Transient Tracers

CMakeLists.txt

@@ -13,5 +13,6 @@ set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs F
 set(CRAY OFF CACHE BOOL "compile with cray ftn")
 set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
 #set(VERBOSE OFF CACHE BOOL "toggle debug output")
+set(ASYNC_ICEBERGS ON CACHE BOOL "compile fesom with or without support for asynchronous iceberg computations")
 #add_subdirectory(oasis3-mct/lib/psmile)
 add_subdirectory(src)

config/namelist.config

@@ -54,6 +54,12 @@ use_cavity=.false.              !
 use_cavity_partial_cell=.false. 
 use_floatice = .false.
 use_sw_pene=.true.
+use_transit=.false.
+anthro_transit=.false.
+paleo_transit=.false.
+length_transit=1                ! 166 for anthro_transit=.true.
+ti_start_transit=1              ! 1 for D14C, 80 for CFC-12
+ifile_transit='/work/ollie/mbutzin/fesom2/input/trace_gases/Table_CO2_isoC_CFC12_SF6.txt'
 /
 
 &machine

config/namelist.config.transit

@@ -0,0 +1,63 @@
+! 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/ollie/projects/clidyn/FESOM2/meshes/core2/'
+ClimateDataPath='/work/ollie/projects/clidyn/FESOM2/hydrography/phc3.0/'
+ResultPath='../result_tmp/'
+/
+
+&restart_log
+restart_length=1        !only required for d,h,s cases,  y, m take 1
+restart_length_unit='y' !output period: y,  d, h, s 
+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.
+use_transit=.true.
+/
+
+&machine
+n_levels=2
+n_part= 12, 36          ! 432 number of partitions on each hierarchy level
+/

config/namelist.io.transit

@@ -0,0 +1,46 @@
+&diag_list
+ldiag_solver     =.false.
+lcurt_stress_surf=.false.
+ldiag_curl_vel3  =.false.
+ldiag_energy     =.false.
+ldiag_salt3D     =.false.
+ldiag_dMOC       =.false.
+ldiag_DVD        =.false.
+ldiag_forc       =.false.
+/
+
+&nml_listsize
+io_listsize=100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
+/
+
+! for sea ice related variables use_ice should be true, otherewise there will be no output
+! for 'curl_surf' to work lcurt_stress_surf must be .true. otherwise no output
+! for 'fer_C', 'bolus_u', 'bolus_v', 'bolus_w', 'fer_K' to work Fer_GM must be .true. otherwise no output
+! 'otracers' - all other tracers if applicable
+! for 'dMOC' to work ldiag_dMOC must be .true. otherwise no output
+&nml_list
+io_list =  'sst       ',1, 'm', 4,
+           'sss       ',1, 'm', 4,
+    	   'ssh       ',1, 'm', 4,
+           'uice      ',1, 'm', 4,
+           'vice      ',1, 'm', 4,
+           'a_ice     ',1, 'm', 4,
+           'm_ice     ',1, 'm', 4,
+           'm_snow    ',1, 'm', 4,
+           'MLD1      ',1, 'm', 4,
+           'MLD2      ',1, 'm', 4,
+           'tx_sur    ',1, 'm', 4,
+           'ty_sur    ',1, 'm', 4,
+           'temp      ',1, 'y', 4,
+           'salt      ',1, 'y', 8,
+           'otracers  ',1, 'm', 4,
+           'N2        ',1, 'y', 4,
+           'Kv        ',1, 'y', 4,
+           'u         ',1, 'y', 4,
+           'v         ',1, 'y', 4,
+           'w         ',1, 'y', 4,
+           'Av        ',1, 'y', 4,
+           'bolus_u   ',1, 'y', 4,
+           'bolus_v   ',1, 'y', 4,
+           'bolus_w   ',1, 'y', 4,
+/

