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101 lines
3.8 KiB
Org Mode
101 lines
3.8 KiB
Org Mode
#+TITLE: Description of =surfex= benchmark
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#+AUTHOR: MDL <delucia@gfz-potsdam.de>
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#+DATE: 2023-08-26
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#+STARTUP: inlineimages
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#+LATEX_CLASS_OPTIONS: [a4paper,9pt]
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#+LATEX_HEADER: \usepackage{fullpage}
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#+LATEX_HEADER: \usepackage{amsmath, systeme}
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#+LATEX_HEADER: \usepackage{graphicx}
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#+LATEX_HEADER: \usepackage{charter}
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#+OPTIONS: toc:nil
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* Quick start
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#+begin_src sh :language sh :frame single
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mpirun -np 4 ./poet ex.R ex_res
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mpirun -np 4 ./poet surfex.R surfex_res
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#+end_src
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* List of Files
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- =ex.R=: POET input script for a 100x100 simulation grid, only
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exchange
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- =ExBase.pqi=: PHREEQC input script for the =ex.R= model
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- =surfex.R=: POET input script for a 1000x1000 simulation grid
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considering both cation exchange and surface complexation
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- =SurfExBase.pqi=: PHREEQC input script for the =surfex.R= model
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- =SMILE_2021_11_01_TH.dat=: PHREEQC database containing the
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parametrized data for Surface and Exchange, based on the SMILE
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Thermodynamic Database (Version 01-November-2021)
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* Chemical system
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This model describes migration of Uranium radionuclide in Opalinus
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clay subject to surface complexation and cation exchange on the
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surface of clay minerals. These two processes account for the binding
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of aqueous complexes to the surfaces of minerals, which may have a
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significant impact on safety of underground nuclear waste repository.
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Namely, they can act as retardation buffer for uranium complexes
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entering into a natural system. The system is kindly provided by Dr.
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T. Hennig and is inspired to the sandy facies BWS-A3 sample from the
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Mont Terri underground lab (Hennig and Kühn, 2021).
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This chemical system is highly redox-sensitive, and several elements
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are defined in significant amounts in different valence states. In
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total, 20 elemental concentrations and valences are transported:
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C(-4), C(4), Ca, Cl, Fe(2), Fe(3), K, Mg, Na, S(-2), S(2), S(4), S(6),
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Sr , U(4), U(5), U(6); plus the total H, total O and Charge implicitly
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required by PHREEQC_RM.
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** Exchange
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The SMILE database defines thermodynamical data for exchange of all
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major cations and uranyl-ions on Illite and Montmorillonite. In
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PHREEQC terms:
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- *Y* for Montmorillonite, with a total amount of 1.2585
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milliequivalents and
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- *Z* for Illite, with a total amount of 0.9418 meq
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** Surface
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Here we consider a Donnan diffuse double layer of 0.49 nm. Six
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distinct sorption sites are defined:
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- Kln_aOH (aluminol site) and Kln_siOH (silanol) for Kaolinite
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- For Illite, strong and weak sites Ill_sOH and Ill_wOH respectively
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- For Montmorillonite, strong and weak sites Mll_sOH and Mll_wOH
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respectively
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Refer to the =SurfExBase.pqi= script for the actual numerical values
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of the parameters.
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* POET simulations
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** =ex.R=
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This benchmark only considers EXCHANGE, no mineral or SURFACE
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complexation is involved.
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- Grid discretization: square domain of 1 \cdot 1 m^{2} discretized in
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100x100 cells
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- Boundary conditions: E, S and W sides of the domain are closed.
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*Fixed concentrations* are fixed at the N boundary.
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- Diffusion coefficients: isotropic homogeneous \alpha = 1E-06
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- Time steps & iterations: 10 iterations with \Delta t of 200 s
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- *DHT* is not implemented as of yet for models including SURFACE and
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EXCHANGE geochemical processes *TODO*
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- Hooks: no hooks defined *TODO*
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** =surfex.R=
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- Grid discretization: rectangular domain of 1 \cdot 1 m^{2}
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discretized in 10 \times 10 cells
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- Boundary conditions: E, S and W sides of the domain are closed.
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*Fixed concentrations* are fixed at the N boundary.
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- Diffusion coefficients: isotropic homogeneous \alpha = 1E-06
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- Time steps & iterations: 10 iterations with \Delta t of 200 s
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* References
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- Hennig, T.; Kühn, M.Surrogate Model for Multi-Component Diffusion of
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Uranium through Opalinus Clay on the Host Rock Scale. Appl. Sci.
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2021, 11, 786. https://doi.org/10.3390/app11020786
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