old_contents: """
  Sample input files for predicting thermal conductivity of porous crystals using Lammps
  """
  import os
  
  
  sample_dir = os.path.abspath(os.path.dirname(__file__))
  # Lammps input file with thermal flux measured in single direction
  single_inp_path = os.path.join(sample_dir, 'in_single.cond.sample')        # Single MOF
  # Lammps input file with thermal flux measured in three directions
  single_inp3_path = os.path.join(sample_dir, 'in3_single.cond.sample')      # Single MOF
  ipmof_inp3_path = os.path.join(sample_dir, 'in3_ipmof.cond.sample')        # Interpenetrated MOF
  # Lammps structure files
  single_data_path = os.path.join(sample_dir, 'lammps_single.data.sample')   # Single MOF
  ipmof_data_path = os.path.join(sample_dir, 'lammps_ipmof.data.sample')     # Interpenetrated MOF
  # Job submission file for Frank
  qsub_path = os.path.join(sample_dir, 'lammps_qsub.sh.sample')
  
  samples = dict(ideal_mof=dict(inp=single_inp3_path, data=single_data_path, qsub=qsub_path),
                 ideal_interpenetrated_mof=dict(inp=ipmof_inp3_path, data=ipmof_data_path, qsub=qsub_path))
  
new_contents: """
  Sample input files for predicting thermal conductivity of porous crystals using Lammps
  """
  import os
  from thermof import Simulation, Trajectory
  from thermof.parameters import k_parameters
  
  
  sample_dir = os.path.abspath(os.path.dirname(__file__))
  # Lammps input file with thermal flux measured in single direction
  single_inp_path = os.path.join(sample_dir, 'in_single.cond.sample')        # Single MOF
  # Lammps input file with thermal flux measured in three directions
  single_inp3_path = os.path.join(sample_dir, 'in3_single.cond.sample')      # Single MOF
  ipmof_inp3_path = os.path.join(sample_dir, 'in3_ipmof.cond.sample')        # Interpenetrated MOF
  # Lammps structure files
  single_data_path = os.path.join(sample_dir, 'lammps_single.data.sample')   # Single MOF
  ipmof_data_path = os.path.join(sample_dir, 'lammps_ipmof.data.sample')     # Interpenetrated MOF
  # Job submission file for Frank
  qsub_path = os.path.join(sample_dir, 'lammps_qsub.sh.sample')
  
  samples = dict(ideal_mof=dict(inp=single_inp3_path, data=single_data_path, qsub=qsub_path),
                 ideal_interpenetrated_mof=dict(inp=ipmof_inp3_path, data=ipmof_data_path, qsub=qsub_path))
  
  
  tests_dir = os.path.join(sample_dir, '..', '..', 'tests')
  
  
  def load_sample_simulation(mof='single', setup='run', tests_dir=tests_dir, parameters=k_parameters.copy()):
      """ Load a sample simulation object from the tests directory """
      if mof == 'single':
          trial = os.path.join(tests_dir, 'ideal-mof-trial')
          if setup == 'run':
              sample_simulation = Simulation(read=os.path.join(trial, 'Run1'), setup='run', parameters=parameters)
          elif setup == 'trial':
              sample_simulation = Simulation(read=trial, setup='trial', parameters=parameters)
      else:
          trial = os.path.join(tests_dir, 'ip-mof-trial')
          if setup == 'run':
              sample_simulation = Simulation(read=os.path.join(trial, 'Run1'), setup='run', parameters=parameters)
          elif setup == 'trial':
              sample_simulation = Simulation(read=trial, setup='trial', parameters=parameters)
      return sample_simulation
  
  
  def load_sample_trajectory(mof='single', tests_dir=tests_dir):
      """ Load a sample trajectory file from tests directory """
      if mof == 'single':
          sample_traj = Trajectory(read=os.path.join(tests_dir, 'ideal-mof-trial', 'Run1', 'traj.xyz'))
      else:
          sample_traj = Trajectory(read=os.path.join(tests_dir, 'ip-mof-trial', 'Run1', 'traj.xyz'))
      return sample_traj
  
subject: Add functions to load sample traj and sim objects