Init¶
The init stage is where MARBL is configured, parameters are set, and memory is allocated.
If the GCM wants to specify non-default parameter values, that needs to be done with put_setting() statements before calling init().
There are three different interfaces that can be used; all are equivalent, but different GCMs may find it easiest to call different interfaces.
Two arguments: a string containing the variable name, and then the variable value (in proper datatype)
call marbl_instance%put_setting('ciso_on', .true.)
One argument: a string containing a line from a MARBL settings file (see examples below) of the format
varname = valuecall marbl_instance%put_setting('ciso_on = .true.')
Three arguments: strings containing the variable name, the datatype, and the value
call marbl_instance%put_setting('ciso_on', 'logical', '.true.')
put_setting() calls that do not correspond to defined MARBL parameters will result in an error during init().
There is no check in the put_setting() call itself because allowable parameters may depend on other parameter values.
For example, autotrophs(3)%sname is defined if autotroph_cnt >= 3 but not if autotroph_cnt < 3.
The init() interface¶
subroutine init(this, &
gcm_num_levels, &
gcm_num_PAR_subcols, &
gcm_num_elements_surface_flux, &
gcm_delta_z, &
gcm_zw, &
gcm_zt, &
lgcm_has_global_ops)
.
.
.
class(marbl_interface_class), intent(inout) :: this
integer(int_kind), intent(in) :: gcm_num_levels
integer(int_kind), intent(in) :: gcm_num_PAR_subcols
integer(int_kind), intent(in) :: gcm_num_elements_surface_flux
real(r8), intent(in) :: gcm_delta_z(gcm_num_levels) ! thickness of layer k
real(r8), intent(in) :: gcm_zw(gcm_num_levels) ! thickness of layer k
real(r8), intent(in) :: gcm_zt(gcm_num_levels) ! thickness of layer k
logical, optional, intent(in) :: lgcm_has_global_ops
Note the optional argument:
lgcm_has_global_ops is a way for the GCM to inform MARBL that it can perform global operations such as finding global averages of values.
There are some MARBL configurations that require this, and MARBL will abort unless the GCM verifies it can provide these values.
MARBL does not have an explicit interface to tell a GCM how many tracers are being computed.
Instead, use size(marbl_instance%tracer_metadata) (called after marbl_instance%init()).
MARBL can compute surface fluxes across multiple columns simultaneously, with the number of columns supported set by gcm_num_elements_surface_flux.
There is not a corresponding gcm_num_elements_interior_tendency yet, because currently MARBL computes tracer tendencies one column at a time.
Example from Stand-Alone MARBL¶
The stand-alone MARBL driver / test suite use settings files (*.settings in the tests/input_files/settings/ directory) that are processed in the following manner:
settings_file_line = ''
do while(ioerr .eq. 0)
! (i) broadcast settings_file_line and call put_setting(); abort if error
! calling with empty settings_file_line on first entry to loop is okay, and
! this ensures we don't call put_setting with a garbage line if
! ioerr is non-zero
call marbl_mpi_bcast(settings_file_line, 0)
call marbl_instance%put_setting(settings_file_line)
if (marbl_instance%StatusLog%labort_marbl) then
call marbl_instance%StatusLog%log_error_trace("put_setting(settings_file_line)", subname)
call marbl_io_print_marbl_log(marbl_instance%StatusLog)
end if
! (ii) master task reads next line in settings file
if (my_task .eq. 0) read(97,"(A)", iostat=ioerr) settings_file_line
! (iii) broadcast settings file line to all tasks (along with iostat)
call marbl_mpi_bcast(ioerr, 0)
end do
if (.not.is_iostat_end(ioerr)) then
if (my_task .eq. 0) then
write(*,"(A,I0)") "ioerr = ", ioerr
write(*,"(2A)") "ERROR encountered when reading MARBL settings file ", trim(settings_file)
end if
call marbl_mpi_abort()
end if
init() is then called from the individual test:
! Call marbl%init
call marbl_instance%init(gcm_num_levels = km, &
gcm_num_PAR_subcols = 1, &
gcm_num_elements_surface_flux = 1, &
gcm_delta_z = delta_z, &
gcm_zw = zw, &
gcm_zt = zt)
if (marbl_instance%StatusLog%labort_marbl) then
call marbl_instance%StatusLog%log_error_trace('marbl%init', subname)
return
end if
Default Parameter Values¶
Below are the default parameter values (real variables provided to double precision).
