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Cleanup: float index and unused variables #32

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Apr 5, 2024
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Cleanup: float index and unused variables #32

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0f5cf69
kmld_ref is an index and should be an integer
andrew-c-ross Apr 4, 2024
05357b7
Remove some unused variables
andrew-c-ross Apr 4, 2024
5a8fbcb
Remove tabs
andrew-c-ross Apr 4, 2024
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64 changes: 25 additions & 39 deletions generic_tracers/generic_COBALT.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
! fall below 1/4 maximum values
! 3) The default parameterization has elevated N:P ratios for both
! diazotrophs and small phytoplankton
! 4) Remineralization of sinking detritus is now based on the temperature
! 4) Remineralization of sinking detritus is now based on the temperature
! and oxygen dependences described in Laufkotter et al., 2017; O2
! dependence of other aerobic processes have also been adjusted
! for consistency.
Expand Down Expand Up @@ -160,10 +160,6 @@ module generic_COBALT
use FMS_ocmip2_co2calc_mod, only : FMS_ocmip2_co2calc, CO2_dope_vector

implicit none ; private
!-----------------------------------------------------------------------
character(len=128) :: version = '$Id: generic_COBALT.F90,v 20.0.2.1.2.1 2014/09/29 16:40:08 Niki.Zadeh Exp $'
character(len=128) :: tag = '$Name: bugfix_nnz $'
!-----------------------------------------------------------------------

character(len=fm_string_len), parameter :: mod_name = 'generic_COBALT'
character(len=fm_string_len), parameter :: package_name = 'generic_cobalt'
Expand Down Expand Up @@ -418,7 +414,7 @@ module generic_COBALT

type zooplankton
real :: &
imax, & ! maximum ingestion rate (sec-1)
imax, & ! maximum ingestion rate (sec-1)
ki, & ! half-sat for ingestion (moles N m-3)
gge_max, & ! max gross growth efficiciency (approached as i >> bresp, dimensionless)
nswitch, & ! switching parameter (dimensionless)
Expand Down Expand Up @@ -457,13 +453,13 @@ module generic_COBALT
real, ALLOCATABLE, dimension(:,:,:) :: &
f_n, & ! zooplankton biomass
jzloss_n, & ! Losses of n due to consumption by other zooplankton groups
jzloss_p, & ! Losses of p due to consumption by other zooplankton groups
jzloss_p, & ! Losses of p due to consumption by other zooplankton groups
jhploss_n, & ! Losses of n due to consumption by unresolved higher preds
jhploss_p, & ! Losses of p due to consumption by unresolved higher preds
jhploss_p, & ! Losses of p due to consumption by unresolved higher preds
jingest_n, & ! Total ingestion of n
jingest_p, & ! Total ingestion of p
jingest_sio2, & ! Total ingestion of silicate
jingest_fe, & ! Total ingestion of iron
jingest_fe, & ! Total ingestion of iron
jprod_ndet, & ! production of nitrogen detritus by zooplankton group
jprod_pdet, & ! production of phosphorous detritus by zooplankton group
jprod_ldon, & ! production of labile dissolved organic N by zooplankton group
Expand All @@ -472,17 +468,17 @@ module generic_COBALT
jprod_srdop, & ! production of semi-refractory dissolved organic P by zooplankton group
jprod_sldon, & ! production of semi-labile dissolved organic N by zooplankton group
jprod_sldop, & ! production of semi-labile dissolved organic P by zooplankton group
jprod_fed, & ! production of dissolved iron
jprod_fed, & ! production of dissolved iron
jprod_fedet, & ! production of iron detritus
jprod_sidet, & ! production of silica detritus
jprod_sidet, & ! production of silica detritus
jprod_sio4, & ! production of silicate via rapid dissolution at surface
jprod_po4, & ! phosphate production by zooplankton
jprod_nh4, & ! ammonia production by zooplankton
jprod_n, & ! zooplankton production
o2lim, & ! oxygen limitation of zooplankton activity
temp_lim, & ! Temperature limitation
vmove ! Vertical movement
integer :: &
integer :: &
id_jzloss_n = -1, &
id_jzloss_p = -1, &
id_jhploss_n = -1, &
Expand Down Expand Up @@ -720,7 +716,7 @@ module generic_COBALT
ki_hp, & ! unresolved higher pred. half-sat
ktemp_hp, & ! temperature dependence for higher predators
coef_hp, & ! scaling between unresolved preds and available prey
nswitch_hp, & ! higher predator switching behavior
nswitch_hp, & ! higher predator switching behavior
mswitch_hp, & ! higher predator switching behavior
hp_ipa_smp, & ! innate prey availability of small phytos to hp
hp_ipa_mdp, & ! innate prey availability of medium phytos to hp
Expand All @@ -745,7 +741,7 @@ module generic_COBALT
mask_z_sat_calc

