def exists_in_db(a, db_name):
db = connect(db_name)
atoms = []
#print('Checking database ' + db_name)
for row in db.select(struct_type='initial'):
atoms.append(row.toatoms())
symcheck = SymmetryEquivalenceCheck()
if symcheck.compare(a, atoms):
print(db_name)
return symcheck.compare(a, atoms)
def get_unique_prefixes(
path_to_species: str) -> List[str]:
''' Compare each conformers for a given adsorbate and returns a list
with prefixes of a symmetrty dictinct structures
Parameters
----------
path_to_species : str
a path to species
e.g. ``'Cu_111/minima/CO'``
Returns
-------
unique_minima_prefixes : List[str]
a list with prefixes of symmetry distinct structures for a given
adsorbate
'''
good_minima = []
result_dict = {}
unique_minima_prefixes = []
trajlist = sorted(Path(path_to_species).glob('*traj'), key=str)
for traj in trajlist:
minima = read(traj)
comparator = SymmetryEquivalenceCheck(to_primitive=True)
result = comparator.compare(minima, good_minima)
result_dict[str(os.path.basename(traj).split('.')[0])] = result
if result is False:
good_minima.append(minima)
for prefix, result in result_dict.items():
if result is False:
unique_minima_prefixes.append(prefix)
return unique_minima_prefixes
def sync():
db_server = connect(MYSQL_DB)
db_sqlite = connect(SQLITE_DB)
num_inserted = 0
symm_checker = SymmetryEquivalenceCheck()
atoms_on_server = [r.toatoms() for r in db_server.select(type='initial')]
groups = [row.get('group', -1) for row in db_sqlite.select()]
for g in groups:
rows = []
for r in db_sqlite.select(group=g):
rows.append(r)
exists = False
for r in rows:
if symm_checker.compare(r.toatoms(), atoms_on_server):
exists = True
break
if exists:
continue
for r in rows:
try:
row.__dict__.update(
{'project': 'cluster_expansion_almgsiX_fcc'})
row._keys.append('project')
#db_server.write(row)
num_inserted += 1
except Exception:
pass
print("Inserted {} calculations".format(num_inserted))
def sync(group, db_sqlite, db_server):
num_inserted = 0
symm_checker = SymmetryEquivalenceCheck()
atoms_on_server = [r.toatoms() for r in db_server.select(type='initial')]
rows = []
for r in db_sqlite.select(group=group):
rows.append(r)
for r in rows:
if symm_checker.compare(r.toatoms(), atoms_on_server):
exists = True
print("Structures already exists in DB")
return
for row in rows:
if row.get('struct_type', 'none') == 'initial':
row.__dict__.update({'type': 'initial'})
if 'type' not in row._keys:
row._keys.append('type')
try:
row.__dict__.update({'project': 'cluster_expansion_almgsiX_fcc'})
row._keys.append('project')
db_server.write(row)
num_inserted += 1
except Exception as exc:
print(exc)
print("Inserted {} calculations".format(num_inserted))
def test_spglib_standardize():
for i in [
"../tests/MoS2_2H_1l.xyz",
"../tests/WS2_2H_1l.xyz",
"../tests/graphene.xyz",
]:
atoms = ase.io.read(PROJECT_ROOT_DIR.joinpath(i))
N = [[3, 1, 0], [-1, 2, 0], [0, 0, 1]]
sc = make_supercell(atoms, N)
cppatoms = ase_atoms_to_cpp_atoms(sc)
cppatoms.standardize(1, 0, 1e-5, 5)
cell = (sc.cell, sc.get_scaled_positions(), sc.numbers)
spgcell = spglib.standardize_cell(cell,
to_primitive=True,
no_idealize=False,
symprec=1e-5,
angle_tolerance=5)
atoms = Atoms(
cell=spgcell[0],
scaled_positions=spgcell[1],
numbers=spgcell[2],
pbc=[True, True, True],
)
cppatoms = cpp_atoms_to_ase_atoms(cppatoms)
comp = SymmetryEquivalenceCheck()
is_equal = comp.compare(atoms, cppatoms)
assert (
is_equal
), "Standardization in backend and from spglib do not yield same result."
