Changeset 5d23de2 in sasmodels
- Timestamp:
- Mar 13, 2017 12:05:27 AM (8 years ago)
- Branches:
- master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
- Children:
- 3a45c2c, 9f12fbe
- Parents:
- 4f9e288
- File:
-
- 1 edited
-
sasmodels/models/multilayer_vesicle.py (modified) (4 diffs)
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sasmodels/models/multilayer_vesicle.py
r68f45cb r5d23de2 3 3 ---------- 4 4 5 This model is a trivial extension of the core_shell_sphere function to include6 *N* shells where the core is filled with solvent and the shells are interleaved 7 with layers of solvent. For $N = 1$, this returns the same as the vesicle model, 8 except for the normalisation, which here is to outermost volume. 9 The shell thicknessess and SLD are constant for all shells as expected for 10 a multilayer vesicle.5 This model is a trivial extension of the core_shell_sphere function where the 6 core is filled with solvent and is surrounded by $N$ shells of material 7 (such as lipids) interleaved with $N - 1$ layers of solvent. For $N = 1$, this 8 returns the same as the vesicle model, except for the normalisation, which here 9 is to outermost volume. The shell thicknesses and SLD are constant for all 10 shells as expected for a multilayer vesicle. 11 11 12 12 .. figure:: img/multi_shell_geometry.jpg … … 42 42 $\rho_\text{solv}$ is the scattering length density of the solvent. 43 43 44 The outer-most shell radius $R_N$ is used as the effective radius 45 for $P(Q)$ when $P(Q) * S(Q)$ is applied. 44 USAGE NOTES 46 45 47 For mixed systems in which some vesicles have 1 shell, some have 2, 48 etc., use polydispersity on $N$ to model the data. For example, 49 create a file such as *shell_dist.txt* containing the relative portion 50 of each vesicle size:: 46 * The outer-most shell radius $R_N$ is used as the effective radius 47 for $P(Q)$ when $P(Q) * S(Q)$ is applied. 48 calculations rather slow. 49 * The number of shells is always rounded to an integer value as a non interger 50 number of layers is not physical. 51 * Thus Polydispersity should only be applied to number of shells **VERY 52 CAREFULLY**. A possible legitimate use would be for mixed systems in which 53 some vesicles have 1 shell, some have 2, etc. A polydispersity on $N$ can be 54 used to model the data by using the "array distriubtion" feature. First 55 create a file such as *shell_dist.txt* containing the relative portion 56 of each vesicle size:: 51 57 52 58 1 20 … … 54 60 3 1 55 61 56 Turn on polydispersity and select an array distribution for the *n_shells* 57 parameter. Choose the above *shell_dist.txt* file, and the model will be 58 computed with 80% 1-shell vesicles, 16% 2-shell vesicles and 4% 59 3-shell vesicles. 62 Turn on polydispersity and select an array distribution for the *n_shells* 63 parameter. Choose the above *shell_dist.txt* file, and the model will be 64 computed with 80% 1-shell vesicles, 16% 2-shell vesicles and 4% 65 3-shell vesicles. 66 * This is a highly non-linear, highly oscillatory (especially around the 67 q-values that correspond to the repeat distance of the layers), model 68 function complicated by the fact that the number of water/shell pairs must 69 physically be an integer value, although the optimization treats it as a 70 floating point value. Thus it may be that the resolution interpolation is not 71 sufficiently fine grained in certain cases. Please report any such occurences 72 to the SasView team. Generally, for the best possible experience: 73 * Start with the best possible guess 74 * Using a priori knowledge, hold as many parameters fixed as possible 75 * if N=1, tw (water thickness) must by definition be zero. Both N and tw should 76 be fixed during fitting. 77 * If N>1, use constraints to keep N > 1 78 * Because N only really moves in integer steps, it may get "stuck" if the 79 optimizer step size is too small so care should be taken 80 If you experience problems with this please contact the SasView team and let 81 them know the issue preferably with example data and model which fail to 82 converge. 60 83 61 84 The 2D scattering intensity is the same as 1D, regardless of the orientation … … 69 92 the :ref:`magnetism` documentation. 70 93 71 This code is based on the form factor calculations implemented in the NIST72 Center for Neutron Research provided c-library (Kline, 2006).73 74 94 References 75 95 ---------- 76 96 77 B Cabane, *Small Angle Scattering Methods*, 78 in *Surfactant Solutions: New Methods of Investigation*, 79 Ch.2, Surfactant Science Series Vol. 22, Ed. R Zana and M Dekker, 80 New York, (1987). 97 .. [#] B Cabane, *Small Angle Scattering Methods*, in *Surfactant Solutions: 98 New Methods of Investigation*, Ch.2, Surfactant Science Series Vol. 22, Ed. 99 R Zana and M Dekker, New York, (1987). 81 100 82 **Author:** NIST IGOR/DANSE **on:** pre 2010 101 Authorship and Verification 102 ---------------------------- 83 103 84 **Last Modified by:** Piotr Rozyczko **on:** Feb 24, 2016 85 86 **Last Reviewed by:** Paul Butler **on:** March 20, 2016 104 * **Author:** NIST IGOR/DANSE **Date:** pre 2010 105 * **Converted to sasmodels by:** Piotr Rozyczko **Date:** Feb 24, 2016 106 * **Last Modified by:** Paul Kienzle **Date:** Feb 7, 2017 107 * **Last Reviewed by:** Paul Butler **Date:** March 12, 2017 87 108 88 109 """
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