aesp.func package

aesp.func package#

Submodules#

aesp.func.args_setup module#

aesp.func.args_setup.args_setup()#

aesp.func.database module#

class aesp.func.database.DataConnection(db_file_name)#

Bases: object

Class that handles all database communication.

All data communication is collected in this class in order to make a decoupling of the data representation and the GA method.

A new candidate must be added with one of the functions add_unrelaxed_candidate or add_relaxed_candidate this will correctly initialize a configuration id used to keep track of candidates in the database. After one of the add_*_candidate functions have been used, if the candidate is further modified or relaxed the functions add_unrelaxed_step or add_relaxed_step must be used. This way the configuration id carries through correctly.

Parameters:

db_file_name: Path to the ase.db data file.

add_relaxed_stage(candidate, **kwargs)#
add_unrelaxed_candidate(candidate, **kwargs)#

Adds a new candidate which needs to be relaxed.

get_atoms(id, add_info=True)#

Return the atoms object with the specified id

get_candidates(value='all', **kwargs)#

Return all unrelaxed candidates, useful if they can all be evaluated quickly.

get_diversity(**kwargs)#

种群的多样性

get_energy_base_operator(oper_type_list, **kwargs)#
get_max_continuous_opt_num(population)#
get_max_generation()#
get_max_stage(generation)#
get_next_id()#

Get the id of the next candidate to be added to the database. This is a hacky way of obtaining the id and it only works on a sqlite database.

get_next_s_id()#

获得下一个s_id

get_number_of_candidates(**kwargs)#

Returns the number of candidates not yet queued or relaxed.

get_param(parameter)#

Get a parameter saved when creating the database.

get_participation_in_pairing()#

Get information about how many direct offsprings each candidate has, and which specific pairings have been made. This information is used for the extended fitness calculation described in L.B. Vilhelmsen et al., JACS, 2012, 134 (30), pp 12807-12816

is_duplicate(**kwargs)#

Check if the key-value pair is already present in the database

update_population(generation, pop_size)#

aesp.func.entrypoint_func module#

aesp.func.entrypoint_func.change_logger()#
aesp.func.entrypoint_func.config_check(config)#
aesp.func.entrypoint_func.get_last_step(wf)#
aesp.func.entrypoint_func.get_step_dict(wf)#
aesp.func.entrypoint_func.get_step_list(step_dict)#
aesp.func.entrypoint_func.global_config_workflow(wf_config)#
aesp.func.entrypoint_func.normalize(data)#
aesp.func.entrypoint_func.print_citation()#
aesp.func.entrypoint_func.write_input(config, config_name)#

aesp.func.population module#

class aesp.func.population.Population(pop_list)#

Bases: object

Population class which maintains the current population and proposes which candidates to pair together.

Parameters:

data_connection: DataConnection object

Bla bla bla.

population_size: int

The number of candidates in the population.

comparator: Comparator object

this will tell if two configurations are equal. Default compare atoms objects directly.

logfile: str

Text file that contains information about the population The format is:

timestamp: generation(if available): id1,id2,id3...

Using this file greatly speeds up convergence checks. Default None meaning that no file is written.

use_extinct: boolean

Set this to True if mass extinction and the extinct key are going to be used. Default is False.

rng: Random number generator

By default numpy.random.

get_candidates(size=1)#

Returns two candidates for pairing employing the fitness criteria from L.B. Vilhelmsen et al., JACS, 2012, 134 (30), pp 12807-12816 and the roulete wheel selection scheme described in R.L. Johnston Dalton Transactions, Vol. 22, No. 22. (2003), pp. 4193-4207

get_diversity(comp)#

种群的多样性

aesp.func.population.count_looks_like(a, all_cand, comp)#

Utility method for counting occurrences.

aesp.func.population.get_raw_score(atoms)#

Gets the raw_score of the supplied atoms object.

Parameters#

atomsAtoms object

The atoms object from which the raw_score will be returned.

Returns#

raw_scorefloat or int

The raw_score set previously.

aesp.func.scheduler module#

class aesp.func.scheduler.DPScheduler(max_generation, max_stage, fatal_at_max)#

Bases: STScheduler

next_stage(stage_complete)#
property s_converged#
class aesp.func.scheduler.STScheduler(max_generation, max_stage)#

Bases: object

property g_converged#
next_generation(gen_complete, **kwargs)#
next_stage(**kwargs)#
property s_converged#

aesp.func.traj_render module#

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