This specific page was been generated by running the gen_settings_file regression test with no input settings file.
The test writes this output to marbl_settings.gen.
Note that the order the variables are listed in comes from the order the variables are defined in MARBL, but the order of put_setting() calls does not matter.
PFT_defaults = 'CESM2'
ciso_on = F
lsource_sink = T
lecovars_full_depth_tavg = F
ciso_lsource_sink = T
lflux_gas_o2 = T
lflux_gas_co2 = T
lcompute_nhx_surface_emis = T
lvariable_PtoC = T
ladjust_bury_coeff = F
lo2_consumption_scalef = F
lp_remin_scalef = F
init_bury_coeff_opt = 'settings_file'
particulate_flux_ref_depth = 100
Jint_Ctot_thres_molpm2pyr = 0.10000000000000001E-08
gQsi_0 = 0.13700000000000001E+00
gQsi_max = 0.82199999999999995E+00
gQsi_min = 0.45699999999999998E-01
gQ_Fe_kFe_thres = 0.10000000000000000E+02
gQ_Si_kSi_thres = 0.60000000000000000E+01
parm_Fe_bioavail = 0.10000000000000000E+01
parm_o2_min = 0.50000000000000000E+01
parm_o2_min_delta = 0.50000000000000000E+01
parm_kappa_nitrif_per_day = 0.59999999999999998E-01
parm_nitrif_par_lim = 0.10000000000000000E+01
parm_labile_ratio = 0.93999999999999995E+00
parm_init_POC_bury_coeff = 0.25400000000000000E+01
parm_init_POP_bury_coeff = 0.35999999999999999E+00
parm_init_bSi_bury_coeff = 0.15300000000000000E+01
parm_Fe_scavenge_rate0 = 0.22000000000000000E+02
parm_Lig_scavenge_rate0 = 0.14999999999999999E-01
parm_FeLig_scavenge_rate0 = 0.12000000000000000E+01
parm_Lig_degrade_rate0 = 0.93999999999999994E-04
parm_Fe_desorption_rate0 = 0.99999999999999995E-06
parm_f_prod_sp_CaCO3 = 0.70000000000000007E-01
parm_POC_diss = 0.10000000000000000E+05
parm_SiO2_diss = 0.65000000000000000E+05
parm_SiO2_gamma = 0.00000000000000000E+00
parm_hPOC_SiO2_ratio = 0.10000000000000000E-01
parm_CaCO3_diss = 0.50000000000000000E+05
parm_CaCO3_gamma = 0.20000000000000000E-01
parm_hPOC_CaCO3_ratio = 0.10000000000000000E-01
parm_hPOC_dust_ratio = 0.10000000000000000E-01
o2_sf_o2_range_hi = 0.45000000000000000E+02
o2_sf_o2_range_lo = 0.50000000000000000E+01
o2_sf_val_lo_o2 = 0.26000000000000001E+01
parm_sed_denitrif_coeff = 0.10000000000000000E+01
bury_coeff_rmean_timescale_years = 0.10000000000000000E+02
parm_scalelen_z(1) = 0.10000000000000000E+05
parm_scalelen_z(2) = 0.25000000000000000E+05
parm_scalelen_z(3) = 0.50000000000000000E+05
parm_scalelen_z(4) = 0.10000000000000000E+06
parm_scalelen_vals(1) = 0.10000000000000000E+01
parm_scalelen_vals(2) = 0.36000000000000001E+01
parm_scalelen_vals(3) = 0.47000000000000002E+01
parm_scalelen_vals(4) = 0.47999999999999998E+01
caco3_bury_thres_opt = 'omega_calc'
caco3_bury_thres_depth = 0.30000000000000000E+06
caco3_bury_thres_omega_calc = 0.89000000000000001E+00
PON_bury_coeff = 0.50000000000000000E+00
POM_bury_frac_max = 0.80000000000000004E+00
bSi_bury_frac_max = 0.10000000000000000E+01
ciso_fract_factors = 'Laws'
auto_mort2_exp = 0.17500000000000000E+01
zoo_mort2_exp = 0.15000000000000000E+01
QCaCO3_max = 0.40000000000000002E+00
f_graze_CaCO3_remin = 0.33000000000000002E+00