real, dimension(:,:,:), ALLOCATABLE :: &
f_alk,& ! Other prognostic variables
f_alk,& ! Other prognostic variables
f_cadet_arag,&
f_cadet_calc,&
f_dic,&
Expand Down Expand Up @@ -954,7 +950,7 @@ module generic_COBALT
!==============================================================================================================

real, dimension(:,:), ALLOCATABLE :: &
b_alk,b_dic,b_fed,b_nh4,b_no3,b_o2,b_po4,b_sio4,b_di14c,& ! bottom flux terms
b_alk,b_dic,b_fed,b_nh4,b_no3,b_o2,b_po4,b_sio4,b_di14c,& ! bottom flux terms
co2_csurf,pco2_csurf,co2_alpha,c14o2_csurf,c14o2_alpha,&
nh3_csurf,nh3_alpha,pnh3_csurf,&
fcadet_arag_btm,&
Expand Down Expand Up @@ -1223,7 +1219,7 @@ module generic_COBALT
id_irr_aclm_z = -1, &
id_irr_mem_dp = -1, &
id_cased = -1, &
id_cadet_arag_btf = -1, &
id_cadet_arag_btf = -1, &
id_cadet_calc_btf = -1, &
id_fedet_btf = -1, &
id_lithdet_btf = -1, &
Expand Down Expand Up @@ -1881,13 +1877,6 @@ subroutine generic_COBALT_register_diag(diag_list)
type(vardesc) :: vardesc_temp
integer :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau, axes(3), axesTi(3)
type(time_type):: init_time
character(len=fm_string_len) :: cmor_field_name
character(len=fm_string_len) :: cmor_long_name
character(len=fm_string_len) :: cmor_units
character(len=fm_string_len) :: cmor_standard_name
! real :: conversion


call g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes=axes,init_time=init_time)

! The following vardesc types contain a package of metadata about each tracer,
Expand Down Expand Up @@ -3240,7 +3229,7 @@ subroutine generic_COBALT_register_diag(diag_list)

vardesc_temp = vardesc("jprod_n2amx","Fixed N loss via Anammox layer integral",'h','L','s','mol m-2 s-1','f')
cobalt%id_jprod_n2amx = register_diag_field(package_name, vardesc_temp%name, axes(1:3),&
init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)
init_time, vardesc_temp%longname,vardesc_temp%units, missing_value = missing_value1)

