Introduction to PHREEQC—Introduction to PHREEQC—Chemistry for PHASTChemistry for PHAST
PHAST
HST3D—Flow and transportHST3D—Flow and transport
PHREEQC—ChemistryPHREEQC—Chemistry
Operator splitting—Sequential Operator splitting—Sequential
Non-Iterative ApproachNon-Iterative Approach
Chemistry
Transport
Flow
Chemistry
Transport
Flow
PHREEQCPHREEQC
PHAST chemistry is inherited from PHREEQCPHAST chemistry is inherited from PHREEQC
PHREEQC is run at the beginning of PHASTPHREEQC is run at the beginning of PHAST– Solutions and reactants for initial conditionsSolutions and reactants for initial conditions– Solutions for boundary conditionsSolutions for boundary conditions
PHREEQC is run cell-by-cell for each time PHREEQC is run cell-by-cell for each time step in the reactive-transport simulationstep in the reactive-transport simulation
PHREEQC ReactantsPHREEQC Reactants
Keyword data blocks define reactantsKeyword data blocks define reactants
– SOLUTION—SolutionsSOLUTION—Solutions
– EQUILIBRIUM_PHASES—Equilibrium minerals and gases EQUILIBRIUM_PHASES—Equilibrium minerals and gases
– EXCHANGE—Exchangers EXCHANGE—Exchangers
– SURFACE—Surfaces SURFACE—Surfaces
– KINETICS and RATES—Kinetic reactionsKINETICS and RATES—Kinetic reactions
– SOLID_SOLUTIONS—Solid solutionsSOLID_SOLUTIONS—Solid solutions
– GAS_PHASE—gas bubble (rarely used)GAS_PHASE—gas bubble (rarely used)
Store reactants on shelves by type and numberStore reactants on shelves by type and number
SOLUTION—Chemical SOLUTION—Chemical Composition of a WaterComposition of a Water
Chemical analysisChemical analysis– pHpH– TemperatureTemperature
– Major elements Ca, Mg, Na, K, Alkalinity, Cl, SOMajor elements Ca, Mg, Na, K, Alkalinity, Cl, SO44
– Trace elementsTrace elements– NutrientsNutrients
SOLUTION Data BlockSOLUTION Data Block SOLUTION 1: Oklahoma Brine units mol/kgw
pH 5.713temp 25.Ca .4655
Mg .1609 Na 5.402 Cl 6.642
C .00396 S .004725 As .03 (ug/kgw)
EQUILIBRIUM_PHASESEQUILIBRIUM_PHASESMinerals and gases that react to equilibriumMinerals and gases that react to equilibrium
Calcite reactionCalcite reaction
CaCOCaCO33 = Ca = Ca+2+2 + CO + CO33-2-2
EquilibriumEquilibrium
K = [CaK = [Ca+2+2][CO][CO33-2-2] ]
EQUILIBRIUM_PHASES Data BlockEQUILIBRIUM_PHASES Data Block Mineral or gasMineral or gas Saturation stateSaturation state AmountAmount
Example EQUILIBRIUM_PHASES 5:Example EQUILIBRIUM_PHASES 5:COCO22 Log PCOLog PCO22 = -2, = -2, 10 moles10 moles
CalciteCalcite equilibrium equilibrium 1 moles1 moles
DolomiteDolomite equilibrium equilibrium 1 moles1 moles
Fe(OH)Fe(OH)33 equilibriumequilibrium 0 moles0 moles
EXCHANGEEXCHANGE
Cation exchange compositionCation exchange composition
Reaction:Reaction:
CaCa+2+2 + 2NaX = CaX + 2NaX = CaX22 + 2Na + 2Na++
Equilibrium:Equilibrium:
][][
]][[22
22
CaNaX
NaCaXK
EXCHANGE Data BlockEXCHANGE Data Block
Exchanger nameExchanger name Number of exchange sitesNumber of exchange sites Chemical composition of exchangerChemical composition of exchanger
