[Parameter Testing] Lateral Friction using biharmonic operator

[minghangli-uni]

Parameter Tests Description

Details can be referred in #186.

SMAGORINSKY_AH = True           !   [Boolean] default = False
                                ! If true, use a biharmonic Smagorinsky nonlinear eddy viscosity.
SMAG_BI_CONST = 0.05066         !   [nondim] default = 0.0
                                ! The nondimensional biharmonic Smagorinsky constant, typically 0.015 - 0.06.
LAPLACIAN = True                !   [Boolean] default = False
                                ! If true, use a Laplacian horizontal viscosity.
AH_VEL_SCALE = 0.01             !   [m s-1] default = 0.0
                                ! The velocity scale which is multiplied by the cube of the grid spacing to
                                ! calculate the biharmonic viscosity. The final viscosity is the largest of this
                                ! scaled viscosity, the Smagorinsky and Leith viscosities, and AH.
NOSLIP = False                  !   [Boolean] default = False
                                ! If true, no slip boundary conditions are used; otherwise free slip boundary
                                ! conditions are assumed. The implementation of the free slip BCs on a C-grid is
                                ! much cleaner than the no slip BCs. The use of free slip BCs is strongly
                                ! encouraged, and no slip BCs are not used with the biharmonic viscosity.

Expts_manager Version

dd38b80

YAML input file

# =====================================================================================
# YAML Configuration for Expts_manager.py
# =====================================================================================
# This configuration file defining the parameters and settings required for cloning,
# setting up, and running control and perturbation experiments using `Expts_manager.py`.
# Detailed explanations are provided to ensure the configuration is straightforward.
# =====================================================================================


# ============ Model Selection ========================================================

model: access-om3  # Specify the model to be used. Options: 'access-om2', 'access-om3'

# ============ Utility Tool Configuration (only for access-om3) =======================
# The following configuration provides the necessary tools to:
# 1. Parse parameters and comments from `MOM_input` in MOM6.
# 2. Read and write the `nuopc.runconfig` file.

force_overwrite_tools: False
utils_url: [email protected]:minghangli-uni/om3-utils.git  # Git URL for the utility tool repository
utils_branch_name: main  # The branch for which the utility tool will be checked out
utils_dir_name: om3-utils  # Directory name for the utility tool (user-defined)

# ============ Diagnostic Table (optional) ============================================
# Configuration for customising the diagnostic table.

diag_url: [email protected]:minghangli-uni/make_diag_table.git  # Git URL for the `make_diag_table`
diag_branch_name: general_scheme3  # Branch for the `make_diag_table`
diag_dir_name: make_diag_table  # Directory name for the `make_diag_table` (user-defined)
diag_ctrl: True  # Set to 'True' to modify the diagnostic table for the control experiment
diag_pert: True  # Set to 'True' to modify the diagnostic table for perturbation experiments

# ============ Control Experiment Setup ===============================================

base_url: [email protected]:ACCESS-NRI/access-om3-configs.git  # Git URL for the control experiment repository
base_commit: "f37396e"  # Commit hash to use; Please ensure it is a string!
base_dir_name: Ctrl-1deg_jra55do_ryf  # Directory name for cloning (user-defined)
base_branch_name: ctrl  # Branch name for the experiment (user-defined)
test_path: product1_0.25deg_new_topo_modify_lateral_friction # Relative path for all test (control and perturbation) runs (user-defined)

# ============ Control Experiment Variables ===========================================
# Allows modification of various control experiment settings.
# 1. config.yaml  (access-om2 or access-om3)
# 2. all namelists such as with endswith "_in" or ".nml" etc.  (access-om2 or access-om3)
# 3. cpl_dt (coupling timestep)  (access-om3)
# 4. nuopc.runconfig  (access-om3)
# 5. MOM_input  (access-om3)
# Below are some examples for the illustration purpose, please modify for your own settings.
datm_in:
    datm_nml:
        ny_global: 1142
drof_in:
    drof_nml:
        ny_global: 1142
ice_in:
    domain_nml:
        ny_global: 1142

