.. _output_files: Output Files ============ ClayCode.builder ----------------- There are a number of output files generated by :code:`ClayCode.builder`. The :code:`OUTPATH` directory is specified in the :ref:`.yaml file ` and the created output folder and files will have the same name as the clay system, as specified in the :ref:`.csv ` column header and :ref:`.yaml ` :code:`SYSNAME` parameter. The output file structure, in the order of file creation, in the created :code:`//` directory is as follows: Clay Composition ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * :code:`_exp_df.csv` | new target clay composition * :code:`_match_df.csv` | unit-cell matched clay composition Clay Sheets ~~~~~~~~~~~~~ * :code:`___0.gro` * :code:`___1.gro` * ... * :code:`___.gro` Interlayer Sheet ~~~~~~~~~~~~~~~~~ * :code:`___interlayer.gro` * :code:`___interlayer.top` Box Assembly ~~~~~~~~~~~~~ Combining Sheets ***************** * :code:`__.gro` * :code:`__.top` Extending Box ************** Only created if :code:`YAML:BOX_HEIGHT` is greater than the height of the sheet stack. * :code:`___ext.gro` * :code:`___ext.top` Solvating Box ************** Only created if :code:`YAML:BULK_SOLV` is *True*. * :code:`___solv.gro` * :code:`___solv.top` Adding Ions ************ Only created if :code:`YAML:BULK_IONS` are specified and non-zero. * :code:`___solv_ions.gro` * :code:`___solv_ions.top` Energy Minimisation ~~~~~~~~~~~~~~~~~~~~ An :code:`EM/` directory is created within :code:`//` and energy minimistaion is performed by GROMACS. * :code:`___solv_ions_em.mdp` | MD parameter file * :code:`___solv_ions_em.edr` | energy file * :code:`___solv_ions_em.gro` | structure file * :code:`___solv_ions_em.top` | topology file * :code:`___solv_ions_em.trr` | full precision trajectory file * :code:`___solv_ions_em.log` | log file Finished building ~~~~~~~~~~~~~~~~~~ * :code:`___builder.log`