1 | r""" |
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2 | Definition |
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3 | ---------- |
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4 | |
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5 | This model provides the form factor, $P(q)$, for stacked discs (tactoids) |
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6 | with a core/layer structure which is constructed itself as $P(q) S(Q)$ |
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7 | multiplying a $P(q)$ for individual core/layer disks by a structure factor |
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8 | $S(q)$ proposed by Kratky and Porod in 1949\ [#CIT1949]_ assuming the next |
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9 | neighbor distance (d-spacing) in the stack of parallel discs obeys a Gaussian |
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10 | distribution. As such the normalization of this "composite" form factor is |
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11 | relative to the individual disk volume, not the volume of the stack of disks. |
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12 | This model is appropriate for example for non non exfoliated clay particles |
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13 | such as Laponite. |
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14 | |
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15 | .. figure:: img/stacked_disks_geometry.png |
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16 | |
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17 | Geometry of a single core/layer disk |
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18 | |
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19 | The scattered intensity $I(q)$ is calculated as |
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20 | |
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21 | .. math:: |
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22 | |
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23 | I(q) = N\int_{0}^{\pi /2}\left[ \Delta \rho_t |
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24 | \left( V_t f_t(q,\alpha) - V_c f_c(q,\alpha)\right) + \Delta |
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25 | \rho_c V_c f_c(q,\alpha)\right]^2 S(q,\alpha)\sin{\alpha}\ d\alpha |
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26 | + \text{background} |
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27 | |
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28 | where the contrast |
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29 | |
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30 | .. math:: |
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31 | |
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32 | \Delta \rho_i = \rho_i - \rho_\text{solvent} |
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33 | |
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34 | and $N$ is the number of individual (single) discs per unit volume, $\alpha$ |
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35 | is the angle between the axis of the disc and $q$, and $V_t$ and $V_c$ are the |
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36 | total volume and the core volume of a single disc, respectively, and |
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37 | |
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38 | .. math:: |
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39 | |
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40 | f_t(q,\alpha) = |
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41 | \left(\frac{\sin(q(d+h)\cos{\alpha})}{q(d+h)\cos{\alpha}}\right) |
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42 | \left(\frac{2J_1(qR\sin{\alpha})}{qR\sin{\alpha}} \right) |
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43 | |
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44 | f_c(q,\alpha) = |
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45 | \left(\frac{\sin(qh)\cos{\alpha})}{qh\cos{\alpha}}\right) |
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46 | \left(\frac{2J_1(qR\sin{\alpha})}{qR\sin{\alpha}}\right) |
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47 | |
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48 | where $d$ = thickness of the layer (*thick_layer*), |
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49 | $2h$ = core thickness (*thick_core*), and $R$ = radius of the disc (*radius*). |
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50 | |
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51 | .. math:: |
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52 | |
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53 | S(q,\alpha) = 1 + \frac{1}{2}\sum_{k=1}^n(n-k)\cos{(kDq\cos{\alpha})} |
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54 | \exp\left[ -k(q)^2(D\cos{\alpha}~\sigma_d)^2/2\right] |
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55 | |
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56 | where $n$ is the total number of the disc stacked (*n_stacking*), |
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57 | $D = 2(d+h)$ is the next neighbor center-to-center distance (d-spacing), |
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58 | and $\sigma_d$ = the Gaussian standard deviation of the d-spacing (*sigma_d*). |
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59 | Note that $D\cos(\alpha)$ is the component of $D$ parallel to $q$ and the last |
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60 | term in the equation above is effectively a Debye-Waller factor term. |
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61 | |
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62 | .. note:: |
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63 | |
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64 | 1. Each assembly in the stack is layer/core/layer, so the spacing of the |
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65 | cores is core plus two layers. The 2nd virial coefficient of the cylinder |
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66 | is calculated based on the *radius* and *length* |
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67 | = *n_stacking* * (*thick_core* + 2 * *thick_layer*) |
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68 | values, and used as the effective radius for $S(Q)$ when $P(Q) * S(Q)$ |
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69 | is applied. |
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70 | |
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71 | 2. the resolution smearing calculation uses 76 Gaussian quadrature points |
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72 | to properly smear the model since the function is HIGHLY oscillatory, |
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73 | especially around the q-values that correspond to the repeat distance of |
