! BioCGT processes file
! *********************
! properties of processes:
! name=           fortran variable name for the rate
! description=    e.g. "grazing of zooplankton"
! turnover=       fortran formula for calculating the process turnover [mol/kg or mol/m2]
! equation=       equation which, like a chemical equation, lists reaction agents and products of this process.
!                   example: t_no3 + 1/16*t_po4 -> t_lpp
!                   tracers to the left of the "->" are consumed, tracers to the right of the "->" are produced by this process.
! feedingEfficiency= name of an auxiliary variable (values 0..1) which tells how much of the food in a certain depth is accessible for the predator with vertLoc=FIS. Relevant for vertLoc=FIS only. Default="1.0"
! isActive=       1=active (default); 0=process is switched off
! isOutput=       1=occurs as output in model results; 0=internal use only (default)
! limitation=     TYPE tracer > value else otherProcess
! limitation=     TYPE tracer < value else otherProcess
!                   TYPE = HARD (theta function), MM (Michaelis-Menten), MMQ (quadratic Michaelis-Menten), IV (Ivlev), IVQ (quadratic Ivlev), LIN (linear), TANH (tangens hyperbolicus)
!                   tracer = name of tracer that needs to be present
!                   value = value that needs to be exceeded, may also be a constant or auxiliary
!                   otherProcess = process that takes place instead if this process gets hampered by the availability of "tracer"
!                 several of these lines may exist, the order of them may be relevant for the rate of "otherProcess".
! processType=    type of process, e.g. "propagation", default="standard"
! repaint=        number n of repainting actions to be done by the process, default=0
!                 This line is followed by n lines of this kind:
!   <oldColor> <element> = <newColor>    e.g.: "all  N   = blue "
!                                              "blue P   = none "
!                                              "red  all = green"
! vertLoc=        WAT=z-dependent (default), SED=in the sediment only, SUR=in the surface only, FIS=fish-type behaviour
! comment=        comment, default=""
!
! Process rates are calculated in the given order.
! *************************************************************************************
name        = p_n2_stf_down
description = downward nitrogen flux through the surface
turnover    = w_n2_stf*(n2_sat-t_n2)*theta(n2_sat-t_n2)*cgt_density
comment     = relaxation of nitrogen concentration against saturation at surface using \\piston-velocity, downward oxygen flow
equation    =  -> t_n2
vertLoc     = SUR
processType = gas_exchange
***********************
name        = p_n2_stf_up
description = upward nitrogen flux through the surface
turnover    = w_n2_stf*(t_n2-n2_sat)*theta(t_n2-n2_sat)*cgt_density
comment     = relaxation of nitrogen concentration against saturation at surface using piston-velocity, upward oxygen flow
equation    = t_n2 -> 
vertLoc     = SUR
processType = gas_exchange
***********************
name        = p_o2_stf_down
description = downward oxygen flux through the surface
turnover    = w_o2_stf*(o2_sat-t_o2)*theta(o2_sat-t_o2)*cgt_density
comment     = relaxation of oxygen concentration against saturation at surface using piston-velocity, downward oxygen flow
equation    =  -> t_o2
vertLoc     = SUR
processType = gas_exchange
***********************
name        = p_o2_stf_up
description = upward oxygen flux through the surface
turnover    = w_o2_stf*(t_o2-o2_sat)*theta(t_o2-o2_sat)*cgt_density
comment     = relaxation of oxygen concentration against saturation at surface using piston-velocity, upward oxygen flow
equation    = t_o2 -> 
vertLoc     = SUR
processType = gas_exchange
***********************
name        = p_co2_stf_down
description = downward co2 flux through the surface
turnover    = w_co2_stf*(patm_co2-pco2)*k0_co2*theta(patm_co2-pco2)*cgt_density
comment     = relaxation of co2 concentration against saturation at surface using piston-velocity, downward co2 flow
equation    =  -> t_dic
vertLoc     = SUR
processType = gas_exchange
***********************
name        = p_co2_stf_up
description = upward co2 flux through the surface
turnover    = w_co2_stf*(pco2-patm_co2)*k0_co2*theta(pco2-patm_co2)*cgt_density
comment     = relaxation of co2 concentration against saturation at surface using piston-velocity, upward co2 flow
equation    = t_dic -> 
vertLoc     = SUR
processType = gas_exchange
***********************
name        = p_no3_assim_lpp
description = assimilation of nitrate by large-cell phytoplankton
turnover    = lpp_plus_lpp0*lr_assim_lpp*t_no3/(din+epsilon)*theta(cgt_dayofyear-60.0)*theta(200.0-cgt_dayofyear)
equation    = t_no3 + rfr_p*t_po4 + rfr_c*t_dic + 6.4375*h2o + 1.1875*h3oplus -> t_lpp + 8.625*t_o2
***********************
name        = p_nh4_assim_lpp
description = assimilation of ammonium by large-cell phytoplankton
turnover    = lpp_plus_lpp0*lr_assim_lpp*t_nh4/(din+epsilon)*theta(cgt_dayofyear-60.0)*theta(200.0-cgt_dayofyear)
equation    = 7.4375*h2o + rfr_c*t_dic + rfr_p*t_po4 + t_nh4 -> 0.8125*h3oplus + 6.625*t_o2 + t_lpp
***********************
name        = p_no3_assim_spp
description = assimilation of nitrate by small-cell phytoplankton
turnover    = spp_plus_spp0*lr_assim_spp*t_no3/(din+epsilon)*theta(cgt_dayofyear-60.0)*theta(200.0-cgt_dayofyear)
equation    = t_no3 + rfr_p*t_po4 + rfr_c*t_dic + 6.4375*h2o + 1.1875*h3oplus -> t_spp + 8.625*t_o2
***********************
name        = p_nh4_assim_spp
description = assimilation of ammonium by small-cell phytoplankton
turnover    = spp_plus_spp0*lr_assim_spp*t_nh4/(din+epsilon)*theta(cgt_dayofyear-60.0)*theta(200.0-cgt_dayofyear)
