catmap.scalers package

Submodules

catmap.scalers.generalized_linear_scaler module

class catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler(reaction_model=None)[source]

Bases: catmap.scalers.scaler_base.ScalerBase

TODO:
__getattr__(attr)

Return the value of the reaction model instance if its there. Otherwise return the instances own value (or none if the instance does not have the attribute defined and the attribute is not private)

__init__(reaction_model=None)[source]
__module__ = 'catmap.scalers.generalized_linear_scaler'
__setattr__(attr, val)

Set attribute for the instance as well as the reaction_model instance

get_adsorbate_coefficient_matrix()[source]

Calculate coefficients for scaling all adsorbates and transition states using constrained optimization. Store results in self.total_coefficient_dict and return the coefficient matrix for the adsorbates only.

get_coefficient_matrix()[source]
TODO:
get_electronic_energies(descriptors)[source]
TODO:
get_energetics(descriptors)
get_enthalpies(descriptors, **kwargs)
get_entropies(descriptors, **kwargs)
get_formation_energy_interaction_parameters(descriptors)[source]
TODO:
get_formation_energy_parameters(descriptors)[source]
TODO:
get_free_energies(descriptors, **kwargs)
get_rxn_parameters(descriptors, *args, **kwargs)[source]
TODO:
get_thermodynamic_energies(**kwargs)
get_total_enthalpies(descriptors, **kwargs)
get_transition_state_coefficient_matrix()[source]
TODO:
get_transition_state_scaling_matrix()[source]
TODO:
parameterize()[source]
TODO:
parse_constraints(constraint_dict)[source]

This function converts constraints which are input as a dictionary to lists compatible with the function to obtain scaling coefficients.

set_output_attrs(descriptors)

Function to set output information.

summary_text()[source]
TODO:

catmap.scalers.null_scaler module

class catmap.scalers.null_scaler.NullScaler(reaction_model=None)[source]

Bases: catmap.scalers.scaler_base.ScalerBase

Scaler which passes descriptor values directly to solver

__getattr__(attr)

Return the value of the reaction model instance if its there. Otherwise return the instances own value (or none if the instance does not have the attribute defined and the attribute is not private)

__init__(reaction_model=None)

Class for `scaling’ descriptors to free energies of reaction and activation (or other parameters). This class acts as a base class to be inherited by other scaler classes, but is not functional on its own.

This class contains the description of the microkinetic model (adsorbate_names, gas_names, etc.) along with the temperature and gas_pressures. In most cases these will automatically be populated by the parent reaction_model class. The scaler-specific attributes are:

gas_energies: defines the energies of the gas-phase species.
This sets the references for the system.
gas_thermo_mode: the mode for obtaining thermal contributions in
the gas phase. Default is to use the ideal gas approxmation.
adsorbate_thermo_mode: the mode for obtaining thermal contributions
from adsorbed species. Default is to use the harmonic adsorbate approximation.
frequency_dict: a dictionary of vibrational frequencies (in eV) for
each gas/adsorbate. Should be of the form frequency_dict[ads] = [freq1, freq2,…]. Needed for ideal gas, harmonic adsorbate, or hindered adsorbate approximations.

A functional derived scaler class must also contain the methods:

get_electronic_energies(descriptors): a function to `scale’ the
descriptors to electronic energies. Returns a dictionary of the electronic energies of each species in the model.
get_energetics(descriptors): a function to obtain the reaction
energetics from the descriptors. Should return a list of length N (number of elementary reactions): [[E_rxn1,E_a1],[E_rxn2,E_a2],…[E_rxnN,E_aN]]
get_rxn_parameters(descriptors): a function to obtain all necessary
reaction parameters from the descriptors. Should return a list of length N (number of elementary reactions): [[param1_rxn1,param2_rxn1…]…[param1_rxnN,param2_rxnN…]]. For a simple model this could be the same as get_energetics, but models accounting for interactions may require more parameters which can be scaled.
__module__ = 'catmap.scalers.null_scaler'
__setattr__(attr, val)

Set attribute for the instance as well as the reaction_model instance

get_electronic_energies(descriptors)[source]
get_energetics(descriptors)
get_enthalpies(descriptors, **kwargs)
get_entropies(descriptors, **kwargs)
get_free_energies(descriptors, **kwargs)
get_rxn_parameters(descriptors)[source]
get_thermodynamic_energies(**kwargs)
get_total_enthalpies(descriptors, **kwargs)
set_output_attrs(descriptors)

