Processes > Reactive transport modelling
Am transport in groundwater
Sen:
Dear Prof. Parkhurst
The purpose of this topic is to ask you for help with using the Transport function in PHREEQC. I also found a Topic: Dual Domain Transport of U and Cl in the forum, http://https://phreeqcusers.org/index.php/topic,1339.0.html. But I can't download any attachments and it always shows 404 - Attachment Not Found.If it is convenient for you, please send me a copy of the attachment in the link above.
In my thesis, there is a section to calculate the migration of Am in groundwater, and the model assumes that there is a repository in deep-underground, which is considered as a source of pollution and defined as Solution 0. The main rock of the repository is granite, so it is considered as column, and the whole model is simplified as possible. The groundwater in zone I is greatly influenced by the repository, which I defined as SOLUTION 1-20 in the model, and the groundwater in zone II is the original groundwater of granite, which is defined as SOLUTION 21-70 in the model, please see the attachment for the specific geochemical conditions, it should be noted that there is no Am in the initial water of zone I and zone II, Am does not exist in nature. Am is subjected to adsorption and ion exchange in granite groundwater.
In addition to the parameters used in the code, I have collected as many hydrogeological parameters as possible. transmissibility of groundwater = 8.673×10-8(m2/s)，hydraulic conductivity =5.04×10-7(m/s)，Effective diffusion coefficient of Am on granite =2×10-13(m2/s)，Pore water velocity=0.82×10-7(m/s)，Porosity= 5.8×10-3，Bulk density =3.0×106 (g/cm3)，Grams of sediment per liter (from porosity and bulk density)=5.17×105 (g/L)，Distribution coefficient of Am on granite Kd = 0.005 m3/g.
I wonder if these parameters can make the calculation results more accurate. Here I apologize for my broken knowledge and for adding extra work to you，but I've done my best to understand the meaning of these parameters in the model.
The attached code only calculates the migration of Am in region I. I have rewritten the model according to the PHREEQC manual, and the model seems to run fine, but the plot is obviously incorrect. Can you help me to adjust the code more accurate?
Best wishes，Sen
--- Code: ---DATABASE D:\USGS\Phreeqc Interactive 3.4.0-12927\database\wateq4f.dat
##DATABASE c:\phreeqc\database\wateq4f.dat
SOLUTION_MASTER_SPECIES
Am Am+3 0.0 Am 243.0000
Am(+3) Am+3 0.0 Am
SOLUTION_SPECIES
Am+3 = Am+3
log_k 0.0
Am+3 + H2O - H+ = AmOH+2
log_k -7.200
Am+3 + 2H2O - 2H+ = Am(OH)2+
log_k -15.100
Am+3 + 3H2O - 3H+ = Am(OH)3
log_k -26.200
Am+3 + F- = AmF+2
log_k 3.400
delta_h 2.89 kcal
Am+3 + 2F- = AmF2+
log_k 5.800
delta_h 10.77 kcal
Am+3 + Cl- = AmCl+2
log_k 0.240
Am+3 + 2Cl- = AmCl2+
log_k -0.810
delta_h 13.11 kcal
Am+3 + SO4-2 = AmSO4+
log_k 3.500
delta_h 9.56 kcal
Am+3 + 2SO4-2 = Am(SO4)2-
log_k 5.000
delta_h 16.72 kcal
Am+3 + NO3- = AmNO3+2
log_k 1.28
delta_h 0.43 kcal
Am+3 + 2NO3- = Am(NO3)2+
log_k 0.88
delta_h 2.58 kcal
Am+3 + CO3-2 = AmCO3+
log_k 8.000
