Source code for susmost.latticetask

from .sitestate import SPMI_db, register_property, StateProp

[docs]class LatticeTask(): """Class for description of a lattice model """ def __init__(self, site_state_types, unit_cell, states, edges_dict, IM, INF_E, precission, max_dimensions): """ Constructor of LatticeTask Parameters: :site_state_types: list of types of possible states of lattice sites as :class:`SiteStateType` objects. Usually correspond to considered adsorption complexes, including an empty site. :unit_cell: unit cell of the lattice as :class:`Cell` object :states: list of possible states of lattice sites as :class:`CellState` objects. Usually correspond to various orientations of adsorption complexes from ``site_state_types`` """ self.site_state_types = site_state_types self.unit_cell = unit_cell self.states = states self.edges_dict = edges_dict self.IM = IM self.INF_E = INF_E self.precission = precission self.max_dimensions = max_dimensions def __repr__(self): return "{} {} {} {} {}".format(self.site_state_types, self.states, self.unit_cell, len(self.edges_dict), self.IM.shape) def get_site_state_type(self, name): for s in self.site_state_types: if s.props['name'].value == name: return s assert False, "Unknown site state type name: {}".format(name) def find_state_index(self, prop_name, prop_value): return [i for i,s in enumerate(self.states) if s.get_prop(prop_name) == prop_value][0]
[docs] def set_property(self, property_name, values, default_value=0): ''' Sets a property for all adsoprtion complexes Parameters: :property_name: name of the property :values: dictionary with AC names as keys and new property values as values :default_value: value to be set for ACs not included in :values:, default value - :0:. Returns: None ''' for k in values: self.get_site_state_type(k) # assert for correct AC names if property_name not in SPMI_db: register_property(property_name) print ("Register new AC property", property_name) for s in self.site_state_types: ac_name = s.props['name'].value s.props[property_name] = StateProp(property_name, values.get(ac_name, default_value))
[docs] def get_property(self, property_name, ac_name=None): ''' Returns current value of the property of the specified adsorption complex Parameters: :property_name: name of property :ac_name: name of adsorption complex Returns: Current value of the property of the specified adsorption complex ''' if ac_name is None: return {(s.props['name'].value, s.props[property_name].value) for s in self.site_state_types} return self.get_site_state_type(ac_name).props[property_name].value
[docs] def set_ads_energy(self, ac_name, energy): ''' Sets adsorption energy for adsorption complex by it's name Parameters: :ac_name: name of adsorption complex :energy: new adsorption energy of the adsorption complex Returns: None ''' self.get_site_state_type(ac_name).props['ads_energy'].value = energy
[docs] def get_ads_energy(self, ac_name): ''' Returns current energy of adsorption of the specified adsorption complex Parameters: :ac_name: name of adsorption complex Returns: Сurrent energy of adsorption of the specified adsorption complex ''' return self.get_site_state_type(ac_name).props['ads_energy'].value
@property def zero_coverage_state_index(self): """Get index of the state with zero coverage, that is empty state""" return self.find_state_index('coverage', 0) @property def states_count(self): """Get number of possible cell states""" return len(self.states) @property def edges_count(self): """Get number of different edges in the lattice, that are considered in the model""" return len(self.edges_dict) @property def edges_array(self): """Get edges considered in the model as a two-dimensional array of size *(edges_count, 3)* """ return np.array([e.coords for e in self.edges_dict]) @property def interactions_array(self): """ Get paiwise interactions of the model as a three-dimensional array of size *(states_count, edges_count, states_count)*. Returns: :result [i,j,k]: interaction energy between states i-th and k-th separated by j-th edge """ return self.IM.asarray() def __str__(self): return "LT: {} states, {} edges, state types: {}".format(self.states_count, self.edges_count, [str(s) for s in self.site_state_types])