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74 | the layers. |
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75 | |
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76 | 2d scattering from oriented stacks is calculated in the same way as for |
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77 | cylinders, for further details of the calculation and angular dispersions |
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78 | see :ref:`orientation`. |
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79 | |
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80 | .. figure:: img/cylinder_angle_definition.png |
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81 | |
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82 | Angles $\theta$ and $\phi$ orient the stack of discs relative |
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83 | to the beam line coordinates, where the beam is along the $z$ axis. |
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84 | Rotation $\theta$, initially in the $xz$ plane, is carried out first, |
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85 | then rotation $\phi$ about the $z$ axis. Orientation distributions are |
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86 | described as rotations about two perpendicular axes $\delta_1$ and |
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87 | $\delta_2$ in the frame of the cylinder itself, which when |
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88 | $\theta = \phi = 0$ are parallel to the $Y$ and $X$ axes. |
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89 | |
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90 | |
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91 | Our model is derived from the form factor calculations implemented in a |
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92 | c-library provided by the NIST Center for Neutron Research\ [#CIT_Kline]_ |
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93 | |
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94 | References |
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95 | ---------- |
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96 | |
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97 | .. [#CIT1949] O Kratky and G Porod, *J. Colloid Science*, 4, (1949) 35 |
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98 | .. [#CIT_Kline] S R Kline, *J Appl. Cryst.*, 39 (2006) 895 |
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99 | .. [#] J S Higgins and H C Benoit, *Polymers and Neutron Scattering*, |
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100 | Clarendon, Oxford, 1994 |
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101 | .. [#] A Guinier and G Fournet, *Small-Angle Scattering of X-Rays*, |
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102 | John Wiley and Sons, New York, 1955 |
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103 | |
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104 | Authorship and Verification |
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105 | ---------------------------- |
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106 | |
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107 | * **Author:** NIST IGOR/DANSE **Date:** pre 2010 |
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108 | * **Last Modified by:** Paul Butler and Paul Kienzle **on:** November 26, 2016 |
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109 | * **Last Reviewed by:** Paul Butler and Paul Kienzle **on:** November 26, 2016 |
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110 | """ |
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111 | |
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112 | import numpy as np |
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113 | from numpy import inf, sin, cos, pi |
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114 | |
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115 | name = "stacked_disks" |
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116 | title = "Form factor for a stacked set of non exfoliated core/shell disks" |
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117 | description = """\ |
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118 | One layer of disk consists of a core, a top layer, and a bottom layer. |
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119 | radius = the radius of the disk |
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120 | thick_core = thickness of the core |
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121 | thick_layer = thickness of a layer |
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122 | sld_core = the SLD of the core |
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123 | sld_layer = the SLD of the layers |
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124 | n_stacking = the number of the disks |
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125 | sigma_d = Gaussian STD of d-spacing |
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126 | sld_solvent = the SLD of the solvent |
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127 | """ |
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128 | category = "shape:cylinder" |
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129 | |
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130 | # pylint: disable=bad-whitespace, line-too-long |
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131 | # ["name", "units", default, [lower, upper], "type","description"], |
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132 | parameters = [ |
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133 | ["thick_core", "Ang", 10.0, [0, inf], "volume", "Thickness of the core disk"], |
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134 | ["thick_layer", "Ang", 10.0, [0, inf], "volume", "Thickness of layer each side of core"], |
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135 | ["radius", "Ang", 15.0, [0, inf], "volume", "Radius of the stacked disk"], |
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136 | ["n_stacking", "", 1.0, [1, inf], "volume", "Number of stacked layer/core/layer disks"], |
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137 | ["sigma_d", "Ang", 0, [0, inf], "", "Sigma of nearest neighbor spacing"], |
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138 | ["sld_core", "1e-6/Ang^2", 4, [-inf, inf], "sld", "Core scattering length density"], |
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139 | ["sld_layer", "1e-6/Ang^2", 0.0, [-inf, inf], "sld", "Layer scattering length density"], |
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140 | ["sld_solvent", "1e-6/Ang^2", 5.0, [-inf, inf], "sld", "Solvent scattering length density"], |
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141 | ["theta", "degrees", 0, [-360, 360], "orientation", "Orientation of the stacked disk axis w/respect incoming beam"], |
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142 | ["phi", "degrees", 0, [-360, 360], "orientation", "Rotation about beam"], |
