Changeset f64b154 in sasmodels


Ignore:
Timestamp:
Apr 2, 2019 6:12:24 AM (6 years ago)
Author:
GitHub <noreply@…>
Branches:
master
Parents:
3448301 (diff), b955dd5 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
git-author:
Steve K <smk78@…> (04/02/19 06:12:24)
git-committer:
GitHub <noreply@…> (04/02/19 06:12:24)
Message:

Merge pull request #103 from SasView?/ticket-1263-source-link

Add local link to source files. Refs #1263.

Files:
5 added
86 edited

Legend:

Unmodified
Added
Removed

  • doc/conf.py

    r30b60d2 rf8060c5  
    3434              #'sphinx.ext.pngmath', 
    3535              'sphinx.ext.mathjax', 
    36               #'only_directives', 
    3736              #'matplotlib.sphinxext.mathmpl', 
    38               'matplotlib.sphinxext.only_directives', 
    3937              'matplotlib.sphinxext.plot_directive', 
    4038              'dollarmath', 

  • doc/genmodel.py

    rb866abf rbe0942c  
    77import matplotlib.pyplot as plt 
    88sys.path.insert(0, os.path.abspath('..')) 
     9import sasmodels 
    910from sasmodels import generate, core 
    1011from sasmodels.direct_model import DirectModel, call_profile 
    … …  
    127128    #print("figure saved in",path) 
    128129 
     130def copy_if_newer(src, dst): 
     131    from os.path import dirname, exists, getmtime 
     132    import shutil 
     133    if not exists(dst): 
     134        path = dirname(dst) 
     135        if not exists(path): 
     136            os.makedirs(path) 
     137        shutil.copy2(src, dst) 
     138    elif getmtime(src) > getmtime(dst): 
     139        shutil.copy2(src, dst) 
     140 
     141def link_sources(model_info): 
     142    from os.path import basename, dirname, realpath, join as joinpath 
     143 
     144    # List source files in reverse order of dependency. 
     145    model_file = basename(model_info.filename) 
     146    sources = list(reversed(model_info.source + [model_file])) 
     147 
     148    # Copy files to src dir under models directory.  Need to do this 
     149    # because sphinx can't link to an absolute path. 
     150    root = dirname(dirname(realpath(__file__))) 
     151    src = joinpath(root, "sasmodels", "models") 
     152    dst = joinpath(root, "doc", "model", "src") 
     153    for path in sources: 
     154        copy_if_newer(joinpath(src, path), joinpath(dst, path)) 
     155 
     156    # Link to local copy of the files 
     157    downloads = [":download:`%s <src/%s>`"%(path, path) for path in sources] 
     158 
     159    # Could do syntax highlighting on the model files by creating a rst file 
     160    # beside each source file named containing source file with 
     161    # 
     162    #    src/path.rst: 
     163    # 
     164    #    .. {{ path.replace('/','_') }}: 
     165    # 
     166    #    .. literalinclude:: {{ src/path }} 
     167    #        :language: {{ "python" if path.endswith('.py') else "c" }} 
     168    #        :linenos: 
     169    # 
     170    # and link to it using 
     171    # 
     172    #     colors = [":ref:`%s`"%(path.replace('/','_')) for path in sources] 
     173    # 
     174    # Probably need to dump all the rst files into an index.rst to build them. 
     175 
     176    # Link to github repo (either the tagged sasmodels version or master) 
     177    url = "https://github.com/SasView/sasmodels/blob/v%s"%sasmodels.__version__ 
     178    #url = "https://github.com/SasView/sasmodels/blob/master"%sasmodels.__version__ 
     179    links = ["`%s <%s/sasmodels/models/%s>`_"%(path, url, path) for path in sources] 
     180 
     181    sep = "\n$\\ \\star\\ $ "  # bullet 
     182    body = "\n**Source**\n" 
     183    #body += "\n" + sep.join(links) + "\n\n" 
     184    body += "\n" + sep.join(downloads) + "\n\n" 
     185    return body 
     186 
    129187def gen_docs(model_info): 
    130188    # type: (ModelInfo) -> None 
    … …  
    150208    match = re.search(pattern, docstr.upper()) 
    151209 
     210    sources = link_sources(model_info) 
     211 
     212    insertion = captionstr + sources 
     213 
    152214    if match: 
    153215        docstr1 = docstr[:match.start()] 
    154216        docstr2 = docstr[match.start():] 
    155         docstr = docstr1 + captionstr + docstr2 
     217        docstr = docstr1 + insertion + docstr2 
    156218    else: 
    157219        print('------------------------------------------------------------------') 
    158220        print('References NOT FOUND for model: ', model_info.id) 
    159221        print('------------------------------------------------------------------') 
    160         docstr += captionstr 
    161  
    162     open(sys.argv[2],'w').write(docstr) 
     222        docstr += insertion 
     223 
     224    open(sys.argv[2], 'w').write(docstr) 
    163225 
    164226def process_model(path): 

  • doc/guide/fitting_sq.rst

    r3448301 rf64b154  
    9090   later. 
    9191 
    92 * *radius_effective_mode*: 
     92 *radius_effective_mode*: 
    9393 
    9494    Defines how the effective radius (parameter **radius_effective**) should 

  • doc/index.rst

    r8ae8532 rb955dd5  
    1616polydispersity and orientational dispersion. 
    1717 
    18 .. htmlonly:: 
     18.. only:: html 
     19 
    1920   :Release: |version| 
    2021   :Date:    |today| 
    … …  
    2324 
    2425.. toctree:: 
    25    :numbered: 
    2626   :maxdepth: 4 
    2727 
    … …  
    3737* :ref:`modindex` 
    3838 
    39 .. htmlonly:: 
     39.. only:: html 
     40 
    4041  * :ref:`search` 

  • sasmodels/modelinfo.py

    ra34b811 rb955dd5  
    292292    Control parameters are used for variant models such as :ref:`rpa` which 
    293293    have different cases with different parameters, as well as models 
    294     like :ref:`spherical_sld` with its user defined number of shells. 
     294    like *spherical_sld* with its user defined number of shells. 
    295295    The control parameter should appear in the parameter table along with the 
    296296    parameters it is is controlling.  For variant models, use *[CASES]* in 
    … …  
    957957    structure_factor = None # type: bool 
    958958    #: True if the model defines an Fq function with signature 
    959     #: void Fq(double q, double *F1, double *F2, ...) 
     959    #: ``void Fq(double q, double *F1, double *F2, ...)`` 
    960960    have_Fq = False 
    961961    #: List of options for computing the effective radius of the shape, 

  • sasmodels/models/_spherepy.py

    ra34b811 rd57b06c  
    3939John Wiley and Sons, New York, (1955) 
    4040 
    41 Source 
    42 ------ 
    43  
    44 `_spherepy.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/_spherepy.py>`_ 
    45 `sphere.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/sphere.c>`_ 
    46  
    4741Authorship and Verification 
    4842---------------------------- 
    … …  
    5145* **Last Modified by:** 
    5246* **Last Reviewed by:** S King and P Parker **Date:** 2013/09/09 and 2014/01/06 
    53 * **Source added by :** Steve King **Date:** March 25, 2019 
    5447""" 
    5548 

  • sasmodels/models/adsorbed_layer.py

    r0507e09 rc1e44e5  
    4949   Layers*, *Macromol. Symp.*, 190 (2002) 33-42. 
    5050 
    51 Source 
    52 ------ 
    53  
    54 `adsorbed_layer.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/adsorbed_layer.py>`_ 
    55  
    5651Authorship and Verification 
    5752---------------------------- 
    … …  
    6055* **Last Modified by:** Paul Kienzle **Date:** April 14, 2016 
    6156* **Last Reviewed by:** Steve King **Date:** March 18, 2016 
    62 * **Source added by :** Steve King **Date:** March 25, 2019 
    6357""" 
    6458 

  • sasmodels/models/barbell.py

    ra34b811 rd57b06c  
    8181.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    8282 
    83 Source 
    84 ------ 
    85  
    86 `barbell.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/barbell.py>`_ 
    87  
    88 `barbell.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/barbell.c>`_ 
    89  
    9083Authorship and Verification 
    9184---------------------------- 
    … …  
    9487* **Last Modified by:** Paul Butler **Date:** March 20, 2016 
    9588* **Last Reviewed by:** Richard Heenan **Date:** January 4, 2017 
    96 * **Source added by :** Steve King **Date:** March 25, 2019 
    9789""" 
    9890 

  • sasmodels/models/bcc_paracrystal.py

    r0507e09 rc1e44e5  
    100100   (Corrections to FCC and BCC lattice structure calculation) 
    101101 
    102 Source 
    103 ------ 
    104  
    105 `bcc_paracrystal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/bcc_paracrystal.py>`_ 
    106  
    107 `bcc_paracrystal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/bcc_paracrystal.c>`_ 
    108  
    109102Authorship and Verification 
    110103--------------------------- 
    … …  
    113106* **Last Modified by:** Paul Butler **Date:** September 29, 2016 
    114107* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016 
    115 * **Source added by :** Steve King **Date:** March 25, 2019 
    116108""" 
    117109 

