diff --git a/src/aed_pathogens.F90 b/src/aed_pathogens.F90 index fbad8ff..5dfb6dd 100644 --- a/src/aed_pathogens.F90 +++ b/src/aed_pathogens.F90 @@ -524,12 +524,18 @@ SUBROUTINE aed_calculate_pathogens(data,column,layer_idx) predation = zero_ ! Natural mortality (as impacted by T, S, pH; see Hipsey et al 2008) + ! Hardwiring f_AOC to 1 below means that salinity (and pH) effects are turned off - is this intended? f_AOC = 1.0 ! aoc / (K_AOC + aoc) f_pH = 1.0 ! + c_PH * ( pH_star**delta / (pH_star**delta+K_PH**delta) ) + ! Not consistent with Hipsey et al (2008), and + ! Is the value of coeff_mort_c_SM already inclusive of the /35 in Hipsey et al 2008, or is this needed in the code below? mortality = data%pathogens(pth_i)%coef_mort_kd20 & + (data%pathogens(pth_i)%coef_mort_c_SM*salinity**data%pathogens(pth_i)%coef_mort_alpha) & * ((1.0-f_AOC)**data%pathogens(pth_i)%coef_mort_beta) * f_pH mortality = mortality * (data%pathogens(pth_i)%coef_mort_theta**(temp-20.0)) + ! To summarise the comments above, with the hardwires set as they are, the code above reduces to + ! mortality = data%pathogens(pth_i)%coef_mort_kd20 * (data%pathogens(pth_i)%coef_mort_theta**(temp-20.0)) + ! i.e. no salinity effects ! Sunlight inactivation (as impacted by S, DO and pH; see Hipsey et al 2008)