Changeset d138d43 in sasmodels for sasmodels/models/hollow_cylinder.py


Ignore:
Timestamp:
Nov 30, 2015 2:24:28 PM (8 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
eb69cce
Parents:
1ec7efa
Message:

remove documentation build errors

File:
1 edited

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  • sasmodels/models/hollow_cylinder.py

    r66ebdd6 rd138d43  
    11r""" 
    2 This model provides the form factor, *P(q)*, for a monodisperse hollow right  
     2This model provides the form factor, $P(q)$, for a monodisperse hollow right 
    33angle circular cylinder (tube) where the form factor is normalized by the 
    44volume of the tube 
    55 
    6 *P(q)* = *scale* \* *<F*\ :sup:`2`\ *>* / *V*\ :sub:`shell` + *background* 
     6.. math:: 
    77 
    8 where the averaging < > is applied only for the 1D calculation. 
     8    P(q) = \text{scale} \langle F^2 \rangle/V_\text{shell} + \text{background} 
     9 
     10where the averaging $\langle \rangle$ is applied only for the 1D calculation. 
    911 
    1012The inside and outside of the hollow cylinder are assumed have the same SLD. 
     
    1820 
    1921    \begin{eqnarray} 
    20     P(q)&=&(\text{scale})V_{shell}(\Delta\rho)^2\int_0^{1}\Psi^2[q_z, 
    21     R_{shell}(1-x^2)^{1/2},R_{core}(1-x^2)^{1/2}][\frac{sin(qHx)}{qHx}]^2dx\\ 
    22     \Psi[q,y,z]&=&\frac{1}{1-\gamma^2}[\Lambda(qy)-\gamma^2\Lambda(qz)]\\ 
    23     \Lambda(a)&=&2J_1(a)/a\\ 
    24     \gamma&=&R_{core}/R_{shell}\\ 
    25     V_{shell}&=&\pi(R_{shell}^2-R_{core}^2)L\\ 
    26     J_1(x)&=&\frac{(sin(x)-x\cdot cos(x))}{x^2}\\ 
     22    P(q)           &=& (\text{scale})V_\text{shell}\Delta\rho^2 
     23            \int_0^{1}\Psi^2 
     24            \left[q_z, R_\text{shell}(1-x^2)^{1/2}, 
     25                       R_\text{core}(1-x^2)^{1/2}\right] 
     26            \left[\frac{\sin(qHx)}{qHx}\right]^2 dx \\ 
     27    \Psi[q,y,z]    &=& \frac{1}{1-\gamma^2} 
     28            \left[ \Lambda(qy) - \gamma^2\Lambda(qz) \right] \\ 
     29    \Lambda(a)     &=& 2 J_1(a) / a \\ 
     30    \gamma         &=& R_\text{core} / R_\text{shell} \\ 
     31    V_\text{shell} &=& \pi \left(R_\text{shell}^2 - R_\text{core}^2 \right)L \\ 
     32    J_1(x)         &=& \frac{(\sin(x)-x\cdot \cos(x))}{x^2} \\ 
    2733    \end{eqnarray} 
    2834 
    29 where *scale* is a scale factor and *J1* is the 1st order Bessel function. 
     35where *scale* is a scale factor and $J_1$ is the 1st order 
     36Bessel function. 
    3037 
    3138To provide easy access to the orientation of the core-shell cylinder, we define 
    32 the axis of the cylinder using two angles |theta| and |phi|\ . As for the case  
     39the axis of the cylinder using two angles $\theta$ and $\phi$. As for the case 
    3340of the cylinder, those angles are defined in Figure 2 of the CylinderModel. 
    3441 
    35 NB: The 2nd virial coefficient of the cylinder is calculated based on the radius 
    36 and 2 length values, and used as the effective radius for *S(Q)* when  
    37 *P(Q)* \* *S(Q)* is applied. 
     42**NB**: The 2nd virial coefficient of the cylinder is calculated 
     43based on the radius and 2 length values, and used as the effective radius 
     44for $S(Q)$ when $P(Q) * S(Q)$ is applied. 
    3845 
    3946In the parameters, the contrast represents SLD :sub:`shell` - SLD :sub:`solvent` 
    40 and the *radius* = *R*\ :sub:`shell` while *core_radius* = *R*\ :sub:`core`. 
     47and the *radius* is $R_\text{shell}$ while *core_radius* is $R_\text{core}$. 
    4148 
    42 .. image:: img/image074.jpg 
     49.. figure:: img/hollow_cylinder_1d.jpg 
    4350 
    44 *Figure. 1D plot using the default values (w/1000 data point).* 
     51    1D plot using the default values (w/1000 data point). 
    4552 
    46 Our model uses the form factor calculations implemented in a c-library provided 
    47 by the NIST Center for Neutron Research (Kline, 2006). 
     53.. figure:: img/orientation.jpg 
    4854 
    49 .. image:: img/image061.jpg 
     55    Definition of the angles for the oriented hollow_cylinder model. 
    5056 
    51 *Figure. Definition of the angles for the oriented hollow_cylinder model.* 
     57.. figure:: img/orientation2.jpg 
    5258 
    53 .. image:: img/image062.jpg 
     59    Examples of the angles for oriented pp against the detector plane. 
    5460 
    55 *Figure. Examples of the angles for oriented pp against the detector plane.* 
    56  
    57 REFERENCE 
     61Reference 
     62--------- 
    5863 
    5964L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and 
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