config.yaml:
    ncpus: 1584
    mem: 6336GB
    walltime: 10:00:00

    metadata:
        enable: True
    runlog: True
    restart_freq: 1
    modules:
        use:
            - /g/data/ik11/spack/0.21.2/modules/access-om3/0.x.0/linux-rocky8-cascadelake
            - /g/data/hh5/public/modules
        load:
            - access-om3/63ed4a4777aeac0c62720ddbe7f85e4ed16f82eb_main
            - conda/analysis3-24.01

    input:
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/access-om2-025deg-ESMFmesh.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/access-om2-025deg-nomask-ESMFmesh.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/topog.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/ocean_hgrid.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/ocean_vgrid.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/ocean_temp_salt.res.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/salt_sfc_restore.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/grid.nc
    - /g/data/tm70/ml0072/COMMON/git_repos/COSIMA_om3-scripts/expts_manager/New_grid_input_files_025deg_75zlevels/kmt.nc
    - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-datm-ESMFmesh.nc
    - /g/data/vk83/configurations/inputs/access-om3/share/meshes/share/2024.09.16/JRA55do-drof-ESMFmesh.nc
    - /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data

nuopc.runseq: 1080.0  # Coupling timestep in the `nuopc_runseq`
nuopc.runconfig:
    CLOCK_attributes:
        stop_option: nyears
        stop_n: 1
        restart_option: nyears
        restart_n: 1
    PELAYOUT_attributes:
        atm_ntasks: 240
        rof_ntasks: 240
        cpl_ntasks: 240
        ice_ntasks: 240
        ocn_ntasks: 1344
        ocn_rootpe: 240
    MED_attributes:
        atm_ny: 1142
        ice_ny: 1142
        ocn_ny: 1142
        rof_ny: 1142

MOM_input:
    NJGLOBAL: 1142
    NK: 75
    DT_THERM: 10800.0
    DT: 1080.0
    DIABATIC_FIRST: False
    THERMO_SPANS_COUPLING: True
    DTBT_RESET_PERIOD: 10800.0
    MAXTRUNC: 500

input.nml:
    diag_manager_nml:
        max_axes: 400
        max_files: 200
        max_num_axis_sets: 200

# ============ Namelist Tunning ================================
# Tune parameters across different model components.

namelists:
# ------------------------------------------------------------------------------------- #
    cross_block1:
        cross_block1_dirs: [lateral_friction1]
        MOM_input:
            MOM_list1_combo:
                SMAGORINSKY_AH: [True]
                SMAG_BI_CONST: [0.05066]
                LAPLACIAN: [True]
                AH_VEL_SCALE: [0.01]

# ============ Control experiment and perturbation Runs ===================================
# This section configures the settings for running control experiments and their corresponding perturbation tests.
    
ctrl_nruns: 0
# Number of control experiment runs.            
# Default: 0.            
# Adjust this value to set the number of iterations for the control experiment, which serves as the baseline for perturbations.

run_namelists: True  
# Determines whether to run using the specified namelists.            
# Default: False.            
# Set to 'True' to apply configurations from the namelist section; otherwise, 'False' to skip this step.

check_duplicate_jobs: True  
# Checks if there are duplicate PBS jobs within the same parent directory (`test_path`) based on their names.            
# This check is useful when you have existing running jobs and want to add additional tests, which helps avoid conflicts by ensuring new jobs don't duplicate existing ones in the same `test_path`.            
# The check will not be triggered if the jobs are located in different `test_path`. It only applies to jobs within the same `test_path` directory.            
# Default: True.            
# If duplicates are found, a message will be printed indicating the presence of duplicate runs and those runs will be skipped.

check_skipping: False  
# Checks if certain runs should be skipped based on pre-existing conditions or results. Currently only valid for nml type.            
# Default: False.            
# Set to 'True' if you want the system to skip runs under specific criteria; otherwise, keep it 'False'. Currently only valid for nml type.

force_restart: False  
# Controls whether to force a restart of the experiments regardless of existing initial conditions.            
# Default: False.            
# Set to 'True' to enforce a restart of the control and perturbation runs.

startfrom: 'rest'  
# Defines the starting point for perturbation tests.            
# Options: a specific restart number of the control experiment, or 'rest' to start from the initial state.            
# This parameter determines the initial condition for each perturbation test.

nruns: 10
# Total number of output directories to generate for each Expts_manager member.            
# Default: 0.            
# Specifies how many runs of each perturbation experiment will be started; this number correlates with the different parameter combinations defined in the configuration.

Additional Information

No response