autotroph_cnt = 3
zooplankton_cnt = 1
max_grazer_prey_cnt = 3
autotroph_settings(1)%sname = 'sp'
autotroph_settings(1)%lname = 'Small Phyto'
autotroph_settings(1)%temp_func_form_opt = 'q_10'
autotroph_settings(1)%Nfixer = F
autotroph_settings(1)%imp_calcifier = T
autotroph_settings(1)%exp_calcifier = F
autotroph_settings(1)%silicifier = F
autotroph_settings(1)%is_carbon_limited = F
autotroph_settings(1)%kFe = 0.30000000000000001E-04
autotroph_settings(1)%kPO4 = 0.10000000000000000E-01
autotroph_settings(1)%kDOP = 0.29999999999999999E+00
autotroph_settings(1)%kNO3 = 0.25000000000000000E+00
autotroph_settings(1)%kNH4 = 0.10000000000000000E-01
autotroph_settings(1)%kSiO3 = 0.00000000000000000E+00
autotroph_settings(1)%kCO2 = 0.00000000000000000E+00
autotroph_settings(1)%Qp_fixed = 0.85470085470085479E-02
autotroph_settings(1)%gQfe_0 = 0.30000000000000001E-04
autotroph_settings(1)%gQfe_min = 0.25000000000000002E-05
autotroph_settings(1)%alphaPI_per_day = 0.39000000000000001E+00
autotroph_settings(1)%PCref_per_day = 0.50000000000000000E+01
autotroph_settings(1)%thetaN_max = 0.25000000000000000E+01
autotroph_settings(1)%loss_thres = 0.10000000000000000E-01
autotroph_settings(1)%loss_thres2 = 0.00000000000000000E+00
autotroph_settings(1)%temp_thres = -0.10000000000000000E+02
autotroph_settings(1)%mort_per_day = 0.10000000000000001E+00
autotroph_settings(1)%mort2_per_day = 0.10000000000000000E-01
autotroph_settings(1)%agg_rate_max = 0.50000000000000000E+00
autotroph_settings(1)%agg_rate_min = 0.10000000000000000E-01
autotroph_settings(1)%loss_poc = 0.00000000000000000E+00
autotroph_settings(1)%Ea = 0.32000000000000001E+00
autotroph_settings(2)%sname = 'diat'
autotroph_settings(2)%lname = 'Diatom'
autotroph_settings(2)%temp_func_form_opt = 'q_10'
autotroph_settings(2)%Nfixer = F
autotroph_settings(2)%imp_calcifier = F
autotroph_settings(2)%exp_calcifier = F
autotroph_settings(2)%silicifier = T
autotroph_settings(2)%is_carbon_limited = F
autotroph_settings(2)%kFe = 0.69999999999999994E-04
autotroph_settings(2)%kPO4 = 0.50000000000000003E-01
autotroph_settings(2)%kDOP = 0.50000000000000000E+00
autotroph_settings(2)%kNO3 = 0.50000000000000000E+00
autotroph_settings(2)%kNH4 = 0.50000000000000003E-01
autotroph_settings(2)%kSiO3 = 0.69999999999999996E+00
autotroph_settings(2)%kCO2 = 0.00000000000000000E+00
autotroph_settings(2)%Qp_fixed = 0.85470085470085479E-02
autotroph_settings(2)%gQfe_0 = 0.30000000000000001E-04
autotroph_settings(2)%gQfe_min = 0.25000000000000002E-05
autotroph_settings(2)%alphaPI_per_day = 0.28000000000000003E+00
autotroph_settings(2)%PCref_per_day = 0.50000000000000000E+01
autotroph_settings(2)%thetaN_max = 0.40000000000000000E+01
autotroph_settings(2)%loss_thres = 0.20000000000000000E-01
autotroph_settings(2)%loss_thres2 = 0.00000000000000000E+00
autotroph_settings(2)%temp_thres = -0.10000000000000000E+02
autotroph_settings(2)%mort_per_day = 0.10000000000000001E+00
autotroph_settings(2)%mort2_per_day = 0.10000000000000000E-01
