# Changeset fa8011eb in sasmodels

Ignore:
Timestamp:
Feb 24, 2016 5:51:27 PM (7 years ago)
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:
d51ea74
Parents:
c8dcbdf
Message:

doc cleanup

Location:
sasmodels
Files:
8 edited

Unmodified
Removed
• ## sasmodels/generate.py

 r0a4628d The function :func:make loads the metadata from the module and returns the kernel source.  The function :func:doc extracts the doc string and adds the parameter table to the top.  The function :func:sources and adds the parameter table to the top.  The function :func:model_sources returns a list of files required by the model. """ import numpy as np __all__ = ["make", "doc", "sources", "convert_type"] #__all__ = ["make", "doc", "model_sources", "convert_type"] C_KERNEL_TEMPLATE_PATH = joinpath(dirname(__file__), 'kernel_template.c')
• ## sasmodels/models/core_shell_bicelle.py

 r8007311 The form factor is normalized by the particle volume. .. _core-shell-cylinder-geometry: .. _core-shell-bicelle-geometry: .. figure:: img/core_shell_bicelle_geometry.png
• ## sasmodels/models/core_shell_sphere.py

 r8c9dbc9 .. math:: F^2(q)=\frac{3}{V_s}\left[V_c(\rho_c-\rho_s)\frac{\sin(qr_c)-qr_c\cos(qr_c)}{(qr_c)^3}+ V_s(\rho_s-\rho_{solv})\frac{\sin(qr_s)-qr_s\cos(qr_s)}{(qr_s)^3}\right] our model and the output of the NIST software. .. image:: img/core_shell_sphere_1d.jpg .. figure:: img/core_shell_sphere_1d.jpg Figure 1: Comparison of the SasView scattering intensity for a core-shell sphere with Comparison of the SasView scattering intensity for a core-shell sphere with the output of the NIST SANS analysis software. The parameters were set to: *scale* = 1.0, *radius* = 60 , *contrast* = 1e-6 |Ang^-2|, and
• ## sasmodels/models/elliptical_cylinder.py

 rb7c2fce to any of the orientation angles, and also for the minor radius and the ratio of the ellipse radii. .. image:: img/elliptical_cylinder_geometry.gif .. figure:: img/elliptical_cylinder_geometry.gif *Figure.* *a* = *r_minor* and |nu|\ :sub:n = $r_ratio$ (i.e., $r_major / r_minor$). *a* = *r_minor* and |nu|\ :sub:n = $r_ratio$ (i.e., $r_major / r_minor$). The function calculated is .. math:: I(\mathbf{q})=\frac{1}{V_{cyl}}\int{d\psi}\int{d\phi}\int{p(\theta,\phi,\psi)F^2(\mathbf{q},\alpha,\psi)\sin(\theta)d\theta} .. math:: F(\mathbf{q},\alpha,\psi)=2\frac{J_1(a)\sin(b)}{ab} \\ P(q) = scale  / V The returned value is scaled to units of |cm^-1|. To provide easy access to the orientation of the elliptical cylinder, we define the axis of the cylinder using two angles |theta|, |phi| and |bigpsi|. As for the case of the cylinder, the angles |theta| and |phi| are defined on All angle parameters are valid and given only for 2D calculation; ie, an oriented system. .. image:: img/elliptical_cylinder_geometry_2d.jpg .. figure:: img/elliptical_cylinder_geometry_2d.jpg *Figure. Definition of angles for 2D* Definition of angles for 2D .. image:: img/core_shell_bicelle_fig2.jpg .. figure:: img/core_shell_bicelle_fig2.jpg *Figure. Examples of the angles for oriented elliptical cylinders against the detector plane.* Examples of the angles for oriented elliptical cylinders against the detector plane. NB: The 2nd virial coefficient of the cylinder is calculated based on the averaged radius (= sqrt(*r_minor*\ :sup:2 \* *r_ratio*)) .. image:: img/elliptical_cylinder_comparison_1d.jpg .. figure:: img/elliptical_cylinder_comparison_1d.jpg *Figure. 1D plot using the default values (w/1000 data point).* 1D plot using the default values (w/1000 data point). Validation and 76 degrees are taken for the angles of |theta|, |phi|, and |bigpsi| respectively). .. image:: img/elliptical_cylinder_validation_1d.gif .. figure:: img/elliptical_cylinder_validation_1d.gif *Figure. Comparison between 1D and averaged 2D.* Comparison between 1D and averaged 2D. In the 2D average, more binning in the angle |phi| is necessary to get the proper result. The following figure shows the results of the averaging by varying the number of angular bins. .. image:: img/elliptical_cylinder_averaging.gif .. figure:: img/elliptical_cylinder_averaging.gif *Figure. The intensities averaged from 2D over different numbers of bins and angles.* The intensities averaged from 2D over different numbers of bins and angles. Reference
• ## sasmodels/models/guinier_porod.py

 r21d1031 q = \sqrt{q_x^2+q_y^2} .. image:: img/guinier_porod_model.jpg .. figure:: img/guinier_porod_model.jpg Figure 1: Guinier-Porod model for $R_g=100$ |Ang|, $s=1$, $m=3$, and $background=0.1$. Guinier-Porod model for $R_g=100$ |Ang|, $s=1$, $m=3$, and $background=0.1$.
• ## sasmodels/models/line.py

 re66075f .. note:: For 2D plots intensity has different definition than other shape independent models .. math:: I(q) = I(qx) \cdot I(qy) .. figure:: None References
• ## sasmodels/models/rpa.py

 r8dd6914 component. .. figure:: img/image215.jpg .. figure:: img/rpa_1d.jpg 1D plot using the default values (w/500 data points).
• ## sasmodels/models/vesicle.py

 r068cebd is a flat background level (due for example to incoherent scattering in the case of neutrons), and $j_1$ is the spherical bessel function $j_1 = (sin(x) - x cos(x))/ x^2$. $j_1 = (\sin(x) - x \cos(x))/ x^2$. The functional form is identical to a "typical" core-shell structure, except thickness = $R_{\text{tot}} - R_{\text{core}}$. .. figure: img/vesicle_geometry.jpg .. figure:: img/vesicle_geometry.jpg Vesicle geometry. The 2D scattering intensity is the same as *P(q)* above, regardless of the radius for *S(Q)* when *P(Q)* \* *S(Q)* is applied. .. image:: img/vesicle_1d.jpg .. figure:: img/vesicle_1d.jpg *Figure. 1D plot using the default values given in the table (w/200 data point). Polydispersity and instrumental resolution normally will smear out most of the rapidly oscillating features.* 1D plot using the default values given in the table (w/200 data point). Polydispersity and instrumental resolution normally will smear out most of the rapidly oscillating features. REFERENCE
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