diff --git a/doc/namelists/nam_trc_age b/doc/namelists/nam_trc_age
deleted file mode 100644
index 74e945e62d654a1706cbf597586434d842ce676a..0000000000000000000000000000000000000000
--- a/doc/namelists/nam_trc_age
+++ /dev/null
@@ -1,8 +0,0 @@
- ! Variable setting
- ctrcnm (jp_age) = 'Age'
- ctrcln (jp_age) = 'Sea water age since surface contact'
- ctrcun (jp_age) = 'year'
- ln_trc_ini(jp_age) = .false.
- ln_trc_sbc(jp_age) = .false.
- ln_trc_cbc(jp_age) = .false.
- ln_trc_obc(jp_age) = .false.
diff --git a/doc/namelists/namagrif b/doc/namelists/namagrif
index 743476dd9247a121b1467e75cc29add90c89ef74..f9f449929bbd82d95c5ca504e150d51dc4656957 100644
--- a/doc/namelists/namagrif
+++ b/doc/namelists/namagrif
@@ -4,7 +4,7 @@
ln_agrif_2way = .true. ! activate two way nesting
ln_init_chfrpar = .false. ! initialize child grids from parent
ln_vert_remap = .false. ! use vertical remapping
- ln_spc_dyn = .true. ! use 0 as special value for dynamics
+ ln_spc_dyn = .false. ! use 0 as special value for dynamics
ln_chk_bathy = .true. ! =T check the parent bathymetry
rn_sponge_tra = 0.002 ! coefficient for tracer sponge layer []
rn_sponge_dyn = 0.002 ! coefficient for dynamics sponge layer []
diff --git a/doc/namelists/namdta_dyn_linssh b/doc/namelists/namdta_dyn_linssh
deleted file mode 100644
index 8a41238965711ebd701fef0b806659158cb0bf22..0000000000000000000000000000000000000000
--- a/doc/namelists/namdta_dyn_linssh
+++ /dev/null
@@ -1,23 +0,0 @@
-!-----------------------------------------------------------------------
-&namdta_dyn ! offline ocean input files (OFF_SRC only)
-!-----------------------------------------------------------------------
-
- cn_dir = './' ! root directory for the ocean data location
- !___________!_________________________!___________________!___________!_____________!________!___________!
- ! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
- ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_tem = 'dyna_grid_T' , 120. , 'votemper' , .true. , .true. , 'yearly'
- sn_sal = 'dyna_grid_T' , 120. , 'vosaline' , .true. , .true. , 'yearly'
- sn_mld = 'dyna_grid_T' , 120. , 'somixhgt' , .true. , .true. , 'yearly'
- sn_emp = 'dyna_grid_T' , 120. , 'sowaflup' , .true. , .true. , 'yearly'
- sn_fmf = 'dyna_grid_T' , 120. , 'iowaflup' , .true. , .true. , 'yearly'
- sn_ice = 'dyna_grid_T' , 120. , 'soicecov' , .true. , .true. , 'yearly'
- sn_qsr = 'dyna_grid_T' , 120. , 'soshfldo' , .true. , .true. , 'yearly'
- sn_wnd = 'dyna_grid_T' , 120. , 'sowindsp' , .true. , .true. , 'yearly'
- sn_uwd = 'dyna_grid_U' , 120. , 'uocetr_eff', .true. , .true. , 'yearly'
- sn_vwd = 'dyna_grid_V' , 120. , 'vocetr_eff', .true. , .true. , 'yearly'
- sn_wwd = 'dyna_grid_W' , 120. , 'wocetr_eff', .true. , .true. , 'yearly'
- sn_avt = 'dyna_grid_W' , 120. , 'voddmavs' , .true. , .true. , 'yearly'
- sn_ubl = 'dyna_grid_U' , 120. , 'sobblcox' , .true. , .true. , 'yearly'
- sn_vbl = 'dyna_grid_V' , 120. , 'sobblcoy' , .true. , .true. , 'yearly'
-/
diff --git a/doc/namelists/namdta_dyn_nolinssh b/doc/namelists/namdta_dyn_nolinssh
deleted file mode 100644
index 0660f2436fb671c1b1bb02c6871ed0bbdc8247d3..0000000000000000000000000000000000000000
--- a/doc/namelists/namdta_dyn_nolinssh
+++ /dev/null
@@ -1,28 +0,0 @@
-!-----------------------------------------------------------------------
-&namdta_dyn ! offline ocean input files (OFF_SRC only)
-!-----------------------------------------------------------------------
- ln_dynrnf = .true. ! runoffs option enabled (T) or not (F)
- ln_dynrnf_depth = .false. ! runoffs is spread in vertical (T) or not (F)
- !
