EVROPSKÁ UNIE
Evropské strukturální a investiční fondy Operační program Výzkum, vývoj a vzdělávání
MINISTEHSTVO ŠKOLSTVÍ, MLÁDEŽE A TĚLOVÝCHOVY
Chemical methods in geology
i.
Introduction to geochemica
modelling
Tento učební materiál vznikl v rámci projektu Rozvoj doktorského studia chemie č. CZ.02.2.69/0.0/0.0/16_018/0002593
Modeling
• Regardless of the software used, it is necessary to have an idea of what I am doing and what do the results mean ©
• The goal is to learn how to model sensibly -so that we get valid and useful results
• There are a variety of options and tools -learn basic rules and principles that are useful regardless of the tool used
Model
• Model - a construct describing real conditions
- Conceptual model - a qualitative approximation of the system (used to understand the overall nature - how we think the system works)
— Mathematical model - a mathematical construct based on governing equations and boundary/initial conditions that we assume describe the environment
• Numerical model - approximate solution of the mathematical model (usually using a computer)
ConceptiMniodeJ
pore
Pracný, P., Faimon , J., Všianský, D., Kabelka, L., 2017. Evolution of Mg/Ca Ratios During Limestone Dissolution Under Epikarstic Conditions . Aquat. Geochemistry 23,119-139. https://doi.org/10.1007/sl0498-017-9313-y
Conceptual model
Rainfall +
P-E Correction
Mathematical models
• Include the quantitative expression of processes
• In order to evaluate the model, we need to solve the system of equations
• Solution is possible in two ways
- Analytical solution - exact solution of the mathematical model, applicable to simple problems (e.g. pH calculations in a carbonate system)
- Numerical solution - an approximate solution, typically using a computer, applicable even to very complex models
Mathematical model
0 200 400 600 800
Julian Day
Fig. 8, Equivalent diagram to Fig. 6 for site F5,
0.9
Mathematical mode
0.8 0.7 0.6
o o
° 0.5
8 0.4
co
0.3 0.2 0.1 0.0
y = 0.0190x-0.0942/    >t   J #
y = 0.0205X + 0.0486/ R2 = 0.37
0
10
20
• Vil Lmst. rock
* Laz Lmst. rock
• Vil Lmst. rock (WDS) a  Laz Lmst. rock (WDS)
o Exp. dissolution of Vil Lmst.
Exp. dissolution of Laz Lmst. <>  Regular dripwater
♦ Anomalous dripwater Model evolution
30 40 Mg/Ca x 1000
50
60
70
Mathematical model
Geochemist's Workbench
• Paid software (subscription)
• Graphical interface - more user-friendly
• Speciation, diagrams, reactions, kinetics, spreadsheet...
• Community edition with limited functionality (useful especially for speciation and diagrams)
— Annual license
SpecE8 module
• Speciation calculations for solutions (similar to the SOLUTION command in PHREEQC)
• Input solution composition (directly species) -software calculates the distribution of other species, saturation, etc.
• Interchange of species = "swapping" (e.g. hTfor pH)
• Function „explain"
• Connectivity with Gplot - direct data plotting in diagrams (e.g. Piper)
Model 1: Speciation in seawater
Table 9. Seawater composition.
[Concentration is in parts per million (ppm) unless specified otherwise]
Analysis	PHREEQC notation	Concentration	
Calcium	Ca	4123	
Magnesium	Mg	1291.8	
Sodium	Na	10768.0	
Potassium	K	399.1	
Iron	Fe	0.002	
Manganese	Mn	0.0002	
Silica, as SiOj>	S:	4.28	
Chlonde	Cl	19353.0	CO
Alkalinity as HCO/	Alkalinity'	141.682	o
Sulfate, as S04:	S(6)	27120	CNl O
Nitrate, as NOV	N(5)	0.29	npl
Ammonium, as NH4~	NC-3)	0.03	Q_ <
Uranium	U	0.0033	do
pH, standard units	pH	8.22	+-» to
pe. unitless	pe	8.451	hi i nu
Temperature, °C	temperature	25.0	_^ i_
Density, kilograms per liter	density	1.023	05 CL
• Use the SpecE8 module to find saturation index values for minerals dissolved in seawater
• Which mineral is it most supersaturated with?
• In what form will carbonates be dominant?