  • sasmodels/models/be_polyelectrolyte.py

    r0507e09 rc1e44e5  
    9191.. [#] E Raphael, J F Joanny, *Europhysics Letters*, 11 (1990) 179 
    9292 
    93 Source 
    94 ------ 
    95  
    96 `be_polyelectrolyte.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/be_polyelectrolyte.py>`_ 
    97  
    9893Authorship and Verification 
    9994---------------------------- 
    … …  
    10297* **Last Modified by:** Paul Butler **Date:** September 25, 2018 
    10398* **Last Reviewed by:** Paul Butler **Date:** September 25, 2018 
    104 * **Source added by :** Steve King **Date:** March 25, 2019 
    10599""" 
    106100 

  • sasmodels/models/binary_hard_sphere.py

    r0507e09 rc1e44e5  
    6565.. [#] S R Kline, *J Appl. Cryst.*, 39 (2006) 895 
    6666 
    67 Source 
    68 ------ 
    69  
    70 `binary_hard_sphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/binary_hard_sphere.py>`_ 
    71  
    72 `binary_hard_sphere.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/binary_hard_sphere.c>`_ 
    73  
    7467Authorship and Verification 
    7568---------------------------- 
    … …  
    7871* **Last Modified by:** Paul Butler **Date:** March 20, 2016 
    7972* **Last Reviewed by:** Paul Butler **Date:** March 20, 2016 
    80 * **Source added by :** Steve King **Date:** March 25, 2019 
    8173""" 
    8274 

  • sasmodels/models/broad_peak.py

    r0507e09 rc1e44e5  
    3333None. 
    3434 
    35 Source 
    36 ------ 
    37  
    38 `broad_peak.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/broad_peak.py>`_ 
    39  
    4035Authorship and Verification 
    4136---------------------------- 
    … …  
    4439* **Last Modified by:** Paul kienle **Date:** July 24, 2016 
    4540* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016 
    46 * **Source added by :** Steve King **Date:** March 25, 2019 
    4741""" 
    4842 

  • sasmodels/models/capped_cylinder.py

    ra34b811 rd57b06c  
    8484.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    8585 
    86 Source 
    87 ------ 
    88  
    89 `capped_cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/capped_cylinder.py>`_ 
    90  
    91 `capped_cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/capped_cylinder.c>`_ 
    92  
    9386Authorship and Verification 
    9487---------------------------- 
    … …  
    9790* **Last Modified by:** Paul Butler **Date:** September 30, 2016 
    9891* **Last Reviewed by:** Richard Heenan **Date:** January 4, 2017 
    99 * **Source added by :** Steve King **Date:** March 25, 2019 
    10092""" 
    10193 

  • sasmodels/models/core_multi_shell.py

    ra34b811 rd57b06c  
    3939   Neutron Scattering*, Plenum Press, New York, 1987. 
    4040 
    41 Source 
    42 ------ 
    43  
    44 `core_multi_shell.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_multi_shell.py>`_ 
    45  
    46 `core_multi_shell.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_multi_shell.c>`_ 
    47  
    4841Authorship and Verification 
    4942---------------------------- 
    … …  
    5245* **Last Modified by:** Paul Kienzle **Date:** September 12, 2016 
    5346* **Last Reviewed by:** Paul Kienzle **Date:** September 12, 2016 
    54 * **Source added by :** Steve King **Date:** March 25, 2019 
    5547""" 
    5648from __future__ import division 

  • sasmodels/models/core_shell_bicelle.py

    ra34b811 rd57b06c  
    9292.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    9393 
    94 Source 
    95 ------ 
    96  
    97 `core_shell_bicelle.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_bicelle.py>`_ 
    98  
    99 `core_shell_bicelle.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_bicelle.c>`_ 
    100  
    10194Authorship and Verification 
    10295---------------------------- 
    … …  
    10598* **Last Modified by:** Paul Butler **Date:** September 30, 2016 
    10699* **Last Reviewed by:** Richard Heenan **Date:** January 4, 2017 
    107 * **Source added by :** Steve King **Date:** March 25, 2019 
    108100""" 
    109101 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    ra34b811 rd57b06c  
    101101.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    102102 
    103 Source 
    104 ------ 
    105  
    106 `core_shell_bicelle_elliptical.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_bicelle_elliptical.py>`_ 
    107  
    108 `core_shell_bicelle_elliptical.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_bicelle_elliptical.c>`_ 
    109  
    110103Authorship and Verification 
    111104---------------------------- 
    … …  
    114107* **Last Modified by:**  Richard Heenan **Date:** December 14, 2016 
    115108* **Last Reviewed by:**  Paul Kienzle **Date:** Feb 28, 2018 
    116 * **Source added by :**  Steve King **Date:** March 25, 2019 
    117109""" 
    118110 

  • sasmodels/models/core_shell_bicelle_elliptical_belt_rough.py

    ra34b811 rd57b06c  
    113113.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    114114 
    115 Source 
    116 ------ 
    117  
    118 `core_shell_bicelle_elliptical_belt_rough.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_bicelle_elliptical_belt_rough.py>`_ 
    119  
    120 `core_shell_bicelle_elliptical_belt_rough.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_bicelle_elliptical_belt_rough.c>`_ 
    121  
    122115Authorship and Verification 
    123116---------------------------- 
    … …  
    126119* **Last Modified by:**  Richard Heenan new 2d orientation **Date:** October 5, 2017 
    127120* **Last Reviewed by:**  Richard Heenan 2d calc seems agree with 1d **Date:** Nov 2, 2017 
    128 * **Source added by :**  Steve King **Date:** March 25, 2019 
    129121""" 
    130122 

  • sasmodels/models/core_shell_cylinder.py

    rdb1d9d5 rd57b06c  
    7272.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    7373 
    74 Source 
    75 ------ 
    76  
    77 `core_shell_cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_cylinder.py>`_ 
    78  
    79 `core_shell_cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_cylinder.c>`_ 
    80  
    8174Authorship and Verification 
    8275---------------------------- 
    … …  
    8578* **Last Modified by:** Paul Kienzle **Date:** Aug 8, 2016 
    8679* **Last Reviewed by:** Richard Heenan **Date:** March 18, 2016 
    87 * **Source added by :** Steve King **Date:** March 25, 2019 
    8880""" 
    8981 

  • sasmodels/models/core_shell_ellipsoid.py

    r830cf6b rd57b06c  
    9797.. [#] Berr, S. *J. Phys. Chem.*, 1987, 91, 4760 
    9898 
    99 Source 
    100 ------ 
    101  
    102 `core_shell_ellipsoid.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_ellipsoid.py>`_ 
    103  
    104 `core_shell_ellipsoid.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_ellipsoid.c>`_ 
    105  
    10699Authorship and Verification 
    107100---------------------------- 
    … …  
    110103* **Last Modified by:** Richard Heenan (reparametrised model) **Date:** 2015 
    111104* **Last Reviewed by:** Steve King **Date:** March 27, 2019 
    112 * **Source added by :** Steve King **Date:** March 25, 2019 
    113105""" 
    114106 

  • sasmodels/models/core_shell_parallelepiped.py

    ra34b811 rd57b06c  
    175175.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    176176 
    177 Source 
    178 ------ 
    179  
    180 `core_shell_parallelepiped.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_parallelepiped.py>`_ 
    181  
    182 `core_shell_parallelepiped.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_parallelepiped.c>`_ 
    183  
    184177Authorship and Verification 
    185178---------------------------- 
    … …  
    190183* **Last Reviewed by:** Paul Butler **Date:** May 24, 2018 - documentation 
    191184  updated 
    192 * **Source added by :** Steve King **Date:** March 25, 2019 
    193185""" 
    194186 

  • sasmodels/models/core_shell_sphere.py

    ra34b811 rd57b06c  
    5050.. [#] A Guinier and G Fournet, *Small-Angle Scattering of X-Rays*, John Wiley and Sons, New York, (1955) 
    5151 
    52 Source 
    53 ------ 
    54  
    55 `core_shell_sphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_sphere.py>`_ 
    56  
    57 `core_shell_sphere.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/core_shell_sphere.c>`_ 
    58  
    5952Authorship and Verification 
    6053---------------------------- 
    … …  
    6356* **Last Modified by:** 
    6457* **Last Reviewed by:** 
    65 * **Source added by :** Steve King **Date:** March 25, 2019 
    6658""" 
    6759 

  • sasmodels/models/correlation_length.py

    r0507e09 rc1e44e5  
    3232.. [#] B Hammouda, D L Ho and S R Kline, Insight into Clustering in Poly(ethylene oxide) Solutions, Macromolecules, 37 (2004) 6932-6937 
    3333 
    34 Source 
    35 ------ 
    36  
    37 `correlation_length.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/correlation_length.py>`_ 
    38  
    3934Authorship and Verification 
    4035---------------------------- 
    4136 
    42 * **Author:**  
    43 * **Last Modified by:**  
    44 * **Last Reviewed by:**  
    45 * **Source added by :** Steve King **Date:** March 25, 2019 
     37* **Author:** 
     38* **Last Modified by:** 
     39* **Last Reviewed by:** 
    4640""" 
    4741 

  • sasmodels/models/cylinder.py

    ra34b811 rd57b06c  
    100100.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    101101 
    102 Source 
    103 ------ 
    104  
    105 `cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/cylinder.py>`_ 
    106  
    107 `cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/cylinder.c>`_ 
    108  
    109102Authorship and Verification 
    110103---------------------------- 
    … …  
    113106* **Last Modified by:** 
    114107* **Last Reviewed by:** 
    115 * **Source added by :** Steve King **Date:** March 25, 2019 
    116108""" 
    117109 