- cn_dir = './' ! root directory for the ocean data location
- !___________!_________________________!___________________!_____________!_____________!________!___________!
- ! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
- ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_tem = 'dyna_grid_T' , 120. , 'thetao' , .true. , .true. , 'yearly'
- sn_sal = 'dyna_grid_T' , 120. , 'so' , .true. , .true. , 'yearly'
- sn_div = 'dyna_grid_T' , 120. , 'hdivtr' , .true. , .true. , 'yearly'
- sn_mld = 'dyna_grid_T' , 120. , 'mldr10_1' , .true. , .true. , 'yearly'
- sn_emp = 'dyna_grid_T' , 120. , 'wfo' , .true. , .true. , 'yearly'
- sn_empb = 'dyna_grid_T' , 120. , 'wfob' , .true. , .true. , 'yearly'
- sn_fmf = 'dyna_grid_T' , 120. , 'fmmflx' , .true. , .true. , 'yearly'
- sn_rnf = 'dyna_grid_T' , 120. , 'runoffs' , .true. , .true. , 'yearly'
- sn_ice = 'dyna_grid_T' , 120. , 'siconc' , .true. , .true. , 'yearly'
- sn_qsr = 'dyna_grid_T' , 120. , 'rsntds' , .true. , .true. , 'yearly'
- sn_wnd = 'dyna_grid_T' , 120. , 'windsp' , .true. , .true. , 'yearly'
- sn_uwd = 'dyna_grid_U' , 120. , 'uocetr_eff', .true. , .true. , 'yearly'
- sn_vwd = 'dyna_grid_V' , 120. , 'vocetr_eff', .true. , .true. , 'yearly'
- sn_wwd = 'dyna_grid_W' , 120. , 'wocetr_eff', .true. , .true. , 'yearly'
- sn_avt = 'dyna_grid_W' , 120. , 'difvsolog' , .true. , .true. , 'yearly'
- sn_ubl = 'dyna_grid_U' , 120. , 'ahu_bbl' , .true. , .true. , 'yearly'
- sn_vbl = 'dyna_grid_V' , 120. , 'ahv_bbl' , .true. , .true. , 'yearly'
-/
diff --git a/doc/namelists/namelist_abl_tools b/doc/namelists/namelist_abl_tools
deleted file mode 100644
index 42b2a4cfa5f1cd36578bba9c7b6c81da49eddbd1..0000000000000000000000000000000000000000
--- a/doc/namelists/namelist_abl_tools
+++ /dev/null
@@ -1,53 +0,0 @@
-:
-:-----------------------------------------------------------------------------
-: Atmospheric Boundary Layer preprocessing tool
-:-----------------------------------------------------------------------------
-:
-&nml_dom
- jpka = 50, ! ABL vertical levels number
- hmax = 2000., ! ABL last level altitude
- theta_s = 2., ! vertical grid stretching parameters
- hc = 100., !
- ln_impose_z1 = .true., ! force ABL first level altitude
- z1 = 10., ! ABL firt level imposed altitude [m]
-/
-
-&nml_opt
- ptemp_method = 3 , ! potential temperature computation method
- ln_slp_smth = .true. , ! smooth slp and ghw at high latitudes only
- ln_drw_smth = .false. , ! smooth after drowning
- ln_slp_log = .false. , ! read log(slp)
- ln_read_zsurf = .false. , ! read surface geopotential
- ln_hpg_frc = .true. , ! compute horizontal pressure gradient
- ln_geo_wnd = .false. , ! compute geostrophic wind
- ln_c1d = .false. , ! 1D case
- ln_read_mask = .true. , ! read mask file
- ln_lsm_land = .false. , ! inverse land & sea masks
- ln_perio_latbc = .true. , ! periodic lateral boundary conditions
-/
-
-&nml_fld
- cn_dir = '',
- mask_var = 'LSM',
- file_m = 'MASK.nc',
- file_u = 'U3D.nc',
- file_v = 'V3D.nc',
- file_t = 'T3D.nc',
- file_q = 'Q3D.nc',
- file_p = 'P2D.nc',
- file_z = 'Z2D.nc',
- file_geos = 'UVG_OUT.nc',
- file_hpg = 'HPG_OUT.nc',
-/
-
-&nml_out
- grd_file = 'dom_cfg_abl_L50Z10.nc',
- abl_file = 'ABL_L50Z10_OUT.nc',
- drwn_file = 'ABL_DRWN_L50Z10_OUT.nc',
- var_name = '',
-/
-
-&nml_c1d
- iloc = 283,
- jloc = 52,
-/
diff --git a/doc/namelists/namisf_cfg_eORCA1 b/doc/namelists/namisf_cfg_eORCA1
deleted file mode 100644
index 8cd49301118bb29c61ab35f31be20d71c863e26f..0000000000000000000000000000000000000000
--- a/doc/namelists/namisf_cfg_eORCA1
+++ /dev/null
@@ -1,37 +0,0 @@
-!-----------------------------------------------------------------------
-&namisf ! Top boundary layer (ISF) (default: OFF)
-!-----------------------------------------------------------------------
- !
