def select_cutoff(atoms):
intervals = analyze_dimensionality(atoms, method='RDA', merge=False)
m = intervals[0]
if m.b == float("inf"):
return m.a + 0.1
else:
return (m.a + m.b) / 2
def select_cutoff(atoms):
intervals = analyze_dimensionality(atoms, method='RDA', merge=False)
dimtype = max(merge_intervals(intervals), key=lambda x: x.score).dimtype
m = next(e for e in intervals if e.dimtype == dimtype)
if m.b == float("inf"):
return m.a + 0.1
else:
return (m.a + m.b) / 2
def test_mx2(method):
atoms = ase.build.mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19)
atoms.cell[2, 2] = 7
atoms.set_pbc((1, 1, 1))
atoms *= 2
intervals = analyze_dimensionality(atoms, method=method)
m = intervals[0]
assert m.dimtype == '2D'
assert intervals[0].dimtype == '2D'
assert intervals[0].h == (0, 0, 2, 0)
assert intervals[1].dimtype == '3D'
assert intervals[1].h == (0, 0, 0, 1)
assert intervals[2].dimtype == '0D'
assert intervals[2].h == (24, 0, 0, 0)
def run(args, parser):
files = [os.path.split(path)[1] for path in args.filenames]
lmax = max([len(f) for f in files]) + 2
print('file'.ljust(lmax) +
'type score a b component counts')
print('=' * lmax + '===============================================')
merge = not args.no_merge
# reading CIF files can produce a ton of distracting warnings
with warnings.catch_warnings():
warnings.filterwarnings('ignore')
for path, f in zip(args.filenames, files):
for atoms in iread(path):
result = analyze_dimensionality(atoms, merge=merge)
if not args.full:
result = result[:1]
for i, entry in enumerate(result):
dimtype = entry.dimtype.rjust(4)
score = '{:.3f}'.format(entry.score).ljust(5)
a = '{:.3f}'.format(entry.a).ljust(5)
b = '{:.3f}'.format(entry.b).ljust(5)
if i == 0:
name = f.ljust(lmax)
else:
name = ' ' * lmax
line = ('{}{}' + ' {}' * 4).format(
name, dimtype, score, a, b, entry.h)
print(line)
if args.full:
print()
def test_fcc(method):
atoms = FaceCenteredCubic(size=(2, 2, 2), symbol='Cu', pbc=(1, 1, 1))
intervals = analyze_dimensionality(atoms, method=method)
m = intervals[0]
assert m.dimtype == '3D'
import ase.build from ase.lattice.cubic import FaceCenteredCubic from ase.geometry.dimensionality import analyze_dimensionality # 2D test atoms = ase.build.mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19) atoms.cell[2, 2] = 7 atoms.set_pbc((1, 1, 1)) atoms *= 2 intervals = analyze_dimensionality(atoms, method='TSA') m = intervals[0] assert m.dimtype == '2D' assert intervals[0].dimtype == '2D' assert intervals[0].h == (0, 0, 2, 0) assert intervals[1].dimtype == '3D' assert intervals[1].h == (0, 0, 0, 1) assert intervals[2].dimtype == '0D' assert intervals[2].h == (24, 0, 0, 0) intervals = analyze_dimensionality(atoms, method='RDA') m = intervals[0] assert m.dimtype == '2D' assert intervals[0].dimtype == '2D' assert intervals[0].h == (0, 0, 2, 0)
def on_click_parse(self, event):
"""Load the CIF, unwrap it to P1 using ASE, extract some info, and display it."""
from ase.io import read, write
from ase.io.cif import write_cif
from ase.geometry.dimensionality import analyze_dimensionality
from ase.build import make_supercell
from io import StringIO, BytesIO
import re
# turn "Add CIF" button primary, to remember clicking it again!
self.btn_add_cif.button_type = 'primary'
# assign the filename as the first guess for the COF name, which can be manually corrected
self.inp_name.value = self.inp_cif.filename.split(".")[0]
# read the CIF file and get useful information
cif_str = self.inp_cif.value.decode()
# print(self.inp_cif.param.get_param_values()) # Use for debug!
atoms = read(StringIO(cif_str), format='cif')
formula = atoms.get_chemical_formula()
elements = [e for e in re.split(r'\d+', formula) if e]
self.inp_elements.value = ",".join(elements)
self.inp_modifications.value = 'none'
# If the user selects the proper checkbox, rotate the cell
if self.ckbox_relabel_cab.value:
print("USER CHOICE: relabel cell vectors to CAB")
a, b, c = atoms.cell
atoms.set_cell([ c, a, b ])
if self.ckbox_relabel_bca.value:
print("USER CHOICE: relabel cell vectors to BCA")
a, b, c = atoms.cell
atoms.set_cell([ b, c, a ])
# If the 2x replication was chosen go with that, otherwise check first if there is the need
# NOTE: this is usefull because sometime the layers are close by and ASE recognizes it as a 3D frameworks,
# but you want to force the choice of assuming it is a 2D COF and need 2 layers
if self.ckbox_2x.value:
print("USER CHOICE: force the frameworks to be 2D and duplicate 2x in C direction")
self.inp_dimensionality.value = '2D'
atoms = make_supercell(atoms, np.diag([1,1,2]))
self.inp_modifications.value = 'replicated 2x in C direction'
else:
intervals = analyze_dimensionality(atoms, method='RDA')
if intervals[0].dimtype == '2D':
self.inp_dimensionality.value = '2D'
# Check if it is correcly oriented, and extend to two layers if onyly one is present
z_min_thr = 6 #if less, it is likely a single layer
cell_lengths = atoms.get_cell_lengths_and_angles()[0:3]
if cell_lengths[0] < z_min_thr or cell_lengths[1] < z_min_thr: # X or Y are perpendicular the layer
self.inp_dimensionality.value = "ERROR: you need to rotate the axes to have the layers on XY plane."
self.inp_modifications.value = "ERROR: you need to rotate the axes to have the layers on XY plane."
if cell_lengths[2] < z_min_thr: # Z is perpendicular to a single layer
atoms = make_supercell(atoms, np.diag([1,1,2]))
self.inp_modifications.value = 'replicated 2x in C direction'
else:
self.inp_dimensionality.value = '3D'
self.atoms = atoms
import tempfile
with tempfile.TemporaryFile() as handle:
write(handle, atoms, format='cif')
handle.seek(0)
self.cif_str = handle.read()
print(f"Display: {self.inp_cif.filename}")
self.display(self.cif_str.decode())