  • sasmodels/models/ellipsoid.py

    ra34b811 rd57b06c  
    109109.. [#] A. Isihara. *J. Chem. Phys.*, 18 (1950) 1446-1449 
    110110 
    111 Source 
    112 ------ 
    113  
    114 `ellipsoid.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/ellipsoid.py>`_ 
    115  
    116 `ellipsoid.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/ellipsoid.c>`_ 
    117  
    118111Authorship and Verification 
    119112---------------------------- 
    … …  
    122115* **Converted to sasmodels by:** Helen Park **Date:** July 9, 2014 
    123116* **Last Modified by:** Paul Kienzle **Date:** March 22, 2017 
    124 * **Source added by :** Steve King **Date:** March 25, 2019 
    125117""" 
    126118from __future__ import division 

  • sasmodels/models/elliptical_cylinder.py

    ra34b811 rd57b06c  
    8989.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    9090 
    91 Source 
    92 ------ 
    93  
    94 `elliptical_cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/elliptical_cylinder.py>`_ 
    95  
    96 `elliptical_cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/elliptical_cylinder.c>`_ 
    97  
    9891Authorship and Verification 
    9992---------------------------- 
    … …  
    10295* **Last Modified by:** 
    10396* **Last Reviewed by:**  Richard Heenan - corrected equation in docs **Date:** December 21, 2016 
    104 * **Source added by :** Steve King **Date:** March 25, 2019 
    10597""" 
    10698 

  • sasmodels/models/fcc_paracrystal.py

    r0507e09 rc1e44e5  
    9999   (Corrections to FCC and BCC lattice structure calculation) 
    100100 
    101 Source 
    102 ------ 
    103  
    104 `fcc_paracrystal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fcc_paracrystal.py>`_ 
    105  
    106 `fcc_paracrystal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fcc_paracrystal.c>`_ 
    107  
    108101Authorship and Verification 
    109102--------------------------- 
    … …  
    112105* **Last Modified by:** Paul Butler **Date:** September 29, 2016 
    113106* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016 
    114 * **Source added by :** Steve King **Date:** March 25, 2019 
    115107""" 
    116108 

  • sasmodels/models/flexible_cylinder.py

    r830cf6b rd57b06c  
    9595.. [#] W R Chen, P D Butler and L J Magid, *Incorporating Intermicellar Interactions in the Fitting of SANS Data from Cationic Wormlike Micelles.* Langmuir, 22(15) 2006 6539-6548 
    9696 
    97 Source 
    98 ------ 
    99  
    100 `flexible_cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/flexible_cylinder.py>`_ 
    101  
    102 `flexible_cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/flexible_cylinder.c>`_ 
    103  
    104 `wrc_cyl.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lib/wrc_cyl.c>`_ 
    105  
    10697Authorship and Verification 
    10798---------------------------- 
    … …  
    110101* **Last Modified by:** 
    111102* **Last Reviewed by:** Steve King **Date:** March 26, 2019 
    112 * **Source added by :** Steve King **Date:** March 25, 2019 
    113103""" 
    114104 

  • sasmodels/models/flexible_cylinder_elliptical.py

    rdb1d9d5 rc1e44e5  
    8383.. [#] W R Chen, P D Butler and L J Magid, *Incorporating Intermicellar Interactions in the Fitting of SANS Data from Cationic Wormlike Micelles.* Langmuir, 22(15) 2006 6539-6548 
    8484 
    85 Source 
    86 ------ 
    87  
    88 `flexible_cylinder_elliptical.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/flexible_cylinder_elliptical.py>`_ 
    89  
    90 `flexible_cylinder_elliptical.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/flexible_cylinder_elliptical.c>`_ 
    91  
    92 `wrc_cyl.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lib/wrc_cyl.c>`_ 
    93  
    9485Authorship and Verification 
    9586---------------------------- 
    … …  
    9889* **Last Modified by:** Richard Heenan **Date:** December, 2016 
    9990* **Last Reviewed by:** Steve King **Date:** March 26, 2019 
    100 * **Source added by :** Steve King **Date:** March 25, 2019 
    10191""" 
    10292 

  • sasmodels/models/fractal.py

    r0507e09 rc1e44e5  
    4646.. [#] J Teixeira, *J. Appl. Cryst.*, 21 (1988) 781-785 
    4747 
    48 Source 
    49 ------ 
    50  
    51 `fractal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fractal.py>`_ 
    52  
    53 `fractal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fractal.c>`_ 
    54  
    5548Authorship and Verification 
    5649---------------------------- 
    … …  
    6053* **Last Modified by:** Paul Butler **Date:** March 12, 2017 
    6154* **Last Reviewed by:** Paul Butler **Date:** March 12, 2017 
    62 * **Source added by :** Steve King **Date:** March 25, 2019 
    6355""" 
    6456from __future__ import division 

  • sasmodels/models/fractal_core_shell.py

    r0507e09 rc1e44e5  
    5151.. [#Kline]  S R Kline, *J Appl. Cryst.*, 39 (2006) 895 
    5252 
    53 Source 
    54 ------ 
    55  
    56 `fractal_core_shell.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fractal_core_shell.py>`_ 
    57  
    58 `fractal_core_shell.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fractal_core_shell.c>`_ 
    59  
    6053Authorship and Verification 
    6154---------------------------- 
    … …  
    6457* **Last Modified by:** Paul Butler and Paul Kienzle **Date:** November 27, 2016 
    6558* **Last Reviewed by:** Paul Butler and Paul Kienzle **Date:** November 27, 2016 
    66 * **Source added by :** Steve King **Date:** March 25, 2019 
    6759""" 
    6860 

  • sasmodels/models/fuzzy_sphere.py

    ra34b811 rd57b06c  
    5353.. [#] M Stieger, J. S Pedersen, P Lindner, W Richtering, *Langmuir*, 20 (2004) 7283-7292 
    5454 
    55 Source 
    56 ------ 
    57  
    58 `fuzzy_sphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fuzzy_sphere.py>`_ 
    59  
    60 `fuzzy_sphere.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/fuzzy_sphere.c>`_ 
    61  
    6255Authorship and Verification 
    6356---------------------------- 
    … …  
    6659* **Last Modified by:** 
    6760* **Last Reviewed by:** 
    68 * **Source added by :** Steve King **Date:** March 25, 2019 
    6961""" 
    7062 

  • sasmodels/models/gauss_lorentz_gel.py

    r0507e09 rc1e44e5  
    3434.. [#] G Evmenenko, E Theunissen, K Mortensen, H Reynaers, *Polymer*, 42 (2001) 2907-2913 
    3535 
    36 Source 
    37 ------ 
    38  
    39 `gauss_lorentz_gel.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/gauss_lorentz_gel.py>`_ 
    40  
    4136Authorship and Verification 
    4237---------------------------- 
    4338 
    44 * **Author:**  
    45 * **Last Modified by:**  
    46 * **Last Reviewed by:**  
    47 * **Source added by :** Steve King **Date:** March 25, 2019 
     39* **Author:** 
     40* **Last Modified by:** 
     41* **Last Reviewed by:** 
    4842""" 
    4943 

  • sasmodels/models/gaussian_peak.py

    r0507e09 rc1e44e5  
    2727None. 
    2828 
    29 Source 
    30 ------ 
    31  
    32 `gaussian_peak.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/gaussian_peak.py>`_ 
    33  
    3429Authorship and Verification 
    3530---------------------------- 
    3631 
    37 * **Author:**  
    38 * **Last Modified by:**  
    39 * **Last Reviewed by:**  
    40 * **Source added by :** Steve King **Date:** March 25, 2019 
     32* **Author:** 
     33* **Last Modified by:** 
     34* **Last Reviewed by:** 
    4135""" 
    4236 

  • sasmodels/models/gel_fit.py

    r0507e09 rc1e44e5  
    4141.. [#] Simon Mallam, Ferenc Horkay, Anne-Marie Hecht, Adrian R Rennie, Erik Geissler, *Macromolecules* 1991, 24, 543-548 
    4242 
    43 Source 
    44 ------ 
    45  
    46 `gel_fit.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/gel_fit.py>`_ 
    47  
    48 `gel_fit.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/gel_fit.c>`_ 
    49  
    5043Authorship and Verification 
    5144---------------------------- 
    5245 
    53 * **Author:**  
    54 * **Last Modified by:**  
    55 * **Last Reviewed by:**  
    56 * **Source added by :** Steve King **Date:** March 25, 2019 
     46* **Author:** 
     47* **Last Modified by:** 
     48* **Last Reviewed by:** 
    5749""" 
    5850 

  • sasmodels/models/guinier.py

    r0507e09 rc1e44e5  
    4848.. [#] A Guinier and G Fournet, *Small-Angle Scattering of X-Rays*, John Wiley & Sons, New York (1955) 
    4949 
    50 Source 
    51 ------ 
    52  
    53 `guinier.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/guinier.py>`_ 
    54  
    5550Authorship and Verification 
    5651---------------------------- 
    5752 
    58 * **Author:**  
    59 * **Last Modified by:**  
    60 * **Last Reviewed by:**  
    61 * **Source added by :** Steve King **Date:** March 25, 2019 
     53* **Author:** 
     54* **Last Modified by:** 
     55* **Last Reviewed by:** 
    6256""" 
    6357 

