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refactor symmetry matching and --time-reversal flag
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@mikelgda
mikelgda committed Nov 21, 2024
1 parent 433da71 commit 8624b48
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Showing 3 changed files with 62 additions and 70 deletions.
24 changes: 11 additions & 13 deletions irrep/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -300,6 +300,12 @@ def invoke(self, ctx):
help="File to save the output in JSON format. (without "
"extension, the '.json' will be added automatically)"
)
@click.option(
"--time-reversal",
flag_value=True,
default=False,
help=("Consider TRS a symmetry and use the corresponding gray group.")
)
def cli(
ecut,
fwav,
Expand Down Expand Up @@ -333,6 +339,7 @@ def cli(
correct_ecut0,
trans_thresh,
magmom,
time_reversal,
v,
json_file
):
Expand Down Expand Up @@ -388,23 +395,14 @@ def cli(
try:
magnetic_moments = np.loadtxt(magmom)
except FileNotFoundError:
print("The magnetic moments' file was not found: {}".format(magmom))
print("The magnetic moments file was not found: {}".format(magmom))
except ValueError:
print("Error reading magnetic moments' file: {}".format(magmom))
print("Error reading magnetic moments file: {}".format(magmom))
elif time_reversal:
magnetic_moments = True
else:
magnetic_moments = None

if magmom is not None:
try:
magnetic_moments = np.loadtxt(magmom)
except FileNotFoundError as e:
print(f"The magnetic moments file was not found: {magmom}")
raise e
except ValueError as e:
print(f"Error reading magnetic moments file {magmom}")
raise e
else:
magnetic_moments = None

bandstr = BandStructure(
fWAV=fwav,
Expand Down
104 changes: 49 additions & 55 deletions irrep/spacegroup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -758,9 +758,13 @@ def __init__(
translations = dataset.translations
time_reversal_list = [False] * len(rotations) # to do: change it to implement grey groups

else: # Magnetic moments

elif hasattr(magmom, "__len__"): # Magnetic moments from input
self.magnetic = True
else: # --time-reversal set
self.magnetic = True
magmom = np.zeros((len(self.positions), 3), dtype=float)

if self.magnetic:
dataset = spglib.get_magnetic_symmetry_dataset((*cell,
magmom))
if dataset is None:
Expand Down Expand Up @@ -825,48 +829,36 @@ def __init__(
if no_match_symmetries:
self.spin_transf = np.eye(2) # for printing
else:
au_symmetries = False
sorted_symmetries = []
while True:
try:
ind, dt, signs, U = self.match_symmetries(
signs=self.spinor,
trans_thresh=trans_thresh,
au_symmetries=au_symmetries
)
args = np.argsort(ind)
if not au_symmetries:
symmetries = self.u_symmetries
self.spin_transf = U
N = 0
else:
symmetries = self.au_symmetries
N = len(sorted_symmetries)
for i,i_ind in enumerate(args):
symmetries[i_ind].ind = i+1 + N
symmetries[i_ind].sign = signs[i_ind]
sorted_symmetries.append(symmetries[i_ind])
except RuntimeError:
if search_cell: # symmetries must match to identify irreps
raise RuntimeError((
"refUC and shiftUC don't transform the cell to one where "
"symmetries are identical to those read from tables. "
"Try without specifying refUC and shiftUC."
))
elif refUC is not None or shiftUC is not None:
# User specified refUC or shiftUC in CLI. He/She may
# want the traces in a cell that is not neither the
# one in tables nor the DFT one
msg = ("WARNING: refUC and shiftUC don't transform the cell to "
"one where symmetries are identical to those read from "
"tables. If you want to achieve the same cell as in "
"tables, try not specifying refUC and shiftUC.")
log_message(msg, verbosity, 1)
pass
if au_symmetries or len(self.au_symmetries) == 0:
break
else:
au_symmetries = True
try:
ind, dt, signs, U = self.match_symmetries(
signs=self.spinor,
trans_thresh=trans_thresh,
only_u_symmetries=False
)
args = np.argsort(ind)
self.spin_transf = U
symmetries = self.symmetries
for i,i_ind in enumerate(args):
symmetries[i_ind].ind = i+1
symmetries[i_ind].sign = signs[i_ind]
sorted_symmetries.append(symmetries[i_ind])
except RuntimeError:
if search_cell: # symmetries must match to identify irreps
raise RuntimeError((
"refUC and shiftUC don't transform the cell to one where "
"symmetries are identical to those read from tables. "
"Try without specifying refUC and shiftUC."
))
elif refUC is not None or shiftUC is not None:
# User specified refUC or shiftUC in CLI. He/She may
# want the traces in a cell that is not neither the
# one in tables nor the DFT one
msg = ("WARNING: refUC and shiftUC don't transform the cell to "
"one where symmetries are identical to those read from "
"tables. If you want to achieve the same cell as in "
"tables, try not specifying refUC and shiftUC.")
log_message(msg, verbosity, 1)
self.symmetries = sorted_symmetries