equation    = t_nh4 + rfr_p*t_po4 + rfr_c*t_dic + 0*h2o + 7.4375*h2o -> t_spp + 6.625*t_o2 + 0.8125*h3oplus
***********************
name        = p_n2_assim_cya
description = fixation of dinitrogen by diazotroph cyanobacteria
turnover    = cya_plus_cya0*lr_assim_cya*theta(cgt_dayofyear-60.0)*theta(200.0-cgt_dayofyear)
equation    = 0.1875*h3oplus + 0.5*t_n2 + rfr_p*t_po4 + rfr_c*t_dic + 7.9375*h2o -> t_cya + 7.375*t_o2
repaint     = 1
  all N = blue
***********************
name        = p_lpp_graz_zoo
description = grazing of zooplankton eating large-cell phytoplankton
turnover    = (t_zoo+zoo0)*lr_graz_zoo*t_lpp/max(food_zoo,epsilon)
equation    = t_lpp -> t_zoo
***********************
name        = p_spp_graz_zoo
description = grazing of zooplankton eating small-cell phytoplankton
turnover    = (t_zoo+zoo0)*lr_graz_zoo*t_spp/max(food_zoo,epsilon)
equation    = t_spp -> t_zoo
***********************
name        = p_cya_graz_zoo
description = grazing of zooplankton eating diazotroph cyanobacteria
turnover    = (t_zoo+zoo0)*lr_graz_zoo*(0.5*t_cya)/max(food_zoo,epsilon)
equation    = t_cya -> t_zoo
***********************
name        = p_lpp_resp_nh4
description = respiration of large-cell phytoplankton
turnover    = t_lpp*r_lpp_resp*(1.0-cgt_in_sediment)
equation    = 0.8125*h3oplus + 6.625*t_o2 + t_lpp -> 7.4375*h2o + rfr_c*t_dic + rfr_p*t_po4 + (1-don_fraction)*t_nh4 + don_fraction*t_don
***********************
name        = p_spp_resp_nh4
description = respiration of small-cell phytoplankton
turnover    = t_spp*r_spp_resp*(1.0-cgt_in_sediment)
equation    = t_spp + 6.625*t_o2 + 0.8125*h3oplus -> don_fraction*t_don + (1-don_fraction)*t_nh4 + rfr_p*t_po4 + rfr_c*t_dic + 7.4375*h2o
***********************
name        = p_cya_resp_nh4
description = respiration of diazotroph cyanobacteria
turnover    = t_cya*r_cya_resp*(1.0-cgt_in_sediment)
equation    = t_cya + 6.625*t_o2 + 0.8125*h3oplus -> (1-don_fraction)*t_nh4 + don_fraction*t_don + rfr_p*t_po4 + rfr_c*t_dic + 7.4375*h2o
***********************
name        = p_zoo_resp_nh4
description = respiration of zooplankton
turnover    = zoo_eff*r_zoo_resp*(1.0-cgt_in_sediment)
equation    = t_zoo + 6.625*t_o2 + 0.8125*h3oplus -> don_fraction*t_don + (1-don_fraction)*t_nh4 + rfr_p*t_po4 + rfr_c*t_dic + 7.4375*h2o
***********************
name        = p_don_rec_nh4
description = mineralization of DON
turnover    = t_don*r_don_rec
equation    = t_don -> t_nh4
***********************
name        = p_lpp_mort_det_$t_det
description = mortality of large-cell phytoplankton
turnover    = frac_det_$t_det*t_lpp*r_pp_mort*(1+9*theta(5.0e-6-t_o2))
equation    = t_lpp + (1.0-(1.0/rfr_pc_enrichment_det))*h3oplus -> (1.0/rfr_pc_enrichment_det)*t_detp_$t_det + (1.0/rfr_pc_enrichment_det)*t_det_$t_det + (1.0-(1.0/rfr_pc_enrichment_det))*t_nh4 + (1.0-(1.0/rfr_pc_enrichment_det))*h2o
***********************
name        = p_spp_mort_det_$t_det
description = mortality of small-scale phytoplankton
turnover    = frac_det_$t_det*t_spp*r_pp_mort*(1+9*theta(5.0e-6-t_o2))
equation    = t_spp + (1.0-(1.0/rfr_pc_enrichment_det))*h3oplus -> (1.0/rfr_pc_enrichment_det)*t_detp_$t_det + (1.0/rfr_pc_enrichment_det)*t_det_$t_det + (1.0-(1.0/rfr_pc_enrichment_det))*t_nh4 + (1.0-(1.0/rfr_pc_enrichment_det))*h2o
***********************
name        = p_cya_mort_det_$t_det
description = mortality of diazotroph cyanobacteria
turnover    = frac_det_$t_det*t_cya*r_pp_mort*(1+9*theta(5.0e-6-t_o2))
equation    = (1.0-(1.0/rfr_pc_enrichment_det))*h3oplus + t_cya -> (1.0-(1.0/rfr_pc_enrichment_det))*h2o + (1.0-(1.0/rfr_pc_enrichment_det))*t_nh4 + (1.0/rfr_pc_enrichment_det)*t_det_$t_det + (1.0/rfr_pc_enrichment_det)*t_detp_$t_det
***********************
name        = p_zoo_mort_det_$t_det
description = mortality of zooplankton
turnover    = frac_det_$t_det*zoo_eff*r_zoo_mort*(1+9*theta(5.0e-6-t_o2))
equation    = t_zoo + (1.0-(1.0/rfr_pc_enrichment_det))*h3oplus -> (1.0/rfr_pc_enrichment_det)*t_detp_$t_det + (1.0/rfr_pc_enrichment_det)*t_det_$t_det + (1.0-(1.0/rfr_pc_enrichment_det))*t_nh4 + (1.0-(1.0/rfr_pc_enrichment_det))*h2o
***********************
name        = p_nh4_nit_no3
description = nitrification
turnover    = t_nh4*r_nh4_nitrif*exp(q10_nit*cgt_temp)*(1.0-cgt_in_sediment)
equation    = t_nh4 + 2*t_o2 + h2o -> t_no3 + 2*h3oplus
limitation  = IV t_o2 > o2_min_nit
***********************
name        = p_nh4_nit_no3_sed
description = nitrification in the sediment
turnover    = t_nh4*t_o2*k_nh4_o2*exp(q10_nit*cgt_temp)*cgt_in_sediment
comment     = after Wijsman et al., 2002: A Model for Early Diagenetic Processes in Sediments of \\the Continental Shelf of the Black Sea. Estuarine, Coastal and Shelf Science 54, 403\\-421
equation    = h2o + 2*t_o2 + t_nh4 -> 2*h3oplus + t_no3
limitation  = MM t_o2 > o2_min_nit
***********************
name        = p_sed_$t_sed_resp_nh4
description = recycling of sedimentary detritus to ammonium using oxygen (respiration)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)
equation    = t_sed_$t_sed + rfr_pc_enrichment_det*6.625*t_o2 + h3oplus -> t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic + (1.0+6.625*rfr_pc_enrichment_det)*h2o + rfr_si*t_sil
vertLoc     = SED
isOutput    = 1
***********************
name        = p_sed_$t_sed_denit_nh4
description = recycling of sedimentary detritus to ammonium using nitrate (denitrification)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*pH_inhibition_ironred
comment     = as long as there is enough nitrate, no "negative oxygen" is \\generated (2 NO3- + 2 \\H3O+ -> N2 + 3 H2O + 5/2 O2)
