[321736f] | 1 | r""" |
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| 2 | Definition |
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| 3 | ---------- |
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| 4 | |
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| 5 | The 1D scattering intensity is calculated in the following way (Guinier, 1955) |
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| 6 | |
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| 7 | .. math:: |
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| 8 | |
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[062db5a] | 9 | P(q) = \frac{\phi}{V_\text{shell}} \left[ |
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[321736f] | 10 | \frac{3V_{\text{core}}({\rho_{\text{solvent}} |
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| 11 | - \rho_{\text{shell}})j_1(qR_{\text{core}})}}{qR_{\text{core}}} |
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| 12 | + \frac{3V_{\text{tot}}(\rho_{\text{shell}} |
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| 13 | - \rho_{\text{solvent}}) j_1(qR_{\text{tot}})}{qR_{\text{tot}}} |
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| 14 | \right]^2 + \text{background} |
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| 15 | |
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| 16 | |
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[062db5a] | 17 | where $\phi$ is the volume fraction of shell material, $V_{shell}$ is the volume |
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| 18 | of the shell, $V_{\text{cor}}$ is the volume of the core, $V_{\text{tot}}$ is |
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| 19 | the total volume, $R_{\text{core}}$ is the radius of the core, $R_{\text{tot}}$ |
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| 20 | is the outer radius of the shell, $\rho_{\text{solvent}}$ is the scattering |
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| 21 | length density of the solvent (which is the same as for the core in this case), |
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[321736f] | 22 | $\rho_{\text{scale}}$ is the scattering length density of the shell, background |
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| 23 | is a flat background level (due for example to incoherent scattering in the |
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| 24 | case of neutrons), and $j_1$ is the spherical bessel function |
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[fa8011eb] | 25 | $j_1 = (\sin(x) - x \cos(x))/ x^2$. |
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[321736f] | 26 | |
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| 27 | The functional form is identical to a "typical" core-shell structure, except |
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| 28 | that the scattering is normalized by the volume that is contributing to the |
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| 29 | scattering, namely the volume of the shell alone, the scattering length density |
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| 30 | of the core is fixed the same as that of the solvent, the scale factor when the |
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| 31 | data are on an absolute scale is equivalent to the volume fraction of material |
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| 32 | in the shell rather than the entire core+shell sphere, and the parameterization |
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| 33 | is done in terms of the core radius = $R_{\text{core}}$ and the shell |
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| 34 | thickness = $R_{\text{tot}} - R_{\text{core}}$. |
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| 35 | |
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[fa8011eb] | 36 | .. figure:: img/vesicle_geometry.jpg |
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| 37 | |
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| 38 | Vesicle geometry. |
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[321736f] | 39 | |
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| 40 | The 2D scattering intensity is the same as *P(q)* above, regardless of the |
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| 41 | orientation of the *q* vector which is defined as |
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| 42 | |
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| 43 | .. math:: |
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| 44 | |
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| 45 | q = \sqrt{q_x^2 + q_y^2} |
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| 46 | |
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| 47 | |
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| 48 | NB: The outer most radius (= *radius* + *thickness*) is used as the effective |
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| 49 | radius for *S(Q)* when *P(Q)* \* *S(Q)* is applied. |
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| 50 | |
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| 51 | |
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[aa2edb2] | 52 | References |
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| 53 | ---------- |
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[321736f] | 54 | |
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| 55 | A Guinier and G. Fournet, *Small-Angle Scattering of X-Rays*, John Wiley and |
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| 56 | Sons, New York, (1955) |
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[062db5a] | 57 | |
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[ef07e95] | 58 | * **Author:** NIST IGOR/DANSE **Date:** pre 2010 |
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| 59 | * **Last Modified by:** Paul Butler **Date:** March 20, 2016 |
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| 60 | * **Last Reviewed by:** Paul Butler **Date:** March 20, 2016 |
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[321736f] | 61 | """ |
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| 62 | |
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[2d81cfe] | 63 | import numpy as np |
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[321736f] | 64 | from numpy import pi, inf |
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| 65 | |
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| 66 | name = "vesicle" |
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| 67 | title = "This model provides the form factor, *P(q)*, for an unilamellar \ |
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| 68 | vesicle. This is model is effectively identical to the hollow sphere \ |
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[216fa6d] | 69 | reparameterized to be more intuitive for a vesicle and normalizing the \ |
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| 70 | form factor by the volume of the shell." |
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[321736f] | 71 | description = """ |
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| 72 | Model parameters: |
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| 73 | radius : the core radius of the vesicle |