Am+3 + 2CO3-2 = Am(CO3)2-
log_k 12.900
Am+3 + 3CO3-2 = Am(CO3)3-3
log_k 15.000
Am+3 + HCO3- = AmHCO3+2
log_k 3.100
Am+3 + H3SiO4- = AmSiO(OH)3+2
log_k 8.13
delta_h 4.44 kcal
SOLUTION_SPECIES
Na+ = Na+; -log_k 0; -gamma 1e7 0
Ca+2 = Ca+2; -log_k 0; -gamma 1e7 0
Cl- = Cl-; -log_k 0; -gamma 1e7 0
H2O + 0.01e- = H2O-0.01; -log_k -9
SURFACE_MASTER_SPECIES #Surface Complexation of Am on Granite
Surf SurfOH
SURFACE_SPECIES
SurfOH = SurfOH
log_k 0.0
##Am
SurfOH + Am+3 = SurfOAm+2 + H+
log_k -0.60
SurfOH + Am+3 + 2H2O = SurfOAm(OH)2 + 3H+
log_k -17.20
EXCHANGE_MASTER_SPECIES
X X-
EXCHANGE_SPECIES
X- = X-
log_k 0.0
3NaX + Am+3 = AmX3 + 3Na+
log_k -2.2
SOLUTION 1-20 #Repository groundwater
temp 25
pH 9.0
pe -3
redox pe
units mol/L
density 1.0003
Na 3.23e-2
Ca 3.42e-4
K 1.16e-4
Mg 1.19e-4
Cl 1.79e-2
S 1.15e-4
N 3.67e-4
C(4) 2.05e-3 CO2(g) -5.5
Si 7.05e-5
SURFACE 1-20
SurfOH 7.35e-6 2.3 0.09
-donnan 1e-10
-equil 1
EXCHANGE 1-20
X 4.04e-5
-equil 1
End
SOLUTION 0 Palse solution with Am
temp 25
pH 9.0
pe -3
units mol/L
C(4) 0.0000001 CO2(g) -2.5
Si 7.05e-5
Am 3.51e-10
SURFACE 0
SurfOH 7.35e-6 2.3 0.09
-donnan 1e-10
-equil 0
EXCHANGE 0
X 4.04e-5
-equil 0
End
PRINT;
-reset false;
-status false
SELECTED_OUTPUT
-file Am-000001.sel
-reset false
-solution
-distance true
-time true
-step true
-pH true
-totals Am
-molalities AmSiO(OH)3+2 AmOH+2 Am(OH)2+ AmCO3+ Am(CO3)2- Am(CO3)3-3 SurfOAm+2 SurfOAm(OH)2 AmX3
USER_GRAPH 1
-headings Distance Am
-chart_title "Am transport"
-axis_titles "Distance, in meters" "Millimoles per kilogram water"
-axis_scale x_axis 0 auto
-axis_scale y_axis 0 auto
-initial_solution false
-plot_concentration_vs x
-start
10 x = DIST
20 PLOT_XY x, TOT("Am")*1000, symbol = Circle, color = Orange
30 PLOT_XY x, TOT("AmSiO(OH)3+2 ")*1000, symbol = Plus
40 PLOT_XY x, TOT("AmOH+2 ")*1000, symbol = Plus
50 PLOT_XY x, TOT("Am(OH)2+")*1000, symbol = Plus
60 PLOT_XY x, TOT("AmCO3+ ")*1000, symbol = Plus
70 PLOT_XY x, TOT("Am(CO3)2- ")*1000, symbol = Plus
80 PLOT_XY x, TOT("Am(CO3)3-3 ")*1000, symbol = Plus
90 PLOT_XY x, TOT("SurfOAm+2 ")*1000, symbol = Plus
100 PLOT_XY x, TOT("SurfOAm(OH)2 ")*1000, symbol = Plus
110 PLOT_XY x, TOT("AmX3 ")*1000, symbol = Plus
120 if (x > 10 OR SIM_TIME <= 0) THEN END
-end
TRANSPORT
-cells 20
-length 50 ## total length = length * cells # total length is 1000m
-shifts 20 1 ## total diffusion time is shifts*time_step
-time_step 1.5768e6 ## second 3.1536e7 s= 1a # total time is 1a
-punch_cells 20
-punch_frequency 2
-print_cells 20
-print_frequency 10
-dispersivity 0.078
-flow_direction forward ##diffusion
-boundary_cond flux flux ##constant closed
-correct_disp true
-diffc 2.0e-13 ##diffusion coefficient
-multi_d true 1e-9 5.8e-3 0 1
-porosities 20*5.8e-3
END
PRINT; -user_graph false
SURFACE 0
SOLUTION 0
temp 25
pH 9.0
pe -3
units mol/L
C(4) 0.0000001 CO2(g) -2.5
Si 7.05e-5
##Am 1.27e-7
END
PRINT; -user_graph true
TRANSPORT
-shifts 40 1
END
--- End code ---
dlparkhurst:
Sorry, I do not have the file that was posted. All I can suggest is to look at example 13 in the Version 3 user's manual, which demonstrates the use of a stagnant layer.
