Merge pull request #1234 from esm-tools/feat/fesom26_standalone

Standalone Fesom 2.6 in esm_tools

namelists/fesom2/2.6/namelist.config

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+! This is the namelist file for model general configuration
+
+&modelname
+runid='fesom'
+/
+
+&timestep
+step_per_day=32 !96 !96 !72 !72 !45 !72 !96
+run_length=62 !62 !62 !62 !28
+run_length_unit='y' ! y, m, d, s
+/
+
+&clockinit              ! the model starts at
+timenew=0.0
+daynew=1
+yearnew=1958
+/
+
+&paths
+meshpath = '/work/ab0246/a270092/input/fesom2/core2/'
+climatedatapath = '/work/ab0246/a270092/input/FESOM2/INITIAL/phc3.0/'
+resultpath = '../result_tmp/'
+/
+
+&restart_log
+restart_length=1            ! --> do netcdf restart ( only required for d,h,s cases, y, m take 1)
+restart_length_unit='y'     !output period: y, d, h, s, off
+raw_restart_length=1        ! --> do core dump restart
+raw_restart_length_unit='y' ! e.g. y, d, h, s, off
+bin_restart_length=1        ! --> do derived type binary restart 
+bin_restart_length_unit='y' ! e.g. y, d, h, s, off
+logfile_outfreq=960         !in logfile info. output frequency, # steps
+/
+
+&ale_def
+which_ALE='zstar'       ! 'linfs','zlevel', 'zstar'
+use_partial_cell=.true.
+/
+
+&geometry
+cartesian=.false.
+fplane=.false.
+cyclic_length=360       ![degree]
+rotated_grid=.true.     !option only valid for coupled model case now
+force_rotation=.true.
+alphaEuler=50.          ![degree] Euler angles, convention:
+betaEuler=15.           ![degree] first around z, then around new x,
+gammaEuler=-90.         ![degree] then around new z.
+/
+
+&calendar
+include_fleapyear=.true.
+/
+
+&run_config
+use_ice=.true.                  ! ocean+ice
+use_cavity=.false.              !
+use_cavity_partial_cell=.false. 
+use_floatice = .false.
+use_sw_pene=.true.
+flag_debug=.false.
+use_transit=.false.
+/
+
+&machine
+n_levels=2
+n_part= 5, 128          ! 432 number of partitions on each hierarchy level
+/
+
+&icebergs
+use_icesheet_coupling=.false.
+ib_num=1
+use_icebergs=.false.
+steps_per_ib_step=8
+ib_async_mode=0
+/