Example EXCHANGE 15:Example EXCHANGE 15:CaX2 CaX2 0.05 moles (X is defined in databases)0.05 moles (X is defined in databases)
NaXNaX 0.05 moles0.05 moles
OftenOften
X X 0.15 moles, Equilibrium with solution 10.15 moles, Equilibrium with solution 1
SURFACE—Surface CompositionSURFACE—Surface Composition
Trace elements Zn, Cd, Pb, As, PTrace elements Zn, Cd, Pb, As, P
Reaction:Reaction:
Hfo_wOH + AsOHfo_wOH + AsO44-3-3 = Hfo_wOHAsO = Hfo_wOHAsO44
-3-3
Equilibrium:Equilibrium:
]][_[
]_[3
4
34
AsOwOHHfo
wOHAsOHfoK
SURFACE Data BlockSURFACE Data Block Surface name—Hfo is Hydrous Ferric OxideSurface name—Hfo is Hydrous Ferric Oxide Number of surface sitesNumber of surface sites
Chemical composition of surfaceChemical composition of surface
Example SURFACE 21:Example SURFACE 21:Hfo_wOHHfo_wOH 0.001 moles0.001 moles
Hfo_sOHHfo_sOH 0.00005 moles0.00005 moles
OftenOften
Hfo_wHfo_w 0.001 moles, Equilibrium with solution 10.001 moles, Equilibrium with solution 1
KINETICS—Nonequilibrium ReactionsKINETICS—Nonequilibrium Reactions
Monod KineticsMonod Kinetics
Radioactive decayRadioactive decay
Silicate hydrolosisSilicate hydrolosis
Biological processesBiological processes
)/(max SKSvR half
kCR
KIAPm
m
V
AkR /1
67.
0
mOa
O
Substrates
Substratemmcell bX
CK
C
CK
CXYqR
2
2
KINETICS and RATES Data BlocksKINETICS and RATES Data Blocks Kinetic reaction nameKinetic reaction name Stoichiometry of reactionStoichiometry of reaction Rate expression (RATES)Rate expression (RATES)
Example Example
KINETICS 21:KINETICS 21:DOC_decayDOC_decay
formula formula Doc Doc -1 -1 CH2OCH2O +1 +1
RATESRATES10 Rate = 0.01*TOT(“Doc”)10 Rate = 0.01*TOT(“Doc”)
20 SAVE rate*TIME20 SAVE rate*TIME
PHREEQC—ReactionsPHREEQC—ReactionsFrom the shelfFrom the shelf To the beakerTo the beaker
Solution 1Solution 1
EquilibriumEquilibrium
phases 5phases 5
Surface 21Surface 21
Kinetic reaction Kinetic reaction
and equilibrationand equilibration
Arsenic in the Central Arsenic in the Central Oklahoma AquiferOklahoma Aquifer
Arsenic mostly in Arsenic mostly in confined part of aquiferconfined part of aquifer
Arsenic associated with Arsenic associated with high pHhigh pH
Flow: unconfined to Flow: unconfined to confined back toconfined back tounconfinedunconfined
Geochemical Reactions Geochemical Reactions Brine initially fills the aquiferBrine initially fills the aquifer
Calcite and Dolomite equilibriumCalcite and Dolomite equilibrium
Cation exchange Cation exchange – 2NaX + Ca+2 = CaX2 + 2Na+2NaX + Ca+2 = CaX2 + 2Na+– 2NaX + Mg+2 = MgX2 + 2Na+2NaX + Mg+2 = MgX2 + 2Na+
Surface complexationSurface complexationHfo-HAsO4- + OH- = HfoOH + HAsO4-2Hfo-HAsO4- + OH- = HfoOH + HAsO4-2
Desorption at pH > 8.5Desorption at pH > 8.5
Where we are headedWhere we are headed
Make a brineMake a brine Define exchangerDefine exchanger Define surfaceDefine surface Define recharge waterDefine recharge water Define minerals in aquiferDefine minerals in aquifer Simulate inflow of recharge water Simulate inflow of recharge water
into brine-filled aquiferinto brine-filled aquifer
Solution Definition and Solution Definition and Speciation CalculationsSpeciation Calculations