equation    = rfr_pc_enrichment_det*5.3*t_no3 + (1.0+5.3*rfr_pc_enrichment_det)*h3oplus + t_sed_$t_sed -> rfr_si*t_sil + (1.0+14.575*rfr_pc_enrichment_det)*h2o + rfr_pc_enrichment_det*2.65*t_n2 + t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic
vertLoc     = SED
isOutput    = 1
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 > no3_min_sed_denit
***********************
name        = p_sed_$t_sed_sulf_nh4
description = recycling of sedimentary detritus to ammonium using sulfate (sulfate reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*max(t_so4,0.0)/(max(t_so4,0.0)+so4_min_det_sulf)*pH_inhibition_ironred
equation    = t_sed_$t_sed + rfr_pc_enrichment_det*3.3125*t_so4 + (1.0+rfr_pc_enrichment_det*6.625)*h3oplus -> rfr_si*t_sil + t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic + rfr_pc_enrichment_det*3.3125*t_h2s + (1.0+rfr_pc_enrichment_det*13.25)*h2o
vertLoc     = SED
isOutput    = 1
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_ihs < ihs_min_sed_irred_2d
limitation  = IV t_mos < mos_min_sed_irred_2d
limitation  = IV t_i3i < ihs_min_sed_irred_2d
***********************
name        = p_h2s_oxo2_sul
description = oxidation of hydrogen sulfide with oxygen
turnover    = t_h2s*t_o2*k_h2s_o2*exp(q10_h2s*cgt_temp)
equation    = 0.5*t_o2 + t_h2s -> h2o + t_sul
isOutput    = 1
***********************
name        = p_h2s_oxno3_sul
description = oxidation of hydrogen sulfide with nitrate
turnover    = t_h2s*t_no3*k_h2s_no3*exp(q10_h2s*cgt_temp)
equation    = t_h2s + 0.4*t_no3 + 0.4*h3oplus -> t_sul + 1.6*h2o + 0.2*t_n2
isOutput    = 1
***********************
name        = p_sul_oxo2_so4
description = oxidation of elemental sulfur with oxygen
turnover    = t_sul*t_o2*k_sul_o2*exp(q10_h2s*cgt_temp)
equation    = t_sul + 1.5*t_o2 + 3*h2o -> t_so4 + 2*h3oplus
***********************
name        = p_sul_oxno3_so4
description = oxidation of elemental sulfur with nitrate
turnover    = t_sul*t_no3*k_sul_no3*exp(q10_h2s*cgt_temp)
equation    = t_sul + 1.2*t_no3 + 1.2*h2o -> t_so4 + 0.8*h3oplus + 0.6*t_n2
***********************
name        = p_det_$t_det_sedi_sed
description = detritus sedimentation
turnover    = (1.0-erosion_is_active)*(0.0-w_det_sedi)*t_det_$t_det*cgt_density*(1.0-cgt_in_sediment) + cgt_in_sediment*(t_det_$t_det*cgt_density*cgt_cellheight*0.1)
equation    = t_det_$t_det -> t_sed_$t_det
vertLoc     = SED
***********************
name        = p_detp_$t_det_sedi_sedp
description = detritus sedimentation
turnover    = (1.0-erosion_is_active)*(0.0-w_det_sedi)*t_detp_$t_det*cgt_density*(1.0-cgt_in_sediment) + cgt_in_sediment*(t_detp_$t_det*cgt_density*cgt_cellheight*0.1)
equation    = t_detp_$t_det -> t_sedp_$t_det
vertLoc     = SED
***********************
name        = p_ipw_sedi_ips
description = sedimentation of iron PO4
turnover    = (1.0-erosion_is_active)*(0.0-w_ipw_sedi)*t_ipw*cgt_density*(1.0-cgt_in_sediment)
equation    = t_ipw -> t_ips
vertLoc     = SED
***********************
name        = p_ihw_sedi_ihs
description = sedimentation of iron hydroxide
turnover    = (1.0-erosion_is_active)*(0.0-w_ipw_sedi)*t_ihw*cgt_density*(1.0-cgt_in_sediment)
equation    = t_ihw -> t_ihs
vertLoc     = SED
***********************
name        = p_mow_sedi_mos
description = sedimentation of iron hydroxide
turnover    = (1.0-erosion_is_active)*(0.0-w_ipw_sedi)*t_mow*cgt_density*(1.0-cgt_in_sediment)
equation    = t_mow -> t_mos
vertLoc     = SED
***********************
name        = p_sed_$t_sed_ero_det
description = sedimentary detritus erosion
turnover    = erosion_is_active*r_sed_ero*t_sed_$t_sed*(1.0-cgt_in_sediment)
equation    = t_sed_$t_sed -> t_det_$t_sed
vertLoc     = SED
***********************
name        = p_sedp_$t_sed_ero_detp
description = sedimentary detritus erosion
turnover    = erosion_is_active*r_sed_ero*t_sedp_$t_sed*(1.0-cgt_in_sediment)
equation    = t_sedp_$t_sed -> t_detp_$t_sed
vertLoc     = SED
***********************
name        = p_ips_ero_ipw
description = erosion of iron PO4
turnover    = erosion_is_active*r_ips_ero*t_ips*(1.0-cgt_in_sediment)
equation    = t_ips -> t_ipw
vertLoc     = SED
***********************
name        = p_ihs_ero_ihw
description = erosion of iron PO4
turnover    = erosion_is_active*r_ips_ero*t_ihs*(1.0-cgt_in_sediment)
equation    = t_ihs -> t_ihw
vertLoc     = SED
***********************
name        = p_mos_ero_mow
description = erosion of manganese oxide
turnover    = erosion_is_active*r_ips_ero*t_mos*(1.0-cgt_in_sediment)
equation    = t_mos -> t_mow
vertLoc     = SED
***********************
name        = p_sed_$t_sed_biores_det
description = bio resuspension of sedimentary detritus
turnover    = r_biores*t_sed_$t_sed*(1.0-cgt_in_sediment)
equation    = t_sed_$t_sed -> t_det_$t_sed
vertLoc     = SED
limitation  = MMQ t_o2 > o2_min_sed_resp
***********************
name        = p_sedp_$t_sed_biores_detp
description = bio resuspension of sedimentary detritus
turnover    = r_biores*t_sedp_$t_sed*(1.0-cgt_in_sediment)
equation    = t_sedp_$t_sed -> t_detp_$t_sed
vertLoc     = SED
limitation  = MMQ t_o2 > o2_min_sed_resp
***********************
name        = p_ips_biores_ipw
description = bio resuspension of iron PO4
turnover    = r_biores*t_ips*(1.0-cgt_in_sediment)
equation    = t_ips -> t_ipw
vertLoc     = SED
limitation  = MMQ t_o2 > o2_min_sed_resp
***********************
name        = p_ihs_biores_ihw
description = bio resuspension of iron hydroxyde
turnover    = r_biores*t_ihs*(1.0-cgt_in_sediment)
equation    = t_ihs -> t_ihw
vertLoc     = SED
limitation  = MMQ t_o2 > o2_min_sed_resp
***********************
name        = p_stf_det_$t_det
description = surface flux of detritus
turnover    = frac_det_$t_det*accrate_det_$t_det*2.47e-4*(1.0-cgt_in_sediment)
comment     = 2.47e-4 mol/m2/d ist der Fluss pro Tag, der über das Jahr eine 20m-Deckschicht mit \\4.5 mmol/m3 füllt.