Function to set output information.

summary_text()

catmap.scalers.scaler_base module

class catmap.scalers.scaler_base.ScalerBase(reaction_model=None)[source]

Bases: catmap.ReactionModelWrapper

__getattr__(attr)

Return the value of the reaction model instance if its there. Otherwise return the instances own value (or none if the instance does not have the attribute defined and the attribute is not private)

__init__(reaction_model=None)[source]

Class for `scaling’ descriptors to free energies of reaction and activation (or other parameters). This class acts as a base class to be inherited by other scaler classes, but is not functional on its own.

This class contains the description of the microkinetic model (adsorbate_names, gas_names, etc.) along with the temperature and gas_pressures. In most cases these will automatically be populated by the parent reaction_model class. The scaler-specific attributes are:

gas_energies: defines the energies of the gas-phase species.
This sets the references for the system.
gas_thermo_mode: the mode for obtaining thermal contributions in
the gas phase. Default is to use the ideal gas approxmation.
adsorbate_thermo_mode: the mode for obtaining thermal contributions
from adsorbed species. Default is to use the harmonic adsorbate approximation.
frequency_dict: a dictionary of vibrational frequencies (in eV) for
each gas/adsorbate. Should be of the form frequency_dict[ads] = [freq1, freq2,…]. Needed for ideal gas, harmonic adsorbate, or hindered adsorbate approximations.

A functional derived scaler class must also contain the methods:

get_electronic_energies(descriptors): a function to `scale’ the
descriptors to electronic energies. Returns a dictionary of the electronic energies of each species in the model.
get_energetics(descriptors): a function to obtain the reaction
energetics from the descriptors. Should return a list of length N (number of elementary reactions): [[E_rxn1,E_a1],[E_rxn2,E_a2],…[E_rxnN,E_aN]]
get_rxn_parameters(descriptors): a function to obtain all necessary
reaction parameters from the descriptors. Should return a list of length N (number of elementary reactions): [[param1_rxn1,param2_rxn1…]…[param1_rxnN,param2_rxnN…]]. For a simple model this could be the same as get_energetics, but models accounting for interactions may require more parameters which can be scaled.
__module__ = 'catmap.scalers.scaler_base'
__setattr__(attr, val)

Set attribute for the instance as well as the reaction_model instance

get_electronic_energies(descriptors)[source]
get_energetics(descriptors)[source]
get_enthalpies(descriptors, **kwargs)[source]
get_entropies(descriptors, **kwargs)[source]
get_free_energies(descriptors, **kwargs)[source]
get_rxn_parameters(descriptors)[source]
get_thermodynamic_energies(**kwargs)[source]
get_total_enthalpies(descriptors, **kwargs)[source]
set_output_attrs(descriptors)[source]

Function to set output information.

summary_text()[source]

catmap.scalers.thermodynamic_scaler module

class catmap.scalers.thermodynamic_scaler.ThermodynamicScaler(reaction_model=None)[source]

Bases: catmap.scalers.scaler_base.ScalerBase

Scaler which uses temperature/pressure/potential as descriptors and treates energetics as a constant

__getattr__(attr)

Return the value of the reaction model instance if its there. Otherwise return the instances own value (or none if the instance does not have the attribute defined and the attribute is not private)

__init__(reaction_model=None)[source]
__module__ = 'catmap.scalers.thermodynamic_scaler'
__setattr__(attr, val)

Set attribute for the instance as well as the reaction_model instance

get_electronic_energies(descriptors)[source]
get_energetics(descriptors)
get_enthalpies(descriptors, **kwargs)
get_entropies(descriptors, **kwargs)
get_formation_energy_interaction_parameters(descriptors)[source]
get_formation_energy_parameters(descriptors)[source]
get_free_energies(descriptors, **kwargs)
get_rxn_parameters(descriptors, *args, **kwargs)[source]
get_thermodynamic_energies(descriptors, **kwargs)[source]
get_total_enthalpies(descriptors, **kwargs)
set_output_attrs(descriptors)

Function to set output information.

summary_text()

Module contents