Ca NaSO4Mg
FeCl HCO3
Reaction calculations
Saturation Indices
Speciation calculation
Inverse calculations
PHREEQC Data BlocksPHREEQC Data Blocks SOLUTIONSOLUTION—Define solution composition—Define solution composition
SOLUTION_SPREADSOLUTION_SPREAD—Spreadsheet input for —Spreadsheet input for solution compositionsolution composition
Other data blocks related to speciationOther data blocks related to speciation
SOLUTION_MASTER_SPECIESSOLUTION_MASTER_SPECIES—Redox states and —Redox states and gram formula weightgram formula weight
SOLUTION_SPECIESSOLUTION_SPECIES—Reaction and log K —Reaction and log K
ConstituentConstituent ValueValuepHpH
pEpE
TemperatureTemperature
CaCa
MgMg
NaNa
KK
FeFe
Alkalinity as HCOAlkalinity as HCO33
ClCl
SOSO44
8.228.22
8.458.45
2525
412.3412.3
1291.81291.8
1076810768
399.1399.1
.002.002
141.682141.682
1935319353
27122712
Seawater: units are ppm
PHREEQC Names and Default PHREEQC Names and Default Gram Formula WeightsGram Formula Weights
PHREEQC PHREEQC NameName
SpeciesSpecies Default “as”Default “as”
phreeqc.dat/wateq4f.datphreeqc.dat/wateq4f.dat
AlkalinityAlkalinity AlkalinityAlkalinity CaCOCaCO33
CC Total carbonTotal carbon HCOHCO33
C(4)C(4) TDICTDIC HCOHCO33
C(-4)C(-4) MethaneMethane CHCH44
N(5)N(5) Nitrate, NONitrate, NO33-- NN
N(-3)N(-3) Ammonium, NHAmmonium, NH44++ NN
SiSi SilicaSilica SiOSiO22
POPO44 PhosphatePhosphate PP
S(6)S(6) SulfateSulfate SOSO44
Solution Data BlockSolution Data Block
pH, pe, TemperaturepH, pe, Temperature
Solution CompositionSolution Composition
Set default Set default units!units!
Select Select analytesanalytes
Set “As”, special units
Enter concen-Enter concen-trationstrations
Click OK when done
Run Speciation CalculationRun Speciation CalculationRunRun
Select files, phreeqc.dat
Exercise: Speciate seawaterExercise: Speciate seawater
Use PhreecI to run a speciation calculation for Use PhreecI to run a speciation calculation for seawater using phreeqc.dat database.seawater using phreeqc.dat database.
What is a speciation calculation?What is a speciation calculation? Input: Input:
– pHpH– pepe– ConcentrationsConcentrations
Equations:Equations:Mass-balance—sum of the calcium species = total calciumMass-balance—sum of the calcium species = total calciumMass-action—activity of products divided by reactants = constantMass-action—activity of products divided by reactants = constantActivity coefficients—function of ionic strengthActivity coefficients—function of ionic strength
OutputOutput– Molalities, activitiesMolalities, activities– Saturation indicesSaturation indices
What is pH?What is pH?
QuestionsQuestions
1. How does the pH change when CO1. How does the pH change when CO22 degasses during an alkalinity titration? degasses during an alkalinity titration?
2. How does pH change when plankton 2. How does pH change when plankton respire COrespire CO22??
3. How does pH change when calcite 3. How does pH change when calcite dissolves?dissolves?
pH = 6.3 + log[(HCO3-)/(CO2)]
What is pe?What is pe?