• For raw data see the file Data_pro_modely.xlsx
Speciation in seawater
In the publication
Edited for input into GSS
Table 9. Seawater composition.
[Concentration is in parts per million (ppm) unless specified otherwise]
Analysis	PHREEQC notation	Concentration
Calcium	Ca	412.3
Magnesium	Mg	1291.8
Sodium	Na	10768.0
Potassium	K	399.1
Iron	Fe	0.002
Manganese	Mn	0.0002
Silica, as S1O2	Si	4.28
Chloride	CI	19353.0
Alkalinity as HC03"	Alkalinity	141.682
Sulfate, as S042~	S(6)	2712.0
Nitrate as NOV	N<5)	0.29
Ammonium, as NH4-	N(-3)	0.03
Uranium	U	0.0033
pH, standard units	PH	8.22
pe, imitless	pe	8.451
Temperature, °C	temperature	25.0
Density, kilograms per liter	density	1.023
	Unit	Seawater
PH	PH	
Fr	Fr	8.451
	mg/kg	412.3
Mg++	mg/kg	1292
On+ H	mg/kg ^|	10768.0 ^|
K+	mg/kg	399.1
HC03-^^H	mg/kg	141.7
S04-	mg/kg	2712
Cl-	mg/kg	19353.0
N03-	mg/kg	0.29
Fe++	mg/kg	0.002
Mn++	mg/kg	200E-6
Si02(aq)	mg/kg	4.28
c:\user5\a dminVdisk google\vyuka\g9311 geochernie excgenni'ch procesu\materialy\2Q20\Q9_gwb
File   Edit   Run   Config   Window Help Basis
Command
Run
Constraints on initial system						
H20			1		free kg	w solvent
Ca++			412.3	▼	mg/kg	
Mg++			1292		mg/kg	
Na +			10768		nng/kg	
K+			399.1		nng/kg	W
HC03-			141.7		mg/kg	
S04-			2712	T	mg/kg	T
Cl-			19353		ring/kg	
N03-			.29	▼	mg/kg	T
Fe++			.002	W	mg/kg	W
Mn++			2e-4		mg/kg	
Si02(aq)			4.28	▼	mg/kg	
H +			8.22		PH	
e-		0 02[aq)	8.451	T	pe	
add						
Temperature
25 T °C
>
Model 2: Groundwater speciation
• By interacting with the rocks, groundwater acquired a specific composition.
a) What complexes and species will be in the water?
b) What will be the saturation states of the various minerals?
• Same input as Model 0 for PHREEQC
Phreeqc input:
TITLE Speciation of water
SOLUTION 1
Temp 15
pH 6.05
units mol/L
Al 1E-6
Si 1E-5
Na 1.3E-5
CI 5E-5
Ca 5.5E-4
S 3.5E-4
C 1E-3
END
GSS module
• Spreadsheet Manager (i.e. from the same rank as Excel)
• Enables convenient work with geochemical data, their conversions, calculations and export to graphic outputs
Model 3: Karst water
mol/L
		
Mg	6.17E-05	5.76E-05
Ca	1.31E-03	3.50E-03
S04--	4.07E-04	5.53E-04
Cl	2.26E-04	1.97E-04
Alkalinity as HC03-	1.92E-03	6.02E-03
Sr	9.99E-07	1.18E-06
Na	8.70E-05	9.13E-05
K	1.82E-05	1.92E-05
N03-	1.05E-04	5.97E-05
Si	8.76E-05	9.62E-05
PH	8.08	8.09
Temp	7	
• Enter the following data into the GSS and calculate the saturation indices for calcite and dolomite, the total content of dissolved substances (total dissolved solids TDS) and charge imbalance in %.
