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fixed freox and fanox diags, added units, fixed reference #178

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Merged
hpowley merged 2 commits into from
Jul 27, 2026
Merged

fixed freox and fanox diags, added units, fixed reference #178

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fbc4447
fixed freox and fanox diags, added units, fixed reference
glessin Jul 27, 2026
9363520
added long names for freox and fanox
glessin Jul 27, 2026
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20 changes: 10 additions & 10 deletions src/bacteria_docdyn.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ module ersem_bacteria_docdyn
real(rk) :: DeniX,reoX,omroX,omonX,chN3oX
integer :: denit

! Remineralization
! Remineralisation
real(rk) :: sR1N1X,sR1N4X
real(rk) :: fsinkX
contains
Expand Down Expand Up @@ -98,12 +98,12 @@ subroutine initialize(self,configunit)
call self%register_state_dependency(self%id_N3n,'N3n','mmol N/m^3','nitrate')
call self%register_state_dependency(self%id_N6,'N6','mmol HS-/m^3','reduction equivalent')

call self%register_diagnostic_variable(self%id_fdenit,'fdenit','mmol N/m^3/d','denitrification', missing_value=0._rk)
call self%register_diagnostic_variable(self%id_fanox,'fanox', '-', 'fanox', missing_value=0._rk)
call self%register_diagnostic_variable(self%id_freox,'freox', '-', 'freox', missing_value=0._rk)
call self%register_diagnostic_variable(self%id_fdenit, 'fdenit', 'mmol N/m^3/d', 'denitrification', missing_value=0._rk)
call self%register_diagnostic_variable(self%id_fanox, 'fanox', 'mmol HS-/m^3/d', 'formation of reduction equivalents', missing_value=0._rk)
call self%register_diagnostic_variable(self%id_freox, 'freox','mmol HS-/m^3/d', 'reoxidation of reduction equivalents', missing_value=0._rk)
end if

! Remineralization parameters
! Remineralisation parameters
call self%get_parameter(self%sR1N1X, 'sR1N1', '1/d', 'mineralisation rate of labile dissolved organic phosphorus')
call self%get_parameter(self%sR1N4X, 'sR1N4', '1/d', 'mineralisation rate of labile dissolved organic nitrogen')
call self%get_parameter(self%fsinkX, 'fsink', '1/d', 'scavenging rate for iron')
Expand Down Expand Up @@ -322,7 +322,7 @@ subroutine do(self,_ARGUMENTS_DO_)
fB1R3c=self%frB1R3*rraB1
fB1RDc = fB1R1c + fB1R2c + fB1R3c

! Denitrification implemented as in Sankar et al. (2008), doi.org/10.1016/j.ecolmodel.2018.01.016
! Denitrification implemented as in Sankar et al. (2018), doi.org/10.1016/j.ecolmodel.2018.01.016
if (self%denit == 1) then
denitpot = self%DeniX * N3n !eq.6
deniteff = max(0._rk, self%urB1_O2X * (1._rk-o2state) * fB1O3c / self%omonX) !eq.7
Expand All @@ -331,12 +331,12 @@ subroutine do(self,_ARGUMENTS_DO_)
_SET_DIAGNOSTIC_(self%id_fdenit,fdenit)
_SET_ODE_(self%id_N3n, -fdenit)

! Reduced sulfur formation corresponds to eq.9 in Sankar et al. (2008)
! Reduced sulfur formation corresponds to eq.9 in Sankar et al. (2018)
fanox = self%omroX * (self%urB1_O2X * (1._rk-o2state) * fB1O3c - self%omonX * fdenit)
freox = self%reoX * etB1 * o2state * N6

_SET_DIAGNOSTIC_(self%id_fanox,freox)
_SET_DIAGNOSTIC_(self%id_freox,fanox)
_SET_DIAGNOSTIC_(self%id_fanox,fanox)
_SET_DIAGNOSTIC_(self%id_freox,freox)

_SET_ODE_(self%id_N6, fanox - freox)
end if
Expand Down Expand Up @@ -497,7 +497,7 @@ subroutine remineralization(self,_ARGUMENTS_DO_)
_SET_DIAGNOSTIC_(self%id_minp,fR1N1p)

if (use_iron) then
! remineralization of particulate iron to Fe
! remineralisation of particulate iron to Fe
do iRP=1,self%nRP
_GET_(self%id_RPf(iRP),RPfP(iRP))
end do
Expand Down
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