Bug fix for reading First_direction from restart#18
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Hallberg-NOAA merged 2 commits intoDec 6, 2021
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* A bug on reading parameter First_direction from the restart is fixed. Previously, it only works when rotate_index is .true. * A FATAL error is now issued when both ROTATE_INDEX and ALTERNATE_FIRST_DIRECTION are .true. This should only be treated as a temporary patch. * Local variable first_direction in initialize_MOM is slightly repurposed to exclude any modication by rotate_index turns. This helps clarify the meaning of First_direction in restart files, making it independent from index rotation.
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@@ Coverage Diff @@
## dev/gfdl #18 +/- ##
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Coverage 29.17% 29.17%
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Files 240 240
Lines 71488 71493 +5
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+ Hits 20854 20856 +2
- Misses 50634 50637 +3
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Hallberg-NOAA
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I have carefully examined this PR, and I agree that these changes do properly correct a bug and adds an appropriate error for cases that are not yet being handled. This PR has passed TC testing and it passed pipeline testing at https://gitlab.gfdl.noaa.gov/ogrp/MOM6/-/pipelines/14277.
This was referenced Jan 29, 2022
marshallward
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* 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>
theresa-cordero
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Nov 18, 2024
Remove eqn_of_state from generic tracer interfaces because the photoacclimation mixed layer depth is now calculated in MOM6 and passed to MOM6. Co-authored-by: Theresa Morrison <Theresa.Morrison@gaea53.ncrc.gov>
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Remove eqn_of_state from generic tracer interfaces because the photoacclimation mixed layer depth is now calculated in MOM6 and passed to MOM6. Co-authored-by: Theresa Morrison <Theresa.Morrison@gaea53.ncrc.gov>
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This PR address issue mom-ocean#1546 .
First_directionis not correctly read from restart files. Previously, the code was only added in an if-block that rotate_index is true.FIRST_DIRECTIONfrom MOM_input and float fieldFirst_directionwritten to and read from the restart files have a physical meaning, i.e. their meanings and values should be independent from index rotation.first_directionin subroutineinitialize_MOMis slightly repurposed. Now it is only used to store parameterFIRST_DIRECTIONread from MOM_input. In this way, the modification of "turns" toG%first_directionis more explicit.CS%first_dir_restartis moved after state initialization to increase readability.FATALerror is now raised when bothROTATE_INDEXandALTERNATE_FIRST_DIRECTIONare true. This is mainly to avoid the potential ambiguous meaning of first_direction. It is probably not ideal but can be changed in the future if needed. (e.g. One can addturnsparameter to the control structure and use it to updateCS%first_dir_restartevery dynamical time step.)