  • sasmodels/models/guinier_porod.py

    r7a5f8af rc1e44e5  
    6363.. [#] B Hammouda, *Analysis of the Beaucage model, J. Appl. Cryst.*, (2010), 43, 1474-1478 
    6464 
    65 Source 
    66 ------ 
    67  
    68 `guinier_porod.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/guinier_porod.py>`_ 
    69  
    7065Authorship and Verification 
    7166---------------------------- 
    7267 
    73 * **Author:**  
    74 * **Last Modified by:**  
    75 * **Last Reviewed by:**  
    76 * **Source added by :** Steve King **Date:** March 25, 2019 
     68* **Author:** 
     69* **Last Modified by:** 
     70* **Last Reviewed by:** 
    7771""" 
    7872 

  • sasmodels/models/hardsphere.py

    r4d00de6 r0d5dc05  
    5454.. [#] J K Percus, J Yevick, *J. Phys. Rev.*, 110, (1958) 1 
    5555 
    56 Source 
    57 ------ 
    58  
    59 `hardsphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hardsphere.py>`_ 
    60  
    6156Authorship and Verification 
    6257---------------------------- 
    … …  
    6560* **Last Modified by:** 
    6661* **Last Reviewed by:** 
    67 * **Source added by :** Steve King **Date:** March 25, 2019 
    6862""" 
    6963 

  • sasmodels/models/hayter_msa.py

    r4d00de6 r0d5dc05  
    6363.. [#] C G Malmberg and A A Maryott, *J. Res. Nat. Bureau Standards*, 56 (1956) 2641 
    6464 
    65 Source 
    66 ------ 
    67  
    68 `hayter_msa.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hayter_msa.py>`_ 
    69  
    70 `hayter_msa.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hayter_msa.c>`_ 
    71  
    7265Authorship and Verification 
    7366---------------------------- 
    … …  
    7669* **Last Modified by:** 
    7770* **Last Reviewed by:** Steve King **Date:** March 28, 2019 
    78 * **Source added by :** Steve King **Date:** March 25, 2019 
    7971""" 
    8072 

  • sasmodels/models/hollow_cylinder.py

    ra34b811 rd57b06c  
    6262.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    6363 
    64 Source 
    65 ------ 
    66  
    67 `hollow_cylinder.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hollow_cylinder.py>`_ 
    68  
    69 `hollow_cylinder.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hollow_cylinder.c>`_ 
    70  
    7164Authorship and Verification 
    7265---------------------------- 
    … …  
    7669   (corrected VR calculation) 
    7770* **Last Reviewed by:** Paul Butler **Date:** September 06, 2018 
    78 * **Source added by :** Steve King **Date:** March 25, 2019 
    7971""" 
    8072from __future__ import division 

  • sasmodels/models/hollow_rectangular_prism.py

    ra34b811 rd57b06c  
    100100.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    101101 
    102 Source 
    103 ------ 
    104  
    105 `hollow_rectangular_prism.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hollow_rectangular_prism.py>`_ 
    106  
    107 `hollow_rectangular_prism.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hollow_rectangular_prism.c>`_ 
    108  
    109102Authorship and Verification 
    110103---------------------------- 
    … …  
    113106* **Last Modified by:** Paul Kienzle **Date:** December 14, 2017 
    114107* **Last Reviewed by:** Paul Butler **Date:** September 06, 2018 
    115 * **Source added by :** Steve King **Date:** March 25, 2019 
    116108""" 
    117109 

  • sasmodels/models/hollow_rectangular_prism_thin_walls.py

    ra34b811 rd57b06c  
    7474.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    7575 
    76 Source 
    77 ------ 
    78  
    79 `hollow_rectangular_prism_thin_walls.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hollow_rectangular_prism_thin_walls.py>`_ 
    80  
    81 `hollow_rectangular_prism_thin_walls.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hollow_rectangular_prism_thin_walls.c>`_ 
    82  
    8376Authorship and Verification 
    8477---------------------------- 
    … …  
    8780* **Last Modified by:** Paul Kienzle **Date:** October 15, 2016 
    8881* **Last Reviewed by:** Paul Butler **Date:** September 07, 2018 
    89 * **Source added by :** Steve King **Date:** March 25, 2019 
    9082""" 
    9183 

  • sasmodels/models/lamellar.py

    r0507e09 rc1e44e5  
    4343.. [#] J Berghausen, J Zipfel, P Lindner, W Richtering, *J. Phys. Chem. B*, 105, (2001) 11081-11088 
    4444 
    45 Source 
    46 ------ 
    47  
    48 `lamellar.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar.py>`_ 
    49  
    5045Authorship and Verification 
    5146---------------------------- 
    5247 
    53 * **Author:**  
    54 * **Last Modified by:**  
    55 * **Last Reviewed by:**  
    56 * **Source added by :** Steve King **Date:** March 25, 2019 
     48* **Author:** 
     49* **Last Modified by:** 
     50* **Last Reviewed by:** 
    5751""" 
    5852 

  • sasmodels/models/lamellar_hg.py

    r0507e09 rc1e44e5  
    4545.. [#] J Berghausen, J Zipfel, P Lindner, W Richtering, *J. Phys. Chem. B*, 105, (2001) 11081-11088 
    4646 
    47 Source 
    48 ------ 
    49  
    50 `lamellar_hg.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_hg.py>`_ 
    51  
    5247Authorship and Verification 
    5348---------------------------- 
    5449 
    55 * **Author:**  
    56 * **Last Modified by:**  
     50* **Author:** 
     51* **Last Modified by:** 
    5752* **Last Reviewed by:** S King and P Butler **Date** April 17, 2014 
    58 * **Source added by :** Steve King **Date:** March 25, 2019 
    5953""" 
    6054 

  • sasmodels/models/lamellar_hg_stack_caille.py

    r0507e09 rc1e44e5  
    7272.. [#] J Berghausen, J Zipfel, P Lindner, W Richtering, *J. Phys. Chem. B*, 105, (2001) 11081-11088 
    7373 
    74 Source 
    75 ------ 
    76  
    77 `lamellar_hg_stack_caille.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_hg_stack_caille.py>`_ 
    78  
    79 `lamellar_hg_stack_caille.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_hg_stack_caille.c>`_ 
    80  
    8174Authorship and Verification 
    8275---------------------------- 
    8376 
    84 * **Author:**  
    85 * **Last Modified by:**  
    86 * **Last Reviewed by:**  
    87 * **Source added by :** Steve King **Date:** March 25, 2019 
     77* **Author:** 
     78* **Last Modified by:** 
     79* **Last Reviewed by:** 
    8880""" 
    8981 

  • sasmodels/models/lamellar_stack_caille.py

    r0507e09 rc1e44e5  
    6868.. [#] J Berghausen, J Zipfel, P Lindner, W Richtering, *J. Phys. Chem. B*, 105, (2001) 11081-11088 
    6969 
    70 Source 
    71 ------ 
    72  
    73 `lamellar_stack_caille.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_stack_caille.py>`_ 
    74  
    75 `lamellar_stack_caille.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_stack_caille.c>`_ 
    76  
    7770Authorship and Verification 
    7871---------------------------- 
    7972 
    80 * **Author:**  
    81 * **Last Modified by:**  
    82 * **Last Reviewed by:**  
    83 * **Source added by :** Steve King **Date:** March 25, 2019 
     73* **Author:** 
     74* **Last Modified by:** 
     75* **Last Reviewed by:** 
    8476""" 
    8577 

  • sasmodels/models/lamellar_stack_paracrystal.py

    r0507e09 rc1e44e5  
    9090.. [#] M Bergstrom, J S Pedersen, P Schurtenberger, S U Egelhaaf, *J. Phys. Chem. B*, 103 (1999) 9888-9897 
    9191 
    92 Source 
    93 ------ 
    94  
    95 `lamellar_stack_paracrystal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_stack_paracrystal.py>`_ 
    96  
    97 `lamellar_stack_paracrystal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lamellar_stack_paracrystal.c>`_ 
    98  
    9992Authorship and Verification 
    10093---------------------------- 
    10194 
    102 * **Author:**  
    103 * **Last Modified by:**  
    104 * **Last Reviewed by:**  
    105 * **Source added by :** Steve King **Date:** March 25, 2019 
     95* **Author:** 
     96* **Last Modified by:** 
     97* **Last Reviewed by:** 
    10698""" 
    10799import numpy as np 

  • sasmodels/models/line.py

    r0507e09 rc1e44e5  
    2323None. 
    2424 
    25 Source 
    26 ------ 
    27  
    28 `line.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/line.py>`_ 
    29  
    3025Authorship and Verification 
    3126---------------------------- 
    3227 
    33 * **Author:**  
    34 * **Last Modified by:**  
    35 * **Last Reviewed by:**  
    36 * **Source added by :** Steve King **Date:** March 25, 2019""" 
     28* **Author:** 
     29* **Last Modified by:** 
     30* **Last Reviewed by:** 
     31""" 
    3732 
    3833import numpy as np 

