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'})
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']
halar_po = []
slac_id = []
for i in ids:
print('Processing: {0}'.format(i))
launch = launchpad.get_fw_dict_by_id(i)
launchdir = launch['launches'][-1]['launch_dir']
cluster = launch['launches'][-1]['fworker']['name']
print(cluster)
if cluster == 'SLAC':
print('Dis calculation was done in SLAC cluster!')
slac_id += [i]
continue
encoding = launch['launches'][-1]['action']['stored_data']['trajectory']
atoms = encode_to_atoms(encoding)
if len(atoms[-1]) != 13:
continue
if len(set(atoms[-1].get_chemical_symbols()[-5:-1])) == 1:
m1, m2 = atoms[-1].get_chemical_symbols()[-1], None
if len(set(atoms[-1].get_chemical_symbols()[-5:-1])) == 2:
m1, m2 = set(atoms[-1].get_chemical_symbols()[-5:-1])
print(m1, m2)
pol_metal = ['Fe', 'Co', 'Ni', 'Mn']
if m1 in pol_metal or m2 in pol_metal:
if atoms[-1].info['spinpol'] == False:
IDS = launchpad.get_fw_ids(query={'state': 'COMPLETED'})
IDS = [i for i in IDS if i > 4610]
IDS = IDS[::-1]
pol_metal = ['Fe', 'Co', 'Ni', 'Mn']
weak_pol = ['Co']
strong_pol = ['Fe', 'Ni', 'Mn']
count = 0
j = 1
for ID in IDS: #print ID
#for db in db_error.select():
#ID = db.fw_id
launch = launchpad.get_fw_dict_by_id(ID)
#atoms = encode_to_atoms(launch['spec']['_tasks'][0]['args'][0])[-1]
atoms = encode_to_atoms(
launch['launches'][-1]['action']['stored_data']['trajectory'])[-1]
formula = atoms.get_chemical_formula()
if not np.any([p in formula for p in pol_metal]):
continue
data = atoms.info
if not data['spinpol']:
data['spinpol'] = True
if not np.all(atoms.get_initial_magnetic_moments() == 0):
continue
atoms.info = data
atoms.set_initial_magnetic_moments([
2.2 if atom.symbol == 'Fe' else 1.7 if atom.symbol == 'Co' else
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': 'COMPLETED'})
for i in ids:
print('Processing: {0}'.format(i))
launch = launchpad.get_fw_by_id(i)
atoms = encode_to_atoms(launch.spec['_tasks'][0]['args'][0])[0]
try:
launch2 = launchpad.get_fw_dict_by_id(i)
atoms = encode_to_atoms(
launch2['launches'][-1]['action']['stored_data']['trajectory'])[-1]
continue
except KeyError:
pass
pol_metal = ['Fe', 'Co', 'Ni', 'Mn']
if metal in pol_metal:
if atoms.info['spinpol'] == True:
launchpad.defuse_fw(i)
atoms.set_initial_magnetic_moments(
IDS = launchpad.get_fw_ids(query={'state': 'COMPLETED'})
IDS_A = [i for i in IDS if i < 700]
IDS_A = sorted(IDS_A)
if os.path.exists('All_ads_slab.db'):
os.remove('All_ads_slab.db')
db = connect('All_ads_slab.db')
#Processing A calculations
for ID in IDS_A:
print('Processing id: {0}'.format(ID))
launch = launchpad.get_fw_dict_by_id(ID)
launch2 = launchpad.get_fw_by_id(ID)
atoms0 = encode_to_atoms(launch2.spec['_tasks'][0]['args'][0])[0]
encoding = launch['launches'][-1]['action']['stored_data']['trajectory']
atoms = encode_to_atoms(encoding)
try:
keys['metal'] = launch['name']['calc']['metal']
keys['unique_slab_formula'] = keys['metal']
keys['adsorbate'] = launch['name']['calc']['adsorbate']
keys['site'] = launch['name']['calc']['site']
keys['SBS_symbol'] = 'A1'
except KeyError:
continue
db.write(atoms0, key_value_pairs=keys, data=parameters)
db.write(atoms[-1], key_value_pairs=keys, data=parameters)
