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User/z1l/openmp #12

Merged
merged 15 commits into from
Apr 15, 2014
Merged

User/z1l/openmp #12

merged 15 commits into from
Apr 15, 2014

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Zhi-Liang
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Zhi-Liang added a commit that referenced this pull request Apr 15, 2014
@Zhi-Liang Zhi-Liang merged commit 827d70f into dev/master Apr 15, 2014
@adcroft
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adcroft commented Apr 15, 2014

Zhi, I was just in the middle of testing this! Did you mean to close this request?

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adcroft commented Apr 15, 2014

Passed all tests.

gustavo-marques pushed a commit to gustavo-marques/MOM6 that referenced this pull request Jul 25, 2017
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this pull request Oct 9, 2017
- NOAA-GFDL/MOM6@ae22a0f Merge pull request mom-ocean#578 from NCAR/dev/ncar
- NOAA-GFDL/MOM6@f4f882f Merge pull request mom-ocean#23 from gustavo-marques/combine_mct_modules
- NOAA-GFDL/MOM6@a85b728 Merge MCT modules
- NOAA-GFDL/MOM6@ba5b5ba Merge pull request mom-ocean#22 from gustavo-marques/check_fluxes
- NOAA-GFDL/MOM6@f5a8483 Adds option to write restart files
- NOAA-GFDL/MOM6@8745b4b Fills additional IOB fluxes
- NOAA-GFDL/MOM6@f6b22ff Merge branch 'dev/ncar' into check_fluxes
- NOAA-GFDL/MOM6@369d5d6 Merge pull request mom-ocean#21 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@2582e0a Adds run paramaters to control SW decomposition
- NOAA-GFDL/MOM6@58f78b9 Fill IOB, some fluxes still need to be checked
- NOAA-GFDL/MOM6@06a30ab Fixed clock and timing
- NOAA-GFDL/MOM6@1bca79b Merge pull request mom-ocean#20 from gustavo-marques/fix_merge
- NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge
- NOAA-GFDL/MOM6@7480492 Merge pull request mom-ocean#19 from gustavo-marques/new_merge
- NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar
- NOAA-GFDL/MOM6@76565cb Merge pull request mom-ocean#17 from gustavo-marques/fix_ssh_slopes
- NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation
- NOAA-GFDL/MOM6@17d4586 Merge pull request mom-ocean#16 from adcroft/ncar-cherry-picked-fixes
- NOAA-GFDL/MOM6@be46fee (*)Fixes gprime(1) when no layer coordinates are set
- NOAA-GFDL/MOM6@fccb7ae Avoids a SEGV when OBC are not in use with bi-harmonic friction
- NOAA-GFDL/MOM6@f42c970 Merge pull request mom-ocean#15 from gustavo-marques/small_fixes
- NOAA-GFDL/MOM6@31787c2 Adds reference to set_time that was lost during a conflict handling
- NOAA-GFDL/MOM6@d77936e Fix intent(inout) in ice_ocean_boundary
- NOAA-GFDL/MOM6@b403edd Merge pull request mom-ocean#14 from gustavo-marques/docs
- NOAA-GFDL/MOM6@4d346ca Merge branch 'dev/ncar' into docs
