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 parseoutput-filename
- The file name and location for a lammps outputd
ordebug
- Used for debugging output, lines in cml.py will help print out debugging info can be specified anywhere in the inputh
orhelp
- 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.