ClayCode.builder System Specifications YAML file

ClayCode.builder reads the parameters specified in this file.

Required Parameters

The first section contains general parameters that are required for the model construction.

OUTPATH - output directory path [str]
Directory in which output folder is created.

SYSNAME - clay system name [str]
Th name for clay type, must to match a column header in the CSV file, the created output folder will also have this name. Avoid spaces and unusual symbols.

CLAY_COMP - filename.csv [str]
Name of CSV file where the target stoichiometry for the system specified under SYSNAME.

CLAY_TYPE - unit cell type [str]
Clay unit cell type, available in data/UCS directory.
Such as:
Dioctahedral 2:1 - D21
Trioctahedral 2:1 - T21
Dioctahedral 1:1 - D11
Trioctahedral 1:1 - T11
layered double hydroxide 3:1 - L31
layered double hydroxide 2:1 - L21
Sepiolite - SEP
Note: Only D21, D11 and L31 are supplied with current release.

Example:

# output directory path
OUTPATH: /path/to/output/directory

# name of system
SYSNAME: NAu-1-fe

# name of CSV file with target stoichiometry
CLAY_COMP: /path/to/clay_comp.csv

# clay type
CLAY_TYPE: D21
# Dioctahedral 2:1 - D21


Optional Parameters

This is an optional parameter section, if the directives are not given by the user, ClayCode.builder will use default values.

Clay Sheet Size

X_CELLS - Unit cell number [int] (Default: 7)
Number of unit cells in x-direction.
Note: Future version will have the option to specify target x-dimensions X_DIM

Y_CELLS - Unit cell number [int] (Default: 5)
Number of unit cells in y-direction.
Note: Future version will have the option to specify target y-dimensions Y_DIM

N_SHEETS - Unit cell number [int] (Default: 3)
Number of sheets of 1 unit cell thickness to be stacked in z-direction.

Example:

# 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


Clay Composition

ClayCode.builder calculates the number and type of unit cells necessary to match the desired composition, as given in CSV file.
If, instead, the user would like to specify this manually, the following parameters can be used:

UC_INDEX_LIST - unit cell list [list]
required unit cells, as specified in data/UCS directory, to use for building the system

UC_RATIOS_LIST - probabilities [list]
probability list for the above unit cells, total probability must be 1.00

Example:

The following script will use the dioctohedral 2:1 unit cells, which are both neutral smectite unit cells, with the latter having 1 octohedral Al substitution for the Fe3.

This will produce a neutral smectite with the following stoichiometry: .

# required UCs to builder system as list
UC_INDEX_LIST: [D221 D228]

# probability list of unit cells in system
UC_RATIOS_LIST: [0.8 0.2]


Interlayer Solvent and Ions

IL_SOLV - interlayer solvent presence [bool] (Default: True)
If True interlayer space should be solvated, otherwise False will produce non-hydrated clay.

There are three options to handle interlayer water and interlayer ions, only one should be specified:

  1. ION_WATERS - number of waters per ion [int, Dict[str: int]]
    Number of water molecules that should be added per ion.
    If a single number [int] is given, all of the ions will be hydrated by the same number of waters.
    To specify number of waters per ion-type the entry should be a citionary, then the total number of water molecules will be mapped to the specifications given for each of the interlayer occupancies I in the CSV entry.

    Example:
    A given number of waters will be added for each cation, which quantity is specified in the clay stoichiometry CSV file.

      ION_WATERS: 
        Ca: 12
        Na: 12
        K: 10

  2. UC_WATERS - number of water molecules per unit cell [int]
    The specified number of water molecules multiplied by the number of unit cells is added into each of the interlayer spaces.

  3. SPACING_WATERS - hydrated interleyer spacing, in A [float] (Default 10.0 A)
    Target interlayer spacing filled with water, final value may vary due to the water rearrangement when in contact with clay surface and packing around ions.


Simulation Box Specifications

BOX_HEIGHT - simulation box height in A [float]
Size of the final simulation box in z-direction in A, note the clay layers are positioned in xy-plane.

BULK_SOLV - bulk solvent presence [bool] (Default: True)
If True the box space will be filled with water, otherwise False will keep the box empty. This is useful if further plan is to add other species, such as oil, into the system.

BULK_IONS - type of ions and their concentration in mol/L [int, Dict[str: int]]
Ions to be added into the bulk solvated space.
Note: GROMACS will not be happy if the system is not neutral!

Example:

This will create a simulation box of 120 A height, filled with 0.1 M NaCl solution.


# full simulation box height in A 
BOX_HEIGHT: 120.0

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

BULK_IONS:
  Na: 0.1
  Cl: 0.1


GROMACS version specification

Sometimes more than one version of GROMACS may be installed, this allows user to specify the one to use.

GMX - bash alias for your favourite GROMACS version [str]

Example:

To use your MPI-compiled version:

GMX: gmx_mpi


ClayCode.siminp System Specifications YAML file

ClayCode.simpinp reads the parameters specified in this file and generates simulation inputs for GROMACS.

Coming soon...