- ! ---------------- ice shelf melt formulation -------------------------------
- !
- ln_isf = .true. ! activate ice shelf module
- !
- ! ---------------- cavities opened -------------------------------
- !
- ln_isfcav_mlt = .false. ! ice shelf melting into the cavity (need ln_isfcav = .true. in domain_cfg.nc)
- cn_isfcav_mlt = '3eq' ! ice shelf melting formulation (spe/2eq/3eq/oasis)
- ! ! spe = fwfisf is read from a forcing field
- ! ! 2eq = ISOMIP like: 2 equations formulation (Hunter et al., 2006 for a short description)
- ! ! 3eq = ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2016 for a short description
- rn_htbl = 30. ! thickness of the top boundary layer (Losh et al. 2008)
- ! ! 0 => thickness of the tbl = thickness of the first wet cell
- !
- !* 'spe' and 'oasis' case
- !---------------------------------------------------------------------------------------------
- ! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
- ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_isfcav_fwf = 'isfmlt_cav', -12. , 'fwflisf' , .false. , .true. , 'yearly'
- !
- ! ---------------- cavities parametrised -------------------------------
- !
- ln_isfpar_mlt = .true. ! ice shelf melting parametrised
- cn_isfpar_mlt = 'spe' ! ice shelf melting parametrisation (spe/bg03/oasis)
- ! ! spe = fwfisf is read from a forcing field
- !
- !---------------------------------------------------------------------------------------------
- ! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ !
- ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_isfpar_zmax = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sodepmax_isf' , .false. , .true. , 'yearly'
- sn_isfpar_zmin = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sodepmin_isf' , .false. , .true. , 'yearly'
- !* 'spe' and 'oasis' case
- sn_isfpar_fwf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc' , -12 ,'sornfisf', .false. , .true. , 'yearly'
diff --git a/doc/namelists/namsbc_rnf_cfg_eORCA1 b/doc/namelists/namsbc_rnf_cfg_eORCA1
deleted file mode 100644
index 1847997d6d170d0db4e8bf186ae58335532f4884..0000000000000000000000000000000000000000
--- a/doc/namelists/namsbc_rnf_cfg_eORCA1
+++ /dev/null
@@ -1,19 +0,0 @@
-!-----------------------------------------------------------------------
-&namsbc_rnf ! runoffs (ln_rnf =T)
-!-----------------------------------------------------------------------
- ln_rnf_mouth = .false. ! specific treatment at rivers mouths
- rn_hrnf = 15.e0 ! depth over which enhanced vertical mixing is used (ln_rnf_mouth=T)
- rn_avt_rnf = 1.e-3 ! value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T)
- rn_rfact = 1.e0 ! multiplicative factor for runoff
- ln_rnf_icb = .true. ! read iceberg flux
-
- cn_dir = './' ! root directory for the location of the runoff files
- !---------------------------------------------------------------------------------------------
- ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
- ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_rnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', -1 , 'sorunoff', .true. , .true. , 'yearly'
- sn_i_rnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', -1 , 'Icb_flux', .true. , .true. , 'yearly'
- sn_cnf = 'runoff-icb_DaiTrenberth_Depoorter_eORCA1_JD.nc', 0 , 'socoefr' , .false. , .true. , 'yearly'
- sn_s_rnf = 'runoffs' , 24. , 'rosaline', .true. , .true. , 'yearly'
- sn_t_rnf = 'runoffs' , 24. , 'rotemper', .true. , .true. , 'yearly'
- sn_dep_rnf = 'runoffs' , 0. , 'rodepth' , .false. , .true. , 'yearly'
diff --git a/doc/namelists/namsto b/doc/namelists/namsto
index 92016babf1a61e88af82d2658ac6a22a601393e4..48ffdd373d1d497a719ce56a58472eace87d7821 100644
--- a/doc/namelists/namsto
+++ b/doc/namelists/namsto
@@ -1,6 +1,20 @@
!-----------------------------------------------------------------------