- NOAA-GFDL/MOM6@f7c26a5 Clean the module and start doxygenizing it
- NOAA-GFDL/MOM6@cd58e2a Merge pull request mom-ocean#13 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@37a53bc reorganize file structure
- NOAA-GFDL/MOM6@e6c5ddd Merge pull request mom-ocean#12 from gustavo-marques/fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@6b6289a Remove trailing whitespace
- NOAA-GFDL/MOM6@7ce40e5 Fix undefined reference to fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@d517719 Merge branch 'dev/ncar' into fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@b69ab33 Filling ice_ocean_bnd - Draft
- NOAA-GFDL/MOM6@a306c90 Merge pull request mom-ocean#11 from adcroft/use-ocn-public-for-surface
- NOAA-GFDL/MOM6@c83e238 Correct indexing when using ocean_public_type
- NOAA-GFDL/MOM6@1f39c84 Replaces use of "surface" with "ocean_public_type"
- NOAA-GFDL/MOM6@5cd8d7a Filling ice_ocean_bnd, still needs work
- NOAA-GFDL/MOM6@3ceef26 Merge pull request mom-ocean#10 from adcroft/sketch-out-mct-run
- NOAA-GFDL/MOM6@714e8d6 Adds placeholders for stepping foward MOM
- NOAA-GFDL/MOM6@7f2207c Merge pull request #7 from adcroft/fix-mct-whitespace
- NOAA-GFDL/MOM6@a1db77f Cleans up white space
- NOAA-GFDL/MOM6@5700d67 Merge pull request #6 from adcroft/add-use-only-for-imports
- NOAA-GFDL/MOM6@beac3ed Adds "only" for all use statements
- NOAA-GFDL/MOM6@231d19e Merge pull request #5 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@3a923a2 Got initialization working
- NOAA-GFDL/MOM6@8b38141 Wrapped global data
- NOAA-GFDL/MOM6@970f848 added debugging
- NOAA-GFDL/MOM6@2540ed8 Filled empty subroutines in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@ed3ed30 Added ocn_import_export module
- NOAA-GFDL/MOM6@aba7dc2 Completed ocn_init_mct
- NOAA-GFDL/MOM6@5df3bc3 Added method to point ponters to members of ocean_state_type
- NOAA-GFDL/MOM6@57e6086 Added methods to return domain/grid shape
- NOAA-GFDL/MOM6@37e7356 Added ocn_import_export.F90
- NOAA-GFDL/MOM6@2b794da Merge pull request #4 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@fbd405b Added coupler indices module
- NOAA-GFDL/MOM6@fa86163 Merge pull request #3 from NCAR/dev/gfdl
- NOAA-GFDL/MOM6@e8f2999 Merge pull request #2 from gustavo-marques/temp_salt_z_init_file
- NOAA-GFDL/MOM6@86936ba Adds option to read initial temp and salt from separate files
- NOAA-GFDL/MOM6@54f7976 Most initialization working
- NOAA-GFDL/MOM6@426357c Time and calendar initialization in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@346097d Moved blank ocn_comp_mct.F90
- NOAA-GFDL/MOM6@405fecb Merge pull request #1 from gustavo-marques/ice_shelf
- NOAA-GFDL/MOM6@711a613 Removes frazil's contribution to evaporation
nikizadehgfdl pushed a commit to nikizadehgfdl/MOM6 that referenced this pull request Oct 9, 2017
- Updates MOM_parameter_doc files.

