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Feature/update mom6 and retain b4b results for 025x025 resolution #290

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merged 17 commits into from
Dec 4, 2020
Merged

Feature/update mom6 and retain b4b results for 025x025 resolution #290

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263486c
point MOM6 to new branch which corresponding to GFDL 20201022 commit
jiandewang Nov 18, 2020
1dd6f3c
modify fms_files.cmake and mom6_files.cmake to reflect changes in MOM…
jiandewang Nov 18, 2020
018149e
manually set MOM6 parameters in order to retain origonal results for …
jiandewang Nov 18, 2020
17478cc
Merge remote-tracking branch 'upstream/develop' into feature/update-M…
jiandewang Nov 19, 2020
0c5da2a
switch MOM6 to EMC repo
jiandewang Nov 21, 2020
baab6dd
Merge remote-tracking branch 'upstream/develop' into feature/update-M…
jiandewang Nov 23, 2020
0543eda
update MOM6 to include Bugfix for mom6solo to be built
jiandewang Nov 25, 2020
a53ed3f
Merge remote-tracking branch 'upstream/develop' into feature/update-M…
jiandewang Nov 25, 2020
50b1c28
modify compile.sh to allow mom6solo compiling
jiandewang Nov 26, 2020
4877b8a
Merge remote-tracking branch 'upstream/develop' into feature/update-M…
jiandewang Nov 30, 2020
4ae9414
modify MOM_input_template for all resolutions based on GFDL MOM6-exam…
jiandewang Dec 2, 2020
4c84726
Merge remote-tracking branch 'upstream/develop' into feature/update-M…
jiandewang Dec 2, 2020
0a7a600
change executable permissions for CMakeLists.txt
jiandewang Dec 3, 2020
e6762b8
chmod 644 to 6 files Dom pointed out
jiandewang Dec 3, 2020
da049ea
chmod for CMakeLists.txt and tests/compile.sh
jiandewang Dec 3, 2020
98dbd86
change baseline directpory to 20201202 in rt.sh
jiandewang Dec 3, 2020
fe25d2f
upload regression run log, skip-ci
jiandewang Dec 4, 2020
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Empty file modified CMakeLists.txt
100644 → 100755
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2 changes: 1 addition & 1 deletion MOM6-interface/MOM6
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Submodule MOM6 updated 205 files
19 changes: 12 additions & 7 deletions MOM6-interface/mom6_files.cmake
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Expand Up @@ -24,12 +24,13 @@ list(APPEND mom6_src_files
MOM6/src/core/MOM_CoriolisAdv.F90
MOM6/src/core/MOM_PressureForce.F90
MOM6/src/core/MOM_PressureForce_Montgomery.F90
MOM6/src/core/MOM_PressureForce_analytic_FV.F90
MOM6/src/core/MOM_PressureForce_FV.F90
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MOM6/src/core/MOM_barotropic.F90
MOM6/src/core/MOM_boundary_update.F90
MOM6/src/core/MOM_checksum_packages.F90
MOM6/src/core/MOM_continuity.F90
MOM6/src/core/MOM_continuity_PPM.F90
MOM6/src/core/MOM_density_integrals.F90
MOM6/src/core/MOM_dynamics_split_RK2.F90
MOM6/src/core/MOM_dynamics_unsplit.F90
MOM6/src/core/MOM_dynamics_unsplit_RK2.F90
Expand Down Expand Up @@ -214,12 +215,13 @@ list(APPEND mom6_src_files
MOM6/src/user/Kelvin_initialization.F90
MOM6/src/user/MOM_controlled_forcing.F90
MOM6/src/user/MOM_wave_interface.F90
MOM6/src/user/Neverland_initialization.F90
MOM6/src/user/Neverworld_initialization.F90
MOM6/src/user/Phillips_initialization.F90
MOM6/src/user/RGC_initialization.F90
MOM6/src/user/Rossby_front_2d_initialization.F90
MOM6/src/user/SCM_CVMix_tests.F90
MOM6/src/user/adjustment_initialization.F90
MOM6/src/user/basin_builder.F90
MOM6/src/user/baroclinic_zone_initialization.F90
MOM6/src/user/benchmark_initialization.F90
MOM6/src/user/circle_obcs_initialization.F90
Expand All @@ -241,11 +243,15 @@ list(APPEND mom6_src_files
MOM6/src/user/user_revise_forcing.F90

