Changes in / [a57a902:dd02bce] in sasmodels


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  • .travis.yml

    r947a61e rb419c2d  
    11language: python 
    2 sudo: false 
     2 
     3sudo:  false 
     4 
    35matrix: 
    46  include: 
    5   - os: linux 
    6     env: 
    7     - PY=2.7 
    8   - os: linux 
    9     env: 
    10     - PY=3.6 
    11   - os: osx 
    12     language: generic 
    13     env: 
    14     - PY=2.7 
    15   - os: osx 
    16     language: generic 
    17     env: 
    18     - PY=3.5 
     7    - os: linux 
     8      env: 
     9        - PY=2.7 
     10    - os: linux 
     11      env: 
     12        - PY=3.6 
     13    - os: osx 
     14      language: generic 
     15      env: 
     16        - PY=2.7 
     17    - os: osx 
     18      language: generic 
     19      env: 
     20        - PY=3.5 
     21 
     22# whitelist 
    1923branches: 
    2024  only: 
    21   - master 
     25    - master 
     26 
    2227addons: 
    2328  apt: 
    24     packages: opencl-headers 
     29    packages: 
     30      opencl-headers 
     31 
    2532before_install: 
    26 - openssl aes-256-cbc -K $encrypted_fe6026add10a_key -iv $encrypted_fe6026add10a_iv 
    27   -in .travis/travis_rsa.enc -out .travis/travis_rsa -d 
    28 - echo $TRAVIS_OS_NAME 
    29 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh 
    30   -O miniconda.sh; fi; 
    31 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh 
    32   -O miniconda.sh; fi; 
    33 - bash miniconda.sh -b -p $HOME/miniconda 
    34 - export PATH="$HOME/miniconda/bin:$PATH" 
    35 - hash -r 
    36 - conda update --yes conda 
    37 - conda info -a 
    38 - conda install --yes python=$PY numpy scipy cython mako cffi 
     33  - echo $TRAVIS_OS_NAME 
     34 
     35  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then 
     36      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; 
     37    fi; 
     38  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then 
     39      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; 
     40    fi; 
     41 
     42  - bash miniconda.sh -b -p $HOME/miniconda 
     43  - export PATH="$HOME/miniconda/bin:$PATH" 
     44  - hash -r 
     45  - conda update --yes conda 
     46 
     47  # Useful for debugging any issues with conda 
     48  - conda info -a 
     49 
     50  - conda install --yes python=$PY numpy scipy cython mako cffi 
     51 
     52  # Not testing with opencl below, so don't need to install it 
     53  #- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then 
     54  #    pip install pyopencl; 
     55  #  fi; 
     56 
    3957install: 
    40 - pip install bumps 
    41 - pip install unittest-xml-reporting 
     58  - pip install bumps 
     59  - pip install unittest-xml-reporting 
     60 
    4261script: 
    4362- python --version 
    4463- python -m sasmodels.model_test -v dll all 
    45 before_deploy: 
    46 - echo -e "Host danse.chem.utk.edu\n\tStrictHostKeyChecking no\n" >> ~/.ssh/config 
    47 deploy: 
    48     skip_cleanup: true 
    49     provider: script 
    50     script: /bin/sh -ex ./deploy.sh 
    51     on: 
    52         branch: master 
     64 
    5365notifications: 
    5466  slack: 

  • doc/conf.py

    r30b60d2 r8ae8532  
    211211#latex_preamble = '' 
    212212LATEX_PREAMBLE=r""" 
    213 \newcommand{\lt}{<} 
    214 \newcommand{\gt}{>} 
    215213\renewcommand{\AA}{\text{\r{A}}} % Allow \AA in math mode 
    216214\usepackage[utf8]{inputenc}      % Allow unicode symbols in text 

  • doc/guide/magnetism/magnetism.rst

    r990d8df r990d8df  
    1616 
    1717.. figure:: 
    18     mag_img/mag_vector.png 
     18    mag_img/mag_vector.bmp 
    1919 
    2020The magnetic scattering length density is then 
    … …  
    3636 
    3737.. figure:: 
    38     mag_img/M_angles_pic.png 
     38    mag_img/M_angles_pic.bmp 
    3939 
    4040If the angles of the $Q$ vector and the spin-axis $x'$ to the $x$ - axis are 

