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#!/usr/bin/env python3
""" Program for extracting all relaxed structures from a GA run. """
from optparse import OptionParser
from ase.ga.data import DataConnection
from ase.io import write
description = 'Extracts all relaxed structures and ' + \
'saves them to all_candidates.traj'
p = OptionParser(usage='%prog',
description=description)
p.add_option('-o', '--output',
default='all_candidates.traj',
help='Traj file to save the candidates to')
p.add_option('-d', '--db',
default='gadb.db',
help='SQLite db file')
p.add_option('-s', '--sort',
default='energy',
help='Valid values are energy and time,'
'if the candidates should be sorted by'
'energy or by creation time.')
opt, args = p.parse_args()
dbfile = opt.db
outputfile = opt.output
sort = opt.sort
da = DataConnection(dbfile)
all_trajs = da.get_all_relaxed_candidates()
if sort == 'energy':
all_trajs.sort(key=lambda x: -x.get_potential_energy())
elif sort == 'time':
all_trajs.sort(key=lambda x: x.info['confid'])
write(outputfile, all_trajs)
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