Changeset 30b60d2 in sasmodels


Ignore:
Timestamp:
Sep 5, 2017 12:39:41 PM (7 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
3a45c2c
Parents:
64eecf7
Message:

allow build of both latex and html

Files:
1 added
1 deleted
14 edited
1 moved

Legend:

Unmodified
Added
Removed

  • doc/conf.py

    r8ae8532 r30b60d2  
    211211#latex_preamble = '' 
    212212LATEX_PREAMBLE=r""" 
     213\newcommand{\lt}{<} 
     214\newcommand{\gt}{>} 
    213215\renewcommand{\AA}{\text{\r{A}}} % Allow \AA in math mode 
    214216\usepackage[utf8]{inputenc}      % Allow unicode symbols in text 

  • doc/guide/plugin.rst

    r870a2f4 r30b60d2  
    117117Models that do not conform to these requirements will *never* be incorporated 
    118118into the built-in library. 
    119  
    120 More complete documentation for the sasmodels package can be found at 
    121 `<http://www.sasview.org/sasmodels>`_. In particular, 
    122 `<http://www.sasview.org/sasmodels/api/generate.html#module-sasmodels.generate>`_ 
    123 describes the structure of a model. 
    124119 
    125120 
    … …  
    613608 
    614609    sas_gamma(x): 
    615         Gamma function $\text{sas_gamma}(x) = \Gamma(x)$. 
     610        Gamma function sas_gamma\ $(x) = \Gamma(x)$. 
    616611 
    617612        The standard math function, tgamma(x) is unstable for $x < 1$ 
    … …  
    623618    sas_erf(x), sas_erfc(x): 
    624619        Error function 
    625         $\text{sas_erf}(x) = \frac{2}{\sqrt\pi}\int_0^x e^{-t^2}\,dt$ 
     620        sas_erf\ $(x) = \frac{2}{\sqrt\pi}\int_0^x e^{-t^2}\,dt$ 
    626621        and complementary error function 
    627         $\text{sas_erfc}(x) = \frac{2}{\sqrt\pi}\int_x^{\infty} e^{-t^2}\,dt$. 
     622        sas_erfc\ $(x) = \frac{2}{\sqrt\pi}\int_x^{\infty} e^{-t^2}\,dt$. 
    628623 
    629624        The standard math functions erf(x) and erfc(x) are slower and broken 
    … …  
    634629 
    635630    sas_J0(x): 
    636         Bessel function of the first kind $\text{sas_J0}(x)=J_0(x)$ where 
     631        Bessel function of the first kind sas_J0\ $(x)=J_0(x)$ where 
    637632        $J_0(x) = \frac{1}{\pi}\int_0^\pi \cos(x\sin(\tau))\,d\tau$. 
    638633 
    … …  
    643638 
    644639    sas_J1(x): 
    645         Bessel function of the first kind  $\text{sas_J1}(x)=J_1(x)$ where 
     640        Bessel function of the first kind  sas_J1\ $(x)=J_1(x)$ where 
    646641        $J_1(x) = \frac{1}{\pi}\int_0^\pi \cos(\tau - x\sin(\tau))\,d\tau$. 
    647642 
    … …  
    652647 
    653648    sas_JN(n, x): 
    654         Bessel function of the first kind and integer order $n$: 
    655         $\text{sas_JN}(n, x)=J_n(x)$ where 
     649        Bessel function of the first kind and integer order $n$, 
     650        sas_JN\ $(n, x) =J_n(x)$ where 
    656651        $J_n(x) = \frac{1}{\pi}\int_0^\pi \cos(n\tau - x\sin(\tau))\,d\tau$. 
    657         If $n$ = 0 or 1, it uses sas_J0(x) or sas_J1(x), respectively. 
     652        If $n$ = 0 or 1, it uses sas_J0($x$) or sas_J1($x$), respectively. 
    658653 
    659654        The standard math function jn(n, x) is not available on all platforms. 
    … …  
    663658 
    664659    sas_Si(x): 
    665         Sine integral $\text{Si}(x) = \int_0^x \tfrac{\sin t}{t}\,dt$. 
     660        Sine integral Si\ $(x) = \int_0^x \tfrac{\sin t}{t}\,dt$. 
    666661 
    667662        This function uses Taylor series for small and large arguments: 
    … …  
    688683    sas_3j1x_x(x): 
    689684        Spherical Bessel form 
    690         $\text{sph_j1c}(x) = 3 j_1(x)/x = 3 (\sin(x) - x \cos(x))/x^3$, 
     685        sph_j1c\ $(x) = 3 j_1(x)/x = 3 (\sin(x) - x \cos(x))/x^3$, 
    691686        with a limiting value of 1 at $x=0$, where $j_1(x)$ is the spherical 
    692687        Bessel function of the first kind and first order. 
    … …  
    699694 
    700695    sas_2J1x_x(x): 
    701         Bessel form $\text{sas_J1c}(x) = 2 J_1(x)/x$, with a limiting value 
     696        Bessel form sas_J1c\ $(x) = 2 J_1(x)/x$, with a limiting value 
    702697        of 1 at $x=0$, where $J_1(x)$ is the Bessel function of first kind 
    703698        and first order. 

