Output Files

ClayCode.builder

There are a number of output files generated by ClayCode.builder. The OUTPATH directory is specified in the .yaml file and the created output folder and files will have the same name as the clay system, as specified in the .csv column header and .yaml SYSNAME parameter.

The output file structure, in the order of file creation, in the created <OUTPATH>/<SYSNAME>/ directory is as follows:

Clay Composition

<SYSNAME>_exp_df.csv | new target clay composition
<SYSNAME>_match_df.csv | unit-cell matched clay composition

Clay Sheets

<SYSNAME>_<X_CELLS>_<Y_CELLS>_0.gro
<SYSNAME>_<X_CELLS>_<Y_CELLS>_1.gro
…
<SYSNAME>_<X_CELLS>_<Y_CELLS>_<N_SHEETS>.gro

Interlayer Sheet

<SYSNAME>_<X_CELLS>_<Y_CELLS>_interlayer.gro
<SYSNAME>_<X_CELLS>_<Y_CELLS>_interlayer.top

Box Assembly

Combining Sheets

<SYSNAME>_<X_CELLS>_<Y_CELLS>.gro
<SYSNAME>_<X_CELLS>_<Y_CELLS>.top

Extending Box

Only created if YAML:BOX_HEIGHT is greater than the height of the sheet stack.

<SYSNAME>_<X_CELLS>_<Y_CELLS>_ext.gro
<SYSNAME>_<X_CELLS>_<Y_CELLS>_ext.top

Solvating Box

Only created if YAML:BULK_SOLV is True.

<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv.gro
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv.top

Adding Ions

Only created if YAML:BULK_IONS are specified and non-zero.

<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions.gro
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions.top

Energy Minimisation

An EM/ directory is created within <OUTPATH>/<SYSNAME>/ and energy minimistaion is performed by GROMACS.

<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions_em.mdp | MD parameter file
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions_em.edr | energy file
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions_em.gro | structure file
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions_em.top | topology file
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions_em.trr | full precision trajectory file
<SYSNAME>_<X_CELLS>_<Y_CELLS>_solv_ions_em.log | log file

Finished building

<SYSNAME>_<X_CELLS>_<Y_CELLS>_builder.log