Parses avogadro created .cml files

Uses a command line argument specifying the location of the file to parse. It doesn't check the filename for the extention cml, so be sure it is a cml file otherwise there may be issues.

There are a few command line flags to be aware of (show in parens):

python cml.py (cml-filename) (output-filename) (d)

• cml-filename - The name and location of the cml file you would like to parse
• output-filename - The file name and location for a lammps output
• d or debug - Used for debugging output, lines in cml.py will help print out debugging info can be specified anywhere in the input
• h or help - Used when you are unsure on how to write a lammps file
• -f (file) - Specifies there is an lammps input file that just needs read_data changed. File is the input file

An example of use would be:

python cml.py -imol molecules/smdppeh.cml -od outputs/data.molecule_smdppeh -oi outputs/in.molecule_smdppeh -d for molecules

or python cml.py -imono monomers/p3htn.cml -od outputs/data.monomer_p3ht -oi outputs/data.monomer_p3ht -d for monomers

This would effectively run the program, using the molecules/smdppeh.cml molecule as its input. The flag outputs/data.first is the data file to output and for lammps to read. It also states outputs/in.rewriteout as the file to input into lammps The final d at the end is to get some debugging output.