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Modified ePBL_column to calculate Te and Se when EPBL_ORIGINAL_PE_CALC is False and there are no temperature change diagnostics being requested, and to return dPEc_dKd from one of the calls to find_PE_chg. This avoids the use of uninitialized values in EPBL_ORIGINAL_PE_CALC is false, and some solutions appear to be similar, but others give large qualitative changes, so there are probably still problems with EPBL_ORIGINAL_PE_CALC = False. When this was originally developed, it was verified to be mathematically equivalent, but in the years that this code was not tested, problems have crept it. All answers in the MOM6-examples test cases are bitwise identical.
Added an explicit MOM6 interface for cpu_clock_id, rather than simply passing the call through to mpp_clock_id, both to explicitly document the interface and arguments and to use the FMS run-time defaults for clock synchronization. This will enable SIS2 to use the MOM_cpu_clock module with the same behavior. All answers and output are bitwise identical.
Added code to handle discrepancies between compliers in how "\t" is handled in strings, so that the MOM6 documentation files are identical across compilers. All answers are bitwise identical.
Added an H_subroundoff term to the denominator of an expression in calculate_bkgnd_mixing for the inverse of the mixed layer thickness, so that NaNs will not be created when taking this inverse if CS%HMix is set to 0. All answers are bitwise identical in the MOM6-examples test cases.
Minor correction to avoid scanning past the end of a string. With sensitive settings, this bug was causing sensitive models to abort, but if the model ran it was giving bitwise identical answers.
Slight revision to writeMessageAndDesc to handle the case when a change in tab spacing will cause a line to exactly the maximum line length. All answers are bitwise identical answers.
- Modules, routines and labels in code changed from Neverland to Neverworld. - Add aliases for parameters so that existing configurations still work (given that Neverworld was published but the runs used Neverland).
- was operating on segments not on core, oh no.
(*)Improve ePBL when EPBL_ORIGINAL_PE_CALC=False
MOM6: +Minor improvements in framework code
- The single subroutine that defined the wind stresses for Neverworld (renamed from Neverland) has been moved into MOM_surface_forcing.F90 since an entire module for a single function that had no runtime parameters was overkill. # Conflicts: # src/initialization/MOM_fixed_initialization.F90
- Allows a piecewise scurve (cubics with zero gradients at nodes) to be defined to construct a zonal wind stress profile - Enabled with WIND_CONFIG="scurves" - Requires mandatory parameters WIND_SCURVES_LATS and WIND_SCURVES_TAUX that define the nodal positions and values. - Used in Neverworld2
- This topography is working but still likely to evolve. - The code will be superseded by a more general approach.
Added the new runtime parameter Z_INIT_SEPARATE_MIXED_LAYER and eliminated the extra get_param calls for NKML and NKBL in MOM_temp_salt_initilaize_from_Z with default values that are inconsistent with the defaults in MOM.F90. Also revised tracer_z_init_array and find_interfaces to eliminate unused arguments and added grid type arguments so that these routines follow the rest of the MOM6 code in how it deals with memory and indexing. There are interface changes, and unless Z_INIT_SEPARATE_MIXED_LAYER is explicitly set to true, some non-ALE cases that explicitly set NKML (and do not just take the default value) will have changed answers. However, a preceeding PR to MOM6-examples will avoid these answer changes and this PR fixes the problem that was in MOM6 with conflicting default values for NKML and NKBL. Reusing MOM_parameter_doc.short for MOM_input will once again give the same answers (perhaps with added layout parameters to set a non-default halo size in memory) in the MOM6-examples test suite.
- Allows run-time construction of topography defined by a list of
functions with parameters, e.g.
```
BBUILDER_007_FUNC = "circ_conic_ridge" !
! The basin builder function to apply with parameters BBUILDER_007_PARS. Choices
! are: NS_COAST, EW_COAST, CIRC_CONIC_RIDGE, NS_CONIC_RIDGE.
BBUILDER_007_PARS = 0.0, -50.0, 10.0, 2.0, 200. ! [degrees_E,degrees_N,degrees,degrees,m]
! CIRC_CONIC_RIDGE parameters: center longitude, center latitude, ring radius,
! footprint radius, ridge height.
```
- The hard-coded implementation of the Neverworld2 topography has been replaced by the basin_builder approach so I'm deleting to avoid more unused code. This was added on the branch so the this minimizes net changes from dev/gfdl.
