# cylinder

Right circular cylinder with uniform scattering length density.

Parameter Description Units Default value
scale Source intensity None 1
background Source background cm-1 0.001
sld Cylinder scattering length density 10-6-2 4
sld_solvent Solvent scattering length density 10-6-2 1
length Cylinder length 400
theta latitude degree 60
phi longitude degree 60

The returned value is scaled to units of cm-1 sr-1, absolute scale.

For information about polarised and magnetic scattering, see the Polarisation/Magnetic Scattering documentation.

Definition

The output of the 2D scattering intensity function for oriented cylinders is given by (Guinier, 1955)

$P(q,\alpha) = \frac{\text{scale}}{V} F^2(q,\alpha).sin(\alpha) + \text{background}$

where

$F(q,\alpha) = 2 (\Delta \rho) V \frac{\sin \left(\tfrac12 qL\cos\alpha \right)} {\tfrac12 qL \cos \alpha} \frac{J_1 \left(q R \sin \alpha\right)}{q R \sin \alpha}$

and $$\alpha$$ is the angle between the axis of the cylinder and $$\vec q$$, $$V =\pi R^2L$$ is the volume of the cylinder, $$L$$ is the length of the cylinder, $$R$$ is the radius of the cylinder, and $$\Delta\rho$$ (contrast) is the scattering length density difference between the scatterer and the solvent. $$J_1$$ is the first order Bessel function.

For randomly oriented particles:

$F^2(q)=\int_{0}^{\pi/2}{F^2(q,\alpha)\sin(\alpha)d\alpha}=\int_{0}^{1}{F^2(q,u)du}$

Numerical integration is simplified by a change of variable to $$u = cos(\alpha)$$ with $$sin(\alpha)=\sqrt{1-u^2}$$.

The output of the 1D scattering intensity function for randomly oriented cylinders is thus given by

$P(q) = \frac{\text{scale}}{V} \int_0^{\pi/2} F^2(q,\alpha) \sin \alpha\ d\alpha + \text{background}$

NB: The 2nd virial coefficient of the cylinder is calculated based on the radius and length values, and used as the effective radius for $$S(q)$$ when $$P(q) \cdot S(q)$$ is applied.

For oriented cylinders, we define the direction of the axis of the cylinder using two angles $$\theta$$ (note this is not the same as the scattering angle used in q) and $$\phi$$. Those angles are defined in Fig. 17 .

The $$\theta$$ and $$\phi$$ parameters only appear in the model when fitting 2d data.

Validation

Validation of the code was done by comparing the output of the 1D model to the output of the software provided by the NIST (Kline, 2006). The implementation of the intensity for fully oriented cylinders was done by averaging over a uniform distribution of orientations using

$P(q) = \int_0^{\pi/2} d\phi \int_0^\pi p(\theta) P_0(q,\theta) \sin \theta\ d\theta$

where $$p(\theta,\phi) = 1$$ is the probability distribution for the orientation and $$P_0(q,\theta)$$ is the scattering intensity for the fully oriented system, and then comparing to the 1D result.

References

J. S. Pedersen, Adv. Colloid Interface Sci. 70, 171-210 (1997). G. Fournet, Bull. Soc. Fr. Mineral. Cristallogr. 74, 39-113 (1951).