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))
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()
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 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 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 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 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)