[fb7fcec] | 1 | .. corfunc_help.rst |
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| 2 | |
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[da456fb] | 3 | .. _Correlation_Function_Analysis: |
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| 4 | |
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[32c5983] | 5 | Correlation Function Analysis |
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| 6 | ============================= |
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[fb7fcec] | 7 | |
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| 8 | Description |
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| 9 | ----------- |
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| 10 | |
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[ad476d1] | 11 | This currently performs correlation function analysis on SAXS/SANS data, |
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| 12 | but in the the future is also planned to generate model-independent volume |
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| 13 | fraction profiles from the SANS from adsorbed polymer/surfactant layers. |
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| 14 | The two types of analyses differ in the mathematical transform that is |
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| 15 | applied to the data (Fourier vs Hilbert). However, both functions are |
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| 16 | returned in *real space*. |
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[fb7fcec] | 17 | |
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[d78b5cb] | 18 | A correlation function may be interpreted in terms of an imaginary rod moving |
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[ad476d1] | 19 | through the structure of the material. Î(x) is the probability that a rod of |
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| 20 | length x has equal electron/neutron scattering length density at either end. |
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| 21 | Hence a frequently occurring spacing within a structure will manifest itself |
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| 22 | as a peak in Î(x). *SasView* will return both the one-dimensional ( Î\ :sub:`1`\ (x) ) |
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| 23 | and three-dimensional ( Î\ :sub:`3`\ (x) ) correlation functions, the difference |
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| 24 | being that the former is only averaged in the plane of the scattering vector. |
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| 25 | |
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| 26 | A volume fraction profile :math:`\Phi`\ (z) describes how the density of polymer |
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| 27 | segments/surfactant molecules varies with distance, z, normal to an (assumed |
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| 28 | locally flat) interface. The form of :math:`\Phi`\ (z) can provide information |
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| 29 | about the arrangement of polymer/surfactant molecules at the interface. The width |
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| 30 | of the profile provides measures of the layer thickness, and the area under |
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| 31 | the profile is related to the amount of material that is adsorbed. |
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| 32 | |
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| 33 | Both analyses are performed in 3 stages: |
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| 34 | |
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| 35 | * Extrapolation of the scattering curve to :math:`Q = 0` and toward |
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[fb7fcec] | 36 | :math:`Q = \infty` |
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[1404cce] | 37 | * Smoothed merging of the two extrapolations into the original data |
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| 38 | * Fourier / Hilbert Transform of the smoothed data to give the correlation |
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[ad476d1] | 39 | function or volume fraction profile, respectively |
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| 40 | * (Optional) Interpretation of Î\ :sub:`1`\ (x) assuming the sample conforms |
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| 41 | to an ideal lamellar morphology |
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[fb7fcec] | 42 | |
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| 43 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 44 | |
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[ad476d1] | 45 | |
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[fb7fcec] | 46 | Extrapolation |
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| 47 | ------------- |
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| 48 | |
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| 49 | To :math:`Q = 0` |
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[1404cce] | 50 | ................ |
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[fb7fcec] | 51 | |
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[ad476d1] | 52 | The data are extrapolated to q = 0 by fitting a Guinier function to the data |
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| 53 | points in the low-q range. |
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[1404cce] | 54 | |
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[fb7fcec] | 55 | The equation used is: |
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| 56 | |
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| 57 | .. math:: |
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[ad476d1] | 58 | I(q) = A e^{Bq^2} |
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[fb7fcec] | 59 | |
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[ad476d1] | 60 | Where the parameter :math:`B` is related to the effective radius-of-gyration of |
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| 61 | a spherical object having the same small-angle scattering in this region. |
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| 62 | |
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| 63 | Note that as q tends to zero this function tends to a limiting value and is |
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| 64 | therefore less appropriate for use in systems where the form factor does not |
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| 65 | do likewise. However, because of the transform, the correlation functions are |
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| 66 | most affected by the Guinier back-extrapolation at *large* values of x where |
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| 67 | the impact on any extrapolated parameters will be least significant. |
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[fb7fcec] | 68 | |
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| 69 | To :math:`Q = \infty` |
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[1404cce] | 70 | ..................... |
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[fb7fcec] | 71 | |
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[ad476d1] | 72 | The data are extrapolated towards q = :math:`\infty` by fitting a Porod model to |