  • doc/guide/plugin.rst

    r30b60d2 r870a2f4  
    117117Models that do not conform to these requirements will *never* be incorporated 
    118118into the built-in library. 
     119 
     120More 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>`_ 
     123describes the structure of a model. 
    119124 
    120125 
    … …  
    608613 
    609614    sas_gamma(x): 
    610         Gamma function sas_gamma\ $(x) = \Gamma(x)$. 
     615        Gamma function $\text{sas_gamma}(x) = \Gamma(x)$. 
    611616 
    612617        The standard math function, tgamma(x) is unstable for $x < 1$ 
    … …  
    618623    sas_erf(x), sas_erfc(x): 
    619624        Error function 
    620         sas_erf\ $(x) = \frac{2}{\sqrt\pi}\int_0^x e^{-t^2}\,dt$ 
     625        $\text{sas_erf}(x) = \frac{2}{\sqrt\pi}\int_0^x e^{-t^2}\,dt$ 
    621626        and complementary error function 
    622         sas_erfc\ $(x) = \frac{2}{\sqrt\pi}\int_x^{\infty} e^{-t^2}\,dt$. 
     627        $\text{sas_erfc}(x) = \frac{2}{\sqrt\pi}\int_x^{\infty} e^{-t^2}\,dt$. 
    623628 
    624629        The standard math functions erf(x) and erfc(x) are slower and broken 
    … …  
    629634 
    630635    sas_J0(x): 
    631         Bessel function of the first kind sas_J0\ $(x)=J_0(x)$ where 
     636        Bessel function of the first kind $\text{sas_J0}(x)=J_0(x)$ where 
    632637        $J_0(x) = \frac{1}{\pi}\int_0^\pi \cos(x\sin(\tau))\,d\tau$. 
    633638 
    … …  
    638643 
    639644    sas_J1(x): 
    640         Bessel function of the first kind  sas_J1\ $(x)=J_1(x)$ where 
     645        Bessel function of the first kind  $\text{sas_J1}(x)=J_1(x)$ where 
    641646        $J_1(x) = \frac{1}{\pi}\int_0^\pi \cos(\tau - x\sin(\tau))\,d\tau$. 
    642647 
    … …  
    647652 
    648653    sas_JN(n, x): 
    649         Bessel function of the first kind and integer order $n$, 
    650         sas_JN\ $(n, x) =J_n(x)$ where 
     654        Bessel function of the first kind and integer order $n$: 
     655        $\text{sas_JN}(n, x)=J_n(x)$ where 
    651656        $J_n(x) = \frac{1}{\pi}\int_0^\pi \cos(n\tau - x\sin(\tau))\,d\tau$. 
    652         If $n$ = 0 or 1, it uses sas_J0($x$) or sas_J1($x$), respectively. 
     657        If $n$ = 0 or 1, it uses sas_J0(x) or sas_J1(x), respectively. 
    653658 
    654659        The standard math function jn(n, x) is not available on all platforms. 
    … …  
    658663 
    659664    sas_Si(x): 
    660         Sine integral Si\ $(x) = \int_0^x \tfrac{\sin t}{t}\,dt$. 
     665        Sine integral $\text{Si}(x) = \int_0^x \tfrac{\sin t}{t}\,dt$. 
    661666 
    662667        This function uses Taylor series for small and large arguments: 
    … …  
    683688    sas_3j1x_x(x): 
    684689        Spherical Bessel form 
    685         sph_j1c\ $(x) = 3 j_1(x)/x = 3 (\sin(x) - x \cos(x))/x^3$, 
     690        $\text{sph_j1c}(x) = 3 j_1(x)/x = 3 (\sin(x) - x \cos(x))/x^3$, 
    686691        with a limiting value of 1 at $x=0$, where $j_1(x)$ is the spherical 
    687692        Bessel function of the first kind and first order. 
    … …  
    694699 
    695700    sas_2J1x_x(x): 
    696         Bessel form sas_J1c\ $(x) = 2 J_1(x)/x$, with a limiting value 
     701        Bessel form $\text{sas_J1c}(x) = 2 J_1(x)/x$, with a limiting value 
    697702        of 1 at $x=0$, where $J_1(x)$ is the Bessel function of first kind 
    698703        and first order. 