config/namelist.oce

@@ -91,3 +91,24 @@ filelist = 'phc3.0_winter.nc', 'phc3.0_winter.nc' ! list of files in ClimateData
 varlist  = 'salt', 'temp'                 ! variables to read from specified files
 t_insitu = .true.                         ! if T is insitu it will be converted to potential after reading it
 /
+
+&transit_param
+r14c_nh = 1.0000   	! atm. F14C ratio, 30°N-90°N
+r14c_tz = 1.0000   	! atm. F14C ratio, ITCZ
+r14c_sh = 1.0000   	! atm. F14C ratio, 30°S-90°S
+r39ar_a = 1.0000	! atm. 39Ar/Ar ratio, global mean
+xarg_a  = 9.34e-3	! atm. Argon concn. (mole fraction), global mean
+xco2_a  = 284.32e-6	! atm. CO2 concn. (mole fraction), global mean
+xf12_nh = 0.0e-12	! atm. CFC-12 concn. (ppt), 10°N-90°N
+xf12_sh = 0.0e-12	! atm. CFC_12 concn. (ppt), 10°S-90°S
+xsf6_nh = 0.0e-12	! atm. SF6 concn. (ppt), 10°N-90°N
+xsf6_sh = 0.0e-12	! atm. SF6 concn. (ppt), 10°S-90°S
+f12t_nh = 0.0e-12	! atm. CFC-12 trend (ppt / mon), 10°N-90°N
+f12t_sh = 0.0e-12	! atm. CFC-12 trend (ppt / mon), 10°S-90°S
+sf6t_nh = 0.0e-12	! atm. SF6 trend (ppt / mon), 10°N-90°N
+sf6t_sh = 0.0e-12	! atm. SF6 trend (ppt / mon), 10°S-90°S
+dic_0   = 2.00          ! mixed layer DIC concn. (mol / m**3), global mean
+arg_0   = 0.01          ! mixed layer Argon concn. (mol / m**3), global mean
+decay14 = 3.8561e-12    ! decay constant of 14C (1 / s), 1 a = 365.0 d
+decay39 = 8.1708e-11    ! decay constant of 39Ar (1 / s), 1 a = 365.0 d
+/