namelists/fesom2/2.6/namelist.cvmix

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+! namelist for Turbulent Kinetic Energy (TKE) 
+&param_tke
+tke_c_k            = 0.1              
+tke_c_eps          = 0.7               
+tke_alpha          = 30.0              
+tke_mxl_min        = 1.0e-8            
+tke_kappaM_min     = 0.0                
+tke_kappaM_max     = 100.0              
+tke_cd            = 3.75 ! for Dirichlet boundary conditions
+!tke_cd             = 1.0  ! for Neumann boundary conditions 
+tke_surf_min       = 1.0e-4             
+tke_min            = 1.0e-6
+! tke_mxl_choice ... Can only be 1 or 2, choice of calculation of mixing 
+! length; currently only Blanke, B., P. Delecluse option is implemented
+tke_mxl_choice     = 2     
+tke_dolangmuir     = .false.    
+/
+
+! namelist for IDEMIX von Pollman et al. (2017)
+&param_idemix
+idemix_tau_v       = 172800.0   ! 2days ! time scale for vertical symmetrisation (sec)
+idemix_tau_h       = 1296000.0  !15days ! time scale for horizontal symmetrisation
+idemix_gamma       = 1.570      ! constant of order one derived from the shape of the spectrum in m space (dimensionless)
+idemix_jstar       = 5.0        ! spectral bandwidth in modes (dimensionless)
+idemix_mu0         = 0.33333333 ! dissipation parameter (dimensionless)
+idemix_sforcusage  = 0.2
+idemix_n_hor_iwe_prop_iter = 5  ! iterations for contribution from horiz. wave propagation
+idemix_surforc_file = '/work/ollie/clidyn/forcing/IDEMIX/fourier_smooth_2005_cfsr_inert_rgrid.nc'
+idemix_surforc_vname= 'var706'
+idemix_botforc_file = '/work/ollie/clidyn/forcing/IDEMIX/tidal_energy_gx1v6_20090205_rgrid.nc'
+idemix_botforc_vname= 'wave_dissipation'
+/
+
+! namelist for PP
+&param_pp
+pp_use_fesompp     = .true.     ! if true use fesom flavor off PP if false use original PP of Pacanowski & Philander
+pp_Av0             = 0.01       ! mixing coeff. for PP
+pp_alpha           = 5.0        ! alpha param eq. (1) in Pacanowski and Philander 1981
+pp_exp             = 2.0        ! n param eq. (1) in Pacanowski and Philander 1981
+pp_Avbckg          = 1.0e-4     ! const. pp background viscosity
+pp_Kvbckg          = 1.0e-5     ! const. pp background diffusivity
+pp_use_nonconstKvb = .true.     ! use lat and depth dependent background diffusivity
+/
+
+! namelist for KPP
+&param_kpp
+kpp_use_fesomkpp   = .false.     ! if true use cvmix MOM5 like kpp if false use cvmix MOM6 like kpp
+kpp_use_enhanceKv  = .true.     ! If true, add enhanced diffusivity at base of boundary layer
+kpp_use_compEkman  = .true.     ! If true, compute Ekman depth limit for OBLdepth 
+kpp_use_monob      = .true.     ! If true, compute Monin-Obukhov limit for OBLdepth
+kpp_interptype_ri  = "linear"    ! Type of interpolation in determining OBL depth: linear,quadratic,cubic
+kpp_interptype_atobl= "LMD94"   ! Type of interpolation of visc and diff at obl depth: linear,quadratic,cubic,LMD94
+kpp_matchtechc     = "ParabolicNonLocal" ! Setting diffusivity and NLT profile functions:SimpleShapes, MatchGradient, MatchBoth, ParabolicNonLocal
+kpp_internalmix    = "KPP"      ! Ri-number dependet mixing scheme below the OBL: 'PP' or 'KPP'
+kpp_reduce_tauuice = .false.    ! If True, reduce the wind stress (ustar) under sea ice.
+kpp_Av0            = 5.0e-3     ! leading coefficient of shear mixing formula, units: m^2/s: default= 5e-3  
+kpp_Kv0            = 5.0e-3 
+kpp_Ri0            = 0.7        ! critical Richardson number value, units: unitless (0.7 in LMD94)
+kpp_pp_Av0         = 0.01       ! Parameter in case of PP mixing below the OBL
+kpp_use_nonconstKvb= .true.     ! If True use non constant background diffusivity of Qiang from FESOM1.4
+kpp_Avbckg         = 1.0e-4     ! Values for const. background viscosity and diffusivity
+kpp_Kvbckg         = 1.0e-5
+/
+
+! namelist for TIDAL
+&param_tidal
+tidal_mixscheme    = "Simmons"
+tidal_efficiency   = 0.2         ! units: unitless (fraction); (Gamma in Simmons et al.)
+tidal_vert_decayscale= 500.0     ! units: m; zeta in Simmons et al. (used to compute the vertical deposition function)   
+tidal_max_coeff    = 50e-4       ! units: m^2/s; largest acceptable value for diffusivity          
+tidal_lcl_mixfrac  = 0.33        !tidal dissipation efficiency (q in Simmons et al.), i.e. fraction of energy that dissipates locally
+tidal_depth_cutoff = 0.0         !depth of the shallowest column where tidal mixing is computed (positive below surface)
+tidal_botforc_file = '/albedo/work/projects/p_pool_fesom1/fesom2.0/forcing/idemix/tidal_energy_gx1v6_20090205_rgrid.nc'
+/
+