• Data - Calculate
				1 ■	2 •
Sample ID			►	TC	CP
Mg++ *	mo	ar	►	61.7E-6	57.6E-6
Ca~ *	mo	ar	►	0.00131	0.0035
S04" *	mo	ar	►	407E-6	553E-6
cr n T	mo	ar	►	226E-6	197E-6
HC03" I	mo	ar		0.00192	0.00602
sr A	mo	ar		999E-9	1.18E-6
Na+ ▼	mo	ar		87E-B	91.3E-B
K+ ♦ T	mo	ar	►	18.2E-6	19.2E-6
N03" I	mo	ar		105E-6	59.7E-6
Si02(aq) ^	mo	ar		87.6E-6	96.2E-6
PH °				8.08	8.09
Temperature	C			7	8
Model 4: Water from sanitation
• The following slide shows water analyzes from the area of Stráž pod Ralskem, where remediation is taking place after uranium mining by leaching
• Input water solution to GSS, calculate charge balance and TDS
• Plot the data in diagrams
- Piper
— Column
• Graphs-Piper
Příloha 6. Parametry vybraných vod upravené pro použití v modelu a parametry po nábojovém vyrovnání
Původní složení upravené pro GWB
		1	6	8	Cenoman	1	6	8	Cenoman
pH		U	1,9	3,68	7,63	1,10	1,90	3,68	7,63
Eh	mV		407			273	407	112	744
Electrical conductivíty	uS/cm	4560	1087	79,7	327		7556	712	308
TDS	mg/l	90380	19310	764	286	71138	15040	564	292
AI+++	mg/1	8100	1740	26,83	0,025	8230	1747	26,84	0,025
Ca++	mg/1	231	198	72,13	48,1	235	199	72,14	48,1
Cl	mg/l	16	7,5	7,2	1,9	16	7,5	7,2	1,9
h	mg/l	460	79	4,88	0,3	467	79	4,88	0,3
Fe++	mg/l	1230	261	7,90	5,E-05*	1250	262	7,90	5,E-05
HC03--	mg/l	l,E-30	l,E-30	l,E-30	210	l,E-30	l,E-30	l,E-30	226,683
HP04--	mg/l	152	40	0r078	l,E-30	162	41	0,079	l,E-30
K+	mg/l	151	1G	4,42	4,6	153	1G	4,42	4,6
Mg++	mg/l	67	36,5	10,82	10,2	68	36,6	10,82	10,2
Mn++	mg/l	14	2,1	3,39	0,074	14	2,1	3,39	0,074
Na+	mg/l	18	5,2	7,69	6,1	18	5,2	7,69	6,1
NH4+**	mg/l	1163	257	8,86	0,19*	1182	258	8,86	0,19
02(aq)	mg/l	l,E-30	l,E-30	0,62	0,2	3,E-13	l,E-03	-4.E-17	0,2
S04--	mg/l	52000	12160	473	0,3	62318	12j8S	415	0,3
Zn++	mg/l	59	63	0747	0,01	60	63	0,747	0,01
H+	mg/l					278	34	0	0,153
Složení po nábojovém vyrovnání
00 O
_o> Q_
Pozn.: * hodnota nastavena na detekční limit. **po užité hodnoty NH4+ zahrnují původní koncentraci NH4 a koncentraci NO^- přepočtenou na NH4+.
			1 ▼	2         "I           3         #|           4 A T j                                                          T I T		
Sample ID			Vodal	Voda 6	Voda 8	Cenoman
Al"" v	mg/1		8230	1747	26.84	0.025
	mg/l		235	199	72 14	48.1
er D	mg/l		16	7.5	7.2	1.9
F "	mg/l		467	79	4.88	0.3
Fe~	mg/l (as Fe)		1260	262	7.9	50E-6
HCO3 l	mg/l		1E-30	1E-30	1E-30	226.7
HPO4" z	mg/l		162	41	0.079	0.001
	mg/l		153	16	4.42	4.6
Mg~ t	mg/l		68	36.6	10.82	10.2
	mg/l		14	2.1	3 39	0.074
Na+ T T"	mg/l		18	5 2	7.69	6.1
NH4+	mg/l		1182	258	8.86	0.19
S04~ *	mg/l		62318.0	12588.0	415	0.3
Zn" A	mg/l		60	63	0.747	0.01
PH °			1.1	1.9	3.68	7.63
Eh A	mV		273	407	112	744
H+ T	molal		0.2842	0.0337	-0.01252	150E-6
H+ ♦	molal		0.2842	0.0337	-0.01252	150E-6
Act2 module
• Used to construct diagrams - speciation , activity, Eh-pH...