autotroph_settings(2)%agg_rate_max = 0.50000000000000000E+00
autotroph_settings(2)%agg_rate_min = 0.20000000000000000E-01
autotroph_settings(2)%loss_poc = 0.00000000000000000E+00
autotroph_settings(2)%Ea = 0.32000000000000001E+00
autotroph_settings(3)%sname = 'diaz'
autotroph_settings(3)%lname = 'Diazotroph'
autotroph_settings(3)%temp_func_form_opt = 'q_10'
autotroph_settings(3)%Nfixer = T
autotroph_settings(3)%imp_calcifier = F
autotroph_settings(3)%exp_calcifier = F
autotroph_settings(3)%silicifier = F
autotroph_settings(3)%is_carbon_limited = F
autotroph_settings(3)%kFe = 0.45000000000000003E-04
autotroph_settings(3)%kPO4 = 0.14999999999999999E-01
autotroph_settings(3)%kDOP = 0.74999999999999997E-01
autotroph_settings(3)%kNO3 = 0.20000000000000000E+01
autotroph_settings(3)%kNH4 = 0.20000000000000001E+00
autotroph_settings(3)%kSiO3 = 0.00000000000000000E+00
autotroph_settings(3)%kCO2 = 0.00000000000000000E+00
autotroph_settings(3)%Qp_fixed = 0.27350427350427355E-02
autotroph_settings(3)%gQfe_0 = 0.60000000000000002E-04
autotroph_settings(3)%gQfe_min = 0.25000000000000002E-05
autotroph_settings(3)%alphaPI_per_day = 0.39000000000000001E+00
autotroph_settings(3)%PCref_per_day = 0.25000000000000000E+01
autotroph_settings(3)%thetaN_max = 0.25000000000000000E+01
autotroph_settings(3)%loss_thres = 0.20000000000000000E-01
autotroph_settings(3)%loss_thres2 = 0.10000000000000000E-02
autotroph_settings(3)%temp_thres = 0.15000000000000000E+02
autotroph_settings(3)%mort_per_day = 0.10000000000000001E+00
autotroph_settings(3)%mort2_per_day = 0.10000000000000000E-01
autotroph_settings(3)%agg_rate_max = 0.50000000000000000E+00
autotroph_settings(3)%agg_rate_min = 0.10000000000000000E-01
autotroph_settings(3)%loss_poc = 0.00000000000000000E+00
autotroph_settings(3)%Ea = 0.32000000000000001E+00
zooplankton_settings(1)%sname = 'zoo'
zooplankton_settings(1)%lname = 'Zooplankton'
zooplankton_settings(1)%temp_func_form_opt = 'q_10'
zooplankton_settings(1)%z_mort_0_per_day = 0.10000000000000001E+00
zooplankton_settings(1)%loss_thres = 0.74999999999999997E-01
zooplankton_settings(1)%z_mort2_0_per_day = 0.40000000000000002E+00
zooplankton_settings(1)%Ea = 0.65000000000000002E+00
grazing_relationship_settings(1,1)%sname = 'grz_sp_zoo'
grazing_relationship_settings(1,1)%lname = 'Grazing of sp by zoo'
grazing_relationship_settings(1,1)%auto_ind_cnt = 1
grazing_relationship_settings(1,1)%zoo_ind_cnt = 0
grazing_relationship_settings(1,1)%grazing_function = 1
grazing_relationship_settings(1,1)%z_umax_0_per_day = 0.32999999999999998E+01
grazing_relationship_settings(1,1)%z_grz = 0.12000000000000000E+01
grazing_relationship_settings(1,1)%graze_zoo = 0.29999999999999999E+00
grazing_relationship_settings(1,1)%graze_poc = 0.00000000000000000E+00
grazing_relationship_settings(1,1)%graze_doc = 0.59999999999999998E-01
grazing_relationship_settings(1,1)%f_zoo_detr = 0.12000000000000000E+00
grazing_relationship_settings(1,1)%auto_ind(1) = 1
grazing_relationship_settings(2,1)%sname = 'grz_diat_zoo'
