1 | .. _capped-cylinder: |
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2 | |
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3 | Capped cylinder |
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4 | ======================================================= |
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5 | |
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6 | Right circular cylinder with spherical end caps and uniform SLD |
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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 | cap_radius Cap radius |Ang| 20 |
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17 | length Cylinder length |Ang| 400 |
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18 | theta In plane angle degree 60 |
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19 | phi Out of plane angle degree 60 |
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20 | =========== ================================== ============ ============= |
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21 | |
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22 | The returned value is scaled to units of |cm^-1|. |
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23 | |
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24 | |
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25 | Calculates the scattering from a cylinder with spherical section end-caps. |
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26 | This model simply becomes the a convex lens when the length of the cylinder |
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27 | $L=0$, that is, a sphereocylinder with end caps that have a radius larger |
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28 | than that of the cylinder and the center of the end cap radius lies within |
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29 | the cylinder. See the diagram for the details of the geometry and |
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30 | restrictions on parameter values. |
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31 | |
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32 | Definitions |
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33 | ----------- |
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34 | |
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35 | The returned value is scaled to units of |cm^-1|\ |sr^-1|, absolute scale. |
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36 | |
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37 | The capped cylinder geometry is defined as |
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38 | |
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39 | .. image:: img/capped_cylinder_geometry.jpg |
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40 | |
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41 | where $r$ is the radius of the cylinder. All other parameters are as defined |
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42 | in the diagram. Since the end cap radius $R \ge r$ and by definition for this |
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43 | geometry $h < 0$, $h$ is then defined by $r$ and $R$ as |
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44 | |
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45 | .. math:: |
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46 | |
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47 | h = - \sqrt{R^2 - r^2} |
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48 | |
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49 | The scattered intensity $I(Q)$ is calculated as |
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50 | |
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51 | .. math:: |
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52 | |
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53 | I(Q) = \frac{(\Delta \rho)^2}{V} \left< A^2(Q)\right> |
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54 | |
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55 | where the amplitude $A(Q)$ is given as |
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56 | |
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57 | .. math:: |
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58 | |
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59 | A(Q) =&\ \pi r^2L |
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60 | {\sin\left(\tfrac12 QL\cos\theta\right) |
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61 | \over \tfrac12 QL\cos\theta} |
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62 | {2 J_1(Qr\sin\theta) \over Qr\sin\theta} \\ |
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63 | &\ + 4 \pi R^3 \int_{-h/R}^1 dt |
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64 | \cos\left[ Q\cos\theta |
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65 | \left(Rt + h + {\tfrac12} L\right)\right] |
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66 | \times (1-t^2) |
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67 | {J_1\left[QR\sin\theta \left(1-t^2\right)^{1/2}\right] |
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68 | \over QR\sin\theta \left(1-t^2\right)^{1/2}} |
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69 | |
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70 | The $\left< \ldots \right>$ brackets denote an average of the structure over |
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71 | all orientations. $\left< A^2(Q)\right>$ is then the form factor, $P(Q)$. |
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72 | The scale factor is equivalent to the volume fraction of cylinders, each of |
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73 | volume, $V$. Contrast is the difference of scattering length densities of |
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74 | the cylinder and the surrounding solvent. |
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75 | |
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76 | The volume of the capped cylinder is (with $h$ as a positive value here) |
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77 | |
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78 | .. math:: |
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79 | |
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80 | V = \pi r_c^2 L + \tfrac{2\pi}{3}(R-h)^2(2R + h) |
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81 | |
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82 | |
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83 | and its radius-of-gyration is |
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84 | |
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85 | .. math:: |
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86 | |
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87 | R_g^2 =&\ \left[ \tfrac{12}{5}R^5 |
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88 | + R^4\left(6h+\tfrac32 L\right) |
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89 | + R^2\left(4h^2 + L^2 + 4Lh\right) |
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90 | + R^2\left(3Lh^2 + \tfrac32 L^2h\right) \right. \\ |
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91 | &\ \left. + \tfrac25 h^5 - \tfrac12 Lh^4 - \tfrac12 L^2h^3 |
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92 | + \tfrac14 L^3r^2 + \tfrac32 Lr^4 \right] |
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93 | \left( 4R^3 6R^2h - 2h^3 + 3r^2L \right)^{-1} |
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94 | |
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95 | |
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96 | .. note:: |
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97 | |
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98 | The requirement that $R \ge r$ is not enforced in the model! |
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99 | It is up to you to restrict this during analysis. |
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100 | |
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101 | :num:`Figure #capped-cylinder-1d` shows the output produced by |
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102 | a running the 1D capped cylinder model, using *qmin* = 0.001 |Ang^-1|, |
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103 | *qmax* = 0.7 |Ang^-1| and the default values of the parameters. |
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104 | |
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105 | .. _capped-cylinder-1d: |
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106 | |
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107 | .. figure:: img/capped_cylinder_1d.jpg |
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108 | |
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109 | 1D plot using the default values (w/256 data point). |
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110 | |
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111 | The 2D scattering intensity is calculated similar to the 2D cylinder model. |
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112 | :num:`Figure #capped-cylinder-2d` shows the output for $\theta=45^\circ$ |
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113 | and $\phi=0^\circ$ with default values for the other parameters. |
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114 | |
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115 | .. _capped-cylinder-2d: |
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116 | |
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117 | .. figure:: img/capped_cylinder_2d.jpg |
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118 | |
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119 | 2D plot (w/(256X265) data points). |
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120 | |
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121 | .. figure:: img/orientation.jpg |
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122 | |
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123 | Definition of the angles for oriented 2D cylinders. |
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124 | |
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125 | .. figure:: img/orientation2.jpg |
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126 | |
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127 | Examples of the angles for oriented pp against the detector plane. |
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128 | |
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129 | REFERENCE |
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130 | |
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131 | H Kaya, *J. Appl. Cryst.*, 37 (2004) 223-230 |
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132 | |
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133 | H Kaya and N-R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda and errata) |
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134 | |
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