Need help with kinetic transport

[mdangelm]

I'm still new to PHREEQC especially the kinetics option, and could use some basic tips on how to set up the kinetics in this model.

The problem is relatively simple, we have a dissolved organic contaminant (that's not in the database) and it is moving through a soil horizon. On it's way it reacts irreversibly with certain components of the sediment organic matter which are also consumed in the process together with the contaminant. Unfortunately we don't know the amount of reactive components in the sediment which is where we need to fit a PHREEQC model to experimental data and get an estimate from that.

The key is that the entire process is kinetically controlled, since flow velocities change the removal capacity, and also that the reactive components of the sediment organic matter can become depleted in each cell over time. My current PHREEQC input file looks like this, but it is obviously not working...

SOLUTION_MASTER_SPECIES
DFBA      DFBA-   -1      156      156

SOLUTION_SPECIES
DFBA- = DFBA-
log_k = 0

DFBA- + H+ = DFBAH
log_k = 5.3

DFBA- + Na+ = DFBANa
log_k = 3.1

PHASES
SedOM
   SedOM = SedOM
   log_k = -20

SOLUTION 0
-temp   22
-unit   mmol/L
-pH         6.4
Alkalinity      0.56   as HCO3-
Ca         0.92
Mg         1.07
Na         4.49
Cl         4.04
S(6)         0.7   as SO4-2
K         0.26
Si         0.25   as H4SiO4
DFBA-           0.001

SOLUTION 1-12
-temp   22
-unit   mmol/L
-pH         6.4
Alkalinity           0.56   as HCO3-
Ca         0.92
Mg         1.07
Na         4.49
Cl         4.04
S(6)                  0.7   as SO4-2
K         0.26
Si         0.25   as H4SiO4
 
EQUILIBRIUM_PHASES 1-12
   Calcite      0.0      0.01
   SedOM      0.0      0.002      
 
KINETICS 1-12
   DFBA_degr
   -formula DFBA-
   -step 86400 in 10
 
RATES 1-12
   DFBA_degr
   -start
   10 k = 1.0e-5 # 1/sec
   20 rate = -k * TOT("DFBA-") * TOT("SedOM")
   90 moles = rate * TIME
   91 SAVE MOLES
   -end
 

SELECTED_OUTPUT 1
   -file            DFBA-degrd.txt   
   -high_precision      true
   -reset         false   
   -distance         false
   -time            true
   -step            false
   -pH                        true
   -alkalinity         true
   -temp         false
   -totals         DFBA
   -kinetic_reactants   DFBA_degrd
   -equilibrium_phases     SedOM
 
 
TRANSPORT
       -cells                               12
       -shifts                              20
       -time_step                    7200    
       -lengths                        12*0.5    
   -dispersivities                 12*0.01    
   -diffusion_coefficient      0.3e-9
       -print_cells                  12
       -punch_cells                   12
       -multi_d                            false
 
END

Any input appreciated!

[dlparkhurst]

First, chemical formulas are case sensitive. An aqueous species DFBA is composed of elements D, F, B, and A.

I think the following is what you need.

Code: [Select]

SOLUTION_MASTER_SPECIES
Dfba      Dfba-   -1      156      156

SOLUTION_SPECIES
Dfba- = Dfba-
log_k = 0

Dfba- + H+ = DfbaH
log_k = 5.3

Dfba- + Na+ = DfbaNa
log_k = 3.1

SOLUTION 0
    temp      22
    pH        6.4
    pe        4
    redox     pe
    units     mmol/l
    density   1
    Alkalinity 0.56 as HCO3-
    Ca        0.92
    Cl        4.04
    Dfba      0.001
    K         0.26
    Mg        1.07
    Na        4.49
    S(6)      0.7 as SO4-2
    Si        0.25 as H4SiO4
    -water    1 # kg

Second, I think you probably want a kinetic reaction for organic matter in addition to the degradation of Dfba. I do not know what stoichimetry you want to attach to the reactions other than DfbaH decreases. Charge is not considered in the formula; you should use a charge balanced formula like DfbaH. If you have a kinetic reaction for organic matter, the amount of reactant left is given by the function KIN. (If you keep an equilibrium phase for the organic matter, the amount remaining is given by the function EQUI.) The function TOT takes an element name, like Dfba, not an aqueous species like Dfba-. The concentration of Dfba- is found with the function MOL.

[mdangelm]

Thanks, the errors have decreased. However I still have a problem in making PHREEQC recognize the sediment organic matter as a phase (it says species not defined).

I was wondering if there is a way to avoid using the equilibrium phases for the sediment organic matter altogether. In our model the organic matter doesn't react with anything else but the DFBA. If there is a way to integrate a finite reactant (that doesn't transport) into the rates/kinetics blocks that would be greatly helpful.

[dlparkhurst]

Perhaps the following. Note that for positive moles in "SAVE moles", the amount of kinetic reactant, M, decreases, and combined with -1 for the -formula, DbfaH also decreases.

Code: [Select]

RATES
   Dfba_degr
   -start
   10 k = 1.0e-5 # 1/sec
   20 rate = k * TOT("Dfba") * M
   90 moles = rate * TIME
   91 SAVE MOLES
   -end
KINETICS 1-12
   Dfba_degr
   -m  0.002
   -formula DfbaH -1