  • doc/guide/resolution.rst

    rf8a2baa r30b60d2  
    212212elliptical Gaussian distribution. The $A$ is a normalization factor. 
    213213 
    214 .. figure:: resolution_2d_rotation.gif 
     214.. figure:: resolution_2d_rotation.png 
    215215 
    216216    Coordinate axis rotation for 2D resolution calculation. 

  • doc/rst_prolog

    refb7615 r30b60d2  
    11.. Set up some substitutions to make life easier... 
    2 .. Remove |biggamma|, etc. when they are no longer needed. 
    3  
    4  
    5     .. |alpha| unicode:: U+03B1 
    6     .. |beta| unicode:: U+03B2 
    7     .. |gamma| unicode:: U+03B3 
    8     .. |delta| unicode:: U+03B4 
    9     .. |epsilon| unicode:: U+03B5 
    10     .. |zeta| unicode:: U+03B6 
    11     .. |eta| unicode:: U+03B7 
    12     .. |theta| unicode:: U+03B8 
    13     .. |iota| unicode:: U+03B9 
    14     .. |kappa| unicode:: U+03BA 
    15     .. |lambda| unicode:: U+03BB 
    16     .. |mu| unicode:: U+03BC 
    17     .. |nu| unicode:: U+03BD 
    18     .. |xi| unicode:: U+03BE 
    19     .. |omicron| unicode:: U+03BF 
    20     .. |pi| unicode:: U+03C0 
    21     .. |rho| unicode:: U+03C1 
    22     .. |sigma| unicode:: U+03C3 
    23     .. |tau| unicode:: U+03C4 
    24     .. |upsilon| unicode:: U+03C5 
    25     .. |phi| unicode:: U+03C6 
    26     .. |chi| unicode:: U+03C7 
    27     .. |psi| unicode:: U+03C8 
    28     .. |omega| unicode:: U+03C9 
    29  
    30  
    31     .. |biggamma| unicode:: U+0393 
    32     .. |bigdelta| unicode:: U+0394 
    33     .. |bigzeta| unicode:: U+039E 
    34     .. |bigpsi| unicode:: U+03A8 
    35     .. |bigphi| unicode:: U+03A6 
    36     .. |bigsigma| unicode:: U+03A3 
    37     .. |Gamma| unicode:: U+0393 
    38     .. |Delta| unicode:: U+0394 
    39     .. |Zeta| unicode:: U+039E 
    40     .. |Psi| unicode:: U+03A8 
    41  
    42     .. |drho| replace:: |Delta|\ |rho| 
    43     .. |equiv| unicode:: U+2261 
    44     .. |noteql| unicode:: U+2260 
    45     .. |TM| unicode:: U+2122 
    46     .. |P0| replace:: P\ :sub:`0`\ 
    47     .. |A2| replace:: A\ :sub:`2`\ 
    482 
    493.. |Ang| unicode:: U+212B 
    … …  
    6317.. |sr^-1| replace:: sr\ :sup:`-1` 
    6418 
    65  
    66  
    6719.. |cdot| unicode:: U+00B7 
    6820.. |deg| unicode:: U+00B0 

  • sasmodels/generate.py

    r573ffab r30b60d2  
    210210 
    211211# Conversion from units defined in the parameter table for each model 
    212 # to units displayed in the sphinx documentation.  
     212# to units displayed in the sphinx documentation. 
    213213# This section associates the unit with the macro to use to produce the LaTex 
    214214# code.  The macro itself needs to be defined in sasmodels/doc/rst_prolog. 
    … …  
    216216# NOTE: there is an RST_PROLOG at the end of this file which is NOT 
    217217# used for the bundled documentation. Still as long as we are defining the macros 
    218 # in two places any new addition should define the macro in both places.  
     218# in two places any new addition should define the macro in both places. 
    219219RST_UNITS = { 
    220220    "Ang": "|Ang|", 
    … …  
    898898.. |cm^-3| replace:: cm\ :sup:`-3` 
    899899.. |sr^-1| replace:: sr\ :sup:`-1` 
    900 .. |P0| replace:: P\ :sub:`0`\ 
    901  
    902 .. |equiv| unicode:: U+2261 
    903 .. |noteql| unicode:: U+2260 
    904 .. |TM| unicode:: U+2122 
    905900 
    906901.. |cdot| unicode:: U+00B7 

