Merge pull request #19 from PALEOtoolkit/O2AlkUptakeRemin_bugfix

Bugfix O2AlkUptakeRemin (missing P contribution to TAlk change)

src/PALEOaqchem.jl

@@ -5,27 +5,31 @@ import PALEOboxes as PB
 """
     O2AlkUptakeRemin(Corg, (NO3, TNH3, Ngas), TPO4, Ccarb; rO2Corg=1) -> (O2, Alk)
 
-Oxygen and alkalinity assimilated for production (or released by remineralisation) of particulate matter
-with specified Corg, Ccarb from specified nitrate NO3, total ammonia TNH3, gaseous N, total phosphate TPO4
+Oxygen and alkalinity released by remineralisation
+of particulate matter with specified Corg, Ccarb to specified nitrate NO3, total ammonia TNH3, gaseous N, total phosphate TPO4
 
-NB sign: for Corg +ve, O2 is -ve (ie quantity to subtract from tracer sms for production, or add for remineralisation)
+NB sign: 
+- for remineralization, Corg, NO3, TNH3, Ngas, TPO4, Ccarb are +ve, O2 is -ve 
+  (ie provides O2eq (-ve) required and Alk to add to ocean solute tracers sms, for remineralisation of POC with C:N:P stoichiometry defined by Corg:sum(NO3, TNH3, Ngas):TPO4)
+- for production by oxygenic photosynthesis, Corg, NO3, TNH3, Ngas, Ccarb are -ve, O2 is +ve 
+ (ie provides O2 and Alk to add to ocean solute tracers sms for production of POC with C:N:P stoichiometry defined by Corg:sum(NO3, TNH3, Ngas):TPO4)
 
 # Examples
 ```jldoctest; setup=:(import PALEOaqchem)
 julia> PALEOaqchem.O2AlkUptakeRemin(106.0, (0.0, 0.0, 0.0), 1.0, 0.0) # Corg:P = 106:1, no N
-(-106.0, 0.0)
+(-106.0, -1.0)
 
 julia> PALEOaqchem.O2AlkUptakeRemin(106.0, (16.0, 0.0, 0.0), 1.0, 0.0) # Corg:NO3:P = 106:16:1
-(-138.0, -16.0)
+(-138.0, -17.0)
 
 julia> PALEOaqchem.O2AlkUptakeRemin(106.0, (0.0, 16.0, 0.0), 1.0, 0.0) # Corg:TNH3:P = 106:16:1
-(-106.0, 16.0)
+(-106.0, 15.0)
 ```
 """
 function O2AlkUptakeRemin(Corg, (NO3, TNH3, Ngas), TPO4, Ccarb; rO2Corg=1)
 
-    O2 = -(rO2Corg*PB.get_total(Corg) +2.0*PB.get_total(NO3) + 3.0/4.0*PB.get_total(Ngas))  # -ve uptake/remin, ie oxygen released by production and consumed by remin
-    Alk = - PB.get_total(NO3) + PB.get_total(TNH3) + 2.0*PB.get_total(Ccarb)                # production leads to increase in Alk with NO3 source, decrease with NH3 source
+    O2 = -(rO2Corg*PB.get_total(Corg) +2.0*PB.get_total(NO3) + 3.0/4.0*PB.get_total(Ngas))  # -ve uptake/remin, ie oxygen released by production and consumed by remin          
+    Alk = - PB.get_total(NO3) + PB.get_total(TNH3) - PB.get_total(TPO4) + 2.0*PB.get_total(Ccarb)  # production leads to increase in Alk with NO3 source, decrease with NH3 source
 
     # Biomass organic carbon stoichiometry is CH2Ox, where x follows from k_O_rO2Corg
     # CorgOx = 3 - 2*rO2Corg