old_contents: 
  """Example of irreversible reaction."""
  
  import os
  from chemkinlib.utils import Parser
  from chemkinlib.utils import visualizer
  from chemkinlib.reactions import ReactionSystems
  from chemkinlib.config import DATA_DIRECTORY
  import numpy
  
  # USER INPUT: reaction (xml) file
  xml_filename = os.path.join(DATA_DIRECTORY, "rxnset_long.xml")
  
  parser = Parser.ReactionParser(xml_filename)
  
  # USER INPUTS (concentrations and temperatures)
  concentration = ({'H':1, 'H2':1, 'H2O':0, 'H2O2':1, 'HO2':1, 'O':1, "O2":1, "OH":1})
  temperature = 1000
  
  
  # Set up reaction system
  rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
                          parser.NASA_poly_coefs,
                          temperature,
                          concentration)
  
  target = "outputs/"
  graph_dict = {'node_color':True,'rate':False,'arrow_size':True,'arrow_color':True,'init_con':True,'prod_con': True}
  #compute the concentration change with timestep
  
  for i in range(3):
      graph = visualizer.ReactionPathDiagram(target+str(i), rxnsys, integrate=True, time=1e-15, cluster=True)
      graph.fit()
      graph.connect(graph_dict, size=5, separate = True)
      graph.plot()
  
  imgs = [target+str(i)+".gv.png" for i in range(3)]
  graph.create_video(imgs, target)
  
  # Compute and sort reaction rates
  rxnrates_dict = rxnsys.sort_reaction_rates()
  
  # display reaction rates by species
  for k, v in rxnrates_dict.items():
      print("d[{0}]/dt : \t {1:e}".format(k, v))
  
  
  
  
  
new_contents: 
  """Example of irreversible reaction."""
  
  import os
  from chemkinlib.utils import Parser
  from chemkinlib.utils import visualizer
  from chemkinlib.reactions import ReactionSystems
  from chemkinlib.config import DATA_DIRECTORY
  import numpy
  
  # USER INPUT: reaction (xml) file
  xml_filename = os.path.join(DATA_DIRECTORY, "rxnset_long.xml")
  
  parser = Parser.ReactionParser(xml_filename)
  
  # USER INPUTS (concentrations and temperatures)
  concentration = ({'H':1, 'H2':1, 'H2O':0, 'H2O2':1, 'HO2':1, 'O':1, "O2":1, "OH":1})
  temperature = 1000
  
  
  # Set up reaction system
  rxnsys = ReactionSystems.ReactionSystem(parser.reaction_list,
                          parser.NASA_poly_coefs,
                          temperature,
                          concentration)
  
  target = "outputs/"
  graph_dict = {'node_color':True,'rate':False,'arrow_size':True,'arrow_color':True,'init_con':True,'prod_con': True}
  #compute the concentration change with timestep
  
  for i in range(3):
      graph = visualizer.ReactionPathDiagram(target+str(i), rxnsys, integrate=True, time=1e-15, cluster=True)
      graph.fit()
      graph.connect(graph_dict, size=5, separate = True)
      graph.plot()
  
  imgs = [target+str(i)+".gv.png" for i in range(3)]
  graph.create_video(imgs, target+'output_video')
  
  # Compute and sort reaction rates
  rxnrates_dict = rxnsys.sort_reaction_rates()
  
  # display reaction rates by species
  for k, v in rxnrates_dict.items():
      print("d[{0}]/dt : \t {1:e}".format(k, v))
  
  
  
  
  
subject: Update irrev_rxns.py