Sen:
Dear Prof. Parkhurst
apologize for my rush reply, Before I created this topic, I spent about half a month learning about it, but there were so many formulas that I may not have fully grasped the meaning of migration calculation, and I was very unskilled in the use of transport.
The above code is also the result of my rewrite according to Ex11-15, I hope you can take some time to help me to see the possible problems of the code.
Best wishes，
Sen
dlparkhurst:
I suggest you start with batch or simple advection calculations. Below is a 1-cell model that allows 1000 pore volumes to move through the cell (using phreeqc.dat). If you look at the output file, you will see that all of the Am is sequestered in the exchanger; very little is dissolved; and the amount on the surface is negligible.
So, the first thing to consider is whether your exchange and surface reactions are reasonable. If so, you really need not do to much more modeling. The transport of Am will be extremely limited. If you are not satisfied with the reactions, consider how to modify the exchange and surface reactions to simulate the appropriate chemistry better.
--- Code: ---SOLUTION_MASTER_SPECIES
Am Am+3 0.0 Am 243.0000
Am(+3) Am+3 0.0 Am
SOLUTION_SPECIES
Am+3 = Am+3
log_k 0.0
Am+3 + H2O - H+ = AmOH+2
log_k -7.200
Am+3 + 2H2O - 2H+ = Am(OH)2+
log_k -15.100
Am+3 + 3H2O - 3H+ = Am(OH)3
log_k -26.200
Am+3 + F- = AmF+2
log_k 3.400
delta_h 2.89 kcal
Am+3 + 2F- = AmF2+
log_k 5.800
delta_h 10.77 kcal
Am+3 + Cl- = AmCl+2
log_k 0.240
Am+3 + 2Cl- = AmCl2+
log_k -0.810
delta_h 13.11 kcal
Am+3 + SO4-2 = AmSO4+
log_k 3.500
delta_h 9.56 kcal
Am+3 + 2SO4-2 = Am(SO4)2-
log_k 5.000
delta_h 16.72 kcal
Am+3 + NO3- = AmNO3+2
log_k 1.28
delta_h 0.43 kcal
Am+3 + 2NO3- = Am(NO3)2+
log_k 0.88
delta_h 2.58 kcal
Am+3 + CO3-2 = AmCO3+
log_k 8.000
Am+3 + 2CO3-2 = Am(CO3)2-
log_k 12.900
Am+3 + 3CO3-2 = Am(CO3)3-3
log_k 15.000
Am+3 + HCO3- = AmHCO3+2
log_k 3.100
Am+3 + H3SiO4- = AmSiO(OH)3+2
log_k 8.13
delta_h 4.44 kcal
SURFACE_MASTER_SPECIES #Surface Complexation of Am on Granite
Surf SurfOH
SURFACE_SPECIES
SurfOH = SurfOH
log_k 0.0
##Am
SurfOH + Am+3 = SurfOAm+2 + H+
log_k -0.60
SurfOH + Am+3 + 2H2O = SurfOAm(OH)2 + 3H+
log_k -17.20
EXCHANGE_SPECIES
3NaX + Am+3 = AmX3 + 3Na+
log_k -2.2
SOLUTION 1 #Repository groundwater
temp 25
pH 9.0
pe -3
redox pe
units mol/L
density 1.0003
Na 3.23e-2
Ca 3.42e-4
K 1.16e-4
Mg 1.19e-4
Cl 1.79e-2
S 1.15e-4
N 3.67e-4
C(4) 2.05e-3 CO2(g) -5.5
Si 7.05e-5
END
SURFACE 1
SurfOH 7.35e-6 2.3 0.09
#-donnan 1e-10
-equil 1
END
EXCHANGE 1
X 4.04e-5
-equil 1
END
SOLUTION 0 Palse solution with Am
temp 25
pH 9.0
pe -3
units mol/L
C(4) 0.0000001 CO2(g) -2.5
Si 7.05e-5
Am 3.51e-10
END
ADVECTION
-cells 1
-shifts 1000
-punch_frequency 1000
-warnings true
END
--- End code ---
Sen:
Dear Prof. Parkhurst
I am honored to have the help and guidance of a geochemist of your historical stature. I should have replied in the first place and with continued discussions with you, but I unfortunately infected with Omicron and my fever didn't go down until a few hours ago.
