def trig_to_hex(cell, tol=1e-5):
try:
assert np.isclose(cell.box.a, cell.box.b, rtol=tol)
assert np.isclose(cell.box.a, cell.box.c, rtol=tol)
assert np.isclose(cell.box.alpha, cell.box.beta, rtol=tol)
assert np.isclose(cell.box.alpha, cell.box.beta, rtol=tol)
assert cell.box.alpha < 120.0
except:
raise ValueError('Not a standard trigonal box')
newcell = supersize(cell, 3, 1, 1)
newcell.box_set(avect = cell.box.bvect - cell.box.avect,
bvect = cell.box.avect - cell.box.cvect,
cvect = cell.box.avect + cell.box.bvect + cell.box.cvect,
origin= cell.box.origin)
newcell.wrap()
return newcell
def hex_to_ortho(cell, tol=1e-5):
try:
assert np.isclose(cell.box.a, cell.box.b, rtol=tol)
assert not np.isclose(cell.box.a, cell.box.c, rtol=tol)
assert np.isclose(cell.box.alpha, 90.0, rtol=tol)
assert np.isclose(cell.box.beta, 90.0, rtol=tol)
assert np.isclose(cell.box.gamma, 120.0, rtol=tol) or np.isclose(cell.box.gamma, 60.0, rtol=tol)
except:
raise ValueError('Not a standard hexagonal box')
newcell = supersize(cell, 1, 2, 1)
newcell.normalize(style='lammps')
new_b = cell.box.b * 3.**0.5
newcell.box_set(origin=[0.0, 0.0, 0.0], scale=True)
newcell.box_set(a=cell.box.a, b=new_b, c=cell.box.c,
alpha=90.0, beta=90.0, gamma=90.0,
origin=cell.box.origin)
newcell.wrap()
return newcell