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| 73 | the data points in the high-q range and then computing the extrapolation to 100 |
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| 74 | times the maximum q value in the experimental dataset. This should be more than |
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| 75 | sufficient to ensure that on transformation any truncation artefacts introduced |
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| 76 | are at such small values of x that they can be safely ignored. |
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[fb7fcec] | 77 | |
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| 78 | The equation used is: |
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| 79 | |
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| 80 | .. math:: |
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[ad476d1] | 81 | I(q) = K q^{-4}e^{-q^2\sigma^2} + Bg |
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[fb7fcec] | 82 | |
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[ad476d1] | 83 | Where :math:`Bg` is the background, :math:`K` is the Porod constant, and :math:`\sigma` (which |
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| 84 | must be > 0) describes the width of the electron/neutron scattering length density |
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| 85 | profile at the interface between the crystalline and amorphous regions as shown below. |
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[fb7fcec] | 86 | |
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[6aad2e8] | 87 | .. figure:: fig1.png |
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[fb7fcec] | 88 | :align: center |
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| 89 | |
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[d78b5cb] | 90 | |
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[fb7fcec] | 91 | Smoothing |
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[1404cce] | 92 | --------- |
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[fb7fcec] | 93 | |
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[ad476d1] | 94 | The extrapolated data set consists of the Guinier back-extrapolation from q ~ 0 |
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| 95 | up to the lowest q value in the original data, then the original scattering data, |
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| 96 | and then the Porod tail-fit beyond this. The joins between the original data and |
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| 97 | the Guinier/Porod extrapolations are smoothed using the algorithm below to try |
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| 98 | and avoid the formation of truncation ripples in the transformed data: |
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[fb7fcec] | 99 | |
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[2fe78566] | 100 | Functions :math:`f(x_i)` and :math:`g(x_i)` where :math:`x_i \in \left\{ |
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| 101 | {x_1, x_2, ..., x_n} \right\}`, are smoothed over the range :math:`[a, b]` |
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| 102 | to produce :math:`y(x_i)`, by the following equations: |
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[fb7fcec] | 103 | |
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| 104 | .. math:: |
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| 105 | y(x_i) = h_ig(x_i) + (1-h_i)f(x_i) |
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| 106 | |
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| 107 | where: |
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| 108 | |
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| 109 | .. math:: |
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| 110 | h_i = \frac{1}{1 + \frac{(x_i-b)^2}{(x_i-a)^2}} |
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[41345d7e] | 111 | |
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[d78b5cb] | 112 | |
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[ad476d1] | 113 | Transformation |
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| 114 | -------------- |
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[41345d7e] | 115 | |
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| 116 | Fourier |
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[1404cce] | 117 | ....... |
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[41345d7e] | 118 | |
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[ad476d1] | 119 | If "Fourier" is selected for the transform type, *SasView* will perform a |
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[0390040] | 120 | discrete cosine transform on the extrapolated data in order to calculate the |
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[ad476d1] | 121 | 1D correlation function as: |
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[1404cce] | 122 | |
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| 123 | .. math:: |
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[ad476d1] | 124 | \Gamma _{1}(x) = \frac{1}{Q^{*}} \int_{0}^{\infty }I(q) q^{2} cos(qx) dq |
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[1404cce] | 125 | |
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[ad476d1] | 126 | where Q\ :sup:`*` is the Scattering (also called Porod) Invariant. |
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[1404cce] | 127 | |
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| 128 | The following algorithm is applied: |
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[41345d7e] | 129 | |
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| 130 | .. math:: |
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| 131 | \Gamma(x_k) = 2 \sum_{n=0}^{N-1} x_n \cos{\left[ \frac{\pi}{N} |
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[4b4b746] | 132 | \left(n + \frac{1}{2} \right) k \right] } \text{ for } k = 0, 1, \ldots, |
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[41345d7e] | 133 | N-1, N |
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| 134 | |
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[ad476d1] | 135 | The 3D correlation function is calculated as: |
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[d78b5cb] | 136 | |
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| 137 | .. math:: |
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[ad476d1] | 138 | \Gamma _{3}(x) = \frac{1}{Q^{*}} \int_{0}^{\infty}I(q) q^{2} |
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| 139 | \frac{sin(qx)}{qx} dq |
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| 140 | |
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| 141 | .. note:: It is always advisable to inspect Î\ :sub:`1`\ (x) and Î\ :sub:`3`\ (x) |
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| 142 | for artefacts arising from the extrapolation and transformation processes: |
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| 143 | |
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| 144 | - do they tend to zero as x tends to :math:`\infty`? |
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| 145 | - do they smoothly curve onto the ordinate at x = 0? (if not check the value |
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| 146 | of :math:`\sigma` is sensible) |
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| 147 | - are there ripples at x values corresponding to (2 :math:`pi` over) the two |
