# source:sasmodels/sasmodels/models/pearl_necklace.py@4b541ac

core_shell_microgelscostrafo411magnetic_modelticket-1257-vesicle-productticket_1156ticket_1265_superballticket_822_more_unit_tests
Last change on this file since 4b541ac was 4b541ac, checked in by wojciech, 6 years ago

sas_Si fixes in py files

• Property mode set to 100644
File size: 4.7 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
55"""
56
57from numpy import inf, pi
58
59name = "pearl_necklace"
60title = "Colloidal spheres chained together with no preferential orientation"
61description = """
62Calculate form factor for Pearl Necklace Model
63[Macromol. Symp. 2004, 211, 25-42]
64Parameters:
65background:background
66scale: scale factor
67sld: the SLD of the pearl spheres
68sld_string: the SLD of the strings
69sld_solvent: the SLD of the solvent
70num_pearls: number of the pearls
72edge_sep: the length of string segment; surface to surface
73thick_string: thickness (ie, diameter) of the string
74"""
75category = "shape:cylinder"
76
77#             ["name", "units", default, [lower, upper], "type","description"],
78parameters = [["radius", "Ang", 80.0, [0, inf], "volume",
79               "Mean radius of the chained spheres"],
80              ["edge_sep", "Ang", 350.0, [0, inf], "volume",
81               "Mean separation of chained particles"],
82              ["thick_string", "Ang", 2.5, [0, inf], "volume",
83               "Thickness of the chain linkage"],
84              ["num_pearls", "none", 3, [0, inf], "volume",
85               "Number of pearls in the necklace (must be integer)"],
86              ["sld", "1e-6/Ang^2", 1.0, [-inf, inf], "sld",
87               "Scattering length density of the chained spheres"],
88              ["sld_string", "1e-6/Ang^2", 1.0, [-inf, inf], "sld",
89               "Scattering length density of the chain linkage"],
90              ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "sld",
91               "Scattering length density of the solvent"],
92             ]
93
94source = ["lib/sas_Si.c", "lib/sas_3j1x_x.c", "pearl_necklace.c"]
95single = False  # use double precision unless told otherwise
96
98    """
99    Calculates the total particle volume of the necklace.
100    Redundant with form_volume.
101    """
102    number_of_strings = num_pearls - 1.0
103    string_vol = edge_sep * pi * pow((thick_string / 2.0), 2.0)
104    pearl_vol = 4.0 /3.0 * pi * pow(radius, 3.0)
105    total_vol = number_of_strings * string_vol
106    total_vol += num_pearls * pearl_vol
107    return total_vol
108
110    """
112    """
113    tot_vol = volume(radius, edge_sep, thick_string, num_pearls)
114    rad_out = (tot_vol/(4.0/3.0*pi)) ** (1./3.)