def slabs(self, structure=None):
layers = super(LipidLeafletTest, self).slabs(structure=structure)
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
# tail region
volfrac = self.vm_tails.value / (self.apm.value *
self.thickness_tails.value)
layers[0, 4] = 1 - volfrac
if self.head_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[0] = Structure.overall_sld(layers[0], self.head_solvent)
layers[0, 4] = 0
# tail region
volfrac = self.vm_tails.value / (self.apm.value *
self.thickness_tails.value)
layers[1, 4] = 1 - volfrac
if self.tail_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[1] = Structure.overall_sld(layers[1], self.tail_solvent)
layers[1, 4] = 0
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
def slabs(self, structure=None):
"""
Slab representation of monolayer, as an array
Parameters
----------
structure : refnx.reflect.Structure
The Structure hosting this Component
"""
layers = np.zeros((2, 5))
# thicknesses
layers[0, 0] = float(self.thickness_heads)
layers[1, 0] = float(self.thickness_tails)
# real and imag SLD's
head_sld_real, tail_sld_real = self.sld_(
self.b_heads_real, #real
self.b_tails_real,
self.b_mscl_real)
head_sld_imag, tail_sld_imag = self.sld_(
self.b_heads_imag, #imaginary
self.b_tails_imag,
self.b_mscl_imag)
layers[0, 1] = head_sld_real
layers[0, 2] = head_sld_imag
layers[1, 1] = tail_sld_real
layers[1, 2] = tail_sld_imag
# roughnesses
layers[0, 3] = float(self.rough_preceding_mono)
layers[1, 3] = float(self.rough_head_tail)
# volume fractions
# head region
volfrac = self.vm_head() / (self.apm.value *
self.thickness_heads.value)
layers[0, 4] = 1 - volfrac
if self.head_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[0] = Structure.overall_sld(layers[0], self.head_solvent)
layers[0, 4] = 0
# tail region
volfrac = self.vm_tail() / (self.apm.value *
self.thickness_tails.value)
layers[1, 4] = 1 - volfrac
if self.tail_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[1] = Structure.overall_sld(layers[1], self.tail_solvent)
layers[1, 4] = 0
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
return layers
def test_left_right_influence(self):
# make sure that if the left and right components change, so does the
# spline
a = Spline(100, [2], [0.5], zgrad=False, microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
# change the SLD of the left component, spline should respond
self.left.sld.real.value = 2.0
assert_almost_equal(a(0, s), 2)
# check that the spline responds if it's a vfsolv that changes
self.left.vfsolv.value = 0.5
assert_almost_equal(
Structure.overall_sld(self.left.slabs(), self.solvent)[0, 1], 6.0)
assert_almost_equal(a(0, s), 6.0)
# check that the right side responds.
self.right.sld.real.value = 5.0
assert_almost_equal(a(100, s), 5.0)
# the spline should respond if the knot SLD's are changed
a.vs[0].value = 3.0
assert_almost_equal(a(50, s), 3.0)
# spline responds if the interval knot spacing is changed
a.dz[0].value = 0.9
assert_almost_equal(a(90, s), 3.0)
def slabs(self, structure=None):
"""
Slab representation of monolayer, as an array
Parameters
----------
structure : refnx.reflect.Structure
The Structure hosting this Component
"""
layers = super(LipidLeafletWithProtien,
self).slabs(structure=structure)
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
# volume fractions
# head region
# volfrac = self.vm_heads.value / (self.apm.value *
# self.thickness_heads.value)
layers[0,
4] = (1 - self.PLRatio.value
) * self.thickness_heads.value / self.total_thickness()
if self.protein_head_SLD() is not None:
# we do the solvation here, not in Structure.slabs
layers[0] = Structure.overall_sld(layers[0],
self.protein_head_SLD())
layers[0, 4] = 0
# tail region
# volfrac = self.vm_tails.value / (self.apm.value *
# self.thickness_tails.value)
layers[1,
4] = (1 - self.PLRatio.value
) * self.thickness_heads.value / self.total_thickness()
if self.protein_tail_SLD() is not None:
# we do the solvation here, not in Structure.slabs
layers[1] = Structure.overall_sld(layers[1],
self.protein_tail_SLD())
layers[1, 4] = 0
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
return layers
def slabs(self):
"""
Slab representation of monolayer, as an array
"""
layers = np.zeros((2, 5))
# thicknesses
layers[0, 0] = float(self.thickness_heads)
layers[1, 0] = float(self.thickness_tails)
# real and imag SLD's
layers[0, 1] = float(self.b_heads_real) / float(self.vm_heads) * 1.e6
layers[0, 2] = float(self.b_heads_imag) / float(self.vm_heads) * 1.e6
layers[1, 1] = float(self.b_tails_real) / float(self.vm_tails) * 1.e6
layers[1, 2] = float(self.b_tails_imag) / float(self.vm_tails) * 1.e6
# roughnesses
layers[0, 3] = float(self.rough_preceding_mono)
layers[1, 3] = float(self.rough_head_tail)
# volume fractions
# head region
volfrac = self.vm_heads.value / (self.apm.value *
self.thickness_heads.value)
layers[0, 4] = 1 - volfrac
if self.head_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[0] = Structure.overall_sld(layers[0], self.head_solvent)
layers[0, 4] = 0
# tail region
volfrac = self.vm_tails.value / (self.apm.value *
self.thickness_tails.value)
layers[1, 4] = 1 - volfrac
if self.tail_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[1] = Structure.overall_sld(layers[1], self.tail_solvent)
layers[1, 4] = 0
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
return layers
def _interpolator(self):
dz = np.array(self.dz)
zeds = np.cumsum(dz)