Fe+2 = Fe+3 + e-
pe = log( [Fe+3]/[Fe+2] ) + 13
HS- + 4H2O = SO4-2 + 9H+ + 8e-
pe = log( [SO4-2]/[HS-] ) – 9/8pH + 4.21
N2 + 6H2O = 2:NO3- + 12H+ + 10e-
pe = 0.1log( [NO3-]2/[N2] ) –1.2pH + 20.7
pe = 16.9Eh, Eh platinum electrode measurement
Mass-Action EquationsMass-Action Equations
HH++ + CO + CO33-2-2 = HCO = HCO33
--
]][[
][2
3
3
HCO
HCOK
]log[]log[]log[log 233
HCOHCOK
][
][loglog
23
3
CO
HCOKpH
Mass BalanceMass BalanceCalcium mass balance:Calcium mass balance:
CaCatottot = (Ca = (Ca+2+2) + (CaSO) + (CaSO44) + (CaHCO) + (CaHCO33++) + (CaCO) + (CaCO33) + (CaOH) + (CaOH++) + (CaHSO) + (CaHSO44
++))
In millimoles per kilogram of water:In millimoles per kilogram of water:
10.7 = 9.5 + 1.1 + 0.05 + 0.03 + 0.0009 + 6e-810.7 = 9.5 + 1.1 + 0.05 + 0.03 + 0.0009 + 6e-8
Activity CoefficientsActivity Coefficients
iii ma
i
i
ii b
Ba
Az
0
2
1log
0
0.2
0.4
0.6
0.8
1
1.2
0 0.5 1 1.5
IONIC STRENGTH
AC
TIV
ITY
CO
EF
FIC
IEN
T
gamma_Na+
gamma_Z-2
gamma_SO4-2
WATEQ activity coefficient
iii Az 3.01
log 2
Davies activity coefficient
ii
i mz 2
2
1
Pitzer activity coefficientsHigh ionic strengthLimited model
Results of Speciation CalculationResults of Speciation Calculation
SATURATION INDEXSATURATION INDEXThe thermodynamic state of a mineral relative to a solutionThe thermodynamic state of a mineral relative to a solution
SI < 0, Mineral should dissolveSI < 0, Mineral should dissolve
SI > 0, Mineral should precipitateSI > 0, Mineral should precipitate
SI ~ 0, Mineral reacts fast enough to SI ~ 0, Mineral reacts fast enough to maintain equilibriummaintain equilibrium
MaybeMaybe– KineticsKinetics– UncertaintiesUncertainties
Useful Mineral ListUseful Mineral ListMinerals that may react to equilibrium relatively quicklyMinerals that may react to equilibrium relatively quickly
Carbonates PhosphatesCO2(g) CO2 Hydroxyapatite Ca5(PO4)3OHCalcite CaCO3 Vivianite Fe3(PO4)2Dolomite CaMgCO3 OxyhydroxidesSiderite FeCO3 Fe(OH)3(a) Fe(OH)3Rhodochrosite MnCO3 Goethite FeOOH
Sulfates Gibbsite Al(OH)3Gypsum CaSO4 Birnessite MnO2Celestite SrSO4 Manganite Mn(OH)3Barite BaSO4 Aluminosilicates
Sulfides Silica gel SiO2-2H2OFeS(a) FeS Silica glass SiO2-H2OMackinawite FeS Chalcedony SiO2
Kaolinite Al2Si2O5(OH)
Other SOLUTION CapabilitiesOther SOLUTION Capabilities Define pe by ratio of redox states—O(0)/H2O, Define pe by ratio of redox states—O(0)/H2O,
N(5)/N(-3), Fe(3)/Fe(2), S(6)/S(-2)N(5)/N(-3), Fe(3)/Fe(2), S(6)/S(-2)
Charge balance—pH or ionic elementCharge balance—pH or ionic element
Adjust element concentration to phase boundaryAdjust element concentration to phase boundary—Al to gibbsite—Al to gibbsite
Calculate pH from Alkalinity and C(4) (TDIC)Calculate pH from Alkalinity and C(4) (TDIC)
SOLUTION_SPREAD—Spreadsheet formatSOLUTION_SPREAD—Spreadsheet format
Modifying the DatabaseModifying the Database
Problems with arsenic thermo dataProblems with arsenic thermo data
– Arsenic aqueous model (Nordstrom) not Arsenic aqueous model (Nordstrom) not consistent with sorption model consistent with sorption model (Dzombak and Morel)(Dzombak and Morel)
