catmap.mappers package

Submodules

catmap.mappers.mapper_base module

Class for `mapping’ equilibrium coverages and rates through descriptor space. This class acts as a base class to be inherited by other mapper classes, but is not functional on its own.

get_rxn_parameter_map(descriptor_ranges,resolution): Uses a

scaler object to determine the reaction parameters as a function of descriptor space. May be useful for debugging or providing intuition about rate determining steps. Should return a list of the form

[[descriptor_1,descriptor_2,…],[rxn_parameter1, rxn_parameter2, …]]

save_map(map,map_file): creates a pickle of the “map” list and dumps it

to the map_file

load_map(map_file): loads a “map” list by loading a pickle from

the map_file

A functional derived mapper class must also contain the methods:

get_coverage_map(descriptor_ranges,resolution): a function which

returns a list of the form [[descriptor_1,descriptor_2,…], [cvg_ads1,cvg_ads2,…]]

get_rates_map(descriptor_ranges,resolution): a function which returns

a list of the form [[descriptor_1,descriptor_2,…], [rate_rxn1,rate_rxn2,…]]

class catmap.mappers.mapper_base.MapperBase(reaction_model=None)

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)

__module__ = 'catmap.mappers.mapper_base'

__setattr__(attr, val)

Set attribute for the instance as well as the reaction_model instance

get_output_map(descriptor_ranges, resolution, *args, **kwargs)

get_point_output(descriptors, *args, **kwargs)

process_resolution(descriptor_ranges=None, resolution=None)

catmap.mappers.min_resid_mapper module

class catmap.mappers.min_resid_mapper.MinResidMapper(reaction_model=None)

Bases: catmap.mappers.mapper_base.MapperBase

Mapper which uses initial guesses with minimum residual.

__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)

__module__ = 'catmap.mappers.min_resid_mapper'

__setattr__(attr, val)

Set attribute for the instance as well as the reaction_model instance

bisect_descriptor_line(new_descriptors, old_descriptors, initial_guess_coverages)

Find coverages at point new_descriptors given that coverages are initial_guess_coverages at old_descriptors by incrementally halving the distance between points upon failure to converge.

param new_descriptors:  list of descriptors that fails type new_descriptors:  [float] param old_descriptors:  list of descriptors that is known to work type old_descriptors:  [float] param inititial_guess_coverages:  List of best of guess for coverages type initial_guess_coverages:  [float]

get_coverage_map(descriptor_ranges=None, resolution=None, initial_guess_adsorbate_names=None)

Creates coverage map by computing residuals from nearby points and trying points with lowest residuals first

get_initial_coverage(descriptors, *args, **kwargs)

Return initial guess for coverages based on Boltzmann weights. The return format is [descriptors, [coverages]] where the list of coverages represents the initial guess for different choices for gas phase-reservoirs that are in equilibrium with the surface coverages.

Parameters:

• descriptors (A list of descriptor values, like [5, 5]) – [float]
• *args –

  see catmap.solver.get_initial_coverages

• **kwargs –

  see catmap.solver.get_initial_coverages

get_initial_coverage_from_map(descriptors, *args, **kwargs)

get_output_map(descriptor_ranges, resolution, *args, **kwargs)

get_point_coverage(descriptors, *args, **kwargs)

Shortcut to get final coverages at a point.

Parameters:

• descriptors ([float]) – List of chemical descriptors, like [-.5, -.5]
• *args –

  see catmap.solvers.get_coverage

• **kwargs –

  see catmap.solver.get_coverage

get_point_output(descriptors, *args, **kwargs)

process_resolution(descriptor_ranges=None, resolution=None)

Module contents