for i in ids:
if i > 26470:
print('Processing: {0}'.format(i))
launch = launchpad.get_fw_by_id(i)
atoms = encode_to_atoms(launch.spec['_tasks'][0]['args'][0])[0]
try:
metal = launch.name['metal']
print(metal)
if '2' in metal:
a, b, _ = metal.split('2')
elif '3' in metal:
a, b = metal.split('3')
else:
continue
except KeyError:
continue
pol_metal = ['Fe', 'Co', 'Ni', 'Mn']
if a in pol_metal or b in pol_metal:
if atoms.info['spinpol'] == True:
atoms.set_initial_magnetic_moments(
[2.0 if atom.symbol in pol_metal else 0 for atom in atoms])
atoms._calc = None
encoding = atoms_to_encode(atoms)
launchpad.update_spec(
[i], spec_document={'_tasks.0.args.0': encoding})
'spinpol': False,
'mixing_beta': 0.2,
'electron_maxstep': 2000}
formula = set(atoms.get_chemical_symbols())
if np.array([a in pol_metal for a in formula]).any():
atoms.set_initial_magnetic_moments([3 if atom.symbol == 'Fe'
else 2 if atom.symbol == 'Co'
else 1 if atom.symbol == 'Ni'
else 3 if atom.symbol == 'Mn'
else 0 for atom in atoms])
atoms.info['calculator_parameters'].update({'spinpol': True,
'mixing_beta': 0.1,
'electron_maxstep': 4000})
print(atoms.info)
atoms._calc = None
encoding = atoms_to_encode(atoms)
print('Submitting job ....')
launchpad.rerun_fw(i)
launchpad.update_spec([i],
spec_document={'_tasks.0.args.0': encoding,
'_tasks.0.func': 'catkit.flow.fwio.encode_to_atoms',
'_tasks.1.args': ['decaf.Espresso'],
'_tasks.1.func':
'catkit.flow.fwase.get_potential_energy'})
if os.path.exists('input.traj'):
os.remove('input.traj')
launch.name['calc']['facet'] = '(1, 1, 1)'
launch.name['calc']['layer'] = 3
launch.name['calc']['crystal'] = 'fcc'
launch.name['calc']['vacuum'] = 10
launch.name['calc']['SBS_symbol'] = 'L12'
launch.name['calc']['PS_symbol'] = 'cP4'
site_id, a, c, BID = get_info(atoms)
launch.name['calc']['site_id'] = site_id
launch.name['calc']['a'] = a
launch.name['calc']['c'] = c
launchpad.update_spec(
[i],
spec_document={
'calc': {
'symbol': symbol,
'adsorbate': ads,
'facet': '(1, 1, 1)',
'layer': 3,
'crystal': 'fcc',
'vacuum': 10,
'SBS_symbol': 'L12',
'PS_symbol': 'cP4',
'site_id': site_id,
'a': a,
'c': c,
'bulk_id': BID
}
})
#launchpad.rerun_fw(i)
#!/usr/bin/env python
from fireworks import LaunchPad, Firework, Workflow, PyTask
from ase.io import read
from catkit.flow.fwio import atoms_to_encode, encode_to_atoms
from ase.db import connect
from ase.visualize import view
host = 'suncatls2.slac.stanford.edu'
username, name, password = netrc().authenticators(host)
launchpad = LaunchPad(
host=host,
name=name,
username=username,
password=password)
IDS = launchpad.get_fw_ids(query={'state': 'READY'})
IDS = [i for i in IDS if i != 52118]
#IDS = [31032]
for i in IDS:
print('Processing: {0}'.format(i))
launch = launchpad.get_fw_by_id(i)
launchpad.update_spec([i], spec_document={'_tasks.0.func':
'catkit.flow.fwio.encode_to_atoms'})
launchpad.update_spec([i], spec_document={'_tasks.1.func':
'catkit.flow.fwase.get_potential_energy'})