– Competition for surface sites between Competition for surface sites between minor anion and major cations appears minor anion and major cations appears unrealisticunrealistic
Arsenic Thermodynamic Data from Arsenic Thermodynamic Data from Dzombak and MorelDzombak and Morel
SOLUTION_MASTER_SPECIESSOLUTION_MASTER_SPECIES As H3AsO4 -1.0 74.9216 74.9216As H3AsO4 -1.0 74.9216 74.9216SOLUTION_SPECIESSOLUTION_SPECIES#H3AsO4 primary master species#H3AsO4 primary master species H3AsO4 = H3AsO4H3AsO4 = H3AsO4 log_k 0.0log_k 0.0#H2AsO4- #H2AsO4- H3AsO4 = H2AsO4- + H+ H3AsO4 = H2AsO4- + H+ log_k -2.243log_k -2.243 delta_h -1.69 kcaldelta_h -1.69 kcal#HAsO4-2 #HAsO4-2 H3AsO4 = HAsO4-2 + 2H+ H3AsO4 = HAsO4-2 + 2H+ log_k -9.001log_k -9.001 delta_h -0.92 kcaldelta_h -0.92 kcal#AsO4-3 #AsO4-3 H3AsO4 = AsO4-3 + 3H+H3AsO4 = AsO4-3 + 3H+ log_k -20.597log_k -20.597 delta_h 3.43 kcaldelta_h 3.43 kcal
Arsenic Surface Complexation from Arsenic Surface Complexation from Dzombak and Morel Dzombak and Morel
SURFACE_MASTER_SPECIESSURFACE_MASTER_SPECIES Surf SurfOHSurf SurfOHSURFACE_SPECIESSURFACE_SPECIES SurfOH = SurfOHSurfOH = SurfOH log_k 0.0log_k 0.0 SurfOH + H+ = SurfOH2+SurfOH + H+ = SurfOH2+ log_k 7.29log_k 7.29 SurfOH = SurfO- + H+SurfOH = SurfO- + H+ log_k -8.93log_k -8.93 SurfOH + AsO4-3 + 3H+ = SurfH2AsO4 + H2OSurfOH + AsO4-3 + 3H+ = SurfH2AsO4 + H2O log_k 29.31log_k 29.31 SurfOH + AsO4-3 + 2H+ = SurfHAsO4- + H2OSurfOH + AsO4-3 + 2H+ = SurfHAsO4- + H2O log_k 23.51log_k 23.51 SurfOH + AsO4-3 = SurfOHAsO4-3SurfOH + AsO4-3 = SurfOHAsO4-3 log_k 10.58log_k 10.58
Exercise: Define Arsenic ChemistryExercise: Define Arsenic Chemistry
Cut and paste As aqueous species defined aboveCut and paste As aqueous species defined above
Cut and paste As surface complexation defined Cut and paste As surface complexation defined aboveabove
Add As to the SOLUTION definition for seawater Add As to the SOLUTION definition for seawater 0.03 ppb 0.03 ppb
Run speciationRun speciation
Arsenic SpeciationArsenic Speciation
Arsenic has been added as a new Arsenic has been added as a new elementelement
Predominant species is HAsOPredominant species is HAsO44-2 -2 at pH at pH
8.228.22 Although not used yet, arsenic Although not used yet, arsenic
sorption has been definedsorption has been defined
Reaction CalculationsReaction CalculationsSOLUTION EQUILIBRIUM
_PHASESEXCHANGE SURFACE KINETICSMIX REACTION+
SOLUTIONEQUILIBRIUM_
PHASESEXCHANGE SURFACE KINETICS
EQUILIBRATION REACTOR
EQUILIBRIUM REACTIONSEQUILIBRIUM REACTIONS
Can be used as PHAST initial conditionsCan be used as PHAST initial conditions– SURFACESURFACE– EXCHANGEEXCHANGE– SOLID_SOLUTIONSSOLID_SOLUTIONS– EQUILIBRIUM_PHASESEQUILIBRIUM_PHASES
NON-EQUILIBRIUM REACTIONSNON-EQUILIBRIUM REACTIONS
REACTIONREACTION REACTION_TEMPERATUREREACTION_TEMPERATURE KINETICS (PHAST initial condition)KINETICS (PHAST initial condition)
SAVE and USESAVE and USE
Save results of calculationsSave results of calculations Use previously defined SOLUTIONS, Use previously defined SOLUTIONS,
