def expressAtomsInCoordinates(atoms, vectors):
positions = convertToBasis(atoms.get_positions(), vectors)
unit_cell = convertToBasis(atoms.get_cell(), vectors)
new_atoms = atoms.copy()
new_atoms.set_positions(positions)
new_atoms.set_cell(unit_cell)
return new_atoms
def groupAtoms(atoms, order=(2,), tolerance=1e-2):
atoms = atoms.copy()
del atoms.constraints
pbc = atoms.get_pbc()
atoms.set_pbc([True]*3)
cell = atoms.get_cell()
positions, remainder = convertToBasis(atoms.get_positions(), cell)
atoms.set_positions(positions)
tolerance1 = convertToBasis(np.array([1,1,1])*tolerance, cell)[0][0]
tolerance2 = convertToBasis(np.array([-1,1,-1])*tolerance, cell)[0][0]
tolerance1 = map(abs, tolerance1)
tolerance2 = map(abs, tolerance2)
tolerance = np.max((tolerance1, tolerance2), 0)
indices = np.arange(len(atoms))
groups = [(atoms, indices)]
for i in order:
new_groups = []
for atoms, indices in groups:
while len(atoms) > 0:
positions = atoms.get_positions()
min_value = np.min(positions[:, i])
group_mask = abs(positions[:, i] - min_value) < tolerance[i]
atom_group = atoms[group_mask]
indices_group = indices[group_mask]
atoms = atoms[np.logical_not(group_mask)]
indices = indices[np.logical_not(group_mask)]
new_groups.append((atom_group, indices_group))
groups = new_groups
for atoms, indices in groups:
positions = convertFromBasis(atoms.get_positions(), cell)
atoms.set_positions(positions)
atoms.set_cell(cell)
return groups
def findPeriodicallyEqualAtoms(atoms, other_atoms):
center = atoms.positions.mean(axis=0)
center, remain = convertToBasis(center, other_atoms.cell)
center = (np.array([.5, .5, .5]) - center)[0]
other_atoms = wrap(other_atoms, center=center)
cell = other_atoms.get_cell()
pbc = atoms.get_pbc()
cell = atoms.cell[pbc]
group = -np.ones(len(other_atoms), dtype=np.int)
for i, atom in enumerate(atoms):
diff = other_atoms.get_positions() - atom.position
pos = minimalDistance(diff, cell)
mask = vectorLength(pos, 1) < 1e-5
indices = np.arange(len(other_atoms))[mask]
group[indices] = i
return group
