES_BACKGROUND runtime parameter
Hallberg-NOAA Jan 1, 2023
85fffee
+Add WAVE_INTERFACE_ANSWER_DATE runtime parameter
Hallberg-NOAA Jan 1, 2023
5047692
+Make get_StokesSL_LiFoxKemper more robust
Hallberg-NOAA Jan 1, 2023
6096166
+Make Update_Stokes_Drift more robust
Hallberg-NOAA Jan 1, 2023
758c792
+Eliminate wave_parameters_CS%StkLevelMode
Hallberg-NOAA Jan 2, 2023
78c91cd
+Renamed internal Cd variables
Hallberg-NOAA Jan 7, 2023
3f57d75
Add GL90 diagnostics (#293)
NoraLoose Jan 9, 2023
1d918b6
Updates to ODA driver suggested by @Hallberg-NOAA Issue#277 (#297)
MJHarrison-GFDL Jan 12, 2023
237194d
+Add DOME_tracer and tracer_example runtime params
Hallberg-NOAA Jan 4, 2023
54b0701
Named argument assignment white-space clean-up
Hallberg-NOAA Jan 4, 2023
3a9f6c7
+Make z_tol arg non-optional to cut_off_column_top
Hallberg-NOAA Jan 4, 2023
68aefe1
Revise tc4/MOM_input with updated parameter names
Hallberg-NOAA Jan 5, 2023
a3ef1ac
+Obsoleted the runtime parameter NEW_SPONGES
Hallberg-NOAA Jan 5, 2023
3f82a92
Updated comments in MOM_initialize_topography
Hallberg-NOAA Jan 5, 2023
4be437a
Added units to comments in MOM_grid_initialization
Hallberg-NOAA Jan 5, 2023
297cc89
Document units of variables in MOM_wave_speed
Hallberg-NOAA Jan 9, 2023
b9daf2f
+Add runtime parameter INTERNAL_WAVE_CG1_THRESH
Hallberg-NOAA Jan 9, 2023
c60aff1
Add KE_visc_gl90 diagnostic (#305)
NoraLoose Jan 22, 2023
321ee0b
Generic I/O layer for infra and netCDF
marshallward Oct 25, 2022
b7e5b33
pipeline: compile preproc executables on login nodes
adcroft Jan 13, 2023
86c3954
.testing: Add WORKSPACE cpp macro to control scratch space
adcroft Jan 13, 2023
1fe52f7
pipeline: Show list of PASSes
adcroft Jan 13, 2023
b22617c
+(*)Use reproducing sums to homogenize fields
Hallberg-NOAA Jan 7, 2023
3348172
(*)Corrected the units of VarMix_CS%slope_x
Hallberg-NOAA Jan 25, 2023
0b857c0
Cancel out rescaling factors in wave_speed
Hallberg-NOAA Jan 28, 2023
1a51c50
Use rescaled variables for global mean T & S diags
Hallberg-NOAA Jan 7, 2023
f3b1a61
+Add optional unscale argument to check_redundant
Hallberg-NOAA Jan 31, 2023
09880a8
Use unscale args to check_redundant calls
Hallberg-NOAA Jan 31, 2023
915679d
Document units of variables in MOM_spatial_means
Hallberg-NOAA Jan 10, 2023
ff15a76
Document units of variables in MOM_checksums
Hallberg-NOAA Jan 31, 2023
0ab7744
Document units of arguments in MOM_io
Hallberg-NOAA Jan 31, 2023
15ce275
Document units of arguments in MOM_restart
Hallberg-NOAA Jan 31, 2023
6c34e7f
Document units of arguments in MOM_array_transform
Hallberg-NOAA Jan 31, 2023
94f97a5
Revise argument units in MOM_horizontal_regridding
Hallberg-NOAA Jan 31, 2023
a3b61c8
Document units of invcosh and its argument
Hallberg-NOAA Jan 31, 2023
19f683d
Document units of variables in MOM_energetic_PBL
Hallberg-NOAA Jan 3, 2023
cd9ef0a
Document units of variables in MOM_diapyc_energy_req
Hallberg-NOAA Jan 21, 2023
7a9d151
Document units of 16 variables in MOM_opacity
Hallberg-NOAA Jan 23, 2023
9054939
Document units of 21 variables in MOM_bulk_mixed_layer
Hallberg-NOAA Jan 23, 2023
05c2983
Clean up of a get_param call in vertvisc_init
Hallberg-NOAA Jan 23, 2023
f9649d3
Document units of 14 variables in MOM_tidal_mixing
Hallberg-NOAA Jan 23, 2023
6927909
Document units of a variable in MOM_ALE_sponge
Hallberg-NOAA Jan 23, 2023
536d649
Document units of a variable in MOM_kappa_shear
Hallberg-NOAA Jan 23, 2023
5c28263
Document units of an argument to find_maxF_kb
Hallberg-NOAA Jan 23, 2023
6f5c2f4
Document units of 2 variables in MOM_CVMix_KPP
Hallberg-NOAA Jan 23, 2023
9f53a8e
Document units of 3 variables in MOM_CVMix_conv
Hallberg-NOAA Jan 23, 2023
b29ed5c
Document units of a variable in MOM_bkgnd_mixing
Hallberg-NOAA Jan 23, 2023
aa0ec8c
Document units of a variable in MOM_regularize_layers
Hallberg-NOAA Jan 23, 2023
fdab7fd
Document units of a variable in MOM_set_viscosity
Hallberg-NOAA Jan 23, 2023
cf846eb
Document units of 7 variables in MOM_sponge
Hallberg-NOAA Jan 23, 2023
7e7b279
Document units of variables in MOM_internal_tides
Hallberg-NOAA Jan 23, 2023
e85260a
Document units of variables in MOM_tidal_forcing
Hallberg-NOAA Jan 30, 2023
a139bc4
