def test(cell, numops):
""" Test structure initialization. """
from numpy import all, abs, dot, array
from numpy.linalg import inv, det
from pylada.crystal.cppwrappers import cell_invariants, Structure
from pylada.math import is_integer
ops = cell_invariants(cell)
if isinstance(cell, Structure): cell = cell.cell.copy()
assert len(ops) == numops
for op in ops:
assert op.shape == (4, 3)
assert all(abs(op[3, :]) < 1e-8)
transformation = dot(dot(inv(cell), op[:3]), cell)
assert is_integer(transformation)
assert abs(abs(det(transformation)) - 1e0) < 1e-8
if numops != 48:
allops = cell_invariants(
array([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]))
failed = 0
for op in allops:
transformation = dot(dot(inv(cell), op[:3]), cell)
if not (is_integer(transformation)
and abs(abs(det(transformation)) - 1e0) < 1e-8):
failed += 1
assert failed == 48 - numops
def motif(A, B):
""" Check changes in motif. """
from numpy import dot
from pylada.crystal.cppwrappers import cell_invariants
for op in cell_invariants(A)[1:]:
print "op: ", op
C = B.copy()
for atom in C:
atom.pos = dot(op[:3], atom.pos)
scale(A, C)
def motif(A, B):
""" Check changes in motif. """
from numpy import dot
from pylada.crystal.cppwrappers import cell_invariants
for op in cell_invariants(A)[1:]:
print "op: ", op
C = B.copy()
for atom in C:
atom.pos = dot(op[:3], atom.pos)
scale(A, C)
def test(cell, numops):
""" Test structure initialization. """
from numpy import all, abs, dot, array
from numpy.linalg import inv, det
from pylada.crystal.cppwrappers import cell_invariants, Structure
from pylada.math import is_integer
ops = cell_invariants(cell)
if isinstance(cell, Structure): cell = cell.cell.copy()
assert len(ops) == numops
for op in ops:
assert op.shape == (4, 3)
assert all(abs(op[3, :]) < 1e-8)
transformation = dot(dot(inv(cell), op[:3]), cell)
assert is_integer(transformation)
assert abs(abs(det(transformation))-1e0) < 1e-8
if numops != 48:
allops = cell_invariants(array([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]))
failed = 0
for op in allops:
transformation = dot(dot(inv(cell), op[:3]), cell)
if not (is_integer(transformation) and abs(abs(det(transformation))-1e0) < 1e-8):
failed += 1
assert failed == 48 - numops