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| 74 | thickness: the shell thickness |
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| 75 | sld: the shell SLD |
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[e77872e] | 76 | sld_solvent: the solvent (and core) SLD |
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[321736f] | 77 | background: incoherent background |
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[062db5a] | 78 | volfraction: shell volume fraction |
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| 79 | scale : scale factor = 1 if on absolute scale""" |
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[321736f] | 80 | category = "shape:sphere" |
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| 81 | |
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| 82 | # [ "name", "units", default, [lower, upper], "type", "description"], |
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[42356c8] | 83 | parameters = [["sld", "1e-6/Ang^2", 0.5, [-inf, inf], "sld", |
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[321736f] | 84 | "vesicle shell scattering length density"], |
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[42356c8] | 85 | ["sld_solvent", "1e-6/Ang^2", 6.36, [-inf, inf], "sld", |
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[321736f] | 86 | "solvent scattering length density"], |
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[062db5a] | 87 | ["volfraction", "", 0.05, [0, 1.0], "", |
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| 88 | "volume fraction of shell"], |
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[321736f] | 89 | ["radius", "Ang", 100, [0, inf], "volume", |
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| 90 | "vesicle core radius"], |
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| 91 | ["thickness", "Ang", 30, [0, inf], "volume", |
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| 92 | "vesicle shell thickness"], |
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| 93 | ] |
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| 94 | |
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[925ad6e] | 95 | source = ["lib/sas_3j1x_x.c", "vesicle.c"] |
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[71b751d] | 96 | have_Fq = True |
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[321736f] | 97 | |
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| 98 | def ER(radius, thickness): |
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| 99 | ''' |
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| 100 | returns the effective radius used in the S*P calculation |
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| 101 | |
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| 102 | :param radius: core radius |
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| 103 | :param thickness: shell thickness |
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| 104 | ''' |
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| 105 | return radius + thickness |
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| 106 | |
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| 107 | def VR(radius, thickness): |
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| 108 | ''' |
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| 109 | returns the volumes of the shell and of the whole sphere including the |
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| 110 | core plus shell - is used to normalize when including polydispersity. |
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| 111 | |
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| 112 | :param radius: core radius |
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| 113 | :param thickness: shell thickness |
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| 114 | :return whole: volume of core and shell |
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| 115 | :return whole-core: volume of the shell |
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| 116 | ''' |
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| 117 | |
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[3a48772] | 118 | whole = 4./3. * pi * (radius + thickness)**3 |
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| 119 | core = 4./3. * pi * radius**3 |
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[321736f] | 120 | return whole, whole - core |
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| 121 | |
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[48462b0] | 122 | def random(): |
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| 123 | total_radius = 10**np.random.uniform(1.3, 5) |
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| 124 | radius = total_radius * np.random.uniform(0, 1) |
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| 125 | thickness = total_radius - radius |
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| 126 | volfraction = 10**np.random.uniform(-3, -1) |
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| 127 | pars = dict( |
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| 128 | #background=0, |
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| 129 | scale=1, # volfraction is part of the model, so scale=1 |
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| 130 | radius=radius, |
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| 131 | thickness=thickness, |
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| 132 | volfraction=volfraction, |
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| 133 | ) |
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| 134 | return pars |
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[321736f] | 135 | |
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| 136 | # parameters for demo |
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[062db5a] | 137 | demo = dict(sld=0.5, sld_solvent=6.36, |
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| 138 | volfraction=0.05, |
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[321736f] | 139 | radius=100, thickness=30, |
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| 140 | radius_pd=.2, radius_pd_n=10, |
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| 141 | thickness_pd=.2, thickness_pd_n=10) |
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| 142 | |
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[6dd90c1] | 143 | # NOTE: test results taken from values returned by SasView 3.1.2, with |
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| 144 | # 0.001 added for a non-zero default background. |
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[062db5a] | 145 | tests = [[{}, 0.0005, 859.916526646], |
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| 146 | [{}, 0.100600200401, 1.77063682331], |
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| 147 | [{}, 0.5, 0.00355351388906], |
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[321736f] | 148 | [{}, 'ER', 130.], |
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| 149 | [{}, 'VR', 0.54483386436], |
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| 150 | ] |
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