old_contents: """
  TherMOF command line interface.
  """
  import argparse
  from thermof import Simulation, Parameters, Trajectory
  from thermof.parameters import k_parameters, plot_parameters
  
  
  parser = argparse.ArgumentParser(
      description="""
  ----------------------------------------------------------------------------
  ████████╗██╗  ██╗███████╗██████╗ ███╗   ███╗ ██████╗ ███████╗
  ╚══██╔══╝██║  ██║██╔════╝██╔══██╗████╗ ████║██╔═══██╗██╔════╝
     ██║   ███████║█████╗  ██████╔╝██╔████╔██║██║   ██║█████╗
     ██║   ██╔══██║██╔══╝  ██╔══██╗██║╚██╔╝██║██║   ██║██╔══╝
     ██║   ██║  ██║███████╗██║  ██║██║ ╚═╝ ██║╚██████╔╝██║
     ╚═╝   ╚═╝  ╚═╝╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝ ╚═════╝ ╚═╝
  
  TherMOF: Thermal transport in Metal-Organic Frameworks
  -----------------------------------------------------------------------------
      """,
      epilog="""
  Example:
  python thermof_read.py IRMOF-1
  
  would read simulation results from IRMOF-1 directory.
  You would need a Lammps log file and simpar.yaml (produced by thermof) to be able to
  read simulation results.
      """,
      formatter_class=argparse.RawDescriptionHelpFormatter)
  
  
  default_params = {}
  
  # Positional arguments
  parser.add_argument('simdir', type=str, help='Lammps simulation directory.')
  
  # Optional arguments
  parser.add_argument('--setup', '-s', default='run', type=str, metavar='',
                      help='Simulation setup (run | trial | trial_set).')
  parser.add_argument('--no_parameters', '-np', action='store_true', default=False,
                      help='Dont read simulation parameters, use default.')
  parser.add_argument('--plot', '-p', action='store_true', default=False,
                      help='Plot HCACF, k, and thermodynamic properties.')
  parser.add_argument('--write', '-w', action='store_true', default=False,
                      help='Write results to a file.')
  
  # Parse arguments
  args = parser.parse_args()
  
  sim = Simulation()
  sim.read(args.simdir, setup=args.setup, read_parameters=(not args.no_parameters))
  
  # Plotting
  
new_contents: """
  TherMOF command line interface.
  """
  import os
  import argparse
  from thermof import Simulation, Parameters, Trajectory
  from thermof.parameters import k_parameters, plot_parameters
  
  
  parser = argparse.ArgumentParser(
      description="""
  ----------------------------------------------------------------------------
  ████████╗██╗  ██╗███████╗██████╗ ███╗   ███╗ ██████╗ ███████╗
  ╚══██╔══╝██║  ██║██╔════╝██╔══██╗████╗ ████║██╔═══██╗██╔════╝
     ██║   ███████║█████╗  ██████╔╝██╔████╔██║██║   ██║█████╗
     ██║   ██╔══██║██╔══╝  ██╔══██╗██║╚██╔╝██║██║   ██║██╔══╝
     ██║   ██║  ██║███████╗██║  ██║██║ ╚═╝ ██║╚██████╔╝██║
     ╚═╝   ╚═╝  ╚═╝╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝ ╚═════╝ ╚═╝
  
  TherMOF: Thermal transport in Metal-Organic Frameworks
  -----------------------------------------------------------------------------
      """,
      epilog="""
  Example:
  python thermof_read.py IRMOF-1
  
  would read simulation results from IRMOF-1 directory.
  You would need a Lammps log file and simpar.yaml (produced by thermof) to be able to
  read simulation results.
      """,
      formatter_class=argparse.RawDescriptionHelpFormatter)
  
  
  default_params = {}
  
  # Positional arguments
  parser.add_argument('simdir', type=str, help='Lammps simulation directory.')
  
  # Optional arguments
  parser.add_argument('--setup', '-s', default='run', type=str, metavar='',
                      help='Simulation setup (run | trial | trial_set).')
  parser.add_argument('--no_parameters', '-np', action='store_true', default=False,
                      help='Dont read simulation parameters, use default.')
  parser.add_argument('--plot', '-p', nargs='+', default=[],
                      help='Plot HCACF, k, and thermodynamic properties.')
  parser.add_argument('--write', '-w', action='store_true', default=False,
                      help='Write results to a file.')
  
  # Parse arguments
  args = parser.parse_args()
  
  # Initialize simulation and read
  sim = Simulation()
  simdir = os.path.abspath(args.simdir)
  sim.read(simdir, setup=args.setup, read_parameters=(not args.no_parameters))
  
  # Plotting
  if len(args.plot) > 0:
      sim.parameters.plot = plot_parameters.copy()
      for plt in args.plot:
          sim.parameters.plot[plt]['save'] = os.path.join(simdir, '%s-%s.png' % (os.path.basename(simdir), plt))
          sim.plot(plt)
  
subject: Add plotting option to CLI(read).