  • sasmodels/models/binary_hard_sphere.py

    r8f04da4 r30b60d2  
    2323    :nowrap: 
    2424 
    25     \begin{align} 
     25    \begin{align*} 
    2626    x &= \frac{(\phi_2 / \phi)\alpha^3}{(1-(\phi_2/\phi) + (\phi_2/\phi) 
    2727    \alpha^3)} \\ 
    2828    \phi &= \phi_1 + \phi_2 = \text{total volume fraction} \\ 
    2929    \alpha &= R_1/R_2 = \text{size ratio} 
    30     \end{align} 
     30    \end{align*} 
    3131 
    3232The 2D scattering intensity is the same as 1D, regardless of the orientation of 

  • sasmodels/models/core_shell_bicelle.py

    r64eecf7 r30b60d2  
    2525scattering length density variation along the cylinder axis is: 
    2626 
    27 .. 
    28  
    29   .. math:: 
     27.. math:: 
    3028 
    3129    \rho(r) = 
    … …  
    5048    :nowrap: 
    5149 
    52     \begin{align} 
     50    \begin{align*} 
    5351    F(Q,\alpha) = &\bigg[ 
    5452    (\rho_c - \rho_f) V_c \frac{2J_1(QRsin \alpha)}{QRsin\alpha}\frac{sin(QLcos\alpha/2)}{Q(L/2)cos\alpha} \\ 
    … …  
    5654    &+(\rho_r - \rho_s) V_t \frac{2J_1(Q(R+t_r)sin\alpha)}{Q(R+t_r)sin\alpha}\frac{sin(Q(L/2+t_f)cos\alpha)}{Q(L/2+t_f)cos\alpha} 
    5755    \bigg] 
    58     \end{align} 
     56    \end{align*} 
    5957 
    6058where $V_t$ is the total volume of the bicelle, $V_c$ the volume of the core, 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    r64eecf7 r30b60d2  
    4949    :nowrap: 
    5050 
    51     \begin{align} 
     51    \begin{align*} 
    5252    F(Q,\alpha,\psi) = &\bigg[ 
    5353    (\rho_c - \rho_f) V_c \frac{2J_1(QR'sin \alpha)}{QR'sin\alpha}\frac{sin(QLcos\alpha/2)}{Q(L/2)cos\alpha} \\ 
    … …  
    5555    &+(\rho_r - \rho_s) V_t \frac{2J_1(Q(R'+t_r)sin\alpha)}{Q(R'+t_r)sin\alpha}\frac{sin(Q(L/2+t_f)cos\alpha)}{Q(L/2+t_f)cos\alpha} 
    5656    \bigg] 
    57     \end{align} 
     57    \end{align*} 
    5858 
    5959where 

  • sasmodels/models/core_shell_ellipsoid.py

    r64eecf7 r30b60d2  
    4646    :nowrap: 
    4747 
    48     \begin{align} 
     48    \begin{align*} 
    4949    F(q,\alpha) = &f(q,radius\_equat\_core,radius\_equat\_core.x\_core,\alpha) \\ 
    5050    &+ f(q,radius\_equat\_core + thick\_shell,radius\_equat\_core.x\_core + thick\_shell.x\_polar\_shell,\alpha) 
    51     \end{align} 
     51    \end{align*} 
    5252 
    5353where 

  • sasmodels/models/hollow_rectangular_prism.py

    r8f04da4 r30b60d2  
    3131  :nowrap: 
    3232 
    33   \begin{align} 
     33  \begin{align*} 
    3434  A_{P\Delta}(q) & =  A B C 
    3535    \left[\frac{\sin \bigl( q \frac{C}{2} \cos\theta \bigr)} 
    … …  
    4747    \left[ \frac{\sin \bigl[ q \bigl(\frac{B}{2}-\Delta\bigr) \sin\theta \cos\phi \bigr]} 
    4848    {q \bigl(\frac{B}{2}-\Delta\bigr) \sin\theta \cos\phi} \right] 
    49   \end{align} 
     49  \end{align*} 
    5050 
    5151where $A$, $B$ and $C$ are the external sides of the parallelepiped fulfilling 

  • sasmodels/models/parallelepiped.py

    r8f04da4 r30b60d2  
    2020   Parallelepiped with the corresponding definition of sides. 
    2121 
    22 .. note:: 
    23  
    24 The three dimensions of the parallelepiped (strictly here a cuboid) may be given in 
    25 $any$ size order. To avoid multiple fit solutions, especially 
    26 with Monte-Carlo fit methods, it may be advisable to restrict their ranges. There may 
    27 be a number of closely similar "best fits", so some trial and error, or fixing of some 
    28 dimensions at expected values, may help. 
     22The three dimensions of the parallelepiped (strictly here a cuboid) may be 
     23given in *any* size order. To avoid multiple fit solutions, especially 
     24with Monte-Carlo fit methods, it may be advisable to restrict their ranges. 
     25There may be a number of closely similar "best fits", so some trial and 
     26error, or fixing of some dimensions at expected values, may help. 
    2927 
    3028The 1D scattering intensity $I(q)$ is calculated as: 