  • doc/guide/resolution.rst

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

  • doc/rst_prolog

    r30b60d2 ra0fb06a  
    11.. Set up some substitutions to make life easier... 
     2.. Remove |biggamma|, etc. when they are no longer needed. 
    23 
     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 
     43.. |drho| replace:: |Delta|\ |rho| 
    344.. |Ang| unicode:: U+212B 
    445.. |Ang^-1| replace:: |Ang|\ :sup:`-1` 
    … …  
    1657.. |cm^-3| replace:: cm\ :sup:`-3` 
    1758.. |sr^-1| replace:: sr\ :sup:`-1` 
     59.. |P0| replace:: P\ :sub:`0`\ 
     60.. |A2| replace:: A\ :sub:`2`\ 
     61 
     62 
     63.. |equiv| unicode:: U+2261 
     64.. |noteql| unicode:: U+2260 
     65.. |TM| unicode:: U+2122 
     66 
    1867 
    1968.. |cdot| unicode:: U+00B7 

  • sasmodels/generate.py

    r30b60d2 r573ffab  
    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 
    900905 
    901906.. |cdot| unicode:: U+00B7 

  • sasmodels/models/binary_hard_sphere.py

    r30b60d2 r8f04da4  
    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

    r30b60d2 ra151caa  
    4141 
    4242    I(Q,\alpha) = \frac{\text{scale}}{V_t} \cdot 
    43         F(Q,\alpha)^2 \cdot sin(\alpha) + \text{background} 
     43        F(Q,\alpha)^2.sin(\alpha) + \text{background} 
    4444 
    4545where 
    4646 
    4747.. math:: 
    48     :nowrap: 
    4948 
    50     \begin{align*} 
     49    \begin{align} 
    5150    F(Q,\alpha) = &\bigg[ 
    5251    (\rho_c - \rho_f) V_c \frac{2J_1(QRsin \alpha)}{QRsin\alpha}\frac{sin(QLcos\alpha/2)}{Q(L/2)cos\alpha} \\ 
    … …  
    5453    &+(\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} 
    5554    \bigg] 
    56     \end{align*} 
     55    \end{align} 
    5756 
    5857where $V_t$ is the total volume of the bicelle, $V_c$ the volume of the core, 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    r30b60d2 r8f04da4  
    4242 
    4343    I(Q,\alpha,\psi) = \frac{\text{scale}}{V_t} \cdot 
    44         F(Q,\alpha, \psi)^2 \cdot sin(\alpha) + \text{background} 
     44        F(Q,\alpha, \psi)^2.sin(\alpha) + \text{background} 
    4545 
    46 where a numerical integration of $F(Q,\alpha, \psi)^2 \cdot sin(\alpha)$ is carried out over \alpha and \psi for: 
     46where a numerical integration of $F(Q,\alpha, \psi)^2.sin(\alpha)$ is carried out over \alpha and \psi for: 
    4747 
    4848.. math:: 
    49     :nowrap: 
    5049 
    51     \begin{align*} 
     50        \begin{align} 
    5251    F(Q,\alpha,\psi) = &\bigg[ 
    5352    (\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} \\ 
    … …  
    5554    &+(\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} 
    5655    \bigg] 
    57     \end{align*} 
     56    \end{align} 
    5857 
    5958where 

  • sasmodels/models/core_shell_ellipsoid.py

    r30b60d2 r9f6823b  
    4444 
    4545.. math:: 
    46     :nowrap: 
    47  
    48     \begin{align*} 
     46    \begin{align} 
    4947    F(q,\alpha) = &f(q,radius\_equat\_core,radius\_equat\_core.x\_core,\alpha) \\ 
    5048    &+ f(q,radius\_equat\_core + thick\_shell,radius\_equat\_core.x\_core + thick\_shell.x\_polar\_shell,\alpha) 
    51     \end{align*} 
     49    \end{align} 
    5250 
    5351where 

  • sasmodels/models/fractal_core_shell.py

    r8f04da4 r8f04da4  
    3131$\rho_{solv}$ are the scattering length densities of the core, shell, and 
    3232solvent respectively, $r_c$ and $r_s$ are the radius of the core and the radius 
    33 of the whole particle respectively, $D_f$ is the fractal dimension, and $\xi$ the 
     33of the whole particle respectively, $D_f$ is the fractal dimension, and |xi| the 
    3434correlation length. 
    3535 