namelists/fesom2/2.6/namelist.dyn

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+&dynamics_visc
+visc_gamma0  = 0.003 ! [m/s],   backgroung viscosity= gamma0*len, it should be as small a s possible (keep it < 0.01 m/s).
+visc_gamma1  = 0.1   ! [nodim], for computation of the flow aware viscosity
+visc_gamma2  = 0.285 ! [s/m],   is only used in easy backscatter option
+visc_easybsreturn= 1.5
+
+opt_visc     = 5     
+check_opt_visc=.true.  ! check if optvisc=5 is valid based on ratio resol/rossbyR
+! 5=Kinematic (easy) Backscatter
+! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian)
+! 7=Biharmonic flow aware (viscosity depends on velocity differences)
+! 8=Dynamic Backscatter
+
+use_ivertvisc= .true.  
+/
+
+&dynamics_general
+momadv_opt   = 2       ! option for momentum advection in moment only =2
+use_freeslip = .false. ! Switch on free slip
+use_wsplit   = .false. ! Switch for implicite/explicte splitting of vert. velocity
+wsplit_maxcfl= 1.0     ! maximum allowed CFL criteria in vertical (0.5 < w_max_cfl < 1.) 
+                       ! in older FESOM it used to be w_exp_max=1.e-3
+ldiag_KE=.false.       ! activates energy diagnostics
+AB_order=2
+
+use_ssh_se_subcycl = .false.
+se_BTsteps     = 50   
+se_BTtheta     = 0.14   ! default: 0.14, 
+se_bottdrag    = .true.
+se_bdrag_si    = .true. ! bottomdrag semi-implicite/explicite
+se_visc        = .true.
+se_visc_gamma0 = 10  
+se_visc_gamma1 = 19500  !19500 (core2@32spd), 2750 (core2@72spd)
+se_visc_gamma2 = 0
+/
+

