Clay stoicheometry in CSV format

Including into Input Parameter File

The .CSV file must be included into the INPUT .YAML file:

• the path to the CSV file is specified under CLAY_COMP,
• target occupancies from the CSV file are given by SYSNAME, corresponding to the clay name.

e.g.:

CLAY_COMP: /path/to/clay_comp.csv
SYSNAME: NAu-1-fe

File Structure

• First column: sheet

  • for tetrahedral (T) and octahedral (O) occupancies;
  • interlayer ion (I) ocupansies, if the total charge (tot second column) is non-zero;
  • T, O and total (tot) average unit cell charge (C).

• Second column with element:

  • Atom names (if atom is not supported by ClayFF.FF, ClayCode.builder will try to assign it to the supported atom of same charge and re-assign the ocupansies);
  • charges for the T layer, O layer and tot total;
  • The oxidation state of clay atoms can be specified by adding the charge after the element name (e.g. Fe2).

Rules

Occupancies:

• Total occupancies for each dioctahedral/trioctahedral tetrahedral (T) sheet should sum up to 4.
• For octahedral (O) sheets, the total occupancies should amount to 4/3 for dioctahedral/trioctahedral unit cell types, respectively.
• For example, the occupancies of a dioctahedral 2:1 clay (TOT) should have T occupancies of 8, and O occupancies of 4;
• Experimental stoichiometries do not necessarily sum up to interger occupancies. ClayCode.builder will first process the target composition such that the occupancies match those expected for the specified unit cell type.

Interlayer Ions:

• Interlayer ions will be added to compensate the total charge imbalance resulting from substitutions.
• The ratio of these ions can be specified in the I section. The sum of all ion contributions should sum to 1.
• Only ion species of the opposite sign to the layer charge will be considered.

Iron 2+/3+:

• There is no need to specify how much of the total iron is Fe3+ or Fe2+ if at least two values among the total, T and O unit cell charge are specified.
• ClayCode.builder can perform the splitting between the two iron species.

Supplied CSV file

The supplied file within directory Tutorial is exp_clay.csv and contains clay structures corresponding to the Source Clays listed under "Physical and Chemical Data of Source Clays" clays.org.

• 1:1 (TO) dioctohedral smectite:

  • Kaolin KGa-1;

• 2:1 (TOT) dioctohedral smectite:

  • Na-Montmorillonite (Wyoming) SWy-1,
  • Illite IMt-1,
  • Ferruginous Smectite SWa-1,
  • Nontronite NAu-1-fe,
  • Nontronite NAu-2-fe,
  • Nontronite NG-1;

• example Al-Mg 3:1 layered double hydroxide (not via clays.org):

  • LDH31.

Example

Example from clay_comp.csv file for NAu-1 and NAu-2 nontronite clays:

sheet	element	NAu-1-fe	NAu-2-fe
T	Si	6.98	7.55
T	Al	0.95	0.16
T	Fe3	0.07	0.29
O	Fe	3.61	3.54
O	Al	0.36	0.34
O	Mg	0.04	0.05
I	Ca	0.525	0.36
I	Na	0	0
I	Mg	0	0
I	K	0	0
I	Cl	0	0
C	T	-1.02	-0.45
C	O	-0.03	-0.27
C	tot	-1.05	-0.72