Changeset 9802ab3 in sasmodels


Ignore:
Timestamp:
Apr 10, 2017 11:56:55 AM (8 months ago)
Author:
richardh
Branches:
master, boltzmann, costrafo411, doc_update, generic_integration_loop, ticket-1043, ticket-786
Children:
69e1afc
Parents:
dedcf34
Message:

changes to docs, anticipating new orientation angle integrals

Location:
sasmodels/models
Files:
1 added
1 deleted
12 edited

Legend:

Unmodified
Added
Removed
  • sasmodels/models/barbell.py

    r9b79f29 r9802ab3  
    6868The 2D scattering intensity is calculated similar to the 2D cylinder model. 
    6969 
    70 .. figure:: img/cylinder_angle_definition.jpg 
     70.. figure:: img/cylinder_angle_definition.png 
    7171 
    7272    Definition of the angles for oriented 2D barbells. 
  • sasmodels/models/capped_cylinder.py

    r9b79f29 r9802ab3  
    7171The 2D scattering intensity is calculated similar to the 2D cylinder model. 
    7272 
    73 .. figure:: img/cylinder_angle_definition.jpg 
     73.. figure:: img/cylinder_angle_definition.png 
    7474 
    7575    Definition of the angles for oriented 2D cylinders. 
  • sasmodels/models/core_shell_bicelle.py

    r9b79f29 r9802ab3  
    6363cylinders is then given by integrating over all possible $\theta$ and $\phi$. 
    6464 
    65 The *theta* and *phi* parameters are not used for the 1D output. 
     65For oriented bicelles the *theta*, and *phi* orientation parameters will appear when fitting 2D data,  
     66see the :ref:`cylinder` model for further information. 
    6667Our implementation of the scattering kernel and the 1D scattering intensity 
    6768use the c-library from NIST. 
    6869 
    69 .. figure:: img/cylinder_angle_definition.jpg 
     70.. figure:: img/cylinder_angle_definition.png 
    7071 
    7172    Definition of the angles for the oriented core shell bicelle model, 
  • sasmodels/models/core_shell_bicelle_elliptical.py

    r9b79f29 r9802ab3  
    7676bicelles is then given by integrating over all possible $\alpha$ and $\psi$. 
    7777 
    78 For oriented bicellles the *theta*, *phi* and *psi* orientation parameters only appear when fitting 2D data,  
     78For oriented bicelles the *theta*, *phi* and *psi* orientation parameters will appear when fitting 2D data,  
    7979see the :ref:`elliptical-cylinder` model for further information. 
    8080 
  • sasmodels/models/core_shell_ellipsoid.py

    r9b79f29 r9802ab3  
    7777   F^2(q)=\int_{0}^{\pi/2}{F^2(q,\alpha)\sin(\alpha)d\alpha} 
    7878 
     79For oriented ellipsoids the *theta*, *phi* and *psi* orientation parameters will appear when fitting 2D data,  
     80see the :ref:`elliptical-cylinder` model for further information. 
    7981 
    8082References 
  • sasmodels/models/cylinder.py

    r9b79f29 r9802ab3  
    6161.. _cylinder-angle-definition: 
    6262 
    63 .. figure:: img/cylinder_angle_definition.jpg 
     63.. figure:: img/cylinder_angle_definition.png 
    6464 
    65     Definition of the angles for oriented cylinders. 
     65    Definition of the $\theta$ and $\phi$ orientation angles for a cylinder relative  
     66    to the beam line coordinates, plus an indication of their orientation distributions  
     67    which are described as rotations about each of the perpendicular axes $\delta_1$ and $\delta_2$  
     68    in the frame of the cylinder itself, which when $\theta = \phi = 0$ are parallel to the $Y$ and $X$ axes. 
    6669 
    6770.. figure:: img/cylinder_angle_projection.png 
     
