Changeset 15a90c1 in sasmodels


Ignore:
Timestamp:
Apr 6, 2017 1:20:47 PM (7 months ago)
Author:
richardh
Branches:
master, costrafo411, doc_update, flexible-cylinder, ticket-776-orientation
Children:
14207bb
Parents:
4aaf89a
Message:

more changes for new axes, and a bug in cylinder.py docs

Location:
sasmodels/models
Files:
6 added
5 deleted
6 edited

Legend:

Unmodified
Added
Removed
  • sasmodels/models/core_shell_bicelle_elliptical.py

    r3b9a526 r15a90c1  
    8080 
    8181 
    82 .. figure:: img/elliptical_cylinder_angle_definition.jpg 
     82.. figure:: img/elliptical_cylinder_angle_definition.png 
    8383 
    84     Definition of the angles for the oriented core_shell_bicelle_elliptical model. 
    85     Note that *theta* and *phi* are currently defined differently to those for the core_shell_bicelle model. 
     84    Definition of the angles for the oriented core_shell_bicelle_elliptical particles.    
     85 
    8686 
    8787 
  • sasmodels/models/core_shell_parallelepiped.py

    r933af72 r15a90c1  
    3333$(=t_C)$ faces. The projection in the $AB$ plane is then 
    3434 
    35 .. image:: img/core_shell_parallelepiped_projection.jpg 
     35.. image:: img/core_shell_parallelepiped_projection.png 
    3636 
    3737The volume of the solid is 
     
    8080NB: The 2nd virial coefficient of the core_shell_parallelepiped is calculated 
    8181based on the the averaged effective radius $(=\sqrt{(A+2t_A)(B+2t_B)/\pi})$ 
    82 and length $(C+2t_C)$ values, and used as the effective radius 
    83 for $S(Q)$ when $P(Q) * S(Q)$ is applied. 
     82and length $(C+2t_C)$ values, after appropriately 
     83sorting the three dimensions to give an oblate or prolate particle, to give an  
     84effective radius, for $S(Q)$ when $P(Q) * S(Q)$ is applied. 
    8485 
    8586To provide easy access to the orientation of the parallelepiped, we define the 
     
    9091*x*-axis of the detector. 
    9192 
    92 .. figure:: img/parallelepiped_angle_definition.jpg 
     93.. figure:: img/parallelepiped_angle_definition.png 
    9394 
    9495    Definition of the angles for oriented core-shell parallelepipeds. 
  • sasmodels/models/cylinder.py

    rb7e8b94 r15a90c1  
    6464 
    6565    Definition of the angles for oriented cylinders. 
     66 
     67.. figure:: img/cylinder_angle_projection.png 
     68 
     69    Examples for oriented cylinders. 
    6670 
    6771The $\theta$ and $\phi$ parameters only appear in the model when fitting 2d data. 
  • sasmodels/models/elliptical_cylinder.py

    rfcb33e4 r15a90c1  
    6464oriented system. 
    6565 
    66 .. figure:: img/elliptical_cylinder_angle_definition.jpg 
     66.. figure:: img/elliptical_cylinder_angle_definition.png 
    6767 
    68     Definition of angles for 2D 
     68    Definition of angles for oriented elliptical cylinder, where axis_ratio >1, 
     69    and angle $\Psi$ is a rotation around the axis of the cylinder. 
    6970 
    70 .. figure:: img/cylinder_angle_projection.jpg 
     71.. figure:: img/elliptical_cylinder_angle_projection.png 
    7172 
    7273    Examples of the angles for oriented elliptical cylinders against the 
    73     detector plane. 
     74    detector plane, with $\Psi$ = 0. 
    7475 
    7576NB: The 2nd virial coefficient of the cylinder is calculated based on the 
  • sasmodels/models/parallelepiped.py

    r4aaf89a r15a90c1  
    2121.. note:: 
    2222 
    23    The edge of the solid must satisfy the condition that $A < B < C$. 
    24    This requirement is not enforced in the model, so it is up to the 
    25    user to check this during the analysis. 
     23   The edge of the solid used to have to satisfy the condition that $A < B < C$. 
     24   After some improvements to the effective radius calculation, used with an S(Q), 
     25   it is beleived that this is no longer the case.  
    2626 
    2727The 1D scattering intensity $I(q)$ is calculated as: 
     
    7171 
    7272NB: The 2nd virial coefficient of the parallelepiped is calculated based on 
    73 the averaged effective radius $(=\sqrt{A B / \pi})$ and 
     73the averaged effective radius, after appropriately 
     74sorting the three dimensions, to give an oblate or prolate particle, $(=\sqrt{A B / \pi})$ and 
    7475length $(= C)$ values, and used as the effective radius for 
    7576$S(q)$ when $P(q) \cdot S(q)$ is applied. 
     