namelists/fesom2/2.6/namelist.forcing

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+! This is the namelist file for forcing
+
+&forcing_exchange_coeff
+Ce_atm_oce=0.00175 ! exchange coeff. of latent heat over open water
+Ch_atm_oce=0.00175 ! exchange coeff. of sensible heat over open water
+Cd_atm_oce=0.001  ! drag coefficient between atmosphere and water
+Ce_atm_ice=0.00175 ! exchange coeff. of latent heat over ice
+Ch_atm_ice=0.00175 ! exchange coeff. of sensible heat over ice
+Cd_atm_ice=0.0012  ! drag coefficient between atmosphere and ice 
+Swind     =0.0     ! parameterization for coupled current feedback
+/
+
+&forcing_bulk
+AOMIP_drag_coeff=.false.
+ncar_bulk_formulae=.true.
+ncar_bulk_z_wind=10.0 ! height at which wind forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
+ncar_bulk_z_tair=10.0 ! height at which temp forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
+ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
+
+/
+
+&land_ice
+use_landice_water=.false.
+landice_start_mon=5
+landice_end_mon=10
+fwf_path='./mesh/'
+
+/
+
+&age_tracer
+use_age_tracer=.false.
+use_age_mask=.false.
+age_tracer_path='./mesh/'
+age_start_year=2000
+
+/
+
+&nam_sbc
+   nm_xwind_file = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/uas.'        ! name of file with wind speeds x
+   nm_ywind_file = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/vas.'        ! name of file with wind speeds y
+   nm_xstre_file = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/uas.'        ! name of file with wind stress x
+   nm_ystre_file = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/vas.'        ! name of file with wind stress y
+   nm_humi_file  = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/huss.'        ! name of file with humidity
+   nm_qsr_file   = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/rsds.'    ! name of file with solar heat
+   nm_qlw_file   = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/rlds.'    ! name of file with Long wave
+   nm_tair_file  = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/tas.'        ! name of file with 2m air temperature
+   nm_prec_file  = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/prra.' ! name of file with total precipitation
+   nm_snow_file  = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/prsn.' ! name of file with snow  precipitation
+   nm_mslp_file  = '/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/psl.'         ! air_pressure_at_sea_level
+   nm_xwind_var  = 'uas'   ! name of variable in file with wind
+   nm_ywind_var  = 'vas'   ! name of variable in file with wind
+   nm_xstre_var  = 'uas'   ! name of variable in file with wind
+   nm_ystre_var  = 'vas'   ! name of variable in file with wind
+   nm_humi_var   = 'huss'  ! name of variable in file with humidity
+   nm_qsr_var    = 'rsds'  ! name of variable in file with solar heat
+   nm_qlw_var    = 'rlds'  ! name of variable in file with Long wave
+   nm_tair_var   = 'tas'   ! name of variable in file with 2m air temperature
+   nm_prec_var   = 'prra'  ! name of variable in file with total precipitation
+   nm_snow_var   = 'prsn'  ! name of variable in file with total precipitation
+   nm_mslp_var   = 'psl'   ! name of variable in file with air_pressure_at_sea_level
+   nm_nc_iyear   = 1900
+   nm_nc_imm     = 1            ! initial month of time axis in netCDF 
+   nm_nc_idd     = 1            ! initial day of time axis in netCDF
+   nm_nc_freq    = 1            ! data points per day (i.e. 86400 if the time axis is in seconds)
+   nm_nc_tmid    = 0            ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55)
+   l_xwind=.true. l_ywind=.true. l_xstre=.false. l_ystre=.false. l_humi=.true. l_qsr=.true. l_qlw=.true. l_tair=.true. l_prec=.true. l_mslp=.false. l_cloud=.false. l_snow=.true.
+   runoff_data_source ='CORE2'	!Dai09, CORE2
+   nm_runoff_file     ='/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/CORE2_runoff.nc'
+   !nm_runoff_file     ='/work/ollie/qwang/FESOM2_input/mesh/CORE2_finaltopo_mean/forcing_data_on_grid/runoff_clim.nc'
+   !runoff_data_source ='Dai09'  !Dai09, CORE2, JRA55
+   !runoff_climatology =.true.
+   sss_data_source    ='CORE2'
+   nm_sss_data_file   ='/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/PHC2_salx.nc'
+   chl_data_source    ='None' !'Sweeney' monthly chlorophyll climatology or 'NONE' for constant chl_const (below). Make use_sw_pene=.TRUE. in namelist.config!
+   nm_chl_data_file   ='/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/Sweeney/Sweeney_2005.nc'
+   chl_const          = 0.1
+   use_runoff_mapper  = .FALSE.
+   runoff_basins_file = 'runoff_maps_regular.nc'
+   runoff_radius      = 500000.
+/

namelists/fesom2/2.6/namelist.ice

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+! Ice namelist
+&ice_dyn
+whichEVP=0             ! 0=standart; 1=mEVP; 2=aEVP
+Pstar=30000.0          ! [N/m^2]
+ellipse=2.0
+c_pressure=20.0        ! ice concentration parameter used in ice strength computation
+delta_min=1.0e-11      ! [s^(-1)]
+evp_rheol_steps=120    ! number of EVP subcycles
+alpha_evp=250          ! constant that control numerical stability of mEVP. Adjust with resolution. 
+beta_evp=250           ! constant that control numerical stability of mEVP. Adjust with resolution.
+c_aevp=0.15            ! a tuning constant in aEVP. Adjust with resolution.
+Cd_oce_ice=0.0055      ! drag coef. oce - ice 
+ice_gamma_fct=0.5      ! smoothing parameter
+ice_diff=0.0           ! diffusion to stabilize
+theta_io=0.0           ! rotation angle
+ice_ave_steps=1        ! ice step=ice_ave_steps*oce_step
+/
+
+&ice_therm
+Sice=4.0               ! Ice salinity 3.2--5.0 ppt.
+h0=.5                  ! Lead closing parameter [m] 
+emiss_ice=0.97         ! Emissivity of Snow/Ice,
+emiss_wat=0.97         ! Emissivity of open water
+albsn=0.81             ! Albedo: frozen snow
+albsnm=0.77            !         melting snow
+albi=0.7               !         frozen ice
+albim=0.68             !         melting ice
+albw=0.1               !         open water
+con=2.1656             ! Thermal conductivities: ice; W/m/K
+consn=0.31             !                         snow
+/