Unexpected output in distribution of species section

[Marino Vetuschi Zuccolini]

Hello to all,

I'm using a 3.6.1-15000 version and running the input below with sit.dat database I receive in the O(0) section something that is not apparently consistent with what I expect, i.e anionic sulphur species without oxygen, or Cl2
But maybe one reason exists and I would like to know, please.

Thanks

Marino

O(0)          5.569e-04
   O2              2.785e-04   2.785e-04    -3.555    -3.555     0.000     (0) 
   S5-2            6.237e-10   1.019e-10    -9.205    -9.992    -0.787     (0) 
   MnO4-           1.956e-10   1.243e-10    -9.709    -9.905    -0.197     (0) 
   MnO4-2          7.595e-13   1.241e-13   -12.119   -12.906    -0.787     (0) 
   S4-2            9.053e-16   1.479e-16   -15.043   -15.830    -0.787     (0) 
   MnO4-3          7.641e-19   1.296e-20   -18.117   -19.887    -1.771     (0) 
   S3-2            7.925e-22   1.294e-22   -21.101   -21.888    -0.787     (0) 
   Mn+3            6.451e-22   1.094e-23   -21.190   -22.961    -1.771     (0) 
   Cl2             6.686e-24   6.686e-24   -23.175   -23.175     0.000     (0) 
   ClO4-           3.678e-24   2.489e-24   -23.434   -23.604    -0.170     (0) 
   S2-2            5.505e-29   8.992e-30   -28.259   -29.046    -0.787     (0) 
   HSO5-           5.181e-30   3.294e-30   -29.286   -29.482    -0.197     (0) 
   S2O8-2          0.000e+00   0.000e+00   -44.340   -45.127    -0.787     (0) 


Input:
SOLUTION <N>         #incrementale ad ogni chiamata phreeqc
units mg/kgw
pH 8.23
pe 6.67
temp 25
press 1.5
Ca 658
C(4) -3.45 CO2(g)
C(-4) -4 CH4(g)
H(0) -6 H2(g)
O(0)  8.91
S(-2) .0001   
N(+5) 31 as NO3
N(-2) .6 as NO2
N(-3) .06 as NH4+
P 0.06 as PO4
Mg 2025
Na 13267
K 482
Al 7 ug/kgw
Fe 7 ug/kgw
Mn 0.3 ug/kgw
B 4523 ug/kgw
Si 4.28 as SiO2
Alkalinity 181 as HCO3
Cl 23200.0
S(6) 5188
END

[dlparkhurst]

Looks like the developers of sit.dat have left out a few definitions. The rules for definitions of redox states are obscure (SOLUTION_MASTER_SPECIES), but every reaction that contains O2(aq) or e- should be defined as a "secondary master species" to have the bookkeeping work correctly. (And, only one species of a redox state should be defined with a reaction containing O2 or e-.) The sit.dat has quite a few species that are defined with O2(aq), but are not specified to be secondary master species; as a result, they show up in the O(0) distribution of species.

For the polysulfide species (S2-, S3-...) a different approach is used. Instead of writing all the reactions with e- and defining a separate redox state for each species, the option -mass_balance is used to put them all in the S-2 distribution of species. I have never been a fan of these species anyway. I think they rely on an assumption that the solution is in equilibrium with native sulfur rather than using e- or O2 in their equations, which makes them different than most aqueous species, and they are probably metastable in any event.

The following will straighten out the distribution of species for O(0):

Code: [Select]

SOLUTION_MASTER_SPECIES
    C(2)          CO               0     C             
    Cl            Cl-              0     Cl              35.4527
    Cl(-1)        Cl-              0     Cl             
    Cl(0)         Cl2              0     Cl             
    Cl(7)         ClO4-            0     Cl             
    Mn            Mn+2             0     Mn              54.938
    Mn(2)         Mn+2             0     Mn             
    Mn(3)         Mn+3             0     Mn             
    Mn(5)         MnO4-3           0     Mn             
    Mn(6)         MnO4-2           0     Mn             
    Mn(7)         MnO4-            0     Mn             
    S             SO4-2            0     SO4             32.066
    S(-2)         HS-              1     S             
    S(2)          S2O3-2           0     S             
    S(3)          S2O4-2           0     S             
    S(4)          SO3-2            0     S             
    S(5)          S2O5-2           0     S             
    S(6)          SO4-2            0     SO4           
    S(7)          S2O8-2           0     S             
    S(8)          HSO5-            0     S             
SOLUTION_SPECIES
2.000HS-     - 1.000H2O     + 0.500O2     = S2-2
     log_k    32.450     
     delta_h -212.123    #kJ/mol       
     # Enthalpy of formation:           35.04        #kJ/mol        #04CHI
     -analytic -4.7123E+0 0E+0 1.10799E+4 0E+0 0E+0
     -mass_balance S(-2)2

1.000H+     + 3.000HS-     - 2.000H2O     + 1.000O2     = S3-2
     log_k    79.470     
     delta_h -484.686    #kJ/mol       
     # Enthalpy of formation:           25.94        #kJ/mol        #74NAU/RYZ
     -analytic -5.44322E+0 0E+0 2.53169E+4 0E+0 0E+0
     -mass_balance S(-2)3

2.000H+     + 4.000HS-     - 3.000H2O     + 1.500O2     = S4-2
     log_k   125.390     
     delta_h -751.079    #kJ/mol       
     # Enthalpy of formation:           23.01        #kJ/mol        #74NAU/RYZ
     -analytic -6.1932E+0 0E+0 3.92315E+4 0E+0 0E+0
     -mass_balance S(-2)4

3.000H+     + 5.000HS-     - 4.000H2O     + 2.000O2     = S5-2
     log_k   171.090     
     delta_h -1016.212   #kJ/mol       
     # Enthalpy of formation:           21.34        #kJ/mol        #74NAU/RYZ
     -analytic -6.94244E+0 0E+0 5.30804E+4 0E+0 0E+0
     -mass_balance S(-2)5
END


[Marino Vetuschi Zuccolini]

Thank you David, it runs but I'll try to understand the intimate meaning of what you've suggested.

Thanks again

m.

[dlparkhurst]

Whether this clarifies or confuses, here is an additional comment.

The way PHREEQC determines where to put a species in the distribution of species is based on the definitions in SOLUTION_MASTER_SPECIES. One species of every redox state is a "secondary master species".

Let's look at sit.dat reaction for aqueous species  S2O3-2; it is written in terms of SO4-2 (secondary master species for S(6)) and O2 (secondary master species of O(0)). If no redox state S(2) is defined in SOLUTION_MASTER_SPECIES, then S2O3-2 will appear in the S(6) section of the distribution of species and in the O(0) section.

If S(2) is defined in SOLUTION_MASTER_SPECIES, then S2O3-2 actually does not appear in the distribution of species for the SOLUTION because it is no longer part of the S(6) redox state; it is in the S(2) redox state. The SOLUTION defines the total of the S(6) redox state, but not the total of the S(2) redox state. If you define S(2) in SOLUTION, then you would get a distribution of species for S(2). Also, if you changed S(6) in SOLUTION to S, then all redox states of S would appear in the distribution of species.

When you move from a SOLUTION calculation to a reaction--reacting a solution with EQUILIBRIUM_PHASES, REACTION, MIX, etc--then redox equilibrium is invoked, and equilibrium is calculated among all redox states of all the redox elements. At that point, every redox state of S will appear in the distribution of species.

 

[Marino Vetuschi Zuccolini]

It is more clear than confuse. :)

Thanks a lot David

m.