&namsto ! Stochastic parametrization of EOS (default: OFF)
!-----------------------------------------------------------------------
+ ln_sto_ldf = .false. ! stochastic lateral diffusion
+ rn_ldf_std = 0.1 ! lateral diffusion standard deviation (in percent)
+ rn_ldf_tcor = 1440. ! lateral diffusion correlation timescale (in timesteps)
+ ln_sto_hpg = .false. ! stochastic pressure gradient
+ rn_hpg_std = 0.1 ! density gradient standard deviation (in percent)
+ rn_hpg_tcor = 1440. ! density gradient correlation timescale (in timesteps)
+ ln_sto_pstar = .false. ! stochastic ice strength
+ rn_pstar_std = 0.1 ! ice strength standard deviation (in percent)
+ rn_pstar_tcor = 1440. ! ice strength correlation timescale (in timesteps)
+ nn_pstar_ord = 1 ! order of autoregressive processes
+ nn_pstar_flt = 0 ! passes of Laplacian filter
+ ln_sto_trd = .false. ! stochastic model trend
+ rn_trd_std = 0.1 ! trend standard deviation (in percent)
+ rn_trd_tcor = 1440. ! trend correlation timescale (in timesteps)
ln_sto_eos = .false. ! stochastic equation of state
nn_sto_eos = 1 ! number of independent random walks
rn_eos_stdxy = 1.4 ! random walk horz. standard deviation (in grid points)
@@ -9,6 +23,14 @@
nn_eos_ord = 1 ! order of autoregressive processes
nn_eos_flt = 0 ! passes of Laplacian filter
rn_eos_lim = 2.0 ! limitation factor (default = 3.0)
+ ln_sto_trc = .false. ! stochastic tracer dynamics
+ nn_sto_trc = 1 ! number of independent random walks
+ rn_trc_stdxy = 1.4 ! random walk horz. standard deviation (in grid points)
+ rn_trc_stdz = 0.7 ! random walk vert. standard deviation (in grid points)
+ rn_trc_tcor = 1440. ! random walk time correlation (in timesteps)
+ nn_trc_ord = 1 ! order of autoregressive processes
+ nn_trc_flt = 0 ! passes of Laplacian filter
+ rn_trc_lim = 3.0 ! limitation factor (default = 3.0)
ln_rststo = .false. ! start from mean parameter (F) or from restart file (T)
ln_rstseed = .true. ! read seed of RNG from restart file
cn_storst_in = "restart_sto" ! suffix of stochastic parameter restart file (input)
diff --git a/doc/namelists/namtrc_ais_cfg b/doc/namelists/namtrc_ais_cfg
deleted file mode 100644
index 209991e6ffc447cda207164ff759a68b70c3a571..0000000000000000000000000000000000000000
--- a/doc/namelists/namtrc_ais_cfg
+++ /dev/null
@@ -1,9 +0,0 @@
-!-----------------------------------------------------------------------
-&namtrc_ais ! Representation of Antarctic Ice Sheet tracers supply
-!-----------------------------------------------------------------------
- rn_trafac(3) = 4.476e-07 ! ( 0.5e-3 / 55.85 * 0.05 )
-!
- nn_ais_tr = 1 ! tracer concentration in iceberg and ice shelf
- ! = 0 (null concentrations)
- ! = 1 prescribed concentrations
- rn_icbdep = 120. ! Mean underwater depth of iceberg (m)
diff --git a/doc/namelists/namtrc_bc_cfg b/doc/namelists/namtrc_bc_cfg
deleted file mode 100644
index 6d7bbb01c551401834b4454fac8adf07ef8eb9f0..0000000000000000000000000000000000000000
--- a/doc/namelists/namtrc_bc_cfg
+++ /dev/null
@@ -1,17 +0,0 @@
-!----------------------------------------------------------------------
-&namtrc_bc ! data for boundary conditions
-!-----------------------------------------------------------------------
-! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
-! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_trcsbc(2) = 'dust.orca.new' , -1 , 'dustfer' , .true. , .true. , 'yearly'
- sn_trcsbc(3) = 'ndeposition.orca', -12 , 'ndep' , .false. , .true. , 'yearly'
- rn_trsfac(2) = 6.266e-04 ! Multiplicative factor
- rn_trsfac(3) = 5.4464e-01 !
-!
- sn_trccbc(1) = 'river.orca' , -12 , 'riverdic' , .true. , .true. , 'yearly'
- sn_trccbc(2) = 'river.orca' , -12 , 'riverdfe' , .true. , .true. , 'yearly'
- sn_trccbc(3) = 'river.orca' , -12 , 'riverdin' , .true. , .true. , 'yearly'
- rn_trcfac(1) = 1.0 ! Multiplicative factor
- rn_trcfac(2) = 1.0 !