@property
Expand Down Expand Up @@ -1334,7 +1326,8 @@ def determine_basis_transf(
ind, dt, signs, _ = self.match_symmetries(
refUC,
shiftUC,
trans_thresh=trans_thresh
trans_thresh=trans_thresh,
only_u_symmetries=True
)
msg = (f'ShiftUC achieved with the centering: {r_center}')
log_message(msg, verbosity, 1)
Expand All @@ -1352,7 +1345,8 @@ def determine_basis_transf(
ind, dt, signs, _ = self.match_symmetries(
refUC,
shiftUC,
trans_thresh=trans_thresh
trans_thresh=trans_thresh,
only_u_symmetries=True
)
msg = ('ShiftUC achieved in 2 steps:\n'
' (1) Place origin of primitive cell on '
Expand All @@ -1377,7 +1371,7 @@ def match_symmetries(
shiftUC=None,
signs=False,
trans_thresh=1e-5,
au_symmetries=False
only_u_symmetries=False
):
"""
Matches symmetry operations of two lists. Translational parts
Expand All @@ -1397,6 +1391,8 @@ def match_symmetries(
each symmetry.
trans_thresh : float, default=1e-5
Threshold used to compare translational parts of symmetries.
only_y_symmetries: boolean, default=False
Only match unitary symmetries. Useful when determining the centering
Returns
-------
Expand All @@ -1422,12 +1418,13 @@ def match_symmetries(

ind = []
dt = []
if au_symmetries:
symmetries = self.au_symmetries
symmetries_tables = self.au_symmetries_tables
else:
if only_u_symmetries:
symmetries = self.u_symmetries
symmetries_tables = self.u_symmetries_tables
else:
symmetries = self.symmetries
symmetries_tables = self.u_symmetries_tables + self.au_symmetries_tables


for j, sym in enumerate(symmetries):
R = sym.rotation_refUC(refUC)
Expand All @@ -1437,7 +1434,7 @@ def match_symmetries(
t1 = refUC.dot(sym2.t - t) % 1
#t1 = np.dot(sym2.t - t, refUC) % 1
t1[1 - t1 < trans_thresh] = 0
if np.allclose(R, sym2.R):
if np.allclose(R, sym2.R) and sym.time_reversal == sym2.time_reversal:
if np.allclose(t1, [0, 0, 0], atol=trans_thresh):
ind.append(i) # au symmetries labeled from 0
dt.append(sym2.t - t)
Expand Down Expand Up @@ -1475,10 +1472,7 @@ def match_symmetries(
"rotational part. \nR(found) = \n{} \nt(found) = {}"
.format(R, t))

if self.au_symmetries:
order = len(self.au_symmetries)
else:
order = len(self.u_symmetries)
order = len(symmetries)
if len(set(ind)) != order:
raise RuntimeError(
"Error in matching symmetries detected by spglib with the \
Expand Down
4 changes: 2 additions & 2 deletions irreptables/irreptables/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -411,14 +411,14 @@ def u_symmetries(self):
'''
List of unitary symmetries
'''
return list(filter(lambda x: not x.time_reversal, self.symmetries))
return [x for x in self.symmetries if not x.time_reversal]

@property
def au_symmetries(self):
'''
List of unitary antisymmetries
'''
return list(filter(lambda x: x.time_reversal, self.symmetries))
return [x for x in self.symmetries if x.time_reversal]

def show(self):
'''
Expand Down

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