Ferruginous Smectite

The term ferruginous smectite is used for dioctahedral smectites when the Fe^{3+} content is greater than 3%. The ferruginous smectite sold by the Clay Mineral Society’s Source Clays, named SWa-1, has an iron content of 12.6 wt%. They are distinguished from Nontronites by only having partial substitution of aluminium by iron.

The structure given by the Clay Mineral Society is:

\[Mg_{0.18} Ca_{0.36} K_{0.01} [Si_{7.09} Al_{0.91} ]^{-0.91} [Al_{0.61} Fe(III)_{3.08} Mg_{0.24} Ti_{0.02} ]^{-0.18} O_{20} (OH)_4\]

Titanium is often identified during clay analysis, but is attributed to TiO inclusions. Therefore, we will omit it in the input.

Model Construction

The provided exp_clay.csv file contains an entry called SWa-1, which corresponds to this ferruginous smectite clay.

Let’s examine the SWya.yaml, which is provided in the Tutorial directory. This file contains all of the information necessary to build the clay model.

Please consult YAML documentation for descriptions of the parameters.

YAML Parameters

# =============================================================================
# General specifications for clay model construction
# =============================================================================

OUTPATH: .

# name of system to call according to CLAY_COMP (exp_clay.csv)
SYSNAME: SWa-1

# specify whether new clay model should be constructed:
BUILD: new

# name of .csv file with target stoichiometry
CLAY_COMP: ./exp_clay.csv

# clay type
# available options in 'UCS' directory:
CLAY_TYPE: TD21

# -----------------------------------------------------------------------------

# number of unit cells in x direction (Default 7)
X_CELLS: 7

# number of unit cells in y direction (Default 5)
Y_CELLS: 5

# number of unit cells in z direction (Default 3)
N_SHEETS: 3

# -----------------------------------------------------------------------------

# interlayer solvent present or not (Default True)
IL_SOLV: True

# target hydrated interlayer spacing in A
SPACING_WATERS: 10

# -----------------------------------------------------------------------------

# full simulation box height in A (Default 150.0)
BOX_HEIGHT: 150.0

# -----------------------------------------------------------------------------

# Bulk solvent added or not (Default: True)
BULK_SOLV: True

# Ion species and concentration in mol/L name to add in bulk solvent
BULK_IONS:
  Na: 0.1
  Cl: 0.05

# -----------------------------------------------------------------------------

# bash alias for used GROMACS version
GMX: gmx

The model can be constructed from within the Tutorial directory using:

ClayCode builder -f SWa1.yaml