[0.6.1] Error creating NH3 molecule

[Youjin1985]

In [1]: from pyxtal.molecule import pyxtal_molecule
In [2]: pyxtal_molecule('NH3')

ValueError Traceback (most recent call last)
Cell In[2], line 1
----> 1 pyxtal_molecule('NH3')

File ~/.pyenv/versions/3.11.7/envs/matsci/lib/python3.11/site-packages/pyxtal/molecule.py:234, in pyxtal_molecule.init(self, mol, symmetrize, fix, torsions, seed, tm)
232 if len(mo) > 1:
233 if symmetrize:
--> 234 pga = PointGroupAnalyzer(mo, 0.5)
235 mo = pga.symmetrize_molecule()["sym_mol"]
236 self.mol = mo

File ~/.pyenv/versions/3.11.7/envs/matsci/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py:964, in PointGroupAnalyzer.init(self, mol, tolerance, eigen_tolerance, matrix_tolerance)
962 self.eig_tol = eigen_tolerance
963 self.mat_tol = matrix_tolerance
--> 964 self._analyze()
965 if self.sch_symbol in ["C1v", "C1h"]:
966 self.sch_symbol = "Cs"

File ~/.pyenv/versions/3.11.7/envs/matsci/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py:1009, in PointGroupAnalyzer._analyze(self)
1007 else:
1008 logger.debug("Symmetric top molecule detected")
-> 1009 self._proc_sym_top()

File ~/.pyenv/versions/3.11.7/envs/matsci/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py:1048, in PointGroupAnalyzer._proc_sym_top(self)
1046 logger.debug(f"Eigenvalues = {self.eigvals}.")
1047 unique_axis = self.principal_axes[ind]
-> 1048 self._check_rot_sym(unique_axis)
1049 logger.debug(f"Rotation symmetries = {self.rot_sym}")
1050 if len(self.rot_sym) > 0:

File ~/.pyenv/versions/3.11.7/envs/matsci/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py:1172, in PointGroupAnalyzer._check_rot_sym(self, axis)
1166 def _check_rot_sym(self, axis):
1167 """Determines the rotational symmetry about supplied axis.
1168
1169 Used only for symmetric top molecules which has possible rotational symmetry
1170 operations > 2.
1171 """
-> 1172 min_set = self._get_smallest_set_not_on_axis(axis)
1173 max_sym = len(min_set)
1174 for i in range(max_sym, 0, -1):

File ~/.pyenv/versions/3.11.7/envs/matsci/lib/python3.11/site-packages/pymatgen/symmetry/analyzer.py:1164, in PointGroupAnalyzer._get_smallest_set_not_on_axis(self, axis)
1161 if len(valid_set) > 0:
1162 valid_sets.append(valid_set)
-> 1164 return min(valid_sets, key=len)

ValueError: min() arg is an empty sequence

[Youjin1985]

Meanwhile pyxtal_molecule('NH3', symmetrize=False) works, and default pymatgen PointGroupAnalyzer tolerance=0.3 works for NH3, problem is with tolerance 0.5 inside pyxtal
This issue makes impossible to generate random crystals with some molecules, for example:
my_crystal.from_random(3, 36, [nh3], [4])
will fail as there is no way to pass tolerance parameter to internal code.
May I suggest to decrease tolerance at line 234 of pyxtal/molecule.py or change from_random() to accept either tolerance or keyword to turn off molecule symmetrization?