source: sasmodels/sasmodels/models/core_shell_bicelle_elliptical.py @ fc3ae1b

core_shell_microgelsmagnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since fc3ae1b was fc3ae1b, checked in by Paul Kienzle <pkienzle@…>, 6 years ago

elliptical bicelle: change description of x_core to r_major/r_minor

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1r"""
2Definition
3----------
4
5This model provides the form factor for an elliptical cylinder with a
6core-shell scattering length density profile. Thus this is a variation
7of the core-shell bicelle model, but with an elliptical cylinder for the core.
8Outer shells on the rims and flat ends may be of different thicknesses and
9scattering length densities. The form factor is normalized by the total
10particle volume.
11
12.. figure:: img/core_shell_bicelle_geometry.png
13
14    Schematic cross-section of bicelle. Note however that the model here
15    calculates for rectangular, not curved, rims as shown below.
16
17.. figure:: img/core_shell_bicelle_parameters.png
18
19   Cross section of model used here. Users will have
20   to decide how to distribute "heads" and "tails" between the rim, face
21   and core regions in order to estimate appropriate starting parameters.
22
23Given the scattering length densities (sld) $\rho_c$, the core sld, $\rho_f$,
24the face sld, $\rho_r$, the rim sld and $\rho_s$ the solvent sld, the
25scattering length density variation along the bicelle axis is:
26
27.. math::
28
29    \rho(r) =
30      \begin{cases}
31      &\rho_c \text{ for } 0 \lt r \lt R; -L \lt z\lt L \\[1.5ex]
32      &\rho_f \text{ for } 0 \lt r \lt R; -(L+2t) \lt z\lt -L;
33      L \lt z\lt (L+2t) \\[1.5ex]
34      &\rho_r\text{ for } 0 \lt r \lt R; -(L+2t) \lt z\lt -L; L \lt z\lt (L+2t)
35      \end{cases}
36
37The form factor for the bicelle is calculated in cylindrical coordinates, where
38$\alpha$ is the angle between the $Q$ vector and the cylinder axis, and $\psi$
39is the angle for the ellipsoidal cross section core, to give:
40
41.. math::
42
43    I(Q,\alpha,\psi) = \frac{\text{scale}}{V_t} \cdot
44        F(Q,\alpha, \psi)^2 \cdot sin(\alpha) + \text{background}
45
46where a numerical integration of $F(Q,\alpha, \psi)^2 \cdot sin(\alpha)$
47is carried out over \alpha and \psi for:
48
49.. math::
50    :nowrap:
51
52    \begin{align*}
53    F(Q,\alpha,\psi) = &\bigg[
54    (\rho_c - \rho_f) V_c
55     \frac{2J_1(QR'sin \alpha)}{QR'sin\alpha}
56     \frac{sin(QLcos\alpha/2)}{Q(L/2)cos\alpha} \\
57    &+(\rho_f - \rho_r) V_{c+f}
58     \frac{2J_1(QR'sin\alpha)}{QR'sin\alpha}
59     \frac{sin(Q(L/2+t_f)cos\alpha)}{Q(L/2+t_f)cos\alpha} \\
60    &+(\rho_r - \rho_s) V_t
61     \frac{2J_1(Q(R'+t_r)sin\alpha)}{Q(R'+t_r)sin\alpha}
62     \frac{sin(Q(L/2+t_f)cos\alpha)}{Q(L/2+t_f)cos\alpha}
63    \bigg]
64    \end{align*}
65
66where
67
68.. math::
69
70    R'=\frac{R}{\sqrt{2}}\sqrt{(1+X_{core}^{2}) + (1-X_{core}^{2})cos(\psi)}
71
72
73and $V_t = \pi.(R+t_r)(Xcore.R+t_r)^2.(L+2.t_f)$ is the total volume of
74the bicelle, $V_c = \pi.Xcore.R^2.L$ the volume of the core,
75$V_{c+f} = \pi.Xcore.R^2.(L+2.t_f)$ the volume of the core plus the volume
76of the faces, $R$ is the radius of the core, $Xcore$ is the axial ratio of
77the core, $L$ the length of the core, $t_f$ the thickness of the face, $t_r$
78the thickness of the rim and $J_1$ the usual first order bessel function.
79The core has radii $R$ and $Xcore.R$ so is circular, as for the
80core_shell_bicelle model, for $Xcore$ =1. Note that you may need to
81limit the range of $Xcore$, especially if using the Monte-Carlo algorithm,
82as setting radius to $R/Xcore$ and axial ratio to $1/Xcore$ gives an
83equivalent solution!
84
85The output of the 1D scattering intensity function for randomly oriented
86bicelles is then given by integrating over all possible $\alpha$ and $\psi$.
87
88For oriented bicelles the *theta*, *phi* and *psi* orientation parameters will
89appear when fitting 2D data, see the :ref:`elliptical-cylinder` model
90for further information.
91
92.. figure:: img/elliptical_cylinder_angle_definition.png
93
94    Definition of the angles for the oriented core_shell_bicelle_elliptical particles.
95
96Model verified using Monte Carlo simulation for 1D and 2D scattering.
97
98References
99----------
100
101.. [#]
102
103Authorship and Verification
104----------------------------
105