- NOAA-GFDL/MOM6@cde6d3f Merge branch 'dev/master' into dev/gfdl
- NOAA-GFDL/MOM6@ae22a0f Merge pull request mom-ocean#578 from NCAR/dev/ncar
- NOAA-GFDL/MOM6@f4f882f Merge pull request mom-ocean#23 from gustavo-marques/combine_mct_modules
- NOAA-GFDL/MOM6@a85b728 Merge MCT modules
- NOAA-GFDL/MOM6@ba5b5ba Merge pull request mom-ocean#22 from gustavo-marques/check_fluxes
- NOAA-GFDL/MOM6@f5a8483 Adds option to write restart files
- NOAA-GFDL/MOM6@8745b4b Fills additional IOB fluxes
- NOAA-GFDL/MOM6@f6b22ff Merge branch 'dev/ncar' into check_fluxes
- NOAA-GFDL/MOM6@369d5d6 Merge pull request mom-ocean#21 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@2582e0a Adds run paramaters to control SW decomposition
- NOAA-GFDL/MOM6@58f78b9 Fill IOB, some fluxes still need to be checked
- NOAA-GFDL/MOM6@06a30ab Fixed clock and timing
- NOAA-GFDL/MOM6@1bca79b Merge pull request mom-ocean#20 from gustavo-marques/fix_merge
- NOAA-GFDL/MOM6@fb89b08 Adds code that got lost during merge
- NOAA-GFDL/MOM6@7480492 Merge pull request mom-ocean#19 from gustavo-marques/new_merge
- NOAA-GFDL/MOM6@be1e6cf Merge branch 'dev/master' into dev/ncar
- NOAA-GFDL/MOM6@76565cb Merge pull request mom-ocean#17 from gustavo-marques/fix_ssh_slopes
- NOAA-GFDL/MOM6@c04f081 Fix ssh slope calculation
- NOAA-GFDL/MOM6@17d4586 Merge pull request mom-ocean#16 from adcroft/ncar-cherry-picked-fixes
- NOAA-GFDL/MOM6@be46fee (*)Fixes gprime(1) when no layer coordinates are set
- NOAA-GFDL/MOM6@fccb7ae Avoids a SEGV when OBC are not in use with bi-harmonic friction
- NOAA-GFDL/MOM6@f42c970 Merge pull request mom-ocean#15 from gustavo-marques/small_fixes
- NOAA-GFDL/MOM6@31787c2 Adds reference to set_time that was lost during a conflict handling
- NOAA-GFDL/MOM6@d77936e Fix intent(inout) in ice_ocean_boundary
- NOAA-GFDL/MOM6@b403edd Merge pull request mom-ocean#14 from gustavo-marques/docs
- NOAA-GFDL/MOM6@4d346ca Merge branch 'dev/ncar' into docs
- NOAA-GFDL/MOM6@f7c26a5 Clean the module and start doxygenizing it
- NOAA-GFDL/MOM6@cd58e2a Merge pull request mom-ocean#13 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@37a53bc reorganize file structure
- NOAA-GFDL/MOM6@e6c5ddd Merge pull request mom-ocean#12 from gustavo-marques/fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@6b6289a Remove trailing whitespace
- NOAA-GFDL/MOM6@7ce40e5 Fix undefined reference to fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@d517719 Merge branch 'dev/ncar' into fill_ice_ocean_bnd
- NOAA-GFDL/MOM6@b69ab33 Filling ice_ocean_bnd - Draft
- NOAA-GFDL/MOM6@a306c90 Merge pull request mom-ocean#11 from adcroft/use-ocn-public-for-surface
- NOAA-GFDL/MOM6@c83e238 Correct indexing when using ocean_public_type
- NOAA-GFDL/MOM6@1f39c84 Replaces use of "surface" with "ocean_public_type"
- NOAA-GFDL/MOM6@5cd8d7a Filling ice_ocean_bnd, still needs work
- NOAA-GFDL/MOM6@3ceef26 Merge pull request mom-ocean#10 from adcroft/sketch-out-mct-run