grazing_relationship_settings(2,1)%lname = 'Grazing of diat by zoo'
grazing_relationship_settings(2,1)%auto_ind_cnt = 1
grazing_relationship_settings(2,1)%zoo_ind_cnt = 0
grazing_relationship_settings(2,1)%grazing_function = 1
grazing_relationship_settings(2,1)%z_umax_0_per_day = 0.31499999999999999E+01
grazing_relationship_settings(2,1)%z_grz = 0.12000000000000000E+01
grazing_relationship_settings(2,1)%graze_zoo = 0.25000000000000000E+00
grazing_relationship_settings(2,1)%graze_poc = 0.39000000000000001E+00
grazing_relationship_settings(2,1)%graze_doc = 0.59999999999999998E-01
grazing_relationship_settings(2,1)%f_zoo_detr = 0.23999999999999999E+00
grazing_relationship_settings(2,1)%auto_ind(1) = 2
grazing_relationship_settings(3,1)%sname = 'grz_diaz_zoo'
grazing_relationship_settings(3,1)%lname = 'Grazing of diaz by zoo'
grazing_relationship_settings(3,1)%auto_ind_cnt = 1
grazing_relationship_settings(3,1)%zoo_ind_cnt = 0
grazing_relationship_settings(3,1)%grazing_function = 1
grazing_relationship_settings(3,1)%z_umax_0_per_day = 0.32999999999999998E+01
grazing_relationship_settings(3,1)%z_grz = 0.12000000000000000E+01
grazing_relationship_settings(3,1)%graze_zoo = 0.29999999999999999E+00
grazing_relationship_settings(3,1)%graze_poc = 0.10000000000000001E+00
grazing_relationship_settings(3,1)%graze_doc = 0.59999999999999998E-01
grazing_relationship_settings(3,1)%f_zoo_detr = 0.12000000000000000E+00
grazing_relationship_settings(3,1)%auto_ind(1) = 3
tracer_restore_vars(1) = ''
tracer_restore_vars(2) = ''
tracer_restore_vars(3) = ''
tracer_restore_vars(4) = ''
tracer_restore_vars(5) = ''
tracer_restore_vars(6) = ''
tracer_restore_vars(7) = ''
tracer_restore_vars(8) = ''
tracer_restore_vars(9) = ''
tracer_restore_vars(10) = ''
tracer_restore_vars(11) = ''
tracer_restore_vars(12) = ''
tracer_restore_vars(13) = ''
tracer_restore_vars(14) = ''
tracer_restore_vars(15) = ''
tracer_restore_vars(16) = ''
tracer_restore_vars(17) = ''
tracer_restore_vars(18) = ''
tracer_restore_vars(19) = ''
tracer_restore_vars(20) = ''
tracer_restore_vars(21) = ''
tracer_restore_vars(22) = ''
tracer_restore_vars(23) = ''
tracer_restore_vars(24) = ''
tracer_restore_vars(25) = ''
tracer_restore_vars(26) = ''
tracer_restore_vars(27) = ''
tracer_restore_vars(28) = ''
tracer_restore_vars(29) = ''
tracer_restore_vars(30) = ''
tracer_restore_vars(31) = ''
tracer_restore_vars(32) = ''
A python tool to generate input settings files is also provided: MARBL_tools/MARBL_generate_settings_file.py.
This script creates marbl.settings, and organizes the output better than the Fortran test:
! config PFTs
PFT_defaults = "CESM2"
autotroph_cnt = 3
max_grazer_prey_cnt = 3
zooplankton_cnt = 1
! config flags
ciso_lsource_sink = .true.
ciso_on = .false.
ladjust_bury_coeff = .false.
lcompute_nhx_surface_emis = .true.
lecovars_full_depth_tavg = .false.
lflux_gas_co2 = .true.
lflux_gas_o2 = .true.
lo2_consumption_scalef = .false.
lp_remin_scalef = .false.
lsource_sink = .true.
lvariable_PtoC = .true.