config/namelist.oce.c14

@@ -0,0 +1,105 @@
+! The namelist file for the finite-volume ocean model
+
+&oce_dyn
+C_d=0.0025             ! Bottom drag, nondimensional
+gamma0=0.003            ! [m/s],   backgroung viscosity= gamma0*len, it should be as small as possible (keep it < 0.01 m/s).
+gamma1=0.1          ! [nodim], for computation of the flow aware viscosity
+gamma2=0.285            ! [s/m],   is only used in easy backscatter option
+Div_c=.5  	       ! the strength of the modified Leith viscosity, nondimensional, 0.3 -- 1.0
+Leith_c=.05	       ! the strength of the Leith viscosity
+visc_option=5          ! 1=Harmonic Leith parameterization;
+                       ! 2=Laplacian+Leith+biharmonic background
+                       ! 3=Biharmonic Leith parameterization
+                       ! 4=Biharmonic flow aware
+                       ! 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
+easy_bs_return= 1.5     ! coefficient for returned sub-gridscale energy, to be used with visc_option=5 (easy backscatter)
+A_ver= 1.e-4	       ! Vertical viscosity, m^2/s
+scale_area=5.8e9       ! Visc. and diffus. are for an element with scale_area
+mom_adv=2              ! 1=vector CV, p1 vel, 2=sca. CV, 3=vector inv.
+free_slip=.false.      ! Switch on free slip
+i_vert_visc=.true.    
+w_split=.false.
+w_max_cfl=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
+SPP=.false.                 ! Salt Plume Parameterization
+Fer_GM=.true.               ! to swith on/off GM after Ferrari et al. 2010
+K_GM_max     = 1000 !! 2000.0       ! max. GM thickness diffusivity (m2/s)
+K_GM_min     = 2.0          ! max. GM thickness diffusivity (m2/s)
+K_GM_bvref   = 2            ! def of bvref in ferreira scaling 0=srf,1=bot mld,2=mean over mld,3=weighted mean over mld
+K_GM_rampmax = -1         ! Resol >K_GM_rampmax[km] GM on
+K_GM_rampmin = -1         ! Resol <K_GM_rampmin[km] GM off, in between linear scaled down
+K_GM_resscalorder = 1
+
+scaling_Ferreira   =.false.  ! GM vertical scaling after Ferreira et al.(2005) (as also implemented by Qiang in FESOM 1.4)
+scaling_Rossby     =.false. ! GM is smoothly switched off according to Rossby radius (from 1. in coarse areas to 0. where resolution reaches 2 points/Rossby radius)
+scaling_resolution =.true.  ! GM is spatially scaled with resolution; A value of K_GM corresponds then to a resolution of 100km
+scaling_FESOM14    =.false.  ! special treatment of GM in the NH (as also implemented by Qiang in FESOM 1.4; it is zero within the boundary layer)
+
+Redi  =.true.
+visc_sh_limit=5.0e-3       ! for KPP, max visc due to shear instability
+mix_scheme='KPP'           ! vertical mixing scheme: KPP, PP 
+Ricr   = 0.3               ! critical bulk Richardson Number
+concv  = 1.6               ! constant for pure convection (eqn. 23) (Large 1.5-1.6; MOM default 1.8)
+/
+
+&oce_tra 
+use_momix     = .true.     ! switch on/off  !Monin-Obukhov -> TB04 mixing
