source:sasmodels/sasmodels/models/pearl_necklace.py@2cc8aa2

core_shell_microgelsmagnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since 2cc8aa2 was 2cc8aa2, checked in by richardh, 12 months ago

fixed ER bug in elliptical_cylinder, commented out ER, VR unit tests in 7 models, unit tests now pass

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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
55"""
56
57import numpy as np
58from numpy import inf, pi
59
60name = "pearl_necklace"
61title = "Colloidal spheres chained together with no preferential orientation"
62description = """
63Calculate form factor for Pearl Necklace Model
64[Macromol. Symp. 2004, 211, 25-42]
65Parameters:
66background:background
67scale: scale factor
68sld: the SLD of the pearl spheres
69sld_string: the SLD of the strings
70sld_solvent: the SLD of the solvent
71num_pearls: number of the pearls
73edge_sep: the length of string segment; surface to surface
74thick_string: thickness (ie, diameter) of the string
75"""
76category = "shape:cylinder"
77
78#             ["name", "units", default, [lower, upper], "type","description"],
79parameters = [["radius", "Ang", 80.0, [0, inf], "volume",
80               "Mean radius of the chained spheres"],
81              ["edge_sep", "Ang", 350.0, [0, inf], "volume",
82               "Mean separation of chained particles"],
83              ["thick_string", "Ang", 2.5, [0, inf], "volume",
84               "Thickness of the chain linkage"],
85              ["num_pearls", "none", 3, [1, inf], "volume",
86               "Number of pearls in the necklace (must be integer)"],
87              ["sld", "1e-6/Ang^2", 1.0, [-inf, inf], "sld",
88               "Scattering length density of the chained spheres"],
89              ["sld_string", "1e-6/Ang^2", 1.0, [-inf, inf], "sld",
90               "Scattering length density of the chain linkage"],
91              ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "sld",
92               "Scattering length density of the solvent"],
93             ]
94
95source = ["lib/sas_Si.c", "lib/sas_3j1x_x.c", "pearl_necklace.c"]
96single = False  # use double precision unless told otherwise
97
99    """
100    Calculates the total particle volume of the necklace.
101    Redundant with form_volume.
102    """
103    num_pearls = int(num_pearls + 0.5)
104    number_of_strings = num_pearls - 1.0
105    string_vol = edge_sep * pi * pow((thick_string / 2.0), 2.0)
106    pearl_vol = 4.0 /3.0 * pi * pow(radius, 3.0)
107    total_vol = number_of_strings * string_vol
108    total_vol += num_pearls * pearl_vol
109    return total_vol
110
112    """
114    """
115    num_pearls = int(num_pearls + 0.5)
116    tot_vol = volume(radius, edge_sep, thick_string, num_pearls)
117    rad_out = (tot_vol/(4.0/3.0*pi)) ** (1./3.)
119
120def random():
121    radius = 10**np.random.uniform(1, 3) # 1 - 1000
123    edge_sep = 10**np.random.uniform(0, 3)  # 1 - 1000
124    num_pearls = np.round(10**np.random.uniform(0.3, 3)) # 2 - 1000
125    pars = dict(
127        edge_sep=edge_sep,
128        thick_string=thick_string,
129        num_pearls=num_pearls,
130    )
131    return pars
132
133# parameters for demo
134demo = dict(scale=1, background=0, radius=80.0, edge_sep=350.0,
135            num_pearls=3, sld=1, sld_solvent=6.3, sld_string=1,
136            thick_string=2.5,