# if dz's sum to more than 1, then normalise to unit interval.
if zeds[-1] > 1:
zeds /= zeds[-1]
zeds = np.clip(zeds, 0, 1)
vs = np.array(self.vs)
left_sld = Structure.overall_sld(
np.atleast_2d(self.left_slab.slabs[-1]), self.solvent)[..., 1]
right_sld = Structure.overall_sld(
np.atleast_2d(self.right_slab.slabs[0]), self.solvent)[..., 1]
if self.zgrad:
zeds = np.concatenate([[-1.1, 0 - EPS], zeds, [1 + EPS, 2.1]])
vs = np.concatenate([left_sld, left_sld, vs, right_sld, right_sld])
else:
zeds = np.concatenate([[0 - EPS], zeds, [1 + EPS]])
vs = np.concatenate([left_sld, vs, right_sld])
# cache the interpolator
cache_zeds = self.__cached_interpolator['zeds']
cache_vs = self.__cached_interpolator['vs']
cache_extent = self.__cached_interpolator['extent']
# you don't need to recreate the interpolator
if (np.array_equal(zeds, cache_zeds) and np.array_equal(vs, cache_vs)
and np.equal(self.extent, cache_extent)):
return self.__cached_interpolator['interp']
else:
self.__cached_interpolator['zeds'] = zeds
self.__cached_interpolator['vs'] = vs
self.__cached_interpolator['extent'] = float(self.extent)
# TODO make vfp zero for z > self.extent
interpolator = self.interpolator(zeds, vs)
self.__cached_interpolator['interp'] = interpolator
return interpolator
def slabs(self, structure=None):
"""
Slab representation of monolayer, as an array
Parameters
----------
structure : refnx.reflect.Structure
The Structure hosting this Component
"""
layers = np.zeros((2, 5))
# thicknesses
layers[0, 0] = float(self.thickness_heads)
layers[1, 0] = float(self.thickness_tails)
# real and imag SLD's
head_sld_r, tail_sld_r = self.sld_r()
head_sld_i, tail_sld_i = self.sld_i()
layers[0, 1] = head_sld_r
layers[0, 2] = head_sld_i
layers[1, 1] = tail_sld_r
layers[1, 2] = tail_sld_i
# roughnesses
layers[0, 3] = float(self.rough_preceding_mono)
layers[1, 3] = float(self.rough_head_tail)
# volume fractions
# head region
apm = self.total_vm()/self.total_thickness()
self.apm.value = apm
volfrac = self.vm_head() / (self.apm.value *
self.thickness_heads.value)
layers[0, 4] = 1 - volfrac
# print("volfrac h", volfrac)
# print(layers[0])
if self.head_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[0] = Structure.overall_sld(layers[0], self.head_solvent_true())
layers[0, 4] = 0
# print(layers[0])
# tail region
volfrac = self.vm_tail() / (self.apm.value *
self.thickness_tails.value)
layers[1, 4] = 1 - volfrac
# print("volfrac t", volfrac)
if self.tail_solvent is not None:
# we do the solvation here, not in Structure.slabs
layers[1] = Structure.overall_sld(layers[1], self.tail_solvent_true())
layers[1, 4] = 0
if self.reverse_monolayer:
layers = np.flipud(layers)
layers[:, 3] = layers[::-1, 3]
# print("layers",layers)
return layers
def _interpolator(self, structure):
dz = np.array(self.dz)
zeds = np.cumsum(dz)
# if dz's sum to more than 1, then normalise to unit interval.
if len(zeds) and zeds[-1] > 1:
# there may be no knots
zeds /= zeds[-1]
zeds = np.clip(zeds, 0, 1)
# note - this means you shouldn't use the same Spline more than once in
# a Component, because only the first use will be detected.
try:
loc = structure.index(self)
# figure out SLDs for the bracketing Components.
# note the use of the modulus operator. This means that if the
# Spline is at the end, then the right most Component will be
# assumed to be the first Component. This is to aid the use of
# Spline in a Stack.
left_component = structure[loc - 1]
right_component = structure[(loc + 1) % len(structure)]
except ValueError:
raise ValueError("Spline didn't appear to be part of a super"
" Structure")
if (isinstance(left_component, Spline)
or isinstance(right_component, Spline)):
raise ValueError("Spline must be bracketed by Components that"
" aren't Splines.")
vs = np.array(self.vs)
left_sld = Structure.overall_sld(
np.atleast_2d(left_component.slabs(structure)[-1]),
structure.solvent)[..., 1]
right_sld = Structure.overall_sld(
np.atleast_2d(right_component.slabs(structure)[0]),
structure.solvent)[..., 1]
if self.zgrad:
zeds = np.concatenate([[-1.1, 0 - EPS], zeds, [1 + EPS, 2.1]])
vs = np.concatenate([left_sld, left_sld, vs, right_sld, right_sld])
else:
zeds = np.concatenate([[0 - EPS], zeds, [1 + EPS]])
vs = np.concatenate([left_sld, vs, right_sld])
# cache the interpolator
cache_zeds = self.__cached_interpolator['zeds']
cache_vs = self.__cached_interpolator['vs']
cache_extent = self.__cached_interpolator['extent']
# you don't need to recreate the interpolator
if (np.array_equal(zeds, cache_zeds) and np.array_equal(vs, cache_vs)
and np.equal(self.extent, cache_extent)):
return self.__cached_interpolator['interp']
else:
self.__cached_interpolator['zeds'] = zeds
self.__cached_interpolator['vs'] = vs
self.__cached_interpolator['extent'] = float(self.extent)
# TODO make vfp zero for z > self.extent
interpolator = self.interpolator(zeds, vs)
self.__cached_interpolator['interp'] = interpolator
return interpolator