equation    =  -> t_detp_$t_det + t_det_$t_det
vertLoc     = SED
***********************
name        = p_det_$t_det_resp_nh4
description = recycling of detritus to ammonium using oxygen (respiration)
turnover    = t_det_$t_det*r_det_$t_det_rec*exp(q10_det_rec*cgt_temp)*(1.0-cgt_in_sediment)
equation    = t_det_$t_det + rfr_pc_enrichment_det*6.625*t_o2 + h3oplus -> 0*h2o + 0*h3oplus + t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic + (1.0+6.625*rfr_pc_enrichment_det)*h2o
limitation  = IV t_o2 > o2_min_det_resp
***********************
name        = p_det_$t_det_denit_nh4
description = recycling of detritus to ammonium using nitrate (denitrification)
turnover    = t_det_$t_det*r_det_$t_det_rec*exp(q10_det_rec*cgt_temp)*(1.0-cgt_in_sediment)
equation    = t_det_$t_det + (1.0+5.3*rfr_pc_enrichment_det)*h3oplus + rfr_pc_enrichment_det*5.3*t_no3 -> rfr_pc_enrichment_det*rfr_c*t_dic + t_nh4 + rfr_pc_enrichment_det*2.65*t_n2 + (1.0+14.575*rfr_pc_enrichment_det)*h2o
limitation  = IV t_o2 < o2_min_det_resp
limitation  = IV t_no3 > no3_min_det_denit
***********************
name        = p_det_$t_det_sulf_nh4
description = recycling of sedimentary detritus to ammonium using sulfate (sulfate reduction)
turnover    = t_det_$t_det*r_det_$t_det_rec*exp(q10_det_rec*cgt_temp)*max(t_so4,0.0)/(max(t_so4,0.0)+so4_min_det_sulf)*(1.0-cgt_in_sediment)
equation    = t_det_$t_det + rfr_pc_enrichment_det*3.3125*t_so4 + (1.0+rfr_pc_enrichment_det*6.625)*h3oplus -> t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic + rfr_pc_enrichment_det*3.3125*t_h2s + (1.0+rfr_pc_enrichment_det*13.25)*h2o
limitation  = IV t_o2 < o2_min_det_resp
limitation  = IV t_no3 < no3_min_det_denit
***********************
name        = p_fe2_ox_ihs
description = oxidation of Fe2+ to iron hydroxide in the sediment
turnover    = k_feo2*t_fe2*t_o2*oh*oh*cgt_in_sediment*cgt_cellheight*cgt_density
equation    = 0.25*t_o2 + 4.5*h2o + t_fe2 -> t_ihs + 2*h3oplus
vertLoc     = SED
***********************
name        = p_fe2_ox_ihw
description = oxidation of Fe2+ to iron hydroxide in the sediment
turnover    = k_feo2*t_fe2*t_o2*oh*oh*(1.0-cgt_in_sediment)
equation    = t_fe2 + 4.5*h2o + 0.25*t_o2 -> 2*h3oplus + t_ihw
***********************
name        = p_stf_ihw
description = surface tracer flux of iron hydroxide [mol/m2/d]
turnover    = ihs_deposition_moveaway*r_fluffy_moveaway+accrate_det_6*ihs_deposition*2.47e-4
comment     = 1.1 is mass accumulation rate [kgDW/m2/a]\\0.035 is 3.5% iron in total mass\\55.845 is molar mass of iron\\1.0 means 100% of the iron arrive as iron-III (and 0% as solid iron-II)\\the last quotient is the ratio of the fluxes (fluffy->sediment + fluffy-\\>deep_basins)/(fluffy->sediment)\\0.001 is fluffy layer thickness [m]
equation    =  -> t_ihw
vertLoc     = SED
***********************
name        = p_stf_mow
description = surface tracer flux of manganese oxides [mol/m2/d]
turnover    = ratio_Mn_Fe*p_stf_ihw
equation    =  -> t_mow
vertLoc     = SED
***********************
name        = p_sed_$t_sed_mnred_mn2
description = recycling of sedimentary detritus to ammonium using manganese oxide (manganese reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*pH_inhibition_ironred
equation    = 13.25*rfr_pc_enrichment_det*t_mos + (1.0+26.5*rfr_pc_enrichment_det)*h3oplus + t_sed_$t_sed -> rfr_pc_enrichment_det*rfr_c*t_dic + t_nh4 + 13.25*rfr_pc_enrichment_det*t_mn2 + (1.0+46.375*rfr_pc_enrichment_det)*h2o + rfr_si*t_sil
vertLoc     = SED
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_mos > mos_min_sed_irred_2d
***********************
name        = p_sed_$t_sed_irred_ims
description = recycling of sedimentary detritus to ammonium using iron hydroxide (iron reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*t_ihs/max(fe3_sed,epsilon)*fe2_ims_is_smallest*pH_inhibition_ironred
equation    = t_sed_$t_sed + h3oplus + 26.5*rfr_pc_enrichment_det*t_ihs + 26.5*rfr_pc_enrichment_det*t_h2s -> rfr_si*t_sil + (1.0+72.875*rfr_pc_enrichment_det)*h2o + 26.5*rfr_pc_enrichment_det*t_ims + t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic
vertLoc     = SED
isOutput    = 1
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_mos < mos_min_sed_irred_2d
limitation  = IV t_ihs > ihs_min_sed_irred_2d
***********************
name        = p_sed_$t_sed_irredips_ims
description = recycling of sedimentary detritus to ammonium using iron phosphate (iron reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*t_ips/max(fe3_sed,epsilon)*fe2_ims_is_smallest*pH_inhibition_ironred
equation    = 26.5*rfr_pc_enrichment_det*t_h2s + t_sed_$t_sed + 86.125*rfr_pc_enrichment_det*h2o + (1.0+159.1875*rfr_pc_enrichment_det)*h3oplus + 26.5*rfr_pc_enrichment_det*t_ips -> 238.6875*rfr_pc_enrichment_det*h3oplus + 26.5*rfr_pc_enrichment_det*t_po4 + h2o + 26.5*rfr_pc_enrichment_det*t_ims + t_nh4 + rfr_pc_enrichment_det*rfr_c*t_dic + rfr_si*t_sil
vertLoc     = SED
isOutput    = 1
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_mos < mos_min_sed_irred_2d
limitation  = IV t_ihs > ihs_min_sed_irred_2d
***********************
name        = p_sed_$t_sed_irred_iim
description = recycling of sedimentary detritus to ammonium using iron hydroxide (iron reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*t_ihs/max(fe3_sed,epsilon)*fe2_iim_is_smallest*pH_inhibition_ironred
