def submit(self, prototype, ncpus=None, batch_no=None, calc_parameters=None,
**kwargs):
"""Submit a calculation for a prototype, generating atoms
with build_bulk and enumerator"""
cell_parameters = prototype.get('parameters', None)
BB = BuildBulk(prototype['spacegroup'],
prototype['wyckoffs'],
prototype['species'],
)
atoms = BB.get_atoms(cell_parameters=cell_parameters)
p_name = BB.get_prototype_name(prototype['species'])
formula = atoms.get_chemical_formula()
Sub = self.Submitter(atoms=atoms,
ncpus=ncpus,
calc_parameters=calc_parameters)
Sub.submit_calculation()
key_value_pairs = {'p_name': p_name,
'path': Sub.excpath,
'spacegroup': BB.spacegroup,
'wyckoffs': json.dumps(BB.wyckoffs),
'species': json.dumps(BB.species),
'ncpus': Sub.ncpus}
key_value_pairs.update(kwargs)
if batch_no:
key_value_pairs.update({'batch': batch_no})
self.write_submission(key_value_pairs)
def test6_all_spacegroups(self):
images = []
spacegroups = range(195, 230)
spacegroups, spacegroup_letters = get_wyckoff_letters(spacegroups)
for sg in spacegroups:
wyckoffs = spacegroup_letters[sg - 1][::-1][:5]
species = metals[:len(wyckoffs)]
print('----------', sg, '------------')
BB = BuildBulk(sg, wyckoffs, species)
atoms = BB.get_atoms(primitive_cell=False)
PC = PrototypeClassification(atoms)
prototype = PC.get_classification(include_parameters=False)
if not prototype['spacegroup'] == sg:
print(' change in spacegroup', sg, '----->',
prototype['spacegroup'])
print(' ', prototype['p_name'])
else:
assert prototype['wyckoffs'] == wyckoffs, \
'{} --->> {}'.format(prototype['wyckoffs'], wyckoffs)
def test_write_model_nersc(self):
bb_iron = BuildBulk(225, ['a', 'c'], ['Mn', 'O'])
atoms = bb_iron.get_atoms()
submitter = NerscSubmit(atoms, account='projectname', basepath='.')
submitter.set_execution_path(strict_format=False)
submitter.write_submission_files()
submitter.write_submit_script()
def test2_set_parameters(self):
BB = BuildBulk(225, ['a'], ["Cu"])
atoms = BB.get_atoms(cell_parameters={'a': 5})
unit_cell_lengths = np.linalg.norm(atoms.cell, axis=1)
assert np.all(np.isclose(unit_cell_lengths, 5 / np.sqrt(2)))
atoms = BB.get_atoms(cell_parameters={'a': 5}, primitive_cell=False)
unit_cell_lengths = np.linalg.norm(atoms.cell, axis=1)
assert np.all(np.isclose(unit_cell_lengths, 5))
def setUp(self):
self.bb_iron = BuildBulk(225, ['a', 'c'], ['Mn', 'O'])
atoms = self.bb_iron.get_atoms()
self.submitter = TriSubmit(atoms,
basepath_ext='tests',
calc_parameters={'encut': 300,
'kspacing': 0.5},
ncpus=1,
queue='small'
)
self.pwd = os.getcwd()
self.tempdir = tempfile.mkdtemp()
os.chdir(self.tempdir)
class TriSubmitTest(unittest.TestCase):
def setUp(self):
self.bb_iron = BuildBulk(225, ['a', 'c'], ['Mn', 'O'])
atoms = self.bb_iron.get_atoms()
self.submitter = TriSubmit(atoms,
basepath_ext='tests',
calc_parameters={'encut': 300,
'kspacing': 0.5},
ncpus=1,
queue='small'
)
self.pwd = os.getcwd()
self.tempdir = tempfile.mkdtemp()
os.chdir(self.tempdir)
def tearDown(self):
os.chdir(self.pwd)
shutil.rmtree(self.tempdir)
def test_write_poscar(self):
self.submitter.write_poscar('.')