! config strings
init_bury_coeff_opt = "settings_file"
! general parameters
Jint_Ctot_thres_molpm2pyr = 1e-09
QCaCO3_max = 0.4
auto_mort2_exp = 1.75
bury_coeff_rmean_timescale_years = 10
caco3_bury_thres_depth = 3.0000000000000000e+05
caco3_bury_thres_omega_calc = 0.89
caco3_bury_thres_opt = "omega_calc"
ciso_fract_factors = "Laws"
f_graze_CaCO3_remin = 0.33
gQ_Fe_kFe_thres = 10.0
gQ_Si_kSi_thres = 6.0
gQsi_0 = 0.137
gQsi_max = 0.822
gQsi_min = 0.0457
o2_sf_o2_range_hi = 45.0
o2_sf_o2_range_lo = 5.0
o2_sf_val_lo_o2 = 2.6
parm_CaCO3_gamma = 0.02
parm_Fe_bioavail = 1.0
parm_Fe_desorption_rate0 = 9.9999999999999995e-07
parm_Lig_degrade_rate0 = 9.4e-05
parm_SiO2_gamma = 0.0
parm_f_prod_sp_CaCO3 = 0.07
parm_hPOC_CaCO3_ratio = 0.01
parm_hPOC_SiO2_ratio = 0.01
parm_hPOC_dust_ratio = 0.01
parm_labile_ratio = 0.94
parm_o2_min = 5.0
parm_o2_min_delta = 5.0
parm_sed_denitrif_coeff = 1
particulate_flux_ref_depth = 100
zoo_mort2_exp = 1.5
! general parameters (bury coeffs)
POM_bury_frac_max = 0.8
PON_bury_coeff = 0.5
bSi_bury_frac_max = 1.0
parm_init_POC_bury_coeff = 2.54
parm_init_POP_bury_coeff = 0.36
parm_init_bSi_bury_coeff = 1.53
! general parameters (dissolution)
parm_CaCO3_diss = 5.0000000000000000e+04
parm_POC_diss = 1.0000000000000000e+04
parm_SiO2_diss = 6.5000000000000000e+04
! general parameters (nitrification)
parm_kappa_nitrif_per_day = 0.06
parm_nitrif_par_lim = 1.0
! general parameters (scavenging)
parm_FeLig_scavenge_rate0 = 1.2
parm_Fe_scavenge_rate0 = 22.0
parm_Lig_scavenge_rate0 = 0.015
! Scale lengths
parm_scalelen_vals(1) = 1
parm_scalelen_vals(2) = 3.6
parm_scalelen_vals(3) = 4.7
parm_scalelen_vals(4) = 4.8
parm_scalelen_z(1) = 1.0000000000000000e+04
parm_scalelen_z(2) = 2.5000000000000000e+04
parm_scalelen_z(3) = 5.0000000000000000e+04
parm_scalelen_z(4) = 1.0000000000000000e+05
! autotrophs
autotroph_settings(1)%Ea = 0.32
autotroph_settings(1)%Nfixer = .false.
autotroph_settings(1)%PCref_per_day = 5
autotroph_settings(1)%Qp_fixed = 8.5470085470085479e-03
autotroph_settings(1)%agg_rate_max = 0.5
autotroph_settings(1)%agg_rate_min = 0.01
autotroph_settings(1)%alphaPI_per_day = 0.39
autotroph_settings(1)%exp_calcifier = .false.
autotroph_settings(1)%gQfe_0 = 3.0000000000000001e-05
autotroph_settings(1)%gQfe_min = 2.5e-06
autotroph_settings(1)%imp_calcifier = .true.
autotroph_settings(1)%is_carbon_limited = .false.
autotroph_settings(1)%kCO2 = 0
autotroph_settings(1)%kDOP = 0.3
autotroph_settings(1)%kFe = 3e-05
autotroph_settings(1)%kNH4 = 0.01
autotroph_settings(1)%kNO3 = 0.25
autotroph_settings(1)%kPO4 = 0.01
autotroph_settings(1)%kSiO3 = 0
autotroph_settings(1)%lname = "Small Phyto"
autotroph_settings(1)%loss_poc = 0
autotroph_settings(1)%loss_thres = 0.01
autotroph_settings(1)%loss_thres2 = 0
autotroph_settings(1)%mort2_per_day = 0.01
autotroph_settings(1)%mort_per_day = 0.1
autotroph_settings(1)%silicifier = .false.
