Changeset fa8011eb in sasmodels


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

doc cleanup

Location:
sasmodels
Files:
1 added
8 edited

Legend:

Unmodified
Added
Removed
  • sasmodels/generate.py

    r0a4628d rfa8011eb  
    191191The function :func:`make` loads the metadata from the module and returns 
    192192the kernel source.  The function :func:`doc` extracts the doc string 
    193 and adds the parameter table to the top.  The function :func:`sources` 
     193and adds the parameter table to the top.  The function :func:`model_sources` 
    194194returns a list of files required by the model. 
    195195""" 
     
    206206import numpy as np 
    207207 
    208 __all__ = ["make", "doc", "sources", "convert_type"] 
     208#__all__ = ["make", "doc", "model_sources", "convert_type"] 
    209209 
    210210C_KERNEL_TEMPLATE_PATH = joinpath(dirname(__file__), 'kernel_template.c') 
  • sasmodels/models/core_shell_bicelle.py

    r8007311 rfa8011eb  
    77The form factor is normalized by the particle volume. 
    88 
    9 .. _core-shell-cylinder-geometry: 
     9.. _core-shell-bicelle-geometry: 
    1010 
    1111.. figure:: img/core_shell_bicelle_geometry.png 
  • sasmodels/models/core_shell_sphere.py

    r8c9dbc9 rfa8011eb  
    1515 
    1616.. math:: 
     17 
    1718    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}+ 
    1819    V_s(\rho_s-\rho_{solv})\frac{\sin(qr_s)-qr_s\cos(qr_s)}{(qr_s)^3}\right] 
     
    4142our model and the output of the NIST software. 
    4243 
    43 .. image:: img/core_shell_sphere_1d.jpg 
     44.. figure:: img/core_shell_sphere_1d.jpg 
    4445 
    45     Figure 1: Comparison of the SasView scattering intensity for a core-shell sphere with 
     46    Comparison of the SasView scattering intensity for a core-shell sphere with 
    4647    the output of the NIST SANS analysis software. The parameters were set to: 
    4748    *scale* = 1.0, *radius* = 60 , *contrast* = 1e-6 |Ang^-2|, and 
  • sasmodels/models/elliptical_cylinder.py

    rb7c2fce rfa8011eb  
    1010to any of the orientation angles, and also for the minor radius and the ratio of the ellipse radii. 
    1111 
    12 .. image:: img/elliptical_cylinder_geometry.gif 
     12.. figure:: img/elliptical_cylinder_geometry.gif 
    1313 
    14     *Figure.* *a* = *r_minor* and |nu|\ :sub:`n` = $r_ratio$ (i.e., $r_major / r_minor$). 
     14    *a* = *r_minor* and |nu|\ :sub:`n` = $r_ratio$ (i.e., $r_major / r_minor$). 
    1515 
    1616The function calculated is 
    1717 
    1818.. math:: 
     19 
    1920    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} 
    2021 
     
    2223 
    2324.. math:: 
     25 
    2426    F(\mathbf{q},\alpha,\psi)=2\frac{J_1(a)\sin(b)}{ab} 
    2527    \\ 
     
    4042    P(q) = scale  <F^2> / V 
    4143 
    42 The returned value is scaled to units of |cm^-1|. 
    43  
    4444To provide easy access to the orientation of the elliptical cylinder, we define the axis of the cylinder using two 
    4545angles |theta|, |phi| and |bigpsi|. As for the case of the cylinder, the angles |theta| and |phi| are defined on 
     
    4949All angle parameters are valid and given only for 2D calculation; ie, an oriented system. 
    5050 
    51 .. image:: img/elliptical_cylinder_geometry_2d.jpg 
     51.. figure:: img/elliptical_cylinder_geometry_2d.jpg 
    5252 
    53     *Figure. Definition of angles for 2D* 
     53    Definition of angles for 2D 
    5454 
    55 .. image:: img/core_shell_bicelle_fig2.jpg 
     55.. figure:: img/core_shell_bicelle_fig2.jpg 
    5656 
    57     *Figure. Examples of the angles for oriented elliptical cylinders against the detector plane.* 
     57    Examples of the angles for oriented elliptical cylinders against the detector plane. 
    5858 
    5959NB: The 2nd virial coefficient of the cylinder is calculated based on the averaged radius (= sqrt(*r_minor*\ :sup:`2` \* *r_ratio*)) 
     