  • sasmodels/models/hollow_rectangular_prism.py

    r30b60d2 r8f04da4  
    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/line.py

    rc63a7c8 r48462b0  
    1515 
    1616.. math:: 
    17  
    1817    I(q) = \text{scale} (I(qx) \cdot I(qy)) + \text{background} 
    1918 

  • sasmodels/models/multilayer_vesicle.py

    r870a2f4 r870a2f4  
    3333.. math:: 
    3434 
    35      r_i &= r_c + (i-1)(t_s + t_w) \text{ solvent radius before shell } i \\ 
    36      R_i &= r_i + t_s \text{ shell radius for shell } i 
     35     r_i &= r_c + (i-1)(t_s + t_w) && \text{ solvent radius before shell } i \\ 
     36     R_i &= r_i + t_s && \text{ shell radius for shell } i 
    3737 
    3838$\phi$ is the volume fraction of particles, $V(r)$ is the volume of a sphere 

  • sasmodels/models/parallelepiped.py

    r30b60d2 r8f04da4  
    2020   Parallelepiped with the corresponding definition of sides. 
    2121 
    22 The three dimensions of the parallelepiped (strictly here a cuboid) may be 
    23 given in *any* size order. To avoid multiple fit solutions, especially 
    24 with Monte-Carlo fit methods, it may be advisable to restrict their ranges. 
    25 There may be a number of closely similar "best fits", so some trial and 
    26 error, or fixing of some dimensions at expected values, may help. 
     22.. note:: 
     23 
     24The three dimensions of the parallelepiped (strictly here a cuboid) may be given in 
     25$any$ size order. To avoid multiple fit solutions, especially 
     26with Monte-Carlo fit methods, it may be advisable to restrict their ranges. There may 
     27be a number of closely similar "best fits", so some trial and error, or fixing of some 
     28dimensions at expected values, may help. 
    2729 
    2830The 1D scattering intensity $I(q)$ is calculated as: 

  • sasmodels/models/rpa.py

    r30b60d2 r4f9e288  
    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.* and by 
    33 Hammouda assuming the polymer follows Gaussian statistics such 
     32The models are based on the papers by Akcasu et al. [#Akcasu]_ and by 
     33Hammouda [#Hammouda]_ 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'. 
     37Hammouda's 'SANS Toolbox'[#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 ($b_a$, $b_b$, 
    60       etc.) and $\chi$ parameters ($K_{ab}$, $K_{ac}$, etc). 
     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 
    6162 
    6263References 
    6364---------- 
    6465 
    65 A Z Akcasu, R Klein and B Hammouda, *Macromolecules*, 26 (1993) 4136. 
    66  
    67 B. Hammouda, *Advances in Polymer Science* 106 (1993) 87. 
    68  
    69 B. Hammouda, *SANS Toolbox* 
    70 https://www.ncnr.nist.gov/staff/hammouda/the_sans_toolbox.pdf. 
     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 
    7170 
    7271Authorship and Verification 

  • sasmodels/models/star_polymer.py

    r30b60d2 rd439007  
    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

    r30b60d2 r48462b0  
    99 
    1010.. math:: 
    11     :nowrap: 
    1211 
    13     \begin{align*} 
    1412    I(q) &= \text{scale} \times P(q)S(q) + \text{background} \\ 
    1513    P(q) &= F(qR)^2 \\ 
    … …  
    1715    S(q) &= \Gamma(5-D_S)\xi^{\,5-D_S}\left[1+(q\xi)^2 \right]^{-(5-D_S)/2} 
    1816            \sin\left[-(5-D_S) \tan^{-1}(q\xi) \right] q^{-1} \\ 
    19     \text{scale} &= \text{scale factor}\, N V^1(\rho_\text{particle} - \rho_\text{solvent})^2 \\ 
     17    \text{scale} &= \text{scale_factor}\, N V^2(\rho_\text{particle} - \rho_\text{solvent})^2 \\ 
    2018    V &= \frac{4}{3}\pi R^3 
    21     \end{align*} 
    2219 
    2320where $R$ is the radius of the building block, $D_S$ is the **surface** fractal 
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