+momix_lat     = -50.0      ! latitidinal treshhold for TB04, =90 --> global
+momix_kv      = 0.01       ! PP/KPP, mixing coefficient within MO length
+use_instabmix = .true.     ! enhance convection in case of instable stratification
+instabmix_kv  = 0.1
+use_windmix   = .false.     ! enhance mixing trough wind only for PP mixing (for stability)
+windmix_kv    = 1.e-3
+windmix_nl    = 2
+
+smooth_bh_tra =.false.     ! use biharmonic diffusion (filter implementation) for tracers
+gamma0_tra    = 0.0005     ! gammaX_tra are analogous to those in the dynamical part
+gamma1_tra    = 0.0125
+gamma2_tra    = 0.
+
+diff_sh_limit=5.0e-3            ! for KPP, max diff due to shear instability
+Kv0_const=.true.
+double_diffusion=.false.               ! for KPP,dd switch
+K_ver=1.0e-5
+K_hor=3000.
+surf_relax_T=0.0
+surf_relax_S=1.929e-06       ! 50m/300days 6.43e-07! m/s 10./(180.*86400.)
+balance_salt_water =.true.   ! balance virtual-salt or freshwater flux or not
+clim_relax=0.0	                    ! 1/s, geometrical information has to be supplied
+ref_sss_local=.true.
+ref_sss=34.
+i_vert_diff =.true.  ! true
+tra_adv_hor ='MFCT'  !'MUSCL', 'UPW1'
+tra_adv_ver ='QR4C'  !'QR4C', 'CDIFF', 'UPW1'
+tra_adv_lim ='FCT'   !'FCT', 'NONE' (default)
+tra_adv_ph  = 1. ! a parameter to be used in horizontal advection (for MUSCL it is the fraction of fourth-order contribution in the solution)
+tra_adv_pv  = 1. ! a parameter to be used in horizontal advection (for QR4C  it is the fraction of fourth-order contribution in the solution)
+! Implemented trassers (3d restoring):
+! 301 - Fram strait.
+! 302 - Bering Strait
+! 303 - BSO 
+
+num_tracers=4         ! 6          !number of all tracers
+tracer_ID  =0,1,14,39 ! 6,12,14,39  !their IDs (0 and 1 are reserved for temperature and salinity)
+/
+
+&oce_init3d                               ! initial conditions for tracers
+n_ic3d   = 2                              ! number of tracers to initialize
+idlist   = 1, 0                      ! their IDs (0 is temperature, 1 is salinity, etc.). The reading order is defined here!
+filelist = 'phc3.0_winter.nc', 'phc3.0_winter.nc' ! list of files in ClimateDataPath to read (one file per tracer), same order as idlist
+varlist  = 'salt', 'temp'          ! variables to read from specified files
+t_insitu = .true.
+/
+
+&transit_param
+r14c_a  = 1.0000   	! atm. 14CO2/12CO2 ratio
+r39ar_a = 1.0000	! atm. 39Ar/Ar ratio, global mean
+xarg_a  = 9.34e-3	! atm. Argon concn. (mole fraction), global mean
+xco2_a  = 284.32e-6	! atm. CO2 concn. (mole fraction), global mean
+dic_0   = 2.00          ! mixed layer DIC concn. (mol / m**3), global mean
+arg_0   = 0.01          ! mixed layer Argon concn. (mol / m**3), global mean
+decay14 = 3.8561e-12    ! decay constant of 14C (1 / s), 1 a = 365.0 d
+decay39 = 8.1708e-11    ! decay constant of 39Ar (1 / s), 1 a = 365.0 d
+/

