pmutt.statmech.lsr.LSR

class pmutt.statmech.lsr.LSR(slope, intercept, reaction, surf_species=0.0, gas_species=0.0, notes=None)

Bases: _ModelBase

Represents a linear scaling relationship

\(\Delta E^{AH_x} = \alpha \Delta E^{A} + \beta\)

\(E^{AH_{x}^*}=\Delta E^{AH_x} + E^* + E^{AH_{x(g)}}\)

where:

Symbol	Description	Units
\(\Delta E^{AH_x}\)	Binding energy of adsorbate, AHx, on interested surface.	kcal/mol
\(\Delta E^{A}\)	Binding energy of adsorbate, A, on interested surface.	kcal/mol
\(\alpha\)	Slope of LSR	-
\(\beta\)	Intercept of LSR	kcal/mol
\(E^*\)	Electronic energy of interested surface.	kcal/mol
\(E^{AH_{x(g)}}\)	Electronic energy of AHx in the gas phase.	kcal/mol

slope

Slope of LSR relationship. Represents alpha in above equation

Type:

float

intercept

Intercept of LSR relationship in kcal/mol. Represents beta in above equation

Type:

float

reaction

Reaction to use to calculate reference binding energy. Binding energy calculated using get_delta_E and if that fails, get_delta_H. If the binding energy is specified as a float (in kcal/mol), it will be converted to a Reaction made of StatMech objects

Type:

float or Reaction object

surf_species

Surface species. If the surface’s energy is specified as a float (in kcal/mol), it will be converted to a StatMech object with a single ConstantMode mode. Default is 0.

Type:

float or StatMech object, optional

gas_species

Gas-phase species. If the gas’ energy is specified as a float (in kcal/mol), it will be converted to a StatMech object with a single ConstantMode mode. Default is 0.

Type:

float or StatMech object, optional

notes

Extra notes such as the source of the LSR. Default is None

Type:

str or dict, optional

Notes

If the LSR relationship represents the binding of an adsorbate (AHx) on surface (M2) relative to a reference surface (M1) (see equation below), you may still use this class.

\(\Delta E^{AH_x}_{M_2} = \alpha (\Delta E^{A}_{M_2} - \Delta E^{A}_{M_1}) + \Delta E^{AH_x}_{M_1}\)

The reaction inputted will represent the following stoichiometric reaction.

\(*_{(M_1)} + A^*_{(M_2)} \leftrightarrow A^*_{(M_1)} + *_{(M_2)}\)

__init__(slope, intercept, reaction, surf_species=0.0, gas_species=0.0, notes=None)

Methods

__init__(slope, intercept, reaction[, ...])
from_dict(json_obj)	Recreate an object from the JSON representation.
get_Cp(units, **kwargs)	Calculate the heat capacity (constant P)
get_CpoR()	Calculates the dimensionless heat capacity at constant pressure.
get_Cv(units, **kwargs)	Calculate the heat capacity (constant V)
get_CvoR()	Calculates the dimensionless heat capacity at constant volume.
get_F(units[, T])	Calculate the Helmholtz energy
get_FoRT([T])	Calculates the dimensionless Helmholtz energy using the LSR relationship
get_G(units[, T])	Calculate the Gibbs energy
get_GoRT([T])	Calculates the dimensionless Gibbs energy using the LSR relationship
get_H(units[, T])	Calculate the enthalpy
get_HoRT([T])	Calculates the dimensionless enthalpy using the LSR relationship
get_S(units, **kwargs)	Calculate the entropy
get_SoR()	Calculates the dimensionless entropy using the LSR relationship
get_U(units[, T])	Calculate the internal energy
get_UoRT([T])	Calculates the dimensionless internal energy using the LSR relationship
get_q()	Default method to calculate the partition coefficient.
to_dict()	Represents object as dictionary with JSON-accepted datatypes

Attributes

gas_species
reaction
surf_species

classmethod from_dict(json_obj)

Recreate an object from the JSON representation.

Parameters:

json_obj (dict) – JSON representation

Returns:

LSR

Return type:

LSR object

property gas_species

get_Cp(units, **kwargs)

Calculate the heat capacity (constant P)

Parameters:

• units (str) – Units as string. See R() for accepted units.

• kwargs (keyword arguments) – Parameters needed by get_CpoR

Returns:

Cp – Heat capacity (constant P) in appropriate units

Return type:

float

get_CpoR()

Calculates the dimensionless heat capacity at constant pressure.

\(\frac{C_V^{LSR}}{R}=0\)

get_Cv(units, **kwargs)

Calculate the heat capacity (constant V)

Parameters:

• units (str) – Units as string. See R() for accepted units.

• kwargs (keyword arguments) – Parameters needed by get_CvoR

Returns:

Cv – Heat capacity (constant V) in appropriate units

Return type:

float

get_CvoR()

Calculates the dimensionless heat capacity at constant volume.

\(\frac{C_V^{LSR}}{R}=0\)

get_F(units, T=298.15, **kwargs)

Calculate the Helmholtz energy

Parameters:

• units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters needed by get_FoRT

Returns:

F – Hemholtz energy in appropriate units

Return type:

float

get_FoRT(T=298.15, **kwargs)

Calculates the dimensionless Helmholtz energy using the LSR relationship

Parameters:

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

Returns:

FoRT – Dimensionless Helmholtz energy

Return type:

float

get_G(units, T=298.15, **kwargs)

Calculate the Gibbs energy

Parameters:

• units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters needed by get_GoRT

Returns:

G – Gibbs energy in appropriate units

Return type:

float

get_GoRT(T=298.15, **kwargs)

Calculates the dimensionless Gibbs energy using the LSR relationship

Parameters:

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

Returns:

GoRT – Dimensionless Gibbs energy

Return type:

float

get_H(units, T=298.15, **kwargs)

Calculate the enthalpy

Parameters:

• units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters needed by get_HoRT

Returns:

H – Enthalpy in appropriate units

Return type:

float

get_HoRT(T=298.15, **kwargs)

Calculates the dimensionless enthalpy using the LSR relationship

Parameters:

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

Returns:

HoRT – Dimensionless enthalpy

Return type:

float

get_S(units, **kwargs)

Calculate the entropy

Parameters:

• units (str) – Units as string. See R() for accepted units.

• kwargs (keyword arguments) – Parameters needed by get_SoR

Returns:

S – Entropy in appropriate units

Return type:

float

get_SoR()

Calculates the dimensionless entropy using the LSR relationship

Returns:

SoR – Dimensionless entropy. Since LSR handles binding energies, always returns 0

Return type:

float

get_U(units, T=298.15, **kwargs)

Calculate the internal energy

Parameters:

• units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters needed by get_UoRT

Returns:

U – Internal energy in appropriate units

Return type:

float

get_UoRT(T=298.15, **kwargs)

Calculates the dimensionless internal energy using the LSR relationship

Parameters:

• T (float, optional) – Temperature in K. Default is 298.15 K

• kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

Returns:

UoRT – Dimensionless internal energy

Return type:

float

get_q()

Default method to calculate the partition coefficient.

Returns:

q – Returns 1

Return type:

float

property reaction

property surf_species

to_dict()

Represents object as dictionary with JSON-accepted datatypes

Returns:

obj_dict

Return type:

dict