According to your hint, indeed as you said here the ion exchange reaction is not reasonable and the adsorption reaction is very weak. I have reviewed the literature ion exchange only works at pH < 5. The adsorption of Am by granite in alkaline environment is still not very strong, which is reasonable for the adsorption reaction in the model. I tried to modify the code and the model seems to be working, but the diagrams made by ADVECTION and TRANSPORT are very different, I think the code may not be right, can you take some time to help me?
Best wishes,
Sen
--- Code: ---
--- End code ---
SOLUTION_MASTER_SPECIES
Am Am+3 0.0 Am 243.0000
Am(+3) Am+3 0.0 Am
SOLUTION_SPECIES
Am+3 = Am+3
log_k 0.0
Am+3 + H2O - H+ = AmOH+2
log_k -7.200
Am+3 + 2H2O - 2H+ = Am(OH)2+
log_k -15.100
Am+3 + 3H2O - 3H+ = Am(OH)3
log_k -26.200
Am+3 + F- = AmF+2
log_k 3.400
delta_h 2.89 kcal
Am+3 + 2F- = AmF2+
log_k 5.800
delta_h 10.77 kcal
Am+3 + Cl- = AmCl+2
log_k 0.240
Am+3 + 2Cl- = AmCl2+
log_k -0.810
delta_h 13.11 kcal
Am+3 + SO4-2 = AmSO4+
log_k 3.500
delta_h 9.56 kcal
Am+3 + 2SO4-2 = Am(SO4)2-
log_k 5.000
delta_h 16.72 kcal
Am+3 + NO3- = AmNO3+2
log_k 1.28
delta_h 0.43 kcal
Am+3 + 2NO3- = Am(NO3)2+
log_k 0.88
delta_h 2.58 kcal
Am+3 + CO3-2 = AmCO3+
log_k 8.000
Am+3 + 2CO3-2 = Am(CO3)2-
log_k 12.900
Am+3 + 3CO3-2 = Am(CO3)3-3
log_k 15.000
Am+3 + HCO3- = AmHCO3+2
log_k 3.100
Am+3 + H3SiO4- = AmSiO(OH)3+2
log_k 8.13
delta_h 4.44 kcal
SOLUTION_SPECIES
Na+ = Na+; -log_k 0; -gamma 1e10 0
Ca+2 = Ca+2; -log_k 0; -gamma 1e10 0
Cl- = Cl-; -log_k 0; -gamma 1e10 0
H2O + 0.01e- = H2O-0.01; -log_k -9
SURFACE_MASTER_SPECIES #Surface Complexation of Am on Granite
Surf SurfOH
SURFACE_SPECIES
SurfOH = SurfOH
log_k 0.0
##Am
SurfOH + Am+3 = SurfOAm+2 + H+
log_k -0.60
SurfOH + Am+3 + 2H2O = SurfOAm(OH)2 + 3H+
log_k -17.20
SOLUTION 1-21 #Repository groundwater
temp 25
pH 9.0
pe -3
redox pe
units mol/L
density 1.0003
Na 3.23e-2
Ca 3.42e-4
K 1.16e-4
Mg 1.19e-4
Cl 1.79e-2
S(6) 1.15e-4
N(5) 3.67e-4
C(4) 2.05e-3 CO2(g) -5.5
Si 7.05e-5
SURFACE 1-21
SurfOH 7.35e-6 2.3 0.09
-donnan 1e-10
-equil 1
End
SOLUTION 0 Palse solution with Am
temp 25
pH 9.0
pe -3
units mol/L
C(4) 0.0000001 CO2(g) -2.5
Am 1.0e-7
Si 7.05e-5
SURFACE 0
SurfOH 7.35e-6 2.3 0.09
-donnan 1e-10
-equil 0
End
ADVECTION
-cells 20
-shifts 100
-punch_cells 20
