def profile(self, extra=False):
"""
Calculates the volume fraction profile
Returns
-------
z, vfp : np.ndarray
Distance from the interface, volume fraction profile
"""
s = Structure()
s |= SLD(0)
m = SLD(1.)
for i, slab in enumerate(self.left_slabs):
layer = m(slab.thick.value, slab.rough.value)
if not i:
layer.rough.value = 0
layer.vfsolv.value = slab.vfsolv.value
s |= layer
polymer_slabs = self.slabs()
offset = np.sum(s.slabs()[:, 0])
if polymer_slabs is not None:
for i in range(np.size(polymer_slabs, 0)):
layer = m(polymer_slabs[i, 0], polymer_slabs[i, 3])
layer.vfsolv.value = polymer_slabs[i, -1]
s |= layer
for i, slab in enumerate(self.right_slabs):
layer = m(slab.thick.value, slab.rough.value)
layer.vfsolv.value = 1 - slab.vfsolv.value
s |= layer
s |= SLD(0, 0)
# now calculate the VFP.
total_thickness = np.sum(s.slabs()[:, 0])
zed = np.linspace(0, total_thickness, total_thickness + 1)
# SLD profile puts a very small roughness on the interfaces with zero
# roughness.
zed[0] = 0.01
z, s = s.sld_profile(z=zed)
s[0] = s[1]
# perhaps you'd like to plot the knot locations
zeds = np.cumsum(self.dz)
if np.sum(self.dz) > 1:
zeds /= np.sum(self.dz)
zeds = np.clip(zeds, 0, 1)
zed_knots = zeds * float(self.extent) + offset
if extra:
return z, s, zed_knots, np.array(self.vf)
else:
return z, s
def test_stack(self):
stk = Stack()
slabs = stk.slabs(None)
assert (slabs is None)
si = SLD(2.07)
sio2 = SLD(3.47)
polymer = SLD(1.0)
d2o = SLD(6.36)
# check some initial stack properties
stk.append(sio2(55, 4))
slabs = stk.slabs(None)
assert (slabs.shape == (1, 5))
assert_equal(np.sum(slabs[:, 0]), 55)
assert_equal(slabs[0, 1], 3.47)
stk.repeats.value = 3.2
slabs = stk.slabs(None)
assert (slabs.shape == (3, 5))
assert_equal(np.sum(slabs[:, 0]), 165)
# ior a Stack and a Component
stk |= polymer(110, 3.5)
assert_equal(len(stk), 2)
assert (isinstance(stk, Stack))
assert_almost_equal(stk.repeats, 3.2)
slabs = stk.slabs()
assert (slabs.shape == (6, 5))
assert_equal(np.sum(slabs[:, 0]), 495)
# place a stack into a structure
s = si | d2o(10, 3) | stk | d2o
assert (isinstance(s, Structure))
slabs = s.slabs()
assert_equal(slabs[:, 0], [0, 10, 55, 110, 55, 110, 55, 110, 0])
assert_equal(slabs[:, 1],
[2.07, 6.36, 3.47, 1.0, 3.47, 1.0, 3.47, 1.0, 6.36])
assert_equal(slabs[:, 3], [0, 3, 4, 3.5, 4, 3.5, 4, 3.5, 0])
# what are the interfaces of the Stack
assert_equal(len(stk.interfaces), len(stk.slabs()))
assert_equal(len(list(flatten(s.interfaces))), len(s.slabs()))
# ior a Structure and a Stack
s = Structure(components=[si(), d2o(10, 3)])
s |= stk
s |= d2o
assert (isinstance(s, Structure))
assert_equal(s.slabs()[:, 0], [0, 10, 55, 110, 55, 110, 55, 110, 0])
assert_equal(s.slabs()[:, 1],
[2.07, 6.36, 3.47, 1.0, 3.47, 1.0, 3.47, 1.0, 6.36])
q = repr(s)
r = eval(q)
assert_equal(r.slabs()[:, 0], [0, 10, 55, 110, 55, 110, 55, 110, 0])
assert_equal(r.slabs()[:, 1],
[2.07, 6.36, 3.47, 1.0, 3.47, 1.0, 3.47, 1.0, 6.36])
s |= stk
assert (isinstance(s.components[-1], Stack))
import pytest
with pytest.raises(ValueError):
s.slabs()