def test_one_vs_many():
s1 = Atoms('H3', positions=[[0.5, 0.5, 0], [0.5, 1.5, 0], [1.5, 1.5, 0]],
cell=[2, 2, 2], pbc=True)
# Get the unit used for position comparison
u = (s1.get_volume() / len(s1))**(1 / 3)
comp = SymmetryEquivalenceCheck(stol=.095 / u, scale_volume=True)
s2 = s1.copy()
assert comp.compare(s1, s2)
s2_list = []
s3 = Atoms('H3', positions=[[0.5, 0.5, 0], [0.5, 1.5, 0], [1.5, 1.5, 0]],
cell=[3, 3, 3], pbc=True)
s2_list.append(s3)
for d in np.linspace(0.1, 1.0, 5):
s2 = s1.copy()
s2.positions[0] += [d, 0, 0]
s2_list.append(s2)
assert not comp.compare(s1, s2_list[:-1])
assert comp.compare(s1, s2_list)
def test_original_paper_structures():
# Structures from the original paper:
# Comput. Phys. Commun. 183, 690-697 (2012)
# They should evaluate equal (within a certain tolerance)
syms = ['O', 'O', 'Mg', 'F']
cell1 = [(3.16, 0.00, 0.00), (-0.95, 4.14, 0.00), (-0.95, -0.22, 4.13)]
p1 = [(0.44, 0.40, 0.30), (0.94, 0.40, 0.79), (0.45, 0.90, 0.79),
(0.94, 0.40, 0.29)]
s1 = Atoms(syms, cell=cell1, scaled_positions=p1, pbc=True)
cell2 = [(6.00, 0.00, 0.00), (1.00, 3.00, 0.00), (2.00, -3.00, 3.00)]
p2 = [(0.00, 0.00, 0.00), (0.00, 0.00, 0.50), (0.50, 0.00, 0.00),
(0.00, 0.50, 0.00)]
s2 = Atoms(syms, cell=cell2, scaled_positions=p2, pbc=True)
comp = SymmetryEquivalenceCheck()
assert comp.compare(s1, s2)
assert comp.compare(s2, s1) == comp.compare(s1, s2)
def exists_in_db(a):
db = connect('FeCu.db')
atoms = []
for row in db.select(struct_type = 'initial'):
atoms.append(row.toatoms())
symcheck = SymmetryEquivalenceCheck()
return symcheck.compare(a, atoms)
def check_symm(path: str,
return_unique: bool,
compare_traj: bool = True) -> List[int]:
''' Check for the symmetry equivalent structures in the given path
Parameters
___________
path : str
a path to a directory where are files to be checked,
e.g. ``'Cu_111/TS_estimate_unique'``
return_unique : bool
If True, the method will return a list of unique prefixes.
If False, the method will return a list of non-unique prefixes.
compare_traj : bool
If True, the method will compare .traj files.
If False, .xyz files will be compared
Returns
________
idx_list : list(str)
a list with prefixes of all symmetrically distinct sites
'''
if compare_traj:
keyphrase = '**/*.traj'
else:
keyphrase = '*.xyz'
comparator = SymmetryEquivalenceCheck()
list_of_geoms = sorted(Path(path).glob(keyphrase))
good_adsorbates_atom_obj_list = []
result = []
for geom in list_of_geoms:
adsorbate_atom_obj = read(geom)
adsorbate_atom_obj.pbc = True
comparision = comparator.compare(adsorbate_atom_obj,
good_adsorbates_atom_obj_list)
result.append(comparision)
if comparision is False:
good_adsorbates_atom_obj_list.append(adsorbate_atom_obj)
list_of_prefixes = []
for num, res in enumerate(result):
if res is not return_unique:
list_of_prefixes.append(str(num).zfill(3))
return list_of_prefixes
def test_backend_supercell():
for i in [
"../tests/MoS2_2H_1l.xyz",
"../tests/WS2_2H_1l.xyz",
"../tests/graphene.xyz",
]:
atoms = ase.io.read(PROJECT_ROOT_DIR.joinpath(i))
cppatoms = ase_atoms_to_cpp_atoms(atoms)
N = [[3, 1, 0], [-1, 2, 0], [0, 0, 1]]
atoms = make_supercell(atoms, N)
N = int2dVector([int1dVector(k) for k in N])
cppatoms = cpp_make_supercell(cppatoms, N)
cppatoms = cpp_atoms_to_ase_atoms(cppatoms)
comp = SymmetryEquivalenceCheck()
is_equal = comp.compare(atoms, cppatoms)
assert (
is_equal
), "Supercell generation in backend and from ASE do not yield same result."
def get_unique_final_ts_prefixes(
path_to_ts: str) -> List[str]:
''' Compare each conformers for a given adsorbate and returns a list
with prefixes of a symmetrty dictinct structures
Parameters
----------
path_to_species : str
a path to species
e.g. ``'Cu_111/minima/CO'``
Returns
-------
unique_minima_prefixes : List[str]
a list with prefixes of symmetry distinct structures for a given
adsorbate
'''
unique_ts = []
result_dict = {}
unique_ts_prefixes = []
trajlist = sorted(Path(path_to_ts).glob('**/*traj'), key=str)
for traj in trajlist:
try:
ts = read(traj)
comparator = SymmetryEquivalenceCheck(to_primitive=True)
result = comparator.compare(ts, unique_ts)
result_dict[str(os.path.basename(traj)[:2])] = result
if result is False:
unique_ts.append(ts)
# error handling while calculations are still running/unfinished
except UnknownFileTypeError:
pass
for prefix, result in result_dict.items():
if result is False:
unique_ts_prefixes.append(prefix)
return unique_ts_prefixes