-punch_frequency 1
-print_cells 20
-print_frequency 10
PRINT; -reset false; -status false
SELECTED_OUTPUT
-file Am-adv.sel
-reset false
-step
-totals Am
USER_PUNCH
-heading Pore_vol
10 PUNCH (STEP_NO + .5) / 40.
USER_GRAPH 1 Example 11
-chart_title "Using ADVECTION Data Block"
-headings Am
-axis_titles "Pore volumes" "Millimoles per kilogram water"
-axis_scale x_axis 0 auto
-axis_scale y_axis 0 auto
-plot_concentration_vs time
-start
10 x = (STEP_NO + 0.5) / cell_no
20 PLOT_XY x, TOT("Am")*1000, symbol = None
30 PUT(1, 1)
-end
COPY cell 101 1-20
END
USER_GRAPH 1
-detach
END
SOLUTION 0 Palse solution with Am
temp 25
pH 9.0
pe -3
units mol/L
C(4) 0.0000001 CO2(g) -2.5
Am 1.0e-7
Si 7.05e-5
SURFACE 0
SurfOH 7.35e-6 2.3 0.09
-donnan 1e-10
-equil 0
End
PRINT
-reset false
-echo_input true
-status false
SELECTED_OUTPUT
-file Am-transport.sel
-reset false
-solution
-distance true
-time true
-step true
-pH true
-totals Am
-molalities AmSiO(OH)3+2 AmOH+2 Am(OH)2+ AmCO3+ Am(CO3)2- Am(CO3)3-3 SurfOAm+2 SurfOAm(OH)2
USER_PUNCH
-headings Am_mmol AmSiO(OH)3+2_mmol AmOH+2_mmol Am(OH)2+_mmol AmCO3+_mmol Am(CO3)2-_mmol Am(CO3)3-3_mmol SurfOAm+2_mmol SurfOAm(OH)2_mmol
10 PUNCH TOT("Am")*1000, TOT("AmSiO(OH)3+2")*1000,TOT("AmOH+2")*1000,TOT("AmCO3+")*1000,TOT("Am(CO3)2-")*1000,TOT("Am(CO3)3-3")*1000,TOT("SurfOAm+2")*1000,TOT("SurfOAm(OH)2")*1000,
USER_GRAPH 1
-headings Distance Am
-chart_title "Dual Porosity, First-Order Exchange with Implicit Mixing Factors"
-axis_titles "Distance, in meters" "Millimoles per kilogram water"
-axis_scale x_axis 0 auto
-axis_scale y_axis 0 auto
-plot_concentration_vs x
-start
10 GRAPH_X DIST
20 GRAPH_Y TOT("Am")*1000
-end
END
TRANSPORT
-cells 20
-length 50 # total length = length * cells # total length is 1000m
-shifts 20 1 # total diffusion time is shifts*time_step
-time_step 3.1536e7 # second 1a # total time is 10a
-dispersivity 0.078
-punch_cells 20
-punch_frequency 1-20
-print 20
-print_frequency 10
-flow_direction forward # diffusion
-boundary_cond flux flux
-correct_disp true
-diffc 2.0e-13 #diffusion coefficient
-multi_d true 1e-9 5.8e-3 0 1
-porosities 20*5.8e-3
END
SOLUTION 0
temp 25
pH 9.0
pe -3
units mol/L
C(4) 0.0000001 CO2(g) -2.5
END
PRINT; -user_graph true
TRANSPORT
-shifts 60 1
END
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