The OUTPUT directory:

The <OUTPATH> directory is specified in the YAML file

Output files inside <OUTPATH> directory:

  1. Sheet coordinates <SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>.gro

  2. Interlayer coordinates and topology (with solvent and/or ions) (if interlayer is solvated and/or clay has non-zero charge) <SYSNAME>_<X_CELLS>_<Y_CELLS>_interlayer.gro and <SYSNAME>_<X_CELLS>_<Y_CELLS>_interlayer.top

  3. (Solvated) clay sheet stack coordinates and topology <SYSNAME>_<X_CELLS>_<Y_CELLS>.gro and <SYSNAME>_<X_CELLS>_<Y_CELLS>.top

  4. Sheet stack coordinates and topology in extended box (if specfied box height > height of clay sheet stack) <SYSNAME>_<X_CELLS>_<Y_CELLS>_ext.gro and <SYSNAME>_<X_CELLS>_<Y_CELLS>_ext.top

  5. Sheet stack coordinates and topology in extended and solvated box (if bulk solvation is specified and specfied box height > height of clay sheet stack) <SYSNAME>_<X_CELLS>_<Y_CELLS>_solv.gro and <SYSNAME>_<X_CELLS>_<Y_CELLS>_solv.top

  6. Sheet stack coordinates and topology in extended and solvated box with ions (if bulk solvation is specified and specified box height > height of clay sheet stack) <SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions.gro and <SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions.top

  7. Sheet stack coordinates and topology in box after energy minimisation <SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.gro and <SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.top

  8. Sheet stack energy minimisation parameter file and log<SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.mdp and <SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>_em.log

  9. Setup log file <SYSNAME>_<X_CELLS>_<Y_CELLS>_<sheetnumber>.log

Example:

The output generated in the nontronite tutorial executing command:

ClayCode builder -f Tutorial/NAu1.yaml

asking to generate clay named NAu-1-fe using 7 x 5 x 3 unit cells, featuring adding interlayer water and ions and solvated.

The output files are as follows:

CWD
│   
│ 
└───Tutorials
│      NAu1.yaml
│      clay_conf.csv
│      ...
│   
└─── NAu-1-fe

    │   NAu-1-fe_exp_df.csv
    │   NAu-1-fe_match_df.csv
    │   NAu-1-fe_7_5_0.gro
    │   NAu-1-fe_7_5_1.gro
    │   NAu-1-fe_7_5_2.gro
    │   NAu-1-fe_7_5_interlayer.gro
    │   NAu-1-fe_7_5_interlayer.top
    │   NAu-1-fe_7_5.gro
    │   NAu-1-fe_7_5.top
    │   NAu-1-fe_7_5_ext.gro
    │   NAu-1-fe_7_5_ext.top
    │   NAu-1-fe_7_5_solv.gro
    │   NAu-1-fe_7_5_solv.top
    │   NAu-1-fe_7_5_solv_ions.mdp
    │   NAu-1-fe_7_5_solv_ions.log
    │   NAu-1-fe_7_5_solv_ions.gro
    │   NAu-1-fe_7_5_solv_ions.top
    │   NAu-1-fe_7_5_2307041912.log