Small fixes#15
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alperaltuntas
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Feb 5, 2021
* allows control of MOM6 restarts and MOM6 intermediate restarts using nems.configure settings restart_n and restart_option. Fixes duplicate restart issue when running with CMEPS (#16). * when field dumping is turned on, all fields in import state and export state are written to single file with timestamped file name (#15) * moves call to data_override field lrunoff out of the enclosing do loop (#21 ) Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu>
alperaltuntas
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Aug 2, 2021
merge latest updates into dev/gfdl
gustavo-marques
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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
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Apr 2, 2026
Update diagnostics and default parameters
alperaltuntas
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Apr 8, 2026
* indenting for mom_inline_mod and mom_cap_outputlog.F90 made consistent w/ MOM6 style * several docstrings added or moved; spurious whitespace and comments removed * two word end if and end do changed to one word
gustavo-marques
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Apr 9, 2026
* Fix divide by zero fpe in apply_oda_incupd (#164) Move computation of tmp_h inside the if G%mask2dT test to avoid divide by zero error * Add mom_cap_outputlog.F90 that enables output logging diagnostics at a given hourly output frequency Author: Denise Worthen This feature is required for UFS operational configurations and is used to determine when MOM6 output (diagnostics and restart) have been completed. The log files created by this feature can be queried by the Global Workflow to either trigger downstream jobs or to ensure that if a run fails and a restart is required, model output is available consistent with a given restart file. * Adds the ability to read a CDEPS configuration file to provide in-line forcing. * Adds the ability to read a CDEPS configuration file to provide in-line forcing. Currently this is set up to read a non-climatological lrunoff data stream only. * Add tracing instrumentation to nuopc driver (#162) * adds calls to ufs tracing routines that will create a trace file which can then be visualized, which is found to be useful in identifying various performance issues. * Update CVMix to Apache-2.0 based release This patch updates the CVMix submodule to a more recent version that is licensed under the Apache 2.0 license. There are no code changes to CVMix relative to the current version. * Relicense code to Apache License, Version 2.0 This PR re-licenses the MOM6 source code from the Lesser GNU Public License, version 3 to Apache License, Version 2.0. This is done with the consent of all contributors to the source code. All source files are now tagged with the following disclaimer. ``` This file is part of MOM6, the Modular Ocean Model version 6. See the LICENSE file for licensing information. SPDX-License-Identifier: Apache-2.0 ``` All relevent source code, scripts, and macros are now explicitly identified as part of MOM6. Configuration files containing scripts, such as GitHub Actions, have also been tagged. Any other configurations, such as model inputs, have been excluded. * Address reviewer comments (#14) In mom_cap.F90 rename module variable 'mype' to 'localPet' Rename mom_ufs_trace_wrapper module to mom_cap_profiling Add docstrings * address reviewers comments (#15) * indenting for mom_inline_mod and mom_cap_outputlog.F90 made consistent w/ MOM6 style * several docstrings added or moved; spurious whitespace and comments removed * two word end if and end do changed to one word * Fixes for flang * Change variable not type --------- Co-authored-by: jiandewang <jiande.wang@noaa.gov> Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com> Co-authored-by: Denise Worthen <denise.worthen@noaa.gov> Co-authored-by: Marshall Ward <marshall.ward@noaa.gov> Co-authored-by: Matthew Thompson <matthew.thompson@nasa.gov>
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