# PhreeqcUsers Discussion Forum

## Conceptual Models => Design of conceptual models => Topic started by: mhkaufman on September 19, 2019, 10:51:46 PM

Title: aerobic metabolism in a closed bottle with fixed headspace
Post by: mhkaufman on September 19, 2019, 10:51:46 PM
Hi, I am trying to model the evolution of dissolved oxygen and CO2 in a closed bottle with 40ml of water and 10ml of air, while the system undergoes active metabolism of organic carbon.

I am having a hard time figuring out how to properly specify the headspace equilibration. My system as-written below seems to start with a very low pressure in the headspace.
I am guessing this from the output statement:
"Total pressure:  0.07      atmospheres          (Peng-Robinson calculation)"

Input file:

TITLE synthetic seawater in equilibrium with atmosphere, metabolism of organic carbon

SOLUTION 1 #35ppt water with measured pH
units mol/l
-water 0.041 #mass of water to get ~40ml
temp 19.0
pH 7.36 #starting pH
Na   0.412
K   0.055
Mg   0.057
Ca   0.011
Sr   0.001
Cl   0.557
S(6) 0.023 as SO4-2
Alkalinity   0.002   as HCO3
N(5) 0.0001   as NO3-   #nominal, unknown

EQUILIBRIUM PHASES
CO2(g)   -3.4
O2(g)    -0.7
Ntg(g)   -0.0969

SAVE Solution 1

SELECTED_OUTPUT
-reaction true
-percent_error        true
-molalities O2 CO2 Ntg
-totals   C(4)

END

REACTION 1
CH2O(NH3)0.07 0.01 # 0.1 mol CH2O, 0.007 mol NH3; taken from Parkhurst & Appelo 1999

# steps
0.0001   0.0002   0.0003   0.0004   0.0005   0.0006
0.0007   0.0008   0.0009
0.001   0.002   0.003   0.004   0.005   0.006   0.007   0.008   0.009   0.01   0.015
0.02   0.025   0.03   0.035   0.04   0.045   0.05   0.055   0.06   moles

END

-fixed_volume
-pressure      1
-volume      0.01
-temperature   19
CO2(g)      -3.4
O2(g)         -0.7
Ntg(g)      -0.0969
USE Solution 1
USE Reaction 1
END

Any thoughts greatly appreciated!
Title: Re: aerobic metabolism in a closed bottle with fixed headspace
Post by: dlparkhurst on September 19, 2019, 11:34:42 PM
GAS_PHASE gases are defined in partial pressure (atm), not log10 partial pressure.

You may want to add CH4(g) to GAS_PHASE if you are going as far as methanogenesis.
Title: Re: aerobic metabolism in a closed bottle with fixed headspace
Post by: mhkaufman on September 20, 2019, 01:25:13 AM
Thanks!
Title: Re: aerobic metabolism in a closed bottle with fixed headspace
Post by: mhkaufman on September 20, 2019, 05:06:27 PM
Followup question just for my own understanding:

In a "fixed volume" gas_phase block like this:

-fixed_volume
-pressure      1
-volume      0.01
-temperature   19
CO2(g)      0.0004
O2(g)         0.2
Ntg(g)      0.8

Does the -pressure keyword do anything? What does phreeqc do if the partial pressures specified don't add up to the pressure specified?

Thanks again
Title: Re: aerobic metabolism in a closed bottle with fixed headspace
Post by: dlparkhurst on September 24, 2019, 12:01:51 AM
No, in this case, I do not think -pressure has an effect.