MOM6/src/ocean_data_assim/MOM_oda_driver.F90
MOM6/src/ocean_data_assim/core/ocean_da_core.F90
MOM6/src/ocean_data_assim/core/ocean_da_types.F90
MOM6/src/ocean_data_assim/core/write_ocean_obs.F90

MOM6/src/ocean_data_assim/geoKdTree/kdtree.f90
MOM6/config_src/external/GFDL_ocean_BGC/FMS_coupler_util.F90
MOM6/config_src/external/GFDL_ocean_BGC/generic_tracer.F90
MOM6/config_src/external/GFDL_ocean_BGC/generic_tracer_utils.F90
MOM6/config_src/external/ODA_hooks/kdtree.f90
MOM6/config_src/external/ODA_hooks/ocean_da_core.F90
MOM6/config_src/external/ODA_hooks/ocean_da_types.F90
MOM6/config_src/external/ODA_hooks/write_ocean_obs.F90

)

list(APPEND mom6_nuopc_src_files
Expand All @@ -261,7 +267,6 @@ list(APPEND mom6_solo_src_files
MOM6/config_src/solo_driver/MESO_surface_forcing.F90
MOM6/config_src/solo_driver/MOM_driver.F90
MOM6/config_src/solo_driver/MOM_surface_forcing.F90
MOM6/config_src/solo_driver/Neverland_surface_forcing.F90
MOM6/config_src/solo_driver/atmos_ocean_fluxes.F90
MOM6/config_src/solo_driver/user_surface_forcing.F90
)
1 change: 1 addition & 0 deletions fms_files.cmake
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@@ -1,4 +1,5 @@
list(APPEND fms_src_files
FMS/affinity/fms_affinity.F90
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FMS/amip_interp/amip_interp.F90
FMS/astronomy/astronomy.F90
FMS/axis_utils/axis_utils.F90
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4 changes: 4 additions & 0 deletions tests/compile.sh
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Expand Up @@ -150,6 +150,10 @@ if [[ "${MAKE_OPT}" == *"DATM=Y"* ]]; then
CMAKE_FLAGS="${CMAKE_FLAGS} -DDATM=Y"
fi

if [[ "${MAKE_OPT}" == *"S2S=Y"* ]] || [[ ${MAKE_OPT} == *"DATM=Y"* ]]; then
CMAKE_FLAGS="${CMAKE_FLAGS} -DMOM6SOLO=ON"
fi

CMAKE_FLAGS=$(trim "${CMAKE_FLAGS}")

if [ $clean_before = YES ] ; then
Expand Down
916 changes: 437 additions & 479 deletions tests/parm/MOM_input_template_025
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934 changes: 453 additions & 481 deletions tests/parm/MOM_input_template_050
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71 changes: 50 additions & 21 deletions tests/parm/MOM_input_template_100
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Expand Up @@ -72,15 +72,17 @@ WRITE_GEOM = 2 ! default = 1
! If =0, never write the geometry and vertical grid files. If =1, write the
! geometry and vertical grid files only for a new simulation. If =2, always
! write the geometry and vertical grid files. Other values are invalid.
SAVE_INITIAL_CONDS = True ! [Boolean] default = False
! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.

! === module MOM_domains ===
TRIPOLAR_N = True ! [Boolean] default = False
! Use tripolar connectivity at the northern edge of the domain. With
! TRIPOLAR_N, NIGLOBAL must be even.
NIGLOBAL = NX_GLB !
NIGLOBAL = NX_GLB !
! The total number of thickness grid points in the x-direction in the physical
! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
NJGLOBAL = NY_GLB !
NJGLOBAL = NY_GLB !
! The total number of thickness grid points in the y-direction in the physical
! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.

Expand All @@ -106,7 +108,7 @@ GRID_ROTATION_ANGLE_BUGS = False ! [Boolean] default = True
! If true, use an older algorithm to calculate the sine and
! cosines needed rotate between grid-oriented directions and
! true north and east. Differences arise at the tripolar fold
USE_TRIPOLAR_GEOLONB_BUG = False ! [Boolean] default = False
USE_TRIPOLAR_GEOLONB_BUG = False ! [Boolean] default = True
! If true, use older code that incorrectly sets the longitude in some points
! along the tripolar fold to be off by 360 degrees.
TOPO_CONFIG = "file" !
Expand Down Expand Up @@ -165,6 +167,13 @@ CHANNEL_CONFIG = "list" ! default = "none"
! NetCDF file on the model grid.
CHANNEL_LIST_FILE = "MOM_channels_SPEAR" ! default = "MOM_channel_list"
! The file from which the list of narrowed channels is read.
GRID_ROTATION_ANGLE_BUGS = False ! [Boolean] default = False
! If true, use an older algorithm to calculate the sine and cosines needed
! rotate between grid-oriented directions and true north and east. Differences
! arise at the tripolar fold.
USE_TRIPOLAR_GEOLONB_BUG = False ! [Boolean] default = False
! If true, use older code that incorrectly sets the longitude in some points
! along the tripolar fold to be off by 360 degrees.

