surfinpy.p_vs_t

Functions related to the generation of surface phase diagrams as a function of pressure and temperature. An explanation of theory can be found here <theory.html>

surfinpy.p_vs_t.adsorption_energy(data, stoich, adsorbant_t)[source]

From the dft data provided - calculate the adsorbation energy of a species at the surface.

Parameters:
  • data (list) – list of dictionaries containing info about each calculation
  • stoich (dict) – info about the stoichiometric surface calculation
  • adsorbant_t (array like) – dft energy of adsorbing species as a function of temperature
Returns:

AE – Adsorbtion energy of adsorbing species in each calculation as a function of temperature
Return type:

array like
surfinpy.p_vs_t.calculate(stoich, data, SE, adsorbant, thermochem, coverage=None)[source]

Collects input variables and intitialises the calculation.

Parameters:
  • stoich (dictionary) – information about the stoichiometric surface
  • data (list) – list of dictionaries containing information on the “adsorbed” surfaces
  • SE (float) – surface energy of the stoichiomteric surface
  • adsorbant (float) – dft energy of adsorbing species
  • coverage (array like (default None)) – Numpy array containing the different coverages of adsorbant.
  • thermochem (array like) – Numpy array containing thermochemcial data downloaded from NIST_JANAF for the adsorbing species.
Returns:

system – plotting object
Return type:

class object
surfinpy.p_vs_t.calculate_adsorption_energy(adsorbed_energy, slab_energy, n_species, adsorbant_t)[source]

Calculates the adsorption energy in units of eV

Parameters:
  • adsorbed_energy (float) – slab energy of slab and adsorbed species from DFT
  • slab_energy (float) – bare slab energy from DFT
  • n_species (int) – number of adsorbed species at the surface
  • adsorbant_t (array like) – dft energy of adsorbing species as a function of temperature
Returns:

adsorption energy as a function of temperature
Return type:

array like
surfinpy.p_vs_t.calculate_surface_energy(AE, lnP, T, coverage, SE, nsurfaces)[source]

Calculates the surface energy as a function of pressure and temperature for each surface system according to

\[\gamma_{adsorbed, T, p} = \gamma_{bare} + (C(E_{ads, T} - RTln(\frac{p}{p^o})\]

where \(\gamma_{adsorbed, T, p}\) is the surface energy of the surface with adsorbed species at a given temperature and pressure, \(\gamma_{bare}\) is the suface energy of the bare surface, C is the coverage of adsorbed species, \(E_{ads, T}\) is the adsorption energy, R is the gas constant, T is the temperature, and \(\frac{p}{p^o}\) is the partial pressure.

Parameters:
  • AE (list) – list of adsorption energies
  • lnP (array like) – full pressure range
  • T (array like) – full temperature range
  • coverage (array like) – surface coverage of adsorbing species in each calculation
  • SE (float) – surface energy of stoichiomteric surface
  • data (list) – list of dictionaries containing info on each surface
  • nsurfaces (int) – total number of surface
Returns:

SE_array – array of integers corresponding to lowest surface energies
Return type:

array like
surfinpy.p_vs_t.convert_adsorption_energy_units(AE)[source]

Converts the adsorption energy into units of KJ/mol

Parameters:AE (array like) – array of adsorption energies
Returns:array of adsorption energies in units of KJ/mol
Return type:array like
surfinpy.p_vs_t.inititalise(thermochem, adsorbant)[source]

Builds the numpy arrays for each calculation.

Parameters:
  • thermochem (array like) – array containing NIST_JANAF thermochemical data
  • adsorbant (float) – dft energy of adsorbing species
Returns:

  • lnP (array like) – numpy array of pressure values
  • logP (array like) – log of lnP (hard coded range -13 - 5.0)
  • T (array like) – array of temperature values (hard coded range 2 - 1000 K)
  • adsrobant_t (array like) – dft values of adsorbant scaled to temperature