- CPT discussion suggest a smoother profile for the mid-atlantic ridge which I've implemented as an scurve.
Obsoleted the runtime parameters SALT_REJECT_BELOW_ML, MLE_USE_MLD_AVE_BUG and KG_BG_2D_BUG, and deleted the unused subroutine insert_brine. Also deleted 68 variables that have been obsolete for several years. All answers in the MOM6-examples test cases are bitwise identical, but there are changes in the MOM_parameter_doc files.
Changed the default value of GILL_EQUATORIAL_LD to True. This could change answers in some test cases where GILL_EQUATORIAL_LD is not set explicitly, and there are changes to the MOM_parameter_doc files.
Removed the runtime parameter KELVIN_WAVE_2018_ANSWERS, which is no longer used for anything. All answers are bitwise identical, but there are changes to the MOM_parameter_doc files.
MOM6: (*?)Revised ice_shelf_driver.F90 so it compiles
The "for" loop at L510 should be to nz instead of nz+1. Due to array allocation sizes, this loop was extending beyond the shope of the argument arrays.
Squash merge of following commits: * Testing: tc4 installs python-netCDF4 via venv Currently, users are expected to have numpy and netcdf4 python modules in order to generate the necessary netCDF input files. This fails in environments where these modules are unavailable. This patch now installs the modules into a virtual environment which are accessible when generating the tc4 inputs. This solution is local to tc4 but could be extended to other tests as needed. * Testing: remove Python numpy and netCDF4 modules The numpy and netCDF4 packages are no longer needed since tc4 now installs these locally. * Test: Install virtualenv for Python2 tc4 was using the venv module which appears to be python3-specific, and Travis Ubuntu defaults to python2. Also virtualenv was not installed in either case. This patch adds python-virtualenv to the install packages and uses the virtualenv module. * Test: Add python-dev for ARM64 numpy Travis ARM nodes need to build numpy natively when installed by pip, and thus require Python headers. These are provided by the python-dev package. * Test: Revert to Py3 for tc4 generation scripts Reverting the python 2 support (default for Travis) to use Python 3 syntax. The main reason is that Python 3 includes venv (equivalent to virtualenv) as its standard library, and is therefore guaranteed to exist if Python 3 exists. Python 3's virtualenv must be independently installed, which cannot be confirmed. This will cause problems for people without Python 3, but this is probably the best solution, or at least the starting point for a more general solution. * Test: Adding python3-venv to Travis Ubuntu apparently requires an explicit install of python3-venv despite it being part of the standard library. Go figure... * Test: Arm64 tc4 Configuration support Arm64 Ubuntu environments require explicit installations which are otherwise provided on x86 Ubuntu: * Python 3 Pip must be installed (python3-pip) * Wheel installation must be explicitly installed * Cython is required for numpy * Numpy must be explicitly built before installing python-netCDF4 * Test: tc4 common Python local-env Build times for setting up the virtual environments can be very expensive on the Arm64 Ubuntu nodes, so we now create a shared directory for launching the environments. * Test: Use '.' in place of 'source' for Make * Test: Test for required Python modules in tc4 We have reworked the Makefile to conditionally test for required Python modules in tc4. If unavailable, we install these in a virtual environment. This does not address many scenarios, such as if Python 3 is missing, venv is missing (as in Ubuntu), or handle the situation if they do not exist. It assumes that either the modules exist, or that they can be installed by venv. This should be seen as an iterative step to get things working on Travis x86 and Arm64, as well as GFDL's Gaea and most user Linux platforms. * Test: Explicit python execs for tc4 input build This resolves some issues with python2/3 resolution and limited support of various platforms for module support. Specifically, older platform with basic Python 3 support may not also have numpy support. In this case, we can defer back to Python 2 (or whatever the system Python may be). * Test: Setup Python venv at build time This patch moves the Python virtual environment configuration to the main Makefile, which is setup at build time, rather than in the model configuration Makefile, which will typically not have internet access if run on a compute node. As before, the venv will only be setup when the numpy and netCDF4 modules are unavailable. A minor bug in the logic of the check has also been fixed.
