CVMix Interface

Community Vertical Mixing (CVMix, http://cvmix.github.io) library interface. Provides an optional alternative to the native GOTM two-equation closures for ocean models that use CVMix as their mixing library.

Mixing parameterisations available through CVMix:

• Surface boundary layer (parabolic KPP-style)

• Bottom boundary layer

• Interior non-convective mixing (background diffusivity; PP or KPP shear scheme)

• Interior convective mixing

CVMix community vertical-mixing library interface.

Provides CVMixState — the state container for the Community Vertical Mixing (CVMix) parameterisations. CVMix is an optional alternative to the GOTM two-equation closures, intended for use in ocean general circulation models that use CVMix as their mixing library.

class pygotm.cvmix.CVMixState(zsbl=0.0, zbbl=0.0, cvmix_g=9.81, cvmix_rho0=1027.0, cvmix_gorho0=0.00955209347614411, use_surface_layer=True, use_interior=False, use_bottom_layer=False, use_background=False, use_shear=False, use_convection=False, use_tidal_mixing=False, use_double_diffusion=False, sbl_langmuir_method=0, background_diffusivity=1e-05, background_viscosity=0.0001, shear_mix_scheme=2, shear_num_smooth_Ri=1, shear_PP_nu_zero=0.005, shear_PP_alpha=5.0, shear_PP_exp=2.0, shear_KPP_nu_zero=0.005, shear_KPP_Ri_zero=0.7, shear_KPP_exp=3.0, convection_diffusivity=1.0, convection_viscosity=1.0, convection_basedOnBVF=True, convection_triggerBVF=0.0, z_w=None, z_r=None, h_r=None)

Bases: object

Python-side CVMix interface state.

Parameters:

• zsbl (float)

• zbbl (float)

• cvmix_g (float)

• cvmix_rho0 (float)

• cvmix_gorho0 (float)

• use_surface_layer (bool)

• use_interior (bool)

• use_bottom_layer (bool)

• use_background (bool)

• use_shear (bool)

• use_convection (bool)

• use_tidal_mixing (bool)

• use_double_diffusion (bool)

• sbl_langmuir_method (int)

• background_diffusivity (float)

• background_viscosity (float)

• shear_mix_scheme (int)

• shear_num_smooth_Ri (int)

• shear_PP_nu_zero (float)

• shear_PP_alpha (float)

• shear_PP_exp (float)

• shear_KPP_nu_zero (float)

• shear_KPP_Ri_zero (float)

• shear_KPP_exp (float)

• convection_diffusivity (float)

• convection_viscosity (float)

• convection_basedOnBVF (bool)

• convection_triggerBVF (float)

• z_w (ndarray | None)

• z_r (ndarray | None)

• h_r (ndarray | None)

background_diffusivity: float = 1e-05

background_viscosity: float = 0.0001

convection_basedOnBVF: bool = True

convection_diffusivity: float = 1.0

convection_triggerBVF: float = 0.0

convection_viscosity: float = 1.0

cvmix_g: float = 9.81

cvmix_gorho0: float = 0.00955209347614411

cvmix_rho0: float = 1027.0

h_r: ndarray | None = None

sbl_langmuir_method: int = 0

shear_KPP_Ri_zero: float = 0.7

shear_KPP_exp: float = 3.0

shear_KPP_nu_zero: float = 0.005

shear_PP_alpha: float = 5.0

shear_PP_exp: float = 2.0

shear_PP_nu_zero: float = 0.005

shear_mix_scheme: int = 2

shear_num_smooth_Ri: int = 1

use_background: bool = False

use_bottom_layer: bool = False

use_convection: bool = False

use_double_diffusion: bool = False

use_interior: bool = False

use_shear: bool = False

use_surface_layer: bool = True

use_tidal_mixing: bool = False

z_r: ndarray | None = None

z_w: ndarray | None = None

zbbl: float = 0.0

zsbl: float = 0.0

CVMix interface — translation of gotm_cvmix.F90.

Provides an interface to the Community Ocean Vertical Mixing Project (CVMix, http://cvmix.github.io) in the General Ocean Turbulence Model. CVMix is an optional alternative to the native GOTM two-equation closures for ocean models that use CVMix as their mixing library.

Fortran CVMix library modules (cvmix_background, cvmix_convection, cvmix_kpp, cvmix_shear, cvmix_tidal, cvmix_ddiff) are encapsulated by the Python mixing routines below. All configuration and state are held in CVMixState.

Mixing parameterisations:

• Surface boundary layer — surface_layer() (parabolic KPP-style).

• Bottom boundary layer — bottom_layer().

• Interior non-convective — interior_nonconv() (background diffusivity; Pacanowski–Philander or KPP shear scheme).

• Interior convective — interior_conv().

Public interface: init_cvmix(), init_cvmix_yaml(), post_init_cvmix(), do_cvmix(), clean_cvmix(), surface_layer(), bottom_layer(), interior_nonconv(), interior_conv(), CVMixState.

Original FORTRAN authors: Lars Umlauf; adapted for CVMix by Qing Li.

class pygotm.cvmix.gotm_cvmix.CVMixState(zsbl=0.0, zbbl=0.0, cvmix_g=9.81, cvmix_rho0=1027.0, cvmix_gorho0=0.00955209347614411, use_surface_layer=True, use_interior=False, use_bottom_layer=False, use_background=False, use_shear=False, use_convection=False, use_tidal_mixing=False, use_double_diffusion=False, sbl_langmuir_method=0, background_diffusivity=1e-05, background_viscosity=0.0001, shear_mix_scheme=2, shear_num_smooth_Ri=1, shear_PP_nu_zero=0.005, shear_PP_alpha=5.0, shear_PP_exp=2.0, shear_KPP_nu_zero=0.005, shear_KPP_Ri_zero=0.7, shear_KPP_exp=3.0, convection_diffusivity=1.0, convection_viscosity=1.0, convection_basedOnBVF=True, convection_triggerBVF=0.0, z_w=None, z_r=None, h_r=None)

Bases: object

Python-side CVMix interface state.