  • sasmodels/models/linear_pearls.py

    r0507e09 rc1e44e5  
    3131.. [#] A V Dobrynin, M Rubinstein and S P Obukhov, *Macromol.*, 29 (1996) 2974-2979 
    3232 
    33 Source 
    34 ------ 
    35  
    36 `linear_pearls.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/linear_pearls.py>`_ 
    37  
    38 `linear_pearls.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/linear_pearls.c>`_ 
    39  
    4033Authorship and Verification 
    4134---------------------------- 
    4235 
    43 * **Author:**  
    44 * **Last Modified by:**  
    45 * **Last Reviewed by:**  
    46 * **Source added by :** Steve King **Date:** March 25, 2019""" 
     36* **Author:** 
     37* **Last Modified by:** 
     38* **Last Reviewed by:** 
     39""" 
    4740 
    4841import numpy as np 

  • sasmodels/models/lorentz.py

    r0507e09 rc1e44e5  
    2222.. [#] L.S. Qrnstein and F. Zernike, *Proc. Acad. Sci. Amsterdam* 17, 793 (1914), and *Z. Phys.* 19, 134 (1918), and 27, 761 {1926); referred to as QZ. 
    2323 
    24 Source 
    25 ------ 
    26  
    27 `lorentz.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/lorentz.py>`_ 
    28  
    2924Authorship and Verification 
    3025---------------------------- 
    3126 
    32 * **Author:**  
    33 * **Last Modified by:**  
    34 * **Last Reviewed by:**  
    35 * **Source added by :** Steve King **Date:** March 25, 2019""" 
     27* **Author:** 
     28* **Last Modified by:** 
     29* **Last Reviewed by:** 
     30""" 
    3631 
    3732import numpy as np 

  • sasmodels/models/mass_fractal.py

    r0507e09 rc1e44e5  
    5151.. [#] D Mildner and P Hall, *J. Phys. D: Appl. Phys.*, 19 (1986) 1535-1545 Equation(9) 
    5252 
    53 Source 
    54 ------ 
    55  
    56 `mass_fractal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/mass_fractal.py>`_ 
    57  
    58 `mass_fractal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/mass_fractal.c>`_ 
    59  
    6053Authorship and Verification 
    6154---------------------------- 
    6255 
    63 * **Author:**  
    64 * **Last Modified by:**  
    65 * **Last Reviewed by:**  
    66 * **Source added by :** Steve King **Date:** March 25, 2019""" 
     56* **Author:** 
     57* **Last Modified by:** 
     58* **Last Reviewed by:** 
     59""" 
    6760 
    6861import numpy as np 

  • sasmodels/models/mass_surface_fractal.py

    r0507e09 rc1e44e5  
    5555   35 (1987) 2361-2364 Equation(2) 
    5656 
    57 Source 
    58 ------ 
    59  
    60 `mass_surface_fractal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/mass_surface_fractal.py>`_ 
    61  
    62 `mass_surface_fractal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/mass_surface_fractal.c>`_ 
    63  
    6457Authorship and Verification 
    6558---------------------------- 
    6659 
    6760* **Author:** Piotr Rozyczko **Date:** Jan 20, 2016 
    68 * **Last Modified by:**  
     61* **Last Modified by:** 
    6962* **Last Reviewed by:** Richard Heenan **Date:** May 30, 2018 
    70 * **Source added by :** Steve King **Date:** March 25, 2019 
    7163""" 
    7264 

  • sasmodels/models/mono_gauss_coil.py

    ra34b811 rd57b06c  
    4949.. [#] http://www.ncnr.nist.gov/staff/hammouda/distance_learning/chapter_28.pdf 
    5050 
    51 Source 
    52 ------ 
    53  
    54 `mono_gauss_coil.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/mono_gauss_coil.py>`_ 
    55  
    56 `mono_gauss_coil.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/mono_gauss_coil.c>`_ 
    57  
    5851Authorship and Verification 
    5952---------------------------- 
    … …  
    6255* **Last Modified by:** 
    6356* **Last Reviewed by:** 
    64 * **Source added by :** Steve King **Date:** March 25, 2019""" 
     57""" 
    6558 
    6659import numpy as np 

  • sasmodels/models/multilayer_vesicle.py

    rdb1d9d5 rd57b06c  
    100100   R Zana and M Dekker, New York, (1987). 
    101101 
    102 Source 
    103 ------ 
    104  
    105 `multilayer_vesicle.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/multilayer_vesicle.py>`_ 
    106  
    107 `multilayer_vesicle.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/multilayer_vesicle.c>`_ 
    108  
    109102Authorship and Verification 
    110103---------------------------- 
    … …  
    114107* **Last Modified by:** Paul Kienzle **Date:** Feb 7, 2017 
    115108* **Last Reviewed by:** Steve King **Date:** March 28, 2019 
    116 * **Source added by :** Steve King **Date:** March 25, 2019 
    117109""" 
    118110 

  • sasmodels/models/onion.py

    rdb1d9d5 rd57b06c  
    187187.. [#] L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, Plenum Press, New York, 1987. 
    188188 
    189 Source 
    190 ------ 
    191  
    192 `onion.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/onion.py>`_ 
    193  
    194 `onion.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/onion.c>`_ 
    195  
    196189Authorship and Verification 
    197190---------------------------- 
    … …  
    200193* **Last Modified by:** 
    201194* **Last Reviewed by:** Steve King **Date:** March 28, 2019 
    202 * **Source added by :** Steve King **Date:** March 25, 2019 
    203195""" 
    204196 

  • sasmodels/models/parallelepiped.py

    ra34b811 rd57b06c  
    182182.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    183183 
    184 Source 
    185 ------ 
    186  
    187 `parallelepiped.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/parallelepiped.py>`_ 
    188  
    189 `parallelepiped.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/parallelepiped.c>`_ 
    190  
    191184Authorship and Verification 
    192185---------------------------- 
    … …  
    196189* **Last Reviewed by:**  Miguel Gonzales and Paul Butler **Date:** May 24, 
    197190  2018 - documentation updated 
    198 * **Source added by :** Steve King **Date:** March 25, 2019 
    199191""" 
    200192 

  • sasmodels/models/peak_lorentz.py

    r0507e09 rc1e44e5  
    2727None. 
    2828 
    29 Source 
    30 ------ 
    31  
    32 `peak_lorentz.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/peak_lorentz.py>`_ 
    33  
    34 `peak_lorentz.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/peak_lorentz.c>`_ 
    35  
    3629Authorship and Verification 
    3730---------------------------- 
    3831 
    39 * **Author:**  
    40 * **Last Modified by:**  
    41 * **Last Reviewed by:**  
    42 * **Source added by :** Steve King **Date:** March 25, 2019 
     32* **Author:** 
     33* **Last Modified by:** 
     34* **Last Reviewed by:** 
    4335""" 
    4436 

  • sasmodels/models/pearl_necklace.py

    rdb1d9d5 rd57b06c  
    5555.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    5656 
    57 Source 
    58 ------ 
    59  
    60 `pearl_necklace.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/pearl_necklace.py>`_ 
    61  
    62 `pearl_necklace.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/pearl_necklace.c>`_ 
    63  
    6457Authorship and Verification 
    6558---------------------------- 
    … …  
    6861* **Last Modified by:** Andrew Jackson **Date:** March 28, 2019 
    6962* **Last Reviewed by:** Steve King **Date:** March 28, 2019 
    70 * **Source added by :** Steve King **Date:** March 25, 2019 
    7163""" 
    7264 

  • sasmodels/models/poly_gauss_coil.py

    ra34b811 rc1e44e5  
    4848.. [#] http://www.ncnr.nist.gov/staff/hammouda/distance_learning/chapter_28.pdf 
    4949 
    50 Source 
    51 ------ 
    52  
    53 `poly_gauss_coil.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/poly_gauss_coil.py>`_ 
    54  
    55 `poly_gauss_coil.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/poly_gauss_coil.c>`_ 
    56  
    5750Authorship and Verification 
    5851---------------------------- 
    … …  
    6154* **Last Modified by:** 
    6255* **Last Reviewed by:** 
    63 * **Source added by :** Steve King **Date:** March 25, 2019 
    6456""" 
    6557 

  • sasmodels/models/polymer_excl_volume.py

    r0507e09 rc1e44e5  
    113113.. [#] B Hammouda & M-H Kim, *The empirical core-chain model* 247 (2017) 434-440 
    114114 
    115 Source 
    116 ------ 
    117  
    118 `polymer_excl_volume.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/polymer_excl_volume.py>`_ 
    119  
    120 `polymer_excl_volume.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/polymer_excl_volume.c>`_ 
    121  
    122115Authorship and Verification 
    123116---------------------------- 
    124117 
    125 * **Author:**  
    126 * **Last Modified by:**  
    127 * **Last Reviewed by:**  
    128 * **Source added by :** Steve King **Date:** March 25, 2019 
     118* **Author:** 
     119* **Last Modified by:** 
     120* **Last Reviewed by:** 
    129121""" 
    130122 

  • sasmodels/models/polymer_micelle.py

    r0507e09 rc1e44e5  
    7070.. [#] J Pedersen, *J. Appl. Cryst.*, 33 (2000) 637-640 
    7171 
    72 Source 
    73 ------ 
    74  
    75 `polymer_micelle.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/polymer_micelle.py>`_ 
    76  
    77 `polymer_micelle.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/polymer_micelle.c>`_ 
    78  
    7972Authorship and Verification 
    8073---------------------------- 
    … …  
    8376* **Last modified by:** Paul Kienzle **Date:** November 29, 2017 
    8477* **Last reviewed by:** Steve King **Date:** November 30, 2017 
    85 * **Source added by :** Steve King **Date:** March 25, 2019 
    8678""" 
    8779 

