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GFDL to main (2024-11-27) #1647

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70bfe8f
Spatially variable fields for MLE%Bodner (#617)
kshedstrom Jun 2, 2024
b610226
Flux through static ice-shelf to icebergs/new diagnostics (#622)
alex-huth Jun 2, 2024
d8e714e
+(*)Refactor Idealize_Hurricane
Hallberg-NOAA Apr 5, 2024
9059671
Add rescaling parameter to kappa shear (#643)
theresa-morrison Jun 3, 2024
f0badc6
Prestore axes_data in set_up_ALE_sponge_field
yichengt900 May 29, 2024
08a6106
+Add ROBUST_STOKES_PGF and LA_MISALIGNMENT_BUG
Hallberg-NOAA May 29, 2024
e58b95f
Ice-shelf dynamics updates
alex-huth Jan 18, 2024
7ccea2a
Add units to the descriptions of 79 variables
Hallberg-NOAA Apr 28, 2024
b389a89
+(*)Fix sign of neutral_slope_x diag with no EOS
Hallberg-NOAA May 15, 2024
d6500bc
+Add DETERMINE_TEMP_CONVERGENCE_BUG parameter
Hallberg-NOAA May 27, 2024
9ab5f34
(*)Fix Kd_interface diag in newer diabatic_ALE
Hallberg-NOAA May 16, 2024
270ba59
+(*)Fix rotation of coupler_type variables
Hallberg-NOAA May 17, 2024
b56a640
Deallocate eta_av_bc in MOM_end()
herrwang0 May 6, 2024
8521222
Fix warning message indices in MOM_barotropic
herrwang0 May 16, 2024
a296080
Normalize wt_[uv] in MOM_barotropic
herrwang0 May 16, 2024
66e8891
Use dt for vertvisc_remnant() in predictor
herrwang0 May 16, 2024
337ee73
Fix a typo in USE_CONT_THICKNESS description
herrwang0 May 17, 2024
1d2911f
Remove visc_rem from h_[uv] in continuity solver
herrwang0 May 22, 2024
09774d4
Use Adcroft_reciprocal for Iwt_[uv]_tot
herrwang0 Jun 3, 2024
215b960
Refactor PressureForce_FV before ice shelf fixes
Hallberg-NOAA May 12, 2024
31afce0
(*)Avoid diagnostic seg fault in a 10km deep ocean
Hallberg-NOAA May 16, 2024
36dda7e
+Add BACKSCATTER_UNDERBOUND
Hallberg-NOAA May 29, 2024
f798796
Correct the computation of FrictWork in MOM_hor_visc
Wendazhang33 Jun 20, 2024
9351353
CI: parse_perf.py bugfix
marshallward Jun 3, 2024
10f4312
Cleaned up MOM_remapping to reduce compiler warnings
adcroft Mar 12, 2024
b4e3c64
Add timings_tests/time_MOM_remapping
adcroft Mar 22, 2024
a8105af
Added drivers/unit_tests/test_MOM_remapping.F90
adcroft Mar 26, 2024
622651b
Re-factored remapping_unit_tests()
adcroft Mar 27, 2024
b262955
Refactor/split remap_via_sub_cells() adding intersect_src_tgt_grids()
adcroft Mar 12, 2024
11c50db
Refactor/split remap_via_sub_cells() adding remap_src_to_sub_grid()
adcroft Mar 12, 2024
99363e4
Removed debugging from remap_via_sub_cells() in MOM_remapping.F90
adcroft Apr 2, 2024
40e6d6d
Last refactor of remap_via_sub_cells() adding remap_sub_to_tgt_grid()
adcroft Apr 11, 2024
88d9eb7
Fix remapping of last layer for mismatched ocean depths
adcroft May 22, 2024
7cea6dd
Replace kind=8 with iso_fortran_env kinds
marshallward Jun 4, 2024
f596c81
+(*)Fix problems with generic_tracer_min_max
Hallberg-NOAA Apr 30, 2024
ac9d6a4
Autoconf: Disable LDFLAGS for C testing (#674)
marshallward Jul 9, 2024
659d19b
(*)Fix bug in rotate_ALE_sponge for fixed sponges
Hallberg-NOAA Jun 6, 2024
f8f127c
+Renamed myStats scale argument to unscale
Hallberg-NOAA Jun 7, 2024
c4a72df
+Add a better variant of add_LOTW_BBL_diffusivity
Hallberg-NOAA Jun 9, 2024
e9f59c2
+Add optional unscale arguments to checksums
Hallberg-NOAA Jun 5, 2024
2f2b790
+Add optional unscale arguments to MOM_write_field
Hallberg-NOAA Jun 6, 2024
c5e5e30
Better error messages in interp_for_nondim_pos
Hallberg-NOAA May 29, 2024
b4c91e3
Correct 10 do-loop index cases
Hallberg-NOAA Jul 6, 2024
12af900
Use unscale arguments in 384 checksum calls
Hallberg-NOAA Jun 5, 2024
2c1a9d3
+Add and use query_debugging_checks
Hallberg-NOAA Jul 12, 2024
85c72b8
Inline harmonic analysis
c2xu Jun 12, 2024
caae653
Inline harmonic analysis
c2xu Jul 23, 2024
0440ed4
Perform unit conversion for internal heat only when it is applicable
yichengt900 Jul 19, 2024
a8d43f7
Adding Bodner reference
kshedstrom Jul 23, 2024
d76926c
Failing attempt to link to mle docs.
kshedstrom Jul 23, 2024
780d931
Two more references
kshedstrom Jul 23, 2024
ec40a7c
Working on documentation links
kshedstrom Jul 24, 2024
0e17b73
Added Young reference
kshedstrom Jul 24, 2024
369d716
Fix line length in comment
kshedstrom Jul 24, 2024
86b4c85
Delete duplicate entry
kshedstrom Jul 24, 2024
fb40a4a
Another duplicate bib entry
kshedstrom Jul 24, 2024
4fa86fd
Another duplicate ref
kshedstrom Jul 25, 2024
d93f8bf
Clean out another duplicate ref.
kshedstrom Jul 25, 2024
078ec30
Fix the Accad ref.
kshedstrom Jul 25, 2024
da3ec99
still cleaning the docs
kshedstrom Jul 25, 2024
b7fee4d
Fix case
kshedstrom Jul 26, 2024
4f1ecf4
Cleaning up tides section
kshedstrom Jul 26, 2024
1b39d07
*+Fix non-Boussinesq MASS_WEIGHT_IN_PGF bug
Hallberg-NOAA Jul 23, 2024
c3349ab
Merge branch 'main' into main-to-gfdl_2024-05-31
adcroft Jul 30, 2024
