def submit():
parser = argparse.ArgumentParser(
description="Submit task to yascheduler daemon")
parser.add_argument('script')
args = parser.parse_args()
if not os.path.isfile(args.script):
raise ValueError("Script parameter is not a file name")
inputs = {}
with open(args.script) as f:
for l in f.readlines():
try:
k, v = l.split('=')
inputs[k.strip()] = v.strip()
except ValueError:
pass
config = ConfigParser()
config.read(CONFIG_FILE)
yac = Yascheduler(config)
task_id = yac.queue_submit_task(
inputs['LABEL'], {
'structure': open(inputs['STRUCT']).read(),
'input': open(inputs['INPUT']).read(),
'local_folder': os.getcwd()
})
print("Successfully submitted task: {}".format(task_id))
yac.connection.close()
elem_pair,
more_query_args=dict(lattices='cubic'))
structures_by_sgn = {}
for s in structures:
structures_by_sgn.setdefault(s.info['spacegroup'].no, []).append(s)
for sgn_cls in structures_by_sgn:
if how_many and counter >= how_many: raise SystemExit
# get structures with the minimal number of atoms and find one with the median cell vectors
minimal_struct = min([len(s) for s in structures_by_sgn[sgn_cls]])
cells = np.array([
s.get_cell().reshape(9) for s in structures_by_sgn[sgn_cls]
if len(s) == minimal_struct
])
median_cell = np.median(cells, axis=0)
median_idx = int(
np.argmin(np.sum((cells - median_cell)**2, axis=1)**0.5))
target_obj = structures_by_sgn[sgn_cls][median_idx]
f34_input = Fort34([bs_repo[el] for el in elem_pair])
struct_input = f34_input.from_ase(target_obj)
struct_input = str(struct_input)
setup_input = get_input(calc_setup['parameters']['crystal'], elem_pair,
bs_repo, target_obj.info['phase'])
yac.queue_submit_task(target_obj.info['phase'],
dict(structure=struct_input, input=setup_input))
counter += 1
work_folder = os.path.dirname(target)
setup_input = open(target).read()
try:
sys.argv[2]
except IndexError:
folder = None
print('**To save calc in a local repo**')
else:
folder = work_folder
print('**To save calc in an input folder**')
if os.path.exists(os.path.join(work_folder, 'fort.34')):
assert "EXTERNAL" in setup_input
struct_input = open(os.path.join(work_folder, 'fort.34')).read()
else:
assert "EXTERNAL" not in setup_input
struct_input = "UNUSED"
label = setup_input.splitlines()[0]
config = ConfigParser()
config.read(CONFIG_FILE)
yac = Yascheduler(config)
result = yac.queue_submit_task(
label, dict(structure=struct_input, input=setup_input,
local_folder=folder))
print(label)
print(result)
try: symprec = float(sys.argv[2])
except: symprec = 3E-02 # NB needs tuning
print('symprec = %s' % symprec)
label = sys.argv[1].split(os.sep)[-1].split('.')[0] + \
" " + spglib.get_spacegroup(ase_obj, symprec=symprec)
ase_obj, error = refine(ase_obj, accuracy=symprec, conventional_cell=True)
assert not error, error
yaconfig = ConfigParser()
yaconfig.read(CONFIG_FILE)
yac = Yascheduler(yaconfig)
calc_setup = get_template()
bs_repo = get_basis_sets(calc_setup['basis_family'])
#bs_repo_tzvp = get_basis_sets('./tzvp_RE')
#bs_repo_other = get_basis_sets('./hand_made_bs')
#bs_repo = {**bs_repo_tzvp , **bs_repo_other}
elements = list(set(ase_obj.get_chemical_symbols()))
f34_input = Fort34([bs_repo[el] for el in elements])
struct_input = str(f34_input.from_ase(ase_obj))
setup_input = get_input(calc_setup['parameters']['crystal'], elements, bs_repo, label)
result = yac.queue_submit_task(label, dict(structure=struct_input, input=setup_input))
print(label)
print(result)