! === module MOM_verticalGrid ===
! Parameters providing information about the vertical grid.
Expand Down Expand Up @@ -291,19 +300,22 @@ INIT_LAYERS_FROM_Z_FILE = True ! [Boolean] default = False
! Z-space file on a latitude-longitude grid.

! === module MOM_initialize_layers_from_Z ===
TEMP_SALT_Z_INIT_FILE = "MOM6_IC_TS.nc"
TEMP_SALT_Z_INIT_FILE = "MOM6_IC_TS.nc" ! default = "temp_salt_z.nc"
! The name of the z-space input file used to initialize
! temperatures (T) and salinities (S). If T and S are not
! in the same file, TEMP_Z_INIT_FILE and SALT_Z_INIT_FILE
! must be set.
Z_INIT_FILE_PTEMP_VAR = "temp" ! default = "ptemp"
Z_INIT_FILE_PTEMP_VAR = "temp" ! default = "ptemp"
! The name of the potential temperature variable in
! TEMP_Z_INIT_FILE.
Z_INIT_FILE_SALT_VAR = "salt" ! default = "salt"
! The name of the salinity variable in
! SALT_Z_INIT_FILE.
Z_INIT_ALE_REMAPPING = True ! [Boolean] default = False
! If True, then remap straight to model coordinate from file.
Z_INIT_REMAP_OLD_ALG = True ! [Boolean] default = False
! If false, uses the preferred remapping algorithm for initialization. If true,
! use an older, less robust algorithm for remapping.

! === module MOM_diag_mediator ===
!Jiande NUM_DIAG_COORDS = 2 ! default = 1
Expand All @@ -317,9 +329,25 @@ DIAG_COORDS = "z Z ZSTAR"
! is of the form "MODULE_SUFFIX,PARAMETER_SUFFIX,COORDINATE_NAME".
DIAG_COORD_DEF_Z="FILE:interpolate_zgrid_40L.nc,interfaces=zw"
DIAG_MISVAL = -1e34
!Jiande DIAG_COORD_DEF_RHO2 = "RFNC1:35,999.5,1028,1028.5,8.,1038.,0.0078125" ! default = "WOA09"
! Determines how to specify the coordinate
! resolution. Valid options are:
!AVAILABLE_DIAGS_FILE = "available_diags.002160" ! default = "available_diags.000000"
! A file into which to write a list of all available ocean diagnostics that can
! be included in a diag_table.
!DIAG_COORD_DEF_Z = "FILE:vgrid_75_2m.nc,dz" ! default = "WOA09"
! Determines how to specify the coordinate resolution. Valid options are:
! PARAM - use the vector-parameter DIAG_COORD_RES_Z
! UNIFORM[:N] - uniformly distributed
! FILE:string - read from a file. The string specifies
! the filename and variable name, separated
! by a comma or space, e.g. FILE:lev.nc,dz
! or FILE:lev.nc,interfaces=zw
! WOA09[:N] - the WOA09 vertical grid (approximately)
! FNC1:string - FNC1:dz_min,H_total,power,precision
! HYBRID:string - read from a file. The string specifies
! the filename and two variable names, separated
! by a comma or space, for sigma-2 and dz. e.g.
! HYBRID:vgrid.nc,sigma2,dz
!DIAG_COORD_DEF_RHO2 = "RFNC1:35,999.5,1028,1028.5,8.,1038.,0.0078125" ! default = "WOA09"
! Determines how to specify the coordinate resolution. Valid options are:
! PARAM - use the vector-parameter DIAG_COORD_RES_RHO2
! UNIFORM[:N] - uniformly distributed
! FILE:string - read from a file. The string specifies
Expand Down Expand Up @@ -377,7 +405,7 @@ KH_RES_FN_POWER = 100 ! [nondim] default = 2
! The power of dx/Ld in the Kh resolution function. Any positive integer may be
! used, although even integers are more efficient to calculate. Setting this
! greater than 100 results in a step-function being used.
!JW VISC_RES_FN_POWER = 2 ! [nondim] default = 100
VISC_RES_FN_POWER = 2 ! [nondim] default = 100
! The power of dx/Ld in the Kh resolution function. Any positive integer may be
! used, although even integers are more efficient to calculate. Setting this
! greater than 100 results in a step-function being used. This function affects
Expand Down Expand Up @@ -616,7 +644,7 @@ USE_JACKSON_PARAM = True ! [Boolean] default = False
MAX_RINO_IT = 25 ! [nondim] default = 50
! The maximum number of iterations that may be used to estimate the Richardson
! number driven mixing.
VERTEX_SHEAR = True ! [Boolean] default = False
VERTEX_SHEAR = False ! [Boolean] default = False
! If true, do the calculations of the shear-driven mixing
! at the cell vertices (i.e., the vorticity points).
KD_TRUNC_KAPPA_SHEAR = 2.0E-07 ! [m2 s-1] default = 2.0E-07
Expand All @@ -639,14 +667,14 @@ KAPPA_SHEAR_ALL_LAYER_TKE_BUG = True ! [Boolean] default = False

