Problem with adding new SPECIES

Conceptual Models > Database selection and modification

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gmgmgm:
Dear everyone
I am currently using PHT3D (PHREEQC+MT3DMS) to simulate the reaction model of organic carbon reduction of sulfate and precipitation of Fe and Mn. Since there is no PHREEQC reaction module in PHT3D, the first thing I need to do is to add organic carbon (CH2O) to the PHREEQC database. Then I plan to implement the reaction model in PHREEQC first, but I don't know why S(2) was not generated during the reaction process and the concentration of various ions changed abnormally. I don't know whether it is because I added CH2O improperly or there is a problem with the setting, please help me to answer it. (Since my ultimate goal is to use PHT3D for 3D simulation, and the species CH2O must be present in PHT3D to add it to the model, the addition of CH2O is essential)

--- Code: ---SOLUTION 1
temp 25
pH 5.1
pe 4
redox pe
units mg/l
density 1
Ca 0
Fe(2) 33.2
Fe(3) 186.8
Mn(2) 67.6
S(6) 200 charge
-water 1 # kg

SOLUTION_SPECIES

CO3-2 + 4e- + 6H+ = CH2O + 2H2O
log_k -10

PHASES
Sulfidic
SO4-2 + 2CH2O = H2S + 2HCO3-
log_k -3.5
Orgc
CH2O + 2H2O = CO3-2 + 6H+ + 4e-
log_k 99

EQUILIBRIUM_PHASES 1
Fe(OH)3(a) 0 0
FeS(ppt) 0 0
Goethite 0 0
Hematite 0 0

KINETICS 1
Sulfidic
-formula Sulfidic 1
-m 1
-m0 1
-parms 1
-tol 1
-steps 100 in 50 steps # seconds
-step_divide 1
-runge_kutta 3
-bad_step_max 500

RATES
Sulfidic
-start
30 mS6 = tot("S(6)")
60 rate = parm(1)* mS6
70 moles = rate * time
80 if (moles > m) then moles = m
200 save moles
-end

USE equilibrium_phases 1
USE kinetics 1
USE solution 1

USER_GRAPH 1
-headings C SO4 S(-2)
-axis_titles "TIME" "S(6) Concentration, mol/L" "S(2) Concentration, mol/L"
-initial_solutions true
-connect_simulations true
-plot_concentration_vs x
-start
10 graph_x TOTAL_TIME
20 graph_y tot("S(6)")
30 GRAPH_SY tot("S(-2)")
-end
-active true

USER_GRAPH 2
-headings C Fe(2) Fe(3)
-axis_titles "TIME" "Fe(2) Concentration, mol/L" "Fe(3) Concentration, mol/L"
-initial_solutions true
-connect_simulations true
-plot_concentration_vs x
-start
10 graph_x TOTAL_TIME
20 graph_y tot("Fe(2)")
30 GRAPH_SY tot("Fe(3)")
-end
-active true

USER_GRAPH 3
-headings C Mn pH
-axis_titles "TIME" "Concentration, mol/L" "pH"
-initial_solutions true
-connect_simulations true
-plot_concentration_vs x
-start
10 graph_x TOTAL_TIME
20 graph_y tot("Mn(2)")
30 GRAPH_SY -LA("H+")
-end
-active true

USER_GRAPH 4
-headings C FeS(ppt) Fe(OH)3(a) Goethite Manganite Hematite
-axis_titles "TIME"
-initial_solutions true
-connect_simulations true
-plot_concentration_vs x
-start
10 graph_x TOTAL_TIME
20 graph_y EQUI_DELTA("FeS(ppt)"), EQUI_DELTA("Fe(OH)3(a)"),EQUI_DELTA("Goethite"), EQUI_DELTA("Manganite"), EQUI_DELTA("Hematite")
-end
-active true

USER_GRAPH 5
-headings C S Fe
-axis_titles "TIME" "S Concentration, mol/L" "Fe Concentration, mol/L"
-initial_solutions true
-connect_simulations true
-plot_concentration_vs x
-start
10 graph_x TOTAL_TIME
20 graph_y TOT("S")
30 graph_sy TOT("Fe")
-end
-active true

END

--- End code ---

dlparkhurst:
You don't want to add CH2O as a solution species or Sulfidic as a PHASE. To model organic decomposition and Fe/Mn precipitation, you want to add CH2O as the reactant in REACTION or KINETICS, along with EQUILIBRIUM_PHASES with the minerals that you expect to dissolve or precipitate at equilibrium.

Here is the basic idea without the minerals.

--- Code: ---SOLUTION 1 SEAWATER FROM NORDSTROM AND OTHERS (1979)
units ppm
pH 8.22
pe 8.451
density 1.023
temp 25.0
Ca 412.3
Mg 1291.8
Na 10768.0
K 399.1
Si 4.28
Cl 19353.0
Alkalinity 141.682 as HCO3
S(6) 2712.0
REACTION
CH2O 1
0.10 in 100 steps
USER_GRAPH 1
-headings rxn S(6) S(-2) C(4) C(-4) pe
-axis_titles "CH2O, reacted" "Molality" "pe"
-initial_solutions true
-connect_simulations true
-plot_concentration_vs x
-start
10 GRAPH_X RXN
20 GRAPH_Y TOT("S(6)"), TOT("S(-2)"), TOT("C(4)"), TOT("C(-4)")
30 GRAPH_SY -LA("e-")
-end
-active true
END
--- End code ---

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