  • sasmodels/models/porod.py

    r0507e09 rc1e44e5  
    2121.. [#] L A Feigin, D I Svergun, G W Taylor. *Structure Analysis by Small-Angle X-ray and Neutron Scattering*. Springer. (1987) 
    2222 
    23 Source 
    24 ------ 
    25  
    26 `porod.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/porod.py>`_ 
    27  
    2823Authorship and Verification 
    2924---------------------------- 
    3025 
    31 * **Author:**  
    32 * **Last Modified by:**  
    33 * **Last Reviewed by:**  
    34 * **Source added by :** Steve King **Date:** March 25, 2019 
     26* **Author:** 
     27* **Last Modified by:** 
     28* **Last Reviewed by:** 
    3529""" 
    3630 

  • sasmodels/models/power_law.py

    r0507e09 rc1e44e5  
    2626None. 
    2727 
    28 Source 
    29 ------ 
    30  
    31 `power_law.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/power_law.py>`_ 
    32  
    3328Authorship and Verification 
    3429---------------------------- 
    3530 
    36 * **Author:**  
    37 * **Last Modified by:**  
    38 * **Last Reviewed by:**  
    39 * **Source added by :** Steve King **Date:** March 25, 2019 
     31* **Author:** 
     32* **Last Modified by:** 
     33* **Last Reviewed by:** 
    4034""" 
    4135 

  • sasmodels/models/pringle.py

    ra34b811 rd57b06c  
    4343.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    4444 
    45 Source 
    46 ------ 
    47  
    48 `pringle.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/pringle.py>`_ 
    49  
    50 `pringle.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/pringle.c>`_ 
    51  
    5245Authorship and Verification 
    5346---------------------------- 
    … …  
    5649* **Last Modified by:** Wojciech Wpotrzebowski **Date:** March 20, 2016 
    5750* **Last Reviewed by:** Andrew Jackson **Date:** September 26, 2016 
    58 * **Source added by :** Steve King **Date:** March 25, 2019 
    5951""" 
    6052 

  • sasmodels/models/raspberry.py

    ra34b811 rd57b06c  
    100100.. [#] K Larson-Smith, A Jackson, and D C Pozzo, *Small angle scattering model for Pickering emulsions and raspberry particles*, *Journal of Colloid and Interface Science*, 343(1) (2010) 36-41 
    101101 
    102 Source 
    103 ------ 
    104  
    105 `raspberry.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/raspberry.py>`_ 
    106  
    107 `raspberry.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/raspberry.c>`_ 
    108  
    109102Authorship and Verification 
    110103---------------------------- 
    … …  
    113106* **Last Modified by:** Andrew Jackson **Date:** March 20, 2016 
    114107* **Last Reviewed by:** Andrew Jackson **Date:** March 20, 2016 
    115 * **Source added by :** Steve King **Date:** March 25, 2019 
    116108""" 
    117109 

  • sasmodels/models/rectangular_prism.py

    ra34b811 rd57b06c  
    100100.. [#] L. Onsager, *Ann. New York Acad. Sci.*, 51 (1949) 627-659 
    101101 
    102 Source 
    103 ------ 
    104  
    105 `rectangular_prism.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/rectangular_prism.py>`_ 
    106  
    107 `rectangular_prism.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/rectangular_prism.c>`_ 
    108  
    109102Authorship and Verification 
    110103---------------------------- 
    … …  
    113106* **Last Modified by:** 
    114107* **Last Reviewed by:** 
    115 * **Source added by :** Steve King **Date:** March 25, 2019 
    116108""" 
    117109 

  • sasmodels/models/rpa.py

    rdb1d9d5 rc1e44e5  
    6767.. [#] B. Hammouda, *SANS Toolbox* https://www.ncnr.nist.gov/staff/hammouda/the_sans_toolbox.pdf. 
    6868 
    69 Source 
    70 ------ 
    71  
    72 `rpa.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/rpa.py>`_ 
    73  
    74 `rpa.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/rpa.c>`_ 
    75  
    7669Authorship and Verification 
    7770---------------------------- 
    … …  
    8174* **Last Modified by:** Paul Butler **Date:** March 12, 2017 
    8275* **Last Reviewed by:** Steve King **Date:** March 27, 2019 
    83 * **Source added by :** Steve King **Date:** March 25, 2019 
    8476""" 
    8577 

  • sasmodels/models/sc_paracrystal.py

    r0507e09 rc1e44e5  
    101101.. [#CIT1990] Hideki Matsuoka et. al. *Physical Review B*, 41 (1990) 3854 -3856 (Corrections to FCC and BCC lattice structure calculation) 
    102102 
    103 Source 
    104 ------ 
    105  
    106 `sc_paracrystal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/sc_paracrystal.py>`_ 
    107  
    108 `sc_paracrystal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/sc_paracrystal.c>`_ 
    109  
    110103Authorship and Verification 
    111104--------------------------- 
    … …  
    114107* **Last Modified by:** Steve King **Date:** March 25, 2019 
    115108* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016 
    116 * **Source added by :** Steve King **Date:** March 25, 2019 
    117109""" 
    118110 

  • sasmodels/models/sphere.py

    r934a001 rd57b06c  
    3636References 
    3737---------- 
    38   
     38 
    3939.. [#] A Guinier and G. Fournet, *Small-Angle Scattering of X-Rays*, 
    4040   John Wiley and Sons, New York, (1955) 
    41  
    42 Source 
    43 ------ 
    44  
    45 `sphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/sphere.py>`_ 
    46  
    47 `sphere.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/sphere.c>`_ 
    4841 
    4942Authorship and Verification 
    … …  
    5346* **Last Modified by:** 
    5447* **Last Reviewed by:** S King and P Parker **Date:** 2013/09/09 and 2014/01/06 
    55 * **Source added by :** Steve King **Date:** March 25, 2019 
    5648""" 
    5749 
    … …  
    9385#2345678901234567890123456789012345678901234567890123456789012345678901234567890 
    9486tests = [ 
    95      [{}, 0.2, 0.726362], # each test starts with default parameter values  
     87     [{}, 0.2, 0.726362], # each test starts with default parameter values 
    9688     #            inside { }, unless modified. Then Q and expected value of I(Q) 
    97      # putting None for an expected result will pass the test if there are no  
     89     # putting None for an expected result will pass the test if there are no 
    9890     # errors from the routine, but without any check on the value of the result 
    9991    [{"scale": 1., "background": 0., "sld": 6., "sld_solvent": 1., 
    100        "radius": 120.}, [0.01,0.1,0.2],  
     92       "radius": 120.}, [0.01,0.1,0.2], 
    10193     [1.34836265e+04, 6.20114062e+00, 1.04733914e-01]], 
    10294     [{"scale": 1., "background": 0., "sld": 6., "sld_solvent": 1., 
    103      #  careful tests here R=120 Pd=.2, then with S(Q) at default Reff=50  
     95     #  careful tests here R=120 Pd=.2, then with S(Q) at default Reff=50 
    10496     #  (but this gets changed to 120) phi=0,2 
    10597       "radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, 
    106       [0.01,0.1,0.2], [1.74395295e+04, 3.68016987e+00, 2.28843099e-01]],   
     98      [0.01,0.1,0.2], [1.74395295e+04, 3.68016987e+00, 2.28843099e-01]], 
    10799     # a list of Q values and list of expected results is also possible 
    108100    [{"scale": 1., "background": 0., "sld": 6., "sld_solvent": 1., 
    109101     "radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, 
    110       0.01, 335839.88055473, 1.41045057e+11, 120.0, 8087664.122641933, 1.0],  
    111      # the longer list here checks  F1, F2, R_eff, volume, volume_ratio  
     102      0.01, 335839.88055473, 1.41045057e+11, 120.0, 8087664.122641933, 1.0], 
     103     # the longer list here checks  F1, F2, R_eff, volume, volume_ratio 
    112104    [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, 
    113       0.1, 482.93824329, 29763977.79867414, 120.0, 8087664.122641933, 1.0],  
     105      0.1, 482.93824329, 29763977.79867414, 120.0, 8087664.122641933, 1.0], 
    114106    [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, 
    115107      0.2, 1.23330406, 1850806.1197361, 120.0, 8087664.122641933, 1.0], 
    116108   #  But note P(Q) = F2/volume 
    117    #  F and F^2 are "unscaled", with for  n <F F*>S(q) or for beta approx  
     109   #  F and F^2 are "unscaled", with for  n <F F*>S(q) or for beta approx 
    118110   #          I(q) = n [<F F*> + <F><F*> (S(q) - 1)] 
    119    #  for n the number density and <.> the orientation average, and  
     111   #  for n the number density and <.> the orientation average, and 
    120112   #  F = integral rho(r) exp(i q . r) dr. 
    121113   #  The number density is volume fraction divided by particle volume. 
    122    #  Effectively, this leaves F = V drho form, where form is the usual  
     114   #  Effectively, this leaves F = V drho form, where form is the usual 
    123115   #  3 j1(qr)/(qr) or whatever depending on the shape. 
    124116   # @S RESULTS using F1 and F2 from the longer test strng above: 
    … …  
    128120   # with by default scale=1.0, background=0.001 
    129121   # NOTE currently S(Q) volfraction is also included in scaling 
    130    #  structure_factor_mode 0 = normal decoupling approx,  
     122   #  structure_factor_mode 0 = normal decoupling approx, 
    131123   #                        1 = beta(Q) approx 
    132    # radius_effective_mode  0 is for free choice,  
     124   # radius_effective_mode  0 is for free choice, 
    133125   #                        1 is use radius from F2(Q) 
    134126   #    (sphere only has two choices, other models may have more) 
    … …  
    136128     "radius": 120., "radius_pd": 0.2, "radius_pd_n":45,"volfraction":0.2, 
    137129     #"radius_effective":50.0,    # hard sphere structure factor 
    138      "structure_factor_mode": 1,  # mode 0 = normal decoupling approx,  
     130     "structure_factor_mode": 1,  # mode 0 = normal decoupling approx, 
    139131     #                                   1 = beta(Q) approx 
    140      "radius_effective_mode": 0   # this used default hardsphere Reff=50     
     132     "radius_effective_mode": 0   # this used default hardsphere Reff=50 
    141133     }, [0.01,0.1,0.2], [1.32473756e+03, 7.36633631e-01, 4.67686201e-02]  ], 
    142134    [{"@S": "hardsphere", 
    … …  
    145137     "radius_effective":45.0,     # explicit Reff over rides either 50 or 120 
    146138     "structure_factor_mode": 1,  # beta approx 
    147      "radius_effective_mode": 0   #  
     139     "radius_effective_mode": 0   # 
    148140     }, 0.01, 1316.2990966463444 ], 
    149141    [{"@S": "hardsphere", 
    … …  
    152144     "radius_effective":120.0,    # over ride Reff 
    153145     "structure_factor_mode": 1,  # beta approx 
    154      "radius_effective_mode": 0   # (mode=1 here also uses 120)  
     146     "radius_effective_mode": 0   # (mode=1 here also uses 120) 
    155147     }, [0.01,0.1,0.2], [1.57928589e+03, 7.37067923e-01, 4.67686197e-02  ]], 
    156148    [{"@S": "hardsphere", 