equation    = 53*rfr_pc_enrichment_det*ohminus + 26.5*rfr_pc_enrichment_det*t_ihs + h3oplus + t_sed_$t_sed + 53.0*rfr_pc_enrichment_det*h3oplus -> rfr_pc_enrichment_det*rfr_c*t_dic + t_nh4 + 26.5*rfr_pc_enrichment_det*t_iim + h2o + 125.875*rfr_pc_enrichment_det*h2o + rfr_si*t_sil
vertLoc     = SED
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_mos < mos_min_sed_irred_2d
limitation  = IV t_ihs > ihs_min_sed_irred_2d
***********************
name        = p_sed_$t_sed_irredips_iim
description = recycling of sedimentary detritus to ammonium using iron hydroxide (iron reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*t_ips/max(fe3_sed,epsilon)*fe2_iim_is_smallest*pH_inhibition_ironred
equation    = 53*rfr_pc_enrichment_det*ohminus + 33.125*rfr_pc_enrichment_det*h2o + (1+53.0*rfr_pc_enrichment_det)*h3oplus + t_sed_$t_sed + 26.5*rfr_pc_enrichment_det*t_ips -> 79.5*rfr_pc_enrichment_det*h3oplus + h2o + 26.5*rfr_pc_enrichment_det*t_iim + t_nh4 + rfr_pc_enrichment_det*26.5*t_po4 + rfr_pc_enrichment_det*rfr_c*t_dic + rfr_si*t_sil
vertLoc     = SED
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_mos < mos_min_sed_irred_2d
limitation  = IV t_ihs > ihs_min_sed_irred_2d
***********************
name        = p_i3i_$t_sed_irred_i2i
description = recycling of sedimentary detritus to ammonium using iron-III in clay minerals (iron reduction)
turnover    = t_sed_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*pH_inhibition_ironred
equation    = 26.5*rfr_pc_enrichment_det*t_i3i + h3oplus + t_sed_$t_sed -> rfr_pc_enrichment_det*rfr_c*t_dic + t_nh4 + 26.5*rfr_pc_enrichment_det*i2i + (1.0+19.875*rfr_pc_enrichment_det)*h2o + rfr_si*t_sil
vertLoc     = SED
isOutput    = 1
limitation  = IV t_o2 < o2_min_sed_resp
limitation  = IV t_no3 < no3_min_sed_denit
limitation  = IV t_mos < mos_min_sed_irred_2d
limitation  = IV t_ihs < ihs_min_sed_irred_2d
limitation  = IV t_i3i > ihs_min_sed_irred_2d
***********************
name        = p_ihs_red_iim
description = reduction of sedimentary iron hydroxide to iron-II
turnover    = k_h2s_ihs*t_h2s*ihs_conc_pw*fe2_iim_is_smallest
equation    = 8.0*t_ihs + t_h2s -> 2.0*h3oplus + t_so4 + 2*h2o + 8.0*t_iim
vertLoc     = SED
isOutput    = 1
limitation  = IV t_ihs > ihs_min_sed_irred_2d
***********************
name        = p_ihs_red_ims
description = reduction of sedimentary iron hydroxide to iron-II
turnover    = k_h2s_ihs*t_h2s*ihs_conc_pw*fe2_ims_is_smallest
equation    = 8.0*t_ihs + 9.0*t_h2s -> 2.0*h3oplus + t_so4 + 18*h2o + 8.0*t_ims
vertLoc     = SED
isOutput    = 1
limitation  = IV t_ihs > ihs_min_sed_irred_2d
***********************
name        = p_stf_po4
description = relaxation against typical wintertime concentration
turnover    = theta(1.0e-6-t_po4)*0.1*(1.0e-6-t_po4)*(1.0-cgt_in_sediment)*theta(20.0-cgt_bottomdepth)*theta(cgt_dayofyear-5.0)*theta(55.0-cgt_dayofyear)
equation    =  -> t_po4
***********************
name        = p_stf_po4_up
description = relaxation against typical wintertime concentration
turnover    = theta(t_po4-1.0e-6)*0.1*(t_po4-1.0e-6)*(1.0-cgt_in_sediment)*theta(20.0-cgt_bottomdepth)*theta(cgt_dayofyear-5.0)*theta(55.0-cgt_dayofyear)
equation    = t_po4 -> 
***********************
name        = p_stf_no3
description = relaxation against typical wintertime concentration
turnover    = theta(2.0*4.5e-6-t_no3)*0.1*(2.0*4.5e-6-t_no3)*(1.0-cgt_in_sediment)*theta(20.0-cgt_bottomdepth)*theta(cgt_dayofyear-5.0)*theta(55.0-cgt_dayofyear)
equation    =  -> t_no3
***********************
name        = p_stf_no3_up
description = relaxation against typical wintertime concentration
turnover    = theta(t_no3-2.0*4.5e-6)*0.1*(t_no3-2.0*4.5e-6)*(1.0-cgt_in_sediment)*theta(20.0-cgt_bottomdepth)*theta(cgt_dayofyear-5.0)*theta(55.0-cgt_dayofyear)
equation    = t_no3 -> 
***********************
name        = p_so4_relax_upwards
description = raise SO4 concentration in the water column to salinity-determined default value
turnover    = (0.077*sal_for_so4/(32+4*16)-t_so4)*theta(0.077*sal_for_so4/(32+4*16)-t_so4)*(1.0-cgt_in_sediment)
comment     = see table 2 (salt composition) in http://www.seafriends.org.nz/oceano/seawater.htm
equation    =  -> t_so4
***********************
name        = p_so4_relax_downwards
description = lower SO4 concentration in the water column to salinity-determined default value
turnover    = (t_so4-0.077*sal_for_so4/(32+4*16))*theta(t_so4-0.077*sal_for_so4/(32+4*16))*(1.0-cgt_in_sediment)
comment     = see table 2 (salt composition) in http://www.seafriends.org.nz/oceano/seawater.htm
equation    = t_so4 -> 
***********************
name        = p_ca2_relax_upwards
description = raise Ca2+ concentration in the water column to salinity-determined default value
turnover    = (0.0118*sal_for_so4/(40.1)-t_ca2)*theta(0.0118*sal_for_so4/(40.0)-t_ca2)*(1.0-cgt_in_sediment)
comment     = see table 2 (salt composition) in http://www.seafriends.org.nz/oceano/seawater.htm
equation    =  -> t_ca2
***********************
name        = p_ca2_relax_downwards
description = lower Ca2+ concentration in the water column to salinity-determined default value
turnover    = (t_ca2-0.0118*sal_for_so4/(40.1))*theta(t_ca2-0.0118*sal_for_so4/(40.0))*(1.0-cgt_in_sediment)
equation    = t_ca2 -> 
***********************
name        = p_po4_ads_ips
description = adsorption of phosphate to iron hydroxide particles
turnover    = k_ips_dissolution * (t_po4 - po4_eq_ips) * theta(t_po4 - po4_eq_ips) *cgt_cellheight*cgt_density
comment     = Reaction speed depends on the concentration of phosphate and on the ratio of free \\adsorption sites.
