1 | .. _cylinder: |
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2 | |
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3 | Cylinder |
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4 | ======================================================= |
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5 | |
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6 | Right circular cylinder with uniform scattering length density. |
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7 | |
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8 | =========== ================================== ============ ============= |
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9 | Parameter Description Units Default value |
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10 | =========== ================================== ============ ============= |
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11 | scale Source intensity None 1 |
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12 | background Source background |cm^-1| 0 |
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13 | sld Cylinder scattering length density |1e-6Ang^-2| 4 |
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14 | solvent_sld Solvent scattering length density |1e-6Ang^-2| 1 |
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15 | radius Cylinder radius |Ang| 20 |
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16 | length Cylinder length |Ang| 400 |
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17 | theta In plane angle degree 60 |
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18 | phi Out of plane angle degree 60 |
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19 | =========== ================================== ============ ============= |
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20 | |
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21 | The returned value is scaled to units of |cm^-1|. |
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22 | |
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23 | |
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24 | The form factor is normalized by the particle volume. |
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25 | |
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26 | For information about polarised and magnetic scattering, click here_. |
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27 | |
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28 | Definition |
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29 | ---------- |
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30 | |
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31 | The output of the 2D scattering intensity function for oriented cylinders is |
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32 | given by (Guinier, 1955) |
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33 | |
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34 | .. math:: |
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35 | |
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36 | P(Q,\alpha) = {\text{scale} \over V} F^2(Q) + \text{background} |
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37 | |
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38 | where |
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39 | |
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40 | .. math:: |
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41 | |
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42 | F(Q) = 2 (\Delta \rho) V |
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43 | {\sin \left(Q\tfrac12 L\cos\alpha \right) |
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44 | \over Q\tfrac12 L \cos \alpha} |
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45 | {J_1 \left(Q R \sin \alpha\right) \over Q R \sin \alpha} |
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46 | |
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47 | and $\alpha$ is the angle between the axis of the cylinder and $\vec q$, $V$ |
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48 | is the volume of the cylinder, $L$ is the length of the cylinder, $R$ is the |
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49 | radius of the cylinder, and $\Delta\rho$ (contrast) is the scattering length |
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50 | density difference between the scatterer and the solvent. $J_1$ is the |
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51 | first order Bessel function. |
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52 | |
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53 | To provide easy access to the orientation of the cylinder, we define the |
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54 | axis of the cylinder using two angles $\theta$ and $\phi$. Those angles |
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55 | are defined in :num:`figure #cylinder-orientation`. |
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56 | |
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57 | .. _cylinder-orientation: |
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58 | |
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59 | .. figure:: img/orientation.jpg |
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60 | |
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61 | Definition of the angles for oriented cylinders. |
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62 | |
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63 | .. figure:: img/orientation2.jpg |
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64 | |
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65 | Examples of the angles for oriented cylinders against the detector plane. |
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66 | |
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67 | NB: The 2nd virial coefficient of the cylinder is calculated based on the |
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68 | radius and length values, and used as the effective radius for $S(Q)$ |
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69 | when $P(Q) \cdot S(Q)$ is applied. |
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70 | |
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71 | The output of the 1D scattering intensity function for randomly oriented |
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72 | cylinders is then given by |
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73 | |
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74 | .. math:: |
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75 | |
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76 | P(Q) = {\text{scale} \over V} |
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77 | \int_0^{\pi/2} F^2(Q,\alpha) \sin \alpha\ d\alpha + \text{background} |
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78 | |
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79 | The *theta* and *phi* parameters are not used for the 1D output. Our |
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80 | implementation of the scattering kernel and the 1D scattering intensity |
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81 | use the c-library from NIST. |
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82 | |
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83 | Validation |
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84 | ---------- |
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85 | |
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86 | Validation of our code was done by comparing the output of the 1D model |
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87 | to the output of the software provided by the NIST (Kline, 2006). |
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88 | :num:`Figure #cylinder-compare` shows a comparison of |
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89 | the 1D output of our model and the output of the NIST software. |
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90 | |
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91 | .. _cylinder-compare: |
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92 | |
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93 | .. figure:: img/cylinder_compare.jpg |
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94 | |
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95 | Comparison of the SasView scattering intensity for a cylinder with the |
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96 | output of the NIST SANS analysis software. |
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97 | The parameters were set to: *scale* = 1.0, *radius* = 20 |Ang|, |
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98 | *length* = 400 |Ang|, *contrast* = 3e-6 |Ang^-2|, and |
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99 | *background* = 0.01 |cm^-1|. |
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100 | |
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101 | In general, averaging over a distribution of orientations is done by |
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102 | evaluating the following |
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103 | |
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104 | .. math:: |
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105 | |
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106 | P(Q) = \int_0^{\pi/2} d\phi |
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107 | \int_0^\pi p(\theta, \phi) P_0(Q,\alpha) \sin \theta\ d\theta |
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108 | |
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109 | |
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110 | where $p(\theta,\phi)$ is the probability distribution for the orientation |
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111 | and $P_0(Q,\alpha)$ is the scattering intensity for the fully oriented |
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112 | system. Since we have no other software to compare the implementation of |
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113 | the intensity for fully oriented cylinders, we can compare the result of |
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114 | averaging our 2D output using a uniform distribution $p(\theta, \phi) = 1.0$. |
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115 | :num:`Figure #cylinder-crosscheck` shows the result of |
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116 | such a cross-check. |
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117 | |
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118 | .. _cylinder-crosscheck: |
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119 | |
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120 | .. figure:: img/cylinder_crosscheck.jpg |
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121 | |
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122 | Comparison of the intensity for uniformly distributed cylinders |
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123 | calculated from our 2D model and the intensity from the NIST SANS |
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124 | analysis software. |
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125 | The parameters used were: *scale* = 1.0, *radius* = 20 |Ang|, |
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126 | *length* = 400 |Ang|, *contrast* = 3e-6 |Ang^-2|, and |
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127 | *background* = 0.0 |cm^-1|. |
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128 | |
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