EQUILIBRIUM_PHASES, REACTIONs, etc EQUILIBRIUM_PHASES, REACTIONs, etc Use previously SAVEd SOLUTIONS, Use previously SAVEd SOLUTIONS,
EQUILBRIUM_PHASES, etcEQUILBRIUM_PHASES, etc
ReactionsReactionsEvaporating SeawaterEvaporating Seawater
PHREEQC Processing and OutputPHREEQC Processing and Output Initial-solution calculationInitial-solution calculation Reaction calculation includes any of the Reaction calculation includes any of the
following:following:
Simulation/ENDSimulation/ENDEQUILIBRIUM_PHASES 2EQUILIBRIUM_PHASES 2SOLUTION 1SOLUTION 1SOLUTION 1SOLUTION 1ENDENDSOLUTION 1SOLUTION 1ENDEND
MIXREACTIONREACTION_TEMP
EQUILIBRIUM_PHASESEXCHANGESURFACE SOLID_SOLUTION GAS_PHASEKINETICS
Exercise: Evaporate SeawaterExercise: Evaporate Seawater Append to input file and “save as” Append to input file and “save as” ENDEND USE solution 1 USE solution 1 EQUILIBRIUM_PHASES 1EQUILIBRIUM_PHASES 1
– HaliteHalite SI = 0SI = 0 Alternate formula is H2OAlternate formula is H2O
– Calcite—SI=0, moles=0Calcite—SI=0, moles=0– Dolomite—SI=0, moles=0Dolomite—SI=0, moles=0– CO2(g)—SI=-1.5, moles=10CO2(g)—SI=-1.5, moles=10– Anhydrite—SI=0, moles=0Anhydrite—SI=0, moles=0– Gypsum—SI=0, moles=0Gypsum—SI=0, moles=0
SAVE solution 1SAVE solution 1
Exercise: Evaporate SeawaterExercise: Evaporate Seawater
How much water remains?How much water remains? What is the concentration of Na, Cl?What is the concentration of Na, Cl?
Exercise: Surface composition in Exercise: Surface composition in equilibrium with brineequilibrium with brine
Define a SURFACE 1Define a SURFACE 1–Equilibrium with solution 1 Equilibrium with solution 1 –SurfOHSurfOH–0.14 moles of sites0.14 moles of sites–600 m600 m22/g/g–30 g30 g
Exercise: Exchange composition Exercise: Exchange composition in equilibrium with brinein equilibrium with brine
Define EXCHANGE 1Define EXCHANGE 1–Equilibrium with solution 1Equilibrium with solution 1–0.4 moles of exchange sites0.4 moles of exchange sites
Exercise: Make a Carbonate Exercise: Make a Carbonate Ground WaterGround Water
Append to same fileAppend to same file END END Start with pure water (solution 2)Start with pure water (solution 2) Equilibrate with calcite and dolomiteEquilibrate with calcite and dolomite PCO2 = -1.5PCO2 = -1.5 Save result as solution 2Save result as solution 2
Comprehensive ExamComprehensive Exam We want to simulate the reactions of carbonate We want to simulate the reactions of carbonate
ground water with the aquifer sedimentsground water with the aquifer sediments
Assume the aquifer initially contains a surface Assume the aquifer initially contains a surface and exchanger that have been equilibrated with and exchanger that have been equilibrated with the brine as well as calcite and dolomitethe brine as well as calcite and dolomite
Simulate a volume of aquifer that sequentially Simulate a volume of aquifer that sequentially receives 4 volumes of carbonate ground water receives 4 volumes of carbonate ground water
What pH and arsenic concentrations do you find What pH and arsenic concentrations do you find in each volume of pore water?in each volume of pore water?