equation    = t_ihs + t_po4 -> t_ips + 3*ohminus
vertLoc     = SED
***********************
name        = p_ips_diss_po4
description = dissolution of iron phosphate
turnover    = k_ips_dissolution * (po4_eq_ips-t_po4) * theta(po4_eq_ips-t_po4) *cgt_cellheight*cgt_density
equation    = t_ips + 3*ohminus -> t_ihs + t_po4
vertLoc     = SED
***********************
name        = p_po4_ads_ipw
description = adsorption of phosphate to iron hydroxide particles
turnover    = k_ips_dissolution * (t_po4 - po4_eq_ipw) * theta(t_po4 - po4_eq_ipw)*(1.0-cgt_in_sediment)
equation    = t_po4 + t_ihw -> 3*ohminus + t_ipw
***********************
name        = p_ipw_diss_po4
description = dissolution of iron phosphate
turnover    = k_ips_dissolution * (po4_eq_ipw-t_po4) * theta(po4_eq_ipw-t_po4)*(1.0-cgt_in_sediment)
equation    = t_ipw + 3*ohminus -> t_ihw + t_po4
***********************
name        = p_ihs_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_ihs*(1.0-cgt_in_sediment)
equation    = t_ihs -> 
vertLoc     = SED
***********************
name        = p_ips_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_ips*(1.0-cgt_in_sediment)
equation    = t_ips -> 
vertLoc     = SED
***********************
name        = p_ims_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_ims*(1.0-cgt_in_sediment)
equation    = t_ims -> 
vertLoc     = SED
***********************
name        = p_pyr_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_pyr*(1.0-cgt_in_sediment)
equation    = t_pyr -> 
vertLoc     = SED
***********************
name        = p_mos_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_mos*(1.0-cgt_in_sediment)
equation    = t_mos -> 
vertLoc     = SED
***********************
name        = t_rho_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_rho*(1.0-cgt_in_sediment)
equation    = t_rho -> 
vertLoc     = SED
***********************
name        = p_iim_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_iim*(1.0-cgt_in_sediment)
equation    = t_iim -> 
vertLoc     = SED
***********************
name        = p_ihc_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_ihc*(1.0-cgt_in_sediment)
equation    = t_ihc -> 
vertLoc     = SED
***********************
name        = p_sed_$t_sed_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_sed_$t_sed*(1.0-cgt_in_sediment)
equation    = t_sed_$t_sed -> 
vertLoc     = SED
***********************
name        = p_sedp_$t_sed_removal
description = transport from fluffy layer to deep basins
turnover    = r_fluffy_moveaway*t_sedp_$t_sed*(1.0-cgt_in_sediment)
equation    = t_sedp_$t_sed -> 
vertLoc     = SED
***********************
name        = p_fe2_prec_ims
description = precipitation of iron II as siderite
turnover    = fe2_ims_is_smallest*cgt_in_sediment*theta(t_fe2-fe2_smooth)*(t_fe2-fe2_smooth)/cgt_timestep*cgt_cellheight*cgt_density
equation    = t_fe2 + t_h2s + 2.0*ohminus -> t_ims + 2.0*h2o
vertLoc     = SED
isOutput    = 1
***********************
name        = p_ims_diss_fe2
description = dissolution of magnetite to iron II (precipitating iron hydroxides)
turnover    = fe2_ims_is_smallest*cgt_in_sediment*theta(fe2_smooth-t_fe2)*(fe2_smooth-t_fe2)/cgt_timestep*cgt_cellheight*cgt_density
equation    = t_ims + 2.0*h3oplus -> t_fe2 + t_h2s + 2.0*h2o
vertLoc     = SED
isOutput    = 1
***********************
name        = p_fe2_prec_iim
description = precipitation of iron II as minnesotaite
turnover    = fe2_iim_is_smallest*cgt_in_sediment*theta(t_fe2-fe2_smooth)*(t_fe2-fe2_smooth)/cgt_timestep*cgt_cellheight*cgt_density
equation    = t_fe2 + 2*ohminus -> t_iim
vertLoc     = SED
***********************
name        = p_iim_diss_fe2
description = precipitation of iron II as minnesotaite
turnover    = fe2_iim_is_smallest*cgt_in_sediment*theta(fe2_smooth-t_fe2)*(fe2_smooth-t_fe2)/cgt_timestep*cgt_cellheight*cgt_density
equation    = t_iim -> 2*ohminus + t_fe2
vertLoc     = SED
***********************
name        = p_stf_alk
description = relax alkalinity to default value to compensate for detritus removal
turnover    = theta(0.0024-t_alk)*0.01*(0.0024-t_alk)*(1.0-cgt_in_sediment)*theta(20.0-cgt_bottomdepth)
equation    =  -> ohminus
***********************
name        = p_stf_alk_up
description = relax alkalinity to default value to compensate for detritus removal
turnover    = theta(t_alk-0.0024)*0.01*(t_alk-0.0024)*(1.0-cgt_in_sediment)*theta(20.0-cgt_bottomdepth)
equation    = ohminus -> 
***********************
name        = p_ims_trans_iim
description = iron monosulfide transformation to minnesotaite
turnover    = fe2_iim_is_smallest*theta(ims_dissolution_rate)*ims_dissolution_rate
equation    = t_ims + 2*h2o -> t_iim + t_h2s
vertLoc     = SED
isOutput    = 1
***********************
name        = p_iim_trans_ims
description = minnesotaite transformation to iron monosulfide
turnover    = fe2_ims_is_smallest*theta(iim_dissolution_rate)*iim_dissolution_rate
equation    = t_h2s + t_iim -> 2*h2o + t_ims
vertLoc     = SED
isOutput    = 1
***********************
name        = p_mn2_ox_mos
