source: sasmodels/sasmodels/models/lamellar_stack_caille.py @ 830cf6b

ticket-1257-vesicle-productticket_1156ticket_822_more_unit_tests
Last change on this file since 830cf6b was 0507e09, checked in by smk78, 5 years ago

Added link to source code to each model. Closes #883

  • Property mode set to 100644
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Line 
1r"""
2This model provides the scattering intensity, $I(q) = P(q) S(q)$, for a
3lamellar phase where a random distribution in solution are assumed.
4Here a Caille $S(q)$ is used for the lamellar stacks.
5
6Definition
7----------
8
9The scattering intensity $I(q)$ is
10
11.. math::
12
13    I(q) = 2\pi \frac{P(q)S(q)}{q^2\delta }
14
15The form factor is
16
17.. math::
18
19    P(q) = \frac{2\Delta\rho^2}{q^2}\left(1-\cos q\delta \right)
20
21and the structure factor is
22
23.. math::
24
25    S(q) = 1 + 2 \sum_1^{N-1}\left(1-\frac{n}{N}\right)
26           \cos(qdn)\exp\left(-\frac{2q^2d^2\alpha(n)}{2}\right)
27
28where
29
30.. math::
31    :nowrap:
32
33    \begin{align*}
34    \alpha(n) &= \frac{\eta_{cp}}{4\pi^2} \left(\ln(\pi n)+\gamma_E\right)
35              && \\
36    \gamma_E  &= 0.5772156649
37              && \text{Euler's constant} \\
38    \eta_{cp} &= \frac{q_o^2k_B T}{8\pi\sqrt{K\overline{B}}}
39              && \text{Caille constant}
40    \end{align*}
41
42Here $d$ = (repeat) d_spacing, $\delta$ = bilayer thickness,
43the contrast $\Delta\rho$ = SLD(headgroup) - SLD(solvent),
44$K$ = smectic bending elasticity, $B$ = compression modulus, and
45$N$ = number of lamellar plates (*n_plates*).
46
47NB: **When the Caille parameter is greater than approximately 0.8 to 1.0, the
48assumptions of the model are incorrect.** And due to a complication of the
49model function, users are responsible for making sure that all the assumptions
50are handled accurately (see the original reference below for more details).
51
52Non-integer numbers of stacks are calculated as a linear combination of
53results for the next lower and higher values.
54
55The 2D scattering intensity is calculated in the same way as 1D, where the
56$q$ vector is defined as
57
58.. math::
59
60    q = \sqrt{q_x^2 + q_y^2}
61
62
63
64References
65----------
66
67.. [#] F Nallet, R Laversanne, and D Roux, *J. Phys. II France*, 3, (1993) 487-502
68.. [#] J Berghausen, J Zipfel, P Lindner, W Richtering, *J. Phys. Chem. B*, 105, (2001) 11081-11088
69
70Source
71------
72
73`lamellar_stack_caille.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_stack_caille.py>`_
74
75`lamellar_stack_caille.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_stack_caille.c>`_
76
77Authorship and Verification
78----------------------------
79
80* **Author:**
81* **Last Modified by:**
82* **Last Reviewed by:**
83* **Source added by :** Steve King **Date:** March 25, 2019
84"""
85
86import numpy as np
87from numpy import inf
88
89name = "lamellar_stack_caille"
90title = "Random lamellar sheet with Caille structure factor"
91description = """\
92    [Random lamellar phase with Caille  structure factor]
93    randomly oriented stacks of infinite sheets
94    with Caille S(Q), having polydisperse spacing.
95    sld = sheet scattering length density
96    sld_solvent = solvent scattering length density
97    background = incoherent background
98    scale = scale factor
99"""
100category = "shape:lamellae"
101
102single = False  # TODO: check
103# pylint: disable=bad-whitespace, line-too-long
104#             ["name", "units", default, [lower, upper], "type","description"],
105parameters = [
106    ["thickness",        "Ang",      30.0,  [0, inf],   "volume", "sheet thickness"],
107    ["Nlayers",          "",          20,   [1, inf],   "",       "Number of layers"],
108    ["d_spacing",        "Ang",      400.,  [0.0,inf],  "volume", "lamellar d-spacing of Caille S(Q)"],
109    ["Caille_parameter", "1/Ang^2",    0.1, [0.0,0.8],  "",       "Caille parameter"],
110    ["sld",              "1e-6/Ang^2", 6.3, [-inf,inf], "sld",    "layer scattering length density"],
111    ["sld_solvent",      "1e-6/Ang^2", 1.0, [-inf,inf], "sld",    "Solvent scattering length density"],
112    ]
113# pylint: enable=bad-whitespace, line-too-long
114
115source = ["lamellar_stack_caille.c"]
116
117def random():
118    """Return a random parameter set for the model."""
119    total_thickness = 10**np.random.uniform(2, 4.7)
120    Nlayers = np.random.randint(2, 200)
121    d_spacing = total_thickness / Nlayers
122    thickness = d_spacing * np.random.uniform(0, 1)
123    Caille_parameter = np.random.uniform(0, 0.8)
124    pars = dict(
125        thickness=thickness,
126        Nlayers=Nlayers,
127        d_spacing=d_spacing,
128        Caille_parameter=Caille_parameter,
129    )
130    return pars
131
132# No volume normalization despite having a volume parameter
133# This should perhaps be volume normalized?
134form_volume = """
135    return 1.0;
136    """
137
138demo = dict(scale=1, background=0,
139            thickness=67., Nlayers=3.75, d_spacing=200.,
140            Caille_parameter=0.268, sld=1.0, sld_solvent=6.34,
141            thickness_pd=0.1, thickness_pd_n=100,
142            d_spacing_pd=0.05, d_spacing_pd_n=40)
143
144#
145tests = [
146    [{'scale': 1.0, 'background': 0.0, 'thickness': 30., 'Nlayers': 20.0,
147      'd_spacing': 400., 'Caille_parameter': 0.1, 'sld': 6.3,
148      'sld_solvent': 1.0, 'thickness_pd': 0.0, 'd_spacing_pd': 0.0},
149     [0.001], [28895.13397]]
150    ]
151# ADDED by: RKH  ON: 18Mar2016  converted from sasview previously, now renaming everything & sorting the docs
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