old_contents: from hoomd_script import *
  import random
  from math import pi
  from hoomd_util import try_restart, make_write_restart_file_callback
  
  def simulate(max_walltime, N, density, epsilon, sigma, r_cut, T, random_seed, num_steps, tau):
      if init.is_initialized():
          init.reset()
  
      density /= 100
      r = sigma / 2
      phi_p = 4.0 / 3 * pi * pow(r, 3) * density
  
      try:
          system = try_restart('restart.xml')
      except FileNotFoundError:
          system = init.create_random(
              N = N, phi_p = phi_p, seed = int(random_seed))
          dump.xml('init.xml', vis = True)
  
      # simple lennard jones potential
      lj = pair.lj(r_cut=3.0)
      lj.pair_coeff.set('A', 'A', epsilon=epsilon, sigma=sigma)
  
      # integrate forward in the nvt ensemble
      all = group.all()
      integrate.mode_standard(dt=0.005)
      integrate.nvt(group=all, T = T, tau = tau)
  
      # Setup thermal analysis log
      analyze.log(
          filename = 'thermal.log',
          quantities = ['time', 'volume', 'temperature', 'pressure', 'potential_energy'],
          period = num_steps * 1e-4)
  
      dump.xml('init.xml', vis = True)
      # Setup trajectory storage
      dumping_period = max(1, int(num_steps / 10))
      dump.dcd(
          filename = 'trajectory.dcd',
          period = dumping_period)
  
      # run for 20k steps
      restart_callback = make_write_restart_file_callback('restart.xml')
      def callback(num_steps):
          from signac.contrib import walltime
          restart_callback(num_steps)
          walltime.exit_by(max_walltime)
  
      restart_period = max(1000, int(num_steps / 10))
      run_upto(num_steps, callback=callback, callback_period=restart_period)
  
new_contents: from hoomd_script import *
  from math import pi
  from hoomd_util import try_restart, make_write_restart_file_callback
  
  def simulate(max_walltime, N, density, epsilon, sigma, r_cut, T, random_seed, num_steps, tau):
      if init.is_initialized():
          init.reset()
  
      density /= 100
      r = sigma / 2
      phi_p = 4.0 / 3 * pi * pow(r, 3) * density
  
      try:
          try_restart('restart.xml')
      except FileNotFoundError:
          init.create_random(
              N = N, phi_p = phi_p, seed = int(random_seed))
          dump.xml('init.xml', vis = True)
  
      # simple lennard jones potential
      lj = pair.lj(r_cut=3.0)
      lj.pair_coeff.set('A', 'A', epsilon=epsilon, sigma=sigma)
  
      # integrate forward in the nvt ensemble
      all = group.all()
      integrate.mode_standard(dt=0.005)
      integrate.nvt(group=all, T = T, tau = tau)
  
      # Setup thermal analysis log
      analyze.log(
          filename = 'thermal.log',
          quantities = ['time', 'volume', 'temperature', 'pressure', 'potential_energy'],
          period = num_steps * 1e-4)
  
      dump.xml('init.xml', vis = True)
      # Setup trajectory storage
      dumping_period = max(1, int(num_steps / 10))
      dump.dcd(
          filename = 'trajectory.dcd',
          period = dumping_period)
  
      # run for 20k steps
      restart_callback = make_write_restart_file_callback('restart.xml')
      def callback(num_steps):
          from signac.contrib import walltime
          restart_callback(num_steps)
          walltime.exit_by(max_walltime)
  
      restart_period = max(1000, int(num_steps / 10))
      run_upto(num_steps, callback=callback, callback_period=restart_period)
  
subject: Remove unnecessary variable definition.