def update(self, coords, lattice=None, absolute=False, update_mol=True):
"""
After the geometry relaxation, the returned atomic coordinates
maybe rescaled to [0, 1] bound. In this case, we need to refind
the molecular coordinates according to the original neighbor list.
If the list does not change, we return the new coordinates
otherwise, terminate the calculation.
"""
from pyxtal.molecule import compare_mol_connectivity, Orientation
try:
from openbabel import pybel, openbabel
except:
import pybel, openbabel
if lattice is not None:
self.lattice = lattice
if not absolute:
coords = coords.dot(self.lattice.matrix)
#mol = Molecule(self.symbols, coords-np.mean(coords, axis=0))
center = self.molecule.get_center(coords)
mol = Molecule(self.symbols, coords - center)
#match, _ = compare_mol_connectivity(mol, self.mol, True)
match, _ = compare_mol_connectivity(mol, self.mol)
if match:
#position = np.mean(coords, axis=0).dot(self.lattice.inv_matrix)
position = center.dot(self.lattice.inv_matrix)
#position -= np.floor(position)
self.position = position - np.floor(position)
if update_mol:
self.orientation = Orientation(np.eye(3))
self.mol = mol
else:
m1 = pybel.readstring('xyz', self.mol.to('xyz'))
m2 = pybel.readstring('xyz', mol.to('xyz'))
aligner = openbabel.OBAlign(True, False)
aligner.SetRefMol(m1.OBMol)
aligner.SetTargetMol(m2.OBMol)
if aligner.Align():
print("RMSD: ", aligner.GetRMSD())
rot = np.zeros([3, 3])
for i in range(3):
for j in range(3):
rot[i, j] = aligner.GetRotMatrix().Get(i, j)
if abs(np.linalg.det(rot) - 1) < 1e-2:
self.orientation.matrix = rot
self.orientation.r = R.from_matrix(rot)
else:
raise ValueError("rotation matrix is wrong")
else:
import pickle
with open('wrong.pkl', "wb") as f:
pickle.dump([mol, self.mol], f)
mol.to(filename='Wrong.xyz', fmt='xyz')
self.mol.to(filename='Ref.xyz', fmt='xyz')
raise ValueError("molecular connectivity changes! Exit")
