source: sasmodels/sasmodels/models/pearl_necklace.py @ cf3d0ce

core_shell_microgelsmagnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since cf3d0ce was cf3d0ce, checked in by Paul Kienzle <pkienzle@…>, 10 months ago

remove dead code

  • Property mode set to 100644
File size: 4.8 KB
Line 
1r"""
2This model provides the form factor for a pearl necklace composed of two
3elements: *N* pearls (homogeneous spheres of radius *R*) freely jointed by *M*
4rods (like strings - with a total mass *Mw* = *M* \* *m*\ :sub:`r` + *N* \* *m*\
5:sub:`s`, and the string segment length (or edge separation) *l*
6(= *A* - 2\ *R*)). *A* is the center-to-center pearl separation distance.
7
8.. figure:: img/pearl_necklace_geometry.jpg
9
10    Pearl Necklace schematic
11
12Definition
13----------
14
15The output of the scattering intensity function for the pearl_necklace is
16given by (Schweins, 2004)
17
18.. math::
19
20    I(q)=\frac{ \text{scale} }{V} \cdot \frac{(S_{ss}(q)+S_{ff}(q)+S_{fs}(q))}
21        {(M \cdot m_f + N \cdot m_s)^2} + \text{bkg}
22
23where
24
25.. math::
26
27    S_{ss}(q) &= sm_s^2\psi^2(q)[\frac{N}{1-sin(qA)/qA}-\frac{N}{2}-
28        \frac{1-(sin(qA)/qA)^N}{(1-sin(qA)/qA)^2}\cdot\frac{sin(qA)}{qA}] \\
29    S_{ff}(q) &= sm_r^2[M\{2\Lambda(q)-(\frac{sin(ql/2)}{ql/2})\}+
30        \frac{2M\beta^2(q)}{1-sin(qA)/qA}-2\beta^2(q)\cdot
31        \frac{1-(sin(qA)/qA)^M}{(1-sin(qA)/qA)^2}] \\
32    S_{fs}(q) &= m_r \beta (q) \cdot m_s \psi (q) \cdot 4[
33        \frac{N-1}{1-sin(qA)/qA}-\frac{1-(sin(qA)/qA)^{N-1}}{(1-sin(qA)/qA)^2}
34        \cdot \frac{sin(qA)}{qA}] \\
35    \psi(q) &= 3 \cdot \frac{sin(qR)-(qR)\cdot cos(qR)}{(qR)^3} \\
36    \Lambda(q) &= \frac{\int_0^{ql}\frac{sin(t)}{t}dt}{ql} \\
37    \beta(q) &= \frac{\int_{qR}^{q(A-R)}\frac{sin(t)}{t}dt}{ql}
38
39where the mass *m*\ :sub:`i` is (SLD\ :sub:`i` - SLD\ :sub:`solvent`) \*
40(volume of the *N* pearls/rods). *V* is the total volume of the necklace.
41
42The 2D scattering intensity is the same as $P(q)$ above, regardless of the
43orientation of the *q* vector.
44
45The returned value is scaled to units of |cm^-1| and the parameters of the
46pearl_necklace model are the following
47
48NB: *num_pearls* must be an integer.
49
50References
51----------
52
53R Schweins and K Huber, *Particle Scattering Factor of Pearl Necklace Chains*,
54*Macromol. Symp.* 211 (2004) 25-42 2004
55L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).
56"""
57
58import numpy as np
59from numpy import inf, pi
60
61name = "pearl_necklace"
62title = "Colloidal spheres chained together with no preferential orientation"
63description = """
64Calculate form factor for Pearl Necklace Model
65[Macromol. Symp. 2004, 211, 25-42]
66Parameters:
67background:background
68scale: scale factor
69sld: the SLD of the pearl spheres
70sld_string: the SLD of the strings
71sld_solvent: the SLD of the solvent
72num_pearls: number of the pearls
73radius: the radius of a pearl
74edge_sep: the length of string segment; surface to surface
75thick_string: thickness (ie, diameter) of the string
76"""
77category = "shape:cylinder"
78
79#             ["name", "units", default, [lower, upper], "type","description"],
80parameters = [["radius", "Ang", 80.0, [0, inf], "volume",
81               "Mean radius of the chained spheres"],
82              ["edge_sep", "Ang", 350.0, [0, inf], "volume",
83               "Mean separation of chained particles"],
84              ["thick_string", "Ang", 2.5, [0, inf], "volume",
85               "Thickness of the chain linkage"],
86              ["num_pearls", "none", 3, [1, inf], "volume",
87               "Number of pearls in the necklace (must be integer)"],
88              ["sld", "1e-6/Ang^2", 1.0, [-inf, inf], "sld",
89               "Scattering length density of the chained spheres"],
90              ["sld_string", "1e-6/Ang^2", 1.0, [-inf, inf], "sld",
91               "Scattering length density of the chain linkage"],
92              ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "sld",
93               "Scattering length density of the solvent"],
94             ]
95
96source = ["lib/sas_Si.c", "lib/sas_3j1x_x.c", "pearl_necklace.c"]
97single = False  # use double precision unless told otherwise
98effective_radius_type = [
99    "equivalent volume sphere", 
100    ]
101   
102def random():
103    radius = 10**np.random.uniform(1, 3) # 1 - 1000
104    thick_string = 10**np.random.uniform(0, np.log10(radius)-1) # 1 - radius/10
105    edge_sep = 10**np.random.uniform(0, 3)  # 1 - 1000
106    num_pearls = np.round(10**np.random.uniform(0.3, 3)) # 2 - 1000
107    pars = dict(
108        radius=radius,
109        edge_sep=edge_sep,
110        thick_string=thick_string,
111        num_pearls=num_pearls,
112    )
113    return pars
114
115# parameters for demo
116demo = dict(scale=1, background=0, radius=80.0, edge_sep=350.0,
117            num_pearls=3, sld=1, sld_solvent=6.3, sld_string=1,
118            thick_string=2.5,
119            radius_pd=.2, radius_pd_n=5,
120            edge_sep_pd=25.0, edge_sep_pd_n=5,
121            num_pearls_pd=0, num_pearls_pd_n=0,
122            thick_string_pd=0.2, thick_string_pd_n=5,
123           )
124# ER function is not being used here, not that it is likely very sensible to
125# include an S(Q) with this model, the default in sasview 5.0 would be to the
126# "unconstrained" radius_effective.
127#tests = [[{}, 0.001, 17380.245], [{}, 'ER', 115.39502]]
128tests = [[{}, 0.001, 17380.245]]
Note: See TracBrowser for help on using the repository browser.