- NOAA-GFDL/MOM6@714e8d6 Adds placeholders for stepping foward MOM
- NOAA-GFDL/MOM6@7f2207c Merge pull request #7 from adcroft/fix-mct-whitespace
- NOAA-GFDL/MOM6@a1db77f Cleans up white space
- NOAA-GFDL/MOM6@5700d67 Merge pull request #6 from adcroft/add-use-only-for-imports
- NOAA-GFDL/MOM6@beac3ed Adds "only" for all use statements
- NOAA-GFDL/MOM6@231d19e Merge pull request #5 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@3a923a2 Got initialization working
- NOAA-GFDL/MOM6@8b38141 Wrapped global data
- NOAA-GFDL/MOM6@970f848 added debugging
- NOAA-GFDL/MOM6@2540ed8 Filled empty subroutines in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@ed3ed30 Added ocn_import_export module
- NOAA-GFDL/MOM6@aba7dc2 Completed ocn_init_mct
- NOAA-GFDL/MOM6@5df3bc3 Added method to point ponters to members of ocean_state_type
- NOAA-GFDL/MOM6@57e6086 Added methods to return domain/grid shape
- NOAA-GFDL/MOM6@37e7356 Added ocn_import_export.F90
- NOAA-GFDL/MOM6@2b794da Merge pull request #4 from alperaltuntas/dev/ncar
- NOAA-GFDL/MOM6@fbd405b Added coupler indices module
- NOAA-GFDL/MOM6@fa86163 Merge pull request #3 from NCAR/dev/gfdl
- NOAA-GFDL/MOM6@e8f2999 Merge pull request #2 from gustavo-marques/temp_salt_z_init_file
- NOAA-GFDL/MOM6@86936ba Adds option to read initial temp and salt from separate files
- NOAA-GFDL/MOM6@54f7976 Most initialization working
- NOAA-GFDL/MOM6@426357c Time and calendar initialization in ocn_comp_mct.F90
- NOAA-GFDL/MOM6@346097d Moved blank ocn_comp_mct.F90
- NOAA-GFDL/MOM6@405fecb Merge pull request #1 from gustavo-marques/ice_shelf
- NOAA-GFDL/MOM6@711a613 Removes frazil's contribution to evaporation
SMoorthi-emc pushed a commit to SMoorthi-emc/MOM6 that referenced this pull request Apr 16, 2020
Hallberg-NOAA pushed a commit that referenced this pull request Jan 20, 2021
Resolve conflicts between ODA use framework #1291 and dev/gfdl
gustavo-marques added a commit to gustavo-marques/MOM6 that referenced this pull request Aug 7, 2021
SMoorthi-emc pushed a commit to SMoorthi-emc/MOM6 that referenced this pull request Sep 30, 2021
merge dev/emc into ocean stochastic branch
sditkovsky pushed a commit to sditkovsky/MOM6 that referenced this pull request Nov 29, 2021
Bitwise identical refactoring of the code in DOME_initialize_sponges,
including renaming variables for greater clarity, adding variables for several
dimensional constants, and correcting comments.  This also includes more careful
handling of the DOME OBCs in DOME_set_OBC_data() to hopefully avoid some obvious
problems (noted in a comment about a "fight with T,S") that would arise if a
DOME case were set up that used temperature and salinity. Future revisions
should add more runtime parameters to specify the details of this case, but
properly doing so would involve changing the order of arithmetic; this has not
happened in this case.  All real variables in this module are now described in
comments.  All answers and output are bitwise identical.

