Merging dev/master #9
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ed to figure out why the redistribution of residual does not fully conserve.
in MOM_tracer_registry.F90: MOM_tracer_chkinv. This routine calculates the global inventories of all tracers in the registry. Some of the debugging checksums in the offline tracer routines are updated to use this new function.
This primarily resulted from an error in the indexing when the fields were being updated. Now to test in OM4_05
Added a term proportional to the gradient of divergence to the Leith viscosity, which turns regular 2D Leith into Modified Leith.
Moved the calls to set_viscous_BBL out of the dynamics code and up into step_MOM, eliminating 4-way redundant calls and making the various algorithms more obviously similar. The answers are bitwise identical with 3 of the 4 dynamic solvers, but with MOM_dynamics_unsplit the time level of thicknesses used to calculate the bottom boundary layer properties are replaced with the initial thicknesses (like the other schemes), rather than the average of the initial thicknesses and the predicted thicknesses from the first (of perhaps several) step of the dynamics. All existing test cases are bitwise identical, but if SPLIT=FALSE and USE_RK2=FALSE, answers will change.
Eliminated calc_bbl and bbl_calc_time_interval from the vertvisc_type. Also renamed pass_kd_kv_turb to pass_kv_turb and added local variables inside of step_MOM to take the place of the variables that were eliminated, and added a new clock to step_MOM to record the time taken by calls to set_viscous_BBL. The unused module use statements for set_viscous_BBL were also eliminated from the MOM_dynamics modules. All answers are bitwise identical.
Moving set_viscous_BBL out of dynamics code Passes: https://gitlab.gfdl.noaa.gov/ogrp/MOM6/pipelines/1947
Runs fail with FATAL from PE 107: MPP_RESET_GROUP_UPDATE_FIELD_3D_: group%reset_index_s > group%nscalar etc. " .and. (.not.CS%thickness_diffuse_first .or. CS%t_dyn_rel_adv == 0)) " was removed in a previous update.
Corrected a bug when DIABATIC_FIRST=True in how the compensation for the difference between the dynamic sea surface height used by the barotropic solver and the height that the layers would have if net mass sources were applied gradually instead of abruptly at the start of the thermodynamic time step. This would change answers if both SPLIT and DIABATIC_FIRST are true and the value of BT_MASS_SOURCE_LIMIT > 0.0, but as there are currently no test cases that match these conditions, the answers are unchanged in all of the test cases. In cases where the answers do change, they are unambiguously better based on weaker high frequency gravity waves arising from coupling shocks.
…opass_fix Bugfix to reintroduce group halo pass check removed in 282a160
Corrected spelling errors and content errors in several of the comments describing subroutine arguments. All answers are bitwise identical.
Reverted to the simpler pass_var routines for the single 3-d variable h. This avoids the issue that triggered the recent pull request mom-ocean#520, and it should have no performance impacts. (In fact, by letting each call have its own halo size, it might lead to performance improvements in subsequent commits.) All answers are bitwise identical.
added Doxygen comments to all of the arguments to the subroutines in MOM_checksum_packages.F90. All the answers are bitwise identical.
Change to pass_var for h and correct barotropic mass source ...and it passed (no surprise): https://gitlab.gfdl.noaa.gov/ogrp/MOM6/pipelines/1956
added Doxygen comments to all of the subroutines in MOM_checksum_packages.F90. All the answers are bitwise identical.
Added Doxygen comments to all of the subroutines in the MOM_dynamics_legacy_split.F90. All the answers are bitwise identical.
Added Doxygen comments to all of the subroutines in the MOM_dynamics_unsplit.F90. All the answers are bitwise identical.
Added doxygen comments to all of the subroutines in MOM_dynamics_unsplit_RK2.F90
…line_tracer_updates # Conflicts: # src/core/MOM.F90
…anup code before PR
Added doxygen comments to all of the subroutines in MOM_interface_heights.F90. All the answers are bitwise identical.
- A new local variable was missing from the openmp directives.
committing pull request NCAR#2 to dev/ncar branch
Added coupler indices module
- get_global_shape() returns niglobal, njglobal from domain type. - get_global_grid_shape() returns niglobal, njglobal by calling get_global_shape(). - This avoids exposing members inside opaque types otherwise needed for initializing under MCT.
- To initialize within the MCT coupler we need access to members of ocean_state_type which are private. This method allows us to have local pointers to those members.
First version with working initialization routine
- In keeping with MOM6 style guide, all module use statements now have "only" and each imported entity is explicitly listed.
Adds "only" for all use statements
- something we'll get in the habit of doing...
Cleans up white space
|
This merge passed all the MOM6/examples tests on Cheyenne! |
alperaltuntas
pushed a commit
that referenced
this pull request
Mar 8, 2021
Remove AC_CHECK_FILE for legacy MOM_memory.h
alperaltuntas
pushed a commit
that referenced
this pull request
Apr 22, 2021
Feature/logcleanup (#20)
alperaltuntas
pushed a commit
that referenced
this pull request
Aug 2, 2021
Merge in latest MOM6 dev/gfdl updates
alperaltuntas
pushed a commit
that referenced
this pull request
Oct 20, 2021
Merge dev gfdl 19may2021
gustavo-marques
pushed a commit
that referenced
this pull request
May 7, 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 (#10) * Don't bother calculating tv%varT if stanley_coeff<0 * Missing then added * Merge Ian Grooms Tvar Discretization (#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 (#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 (#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 (#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 (#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 (#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>
alperaltuntas
pushed a commit
that referenced
this pull request
May 19, 2022
Update ocn_stoch branch with dev/emc
alperaltuntas
pushed a commit
that referenced
this pull request
Jun 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 #88 from marshallward/missing_attrib_with_class_bugfix - d380f1d An alternate fix to class(*) issues with FMS 2022-01 - 8ecf333 Merge pull request #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 #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 #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 #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 #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 #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 (#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
alperaltuntas
pushed a commit
that referenced
this pull request
Feb 9, 2024
Remove fms_io_mod import
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR bring dev/ncar up to date with the latest dev/master (as of 07/21/2017).