Electrochemistry

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.
• 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)