def main():
""" Run GA. """
from glob import glob
from sys import argv
from matador.hull import QueryConvexHull
from matador.fingerprints.similarity import get_uniq_cursor
from matador.utils.chem_utils import get_formula_from_stoich
from matador.scrapers.castep_scrapers import res2dict
from ilustrado.ilustrado import ArtificialSelector
cursor = [res2dict(res)[0] for res in glob('seed/*.res')]
hull = QueryConvexHull(cursor=cursor,
no_plot=True,
kpoint_tolerance=0.03,
summary=True,
hull_cutoff=1e-1)
print('Filtering down to only ternary phases... {}'.format(
len(hull.hull_cursor)))
hull.hull_cursor = [
doc for doc in hull.hull_cursor if len(doc['stoichiometry']) == 3
]
print('Filtering unique structures... {}'.format(len(hull.hull_cursor)))
# uniq_list, _, _, _ = list(get_uniq_cursor(hull.hull_cursor[1:-1], debug=False))
# cursor = [hull.hull_cursor[1:-1][ind] for ind in uniq_list]
cursor = hull.hull_cursor
print('Final cursor length... {}'.format(len(cursor)))
print('over {} stoichiometries...'.format(
len(
set([
get_formula_from_stoich(doc['stoichiometry']) for doc in cursor
]))))
print([doc['stoichiometry'] for doc in cursor])
def filter_fn(doc):
""" Filter out any non-ternary phases. """
return True if len(doc['stoichiometry']) == 3 else False
ArtificialSelector(gene_pool=cursor,
seed='KPSn',
compute_mode='slurm',
entrypoint=__file__,
walltime_hrs=12,
slurm_template='template.slurm',
max_num_nodes=100,
hull=hull,
check_dupes=0,
structure_filter=filter_fn,
best_from_stoich=True,
max_num_mutations=3,
max_num_atoms=50,
mutation_rate=0.4,
crossover_rate=0.6,
num_generations=20,
population=30,
num_survivors=20,
elitism=0.5,
loglevel='debug')
from ilustrado.ilustrado import ArtificialSelector
from glob import glob
from sys import argv
nprocs = int(argv[1])
cursor = [res2dict(res)[0] for res in glob('seed/*.res')]
hull = QueryConvexHull(cursor=cursor,
no_plot=True,
kpoint_tolerance=0.03,
summary=True,
hull_cutoff=7.5e-2)
print('Filtering down to only ternary phases... {}'.format(
len(hull.hull_cursor)))
hull.hull_cursor = [
doc for doc in hull.hull_cursor if len(doc['stoichiometry']) == 3
]
print('Filtering unique structures... {}'.format(len(hull.hull_cursor)))
uniq_list, _, _, _ = list(get_uniq_cursor(hull.hull_cursor[1:-1], debug=False))
cursor = [hull.hull_cursor[1:-1][ind] for ind in uniq_list]
print('Final cursor length... {}'.format(len(cursor)))
print('over {} stoichiometries...'.format(
len(set([get_formula_from_stoich(doc['stoichiometry'])
for doc in cursor]))))
print([doc['stoichiometry'] for doc in cursor])
ArtificialSelector(gene_pool=cursor,
seed='KPSn',
hull=hull,
debug=False,
fitness_metric='hull',
def main():
""" Run GA. """
from glob import glob
from sys import argv
from matador.hull import QueryConvexHull
from matador.fingerprints.similarity import get_uniq_cursor
from matador.utils.chem_utils import get_formula_from_stoich
from matador.scrapers.castep_scrapers import res2dict
from ilustrado.ilustrado import ArtificialSelector
nprocs = int(argv[1]) # specify nprocs at the command-line
cursor = [res2dict(res)[0] for res in glob('seed/*.res')]
hull = QueryConvexHull(cursor=cursor,
no_plot=True,
kpoint_tolerance=0.03,
summary=True,
hull_cutoff=1e-1)
print('Filtering down to only ternary phases... {}'.format(
len(hull.hull_cursor)))
hull.hull_cursor = [
doc for doc in hull.hull_cursor if len(doc['stoichiometry']) == 3
]
print('Filtering unique structures... {}'.format(len(hull.hull_cursor)))
uniq_list, _, _, _ = list(
get_uniq_cursor(hull.hull_cursor[1:-1], debug=False))
cursor = [hull.hull_cursor[1:-1][ind] for ind in uniq_list]
print('Final cursor length... {}'.format(len(cursor)))
print('over {} stoichiometries...'.format(
len(
set([
get_formula_from_stoich(doc['stoichiometry']) for doc in cursor
]))))
print([doc['stoichiometry'] for doc in cursor])
def filter_fn(doc):
""" Filter out any non-ternary phases. """
return True if len(doc['stoichiometry']) == 3 else False
relaxer_params = {'bnl': True} # required to use srun instead of mpirun
ArtificialSelector(
gene_pool=cursor,
seed='KPSn',
hull=hull,
debug=False,
fitness_metric='hull',
# number of cores per individual calculation
# to use less than one node, decrease this to e.g. 10
# then increase nprocs to 2*nnodes
ncores=20,
check_dupes=1,
# number of total procs, taken as command-line argument to script
nprocs=nprocs,
executable='castep',
relaxer_params=relaxer_params,
structure_filter=filter_fn,
best_from_stoich=True,
max_num_mutations=3,
max_num_atoms=50,
mutation_rate=0.4,
crossover_rate=0.6,
num_generations=20,
population=30,
num_survivors=20,
elitism=0.5,
loglevel='debug')