Parameters:

• zsbl (float)

• zbbl (float)

• cvmix_g (float)

• cvmix_rho0 (float)

• cvmix_gorho0 (float)

• use_surface_layer (bool)

• use_interior (bool)

• use_bottom_layer (bool)

• use_background (bool)

• use_shear (bool)

• use_convection (bool)

• use_tidal_mixing (bool)

• use_double_diffusion (bool)

• sbl_langmuir_method (int)

• background_diffusivity (float)

• background_viscosity (float)

• shear_mix_scheme (int)

• shear_num_smooth_Ri (int)

• shear_PP_nu_zero (float)

• shear_PP_alpha (float)

• shear_PP_exp (float)

• shear_KPP_nu_zero (float)

• shear_KPP_Ri_zero (float)

• shear_KPP_exp (float)

• convection_diffusivity (float)

• convection_viscosity (float)

• convection_basedOnBVF (bool)

• convection_triggerBVF (float)

• z_w (ndarray | None)

• z_r (ndarray | None)

• h_r (ndarray | None)

zsbl: float = 0.0

zbbl: float = 0.0

cvmix_g: float = 9.81

cvmix_rho0: float = 1027.0

cvmix_gorho0: float = 0.00955209347614411

use_surface_layer: bool = True

use_interior: bool = False

use_bottom_layer: bool = False

use_background: bool = False

use_shear: bool = False

use_convection: bool = False

use_tidal_mixing: bool = False

use_double_diffusion: bool = False

sbl_langmuir_method: int = 0

background_diffusivity: float = 1e-05

background_viscosity: float = 0.0001

shear_mix_scheme: int = 2

shear_num_smooth_Ri: int = 1

shear_PP_nu_zero: float = 0.005

shear_PP_alpha: float = 5.0

shear_PP_exp: float = 2.0

shear_KPP_nu_zero: float = 0.005

shear_KPP_Ri_zero: float = 0.7

shear_KPP_exp: float = 3.0

convection_diffusivity: float = 1.0

convection_viscosity: float = 1.0

convection_basedOnBVF: bool = True

convection_triggerBVF: float = 0.0

z_w: ndarray | None = None

z_r: ndarray | None = None

h_r: ndarray | None = None

pygotm.cvmix.gotm_cvmix.bottom_layer(state, nlev, h, num, nuh, *, u_taub, hbl)

Simple parabolic bottom boundary-layer enhancement.

Return type:

None

Parameters:

• state (CVMixState)

• nlev (int)

• h (ndarray)

• num (ndarray)

• nuh (ndarray)

• u_taub (float)

• hbl (float)

pygotm.cvmix.gotm_cvmix.clean_cvmix(state)

Release CVMix work arrays.

Return type:

None

Parameters:

state (CVMixState)

pygotm.cvmix.gotm_cvmix.do_cvmix(state, nlev, h0, h, rho, u, v, NN, NNT, NNS, SS, u_taus, u_taub, num, nuh, nus, Rig)

Dispatch CVMix contributions into GOTM diffusivity arrays.

Return type:

None

Parameters:

• state (CVMixState)

• nlev (int)

• h0 (float)

• h (ndarray)

• rho (ndarray)

• u (ndarray)

• v (ndarray)

• NN (ndarray)

• NNT (ndarray)

• NNS (ndarray)

• SS (ndarray)

• u_taus (float)

• u_taub (float)

• num (ndarray)

• nuh (ndarray)

• nus (ndarray)

• Rig (ndarray)

pygotm.cvmix.gotm_cvmix.init_cvmix(state=None, branch=None)

Initialise CVMix state from an optional YAML-like branch.

Return type:

CVMixState

Parameters:

• state (CVMixState | None)

• branch (dict[str, Any] | None)

pygotm.cvmix.gotm_cvmix.init_cvmix_yaml(state, branch)

Apply CVMix YAML options.

Return type:

None

Parameters:

• state (CVMixState)

• branch (dict[str, Any])

pygotm.cvmix.gotm_cvmix.interior_conv(state, nlev, NN, num, nuh, nus)

Apply convective interior mixing where the water column is unstable.

Return type:

None

Parameters:

• state (CVMixState)

• nlev (int)

• NN (ndarray)

• num (ndarray)

• nuh (ndarray)

• nus (ndarray)

pygotm.cvmix.gotm_cvmix.interior_nonconv(state, nlev, NN, NNT, NNS, SS, num, nuh, nus, Rig)

Compute non-convective interior CVMix contributions.

Return type:

None

Parameters:

• state (CVMixState)

• nlev (int)

• NN (ndarray)

• NNT (ndarray)

• NNS (ndarray)

• SS (ndarray)

• num (ndarray)

• nuh (ndarray)

• nus (ndarray)

• Rig (ndarray)

pygotm.cvmix.gotm_cvmix.post_init_cvmix(state, nlev, h0, gravity, rho0)

Initialise grid arrays and physical constants.

Return type:

None

Parameters:

• state (CVMixState)

• nlev (int)

• h0 (float)

• gravity (float)

• rho0 (float)

pygotm.cvmix.gotm_cvmix.surface_layer(state, nlev, h, num, nuh, *, u_taus, hbl)

Simple parabolic surface boundary-layer enhancement.

Return type:

None

Parameters:

• state (CVMixState)

• nlev (int)

• h (ndarray)

• num (ndarray)

• nuh (ndarray)

• u_taus (float)

• hbl (float)