    6161 
    6262 
    63 .. image:: img/elliptical_cylinder_comparison_1d.jpg 
     63.. figure:: img/elliptical_cylinder_comparison_1d.jpg 
    6464 
    65     *Figure. 1D plot using the default values (w/1000 data point).* 
     65    1D plot using the default values (w/1000 data point). 
    6666 
    6767Validation 
     
    7373and 76 degrees are taken for the angles of |theta|, |phi|, and |bigpsi| respectively). 
    7474 
    75 .. image:: img/elliptical_cylinder_validation_1d.gif 
     75.. figure:: img/elliptical_cylinder_validation_1d.gif 
    7676 
    77     *Figure. Comparison between 1D and averaged 2D.* 
     77    Comparison between 1D and averaged 2D. 
    7878 
    7979In the 2D average, more binning in the angle |phi| is necessary to get the proper result. The following figure shows 
    8080the results of the averaging by varying the number of angular bins. 
    8181 
    82 .. image:: img/elliptical_cylinder_averaging.gif 
     82.. figure:: img/elliptical_cylinder_averaging.gif 
    8383 
    84     *Figure. The intensities averaged from 2D over different numbers of bins and angles.* 
     84    The intensities averaged from 2D over different numbers of bins and angles. 
    8585 
    8686Reference 
  • sasmodels/models/guinier_porod.py

    r21d1031 rfa8011eb  
    5151    q = \sqrt{q_x^2+q_y^2} 
    5252 
    53 .. image:: img/guinier_porod_model.jpg 
     53.. figure:: img/guinier_porod_model.jpg 
    5454 
    55     Figure 1: Guinier-Porod model for $R_g=100$ |Ang|, $s=1$, $m=3$, and $background=0.1$. 
     55    Guinier-Porod model for $R_g=100$ |Ang|, $s=1$, $m=3$, and $background=0.1$. 
    5656 
    5757 
  • sasmodels/models/line.py

    re66075f rfa8011eb  
    1313.. note:: 
    1414    For 2D plots intensity has different definition than other shape independent models 
     15 
    1516.. math:: 
    1617    I(q) = I(qx) \cdot I(qy) 
    17  
    18 .. figure:: None 
    1918 
    2019References 
  • sasmodels/models/rpa.py

    r8dd6914 rfa8011eb  
    4343component. 
    4444 
    45 .. figure:: img/image215.jpg 
     45.. figure:: img/rpa_1d.jpg 
    4646 
    4747    1D plot using the default values (w/500 data points). 
  • sasmodels/models/vesicle.py

    r068cebd rfa8011eb  
    2424is a flat background level (due for example to incoherent scattering in the 
    2525case of neutrons), and $j_1$ is the spherical bessel function 
    26 $j_1 = (sin(x) - x cos(x))/ x^2$. 
     26$j_1 = (\sin(x) - x \cos(x))/ x^2$. 
    2727 
    2828The functional form is identical to a "typical" core-shell structure, except 
     
    3535thickness = $R_{\text{tot}} - R_{\text{core}}$. 
    3636 
    37 .. figure: img/vesicle_geometry.jpg 
     37.. figure:: img/vesicle_geometry.jpg 
     38 
     39    Vesicle geometry. 
    3840 
    3941The 2D scattering intensity is the same as *P(q)* above, regardless of the 
     
    4850radius for *S(Q)* when *P(Q)* \* *S(Q)* is applied. 
    4951 
    50 .. image:: img/vesicle_1d.jpg 
     52.. figure:: img/vesicle_1d.jpg 
    5153 
    52 *Figure. 1D plot using the default values given in the table 
    53 (w/200 data point). Polydispersity and instrumental resolution normally 
    54 will smear out most of the rapidly oscillating features.* 
     54    1D plot using the default values given in the table (w/200 data point). 
     55    Polydispersity and instrumental resolution normally will smear out most 
     56    of the rapidly oscillating features. 
    5557 
    5658REFERENCE 
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