Kinetic reactions integration order

[Ivan M]

Hi all,

I'm doing some kinetic reactions (dual Monod equations) using a substrate (Benzene), an electron acceptor (O2) and Biomass. Both the substrate and the biomass are modeled using a SOLUTION_MASTER_SPECIES block, detailed below. There are three KINETICS blocks, one for the benzene equation, one for the oxygen equation and one for the biomass. The benzene part depends on the present O2 concentration, and the oxygen one depends on the benzene concentration. 

My question is: what is the integration order and parameter usage? Are the O2 and benzene concentrations used from the same iteration or are the integration order following the KINETICS block? 

<kinetics block>

<iteration>  <reaction>

      1            Benzene

      1            O2

      1            Biomass

or 

<kinetics block>

<iteration>  <reaction>

      1            Benzene

      2            O2

      3            Biomass

Cheers!

TITLE Benzene-O2

# This model degrades benzene using a dual Monod

# equation and biomass generation.

SOLUTION_MASTER_SPECIES

  Benzene   Benzene             0     C6H6  78.108

  Biomass  Biomass    0    22.6 22.6

SOLUTION_SPECIES

  Benzene = Benzene

  log_k 0

  -gamma    0.0000    0.0000

  Biomass = Biomass

  log_k 0

  -gamma    0.0000    0.0000

SOLUTION 1

# -units mol/kgw

# Benzene 0.0001024

# O(0) 0.000063

# Biomass 0.00003125

 -units g/kgw

 Benzene 0.005931

 O(0)  0.0025

 Biomass 0.0000025 #better fit

RATES

 Benzene_degradation

 -start

  10 kB_max   = parm(1)

  20 kB_half  = parm(2)

  30 k02_half = parm(3)

 100 Benz     = tot("Benzene")

 150 EAO2     = mol("O2")

 200 B        = mol("Biomass")

 250 if Benz < 1e-15 then goto 600

 300 if EAO2 < 1e-15 then goto 600

 400 rate =  - kB_max * B * (Benz /(kB_half + Benz)) * (EAO2 /(kO2_half + EAO2)) 

 500 dS = rate * time

 600 save dS

 700 put(rate, 1)

 -end

  EA_degradation

 -start

  10 kB_max   = parm(1)

  20 kB_half  = parm(2)

  30 KO2_half = parm(3)

  40 stoichi  = parm(4)

 100 Benz     = tot("Benzene")

 150 EAO2     = mol("O2")

 200 B = mol("Biomass")

 300 if Benz < 1e-15 then goto 600

 350 if EAO2 < 1e-15 then goto 600

 400 rate =  - stoichi * kB_max * B * (Benz /(kB_half + Benz)) * (EAO2 /(kO2_half + EAO2)) 

 500 dS = rate * time

 600 save dS

 700 put(rate, 2)

 -end

 Biomass_deg

 -start

  1 Y = parm(1); 2 R = 1 + parm(2); 3 k_Bd = parm(3)

 10 rate_S = get(1)

 20 B = mol("Biomass")

 30 rate = -Y  * rate_S - k_Bd * B

 40 dB = rate * time

 50 save -dB

 -end

KINETICS 1

 Benzene_degradation

  -formula Benzene 1 #O2 1

  #        KB_max    KB_half   KO_half    

  -parms   5.224e-6  1.286e-5  3.125e-5   

 EA_degradation

  -formula O2 7.5

  #        KB_max    KB_half   KO_half    stoichi  

  -parms   5.224e-6  1.286e-5  3.125e-5   7.5      

 

 Biomass_deg

  -formula Biomass -1 

  #        Y         R       K_Bd

  -parms   4.28      0    0.00000                             

   -steps 864000 in 150

INCREMENTAL_REACTIONS

SELECTED_OUTPUT

   -file benzene-bionapl.csv

   -reset false

   -time

   -molalities Benzene O2 Biomass

END

_________________________________________

Ivan S.P. Marin, PhD

 

Postdoctoral Associate

Département de géologie et de génie géologique

Pavillon Adrien-Pouliot, local 3744

1065. ave de la Médecine

Université Laval

Québec (Québec) Canada

G1V 0A6

418-656-2131 poste 7246

 ivan.silvestre-...@ulaval.ca

[Parkhurst, David]

> My question is: what is the integration order and parameter usage?

Parameters are available only for the kinetic reaction for which they
are defined. Biomass_deg parameters can only be seen by the
Biomass_deg rate expression.

The rates are evaluated in the order they are given in the KINETICS data block.

> Are the
> O2 and benzene concentrations used from the same iteration or are the
> integration order following the KINETICS block?

Basically, a solution composition is calculated and then all of the
rates are calculated, so all of the rate expressions are looking at
the same solution composition.


David Parkhurst
Hydrologist
dlp...@usgs.gov
Profile: https://profile.usgs.gov/dlpark
Project: http://wwwbrr.cr.usgs.gov/www/projects/GWC_coupled

> --
> You received this message because you are subscribed to the Google Groups
> ""phreeqpy-users" group.
> To post to this group, send email to phreeqp...@googlegroups.com.
> To unsubscribe from this group, send email to
> phreeqpy-user...@googlegroups.com.
> For more options, visit this group at
> https://groups.google.com/d/forum/phreeqpy-users?hl=en.
>
> More information about PhreeqPy can be found at http://www.phreeqpy.com.
> ---
> You received this message because you are subscribed to the Google Groups
> "phreeqpy-users" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to phreeqpy-user...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>