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143 | ] |
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144 | # pylint: enable=bad-whitespace, line-too-long |
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145 | |
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146 | source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "stacked_disks.c"] |
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147 | |
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148 | def random(): |
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149 | radius = 10**np.random.uniform(1, 4.7) |
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150 | total_stack = 10**np.random.uniform(1, 4.7) |
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151 | n_stacking = int(10**np.random.uniform(0, np.log10(total_stack)-1) + 0.5) |
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152 | d = total_stack/n_stacking |
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153 | thick_core = np.random.uniform(0, d-2) # at least 1 A for each layer |
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154 | thick_layer = (d - thick_core)/2 |
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155 | # Let polydispersity peak around 15%; 95% < 0.4; max=100% |
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156 | sigma_d = d * np.random.beta(1.5, 7) |
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157 | pars = dict( |
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158 | thick_core=thick_core, |
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159 | thick_layer=thick_layer, |
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160 | radius=radius, |
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161 | n_stacking=n_stacking, |
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162 | sigma_d=sigma_d, |
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163 | ) |
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164 | return pars |
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165 | |
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166 | demo = dict(background=0.001, |
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167 | scale=0.01, |
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168 | thick_core=10.0, |
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169 | thick_layer=10.0, |
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170 | radius=15.0, |
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171 | n_stacking=1, |
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172 | sigma_d=0, |
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173 | sld_core=4, |
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174 | sld_layer=0.0, |
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175 | sld_solvent=5.0, |
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176 | theta=90, |
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177 | phi=0) |
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178 | # After redefinition of spherical coordinates - |
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179 | # tests had in old coords theta=0, phi=0; new coords theta=90, phi=0 |
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180 | q = 0.1 |
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181 | # april 6 2017, rkh added a 2d unit test, assume correct! |
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182 | qx = q*cos(pi/6.0) |
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183 | qy = q*sin(pi/6.0) |
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184 | # Accuracy tests based on content in test/utest_extra_models.py. |
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185 | # Added 2 tests with n_stacked = 5 using SasView 3.1.2 - PDB; |
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186 | # for which alas q=0.001 values seem closer to n_stacked=1 not 5, |
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187 | # changed assuming my 4.1 code OK, RKH |
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188 | tests = [ |
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189 | [{'thick_core': 10.0, |
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190 | 'thick_layer': 15.0, |
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191 | 'radius': 3000.0, |
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192 | 'n_stacking': 1.0, |
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193 | 'sigma_d': 0.0, |
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194 | 'sld_core': 4.0, |
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195 | 'sld_layer': -0.4, |
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196 | 'sld_solvent': 5.0, |
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197 | 'theta': 90.0, |
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198 | 'phi': 0.0, |
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199 | 'scale': 0.01, |
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200 | 'background': 0.001, |
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201 | }, 0.001, 5075.12], |
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202 | [{'thick_core': 10.0, |
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203 | 'thick_layer': 15.0, |
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204 | 'radius': 3000.0, |
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205 | 'n_stacking': 5, |
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206 | 'sigma_d': 0.0, |
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207 | 'sld_core': 4.0, |
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208 | 'sld_layer': -0.4, |
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209 | 'sld_solvent': 5.0, |
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210 | 'theta': 90.0, |
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211 | 'phi': 0.0, |
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212 | 'scale': 0.01, |
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213 | 'background': 0.001, |
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214 | # n_stacking=1 not 5 ? slight change in value here 11jan2017, |
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215 | # check other cpu types |
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216 | #}, 0.001, 5065.12793824], |
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217 | #}, 0.001, 5075.11570493], |
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218 | }, 0.001, 25325.635693], |
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219 | [{'thick_core': 10.0, |
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220 | 'thick_layer': 15.0, |
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221 | 'radius': 100.0, |
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222 | 'n_stacking': 5, |
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223 | 'sigma_d': 0.0, |
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224 | 'sld_core': 4.0, |
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225 | 'sld_layer': -0.4, |