autotroph_settings(1)%sname = "sp"
autotroph_settings(1)%temp_func_form_opt = "q_10"
autotroph_settings(1)%temp_thres = -10
autotroph_settings(1)%thetaN_max = 2.5
autotroph_settings(2)%Ea = 0.32
autotroph_settings(2)%Nfixer = .false.
autotroph_settings(2)%PCref_per_day = 5
autotroph_settings(2)%Qp_fixed = 8.5470085470085479e-03
autotroph_settings(2)%agg_rate_max = 0.5
autotroph_settings(2)%agg_rate_min = 0.02
autotroph_settings(2)%alphaPI_per_day = 0.28
autotroph_settings(2)%exp_calcifier = .false.
autotroph_settings(2)%gQfe_0 = 3.0000000000000001e-05
autotroph_settings(2)%gQfe_min = 2.5e-06
autotroph_settings(2)%imp_calcifier = .false.
autotroph_settings(2)%is_carbon_limited = .false.
autotroph_settings(2)%kCO2 = 0
autotroph_settings(2)%kDOP = 0.5
autotroph_settings(2)%kFe = 7e-05
autotroph_settings(2)%kNH4 = 0.05
autotroph_settings(2)%kNO3 = 0.5
autotroph_settings(2)%kPO4 = 0.05
autotroph_settings(2)%kSiO3 = 0.7
autotroph_settings(2)%lname = "Diatom"
autotroph_settings(2)%loss_poc = 0
autotroph_settings(2)%loss_thres = 0.02
autotroph_settings(2)%loss_thres2 = 0
autotroph_settings(2)%mort2_per_day = 0.01
autotroph_settings(2)%mort_per_day = 0.1
autotroph_settings(2)%silicifier = .true.
autotroph_settings(2)%sname = "diat"
autotroph_settings(2)%temp_func_form_opt = "q_10"
autotroph_settings(2)%temp_thres = -10
autotroph_settings(2)%thetaN_max = 4
autotroph_settings(3)%Ea = 0.32
autotroph_settings(3)%Nfixer = .true.
autotroph_settings(3)%PCref_per_day = 2.5
autotroph_settings(3)%Qp_fixed = 2.7350427350427355e-03
autotroph_settings(3)%agg_rate_max = 0.5
autotroph_settings(3)%agg_rate_min = 0.01
autotroph_settings(3)%alphaPI_per_day = 0.39
autotroph_settings(3)%exp_calcifier = .false.
autotroph_settings(3)%gQfe_0 = 6.0000000000000002e-05
autotroph_settings(3)%gQfe_min = 2.5e-06
autotroph_settings(3)%imp_calcifier = .false.
autotroph_settings(3)%is_carbon_limited = .false.
autotroph_settings(3)%kCO2 = 0
autotroph_settings(3)%kDOP = 0.075
autotroph_settings(3)%kFe = 4.5e-05
autotroph_settings(3)%kNH4 = 0.2
autotroph_settings(3)%kNO3 = 2
autotroph_settings(3)%kPO4 = 0.015
autotroph_settings(3)%kSiO3 = 0
autotroph_settings(3)%lname = "Diazotroph"
autotroph_settings(3)%loss_poc = 0
autotroph_settings(3)%loss_thres = 0.02
autotroph_settings(3)%loss_thres2 = 0.001
autotroph_settings(3)%mort2_per_day = 0.01
autotroph_settings(3)%mort_per_day = 0.1
autotroph_settings(3)%silicifier = .false.
