ReactionEnergyDiagram [RED]: Plotting reaction mechanisms and reaction energetics using Python

Table of Contents

• Installation
• Structure of the repository
• Usage
• License
• How to cite

How to install:

• You can install the library as: pip install git+https://github.com/hitarth64/ReactionEnergyDiagram

Structure of the repository:

• Most of the functionality is contained inside the ReactionEnergyDiagaram/ReactionEnergyDiagaram.py

Usage:

• To use the ReactionEnergyDiagram package, simply import it as:

  from ReactionEnergyDiagram import ReactionEnergyDiagram

• An example for showing Oxygen Evolution Reaction (OER) over RuCrMnO₂ catalyst

  from ReactionEnergyDiagram import ReactionEnergyDiagram
  rde = ReactionEnergyDiagram(spacing=0.3, epsilon=0.3, figsize=(10,7))
  
  rde.add_step('*',0)
  rde.add_step('*O', -0.320865,connect=True, linestyle='dotted', legend=r'RuCrMnO$_2$')
  rde.add_step('*OH', 1.424233,connect=True, linestyle='dotted')
  rde.add_step('*OOH', 1.508143,connect=True, linestyle='dotted')
  rde.add_step(r'O$_2$', 2.308490,connect=True, linestyle='dotted')
  
  # Save the figure as 'ReactionMechanism.png'
  rde.plot(save=False, filename='ReactionMechanism.png')
  

  The result is:

• You can also plot multiple reactions in the same diagram to compare different reaction energetics and pathways. Key is to use superimpose function before inserting a new reaction.

  from ReactionEnergyDiagram import ReactionEnergyDiagram
  red = ReactionEnergyDiagram(spacing=0.3, epsilon=0.3, figsize=(10,7))
  
  red.add_step('*',0)
  red.add_step('*O', -0.320865,connect=True, linestyle='dotted', legend=r'RuCrMnO$_2$')
  red.add_step('*OH', 1.424233,connect=True, linestyle='dotted')
  red.add_step('*OOH', 1.508143,connect=True, linestyle='dotted')
  red.add_step(r'O$_2$', 2.308490,connect=True, linestyle='dotted')
  
  red.superimpose() # resets the internal counters and pointers
  red.add_step('*',0)
  red.add_step(None, -1.140617,connect=True, linestyle='dotted', color='red', legend=r'RuCrMnSbO$_2$')
  red.add_step(None, 2.097738,connect=True, linestyle='dotted', color='red')
  red.add_step(None, 1.792776,connect=True, linestyle='dotted', color='red')
  red.add_step(None, 2.170103,connect=True, linestyle='dotted', color='red')
  
  # Save the figure as 'ReactionMechanism.png'
  rde.plot(save=False, filename='TwoReactionMechanisms.png')
  

  The result is:

  

License:

ReactionEnergyDiagram is released under the MIT License.