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| 148 | q values at which the extrapolated and experimental data are merged? |
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| 149 | - are there any artefacts at x values corresponding to 2 :math:`pi` / q\ :sub:`max` in |
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| 150 | the experimental data? |
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| 151 | - and lastly, do the significant features/peaks in the correlation functions |
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| 152 | actually correspond to anticpated spacings in the sample?!!! |
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| 153 | |
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| 154 | Finally, the program calculates the interface distribution function (IDF) g\ :sub:`1`\ (x) as |
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| 155 | the discrete cosine transform of: |
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| 156 | |
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| 157 | .. math:: |
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| 158 | -q^{4} I(q) |
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| 159 | |
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| 160 | The IDF is proportional to the second derivative of Î\ :sub:`1`\ (x). |
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[d78b5cb] | 161 | |
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[41345d7e] | 162 | Hilbert |
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[1404cce] | 163 | ....... |
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[ad476d1] | 164 | |
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[1404cce] | 165 | If "Hilbert" is selected for the transform type, the analysis will perform a |
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[2fe78566] | 166 | Hilbert transform on the extrapolated data in order to calculate the Volume |
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[41345d7e] | 167 | Fraction Profile. |
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| 168 | |
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[ad476d1] | 169 | .. note:: The Hilbert transform functionality is not yet implemented in SasView. |
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[1404cce] | 170 | |
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| 171 | |
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[41345d7e] | 172 | Interpretation |
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| 173 | -------------- |
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[1404cce] | 174 | |
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| 175 | Correlation Function |
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| 176 | .................... |
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| 177 | |
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[ad476d1] | 178 | Once the correlation functions have been calculated *SasView* can be asked to |
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| 179 | try and interpret Î\ :sub:`1`\ (x) in terms of an ideal lamellar morphology |
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| 180 | as shown below. |
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[41345d7e] | 181 | |
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[6aad2e8] | 182 | .. figure:: fig2.png |
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[41345d7e] | 183 | :align: center |
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| 184 | |
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[ad476d1] | 185 | The structural parameters extracted are: |
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[41345d7e] | 186 | |
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| 187 | * Long Period :math:`= L_p` |
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| 188 | * Average Hard Block Thickness :math:`= L_c` |
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| 189 | * Average Core Thickness :math:`= D_0` |
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[501712f] | 190 | * Average Interface Thickness :math:`= D_{tr}` |
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[8cc9048] | 191 | * Polydispersity :math:`= \Gamma_{\mathrm{min}}/\Gamma_{\mathrm{max}}` |
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[41345d7e] | 192 | * Local Crystallinity :math:`= L_c/L_p` |
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[0390040] | 193 | |
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[1404cce] | 194 | Volume Fraction Profile |
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| 195 | ....................... |
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| 196 | |
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[ad476d1] | 197 | SasView does not provide any automatic interpretation of volume fraction profiles |
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| 198 | in the same way that it does for correlation functions. However, a number of |
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| 199 | structural parameters are obtainable by other means: |
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[1404cce] | 200 | |
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| 201 | * Surface Coverage :math:`=\theta` |
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| 202 | * Anchor Separation :math:`= D` |
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| 203 | * Bound Fraction :math:`= <p>` |
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| 204 | * Second Moment :math:`= \sigma` |
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[8cc9048] | 205 | * Maximum Extent :math:`= \delta_{\mathrm{h}}` |
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[1404cce] | 206 | * Adsorbed Amount :math:`= \Gamma` |
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| 207 | |
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| 208 | .. figure:: profile1.png |
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| 209 | :align: center |
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[d78b5cb] | 210 | |
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[1404cce] | 211 | .. figure:: profile2.png |
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| 212 | :align: center |
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[d78b5cb] | 213 | |
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[ad476d1] | 214 | The reader is directed to the references for information on these parameters. |
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[1404cce] | 215 | |
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| 216 | References |
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| 217 | ---------- |
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| 218 | |
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[ad476d1] | 219 | Correlation Function |
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| 220 | .................... |
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| 221 | |
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[1404cce] | 222 | Strobl, G. R.; Schneider, M. *J. Polym. Sci.* (1980), 18, 1343-1359 |
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| 223 | |
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| 224 | Koberstein, J.; Stein R. *J. Polym. Sci. Phys. Ed.* (1983), 21, 2181-2200 |
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| 225 | |
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| 226 | Baltá Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 247-251 |