def test_write_model(self):
self.submitter.write_model('.')
with open('model.py') as f:
model_text = f.readlines()
def test_submit(self):
self.submitter.submit_calculation()
# Allow lattice constants to be optimized
for del_param in ['a', 'b', 'c']:
if del_param in cell_parameters:
del cell_parameters[del_param]
spacegroup = int(row[4])
wyckoffs = eval(row[6])
species = eval(row[5])
atomA = species[0]
# Change to TiO2 structure
for i in range(len(species)):
if species[i] == atomA:
species[i] = 'Ti'
else:
species[i] = 'O'
try:
bulk_generator = BuildBulk(spacegroup=int(row[4]),
wyckoffs=eval(row[6]),
species=species,
cell_parameters=cell_parameters)
atoms = bulk_generator.atoms
if atoms:
view(atoms)
database.write(atoms)
except BaseException:
print('Error: something is wrong with this structure')
continue
def test_write_model(self):
bb_iron = BuildBulk(225, ['a', 'c'], ['Mn', 'O'])
atoms = bb_iron.get_atoms()
self.submitter = TriSubmit(atoms, basepath_ext='tests')
self.submitter.write_model('.')
def store_atoms_for_prototype(self, prototype, max_candidates=1):
p_name = prototype['name']
counts = []
for a in p_name.split('_')[0]:
if a.isdigit():
counts[-1] += int(a) - 1
else:
counts += [1]
species_lists = self.get_species_lists(
prototype['species'], prototype['permutations'], counts)
cell_parameters = prototype.get('cell_parameters', None)
if cell_parameters:
cell_parameters = json.load(cell_parameters)
for species in species_lists:
structure_name = str(prototype['spacegroup'])
for spec, wy_spec in zip(species, prototype['wyckoffs']):
structure_name += '_{}_{}'.format(spec, wy_spec)
with PrototypeSQL(filename=self.filename) as DB:
if DB.ase_db.count(structure_name=structure_name) > 0:
continue
for row in DB.ase_db.select(p_name=prototype['name'], limit=1):
cell_parameters = json.loads(row.cell_parameters)
BB = BuildBulk(prototype['spacegroup'],
prototype['wyckoffs'],
species,
)
atoms_list, parameters = \
BB.get_wyckoff_candidate_atoms(proximity=1,
primitive_cell=True,
return_parameters=True,
max_candidates=max_candidates)
key_value_pairs = {'p_name': prototype['name'],
'spacegroup': prototype['spacegroup'],
'wyckoffs':
json.dumps(prototype['wyckoffs']),
'species': json.dumps(species),
'structure_name': structure_name,
'source': 'prototype',
'relaxed': 0,
'completed': 0,
'submitted': 0}
for i, atoms in enumerate(atoms_list):
atoms.info.pop('spacegroup')
if 'spacegroup_kinds' in atoms.info:
atoms.info.pop('spacegroup_kinds')
key_value_pairs.update(atoms.info)
key_value_pairs.update(
{'cell_parameters': json.dumps(parameters[i])})
fitness = get_fitness(atoms)
apf = get_covalent_density(atoms)
key_value_pairs.update({'fitness': fitness,
'apf': apf})
with PrototypeSQL(filename=self.filename) as DB:
DB.ase_db.write(atoms, key_value_pairs)
def test1_no_parameters(self):
BB = BuildBulk(225, ['a'], ["Cu"])
atoms = BB.get_atoms(proximity=1)
unit_cell_lengths = np.linalg.norm(atoms.cell, axis=1)
assert np.all(np.isclose(unit_cell_lengths, 2.629, rtol=0.01))
from protosearch.build_bulk.build_bulk import BuildBulk from ase.visualize import view BB = BuildBulk(47, ['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h'], ['Cu', 'Pd', 'Pt','Au', 'Cu', 'Pd', 'Pt','Au']) atoms = BB.get_atoms(proximity=1) view(atoms)