106* **Author:** Richard Heenan **Date:** December 14, 2016
107* **Last Modified by:**  Richard Heenan **Date:** December 14, 2016
108* **Last Reviewed by:**  Paul Kienzle **Date:** Feb 28, 2018
109"""
110
111import numpy as np
112from numpy import inf, sin, cos, pi
113
114name = "core_shell_bicelle_elliptical"
115title = "Elliptical cylinder with a core-shell scattering length density profile.."
116description = """
117    core_shell_bicelle_elliptical
118    Elliptical cylinder core, optional shell on the two flat faces, and shell of
119    uniform thickness on its rim (extending around the end faces).
120    Please see full documentation for equations and further details.
121    Involves a double numerical integral around the ellipsoid diameter
122    and the angle of the cylinder axis to Q.
123    Compare also the core_shell_bicelle and elliptical_cylinder models.
124      """
125category = "shape:cylinder"
126
127# pylint: disable=bad-whitespace, line-too-long
128#             ["name", "units", default, [lower, upper], "type", "description"],
129parameters = [
130    ["radius",         "Ang",       30, [0, inf],    "volume",      "Cylinder core radius r_minor"],
131    ["x_core",        "None",       3,  [0, inf],    "volume",      "Axial ratio of core, X = r_major/r_minor"],
132    ["thick_rim",  "Ang",            8, [0, inf],    "volume",      "Rim shell thickness"],
133    ["thick_face", "Ang",           14, [0, inf],    "volume",      "Cylinder face thickness"],
134    ["length",         "Ang",       50, [0, inf],    "volume",      "Cylinder length"],
135    ["sld_core",       "1e-6/Ang^2", 4, [-inf, inf], "sld",         "Cylinder core scattering length density"],
136    ["sld_face",       "1e-6/Ang^2", 7, [-inf, inf], "sld",         "Cylinder face scattering length density"],
137    ["sld_rim",        "1e-6/Ang^2", 1, [-inf, inf], "sld",         "Cylinder rim scattering length density"],
138    ["sld_solvent",    "1e-6/Ang^2", 6, [-inf, inf], "sld",         "Solvent scattering length density"],
139    ["theta",       "degrees",    90.0, [-360, 360], "orientation", "Cylinder axis to beam angle"],
140    ["phi",         "degrees",    0,    [-360, 360], "orientation", "Rotation about beam"],
141    ["psi",         "degrees",    0,    [-360, 360], "orientation", "Rotation about cylinder axis"]
142    ]
143
144# pylint: enable=bad-whitespace, line-too-long
145
146source = ["lib/sas_Si.c", "lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c",
147          "core_shell_bicelle_elliptical.c"]
148
149def random():
150    outer_major = 10**np.random.uniform(1, 4.7)
151    outer_minor = 10**np.random.uniform(1, 4.7)
152    # Use a distribution with a preference for thin shell or thin core,
153    # limited by the minimum radius. Avoid core,shell radii < 1
154    min_radius = min(outer_major, outer_minor)
155    thick_rim = np.random.beta(0.5, 0.5)*(min_radius-2) + 1
156    radius_major = outer_major - thick_rim
157    radius_minor = outer_minor - thick_rim
158    radius = radius_major
159    x_core = radius_minor/radius_major
160    outer_length = 10**np.random.uniform(1, 4.7)
161    # Caps should be a small percentage of the total length, but at least one
162    # angstrom long.  Since outer length >= 10, the following will suffice
163    thick_face = 10**np.random.uniform(-np.log10(outer_length), -1)*outer_length
164    length = outer_length - thick_face
165    pars = dict(
166        radius=radius,
167        x_core=x_core,
168        thick_rim=thick_rim,
169        thick_face=thick_face,
170        length=length
171    )
172    return pars
173
174
175q = 0.1
176# april 6 2017, rkh added a 2d unit test, NOT READY YET pull #890 branch assume correct!
177qx = q*cos(pi/6.0)
178qy = q*sin(pi/6.0)
179
180tests = [
181    [{'radius': 30.0, 'x_core': 3.0,
182      'thick_rim': 8.0, 'thick_face': 14.0, 'length': 50.0}, 'ER', 1],
183    [{'radius': 30.0, 'x_core': 3.0,
184      'thick_rim': 8.0, 'thick_face': 14.0, 'length': 50.0}, 'VR', 1],
185
186    [{'radius': 30.0, 'x_core': 3.0,
187      'thick_rim': 8.0, 'thick_face': 14.0, 'length': 50.0,
188      'sld_core': 4.0, 'sld_face': 7.0, 'sld_rim': 1.0,
189      'sld_solvent': 6.0, 'background': 0.0},
190     0.015, 286.540286],
191    #[{'theta':80., 'phi':10.}, (qx, qy), 7.88866563001],
192]
193
194del qx, qy  # not necessary to delete, but cleaner
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