#gpt3 create a mogli xyz file using python for a molecule that is composed of a metal center and a radical, which consists of a cyclopentadienyl group and a methyl group. The metal center can be iron, nickel, or cobalt.

mog.py

#!/usr/bin/env python

import re
import sys
import itertools

import numpy as np

from mogli import *

def main():
  
  # check for correct usage
  if len(sys.argv) != 4:
    print ('Usage: mogli.py -m <metal> -r <radical1> -r <radical2>')
    return
  
  # process command line arguments
  metal = sys.argv[1]
  if metal not in ['Fe', 'Ni', 'Co']:
    print ('Error: invalid metal argument')
    return
  radicals = sys.argv[2:]
  if len(radicals) != 2:
    print ('Error: invalid number of radicals')
    return
  
  # build the molecule
  mol = Molecule()
  mol.add_atom(Atom(metal, 0.0, 0.0, 0.0))
  for radical in radicals:
    if radical == 'Cp*':
      mol.add_atom(Atom('C', 1.39, 0.0, 0.0))
      mol.add_atom(Atom('H', 1.39, 0.927, 0.0))
      mol.add_atom(Atom('H', 1.39, -0.927, 0.0))
      mol.add_atom(Atom('C', 0.0, 1.39, 0.0))
      mol.add_atom(Atom('H', 0.927, 1.39, 0.0))
      mol.add_atom(Atom('H', -0.927, 1.39, 0.0))
      mol.add_atom(Atom('C', -1.39, 0.0, 0.0))
      mol.add_atom(Atom('H', -1.39, -0.927, 0.0))
      mol.add_atom(Atom('H', -1.39, 0.927, 0.0))
      mol.add_atom(Atom('C', 0.0, -1.39, 0.0))
      mol.add_atom(Atom('H', 0.927, -1.39, 0.0))
      mol.add_atom(Atom('H', -0.927, -1.39, 0.0))
    elif radical == 'CH3':
      mol.add_atom(Atom('C', 0.0, 0.0, 1.2))
      mol.add_atom(Atom('H', 0.0, 0.0, 2.2))
      mol.add_atom(Atom('H', 0.0, 0.927, 1.2))
      mol.add_atom(Atom('H', 0.811, -0.464, 1.2))
      mol.add_atom(Atom('H', -0.811, -0.464, 1.2))
    else:
      print ('Error: invalid radical argument')
      return
  
  # write the xyz file
  with open('mogli.xyz', 'w') as fout:
    fout.write('%d\n\n' % len(mol.atoms))
    for atom in mol.atoms:
      fout.write('%-2s %f %f %f\n' % (atom.symbol, atom.x, atom.y, atom.z))

if __name__ == '__main__':
  main()
  
#mog.py -m Fe -r 'Cp*' -r 'CH3'