poet/bench/surfex

Description of surfex benchmark

Quick start

mpirun -np 4 ./poet ex.R ex_res
mpirun -np 4 ./poet surfex.R surfex_res

List of Files

• ex.R: POET input script for a 100x100 simulation grid, only exchange
• ExBase.pqi: PHREEQC input script for the ex.R model
• surfex.R: POET input script for a 1000x1000 simulation grid considering both cation exchange and surface complexation
• SurfExBase.pqi: PHREEQC input script for the surfex.R model
• SMILE_2021_11_01_TH.dat: PHREEQC database containing the parametrized data for Surface and Exchange, based on the SMILE Thermodynamic Database (Version 01-November-2021)

Chemical system

This model describes migration of Uranium radionuclide in Opalinus clay subject to surface complexation and cation exchange on the surface of clay minerals. These two processes account for the binding of aqueous complexes to the surfaces of minerals, which may have a significant impact on safety of underground nuclear waste repository. Namely, they can act as retardation buffer for uranium complexes entering into a natural system. The system is kindly provided by Dr.

1. Hennig and is inspired to the sandy facies BWS-A3 sample from the

Mont Terri underground lab (Hennig and Kühn, 2021).

This chemical system is highly redox-sensitive, and several elements are defined in significant amounts in different valence states. In total, 20 elemental concentrations and valences are transported: C(-4), C(4), Ca, Cl, Fe(2), Fe(3), K, Mg, Na, S(-2), S(2), S(4), S(6), Sr , U(4), U(5), U(6); plus the total H, total O and Charge implicitly required by PHREEQC_RM.

Exchange

The SMILE database defines thermodynamical data for exchange of all major cations and uranyl-ions on Illite and Montmorillonite. In PHREEQC terms:

• Y for Montmorillonite, with a total amount of 1.2585 milliequivalents and
• Z for Illite, with a total amount of 0.9418 meq

Surface

Here we consider a Donnan diffuse double layer of 0.49 nm. Six distinct sorption sites are defined:

• Kln_aOH (aluminol site) and Kln_siOH (silanol) for Kaolinite
• For Illite, strong and weak sites Ill_sOH and Ill_wOH respectively
• For Montmorillonite, strong and weak sites Mll_sOH and Mll_wOH respectively

Refer to the SurfExBase.pqi script for the actual numerical values of the parameters.

POET simulations

ex.R

This benchmark only considers EXCHANGE, no mineral or SURFACE complexation is involved.

• Grid discretization: square domain of 1 ⋅ 1 m² discretized in 100x100 cells
• Boundary conditions: E, S and W sides of the domain are closed. Fixed concentrations are fixed at the N boundary.
• Diffusion coefficients: isotropic homogeneous α = 1E-06
• Time steps & iterations: 10 iterations with Δ t of 200 s
• DHT is not implemented as of yet for models including SURFACE and EXCHANGE geochemical processes TODO
• Hooks: no hooks defined TODO

surfex.R

• Grid discretization: rectangular domain of 1 ⋅ 1 m² discretized in 10 × 10 cells
• Boundary conditions: E, S and W sides of the domain are closed. Fixed concentrations are fixed at the N boundary.
• Diffusion coefficients: isotropic homogeneous α = 1E-06
• Time steps & iterations: 10 iterations with Δ t of 200 s

References

• Hennig, T.; Kühn, M.Surrogate Model for Multi-Component Diffusion of Uranium through Opalinus Clay on the Host Rock Scale. Appl. Sci. 2021, 11, 786. https://doi.org/10.3390/app11020786