# Changeset 9802ab3 in sasmodels

Ignore:
Timestamp:
Apr 10, 2017 11:56:55 AM (6 months ago)
Branches:
master, costrafo411, doc_update, flexible-cylinder, ticket-776-orientation
Children:
69e1afc
Parents:
dedcf34
Message:

changes to docs, anticipating new orientation angle integrals

Location:
sasmodels/models
Files:
1 deleted
12 edited

Unmodified
Removed
• ## sasmodels/models/barbell.py

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

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

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

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

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

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

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

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

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

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