RE: Simulating headspace in a batch system

[Girish Kumar]

Hello Glenn/Fellow Users,

I'm trying to simulate a simple closed batch system of 35 mL in volume with 10 ml of solution and 25 ml of headspace with some gas species in it. Attached is the input file and associated database file (hanford.dat). I have the following questions:

1. How do I simulate a headspace for this batch system in general mode? Is there a way to specify a porosity of 1 and then specify a liquid saturation and/or gas saturation by calculating the fractions of those two phases (i.e., Liq_Sat of 10ml/35 ml and Gas_Sat of 25 ml/35 ml?). I was also trying a work around with RICHARDS mode and including a flow condition to be able to specify saturations. But maybe there is a simpler way?

2. Also, I'm simulating equilibrium partitioning of certain gas species in the system via Henry's constant (included through speciation reaction between gas and liquid forms of the species in the database). I specify these species under ACTIVE_GAS_SPECIES and the acknowledgement of GAS_TRANSPORT_IS_UNVETTED in that block. Do I also need to include a PASSIVE_GAS_SPECIES block. I saw something of this sort here: https://gitlab.amphos21.com/public-projects/pflotran-np-dc/-/blob/1976a774ba589b802f1b055d585c3ba9b7d8ebba/regression_tests/default/column/multiphase_transport_pulse.in

3. For my initial constraint of chemical species concentrations, I specify concentrations of the aqueous forms of the gas species, and I assume that the equilibrium partitioning before time stepping will distribute the mass and/or concentration into the gas and liquid phase through speciation reactions. Is that what I should expect? Or Should I be specifying the concentrations of these aqueous species 

Would greatly appreciate your input/clarifications.

Thanks,

Girish

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[Hammond, Glenn E]

Girish,

Please see my responses in red below.

Glenn

From: pflotra...@googlegroups.com <pflotra...@googlegroups.com> on behalf of Girish Kumar <girish...@gmail.com>
Date: Tuesday, August 19, 2025 at 4:45 PM
To: pflotra...@googlegroups.com <pflotra...@googlegroups.com>
Subject: [pflotran-users: 8532] RE: Simulating headspace in a batch system

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Hello Glenn/Fellow Users,

I'm trying to simulate a simple closed batch system of 35 mL in volume with 10 ml of solution and 25 ml of headspace with some gas species in it. Attached is the input file and associated database file (hanford.dat). I have the following questions:

1. How do I simulate a headspace for this batch system in general mode? Is there a way to specify a porosity of 1 and then specify a liquid saturation and/or gas saturation by calculating the fractions of those two phases (i.e., Liq_Sat of 10ml/35 ml and Gas_Sat of 25 ml/35 ml?). I was also trying a work around with RICHARDS mode and including a flow condition to be able to specify saturations. But maybe there is a simpler way?

I would not use a flow mode. Use solely the SUBSURFACE_TRANSPORT process model (MODE = GIRT) and set a REFERENCE_SATURATION 0.2857 in the SUBSURFACE block. That should set the proper saturation (output LIQUID_SATURATION to verify…I am fairly confident that you can output it with solely transport).

2. Also, I'm simulating equilibrium partitioning of certain gas species in the system via Henry's constant (included through speciation reaction between gas and liquid forms of the species in the database). I specify these species under ACTIVE_GAS_SPECIES and the acknowledgement of GAS_TRANSPORT_IS_UNVETTED in that block. Do I also need to include a PASSIVE_GAS_SPECIES block. I saw something of this sort here: https://gitlab.amphos21.com/public-projects/pflotran-np-dc/-/blob/1976a774ba589b802f1b055d585c3ba9b7d8ebba/regression_tests/default/column/multiphase_transport_pulse.in

You need the PASSIVE_GAS_SPECIES for constraint against gas partial pressures in the CONSTRAINTS. Anytime you have ACTIVE_GAS_SPECIES, you should include them as PASSIVE_GAS_SPECIES.

3. For my initial constraint of chemical species concentrations, I specify concentrations of the aqueous forms of the gas species, and I assume that the equilibrium partitioning before time stepping will distribute the mass and/or concentration into the gas and liquid phase through speciation reactions. Is that what I should expect? Or Should I be specifying the concentrations of these aqueous species 

Constrain against the gas species and gas partial pressure in Bars. The following is an example for O2(g):

https://bitbucket.org/pflotran/pflotran/src/2d5169f01591ed7c34917c211a24d34d6d2a7f6e/shortcourse/exercises/copper_leaching/cu_leaching.in#lines-319. Note that a negative partial pressure (p_bar < 0) is 10^p_bar.

Would greatly appreciate your input/clarifications.

Thanks,

Girish

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