source: sasmodels/sasmodels/models/vesicle.py @ a34b811

ticket-1257-vesicle-productticket_1156ticket_822_more_unit_tests
Last change on this file since a34b811 was a34b811, checked in by Paul Kienzle <pkienzle@…>, 3 months ago

use radius_effective/radius_effective_mode/radius_effective_modes consistently throughout the code

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Line 
1r"""
2Definition
3----------
4
5This model provides the form factor, *P(q)*, for an unilamellar vesicle and is
6effectively identical to the hollow sphere reparameterized to be
7more intuitive for a vesicle and normalizing the form factor by the volume of
8the shell. The 1D scattering intensity is calculated in the following way
9(Guinier,1955\ [#Guinier1955]_)
10
11.. math::
12
13    P(q) = \frac{\phi}{V_\text{shell}} \left[
14           \frac{3V_{\text{core}}({\rho_{\text{solvent}}
15           - \rho_{\text{shell}})j_1(qR_{\text{core}})}}{qR_{\text{core}}}
16           + \frac{3V_{\text{tot}}(\rho_{\text{shell}}
17           - \rho_{\text{solvent}}) j_1(qR_{\text{tot}})}{qR_{\text{tot}}}
18           \right]^2 + \text{background}
19
20
21where $\phi$ is the volume fraction of shell material, $V_{shell}$ is the volume
22of the shell, $V_{\text{cor}}$ is the volume of the core, $V_{\text{tot}}$ is
23the total volume, $R_{\text{core}}$ is the radius of the core, $R_{\text{tot}}$
24is the outer radius of the shell, $\rho_{\text{solvent}}$ is the scattering
25length density of the solvent (which is the same as for the core in this case),
26$\rho_{\text{scale}}$ is the scattering length density of the shell, background
27is a flat background level (due for example to incoherent scattering in the
28case of neutrons), and $j_1$ is the spherical bessel function
29$j_1 = (\sin(x) - x \cos(x))/ x^2$.
30
31The functional form is identical to a "typical" core-shell structure, except
32that the scattering is normalized by the volume that is contributing to the
33scattering, namely the volume of the shell alone, the scattering length density
34of the core is fixed the same as that of the solvent, the scale factor when the
35data are on an absolute scale is equivalent to the volume fraction of material
36in the shell rather than the entire core+shell sphere, and the parameterization
37is done in terms of the core radius = $R_{\text{core}}$ and the shell
38thickness = $R_{\text{tot}} - R_{\text{core}}$.
39
40.. figure:: img/vesicle_geometry.jpg
41
42    Vesicle geometry.
43
44The 2D scattering intensity is the same as *P(q)* above, regardless of the
45orientation of the *q* vector which is defined as
46
47.. math::
48
49    q = \sqrt{q_x^2 + q_y^2}
50
51
52NB: The outer most radius (= *radius* + *thickness*) is used as the effective
53radius for *S(Q)* when *P(Q)* \* *S(Q)* is applied.
54
55
56References
57----------
58
59.. [#Guinier1955] A Guinier and G. Fournet, *Small-Angle Scattering of X-Rays*, John Wiley and
60   Sons, New York, (1955)
61
62Source
63------
64
65`vesicle.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/vesicle.py>`_
66
67`vesicle.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/vesicle.c>`_
68
69Authorship and Verification
70----------------------------
71
72* **Author:** NIST IGOR/DANSE **Date:** pre 2010
73* **Last Modified by:** Paul Butler **Date:** March 20, 2016
74* **Last Reviewed by:** Paul Butler **Date:** September 7, 2018
75* **Source added by :** Steve King **Date:** March 25, 2019
76"""
77
78import numpy as np
79from numpy import inf
80
81name = "vesicle"
82title = "Vesicle model representing a hollow sphere"
83description = """
84    Model parameters:
85        radius : the core radius of the vesicle
86        thickness: the shell thickness
87        sld: the shell SLD
88        sld_solvent: the solvent (and core) SLD
89        background: incoherent background
90        volfraction: shell volume fraction
91        scale : scale factor = 1 if on absolute scale"""
92category = "shape:sphere"
93
94#             [ "name", "units", default, [lower, upper], "type", "description"],
95parameters = [["sld", "1e-6/Ang^2", 0.5, [-inf, inf], "sld",
96               "vesicle shell scattering length density"],
97              ["sld_solvent", "1e-6/Ang^2", 6.36, [-inf, inf], "sld",
98               "solvent scattering length density"],
99              ["volfraction", "", 0.05, [0, 1.0], "",
100               "volume fraction of shell"],
101              ["radius", "Ang", 100, [0, inf], "volume",
102               "vesicle core radius"],
103              ["thickness", "Ang", 30, [0, inf], "volume",
104               "vesicle shell thickness"],
105             ]
106
107source = ["lib/sas_3j1x_x.c", "vesicle.c"]
108have_Fq = True
109radius_effective_modes = ["outer radius"]
110
111def random():
112    """Return a random parameter set for the model."""
113    total_radius = 10**np.random.uniform(1.3, 5)
114    radius = total_radius * np.random.uniform(0, 1)
115    thickness = total_radius - radius
116    volfraction = 10**np.random.uniform(-3, -1)
117    pars = dict(
118        #background=0,
119        scale=1,  # volfraction is part of the model, so scale=1
120        radius=radius,
121        thickness=thickness,
122        volfraction=volfraction,
123    )
124    return pars
125
126# parameters for demo
127demo = dict(sld=0.5, sld_solvent=6.36,
128            volfraction=0.05,
129            radius=100, thickness=30,
130            radius_pd=.2, radius_pd_n=10,
131            thickness_pd=.2, thickness_pd_n=10)
132
133# NOTE: test results taken from values returned by SasView 3.1.2, with
134# 0.001 added for a non-zero default background.
135tests = [[{}, 0.0005, 859.916526646],
136         [{}, 0.100600200401, 1.77063682331],
137         [{}, 0.5, 0.00355351388906],
138         [{}, 0.1, None, None, 130., None, 1./0.54483386436],  # R_eff, form:shell
139        ]
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