vardesc_temp = vardesc("juptake_nh4amx","NH4 uptake via Anammox layer integral",'h','L','s','mol m-2 s-1','f')
cobalt%id_juptake_nh4amx = register_diag_field(package_name, vardesc_temp%name, axes(1:3),&
Expand Down Expand Up @@ -6206,8 +6195,8 @@ subroutine user_add_params
! Effect is to decrease alkalinity by 2 NH4 equivalents.
!
! New Nitrification stoichiometry from JPD, for ESM4.2:
! (16+106*35)*NH4+ + 106*CO2 + (106*35+449*8)*O2 + 62*H2O <->
! C106H172O38N16 + (106*35)*NO3- + (106*35)*H2O + (16+106*35*2)*H+
! (16+106*35)*NH4+ + 106*CO2 + (106*35+449*8)*O2 + 62*H2O <->
! C106H172O38N16 + (106*35)*NO3- + (106*35)*H2O + (16+106*35*2)*H+
! Effect is to decrease alkalinity by 1.996 NH4 equivalents.
!
! Denitrification:
Expand All @@ -6218,12 +6207,12 @@ subroutine user_add_params
!
! Anammox stoichiometry from JPD, for ESM4.2:
!
! (16+106*3*5*5+64)*NH4+ + (106*3*3*5-118*4)*NO3- + 106*5*CO2 + 62*5*H2O <->
! 5*C106H172O38N16 + (106*3*4*5-118*2)*N2 +
! (106*3*9*5-118*2)*H2O + (16+106*3*2*5+118*4+64)*H+
!
! Effect is to decrease alkalinity by
! (16+106*3*2*5+118*4+64)/ (16+106*3*5*5+64) = 0.46 mole equivalents per mole of NH4 removed.
! (16+106*3*5*5+64)*NH4+ + (106*3*3*5-118*4)*NO3- + 106*5*CO2 + 62*5*H2O <->
! 5*C106H172O38N16 + (106*3*4*5-118*2)*N2 +
! (106*3*9*5-118*2)*H2O + (16+106*3*2*5+118*4+64)*H+
!
! Effect is to decrease alkalinity by
! (16+106*3*2*5+118*4+64)/ (16+106*3*5*5+64) = 0.46 mole equivalents per mole of NH4 removed.
!
call g_tracer_add_param('n_2_n_denit', cobalt%n_2_n_denit, 472.0/(5.0*16.0)) ! mol N NO3 mol N org-1
call g_tracer_add_param('no3_2_nh4_amx', cobalt%no3_2_nh4_amx, &
Expand All @@ -6232,7 +6221,7 @@ subroutine user_add_params
! call g_tracer_add_param('o2_2_nfix', cobalt%o2_2_nfix, (118.0+3.0/(5.0+3.0)*(150.0-118.0))/16.0) ! mol O2 mol N-1
call g_tracer_add_param('o2_2_nh4', cobalt%o2_2_nh4, 118.0 / 16.0) ! mol O2 mol N-1
!call g_tracer_add_param('o2_2_nitrif', cobalt%o2_2_nitrif, &
! (106.0*35.0+449.0*8.0)/(16.0+106.0*35.0)) ! mol O2 mol N-1
! (106.0*35.0+449.0*8.0)/(16.0+106.0*35.0)) ! mol O2 mol N-1
call g_tracer_add_param('o2_2_nitrif', cobalt%o2_2_nitrif,2.0)
call g_tracer_add_param('o2_2_no3', cobalt%o2_2_no3, 150.0 / 16.0) ! mol O2 mol N-1
!
Expand Down Expand Up @@ -7877,7 +7866,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
type(EOS_type), optional, intent(in) :: eqn_of_state !< Equation of state structure

character(len=fm_string_len), parameter :: sub_name = 'generic_COBALT_update_from_source'
integer :: isc,iec, jsc,jec,isd,ied,jsd,jed,nk,ntau, i, j, k , m, n, k_100, k_200, kbot
integer :: isc,iec, jsc,jec,isd,ied,jsd,jed,nk,ntau, i, j, k , m, n, k_100, k_200, kmld_ref
real, dimension(:,:,:) ,pointer :: grid_tmask
integer, dimension(:,:),pointer :: mask_coast,grid_kmt
!
Expand All @@ -7889,9 +7878,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
integer :: nb
real :: r_dt
real :: feprime_temp
real :: juptake_di_tot2nterm
real :: P_C_m, k_po4_adjust
real :: p_lim_nhet
real :: TK, PRESS, PKSPA, PKSPC
real :: tmp_hblt, tmp_irrad, tmp_irrad_ML,tmp_opacity,tmp_mu_ML
real :: frac_sfc_irrad_aclm, irrad_aclm_thresh
Expand All @@ -7912,8 +7899,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
real :: fpoc_btm, log10_fpoc_btm
real :: fe_salt
real :: sal,tt,tkb,ts,ts2,ts3,ts4,ts5
real :: rho_mld_ref,rho_k,dK,dKm1,afac,deltaRhoAtK,deltaRhoAtKm1,deltaRhoFlag,kmld_ref
real :: depth_limit
real :: rho_mld_ref,rho_k,dK,dKm1,afac,deltaRhoAtK,deltaRhoAtKm1,deltaRhoFlag
real :: alpha_temp, alpha_step
real :: P_C_max_temp, P_C_max_step, bresp_temp
real :: theta_temp, theta_step, irrlim_temp, P_C_m_temp
Expand Down Expand Up @@ -16072,7 +16058,7 @@ end function calc_pka_nh3
!salting out correction for solubility (Johnson 2010, Ocean Science)
function saltout_correction(kh,vb,salt) result(C)
real, intent(in) :: Kh,vb,salt
real*8 :: T,log_kh,theta2
real*8 :: log_kh
real :: theta,C
log_kh = log(kh)
theta = (7.3353282561828962e-04 + (3.3961477466551352e-05*log_kh) + (-2.4088830102075734e-06*(log_kh)**2) + (1.5711393120941302e-07*(log_kh)**3))*log(vb)
Expand Down
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