description = oxidation of Mn2+ to manganese oxide in the sediment
turnover    = k_mno2*t_mn2*t_o2*cgt_in_sediment*cgt_cellheight*cgt_density
comment     = is biologically controlled, see Kinetics of Mn(II) oxidation by Leptothrix discophora \\SS1
equation    = 3*h2o + 0.5*t_o2 + t_mn2 -> t_mos + 2*h3oplus
vertLoc     = SED
***********************
name        = p_rho_diss_mn2
description = rhodochrosite dissolution to manganese-II
turnover    = 0.1*1.0e-5*theta(1.0-saturation_rhodochrosite)*cgt_in_sediment*cgt_cellheight*cgt_density
equation    = 3.2*h3oplus + t_rho -> 1.6*t_dic + t_mn2 + 0.6*t_ca2 + 4.8*h2o
vertLoc     = SED
***********************
name        = relax_ohm_quickdiff_up
description = relax ohm_quickdiff tracer against actual OH- concentration
turnover    = theta(oh-t_ohm_quickdiff)*(oh-t_ohm_quickdiff)/cgt_timestep
equation    =  -> t_ohm_quickdiff
***********************
name        = relax_ohm_quickdiff_down
description = relax ohm_quickdiff tracer against actual OH- concentration
turnover    = theta(t_ohm_quickdiff-oh)*(t_ohm_quickdiff-oh)/cgt_timestep
equation    = t_ohm_quickdiff -> 
***********************
name        = relax_ohm_slowdiff_up
description = relax ohm_slowdiff tracer against actual OH- concentration
turnover    = theta(oh-t_ohm_slowdiff)*(oh-t_ohm_slowdiff)/cgt_timestep
equation    =  -> t_ohm_slowdiff
***********************
name        = relax_ohm_slowdiff_down
description = relax ohm_slowdiff tracer against actual OH- concentration
turnover    = theta(t_ohm_slowdiff-oh)*(t_ohm_slowdiff-oh)/cgt_timestep
equation    = t_ohm_slowdiff -> 
***********************
name        = p_alk_rise_ohmdiff
description = rise of total alkalinity by quicker-than-assumed diffusion of OH-
turnover    = theta(t_ohm_quickdiff-t_ohm_slowdiff)*(t_ohm_quickdiff-t_ohm_slowdiff)/cgt_timestep
equation    =  -> ohminus
***********************
name        = p_alk_fall_ohmdiff
description = falling of total alkalinity by quicker-than-assumed diffusion of OH-
turnover    = theta(t_ohm_slowdiff-t_ohm_quickdiff)*(t_ohm_slowdiff-t_ohm_quickdiff)/cgt_timestep
equation    =  -> h3oplus
***********************
name        = p_ims_form2_pyr
description = pyrite formation from iron monosulfide
turnover    = t_ims*t_h2s*k_pyrite
equation    = t_ims + 0.75*t_h2s + 0.25*t_so4 + 0.5*h3oplus -> 1.5*h2o + t_pyr
vertLoc     = SED
isOutput    = 1
***********************
name        = p_h3o_ads_hss
description = adsorption of protons to humic acids
turnover    = cgt_in_sediment*theta(hss_eq-t_hss)*(hss_eq-t_hss)*r_h3o_ads
equation    = h3oplus -> h2o + t_hss
vertLoc     = SED
***********************
name        = p_hss_lib_h3o
description = liberation of protons from sheet silicates
turnover    = cgt_in_sediment*theta(t_hss-hss_eq)*(t_hss-hss_eq)*r_h3o_ads
equation    = h2o + t_hss -> h3oplus
vertLoc     = SED
***********************
name        = p_pyr_oxmos_ihs
description = oxidation of pyrite by manganese oxide to iron oxyhydroxide
turnover    = cgt_in_sediment*max(r_max_lib_mn2_pyrox/cgt_cellheight/cgt_density,r_max_ox_pyr*t_pyr)
equation    = t_mos + t_pyr + 1.25*h3oplus + 1.25*h2o -> 0.375*t_so4 + 1.625*t_h2s + t_ihs + t_mn2
vertLoc     = SED
isOutput    = 1
***********************
name        = p_pyr_oxo2_ihs
description = oxidation of pyrite by manganese oxide to iron oxyhydroxide
turnover    = cgt_in_sediment*t_o2*pyr_conc_pw*k_o2_pyr*cgt_cellheight*cgt_density
equation    = 0.25*t_o2 + t_pyr + 4*h2o -> 1.75*t_h2s + 0.25*t_so4 + 0.5*h3oplus + t_ihs
vertLoc     = SED
isOutput    = 1
***********************
name        = p_imm_oxo2_ihs
description = oxidation of minnesotaite by oxygen to iron oxyhydroxide
turnover    = cgt_in_sediment*t_o2*iim_conc_pw*k_o2_pyr*cgt_cellheight*cgt_density
equation    = 0.5*h2o + t_iim + 0.25*t_o2 -> t_ihs
vertLoc     = SED
***********************
name        = p_remove_silicate
description = remove silicate in water column as it gets too much
turnover    = (t_sil-1.0e-5)*0.1*(1.0-cgt_in_sediment)*(20.0-cgt_bottomdepth)
equation    = t_sil -> 
***********************
name        = p_i2i_oxo2_i3i
description = oxidation of iron-II in illite-montmorillonite mixed layer minerals to iron-III
turnover    = cgt_in_sediment*max(i3i_max-t_i3i,0.0)*r_i2i_ox
equation    = i2i + 0.25*t_o2 + 0.5*h2o -> t_i3i
vertLoc     = SED
limitation  = IV t_o2 > o2_min_sed_resp
***********************
name        = p_i3i_redh2s_i2i
description = reduction of iron-III in clay minerals to iron-II consuming h2s
turnover    = r_h2s_ox_i3i*t_h2s
equation    = 8*t_i3i + t_h2s -> t_so4 + 2*h3oplus + 2*h2o + 8*i2i
isOutput    = 1
limitation  = IV t_i3i > ihs_min_sed_irred_2d
***********************
name        = p_ihs_trans_ihc
description = transformation of amorphous iron oxyhydroxides to crystalline phase
turnover    = r_ihs_trans_ihc*t_ihs
comment     = rate is 0.6/year taken from \\Reed, D.C., Slomp, C.P., Gustafssonb, B.G., 2011. Sedimentary phosphorus dynamics and \\the evolution of bottom-water hypoxia: A coupled benthic-pelagic model of a coastal \\system. Limnol. Oceanogr 56, 1075-1092.
