Electrochemistry - SUNCAT-Center/catmap GitHub Wiki

Electrochemistry in CatMAP is implemented as a set of thermodynamic corrections in the enthalpy_entropy module. To run models containing electrochemical reactions in CatMAP, the user needs to provide the following in addition to all of the typical components of a CatMAP model described in the tutorials:

• A fictitious gas molecule called 'pe' that represents the free energy of a proton-electron pair at 0V vs RHE. As part of the Computational Hydrogen Electrode, this species should have the same free energy of 1/2 of a molecule of H₂ gas. This species's energy (usually 0 if an H₂ reference is used) should be defined in the input file of energies.
• In the reaction definitions, any reaction involving the use of a proton-electron pair should have the pe_g gas molecule in the initial (if reductive) or final (if oxidative) state. In addition, in the reaction definitions and input file, transition states for these reactions should contain pe in the species name. For example, the reduction of adsorbed oxygen to adsorbed OH can be written as 'O* + pe_g <-> O-pe* -> OH*'.
• A voltage (vs RHE) defined as a parameter in the .mkm file e.g. voltage = -0.2
• A transfer coefficient defined as a parameter in the .mkm file e.g. beta = 0.5
• In the .mkm file, electrochemical_thermo_mode can be specified to one of three possible values (defaults to simple_electrochemical): simple_electrochemical, hbond_electrochemical, and hbond_with_estimates_electrochemical. "simple" only adds free energy corrections to adsorbates and transition states to account for voltage and beta. "hbond" will take a default or user-provided hbond_dict to correct each species for hydrogen bonding stabilization (see catmap/data/hbond_data.py for the default hbond_dict). "hbond_with_estimates" attempts to estimate a hydrogen bonding correction for a given species based on its chemical formula. This is a very crude process that is described in catmap/thermodynamics/enthalpy_entropy.py.

There are two provided examples of using electrochemistry in CatMAP in the tutorials/electrochemistry directory. The HER example shows the hydrogen evolution reaction in the low-coverage limit, and the provided README file explains the details of the simplest of electrochemical reactions as done in CatMAP. The ORR example is meant to reproduce the results discussed in Hansen et al. (2014) DOI: 10.1021/jp4100608, which used a home-spun microkinetic model. The README in that directory goes into depth on how you can replicate some of the major features of this work with the provided scripts.