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226 | 'sld_solvent': 5.0, |
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227 | 'theta': 90.0, |
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228 | 'phi': 20.0, |
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229 | 'scale': 0.01, |
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230 | 'background': 0.001, |
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231 | }, (qx, qy), 0.0491167089952], |
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232 | [{'thick_core': 10.0, |
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233 | 'thick_layer': 15.0, |
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234 | 'radius': 3000.0, |
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235 | 'n_stacking': 5, |
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236 | 'sigma_d': 0.0, |
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237 | 'sld_core': 4.0, |
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238 | 'sld_layer': -0.4, |
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239 | 'sld_solvent': 5.0, |
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240 | 'theta': 90.0, |
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241 | 'phi': 0.0, |
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242 | 'scale': 0.01, |
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243 | 'background': 0.001, |
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244 | # n_stacking=1 not 5 ? slight change in value here 11jan2017, |
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245 | # check other cpu types |
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246 | #}, 0.164, 0.0127673597265], |
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247 | #}, 0.164, 0.01480812968], |
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248 | }, 0.164, 0.0598367986509], |
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249 | |
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250 | [{'thick_core': 10.0, |
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251 | 'thick_layer': 15.0, |
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252 | 'radius': 3000.0, |
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253 | 'n_stacking': 1.0, |
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254 | 'sigma_d': 0.0, |
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255 | 'sld_core': 4.0, |
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256 | 'sld_layer': -0.4, |
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257 | 'sld_solvent': 5.0, |
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258 | 'theta': 90.0, |
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259 | 'phi': 0.0, |
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260 | 'scale': 0.01, |
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261 | 'background': 0.001, |
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262 | # second test here was at q=90, changed it to q=5, |
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263 | # note I(q) is then just value of flat background |
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264 | }, [0.001, 5.0], [5075.12, 0.001]], |
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265 | |
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266 | [{'thick_core': 10.0, |
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267 | 'thick_layer': 15.0, |
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268 | 'radius': 3000.0, |
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269 | 'n_stacking': 1.0, |
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270 | 'sigma_d': 0.0, |
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271 | 'sld_core': 4.0, |
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272 | 'sld_layer': -0.4, |
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273 | 'sld_solvent': 5.0, |
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274 | 'theta': 90.0, |
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275 | 'phi': 0.0, |
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276 | 'scale': 0.01, |
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277 | 'background': 0.001, |
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278 | }, ([0.4, 0.5]), [0.00105074, 0.00121761]], |
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279 | #[{'thick_core': 10.0, |
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280 | # 'thick_layer': 15.0, |
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281 | # 'radius': 3000.0, |
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282 | # 'n_stacking': 1.0, |
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283 | # 'sigma_d': 0.0, |
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284 | # 'sld_core': 4.0, |
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285 | # 'sld_layer': -0.4, |
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286 | # 'sld_solvent': 5.0, |
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287 | # 'theta': 90.0, |
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288 | # 'phi': 20.0, |
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289 | # 'scale': 0.01, |
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290 | # 'background': 0.001, |
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291 | # 2017-05-18 PAK temporarily suppress output of qx,qy test; j1 is |
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292 | # not accurate for large qr |
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293 | # }, (qx, qy), 0.0341738733124], |
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294 | # }, (qx, qy), None], |
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295 | |
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296 | [{'thick_core': 10.0, |
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297 | 'thick_layer': 15.0, |
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298 | 'radius': 3000.0, |
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299 | 'n_stacking': 1.0, |
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300 | 'sigma_d': 0.0, |
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301 | 'sld_core': 4.0, |
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302 | 'sld_layer': -0.4, |
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303 | 'sld_solvent': 5.0, |
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304 | 'theta': 90.0, |
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305 | 'phi': 0.0, |
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306 | 'scale': 0.01, |
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307 | 'background': 0.001, |
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308 | }, ([1.3, 1.57]), [0.0010039, 0.0010038]], |
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309 | ] |
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310 | # 11Jan2017 RKH checking unit test again, note they are all 1D, no 2D |
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