autotroph_settings(3)%sname = "diaz"
autotroph_settings(3)%temp_func_form_opt = "q_10"
autotroph_settings(3)%temp_thres = 15
autotroph_settings(3)%thetaN_max = 2.5
! zooplankton
zooplankton_settings(1)%Ea = 0.65
zooplankton_settings(1)%lname = "Zooplankton"
zooplankton_settings(1)%loss_thres = 0.075
zooplankton_settings(1)%sname = "zoo"
zooplankton_settings(1)%temp_func_form_opt = "q_10"
zooplankton_settings(1)%z_mort2_0_per_day = 0.4
zooplankton_settings(1)%z_mort_0_per_day = 0.1
! grazing
grazing_relationship_settings(1,1)%auto_ind(1) = 1
grazing_relationship_settings(1,1)%auto_ind_cnt = 1
grazing_relationship_settings(1,1)%f_zoo_detr = 0.12
grazing_relationship_settings(1,1)%graze_doc = 0.06
grazing_relationship_settings(1,1)%graze_poc = 0
grazing_relationship_settings(1,1)%graze_zoo = 0.3
grazing_relationship_settings(1,1)%grazing_function = 1
grazing_relationship_settings(1,1)%lname = "Grazing of sp by zoo"
grazing_relationship_settings(1,1)%sname = "grz_sp_zoo"
grazing_relationship_settings(1,1)%z_grz = 1.2
grazing_relationship_settings(1,1)%z_umax_0_per_day = 3.3
grazing_relationship_settings(1,1)%zoo_ind_cnt = 0
grazing_relationship_settings(2,1)%auto_ind(1) = 2
grazing_relationship_settings(2,1)%auto_ind_cnt = 1
grazing_relationship_settings(2,1)%f_zoo_detr = 0.24
grazing_relationship_settings(2,1)%graze_doc = 0.06
grazing_relationship_settings(2,1)%graze_poc = 0.39
grazing_relationship_settings(2,1)%graze_zoo = 0.25
grazing_relationship_settings(2,1)%grazing_function = 1
grazing_relationship_settings(2,1)%lname = "Grazing of diat by zoo"
grazing_relationship_settings(2,1)%sname = "grz_diat_zoo"
grazing_relationship_settings(2,1)%z_grz = 1.2
grazing_relationship_settings(2,1)%z_umax_0_per_day = 3.15
grazing_relationship_settings(2,1)%zoo_ind_cnt = 0
grazing_relationship_settings(3,1)%auto_ind(1) = 3
grazing_relationship_settings(3,1)%auto_ind_cnt = 1
grazing_relationship_settings(3,1)%f_zoo_detr = 0.12
grazing_relationship_settings(3,1)%graze_doc = 0.06
grazing_relationship_settings(3,1)%graze_poc = 0.1
grazing_relationship_settings(3,1)%graze_zoo = 0.3
grazing_relationship_settings(3,1)%grazing_function = 1
grazing_relationship_settings(3,1)%lname = "Grazing of diaz by zoo"
grazing_relationship_settings(3,1)%sname = "grz_diaz_zoo"
grazing_relationship_settings(3,1)%z_grz = 1.2
grazing_relationship_settings(3,1)%z_umax_0_per_day = 3.3
grazing_relationship_settings(3,1)%zoo_ind_cnt = 0
! tracer restoring
tracer_restore_vars(1) = ""
tracer_restore_vars(2) = ""
tracer_restore_vars(3) = ""
tracer_restore_vars(4) = ""
tracer_restore_vars(5) = ""
tracer_restore_vars(6) = ""
tracer_restore_vars(7) = ""
tracer_restore_vars(8) = ""
tracer_restore_vars(9) = ""
tracer_restore_vars(10) = ""
tracer_restore_vars(11) = ""
tracer_restore_vars(12) = ""
tracer_restore_vars(13) = ""
tracer_restore_vars(14) = ""
tracer_restore_vars(15) = ""
tracer_restore_vars(16) = ""
tracer_restore_vars(17) = ""
tracer_restore_vars(18) = ""
tracer_restore_vars(19) = ""
tracer_restore_vars(20) = ""
tracer_restore_vars(21) = ""
tracer_restore_vars(22) = ""
tracer_restore_vars(23) = ""
tracer_restore_vars(24) = ""
tracer_restore_vars(25) = ""
tracer_restore_vars(26) = ""
tracer_restore_vars(27) = ""
tracer_restore_vars(28) = ""
tracer_restore_vars(29) = ""
tracer_restore_vars(30) = ""
tracer_restore_vars(31) = ""
tracer_restore_vars(32) = ""