Better terminology in thickness_diffuse module
Hallberg-NOAA Jan 30, 2023
f6b4a7d
(*)Fix MEKE scaling issues with SmartRedis options
Hallberg-NOAA Jan 23, 2023
454c5c6
Document units of 75 scattered variables
Hallberg-NOAA Jan 28, 2023
cab1e84
Document units of about 250 EOS variables
Hallberg-NOAA Jan 29, 2023
168305f
Merge branch 'main' into dev/gfdl
marshallward Feb 8, 2023
9412c9a
Fixes build failure in gitlab pipeline
adcroft Feb 10, 2023
6ffbc90
+Make output reproduce across layout if DEBUG=True
Hallberg-NOAA Jan 28, 2023
8b528fd
Document units of 30 driver variables
Hallberg-NOAA Jan 30, 2023
2b46275
Document units of 172 MOM_EOS_NEMO variables
Hallberg-NOAA Feb 4, 2023
f54956e
+Add optional unscale argument to log_param_real
Hallberg-NOAA Feb 6, 2023
ad56b29
Use unscale argument in 10 log_param calls
Hallberg-NOAA Feb 6, 2023
2fe2631
(*)Fix bug in CVMix_shear_is_used if USE_PP81=True
Hallberg-NOAA Feb 8, 2023
4c3b409
Direct netCDF data reads
marshallward Feb 2, 2023
37b030a
Autoconf configuration of Python
marshallward Feb 16, 2023
5f62858
reopen_MOM_file explicitly runs on root PE
marshallward Feb 23, 2023
6dc4de6
GitLab: Extend run test timeouts
marshallward Feb 28, 2023
00854d0
+Correct units in 1 get_param call and 64 comments
Hallberg-NOAA Feb 17, 2023
7af22d6
Merge branch 'main' into dev/gfdl
marshallward Mar 2, 2023
348d7b7
(*)Fix a bug with BULKMIXEDLAYER & ML_MIX_FIRST>0
Hallberg-NOAA Feb 24, 2023
ceb4c92
Only root_PE makes write_energy netcdf file calls
Hallberg-NOAA Feb 28, 2023
37389b5
Fix indexing bugs in get_field_nc (#334)
Hallberg-NOAA Mar 26, 2023
588cf03
Add PPM_CM and HYCOM1_ONLY_IMPROVES
awallcraft Mar 19, 2023
1bb66a4
+Update check_MOM6_scaling_factors with C and S
Hallberg-NOAA Feb 20, 2023
19f8613
+(*)Remove coord_SLight
Hallberg-NOAA Mar 13, 2023
a6f813e
(*)Fix MOM_calc_grad_Coriolis GLOBAL_INDEXING bug
Hallberg-NOAA Mar 13, 2023
fc823f5
Merge branch 'main' into merge_main_20230405
marshallward Apr 5, 2023
ac11984
Reversion of MOM_mixed_layer_restrat growth_time
marshallward Apr 26, 2023
400bd21
Merge pull request #1599 from NOAA-GFDL/dev-gfdl-main-candidate-2023-…
marshallward May 4, 2023
3c457c3
Merge branch 'dev/ncar' into merge_main_20230406
gustavo-marques Jul 7, 2023
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2 changes: 1 addition & 1 deletion .github/actions/macos-setup/action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ runs:
shell: bash
run: |
echo "::group::Install packages"
brew update
brew reinstall gcc
brew install automake
brew install netcdf
brew install netcdf-fortran
Expand Down
12 changes: 0 additions & 12 deletions .github/actions/testing-setup/action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,6 @@ inputs:
description: 'If true, will build the symmetric MOM6 executable'
required: false
default: 'true'
install_python:
description: 'If true, will install the local python env needed for .testing'
required: false
default: 'true'
runs:
using: 'composite'
steps:
Expand Down Expand Up @@ -54,14 +50,6 @@ runs:
test ${{ inputs.build_symmetric }} == true && make build/symmetric/MOM6 -j
echo "::endgroup::"

- name: Install local python venv for generating input data
shell: bash
run: |
echo "::group::Create local python env for input data generation"
cd .testing
test ${{ inputs.install_python }} == true && make work/local-env
echo "::endgroup::"

- name: Set flags
shell: bash
run: |
Expand Down
1 change: 0 additions & 1 deletion .github/workflows/coupled-api.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@ jobs:
- uses: ./.github/actions/testing-setup
with:
build_symmetric: 'false'
install_python: 'false'

- name: Compile MOM6 for the GFDL coupled driver
shell: bash
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/macos-regression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@ jobs:
runs-on: macOS-latest

env:
CC: gcc-11
FC: gfortran-11
CC: gcc
FC: gfortran

defaults:
run:
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/macos-stencil.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@ jobs:
runs-on: macOS-latest

env:
CC: gcc-11
FC: gfortran-11
CC: gcc
FC: gfortran

defaults:
run:
Expand Down
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