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Questions around pathogen mortality calcs #60

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6 changes: 6 additions & 0 deletions src/aed_pathogens.F90
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Expand Up @@ -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)
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