    102103.. _parallelepiped-orientation: 
    103104 
    104 .. figure:: img/parallelepiped_angle_definition.jpg 
    105  
    106     Definition of the angles for oriented parallelepipeds. 
    107  
    108 .. figure:: img/parallelepiped_angle_projection.jpg 
    109  
    110     Examples of the angles for oriented parallelepipeds against the 
     105.. figure:: img/parallelepiped_angle_definition.png 
     106 
     107    Definition of the angles for oriented parallelepiped, shown with $A < B < C$. 
     108 
     109.. figure:: img/parallelepiped_angle_projection.png 
     110 
     111    Examples of the angles for an oriented parallelepiped against the 
    111112    detector plane. 
    112113 
     
    116117.. math:: 
    117118 
    118     P(q_x, q_y) = \left[\frac{\sin(qA\cos\alpha/2)}{(qA\cos\alpha/2)}\right]^2 
    119                   \left[\frac{\sin(qB\cos\beta/2)}{(qB\cos\beta/2)}\right]^2 
    120                   \left[\frac{\sin(qC\cos\gamma/2)}{(qC\cos\gamma/2)}\right]^2 
     119    P(q_x, q_y) = \left[\frac{\sin(\tfrac{1}{2}qA\cos\alpha)}{(\tfrac{1}{2}qA\cos\alpha)}\right]^2 
     120                  \left[\frac{\sin(\tfrac{1}{2}qB\cos\beta)}{(\tfrac{1}{2}qB\cos\beta)}\right]^2 
     121                  \left[\frac{\sin(\tfrac{1}{2}qC\cos\gamma)}{(\tfrac{1}{2}qC\cos\gamma)}\right]^2 
    121122 
    122123with 
     
    154155angles. 
    155156 
    156 This model is based on form factor calculations implemented in a c-library 
    157 provided by the NIST Center for Neutron Research (Kline, 2006). 
    158157 
    159158References 
     
    163162 
    164163R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854 
     164 
     165Authorship and Verification 
     166---------------------------- 
     167 
     168* **Author:** This model is based on form factor calculations implemented in a c-library 
     169provided by the NIST Center for Neutron Research (Kline, 2006). 
     170* **Last Modified by:**  Paul Kienzle **Date:** April 05, 2017 
     171* **Last Reviewed by:**  Richard Heenan **Date:** April 06, 2017 
     172 
    165173""" 
    166174 
  • sasmodels/models/triaxial_ellipsoid.py

    r4aaf89a r15a90c1  
    6565To provide easy access to the orientation of the triaxial ellipsoid, 
    6666we define the axis of the cylinder using the angles $\theta$, $\phi$ 
    67 and $\psi$. These angles are defined on 
    68 :numref:`triaxial-ellipsoid-angles` . 
     67and $\psi$. These angles are defined analogously to the elliptical_cylinder below 
     68 
     69.. figure:: img/elliptical_cylinder_angle_definition.png 
     70 
     71    Definition of angles for oriented triaxial ellipsoid, where radii shown here are $a < b << c$ 
     72    and angle $\Psi$ is a rotation around the axis of the particle. 
     73 
    6974The angle $\psi$ is the rotational angle around its own $c$ axis 
    7075against the $q$ plane. For example, $\psi = 0$ when the 
     
    7378.. _triaxial-ellipsoid-angles: 
    7479 
    75 .. figure:: img/triaxial_ellipsoid_angle_projection.jpg 
     80.. figure:: img/triaxial_ellipsoid_angle_projection.png 
    7681 
    77     The angles for oriented ellipsoid. 
     82    Some example angles for oriented ellipsoid. 
    7883 
    7984The radius-of-gyration for this system is  $R_g^2 = (R_a R_b R_c)^2/5$. 
     
    8186The contrast $\Delta\rho$ is defined as SLD(ellipsoid) - SLD(solvent).  In the 
    8287parameters, $R_a$ is the minor equatorial radius, $R_b$ is the major 
    83 equatorial radius, and $R_c$ is the polar radius of the ellipsoid. 
     88equatorial radius, and $R_c$ is the polar radius of the ellipsoid.  
    8489 
    8590NB: The 2nd virial coefficient of the triaxial solid ellipsoid is 
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