- rn_trcfac(3) = 1.0 !
- rn_cbc_time = 3.1536e+7 ! Time scaling factor for CBC data (seconds in a year)
diff --git a/doc/namelists/namtrc_cfg b/doc/namelists/namtrc_cfg
deleted file mode 100644
index d94f021dbcf117fa1a6d364923f13ed66620b693..0000000000000000000000000000000000000000
--- a/doc/namelists/namtrc_cfg
+++ /dev/null
@@ -1,25 +0,0 @@
-!-----------------------------------------------------------------------
-&namtrc ! tracers definition
-!-----------------------------------------------------------------------
- jp_bgc = 24
-!
- ln_pisces = .true.
- ln_my_trc = .false.
- ln_age = .false.
- ln_cfc11 = .false.
- ln_cfc12 = .false.
- ln_c14 = .false.
-!
- !
- ln_trcdta = .true. ! Initialisation from data input file (T) or not (F)
- ln_trcdmp = .false. ! add a damping termn (T) or not (F)
- ln_trcdmp_clo = .false. ! damping term (T) or not (F) on closed seas
- ln_trcbc = .true. ! Surface, Lateral or Open Boundaries conditions
- ln_trcais = .true. ! Antarctic Ice Sheet nutrient supply
-! ! ! ! ! !
-! ! name ! title of the field ! units ! init ! sbc ! cbc ! obc ! ais
- sn_tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mol-C/L' , .true. , .false., .true. , .false. , .false.
- sn_tracer(2) = 'Fer ' , 'Dissolved Iron Concentration ', 'mol-C/L' , .true. , .true. , .true. , .false. , .true.
- sn_tracer(3) = 'NO3 ' , 'Nitrates Concentration ', 'mol-C/L' , .true. , .true. , .true. , .false. , .false.
- sn_tracer(4) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false.
-
diff --git a/doc/namelists/namtrc_dta_cfg b/doc/namelists/namtrc_dta_cfg
deleted file mode 100644
index 2b612e6911190babe76005a43f172235a5e8cbe0..0000000000000000000000000000000000000000
--- a/doc/namelists/namtrc_dta_cfg
+++ /dev/null
@@ -1,12 +0,0 @@
-!-----------------------------------------------------------------------
-&namtrc_dta ! Initialisation from data input file
-!-----------------------------------------------------------------------
-! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ !
-! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' !
- sn_trcdta(1) = 'data_DIC_nomask.nc', -12 , 'PiDIC' , .false. , .true. , 'yearly' ,
- sn_trcdta(2) = 'data_FER_nomask.nc', -1 , 'Fer' , .true. , .true. , 'yearly' ,
- sn_trcdta(3) = 'data_NO3_nomask.nc', -1 , 'NO3' , .true. , .true. , 'yearly' ,
-!
- rn_trfac(1) = 1.028e-06 ! multiplicative factor
- rn_trfac(2) = 1.0e-06 ! - - - -
- rn_trfac(3) = 7.6e-06 ! - - - -
diff --git a/doc/namelists/namtrc_opt b/doc/namelists/namtrc_opt
index 24ed9988e29b97f8b49ee66a1a91f28755e39bd1..5f8b7febff6a47bd2e6a8121bba79aa12c57fd67 100644
--- a/doc/namelists/namtrc_opt
+++ b/doc/namelists/namtrc_opt
@@ -1,11 +1,11 @@
!-----------------------------------------------------------------------
&namtrc_opt ! light availability in the water column
!-----------------------------------------------------------------------
-! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask !
-! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename !
- sn_par = 'par.orca' , 24 , 'fr_par' , .true. , .true. , 'yearly' , '' , '' , ''
- cn_dir = './' ! root directory for the location of the dynamical files
- ln_varpar = .true. ! Read PAR from file
- parlux = 0.43 ! Fraction of shortwave as PAR
- light_loc = 'center' ! Light location in the water cell ('center', 'integral')
+! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask !
+! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename !
+ sn_par = 'par.orca' , 24 , 'fr_par' , .true. , .true. , 'yearly' , '' , '' , ''
+ cn_dir = './' ! root directory for the location of the dynamical files
+ ln_varpar = .true. ! Read PAR from file
+ parlux = 0.43 ! Fraction of shortwave as PAR
+ light_loc = 'center' ! Light location in the water cell ('center', 'integral')
/