90749f3
Fix logic for reading parameter in MOM_tracer_advect.F90
adcroft Jul 31, 2024
87a0c61
Removes remap_via_sub_cells(), after copying code into remapping_core…
adcroft Jul 25, 2024
0344a76
Add gustless Tau to fluxes extracted from IOB by FMS cap.
breichl Aug 1, 2024
da59eb0
Adds new pre-defined coordinate WOA09INT
adcroft Jul 25, 2024
fee3281
Adds new pre-defined coordinate WOA23INT
adcroft Jul 25, 2024
e30a6e7
Fix bugs in setting GxSpV_u and GxSpV_v in MOM_isopycnal_slopes (#701)
Wendazhang33 Aug 2, 2024
906d96a
Add option to use non-surface density in MLD_003
Aug 2, 2024
f1ba822
Move MLD Diagnostics out of MOM_diabatic_aux.F90
Aug 2, 2024
22c9cbc
+Move array_global_min_max to MOM_spatial_means
Hallberg-NOAA Jul 10, 2024
9b45087
+Add runtime parameter WRITE_TRACER_MIN_MAX
Hallberg-NOAA Jul 10, 2024
a78aa57
* Fix for spatially varying Bodner fields.
kshedstrom Aug 16, 2024
42c1a32
Fix USE_CONT_THICKNESS bug
awallcraft Jul 29, 2024
2024f6f
Directional linear wave drag (#703)
c2xu Aug 21, 2024
d234bce
Restore computation of vorticity in MOM_hor_visc.F90
Pperezhogin Aug 19, 2024
a6dd0fd
Makedep output cleanup and PEP8 fixes
marshallward Aug 6, 2024
1eccd28
Merge branch 'main' into dev/gfdl
Hallberg-NOAA Sep 4, 2024
91eee52
Inline harmonic analysis
c2xu Sep 6, 2024
2316ae5
diffusivities from internal tides ray tracing algo (#677)
raphaeldussin Sep 9, 2024
95744a7
Streaming filter (#675)
c2xu Sep 10, 2024
ffff6f3
+Optionally use SSH in calculate density for PGF
Hallberg-NOAA Jul 29, 2024
9b9c165
(*)Refactor p_ave calculation
Hallberg-NOAA Sep 7, 2024
5fc90eb
Rotate ice shelf forcing and initialization
Hallberg-NOAA Aug 17, 2024
70a48e3
+Add MASS_WEIGHT_IN_PRESSURE_GRADIENT_TOP
claireyung Apr 30, 2024
8520c9f
+Add top mass_weight_in_PGF option to 13 integrals
Hallberg-NOAA Jul 24, 2024
e172fe8
+Add CORRECTION_INTXPA
claireyung Apr 30, 2024
15ea628
+Add CORRECTION_INTXPA_5PT
claireyung Apr 30, 2024
1b9bf67
+Add RESET_INTXPA_INTEGRAL
claireyung Apr 30, 2024
7a9545a
Revisions of sub-ice pressure gradient fixes
Hallberg-NOAA Jul 19, 2024
4cf1590
*Refactor CORRECTION_INTX_PA
Hallberg-NOAA Jul 29, 2024
15fd31c
*Non-Boussinesq code for RESET_INTXPA_INTEGRAL
Hallberg-NOAA Aug 5, 2024
5fceecf
+(*)Add 5-point quadrature in RESET_INTXPA_INTEGRAL
Hallberg-NOAA Aug 20, 2024
bdf4b9e
+(*)Eliminate CORRECTION_INTXPA_5PT
Hallberg-NOAA Sep 16, 2024
0363d2b
*Set MASS_WEIGHT_IN_PRESSURE_GRADIENT in .testing
Hallberg-NOAA Sep 16, 2024
1830b8e
Dummy code to suppress errors in posix.F90
marshallward Sep 6, 2024
e05cc01
F2023: Fix argument orders and IO statements
marshallward Sep 9, 2024
b67e93a
Reorder arguments in FMS_cap functions
marshallward Sep 12, 2024
b2db6bf
CI: Fortran 2018 testing
marshallward Sep 12, 2024
b3d7348
Change the default of VISC_REM_CONT_HVEL_FIX
herrwang0 Sep 12, 2024
ba59078
Separate scalar diagnostics for each ice sheet + parameters to contro…
alex-huth Sep 18, 2024
d3d9fc0
Merge branch 'main' into main-to-gfdl-2024-09-26
marshallward Sep 26, 2024
df2cd12
EBT Backscatter (#706)
ElizabethYankovsky Sep 27, 2024
e24cd3a
change CMOR names, fixes #709
Sep 27, 2024
5dcc8e0
Fix .testing make for regression tests
herrwang0 Sep 29, 2024
cfa8a3d
New diagnostics for flux divergence, strain-rates, deviatorics stress…
alex-huth Sep 19, 2024
9d4f9d1
Use loops instead of array syntax when calculating ice-shelf diagnost…
alex-huth Sep 30, 2024
b240e7e
change default for ice-shelf nonlin_solve_err_mode to 3
alex-huth Oct 1, 2024
f90b071
Ice-shelf FMAs (#729)
alex-huth Oct 7, 2024
80d8b5f
Bugfix in MOM_porous_barriers
herrwang0 Sep 18, 2024
79979a9
Update version of checkout action (@v4)
adcroft Apr 10, 2024
795e982
Switch runner and allow for more run time
adcroft Oct 29, 2024
e189e05
+Eliminated h_neglect argument to remapping_core_h
Hallberg-NOAA Feb 27, 2024
3d37f13
Change default of USE_POROUS_BARRIER to false
herrwang0 Oct 3, 2024
96a91f5
Set truncation file handle check from < 0 to == -1 (#739)
marshallward Nov 1, 2024
88ee9dd
CI: Consolidate unit test rules, codecov pathfix
marshallward Oct 31, 2024
a6d27cf
adding a constant mixing efficiency to internal tides
Oct 24, 2024
76915ff
Revert the change from VISC_REM_CONT_VEL_FIX
herrwang0 Oct 27, 2024
dbb3601
Rename VISC_REM bugfix parameters
herrwang0 Oct 27, 2024
13cc946
Replace hard-coded parameter Rrho0 with runtime parameter Max_Rrho_sa…
breichl Oct 29, 2024
31a4d8b
Add REMAPPING_SCHEME for OBC, ODA and SPONGE (#751)
awallcraft Nov 8, 2024
7a9adbc
Add SQG vertical structure to eddy diffusivities (#738)
Wendazhang33 Nov 13, 2024
2b72682
*+HOR_VISC_ANSWER_DATE logic fix
Hallberg-NOAA Nov 25, 2024
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3 changes: 3 additions & 0 deletions .codecov.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,6 @@ coverage:
default:
threshold: 100%
base: parent

