source: sasmodels/sasmodels/models/core_shell_ellipsoid.py @ 81dd619

r"""
This model provides the form factor, $P(q)$, for a core shell ellipsoid (below)
where the form factor is normalized by the volume of the cylinder.

.. math::

    P(q) = scale * \left<f^2\right>/V + background

where the volume $V = (4/3)\pi(r_{maj}r_{min}^2)$ and the averaging $< >$ is
applied over all orientations for 1D.

.. figure:: img/core_shell_ellipsoid_fig1.gif

    The returned value is in units of $cm^{-1}$, on absolute scale.

Definition
----------

The form factor calculated is

.. math::

    P(q) = \frac{scale}{V}\int_0^1
        \left|F(q,r_{min},r_{max},\alpha)\right|^2d\alpha + background

    \left|F(q,r_{min},r_{max},\alpha)\right|=V\Delta \rho \cdot (3j_1(u)/u)

    u = q\left[ r_{maj}^2\alpha ^2 + r_{min}^2(1-\alpha ^2)\right]^{1/2}

where

.. math::

    j_1(u)=(\sin x - x \cos x)/x^2

To provide easy access to the orientation of the core-shell ellipsoid,
we define the axis of the solid ellipsoid using two angles $\theta$ and $\phi$.
These angles are defined on Figure 2 of the CylinderModel.
The contrast is defined as SLD(core) - SLD(shell) and SLD(shell) - SLD(solvent).

In the parameters, *equat_core* = equatorial core radius, *polar_core* =
polar core radius, *equat_shell* = $r_{min}$ (or equatorial outer radius),
and *polar_shell* = $r_{maj}$ (or polar outer radius).

.. note::
    The 2nd virial coefficient of the solid ellipsoid is calculated based on
    the *radius_a* (= *polar_shell)* and *radius_b (= equat_shell)* values,
    and used as the effective radius for *S(Q)* when $P(Q) * S(Q)$ is applied.

.. figure:: img/core_shell_ellipsoid_1d.jpg

    1D plot using the default values (w/200 data point).

.. figure:: img/core_shell_ellipsoid_fig2.jpg

    The angles for oriented core_shell_ellipsoid.

Our model uses the form factor calculations implemented in a c-library provided
by the NIST Center for Neutron Research (Kline, 2006).

References
----------

M Kotlarchyk, S H Chen, *J. Chem. Phys.*, 79 (1983) 2461

S J Berr, *Phys. Chem.*, 91 (1987) 4760

"""

from numpy import inf, sin, cos, pi

name = "core_shell_ellipsoid"
title = "Form factor for an spheroid ellipsoid particle with a core shell structure."
description = """
    [SpheroidCoreShellModel] Calculates the form factor for an spheroid
    ellipsoid particle with a core_shell structure.
    The form factor is averaged over all possible
    orientations of the ellipsoid such that P(q)
    = scale*<f^2>/Vol + bkg, where f is the
    single particle scattering amplitude.
    [Parameters]:
    equat_core = equatorial radius of core,
    polar_core = polar radius of core,
    equat_shell = equatorial radius of shell,
    polar_shell = polar radius (revolution axis) of shell,
    core_sld = SLD_core
    shell_sld = SLD_shell
    solvent_sld = SLD_solvent
    background = Incoherent bkg
    scale =scale
    Note:It is the users' responsibility to ensure
    that shell radii are larger than core radii.
    oblate: polar radius < equatorial radius
    prolate :  polar radius > equatorial radius
    """
category = "shape:ellipsoid"

# pylint: disable=bad-whitespace, line-too-long
#             ["name", "units", default, [lower, upper], "type", "description"],
parameters = [
    ["equat_core",  "Ang",      200,   [0, inf],    "volume",      "Equatorial radius of core"],
    ["polar_core",  "Ang",       10,   [0, inf],    "volume",      "Polar radius of core"],
    ["equat_shell", "Ang",      250,   [0, inf],    "volume",      "Equatorial radius of shell"],
    ["polar_shell", "Ang",       30,   [0, inf],    "volume",      "Polar radius of shell"],
    ["core_sld",    "1e-6/Ang^2", 2,   [-inf, inf], "",            "Core scattering length density"],
    ["shell_sld",   "1e-6/Ang^2", 1,   [-inf, inf], "",            "Shell scattering length density"],
    ["solvent_sld", "1e-6/Ang^2", 6.3, [-inf, inf], "",            "Solvent scattering length density"],
    ["theta",       "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation wrt incoming beam"],
    ["phi",         "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation in the plane of the detector"],
    ]
# pylint: enable=bad-whitespace, line-too-long

source = ["lib/gfn.c", "lib/gauss76.c", "core_shell_ellipsoid.c"]

demo = dict(scale=1, background=0.001,
            equat_core=200.0,
            polar_core=10.0,
            equat_shell=250.0,
            polar_shell=30.0,
            core_sld=2.0,
            shell_sld=1.0,
            solvent_sld=6.3,
            theta=0,
            phi=0)

oldname = 'CoreShellEllipsoidModel'

oldpars = dict(core_sld='sld_core',
               shell_sld='sld_shell',
               solvent_sld='sld_solvent',
               theta='axis_theta',
               phi='axis_phi')

q = 0.1
phi = pi/6
qx = q*cos(phi)
qy = q*sin(phi)

tests = [
    # Accuracy tests based on content in test/utest_other_models.py
    [{'equat_core': 200.0,
      'polar_core': 20.0,
      'equat_shell': 250.0,
      'polar_shell': 30.0,
      'core_sld': 2.0,
      'shell_sld': 1.0,
      'solvent_sld': 6.3,
      'background': 0.001,
      'scale': 1.0,
     }, 1.0, 0.00189402],

    # Additional tests with larger range of parameters
    [{'background': 0.01}, 0.1, 8.86741],

    [{'equat_core': 20.0,
      'polar_core': 200.0,
      'equat_shell': 54.0,
      'polar_shell': 3.0,
      'core_sld': 20.0,
      'shell_sld': 10.0,
      'solvent_sld': 6.0,
      'background': 0.0,
      'scale': 1.0,
     }, 0.01, 26150.4],

    [{'background': 0.001}, (0.4, 0.5), 0.00170471],

    [{'equat_core': 20.0,
      'polar_core': 200.0,
      'equat_shell': 54.0,
      'polar_shell': 3.0,
      'core_sld': 20.0,
      'shell_sld': 10.0,
      'solvent_sld': 6.0,
      'background': 0.01,
      'scale': 0.01,
     }, (qx, qy), 0.105764],
    ]