Changeset e526a9d in sasmodels for doc


Ignore:
Timestamp:
Feb 4, 2018 9:40:01 PM (7 years ago)
Author:
GitHub <noreply@…>
Branches:
master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
aadec17
Parents:
032646d (diff), 72e41a0 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
git-author:
Paul Butler <butlerpd@…> (02/04/18 21:40:01)
git-committer:
GitHub <noreply@…> (02/04/18 21:40:01)
Message:

Merge pull request #59 from SasView?/boltzmann

add BoltzmannDistribution? and UniformDistribution?

Since Paul K approved the code and the only issue found by R. Heenan and P. Butler has been resolved by sasview PR 141 we should be able to merge this now.

Location:
doc
Files:
2 added
4 edited

Legend:

Unmodified
Added
Removed
  • doc/guide/pd/polydispersity.rst

    reda8b30 r92d330fd  
    4242calculations are generally more robust with more data points or more angles. 
    4343 
    44 The following five distribution functions are provided: 
     44The following distribution functions are provided: 
    4545 
    4646*  *Rectangular Distribution* 
     47*  *Uniform Distribution* 
    4748*  *Gaussian Distribution* 
    4849*  *Lognormal Distribution* 
    4950*  *Schulz Distribution* 
    5051*  *Array Distribution* 
     52*  *Boltzmann Distribution* 
    5153 
    5254These are all implemented as *number-average* distributions. 
     
    8587    Rectangular distribution. 
    8688 
     89 
     90 
     91Uniform Distribution 
     92^^^^^^^^^^^^^^^^^^^^^^^^ 
     93 
     94The Uniform Distribution is defined as 
     95 
     96    .. math:: 
     97 
     98        f(x) = \frac{1}{\text{Norm}} 
     99        \begin{cases} 
     100          1 & \text{for } |x - \bar x| \leq \sigma \\ 
     101          0 & \text{for } |x - \bar x| > \sigma 
     102        \end{cases} 
     103 
     104    where $\bar x$ is the mean of the distribution, $\sigma$ is the half-width, and 
     105    *Norm* is a normalization factor which is determined during the numerical 
     106    calculation. 
     107 
     108    Note that the polydispersity is given by 
     109 
     110    .. math:: \text{PD} = \sigma / \bar x 
     111 
     112    .. figure:: pd_uniform.jpg 
     113 
     114        Uniform distribution. 
     115 
     116The value $N_\sigma$ is ignored for this distribution. 
     117 
    87118.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    88119 
     
    183214^^^^^^^^^^^^^^^^^^ 
    184215 
    185 This user-definable distribution should be given as as a simple ASCII text 
     216This user-definable distribution should be given as a simple ASCII text 
    186217file where the array is defined by two columns of numbers: $x$ and $f(x)$. 
    187218The $f(x)$ will be normalized to 1 during the computation. 
     
    202233given for the model will have no affect, and will be ignored when computing 
    203234the average.  This means that any parameter with an array distribution will 
    204 not be fittable. 
     235not be fitable. 
     236 
     237.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     238 
     239Boltzmann Distribution 
     240^^^^^^^^^^^^^^^^^^^^^^ 
     241 
     242The Boltzmann Distribution is defined as 
     243 
     244.. math:: 
     245 
     246    f(x) = \frac{1}{\text{Norm}} 
     247           \exp\left(-\frac{ | x - \bar x | }{\sigma}\right) 
     248 
     249where $\bar x$ is the mean of the distribution and *Norm* is a normalization 
     250factor which is determined during the numerical calculation. 
     251The width is defined as 
     252 
     253.. math:: \sigma=\frac{k T}{E} 
     254 
     255which is the inverse Boltzmann factor, 
     256where $k$ is the Boltzmann constant, $T$ the temperature in Kelvin and $E$ a 
     257characteristic energy per particle. 
     258 
     259.. figure:: pd_boltzmann.jpg 
     260 
     261    Boltzmann distribution. 
    205262 
    206263.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
  • doc/developer/overview.rst

    r2a7e20e r0d5a655  
    190190*sasmodels.generate.PROJECTION*, with the default *PROJECTION=1* for 
    191191equirectangular and *PROJECTION=2* for sinusoidal.  The more complicated 
    192 Guyou and Postel projections are not implemented. See explore.jitter.draw_mesh 
     192Guyou and Postel projections are not implemented. See jitter.draw_mesh 
    193193for details. 
    194194 
     
    274274code. 
    275275 
    276 *explore/jitter.py* is for exploring different options for handling 
    277 orientation and orientation dispersity.  It uses *explore/guyou.py* to 
     276*sasmodels/jitter.py* is for exploring different options for handling 
     277orientation and orientation dispersity.  It uses *sasmodels/guyou.py* to 
    278278generate the Guyou projection. 
    279279 
  • doc/genapi.py

    r706f466 r0d5a655  
    6969    ('exception', 'Annotate exceptions'), 
    7070    ('generate', 'Model parser'), 
     71    ('jitter', 'Orientation explorer'), 
     72    ('guyou', 'Guyou map projection'), 
    7173    ('kernel', 'Evaluator type definitions'), 
    7274    ('kernelcl', 'OpenCL model evaluator'), 
  • doc/guide/orientation/orientation.rst

    r5fb0634 r0d5a655  
    5252yaw angle $\theta$ about the $b$-axis and pitch angle $\phi$ about the 
    5353$a$-axis. 
     54 
     55You can explore the view and jitter angles interactively using 
     56:func:`sasmodels.jitter.run`.  Enter the following into the python 
     57interpreter:: 
     58 
     59    from sasmodels import jitter 
     60    jitter.run() 
    5461 
    5562More formally, starting with axes $a$-$b$-$c$ of the particle aligned 
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