config/namelist.oce.cfc

@@ -0,0 +1,105 @@
+! The namelist file for the finite-volume ocean model
+
+&oce_dyn
+C_d=0.0025             ! Bottom drag, nondimensional
+gamma0=0.003            ! [m/s],   backgroung viscosity= gamma0*len, it should be as small as possible (keep it < 0.01 m/s).
+gamma1=0.1          ! [nodim], for computation of the flow aware viscosity
+gamma2=0.285            ! [s/m],   is only used in easy backscatter option
+Div_c=.5  	       ! the strength of the modified Leith viscosity, nondimensional, 0.3 -- 1.0
+Leith_c=.05	       ! the strength of the Leith viscosity
+visc_option=5          ! 1=Harmonic Leith parameterization;
+                       ! 2=Laplacian+Leith+biharmonic background
+                       ! 3=Biharmonic Leith parameterization
+                       ! 4=Biharmonic flow aware
+                       ! 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
+easy_bs_return= 1.5     ! coefficient for returned sub-gridscale energy, to be used with visc_option=5 (easy backscatter)
+A_ver= 1.e-4	       ! Vertical viscosity, m^2/s
+scale_area=5.8e9       ! Visc. and diffus. are for an element with scale_area
+mom_adv=2              ! 1=vector CV, p1 vel, 2=sca. CV, 3=vector inv.
+free_slip=.false.      ! Switch on free slip
+i_vert_visc=.true.    
+w_split=.false.
+w_max_cfl=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
+SPP=.false.                 ! Salt Plume Parameterization
+Fer_GM=.true.               ! to swith on/off GM after Ferrari et al. 2010
+K_GM_max     = 1000 !! 2000.0       ! max. GM thickness diffusivity (m2/s)
+K_GM_min     = 2.0          ! max. GM thickness diffusivity (m2/s)
+K_GM_bvref   = 2            ! def of bvref in ferreira scaling 0=srf,1=bot mld,2=mean over mld,3=weighted mean over mld
+K_GM_rampmax = -1         ! Resol >K_GM_rampmax[km] GM on
+K_GM_rampmin = -1         ! Resol <K_GM_rampmin[km] GM off, in between linear scaled down
+K_GM_resscalorder = 1
+
+scaling_Ferreira   =.false.  ! GM vertical scaling after Ferreira et al.(2005) (as also implemented by Qiang in FESOM 1.4)
+scaling_Rossby     =.false. ! GM is smoothly switched off according to Rossby radius (from 1. in coarse areas to 0. where resolution reaches 2 points/Rossby radius)
+scaling_resolution =.true.  ! GM is spatially scaled with resolution; A value of K_GM corresponds then to a resolution of 100km
+scaling_FESOM14    =.false.  ! special treatment of GM in the NH (as also implemented by Qiang in FESOM 1.4; it is zero within the boundary layer)
+
+Redi  =.true.
+visc_sh_limit=5.0e-3       ! for KPP, max visc due to shear instability
+mix_scheme='KPP'           ! vertical mixing scheme: KPP, PP 
+Ricr   = 0.3               ! critical bulk Richardson Number
+concv  = 1.6               ! constant for pure convection (eqn. 23) (Large 1.5-1.6; MOM default 1.8)
+/
+
+&oce_tra 
+use_momix     = .true.     ! switch on/off  !Monin-Obukhov -> TB04 mixing
+momix_lat     = -50.0      ! latitidinal treshhold for TB04, =90 --> global
+momix_kv      = 0.01       ! PP/KPP, mixing coefficient within MO length
+use_instabmix = .true.     ! enhance convection in case of instable stratification
+instabmix_kv  = 0.1
+use_windmix   = .false.     ! enhance mixing trough wind only for PP mixing (for stability)
+windmix_kv    = 1.e-3
+windmix_nl    = 2
+
+smooth_bh_tra =.false.     ! use biharmonic diffusion (filter implementation) for tracers
+gamma0_tra    = 0.0005     ! gammaX_tra are analogous to those in the dynamical part
+gamma1_tra    = 0.0125
+gamma2_tra    = 0.
+
+diff_sh_limit=5.0e-3            ! for KPP, max diff due to shear instability
+Kv0_const=.true.
+double_diffusion=.false.               ! for KPP,dd switch
+K_ver=1.0e-5
+K_hor=3000.
+surf_relax_T=0.0
+surf_relax_S=1.929e-06       ! 50m/300days 6.43e-07! m/s 10./(180.*86400.)
+balance_salt_water =.true.   ! balance virtual-salt or freshwater flux or not
+clim_relax=0.0	                    ! 1/s, geometrical information has to be supplied
+ref_sss_local=.true.
+ref_sss=34.
+i_vert_diff =.true.  ! true
+tra_adv_hor ='MFCT'  !'MUSCL', 'UPW1'
+tra_adv_ver ='QR4C'  !'QR4C', 'CDIFF', 'UPW1'
+tra_adv_lim ='FCT'   !'FCT', 'NONE' (default)
+tra_adv_ph  = 1. ! a parameter to be used in horizontal advection (for MUSCL it is the fraction of fourth-order contribution in the solution)
+tra_adv_pv  = 1. ! a parameter to be used in horizontal advection (for QR4C  it is the fraction of fourth-order contribution in the solution)
+! Implemented trassers (3d restoring):
+! 301 - Fram strait.
+! 302 - Bering Strait
+! 303 - BSO 
+
+num_tracers=4 !!6          !number of all tracers
+tracer_ID  =0,1,6,12       !14,39  !their IDs (0 and 1 are reserved for temperature and salinity)
+/
+
+&oce_init3d                               ! initial conditions for tracers
+n_ic3d   = 2                              ! number of tracers to initialize
+idlist   = 1, 0                      ! their IDs (0 is temperature, 1 is salinity, etc.). The reading order is defined here!
+filelist = 'phc3.0_winter.nc', 'phc3.0_winter.nc' ! list of files in ClimateDataPath to read (one file per tracer), same order as idlist
+varlist  = 'salt', 'temp'          ! variables to read from specified files
+t_insitu = .true.
+/
+
+&transit_param
+r14c_a  = 1.0000   	! atm. 14CO2/12CO2 ratio
+r39ar_a = 1.0000	! atm. 39Ar/Ar ratio, global mean
+xarg_a  = 9.34e-3	! atm. Argon concn. (mole fraction), global mean
+xco2_a  = 284.32e-6	! atm. CO2 concn. (mole fraction), global mean
+dic_0   = 2.00          ! mixed layer DIC concn. (mol / m**3), global mean
+arg_0   = 0.01          ! mixed layer Argon concn. (mol / m**3), global mean
+decay14 = 3.8561e-12    ! decay constant of 14C (1 / s), 1 a = 365.0 d
+decay39 = 8.1708e-11    ! decay constant of 39Ar (1 / s), 1 a = 365.0 d
+/