Changeset 5d23de2 in sasmodels


Ignore:
Timestamp:
Mar 13, 2017 12:05:27 AM (3 years ago)
Author:
butler
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
Message:

Fold caveats from original IGOR documentation back into sasmodels
version as requested on sasmodels pull request 27 addressing ticket 843.
Also reformated refs and authorship section as per ticket #646

File:
1 edited

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  • sasmodels/models/multilayer_vesicle.py

    r68f45cb r5d23de2  
    33---------- 
    44 
    5 This model is a trivial extension of the core_shell_sphere function to include 
    6 *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. 
     5This model is a trivial extension of the core_shell_sphere function where the 
     6core 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 
     8returns the same as the vesicle model, except for the normalisation, which here 
     9is to outermost volume. The shell thicknesses and SLD are constant for all 
     10shells as expected for a multilayer vesicle. 
    1111 
    1212.. figure:: img/multi_shell_geometry.jpg 
     
    4242$\rho_\text{solv}$ is the scattering length density of the solvent. 
    4343 
    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. 
     44USAGE NOTES 
    4645 
    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:: 
    5157 
    5258    1 20 
     
    5460    3  1 
    5561 
    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. 
    6083 
    6184The 2D scattering intensity is the same as 1D, regardless of the orientation 
     
    6992the :ref:`magnetism` documentation. 
    7093 
    71 This code is based on the form factor calculations implemented in the NIST 
    72 Center for Neutron Research provided c-library (Kline, 2006). 
    73  
    7494References 
    7595---------- 
    7696 
    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). 
    81100 
    82 **Author:** NIST IGOR/DANSE **on:** pre 2010 
     101Authorship and Verification 
     102---------------------------- 
    83103 
    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 
    87108 
    88109""" 
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