  • sasmodels/models/spherical_sld.py

    r627b68b rd57b06c  
    187187   and Neutron Scattering, Plenum Press, New York, (1987) 
    188188 
    189 Source 
    190 ------ 
    191  
    192 `spherical_sld.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/spherical_sld.py>`_ 
    193  
    194 `spherical_sld.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/spherical_sld.c>`_ 
    195  
    196189Authorship and Verification 
    197190--------------------------- 
    … …  
    200193* **Last Modified by:** Paul Kienzle **Date:** Dec 20, 2016 
    201194* **Last Reviewed by:** Steve King **Date:** March 29, 2019 
    202 * **Source added by :** Steve King **Date:** March 25, 2019 
    203195""" 
    204196 

  • sasmodels/models/spinodal.py

    r0507e09 rc1e44e5  
    4444.. [#] T. Hashimoto, M. Takenaka & H. Jinnai. Scattering Studies of Self-Assembling Processes of Polymer Blends in Spinodal Decomposition. J. Appl. Cryst. 24, 457-466 (1991). 
    4545 
    46 Source 
    47 ------ 
    48  
    49 `spinodal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/spinodal.py>`_ 
    50  
    5146Authorship and Verification 
    5247---------------------------- 
    … …  
    5550* **Last Modified by:** Steve King **Date:** Oct 25, 2018 
    5651* **Last Reviewed by:** Steve King **Date:** Oct 25, 2018 
    57 * **Source added by :** Steve King **Date:** March 25, 2019 
    5852""" 
    5953 

  • sasmodels/models/squarewell.py

    r4d00de6 r0d5dc05  
    5454.. [#] M Kotlarchyk and S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 
    5555 
    56 Source 
    57 ------ 
    58  
    59 `squarewell.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/squarewell.py>`_ 
    60  
    6156Authorship and Verification 
    6257---------------------------- 
    … …  
    6560* **Last Modified by:** 
    6661* **Last Reviewed by:** Steve King **Date:** March 27, 2019 
    67 * **Source added by :** Steve King **Date:** March 25, 2019 
    6862""" 
    6963 

  • sasmodels/models/stacked_disks.py

    r0507e09 rc1e44e5  
    102102   John Wiley and Sons, New York, 1955 
    103103 
    104 Source 
    105 ------ 
    106  
    107 `stacked_disks.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/stacked_disks.py>`_ 
    108  
    109 `stacked_disks.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/stacked_disks.c>`_ 
    110  
    111104Authorship and Verification 
    112105---------------------------- 
    … …  
    115108* **Last Modified by:** Paul Butler and Paul Kienzle **Date:** November 26, 2016 
    116109* **Last Reviewed by:** Paul Butler and Paul Kienzle **Date:** November 26, 2016 
    117 * **Source added by :** Steve King **Date:** March 25, 2019 
    118110""" 
    119111 

  • sasmodels/models/star_polymer.py

    r0507e09 rc1e44e5  
    5050   B Ewen *Macromolecules*, 22, 468-472 (1989) 
    5151 
    52 Source 
    53 ------ 
    54  
    55 `star_polymer.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/star_polymer.py>`_ 
    56  
    57 `star_polymer.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/star_polymer.c>`_ 
    58  
    5952Authorship and Verification 
    6053---------------------------- 
    … …  
    6356* **Last Modified by:** Paul Butler **Date:** Auguts 26, 2017 
    6457* **Last Reviewed by:** Ziang Li and Richard Heenan **Date:** May 17, 2017 
    65 * **Source added by :** Steve King **Date:** March 25, 2019 
    6658""" 
    6759 

  • sasmodels/models/stickyhardsphere.py

    r4d00de6 r0d5dc05  
    7878.. [#] M Kotlarchyk and S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 
    7979 
    80 Source 
    81 ------ 
    82  
    83 `stickyhardsphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/stickyhardsphere.py>`_ 
    84  
    8580Authorship and Verification 
    8681---------------------------- 
    … …  
    8984* **Last Modified by:** 
    9085* **Last Reviewed by:** Steve King **Date:** March 27, 2019 
    91 * **Source added by :** Steve King **Date:** March 25, 2019 
    9286""" 
    9387 

  • sasmodels/models/surface_fractal.py

    r0507e09 rc1e44e5  
    3838.. [#] D Mildner and P Hall, *J. Phys. D: Appl. Phys.*, 19 (1986) 1535-1545 
    3939 
    40 Source 
    41 ------ 
    42  
    43 `surface_fractal.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/surface_fractal.py>`_ 
    44  
    45 `surface_fractal.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/surface_fractal.c>`_ 
    46  
    4740Authorship and Verification 
    4841---------------------------- 
    4942 
    50 * **Author:**  
    51 * **Last Modified by:**  
    52 * **Last Reviewed by:**  
    53 * **Source added by :** Steve King **Date:** March 25, 2019 
     43* **Author:** 
     44* **Last Modified by:** 
     45* **Last Reviewed by:** 
    5446""" 
    5547 

  • sasmodels/models/teubner_strey.py

    r0507e09 rc1e44e5  
    6565.. [#] H Endo, M Mihailescu, M. Monkenbusch, J Allgaier, G Gompper, D Richter, B Jakobs, T Sottmann, R Strey, and I Grillo, *J. Chem. Phys.*, 115 (2001), 580 
    6666 
    67 Source 
    68 ------ 
    69  
    70 `teubner_strey.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/teubner_strey.py>`_ 
    71  
    72 `teubner_strey.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/teubner_strey.c>`_ 
    73  
    7467Authorship and Verification 
    7568---------------------------- 
    7669 
    77 * **Author:**  
    78 * **Last Modified by:**  
    79 * **Last Reviewed by:**  
    80 * **Source added by :** Steve King **Date:** March 25, 2019 
     70* **Author:** 
     71* **Last Modified by:** 
     72* **Last Reviewed by:** 
    8173""" 
    8274from __future__ import division 

  • sasmodels/models/triaxial_ellipsoid.py

    ra34b811 rd57b06c  
    116116.. [#] Finnigan, J.A., Jacobs, D.J., 1971. *Light scattering by ellipsoidal particles in solution*, J. Phys. D: Appl. Phys. 4, 72-77. doi:10.1088/0022-3727/4/1/310 
    117117 
    118 Source 
    119 ------ 
    120  
    121 `triaxial_ellipsoid.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/triaxial_ellipsoid.py>`_ 
    122  
    123 `triaxial_ellipsoid.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/triaxial_ellipsoid.c>`_ 
    124  
    125118Authorship and Verification 
    126119---------------------------- 
    … …  
    129122* **Last Modified by:** Paul Kienzle (improved calculation) **Date:** April 4, 2017 
    130123* **Last Reviewed by:** Paul Kienzle & Richard Heenan **Date:**  April 4, 2017 
    131 * **Source added by :** Steve King **Date:** March 25, 2019 
    132124""" 
    133125 

  • sasmodels/models/two_lorentzian.py

    r0507e09 rc1e44e5  
    2727None. 
    2828 
    29 Source 
    30 ------ 
    31  
    32 `two_lorentzian.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/two_lorentzian.py>`_ 
    33  
    3429Authorship and Verification 
    3530---------------------------- 
    … …  
    3833* **Last Modified by:** Piotr rozyczko **Date:** January 29, 2016 
    3934* **Last Reviewed by:** Paul Butler **Date:** March 21, 2016 
    40 * **Source added by :** Steve King **Date:** March 25, 2019 
    4135""" 
    4236 

