Illite

The term “illite” is often used to describe 2:1 minerals with a non-expandable interlayer. The specific mineral illite is a dioctahedral 2:1 phyllosilicate that is commonly found in soils and sedimentary rocks. The illite sold by the Clay Mineral Society’s Source Clays, named IMt-1 and IMt-2 has the following structure:

\[Mg_{0.09} Ca_{0.06} K_{1.37} [Si_{6.77} Al_{1.23} ]^{-1.23} [Al_{2.69} Fe(III)_{0.76} Fe(II)_{0.06} Mg_{0.43} Ti_{0.06} ]^{-0.44} O_{20} (OH)_4\]

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

Model Construction

The provided exp_clay.csv file contains an entry called IMt-1, which corresponds to this illite clay with the iron oxidation states specified. It also contains an entry called IMt-2, which corresponds to this illite clay but without the iron oxidation states specified.

There are three .yaml files provided, one for each .csv entry without bulk solvation (IMt1.yaml and IMt2.yaml) and another for IMt-1 with bulk solvation (IMt1_solv.yaml).

IMt1.yaml

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

OUTPATH: .

# name of system to call according to CLAY_COMP (exp_clay.csv)
SYSNAME: IMt-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: CD21

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

# number of unit cells in x direction (Default 7)
X_CELLS: 6

# number of unit cells in y direction (Default 5)
Y_CELLS: 4

# number of unit cells in z direction (Default 3)
N_SHEETS: 2

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

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

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

# full simulation box height in A (Default 150.0)
BOX_HEIGHT: 30.0

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

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

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

# bash alias for used GROMACS version
GMX: gmx

IMt1_solv.yaml

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

OUTPATH: .

# name of system to call according to CLAY_COMP (exp_clay.csv)
SYSNAME: IMt-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: CD21

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

# number of unit cells in x direction (Default 7)
X_CELLS: 6

# number of unit cells in y direction (Default 5)
Y_CELLS: 4

# number of unit cells in z direction (Default 3)
N_SHEETS: 4

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

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

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

# full simulation box height in A (Default 150.0)
BOX_HEIGHT: 100.0

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

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

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

# bash alias for used GROMACS version
GMX: gmx

IMt2.yaml

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

OUTPATH: .

# name of system to call according to CLAY_COMP (exp_clay.csv)
SYSNAME: IMt-2

# 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: CD21

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

# number of unit cells in x direction (Default 7)
X_CELLS: 6

# number of unit cells in y direction (Default 5)
Y_CELLS: 4

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

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

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

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

# full simulation box height in A (Default 150.0)
BOX_HEIGHT: 50.0

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

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

BULK_IONS:
   Na: 0
   Cl: 0

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

# bash alias for used GROMACS version
GMX: gmx