…ureForce Fixing loop bound error in MOM_PressureForce_Montgomery.F90
…-ocean#1163) Squash merge: * New diagnostics for barotropic momentum budget calculations are created. In these, different budget terms multiplied by fractional layer thicknesses are saved. Thus, these terms can be added over the whole to obtain the barotropic momentum budget. 'btstep' subroutine in MOM_barotropic module is modified to return fractional thicknesses. Pressure force acceleration multiplied by fractional thickness as diagnostics are added in this commit. * More thickness weighted diagnostics * Implemented Andrew Shao's suggestions * More fractional thickness multiplied diagnostics * Some barotropic diagnostics obtained from fractional thickness multiplied momentum budget terms * Removed trailing spaces * All fractional-thickness multiplied diagnostics implemented * define diagnostic variables as pointers * Shorter initialization of 2D arrays * Modifications in vertical friction diagnostics * Diagnostics initialization as pointers to save memory allocation * Vertical friction module * Removed commented lines and trailing spaces * Diagnostic description change * Fractional thickness-weighted diagnostics for acceleration due to relative vorticity and gradient of kinetic energy * Modifications in vertical friction diagnostics (fractional thickness-weighted) * Modifications in diag_hfrac_u and diag_hfrac_v calls * Made allocation of hfrac at u/v points optional. These arrays are only allocated if any of the relevant diagnostics are called. * Fractional-thickness weighted 3D diagnostics are now commented out as we do not the proper grid remapping option. * Initialization of 2D diagnostic arrays changed from pointer type to allocatable array style. * Trailing spaces removed and line lengths reduced to be under 120 characters * Comment modified Reviewed by Robert Hallberg <Robert.Hallberg@noaa.gov>
This patch fixes three dimensionality errors in the OBC segments. - We add a missing GV%m_to_H conversion for time-dependent eta segments. - The `adjustSegmentEtaToFitBathymetry` function depends on the `segment%Htot` field when computing the dz_src cell spacings. While the calculation primarily assumes that all quantities scale as Z, the segment%Htot field scales as H, which was causing dimensionality errors. We resolve this by converting Htot from Z to H whenever it is used in the calculation. - Segment barotropic velocitys based on transports were limited to a hard-coded thickness of 1e-12, which was not scaled. We have added H-dimensional scaling to these constants.
The current OBC segment list includes a "segment zero" which corresponds to when the segment maps (segnum_u, segnum_v) point to OBC_NONE, which is set to zero. The purpose of this "segment zero" seems to be for avoiding invalid references, so that OBC%segment(OBC%segnum_[uv](i,j)) always returns a valid result, included when set to OBC_NONE. This results in reading and setting values which are unused or unneeded. This patch replaces these redundant accesses to segment zero with various conditional blocks for avoiding these accesses.
OBC: H-dimensionality fixes
Update to GFDL master
There were a few remaining segnum_[uv] references in MOM_open_boundary which could reference segment zero. This patch fixes those references.
…into remove_obc_seg0
OBC: Removal of segment zero
- Adds a diagnostic of the parameterized SGS T variance used in the Brankart correction to the PGF
- The SGS T variance is measure from the grid-scale variance. It should be a horizontal difference but is approximated as along coordinate. This adds thickness weighting to avoid large values near topography.
Brankart
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*Added a clock for the Stanley parameterization Co-authored-by: jkenigson <jkenigso@gmail.com>
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Explicit domain decomposition of horizontal axes
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Added a new variable, initialized, to the control structures of modules that had been testing for an allocated control structure to verify that it had been initialized before it was going to be used, and then duplicated the tests using this new variable. This was done to enable us to go ahead with MOM6 PR #5, which eliminated many of these checks when converting the control structures from pointers in the parent modules to elements that are always there, and then passing them as simple types instead of as pointers. If we decide that we do not need these tests after all, we can easily delete them, but until this is discussed, this commit avoids losing the messages, as it was easier to do it this way instead of trying to recreate them after they had been removed. All answers and output are bitwise identical.
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Redefine ~500 pointers as local or stack variables
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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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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 (NOAA-EMC#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>
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This PR adds in a stochastic component to the density correction to the equation of date described in Stanley et al. 2020.
There is a new module (src/core/MOM_stoch_eos.F90 which creates random gaussian noise that has a decorrelation timescale dependent on the Kinetic energy of the surface layer.
MOM_stoch_eos_init is called by MOM.F90
and
MOM_stoch_eos_run is called by either
MOM_dynamics_unsplit.F90, src/core/MOM_dynamics_split_RK2.F90, or
src/core/MOM_dynamics_unsplit_RK2.F90
The random pattern is then passed down into MOM_density integrals, where it is used to modify the temperature variance estimate that is used for the density correction.