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AROMODEL

For a more indepth look at AROMODEL look at DETAIL.md

Parses avogadro created .cml files

Performs electronic structure calculations using NWCHEM

Performs MD simulations using LAMMPS

Meant for use on XSEDE National Supercomputing Resources

Developed by Samuel Root, and CJ Pais

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.

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Molecular Dynamics Force Field Builder

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