Capped Cylinder - capped_cylinder.py
r"""
Definitions
-----------
Calculates the scattering from a cylinder with spherical section end-caps.
Like :ref:`barbell`, this is a sphereocylinder with end caps that have a
radius larger than that of the cylinder, but with the center of the end cap
radius lying within the cylinder. This model simply becomes a convex
lens when the length of the cylinder $L=0$. See the diagram for the details
of the geometry and restrictions on parameter values.
.. figure:: img/capped_cylinder_geometry.jpg
Capped cylinder geometry, where $r$ is *radius*, $R$ is *bell_radius* and
$L$ is *length*. Since the end cap radius $R \geq r$ and by definition
for this geometry $h < 0$, $h$ is then defined by $r$ and $R$ as
$h = - \sqrt{R^2 - r^2}$
The scattered intensity $I(q)$ is calculated as
.. math::
I(q) = \frac{\Delta \rho^2}{V} \left<A^2(q,\alpha).sin(\alpha)\right>
where the amplitude $A(q,\alpha)$ with the rod axis at angle $\alpha$ to $q$ is given as
.. math::
A(q) =&\ \pi r^2L
\frac{\sin\left(\tfrac12 qL\cos\alpha\right)}
{\tfrac12 qL\cos\alpha}
\frac{2 J_1(qr\sin\alpha)}{qr\sin\alpha} \\
&\ + 4 \pi R^3 \int_{-h/R}^1 dt
\cos\left[ q\cos\alpha
\left(Rt + h + {\tfrac12} L\right)\right]
\times (1-t^2)
\frac{J_1\left[qR\sin\alpha \left(1-t^2\right)^{1/2}\right]}
{qR\sin\alpha \left(1-t^2\right)^{1/2}}
The $\left<\ldots\right>$ brackets denote an average of the structure over
all orientations. $\left< A^2(q)\right>$ is then the form factor, $P(q)$.
The scale factor is equivalent to the volume fraction of cylinders, each of
volume, $V$. Contrast $\Delta\rho$ is the difference of scattering length
densities of the cylinder and the surrounding solvent.
The volume of the capped cylinder is (with $h$ as a positive value here)
.. math::
V = \pi r_c^2 L + \tfrac{2\pi}{3}(R-h)^2(2R + h)
and its radius of gyration is
.. math::
R_g^2 =&\ \left[ \tfrac{12}{5}R^5
+ R^4\left(6h+\tfrac32 L\right)
+ R^2\left(4h^2 + L^2 + 4Lh\right)
+ R^2\left(3Lh^2 + \tfrac32 L^2h\right) \right. \\
&\ \left. + \tfrac25 h^5 - \tfrac12 Lh^4 - \tfrac12 L^2h^3
+ \tfrac14 L^3r^2 + \tfrac32 Lr^4 \right]
\left( 4R^3 6R^2h - 2h^3 + 3r^2L \right)^{-1}
.. note::
The requirement that $R \geq r$ is not enforced in the model!
It is up to you to restrict this during analysis.
The 2D scattering intensity is calculated similar to the 2D cylinder model.
.. figure:: img/cylinder_angle_definition.png
Definition of the angles for oriented 2D cylinders.
References
----------
.. [#] H Kaya, *J. Appl. Cryst.*, 37 (2004) 223-230
.. [#] H Kaya and N-R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda
and errata)
.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659
Authorship and Verification
----------------------------
* **Author:** NIST IGOR/DANSE **Date:** pre 2010
* **Last Modified by:** Paul Butler **Date:** September 30, 2016
* **Last Reviewed by:** Richard Heenan **Date:** January 4, 2017
"""
import numpy as np
from numpy import inf, sin, cos, pi
name = "capped_cylinder"
title = "Right circular cylinder with spherical end caps and uniform SLD"
description = """That is, a sphereocylinder
with end caps that have a radius larger than
that of the cylinder and the center of the
end cap radius lies within the cylinder.
Note: As the length of cylinder -->0,
it becomes a Convex Lens.
It must be that radius <(=) radius_cap.
[Parameters];
scale: volume fraction of spheres,
background:incoherent background,
radius: radius of the cylinder,
length: length of the cylinder,
radius_cap: radius of the semi-spherical cap,
sld: SLD of the capped cylinder,
sld_solvent: SLD of the solvent.
"""
category = "shape:cylinder"
# pylint: disable=bad-whitespace, line-too-long
# ["name", "units", default, [lower, upper], "type", "description"],
parameters = [["sld", "1e-6/Ang^2", 4, [-inf, inf], "sld", "Cylinder scattering length density"],
["sld_solvent", "1e-6/Ang^2", 1, [-inf, inf], "sld", "Solvent scattering length density"],
["radius", "Ang", 20, [0, inf], "volume", "Cylinder radius"],
# TODO: use an expression for cap radius with fixed bounds.
# The current form requires cap radius R bigger than cylinder radius r.
# Could instead use R/r in [1,inf], r/R in [0,1], or the angle between
# cylinder and cap in [0,90]. The problem is similar for the barbell
# model. Propose r/R in [0,1] in both cases, with the model specifying
# cylinder radius in the capped cylinder model and sphere radius in the
# barbell model. This leads to the natural value of zero for no cap
# in the capped cylinder, and zero for no bar in the barbell model. In
# both models, one would be a pill.
["radius_cap", "Ang", 20, [0, inf], "volume", "Cap radius"],
["length", "Ang", 400, [0, inf], "volume", "Cylinder length"],
["theta", "degrees", 60, [-360, 360], "orientation", "cylinder axis to beam angle"],
["phi", "degrees", 60, [-360, 360], "orientation", "rotation about beam"],
]
# pylint: enable=bad-whitespace, line-too-long
source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "capped_cylinder.c"]
have_Fq = True
radius_effective_modes = [
"equivalent cylinder excluded volume", "equivalent volume sphere",
"radius", "half length", "half total length",
]
def random():
"""Return a random parameter set for the model."""
# TODO: increase volume range once problem with bell radius is fixed
# The issue is that bell radii of more than about 200 fail at high q
volume = 10**np.random.uniform(7, 9)
bar_volume = 10**np.random.uniform(-4, -1)*volume
bell_volume = volume - bar_volume
bell_radius = (bell_volume/6)**0.3333 # approximate
min_bar = bar_volume/np.pi/bell_radius**2
bar_length = 10**np.random.uniform(0, 3)*min_bar
bar_radius = np.sqrt(bar_volume/bar_length/np.pi)
if bar_radius > bell_radius:
bell_radius, bar_radius = bar_radius, bell_radius
pars = dict(
#background=0,
radius_cap=bell_radius,
radius=bar_radius,
length=bar_length,
)
return pars
demo = dict(scale=1, background=0,
sld=6, sld_solvent=1,
radius=260, radius_cap=290, length=290,
theta=30, phi=15,
radius_pd=.2, radius_pd_n=1,
radius_cap_pd=.2, radius_cap_pd_n=1,
length_pd=.2, length_pd_n=10,
theta_pd=15, theta_pd_n=45,
phi_pd=15, phi_pd_n=1)
q = 0.1
# april 6 2017, rkh add unit tests, NOT compared with any other calc method, assume correct!
qx = q*cos(pi/6.0)
qy = q*sin(pi/6.0)
tests = [
[{}, 0.075, 26.0698570695],
[{'theta':80., 'phi':10.}, (qx, qy), 0.561811990502],
]
del qx, qy # not necessary to delete, but cleaner
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