1 | .. _triaxial-ellipsoid: |
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2 | |
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3 | Triaxial ellipsoid |
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4 | ======================================================= |
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5 | |
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6 | Ellipsoid of uniform scattering length density with three independent axes. |
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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 Ellipsoid 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 | req_minor Minor equitorial radius |Ang| 20 |
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16 | req_major Major equatorial radius |Ang| 400 |
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17 | rpolar Polar radius |Ang| 10 |
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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 | psi Out of plane angle degree 60 |
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21 | =========== =================================== ============ ============= |
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22 | |
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23 | The returned value is scaled to units of |cm^-1|. |
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24 | |
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25 | |
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26 | All three axes are of different lengths with $R_a \le R_b <= R_c$ |
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27 | **Users should maintain this inequality for all calculations**. |
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28 | |
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29 | .. math:: |
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30 | |
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31 | P(Q) = \text{scale} V \left< F^2(Q) \right> + \text{background} |
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32 | |
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33 | where the volume $V = 4/3 \pi R_a R_b R_c$, and the averaging |
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34 | $\left< \cdots \right>$ is applied over all orientations for 1D. |
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35 | |
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36 | .. figure:: img/triaxial_ellipsoid_geometry.jpg |
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37 | |
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38 | Ellipsoid schematic. |
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39 | |
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40 | The returned value is in units of |cm^-1|, on absolute scale. |
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41 | |
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42 | Definition |
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43 | ---------- |
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44 | |
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45 | The form factor calculated is |
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46 | |
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47 | .. math:: |
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48 | |
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49 | P(Q) = \frac{\text{scale}}{V}\int_0^1\int_0^1 |
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50 | \Phi^2(QR_a^2\cos^2( \pi x/2) + QR_b^2\sin^2(\pi y/2)(1-y^2) + c^2y^2) |
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51 | dx dy |
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52 | |
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53 | where |
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54 | |
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55 | .. math:: |
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56 | |
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57 | \Phi(u) = 3 u^{-3} (\sin u - u \cos u) |
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58 | |
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59 | To provide easy access to the orientation of the triaxial ellipsoid, |
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60 | we define the axis of the cylinder using the angles $\theta$, $\phi$ |
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61 | and $\psi$. These angles are defined on |
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62 | :num:`figure #triaxial-ellipsoid-angles`. |
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63 | The angle $\psi$ is the rotational angle around its own $c$ axis |
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64 | against the $Q$ plane. For example, $\psi = 0$ when the |
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65 | $a$ axis is parallel to the $x$ axis of the detector. |
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66 | |
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67 | .. _triaxial-ellipsoid-angles: |
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68 | |
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69 | .. figure:: img/triaxial_ellipsoid_angles.jpg |
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70 | |
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71 | The angles for oriented ellipsoid. |
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72 | |
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73 | The radius-of-gyration for this system is $R_g^2 = (R_a R_b R_c)^2/5$. |
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74 | |
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75 | The contrast is defined as SLD(ellipsoid) - SLD(solvent). In the |
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76 | parameters, *a* is the minor equatorial radius, *b* is the major |
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77 | equatorial radius, and c is the polar radius of the ellipsoid. |
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78 | |
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79 | NB: The 2nd virial coefficient of the triaxial solid ellipsoid is |
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80 | calculated based on the polar radius $R_p = R_c$ and equatorial |
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81 | radius $R_e = \sqrt{R_a R_b}$, and used as the effective radius for |
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82 | $S(Q)$ when $P(Q) \cdot S(Q)$ is applied. |
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83 | |
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84 | .. figure:: img/triaxial_ellipsoid_1d.jpg |
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85 | |
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86 | 1D plot using the default values (w/1000 data point). |
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87 | |
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88 | Validation |
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89 | ---------- |
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90 | |
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91 | Validation of our code was done by comparing the output of the |
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92 | 1D calculation to the angular average of the output of 2D calculation |
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93 | over all possible angles. |
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94 | :num:`Figure #triaxial-ellipsoid-comparison` shows the comparison where |
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95 | the solid dot refers to averaged 2D while the line represents the |
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96 | result of 1D calculation (for 2D averaging, 76, 180, and 76 points |
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97 | are taken for the angles of $\theta$, $\phi$, and $\psi$ respectively). |
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98 | |
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99 | .. _triaxial-ellipsoid-comparison: |
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100 | |
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101 | .. figure:: img/triaxial_ellipsoid_comparison.png |
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102 | |
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103 | Comparison between 1D and averaged 2D. |
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104 | |
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105 | Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research |
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106 | (Kline, 2006) |
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107 | |
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108 | REFERENCE |
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109 | |
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110 | L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, Plenum, |
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111 | New York, 1987. |
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112 | |
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