• We can input data from GSS and plot it as points in diagrams
• Using the "suppress" command, we can suppress phases and species that will not occur or for some other reason we do not want in the diagram
Model 5a: Carbonate speciation
• Construct the Eh-pH diagram for HC03~ speciation
• Activity of HCO3- = 3xl0"3 mol/L
• Plot data from Stráž (Model 4)
• File - Open - Scatter Data
Model 5b: Al speciation
• Construct an Eh-pH diagram for aluminum
• Al activity = 1CT7-8 mol/L
Model 5c: Speciation of As
• Construct an Eh-pH diagram for arsenic
• As activity = 10~6 mol/L
• In the presence of sulfur with an activity of 10"2 mol/L
Model 5d: Speciation of Fe
• Fe2+activity = 1CT6
• Suppression of unwanted species with "suppress"
• Config - Suppress
Other modules
• Rxn - balance of reactions
• React - reaction models
• Modules for the construction of other types of diagrams (P-T, phase)
• Reaction transport modeling
PHREEQC
• Freely available in versions for Windows, Mac and Linux
• Coding
• Speciation, interaction, mixing, kinetics, reaction-transport calculations...
• Possibility of programming in Basic, connection with R, Matlab, etc.
• There is a GUI version for Windows (Phreeqci)
Possible problems
• All numbers must be entered with a decimal point - commas will not work!
• Output path issues (diacritics in folder names) - issue especially with PHREEQCi
Modeling
• Regardless of the software used, it is necessary to have an idea of what I am doing and what I am finding out ©
• A geochemical model is a mathematical model
- In order to evaluate the model, we need to solve the system of governing equations
- The solution is possible in two ways
1. Analytical solution - exact solution to the mathematical model, applicable to simple problems (last week's pH calculation)
2. Numerical solution - an approximate solution, typically using a computer, applicable even to very complex models
Types of geochemical models
1. Speciation modeling
2. Water mixing
3. Modeling of direct interactions
a) Equilibrium
b) Irreversible processes
4. Inverse modeling
5. Reaction-transport modeling
6. Kinetic modeling
7. And more...
Speciation models
• Evaluation of the composition of the water sample
- Distribution of total concentrations on the activities of individual species in solution
- E.g. distribution of total carbonates
- It only counts components and species defined in the database (it may be necessary to define new ones)
- It does not consider kinetics - only a thermodynamic assessment of stabilities
- Pure mineral phases only (no solid solutions, impurities or non-ideal stoichiometry)
- Generally a problem with organics (not enough thermodynamic data)
Model 0
• By interacting with the rock, groundwater acquired a specific composition.
a) What complexes and species will be in the water?
b) What will be the saturation states of the various minerals?
Phreeqc input
TITLE Speciation of water
SOLUTION 1
Temp 15
pH 6.05
units mol/L
Al 1E-6
Si 1E-5
Na 1.3E-5
CI 5E-5
Ca 5.5E-4
S 3.5E-4
C 1E-3
END
Direct interaction models
• Predicts final composition of water after interactions (with other phases or after the reaction of components in water).
• Again, it does not assess kinetics, it is based purely on the thermodynamics of processes.
• EQUILIBRIUM_PHASES command
- Phase name, saturation index (SI) and amount in moles
- SI = 0 ... the system will calculate to balance
- In the case of gases, it is the log of fugacity
Model 1
What is the pH of pure water in equilibrium with atmospheric C02?
T = 25°C
PCO2 = 4xl0"4
-Log PC02=-3.4
— When calculating the equilibrium with gases, we enter the value of the logarithm of the partial pressure (orfugacity) and then we can also enter the molar content (how many moles are available; the default value is 10)
Model 2
What is the pH of pure water in equilibrium with atmospheric C02and calcite (open system conditions)?
T = 25°C
PCO2 = 4xl0-4 -Log PC02=-3.4
calcite = 0
- When balancing with minerals, we enter the value of the saturation index, and then we can also enter the molar content (how many moles are available; the default value is 10)
Model 3
What is the pH of pure water in equilibriu with atmospheric C02and calcite (closed system conditions)?
T = 25°C
PCO2=4xl0"4
-Log PC02=-3.4
S'calcite = 0
Model 3b
What is the pH of pure water in equilibrium with atmospheric C02and calcite (closed system conditions) if the temperature drops at the same time before contact with calcite?