fixes:
- "MOM6/::"
2 changes: 1 addition & 1 deletion .github/actions/ubuntu-setup/action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ runs:
run: |
echo "::group::config.mk"
cd .testing
echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
echo "FCFLAGS_DEBUG = -g -O0 -std=f2018 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/coupled-api.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
16 changes: 5 additions & 11 deletions .github/workflows/coverage.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,25 +11,19 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

- uses: ./.github/actions/ubuntu-setup

- uses: ./.github/actions/testing-setup

- name: Compile file parser unit tests
run: make -j build/unit/test_MOM_file_parser

- name: Run file parser unit tests
run: make run.cov.unit

- name: Compile unit testing
- name: Compile unit tests
run: make -j build.unit

- name: Run (single processor) unit tests
run: make run.unit
- name: Run unit tests
run: make run.cov.unit

- name: Report unit test coverage to CI
run: make report.cov.unit
Expand All @@ -40,7 +34,7 @@ jobs:
run: make -j build/cov/MOM6

- name: Run coverage tests
run: make -j -k run.cov
run: make -k run.cov

- name: Report coverage to CI
run: make report.cov
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/documentation-and-style.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ jobs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/expression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/macos-regression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/macos-stencil.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/other.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/perfmon.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/regression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/stencil.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
working-directory: .testing

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
submodules: recursive

Expand Down
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