equation    = t_ihs -> t_ihc
vertLoc     = SED
***********************
name        = p_ihc_red_iim
description = reduction of sedimentary iron hydroxide to iron-II
turnover    = k_h2s_ihs*t_h2s*ihc_conc_pw*fe2_iim_is_smallest
equation    = 8.0*t_ihc + t_h2s -> 2.0*h3oplus + t_so4 + 2*h2o + 8.0*t_iim
vertLoc     = SED
isOutput    = 1
limitation  = IV t_ihc > ihs_min_sed_irred_2d
***********************
name        = p_ihc_red_ims
description = reduction of sedimentary iron hydroxide to iron-II
turnover    = k_h2s_ihs*t_h2s*ihc_conc_pw*fe2_ims_is_smallest
equation    = 8.0*t_ihc + 9.0*t_h2s -> 2.0*h3oplus + t_so4 + 18*h2o + 8.0*t_ims
vertLoc     = SED
isOutput    = 1
limitation  = IV t_ihc > ihs_min_sed_irred_2d
***********************
name        = p_po4_ads_pim
description = phosphate adsorption to illite-montmorillonite mixed layer minerals
turnover    = cgt_in_sediment*min(t_po4*cgt_cellheight*cgt_density,max(0.0,pim_eq-t_pim))*r_po4_ads_pim
equation    = 3*h3oplus + t_po4 -> 3*h2o + t_pim
vertLoc     = SED
isOutput    = 1
***********************
name        = p_pim_lib_po4
description = phosphate liberation from illite-montmorillonite mixed layer minerals
turnover    = cgt_in_sediment*min(po4_ads_pim*cgt_cellheight*cgt_density,max(0.0,t_pim-pim_eq))*r_po4_ads_pim+(1.0-cgt_in_sediment)*t_pim*r_po4_ads_pim
equation    = 3*h2o + t_pim -> 3*h3oplus + t_po4
vertLoc     = SED
isOutput    = 1
***********************
name        = p_nh4_ads_aim
description = ammonium adsorption to illite-montmorillonite mixed layer minerals
turnover    = cgt_in_sediment*min(t_nh4*cgt_cellheight*cgt_density,max(0.0,aim_eq-t_aim))*r_nh4_ads_aim
equation    = t_nh4 + ohminus -> t_aim + h2o
vertLoc     = SED
***********************
name        = p_aim_lib_nh4
description = ammonium liberation from illite-montmorillonite mixed layer minerals
turnover    = cgt_in_sediment*min(nh4_ads_aim*cgt_cellheight*cgt_density,max(0.0,t_aim-aim_eq))*r_nh4_ads_aim+(1.0-cgt_in_sediment)*t_aim*r_nh4_ads_aim
equation    = t_aim + h2o -> t_nh4 + ohminus
vertLoc     = SED
***********************
name        = p_aim_nit_no3_sed
description = nitrification in the sediment
turnover    = t_aim*t_o2*k_nh4_o2*exp(q10_nit*cgt_temp)*cgt_in_sediment
equation    = t_aim + 2*t_o2 -> t_no3 + h3oplus
vertLoc     = SED
limitation  = MM t_o2 > o2_min_nit
***********************
name        = p_fe2_mnox_ihs
description = oxidation of Fe2+ by reduction of MnO2
turnover    = t_fe2*mos_conc_pw*k_mno2_fe2*cgt_cellheight*cgt_density
equation    = 6.0*h2o + 2.0*t_fe2 + t_mos -> 2.0*t_ihs + t_mn2 + 2.0*h3oplus
vertLoc     = SED
isOutput    = 1
***********************
name        = p_h2s_mnox_so4
description = oxidation of h2s by reduction of MnO2
turnover    = t_h2s*mos_conc_pw*k_mno2_h2s*cgt_cellheight*cgt_density
equation    = t_mos + 1.5*h3oplus + 0.25*t_h2s -> 0.25*t_so4 + 2.5*h2o + t_mn2
vertLoc     = SED
isOutput    = 1
***********************
name        = p_ims_oxo2_ihs
description = iron monosulfide oxidation to iron oxihydroxides
turnover    = k_ims_o2*ims_conc_pw*t_o2*cgt_cellheight*cgt_density
equation    = 4.5*h2o + 2.25*t_o2 + t_ims -> 2*h3oplus + t_ihs + t_so4
vertLoc     = SED
***********************
name        = p_detp_$t_det_remin_po4
description = recycling of detritus to ammonium using oxygen (respiration)
turnover    = t_detp_$t_det*r_det_$t_det_rec*exp(q10_det_rec*cgt_temp)*(1.0-cgt_in_sediment)*(1.0+(factor_pref_remin_p-1.0)*o2_min_sed_resp/(t_o2 + o2_min_sed_resp))
equation    = 3*rfr_pc_enrichment_det*rfr_p*h2o + t_detp_$t_det -> rfr_pc_enrichment_det*rfr_p*t_po4 + 3*rfr_pc_enrichment_det*rfr_p*h3oplus
***********************
name        = p_sedp_$t_sed_remin_po4
description = recycling of sediment detrital phosphate
turnover    = t_sedp_$t_sed*r_det_$t_sed_rec*exp(q10_det_rec*cgt_temp)*(1.0+(factor_pref_remin_p-1.0)*o2_min_sed_resp/(t_o2 + o2_min_sed_resp))
equation    = 3*rfr_pc_enrichment_det*rfr_p*h2o + t_sedp_$t_sed -> rfr_pc_enrichment_det*rfr_p*t_po4 + 3*rfr_pc_enrichment_det*rfr_p*h3oplus
vertLoc     = SED
***********************
name        = p_mn2_prec_rho
description = manganese-II precipitation to rhodochrosite
turnover    = 0.1*t_mn2*theta(saturation_rhodochrosite-1.0)*cgt_in_sediment*cgt_cellheight*cgt_density
equation    = 4.8*h2o + 0.6*t_ca2 + t_mn2 + 1.6*t_dic -> t_rho + 3.2*h3oplus
vertLoc     = SED
isOutput    = 1
***********************
name        = p_sed_$t_sed_sulfdeep_nh4
description = parameterization for recycling of sedimentary detritus to ammonium below the deepest sediment layer (sulfate reduction / methane formation)
turnover    = t_sed_$t_sed*vel_remin_deep*24.0*3600.0/0.02*theta(k-21)
comment     = Deposition of inert material to the sediment removes tracers from the deepest layer of \\the sediment model (burial).\\This process mineralizes part of the material in the deepest cell by sulfate reduction \\before it is buried.\\The constant vel_remin_deep describes an effective velocity of the burial [m/s] and can \\be calculated by sed_inert_deposition*ratio_deep_mineralization/(1.0-POR)
equation    = (1.0+rfr_pc_enrichment_det*6.625)*h3oplus + rfr_pc_enrichment_det*3.3125*t_so4 + t_sed_$t_sed -> (1.0+rfr_pc_enrichment_det*13.25)*h2o + rfr_pc_enrichment_det*3.3125*t_h2s + rfr_pc_enrichment_det*rfr_c*t_dic + t_nh4 + rfr_si*t_sil
vertLoc     = SED
isOutput    = 1
***********************
name        = p_sedp_$t_sed_sulfdeep_po4
description = parameterization for recycling of sedimentary detritus to ammonium below the deepest sediment layer (sulfate reduction / methane formation)
turnover    = t_sedp_$t_sed*vel_remin_deep*24.0*3600.0/0.02*theta(k-21)
equation    = t_sedp_$t_sed + 3*rfr_pc_enrichment_det*rfr_p*h2o -> 3*rfr_pc_enrichment_det*rfr_p*h3oplus + rfr_pc_enrichment_det*rfr_p*t_po4
vertLoc     = SED
isOutput    = 1
***********************