Co-authored-by: Marshall Ward <marshall.ward@noaa.gov>
marshallward referenced this pull request in marshallward/MOM6 May 3, 2022
Note that most of these commits are from previously squashed pull
requests, and this PR is restoring them.

- 6360dbb Merge branch 'main' into main_to_dev
- bac8031 Merge pull request mom-ocean#1566 from jiandewang/EMC-FMS-mixed-mode-20220411
- e532d86 Merge pull request mom-ocean#88 from marshallward/missing_attrib_with_class_bugfix
- d380f1d An alternate fix to class(*) issues with FMS 2022-01
- 8ecf333 Merge pull request mom-ocean#87 from jiandewang/feature/update-to-main-20220317
- ba37f94 Merge remote-tracking branch 'FSU/main' into feature/update-to-main-20220317 this is corresponding to MOM6 main 20220317 commit (hash # 399a7db)
- 44313d9 Merge pull request mom-ocean#85 from jiandewang/feature/update-to-main-20220217
- 966707f Merge remote-tracking branch 'GFDL/main' into feature/update-to-main-20220217 this is corresponding to MOM6 main branch 20220217 commit (hash # 6f6d4d6), which originally based on GFDL-candidate-20220129
- 32c0e1e Merge pull request mom-ocean#81 from jiandewang/feature/update-to-main-20211220
- 9642b1d delete external/OCEAN_stochastic_phyiscs directory as Phil re-coded in external/stochastic_physics directory
- e7c9ada solve minor conflict in mom_cap.F90 mom_ocean_model_nuopc.F90 and MOM_energetic_PBL.F90, add two new files: src/parameterizations/stochastic/MOM_stochastics.F90 and config_src/external/stochastic_physics/stochastic_physics.F90
- 90d5961 Merge pull request mom-ocean#78 from jiandewang/feature/update-to-GFDL-20211019
- fd02017 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20211019
- 36f17eb Merge pull request mom-ocean#72 from pjpegion/ocn_stoch_july2021
- a9a957e return a more accurate error message in MOM_stochasics
- 56bb41e Merge branch 'ocn_stoch_july2021' of https://github.com/pjpegion/MOM6 into ocn_stoch_july2021
- ca2ae1c update to dev/emc
- 14ca4a1 Merge pull request mom-ocean#76 from jiandewang/feature/update-to-GFDL-20210914
- 29016c2 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210914 merge GFDL main 20210914 commit (hash # c09e199)
- a8577df Merge branch 'NOAA-EMC:dev/emc' into ocn_stoch_july2021
- f8a8e4c update to gfdl 20210806 (mom-ocean#74)
- 16e6af0 update to dev/emc
- 237a510 add comments
- 1b4273d revert logic wrt increments
- 5b2040e add logic to remove incrments from restart if outside IAU window
- c5f2b72 add write_stoch_restart_ocn to MOM_stochastics
- bdf2dc7 doxygen cleanup
- 8bc4acc move stochastics to external directory
- a3fa3a1 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch_july2021
- e4bc007 stochastic physics re-write
- 202cbd4 update to dev/emc
- 61717ee Merge remote-tracking branch 'origin/dev/emc' into ocn_stoch
- 565e0bb remove debug statements
- a4c0411 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 689a73f remove PE_here from mom_ocean_model_nuopc.F90
- 8afe969 clean up of mom_ocean_model_nuopc.F90
- 25ed4fc revert MOM_domains.F90
- b8d9888 place stochastic array in fluxes container and make SPPT specific arrays allocatable
- d984a7e remove stochastics container
- eb88219 clean up of code for MOM6 coding standards
- 6e3ea1b correct coupled_driver/ocean_model_MOM.F90 and other cleanup
- 0b99c1f make stochastics optional
- 85023f8 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 80f9f44 clean up MOM_domains
- 5443f8e remove blank link in MOM_diagnostics
- 1727d9a re-write of stochastic code to remove CPP directives
- 600ebf9 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 6bb9d0b fix non stochastic ePBL calculation
- 1d7ffa3 clean up code
- 040e1f1 Merge pull request #13 from NOAA-EMC/dev/emc
- 2cba995 Merge branch 'dev/emc' into ocn_stoch
- 1dc0f4f Merge remote-tracking branch 'upstream/dev/emc' into dev/emc
- 4bd9b9e clean up debug statements
- 25ed5ef additions for stochy restarts
- a2a374b add stochy_restart writing to mom_cap
- 0c15f4c Update MOM_diabatic_driver.F90
- 167a62e Merge pull request #12 from pjpegion/dev/emc
- bd477a9 Update MOM_diabatic_driver.F90
- 7212400 Update MOM_diabatic_driver.F90
- 7de295c cleanup of code and enhancement of ePBL perts
- cd06356 Merge pull request #11 from NOAA-EMC/dev/emc
- 9896d61 Merge pull request #9 from pjpegion/dev/emc_merge
- 0a62737 Merge branch 'ocn_stoch' into dev/emc_merge
- 3cad1ba Merge pull request #8 from NOAA-EMC/dev/emc
- c2aa2a8 updates from dev/emc
- 182ef34 additions for stochastic physics and ePBL perts
- 671c714 Merge pull request #1 from NOAA-EMC/dev/emc
gustavo-marques pushed a commit to gustavo-marques/MOM6 that referenced this pull request May 6, 2022
* Update MOM_stoch_eos.F90

