old_contents: """
  TherMOF command line interface.
  """
  import argparse
  
  
  parser = argparse.ArgumentParser(
      description="""
  ----------------------------------------------------------------------------
  ████████╗██╗  ██╗███████╗██████╗ ███╗   ███╗ ██████╗ ███████╗
  ╚══██╔══╝██║  ██║██╔════╝██╔══██╗████╗ ████║██╔═══██╗██╔════╝
     ██║   ███████║█████╗  ██████╔╝██╔████╔██║██║   ██║█████╗
     ██║   ██╔══██║██╔══╝  ██╔══██╗██║╚██╔╝██║██║   ██║██╔══╝
     ██║   ██║  ██║███████╗██║  ██║██║ ╚═╝ ██║╚██████╔╝██║
     ╚═╝   ╚═╝  ╚═╝╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝ ╚═════╝ ╚═╝
  
  TherMOF: Thermal transport in Metal-Organic Frameworks
  -----------------------------------------------------------------------------
      """,
      epilog="""
  Example:
  python thermof_write.py IRMOF-1.cif
  
  would read IRMOF-1 cif file, analyze topology, assign force field (default: UFF) and
  create input files for a Lammps simulation.
      """,
      formatter_class=argparse.RawDescriptionHelpFormatter)
  
  
  default_params = {}
  
  # Positional arguments
  parser.add_argument('molecule', type=str, help='Molecule file to read.')
  
  # Optional arguments
  parser.add_argument('--forcefield', '-ff', default='UFF', type=str, metavar='',
                      help='Force field for molecule file.')
  
  # Parse arguments
  args = parser.parse_args()
  
new_contents: """
  TherMOF command line interface.
  """
  import os
  import argparse
  from thermof import Simulation
  from thermof import Parameters
  
  
  parser = argparse.ArgumentParser(
      description="""
  ----------------------------------------------------------------------------
  ████████╗██╗  ██╗███████╗██████╗ ███╗   ███╗ ██████╗ ███████╗
  ╚══██╔══╝██║  ██║██╔════╝██╔══██╗████╗ ████║██╔═══██╗██╔════╝
     ██║   ███████║█████╗  ██████╔╝██╔████╔██║██║   ██║█████╗
     ██║   ██╔══██║██╔══╝  ██╔══██╗██║╚██╔╝██║██║   ██║██╔══╝
     ██║   ██║  ██║███████╗██║  ██║██║ ╚═╝ ██║╚██████╔╝██║
     ╚═╝   ╚═╝  ╚═╝╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝ ╚═════╝ ╚═╝
  
  TherMOF: Thermal transport in Metal-Organic Frameworks
  -----------------------------------------------------------------------------
      """,
      epilog="""
  Example:
  python thermof_write.py IRMOF-1.cif
  
  would read IRMOF-1 cif file, analyze topology, assign force field (default: UFF) and
  create input files for a Lammps simulation.
      """,
      formatter_class=argparse.RawDescriptionHelpFormatter)
  
  
  default_params = {}
  
  # Positional arguments
  parser.add_argument('molecule', type=str, help='Molecule file to read.')
  
  # Optional arguments
  parser.add_argument('--forcefield', '-ff', default='UFF', type=str, metavar='',
                      help='Force field for molecule file.')
  
  # Parse arguments
  args = parser.parse_args()
  
  # Initialize simulation
  simpar = Parameters()
  sim = Simulation(mof=args.molecule, parameters=simpar)
  mof_name = os.path.splitext(os.path.basename(args.molecule))[0]
  sim.simdir = os.path.join(os.path.dirname(args.molecule), mof_name)
  try:
      sim.initialize()
  except Exception as e:
      print(e)
  
subject: Add simulation initialization for CLI(write).