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