In progress updating stencil for$ | dx \times \nabla T|^2$ calculation

* New discretization of |dx\circ\nablaT|^2

* AR1 timescale land mask

Adds land mask to the computation of the AR1 decorrelation time

* Update dt in call to MOM_stoch_eos_run

The call to `MOM_stoch_eos_run` (which time steps the noise) is from within `step_MOM_dynamics`. `step_MOM_dynamics` advances on time step `dt` (per line 957), but the noise is updated using `dt_thermo`. It seems more appropriate to update the noise using `dt`, since it gets called from within `step_MOM_dynamics`.

* Fixed the units for r_sm_H

* Remove vestigial declarations

The variables `hl`, `Tl`, `mn_T`, `mn_T2`, and `r_sm_H` are no longer used, so I removed their declarations and an OMP private clause

Co-authored-by: Ian Grooms <ian.grooms@colorado.edu>
gustavo-marques pushed a commit to gustavo-marques/MOM6 that referenced this pull request May 17, 2022
* initial hooks for stochastic EOS modifications

* remove debug statements

* add documentation

* Change ampltiude from 0.39 to sqrt(.39)

* remove global_indexing logic from stoch_eos_init

* switch to using MOM_random and add restart capability

* update random sequence to update each each time-step

* remove tseed0 from MOM_random (leftover from debugging)

* Added necessary submodules and S^2, T^2 diagnostics to MOM_diagnostics

* Added diagnostics for outputting variables related to the stochastic parameterization.

* Diagnostics in MOM_PressureForce_FV updated for stochastic (rather than deterministic) Stanley SGS T variance parameterization.

* Added parentheses for reproducibility.

* Changed diagnostics to account for possible absence of stoch_eos_pattern in MOM_PressureForce_FV,
when deterministic parameterization is on.

* remove mom6_da_hooks and geoKdTree from pkg

* add stochastic compoment to MOM_thickness_diffuse

* fix array size declaration and post_data

* Corrected indexing of loops in MOM_calc_varT

* Changed how parameterization of SGS T variance (deterministic and stochastic) is switched on in PGF and thickness diffusion codes

* Corrected a few typos

* Cleaned up indices, redundant diagnostic, printing

* Fixed diagnostic IDs

* Fixed diagnostics typo

* Corrected indices in calculation of tv%varT

* Minor index fix

* Corrected bug in pressure in Stanley diagnostics

* Fixed whitespace error

* Stoch eos clock (#5)

*Added a clock for the Stanley parameterization

Co-authored-by: jkenigson <jkenigso@gmail.com>

* add halo update to random pattern

* Update MOM_stoch_eos.F90

Fix bug for looping over compute domain (is -> isc etc.)

* Avoid unnessary computations on halo (MOM_stoch_eos) and code clean-up (MOM_thickness_diffuse)

* Removed halo updates before determ param calc

* Update MOM_stoch_eos.F90

Removed unnecessary code

* Bug - indices are transposed

* Changed Stanley stochastic coefficient from exp(X) to exp(aX) (#9)

* Changed Stanley stochastic coefficient from exp(X) to exp(aX)

* Extra spaces removed

* Stoch eos init fix (mom-ocean#10)

* Don't bother calculating tv%varT if stanley_coeff<0

* Missing then added

* Merge Ian Grooms Tvar Discretization (mom-ocean#11)

* Update MOM_stoch_eos.F90

In progress updating stencil for$ | dx \times \nabla T|^2$ calculation

* New discretization of |dx\circ\nablaT|^2

Co-authored-by: Ian Grooms <ian.grooms@colorado.edu>

* Multiplied tvar%SGS by grid cell thickness ratio

* Added limiter for tv%varT

* Stoch eos ncar linear disc (mom-ocean#12)

* Update MOM_stoch_eos.F90

In progress updating stencil for$ | dx \times \nabla T|^2$ calculation

* New discretization of |dx\circ\nablaT|^2

* AR1 timescale land mask

Adds land mask to the computation of the AR1 decorrelation time

* Update dt in call to MOM_stoch_eos_run

The call to `MOM_stoch_eos_run` (which time steps the noise) is from within `step_MOM_dynamics`. `step_MOM_dynamics` advances on time step `dt` (per line 957), but the noise is updated using `dt_thermo`. It seems more appropriate to update the noise using `dt`, since it gets called from within `step_MOM_dynamics`.