T = 8°C
PCO2 = 4xl0"4
-LogPc02=-3.4
S'calcite = 0
Model 4a
• We have water of given initial composition:
• pH = 7.3
• T = 25°C
• Units mol/L
• Ca = 1.64xl0-3 mol/L
• Alkalinity = 3.30xl(r3 eq/L as HC03"
• What will be the saturation with respect to calcite?
• What will the "partial pressure of C02 in water" be?
— (The partial pressure of C02 above the water with which the dissolved carbonates would be in equilibrium).
Model 4b
l/l/e have water of given initial composition: T = 25°C
Ca = 1.64xlcr3mol/L
Alkalinity = 3.30xlO-3 mol/L as HC03"
pH = 7.3
The solution will establish equilibrium with atmospheric PC02
PC02 = 4xl0"4 - Log PC02=-3.4
What will be the saturation index value with to calcite?
Model 4c
We have water of given initial composition: T = 25°C
Ca = 1.64xl0"3 mol/L Alkalinity = 3.30xl0"3 mol/L as HCO3-pH = 7.3
The solution establishes equilibrium with atmospheric PC02 PC02 = 4xl0-4
- LogPc02=-3.4
• The solution will also balance with calcite (ie, excess calcium and carbonates will precipitate).
^'calcite u
• What will be the concentrations of Ca 2+, total carbonates and the resulting pH?
Other models according to the samples in the PHREEQC documentation
Solution to Model 1
Title Model 1 Solution 1 Temp 2 5
Equilibrium_phases C02(g) -3.4
end
Solution to Model 2
Title Model 2 Solution 1 Temp 2 5
Equilibrium_phases C02(g) -3.4 Calcite 0
end
Solution to Model 3
Title Model 3 Solution 1 Temp 2 5
Equilibrium_phases C02(g) -3.4
Save Solution 2
end
Use Solution 2 Equilibrium_phases Calcite 0
end
Solution to Model 3
Title Model 3b Solution 1 Temp 2 5
Equilibrium phases C02(g) -3.4
Save Solution 2
end
# here we enter a lower temperature for further interaction
Reaction Temperature
8
Use Solution 2 Equilibrium phases Calcite 0
end
Solution to Model 4a
Title Model 4a Solution 1 Temp 2 5
Equilibrium_phases C02(g) -3.4
Save Solution 2
end
Use Solution 2 Equilibrium_phases Calcite 0
end
Solution to Model 4b
Title Model 4b
#we are interested in saturation with respect to calcite and C02 Solution 1 Temp 2 5 pH 7 . 3 Units mol/L
Ca 1.64e-3 Alkalinity 3.30e-3 as HC03-
Save Solution 1 end
# water in next step attains balance with atmospheric C02 Use Solution 1 Equilibrium_Phases C02(g) -3.4
end
Solution to Model 4c
Title Model 4c
# we are interested in saturation with respect to calcite and C02 Solution 1
Temp 25 pH 7.3 Units mol/L
Ca 1.64e-3
Alkalinity 3.30e-3 as HC03-
Save Solution 1 end
# water in next step attains balance with atmospheric C02 Use Solution 1
Equilibrium_Phases C02(g) -3.4
Save Solution 2 end
# in the last step water precipitates calcite, with respect to which it is supersaturated Use Solution 2
Equilibrium_Phases Calcite 0 C02(g) -3.4
end
EVROPSKÁ UNIE
Evropské strukturální a investiční fondy Operační program Výzkum, vývoj a vzdělávání
MINISTERSTVO ŠKOLSTVÍ, MLÁDEŽE A TELOVÝCHOVY
Tento učební materiál vznikl v rámci projektu Rozvoj doktorského studia
chemie
č. CZ.02.2.69/0.0/0.0/16_018/0002593
Resources
• Parkhurst, DL, and Appelo, CAJ, 2013, Description of input and examples for PHREEQC version 3 — A computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations: US Geological Survey Techniques and Methods, book 6, chap. A43, 497 p., available only at http://pubs.usgs.gov/tm/06/a43/.
• SCHRIMPELOVA, Kateřina. A Geochemical Model of the Groundwater of the Guardian Area Leach Fields [online]. Brno, 2018 [cit. 2020-12-01]. Available from: <https://theses.cz/id/ puiiey/>. Thesis. Masaryk University, Faculty of Science. Supervisor doc. RNDr. Josef Zeman, CSc.