Chemical ReactionsChemical Reactions
Ca, Mg exchanged for NaCa, Mg exchanged for Na Calcite, dolomite dissolveCalcite, dolomite dissolve pH increasespH increases Arsenic is released from surface sitesArsenic is released from surface sites
Kinetic ReactionsKinetic Reactions
RATES Datablock—defines rates of RATES Datablock—defines rates of reaction as function of solution reaction as function of solution compositioncomposition
KINETICS DatablockKINETICS Datablock– Select rate expression(s)Select rate expression(s)– Amount of reactantAmount of reactant– Stoichiometry of reactionStoichiometry of reaction– ParametersParameters
Monod Kinetics Rate DefinitionMonod Kinetics Rate DefinitionCell GrowthCell Growth
22
2
maxOO
OX CK
CXvR
ParameterParameter ValueValue
VVmaxmax, 1/s, 1/s 1e-51e-5
KKO2O2, mol/L, mol/L 1e-51e-5
XX00, mol/L, mol/L 0.4e-3 0.4e-3
RATES Data BlockRATES Data BlockSee RATES in documentation for description of Basic statementsSee RATES in documentation for description of Basic statements
RATES RATES BiomassBiomass-start-start5 5 REM Biomass is the name applied to this rate expressionREM Biomass is the name applied to this rate expression10 vmax = 1e-510 vmax = 1e-520 KO2 = 1e-520 KO2 = 1e-525 25 REM KIN returns current amount for kinetic reactantREM KIN returns current amount for kinetic reactant30 X = KIN("Biomass")30 X = KIN("Biomass")35 35 REM MOL returns molality of speciesREM MOL returns molality of species40 O2 = MOL("O2")40 O2 = MOL("O2")50 rate = vmax * X * O2/(KO2 + O2)50 rate = vmax * X * O2/(KO2 + O2)55 55 REM TIME is internally defined time step for integrationREM TIME is internally defined time step for integration60 moles = rate*TIME60 moles = rate*TIME70 save -moles70 save -moles-end-end
KINETICS Data BlockKINETICS Data Block
CHCH22O + OO + O22 = CO = CO22 + H + H22OO
KINETICS 1KINETICS 1BiomassBiomass
-formula -formula CH2O -1 CH2O -1 Sub 1Sub 1-m -m 0.00040.0004 # moles# moles-steps -steps 86400 in 4 steps 86400 in 4 steps # seconds# seconds-tol -tol 1e-81e-8
Sign ConventionsSign ConventionsSAVE in SAVE in RATESRATES
Coefficient inCoefficient in
KINETICSKINETICSKinetic Kinetic
reactant (KIN, reactant (KIN, M)M)
Aqueous Aqueous concentrationconcentration
+ + Decrease Increase
+ - Decrease Decrease
- + Increase Decrease
- - Increase Increase
ExerciseExercise Define a new element “Sub” with one Define a new element “Sub” with one
species, Sub.species, Sub. Start with water in equilibrium with Start with water in equilibrium with
atmospheric O2, 1 mmol/kgw Sub.atmospheric O2, 1 mmol/kgw Sub. Define a Monod kinetics with the Define a Monod kinetics with the
parameters from the previous slidesparameters from the previous slides Initial amount of biomass is 4e-4 molesInitial amount of biomass is 4e-4 moles The stoichiometry of the reaction replaces The stoichiometry of the reaction replaces
Sub with CH2OSub with CH2O Run the simulation for 1 day printing Run the simulation for 1 day printing
results every ¼ day.results every ¼ day.
Kinetic ResultsKinetic Results
0.00E+00
2.00E-04
4.00E-04
6.00E-04
8.00E-04
1.00E-03
1.20E-03
0 20000 40000 60000 80000 100000
SECONDS
MO
L/L
Sub
O(0)
C
k_Biomass
PHREEQC ReactantsPHREEQC Reactants Keyword data blocks define reactantsKeyword data blocks define reactants
– SOLUTION—SolutionsSOLUTION—Solutions
– EQUILIBRIUM_PHASES—Equilibrium minerals and gases EQUILIBRIUM_PHASES—Equilibrium minerals and gases
– EXCHANGE—Exchangers EXCHANGE—Exchangers
– SURFACE—Surfaces SURFACE—Surfaces
– KINETICS and RATES—Kinetic reactionsKINETICS and RATES—Kinetic reactions
– SOLID_SOLUTIONS—Solid solutionsSOLID_SOLUTIONS—Solid solutions
– GAS_PHASE—gas bubble (rarely used)GAS_PHASE—gas bubble (rarely used) Store reactants on shelves by type and numberStore reactants on shelves by type and number Put reactants together to define a reaction calculationPut reactants together to define a reaction calculation SAVE/USE reactantsSAVE/USE reactants
Type and number are used to define PHAST reactionsType and number are used to define PHAST reactions
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