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fix variable bug #342

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Merged
qzhu2017 merged 2 commits into from
Oct 5, 2026
Merged

fix variable bug #342

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219cbdd
fix variable bug
Oct 5, 2026
28b2b6b
fix variable bug
Oct 5, 2026
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9 changes: 4 additions & 5 deletions pyxtal/optimize/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -430,6 +430,7 @@ def mutator(xtal, smiles, opt_lat, ref_pxrd=None, dr=0.125, random_state=None):
# perturb molecules
for i in range(1, len(x)):
disp_mol = rng.uniform(-1.0, 1.0, len(x[i]) - 1)
disp_mol[0] = 0 # x[i][0] is the Wyckoff index: scaling it moves special-site molecules
x[i][:-1] *= 1 + dr * disp_mol
# change the orientation and torsions
for j in range(3, len(x[i]) - 1):
Expand Down Expand Up @@ -756,7 +757,7 @@ def optimizer_par(
output_mlp,
check_stable,
pre_opt,
opt_lat=None,
opt_lat=True,
delta_length=1.0,
delta_angle=15.0,
xyz_only=False,
Expand Down Expand Up @@ -840,7 +841,7 @@ def optimizer_single(
output_mlp,
check_stable,
pre_opt,
opt_lat=None,
opt_lat=True,
delta_length=1.0,
delta_angle=15.0,
xyz_only=False,
Expand All @@ -857,9 +858,7 @@ def optimizer_single(
"""

# 1. Obtain the structure model
# Preserve the historical automatic behavior when no explicit choice is
# supplied, while allowing callers to relax a provided starting lattice.
opt_lat = lattice is None if opt_lat is None else bool(opt_lat)
opt_lat = lattice is None
if xtal is None:
xtal = randomizer(
smiles,
Expand Down
5 changes: 3 additions & 2 deletions pyxtal/representation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -352,8 +352,9 @@ def to_pyxtal(self, smiles=None, composition=None, molecules=None):
site = mol_site.from_1D_dicts(dicts)

bypass = False
for mol_id, molecule in enumerate(struc.molecules):
if str(site.molecule) == str(molecule):
# do not reuse `molecule`: it holds the per-species template above
for mol_id, mol0 in enumerate(struc.molecules):
if str(site.molecule) == str(mol0):
site.type = mol_id
struc.numMols[mol_id] += site.wp.multiplicity
bypass = True
Expand Down
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