    6972    Examples for oriented cylinders. 
    7073 
    71 The $\theta$ and $\phi$ parameters only appear in the model when fitting 2d data. 
     74The $\theta$ and $\phi$ parameters to orient the cylinder only appear in the model when fitting 2d data.  
     75On introducing "Orientational Distribution" in the angles, "distribution of theta" and "distribution of phi" parameters will 
     76appear. These are actually rotations about the axes $\delta_1$ and $\delta_2$ of the cylinder, which when $\theta = \phi = 0$ are parallel  
     77to the $Y$ and $X$ axes of the instrument respectively. Some experimentation may be required to understand the 2d patterns fully. 
     78(Earlier implementations had numerical integration issues in some circumstances when orientation distributions passed through 90 degrees, such  
     79situations, with very broad distributions, should still be approached with care.)  
    7280 
    7381Validation 
  • sasmodels/models/elliptical_cylinder.py

    r9b79f29 r9802ab3  
    5757define the axis of the cylinder using two angles $\theta$, $\phi$ and $\Psi$ 
    5858(see :ref:`cylinder orientation <cylinder-angle-definition>`). The angle 
    59 $\Psi$ is the rotational angle around its own long_c axis against the $q$ plane. 
    60 For example, $\Psi = 0$ when the $r_\text{minor}$ axis is parallel to the 
    61 $x$ axis of the detector. 
     59$\Psi$ is the rotational angle around its own long_c axis.  
    6260 
    6361All angle parameters are valid and given only for 2D calculation; ie, an 
     
    6664.. figure:: img/elliptical_cylinder_angle_definition.png 
    6765 
    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. 
     66    Definition of angles for oriented elliptical cylinder, where axis_ratio is drawn >1, 
     67    and angle $\Psi$ is now a rotation around the axis of the cylinder. 
    7068 
    7169.. figure:: img/elliptical_cylinder_angle_projection.png 
     
    7371    Examples of the angles for oriented elliptical cylinders against the 
    7472    detector plane, with $\Psi$ = 0. 
     73 
     74The $\theta$ and $\phi$ parameters to orient the cylinder only appear in the model when fitting 2d data.  
     75On introducing "Orientational Distribution" in the angles, "distribution of theta" and "distribution of phi" parameters will 
     76appear. These are actually rotations about the axes $\delta_1$ and $\delta_2$ of the cylinder, the $b$ and $a$ axes of the  
     77cylinder cross section. (When $\theta = \phi = 0$ these are parallel to the $Y$ and $X$ axes of the instrument.)  
     78The third orientation distribution, in $\psi$, is about the $c$ axis of the particle. Some experimentation may be required to  
     79understand the 2d patterns fully. (Earlier implementations had numerical integration issues in some circumstances when orientation  
     80distributions passed through 90 degrees, such situations, with very broad distributions, should still be approached with care.)  
    7581 
    7682NB: The 2nd virial coefficient of the cylinder is calculated based on the 
  • sasmodels/models/parallelepiped.py

    r3401a7a r9802ab3  
    112112    detector plane. 
    113113 
     114On introducing "Orientational Distribution" in the angles, "distribution of theta" and "distribution of phi" parameters will 
     115appear. These are actually rotations about axes $\delta_1$ and $\delta_2$ of the parallelepiped, perpendicular to the $a$ x $c$ and $b$ x $c$ faces.  
     116(When $\theta = \phi = 0$ these are parallel to the $Y$ and $X$ axes of the instrument.) The third orientation distribution, in $\psi$, is  
     117about the $c$ axis of the particle, perpendicular to the $a$ x $b$ face. Some experimentation may be required to  
     118understand the 2d patterns fully. (Earlier implementations had numerical integration issues in some circumstances when orientation  
     119distributions passed through 90 degrees, such situations, with very broad distributions, should still be approached with care.)  
     120 
     121     
    114122For a given orientation of the parallelepiped, the 2D form factor is 
    115123calculated as 
  • sasmodels/models/stacked_disks.py

    r48438f9 r9802ab3  
    7777the axis of the cylinder using two angles $\theta$ and $\varphi$. 
    7878 
    79 .. figure:: img/cylinder_angle_definition.jpg 
     79.. figure:: img/cylinder_angle_definition.png 
    8080 
    8181    Examples of the angles against the detector plane. 
  • sasmodels/models/triaxial_ellipsoid.py

    r3401a7a r9802ab3  
    7676    of the particle. 
    7777 
    78 The angle $\psi$ is the rotational angle around its own $c$ axis 
    79 against the $q$ plane. For example, $\psi = 0$ when the 
    80 $a$ axis is parallel to the $x$ axis of the detector. 
     78For oriented ellipsoids the *theta*, *phi* and *psi* orientation parameters will appear when fitting 2D data,  
     79see the :ref:`elliptical-cylinder` model for further information. 
    8180 
    8281.. _triaxial-ellipsoid-angles: 
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