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| 227 | |
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| 228 | Baltá Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 257-261 |
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| 229 | |
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| 230 | Baltá Calleja, F. J.; Vonk, C. G. *X-ray Scattering of Synthetic Poylmers*, Elsevier. Amsterdam (1989), 260-270 |
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| 231 | |
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[ad476d1] | 232 | Göschel, U.; Urban, G. *Polymer* (1995), 36, 3633-3639 |
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| 233 | |
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| 234 | Stribeck, N. *X-Ray Scattering of Soft Matter*, Springer. Berlin (2007), 138-161 |
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| 235 | |
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[1404cce] | 236 | :ref:`FDR` (PDF format) |
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| 237 | |
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[ad476d1] | 238 | Volume Fraction Profile |
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| 239 | ....................... |
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| 240 | |
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| 241 | Washington, C.; King, S. M. *J. Phys. Chem.*, (1996), 100, 7603-7609 |
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| 242 | |
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| 243 | Cosgrove, T.; King, S. M.; Griffiths, P. C. *Colloid-Polymer Interactions: From Fundamentals to Practice*, Wiley. New York (1999), 193-204 |
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| 244 | |
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| 245 | King, S. M.; Griffiths, P. C.; Cosgrove, T. *Applications of Neutron Scattering to Soft Condensed Matter*, Gordon & Breach. Amsterdam (2000), 77-105 |
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| 246 | |
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| 247 | King, S.; Griffiths, P.; Hone, J.; Cosgrove, T. *Macromol. Symp.* (2002), 190, 33-42 |
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| 248 | |
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[0390040] | 249 | .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ |
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| 250 | |
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[1404cce] | 251 | |
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[0390040] | 252 | Usage |
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| 253 | ----- |
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[f56770ef] | 254 | Upon sending data for correlation function analysis, it will be plotted (minus |
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[d78b5cb] | 255 | the background value), along with a *red* bar indicating the *upper end of the |
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[ad476d1] | 256 | low-Q range* (used for Guinier back-extrapolation), and 2 *purple* bars indicating |
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| 257 | the range to be used for Porod forward-extrapolation. These bars may be moved by |
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| 258 | grabbing and dragging, or by entering appropriate values in the Q range input boxes. |
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[0390040] | 259 | |
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| 260 | .. figure:: tutorial1.png |
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| 261 | :align: center |
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| 262 | |
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[ad476d1] | 263 | Once the Q ranges have been set, click the "Calculate Bg" button to determine the |
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| 264 | background level. Alternatively, enter your own value into the box. If the box turns |
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| 265 | yellow this indicates that background subtraction has created some negative intensities. |
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[0390040] | 266 | |
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[ad476d1] | 267 | Now click the "Extrapolate" button to extrapolate the data. The graph window will update |
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| 268 | to show the extrapolated data, and the values of the parameters used for the Guinier and |
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| 269 | Porod extrapolations will appear in the "Extrapolation Parameters" section of the SasView |
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| 270 | GUI. |
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[0390040] | 271 | |
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| 272 | .. figure:: tutorial2.png |
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| 273 | :align: center |
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| 274 | |
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[1404cce] | 275 | Now select which type of transform you would like to perform, using the radio |
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[0390040] | 276 | buttons: |
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| 277 | |
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[ad476d1] | 278 | * **Fourier**: to perform a Fourier Transform to calculate the correlation |
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| 279 | functions |
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| 280 | * **Hilbert**: to perform a Hilbert Transform to calculate the volume fraction |
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[1404cce] | 281 | profile |
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| 282 | |
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[ad476d1] | 283 | and click the "Transform" button to perform the selected transform and plot |
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| 284 | the results. |
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[0390040] | 285 | |
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| 286 | .. figure:: tutorial3.png |
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| 287 | :align: center |
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| 288 | |
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[ad476d1] | 289 | If a Fourier Transform was performed, the "Compute Parameters" button can now be |
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| 290 | clicked to interpret the correlation function as described earlier. The parameters |
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| 291 | will appear in the "Output Parameters" section of the SasView GUI. |
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| 292 | |
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| 293 | .. figure:: tutorial4.png |
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| 294 | :align: center |
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| 295 | |
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[d78b5cb] | 296 | |
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[1404cce] | 297 | .. note:: |
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[ad476d1] | 298 | This help document was last changed by Steve King, 26Sep2017 |
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