* Fixed the units for r_sm_H

* Remove vestigial declarations

The variables `hl`, `Tl`, `mn_T`, `mn_T2`, and `r_sm_H` are no longer used, so I removed their declarations and an OMP private clause

Co-authored-by: Ian Grooms <ian.grooms@colorado.edu>

* Update MOM_thickness_diffuse.F90

Changed index for soft convention

* Update CVMix-src

* Ensure use_varT, etc., initialized

* Don't register stanley diagnostics if scheme is off

* Stanley density second derivs at h pts (mom-ocean#15)

* Change discretization of Stanley correction (drho_dT_dT at h points)

* Limit Stanley noise, shrink limiting value

* Revert t variance discretization

* Reverted variable declarations

* Stanley scheme in mixed_layer_restrat, vert_fill in stoch_eos, code cleanup (mom-ocean#19)

* Test Stanley EOS param in mixed_layer_restrat

* Fix size of TS cov, S var in Stanley calculate_density calls

* Test move stanley scheme initialization

* Added missing openMP directives

* Revert Stanley tvar discretization (mom-ocean#18)

* Perform vertical filling in calculation of T variance

* Variable declaration syntax error, remove scaling from get_param

* Fix call to vert_fill_TS

* Code cleanup, whitespace cleanup

Co-authored-by: Jessica Kenigson <jessicak@cheyenne1.cheyenne.ucar.edu>

* Use Stanley (2020) variance; scheme off at coast

* Comment clean-up

* Remove factor of 0.5 in Tvar

* Don't calculate Stanley diagnostics on halo

* Change start indices in stanley_density_1d

* Stanley param in MOM_isopycnal_slopes (mom-ocean#22)

Stanley param in MOM_isopycnal_slopes and thickness diffuse index fix

* Set eady flag to true if use_stored_slopes is true

* Cleanup, docs, whitespace

* Docs and whitespace

* Docs and whitespace

* Docs and whitespace

* Whitespace cleanup

* Whitespace cleanup

* Clean up whitespace

* Docs cleanup

* use_stanley

* Update MOM_lateral_mixing_coeffs.F90

* Adds link to another TEOS10 module

* Set Stanley off for testing

* Line continuation

Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: Philip Pegion <Philip.Pegion@noaa.gov>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne6.cheyenne.ucar.edu>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne3.cheyenne.ucar.edu>
Co-authored-by: jkenigson <jkenigso@gmail.com>
Co-authored-by: jskenigson <jessica.kenigson@colorado.edu>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne1.cheyenne.ucar.edu>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne5.cheyenne.ucar.edu>
Co-authored-by: Philip Pegion <ppegion@Philips-MacBook-Pro.local>
Co-authored-by: Jessica Kenigson <jessicak@cheyenne4.cheyenne.ucar.edu>
jiandewang added a commit that referenced this pull request May 8, 2024
Replace db array default values with real literals
andrew-c-ross added a commit to andrew-c-ross/MOM6 that referenced this pull request Sep 18, 2024
* Apply changes for BGC budgets

# Conflicts:
#	src/tracer/MOM_generic_tracer.F90
#	src/tracer/MOM_tracer_registry.F90

* Updated budget code from Fan

* Enable built in diagnostics

* Cleanup

* Cleanup

* Add boundary_forcing_tend to stub g_tracer_type

* Clean trailing whitespace

* Remove redundant zeroing of boundary_forcing_tend

* Add an attribution

* Clarify which diagnostics are for concentration

* Fix units for _diffusion_xy
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2 participants