Modify Chemical Spectroscopy LAMMPS Tool to better support general inputs for LAMMPS simulations

McDonnell, Marshallrequested to merge
187-lammps-need-better-input-setup-for-tool into dev

Summary of Changes

This updates the chemical spectroscopy lammps tool.

Work for this tool includes:

  • Adding optional filename inputs (force field filenames, starting structure data filenames, and dump output filenames)
  • These new optional filename can change the filenames used in the input file
  • The force field file type is changed from binary -> txt so we can upload non-binary files used by lammps force fields

Checklist

  • The MR has a clear and concise title
  • Code is self-documented and follows style guidelines.
  • Automated tests are written and pass successfully.
  • Regression tests (e.g. manually triggered system tests, manual GUI/tool tests, ...) are performed to make sure the MR does not break anything (when applicable)
  • Readme file is present and up-to-date.

Documentation Updates

Additional Notes

Closes #187 (closed)

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