! === module MOM_diabatic_aux ===
! The following parameters are used for auxiliary diabatic processes.
PRESSURE_DEPENDENT_FRAZIL = false ! [Boolean] default = False
PRESSURE_DEPENDENT_FRAZIL = False ! [Boolean] default = False
! If true, use a pressure dependent freezing temperature when making frazil. The
! default is false, which will be faster but is inappropriate with ice-shelf
! cavities.
VAR_PEN_SW = True ! [Boolean] default = False
! If true, use one of the CHL_A schemes specified by OPACITY_SCHEME to determine
! the e-folding depth of incoming short wave radiation.
CHL_FILE = CHLCLIM
CHL_FILE = CHLCLIM !
! CHL_FILE is the file containing chl_a concentrations in the variable CHL_A. It
! is used when VAR_PEN_SW and CHL_FROM_FILE are true.

Expand Down Expand Up @@ -692,14 +720,6 @@ MIX_LEN_EXPONENT = 1.0 ! [nondim] default = 2.0
USE_LA_LI2016 = MOM6_REPRO_LA ! [nondim] default = False
! A logical to use the Li et al. 2016 (submitted) formula to determine the
! Langmuir number.
EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
! EPBL_LANGMUIR_SCHEME selects the method for including Langmuir turbulence.
! Valid values are:
! NONE - Do not do any extra mixing due to Langmuir turbulence
! RESCALE - Use a multiplicative rescaling of mstar to account for Langmuir
! turbulence
! ADDITIVE - Add a Langmuir turblence contribution to mstar to other
! contributions
USE_WAVES = MOM6_USE_WAVES ! [Boolean] default = False
! If true, enables surface wave modules.
WAVE_METHOD = "SURFACE_BANDS" ! default = "EMPTY"
Expand All @@ -723,6 +743,14 @@ STK_BAND_COUPLER = 3 ! default = 1
! will fail.
SURFBAND_WAVENUMBERS = 0.04, 0.11, 0.3305 ! [rad/m] default = 0.12566
! Central wavenumbers for surface Stokes drift bands.
EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
! EPBL_LANGMUIR_SCHEME selects the method for including Langmuir turbulence.
! Valid values are:
! NONE - Do not do any extra mixing due to Langmuir turbulence
! RESCALE - Use a multiplicative rescaling of mstar to account for Langmuir
! turbulence
! ADDITIVE - Add a Langmuir turblence contribution to mstar to other
! contributions
LT_ENHANCE_COEF = 0.044 ! [nondim] default = 0.447
! Coefficient for Langmuir enhancement of mstar
LT_ENHANCE_EXP = -1.5 ! [nondim] default = -1.33
Expand Down Expand Up @@ -778,13 +806,14 @@ ENERGYSAVEDAYS = 0.25 ! [days] default = 1.0
! other globally summed diagnostics.

! === module ocean_model_init ===

! === module MOM_surface_forcing ===
OCEAN_SURFACE_STAGGER = "A" ! default = "C"
! A case-insensitive character string to indicate the
! staggering of the surface velocity field that is
! returned to the coupler. Valid values include
! 'A', 'B', or 'C'.

! === module MOM_surface_forcing ===
MAX_P_SURF = 0.0 ! [Pa] default = -1.0
! The maximum surface pressure that can be exerted by the atmosphere and
! floating sea-ice or ice shelves. This is needed because the FMS coupling
Expand Down