  • sasmodels/models/rpa.py

    r4f9e288 r30b60d2  
    3030    These case numbers are different from those in the NIST SANS package! 
    3131 
    32 The models are based on the papers by Akcasu et al. [#Akcasu]_ and by 
    33 Hammouda [#Hammouda]_ assuming the polymer follows Gaussian statistics such 
     32The models are based on the papers by Akcasu *et al.* and by 
     33Hammouda assuming the polymer follows Gaussian statistics such 
    3434that $R_g^2 = n b^2/6$ where $b$ is the statistical segment length and $n$ is 
    3535the number of statistical segment lengths. A nice tutorial on how these are 
    3636constructed and implemented can be found in chapters 28 and 39 of Boualem 
    37 Hammouda's 'SANS Toolbox'[#toolbox]_. 
     37Hammouda's 'SANS Toolbox'. 
    3838 
    3939In brief the macroscopic cross sections are derived from the general forms 
    … …  
    4949  are calculated with respect to component D).** So the scattering contrast 
    5050  for a C/D blend = [SLD(component C) - SLD(component D)]\ :sup:`2`. 
    51 * Depending on which case is being used, the number of fitting parameters can  
     51* Depending on which case is being used, the number of fitting parameters can 
    5252  vary. 
    5353 
    … …  
    5757      component are obtained from other methods and held fixed while The *scale* 
    5858      parameter should be held equal to unity. 
    59     * The variables are normally the segment lengths (b\ :sub:`a`, b\ :sub:`b`, 
    60       etc) and $\chi$ parameters (K\ :sub:`ab`, K\ :sub:`ac`, etc). 
    61  
     59    * The variables are normally the segment lengths ($b_a$, $b_b$, 
     60      etc.) and $\chi$ parameters ($K_{ab}$, $K_{ac}$, etc). 
    6261 
    6362References 
    6463---------- 
    6564 
    66 .. [#Akcasu] A Z Akcasu, R Klein and B Hammouda, *Macromolecules*, 26 (1993) 
    67    4136. 
    68 .. [#Hammouda] B. Hammouda, *Advances in Polymer Science* 106 (1993) 87. 
    69 .. [#toolbox] https://www.ncnr.nist.gov/staff/hammouda/the_sans_toolbox.pdf 
     65A Z Akcasu, R Klein and B Hammouda, *Macromolecules*, 26 (1993) 4136. 
     66 
     67B. Hammouda, *Advances in Polymer Science* 106 (1993) 87. 
     68 
     69B. Hammouda, *SANS Toolbox* 
     70https://www.ncnr.nist.gov/staff/hammouda/the_sans_toolbox.pdf. 
    7071 
    7172Authorship and Verification 

  • sasmodels/models/star_polymer.py

    r142a8e2 r30b60d2  
    77emanating from a common central (in the case of this model) point.  It is 
    88derived as a special case of on the Benoit model for general branched 
    9 polymers\ [#CITBenoit]_ as also used by Richter ''et. al.''\ [#CITRichter]_ 
     9polymers\ [#CITBenoit]_ as also used by Richter *et al.*\ [#CITRichter]_ 
    1010 
    1111For a star with $f$ arms the scattering intensity $I(q)$ is calculated as 

  • sasmodels/models/surface_fractal.py

    r48462b0 r30b60d2  
    99 
    1010.. math:: 
     11    :nowrap: 
    1112 
     13    \begin{align*} 
    1214    I(q) &= \text{scale} \times P(q)S(q) + \text{background} \\ 
    1315    P(q) &= F(qR)^2 \\ 
    … …  
    1517    S(q) &= \Gamma(5-D_S)\xi^{\,5-D_S}\left[1+(q\xi)^2 \right]^{-(5-D_S)/2} 
    1618            \sin\left[-(5-D_S) \tan^{-1}(q\xi) \right] q^{-1} \\ 
    17     \text{scale} &= \text{scale_factor}\, N V^2(\rho_\text{particle} - \rho_\text{solvent})^2 \\ 
     19    \text{scale} &= \text{scale factor}\, N V^1(\rho_\text{particle} - \rho_\text{solvent})^2 \\ 
    1820    V &= \frac{4}{3}\pi R^3 
     21    \end{align*} 
    1922 
    2023where $R$ is the radius of the building block, $D_S$ is the **surface** fractal 
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