CSV File

For the .csv file to be read by ClayCode.builder, the relative path needs to be referenced in the .yaml file. See Input files: YAML more for information. A CSV file is supplied with ClayCode within the Tutorial directory. The file (exp_clay.csv) contains clay structures from the Clay Mineral Society’s Source Clays. 1,2

File Structure

The file should be comprised of at least 3 columns:

  • First column - sheet with each row containing one of the following options:

    • T for tetrahedral occupancies

    • O for octahedral occupancies

    • I for interlayer ion occupancies (if the total layer charge is non-zero)

    • C for the tetrahedral, octahedral and total unit cell charges

  • Second column - element containing either:

    • Atom names

      • The oxidation state of clay atoms can be specified by adding the charge after the element name (e.g. Fe2)

      • If the specified atom is not supported by ClayFF.ff, ClayCode.builder will try to assign it to a supported atom of same charge and re-assign the occupancies

    • Whether the charge (sheet: C) is for the T layer, O layer or the tot total

  • Subsequent columns - the clay name(s) with each row giving the corresponding value for that clay. One of these should match the SYSNAME option in the corresponding .yaml file.

CSV structure

The file structure for the CSV file.

Iron Oxidation State

There is no need to specify how much of the total iron content is Fe2+ or Fe3+ if at least two charge values are given (T layer, O layer or the tot total). ClayCode.builder will determine the iron content splitting based on these values.

Rules

Occupancies:

  • Tetrahedral (T) unit cell occupancies should sum to 4 for each sheet

  • Dioctahedral (O) unit cell occupancies should sum to 4 for each sheet

  • Trioctahedral (O) unit cell occupancies should sum to 3 for each sheet

For example, a dioctahedral 2:1 clay (TOT) should have 8 tetrahedral occupancies and 4 octahedral occupancies

Experimental stoichiometries do not necessarily sum up to integer 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 T and O sheet substitutions

  • The sum of all ion contributions should be 1

  • Only ion species of the opposite sign to the layer charge will be considered

Example File

For the Nontronite tutorial clays NAu-1 and NAu-2, the CSV file would be written as follows:

sheet

element

NAu-1

NAu-2

T

Si

6.98

7.55

T

Al

0.95

0.16

T

Fe3

0.07

0.29

O

Al

0.36

0.34

O

Fe

3.61

3.54

O

Mg

0.04

0.05

I

Ca

0.525

0.36

C

T

-1.02

-0.45

C

O

-0.03

-0.27

C

tot

-1.05

-0.72
1

J Fripiat and H van Olphen, editors. Data Handbook for Clay Minerals and Other Non-metallic Minerals. Pergamon Press, 1979.

2

Clay Mineral Society. Physical and chemical data of source clays. URL: https://www.clays.org/sourceclays_data/.