  • sasmodels/models/two_power_law.py

    r0507e09 rc1e44e5  
    3737None. 
    3838 
    39 Source 
    40 ------ 
    41  
    42 `two_power_law.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/two_power_law.py>`_ 
    43  
    4439Authorship and Verification 
    4540---------------------------- 
    … …  
    4843* **Last Modified by:** Wojciech Wpotrzebowski **Date:** February 18, 2016 
    4944* **Last Reviewed by:** Paul Butler **Date:** March 21, 2016 
    50 * **Source added by :** Steve King **Date:** March 25, 2019 
    5145""" 
    5246 

  • sasmodels/models/unified_power_Rg.py

    rb606805 rd57b06c  
    6767.. [#] B Hammouda, *Analysis of the Beaucage model, J. Appl. Cryst.*, (2010), 43, 1474-1478 
    6868 
    69 Source 
    70 ------ 
    71  
    72 `unified_power_Rg.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/unified_power_Rg.py>`_ 
    73  
    7469Authorship and Verification 
    7570---------------------------- 
    7671 
    77 * **Author:**  
    78 * **Last Modified by:**  
    79 * **Last Reviewed by:**  
    80 * **Source added by :** Steve King **Date:** March 25, 2019 
     72* **Author:** 
     73* **Last Modified by:** 
     74* **Last Reviewed by:** 
    8175""" 
    8276 

  • sasmodels/models/vesicle.py

    ra34b811 rd57b06c  
    6060   Sons, New York, (1955) 
    6161 
    62 Source 
    63 ------ 
    64  
    65 `vesicle.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/vesicle.py>`_ 
    66  
    67 `vesicle.c <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/vesicle.c>`_ 
    68  
    6962Authorship and Verification 
    7063---------------------------- 
    … …  
    7366* **Last Modified by:** Paul Butler **Date:** March 20, 2016 
    7467* **Last Reviewed by:** Paul Butler **Date:** September 7, 2018 
    75 * **Source added by :** Steve King **Date:** March 25, 2019 
    7668""" 
    7769 

  • doc/guide/pd/polydispersity.rst

    rd089a00 ra5cb9bc  
    1111-------------------------------------------- 
    1212 
    13 For some models we can calculate the average intensity for a population of  
    14 particles that possess size and/or orientational (ie, angular) distributions.  
    15 In SasView we call the former *polydispersity* but use the parameter *PD* to  
    16 parameterise both. In other words, the meaning of *PD* in a model depends on  
     13For some models we can calculate the average intensity for a population of 
     14particles that possess size and/or orientational (ie, angular) distributions. 
     15In SasView we call the former *polydispersity* but use the parameter *PD* to 
     16parameterise both. In other words, the meaning of *PD* in a model depends on 
    1717the actual parameter it is being applied too. 
    1818 
    19 The resultant intensity is then normalized by the average particle volume such  
     19The resultant intensity is then normalized by the average particle volume such 
    2020that 
    2121 
    … …  
    2424  P(q) = \text{scale} \langle F^* F \rangle / V + \text{background} 
    2525 
    26 where $F$ is the scattering amplitude and $\langle\cdot\rangle$ denotes an  
     26where $F$ is the scattering amplitude and $\langle\cdot\rangle$ denotes an 
    2727average over the distribution $f(x; \bar x, \sigma)$, giving 
    2828 
    2929.. math:: 
    3030 
    31   P(q) = \frac{\text{scale}}{V} \int_\mathbb{R}  
     31  P(q) = \frac{\text{scale}}{V} \int_\mathbb{R} 
    3232  f(x; \bar x, \sigma) F^2(q, x)\, dx + \text{background} 
    3333 
    3434Each distribution is characterized by a center value $\bar x$ or 
    3535$x_\text{med}$, a width parameter $\sigma$ (note this is *not necessarily* 
    36 the standard deviation, so read the description of the distribution carefully),  
    37 the number of sigmas $N_\sigma$ to include from the tails of the distribution,  
    38 and the number of points used to compute the average. The center of the  
    39 distribution is set by the value of the model parameter. 
    40  
    41 The distribution width applied to *volume* (ie, shape-describing) parameters  
    42 is relative to the center value such that $\sigma = \mathrm{PD} \cdot \bar x$.  
    43 However, the distribution width applied to *orientation* parameters is just  
    44 $\sigma = \mathrm{PD}$. 
     36the standard deviation, so read the description carefully), the number of 
     37sigmas $N_\sigma$ to include from the tails of the distribution, and the 
     38number of points used to compute the average. The center of the distribution 
     39is set by the value of the model parameter. The meaning of a polydispersity 
     40parameter *PD* (not to be confused with a molecular weight distributions 
     41in polymer science) in a model depends on the type of parameter it is being 
     42applied too. 
     43 
     44The distribution width applied to *volume* (ie, shape-describing) parameters 
     45is relative to the center value such that $\sigma = \mathrm{PD} \cdot \bar x$. 
     46However, the distribution width applied to *orientation* (ie, angle-describing) 
     47parameters is just $\sigma = \mathrm{PD}$. 
    4548 
    4649$N_\sigma$ determines how far into the tails to evaluate the distribution, 
    … …  
    5255 
    5356Users should note that the averaging computation is very intensive. Applying 
    54 polydispersion and/or orientational distributions to multiple parameters at  
    55 the same time, or increasing the number of points in the distribution, will  
    56 require patience! However, the calculations are generally more robust with  
     57polydispersion and/or orientational distributions to multiple parameters at 
     58the same time, or increasing the number of points in the distribution, will 
     59require patience! However, the calculations are generally more robust with 
    5760more data points or more angles. 
    5861 
    … …  
    6669*  *Schulz Distribution* 
    6770*  *Array Distribution* 
     71*  *User-defined Distributions* 
    6872 
    6973These are all implemented as *number-average* distributions. 
    7074 
    71 Additional distributions are under consideration. 
    7275 
    7376**Beware: when the Polydispersity & Orientational Distribution panel in SasView is** 
    … …  
    7578**This may not be suitable. See Suggested Applications below.** 
    7679 
    77 .. note:: In 2009 IUPAC decided to introduce the new term 'dispersity' to replace  
    78            the term 'polydispersity' (see `Pure Appl. Chem., (2009), 81(2),  
    79            351-353 <http://media.iupac.org/publications/pac/2009/pdf/8102x0351.pdf>`_  
    80            in order to make the terminology describing distributions of chemical  
    81            properties unambiguous. However, these terms are unrelated to the  
    82            proportional size distributions and orientational distributions used in  
     80.. note:: In 2009 IUPAC decided to introduce the new term 'dispersity' to replace 
     81           the term 'polydispersity' (see `Pure Appl. Chem., (2009), 81(2), 
     82           351-353 <http://media.iupac.org/publications/pac/2009/pdf/8102x0351.pdf>`_ 
     83           in order to make the terminology describing distributions of chemical 
     84           properties unambiguous. However, these terms are unrelated to the 
     85           proportional size distributions and orientational distributions used in 
    8386           SasView models. 
    8487 
    … …  
    9295or angular orientations, consider using the Gaussian or Boltzmann distributions. 
    9396 
    94 If applying polydispersion to parameters describing angles, use the Uniform  
    95 distribution. Beware of using distributions that are always positive (eg, the  
     97If applying polydispersion to parameters describing angles, use the Uniform 
     98distribution. Beware of using distributions that are always positive (eg, the 
    9699Lognormal) because angles can be negative! 
    97100 
    98 The array distribution allows a user-defined distribution to be applied. 
     101The array distribution provides a very simple means of implementing a user- 
     102defined distribution, but without any fittable parameters. Greater flexibility 
     103is conferred by the user-defined distribution. 
    99104 
    100105.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    334339.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    335340 
     341User-defined Distributions 
     342^^^^^^^^^^^^^^^^^^^^^^^^^^ 
     343 
     344You can also define your own distribution by creating a python file defining a 
     345*Distribution* object with a *_weights* method.  The *_weights* method takes 
     346*center*, *sigma*, *lb* and *ub* as arguments, and can access *self.npts* 
     347and *self.nsigmas* from the distribution.  They are interpreted as follows: 
     348 
     349* *center* the value of the shape parameter (for size dispersity) or zero 
     350  if it is an angular dispersity.  This parameter may be fitted. 
     351 
     352* *sigma* the width of the distribution, which is the polydispersity parameter 
     353  times the center for size dispersity, or the polydispersity parameter alone 
     354  for angular dispersity.  This parameter may be fitted. 
     355 
     356* *lb*, *ub* are the parameter limits (lower & upper bounds) given in the model 
     357  definition file.  For example, a radius parameter has *lb* equal to zero.  A 
     358  volume fraction parameter would have *lb* equal to zero and *ub* equal to one. 
     359 
     360* *self.nsigmas* the distance to go into the tails when evaluating the 
     361  distribution.  For a two parameter distribution, this value could be 
     362  co-opted to use for the second parameter, though it will not be available 
     363  for fitting. 
     364 
     365* *self.npts* the number of points to use when evaluating the distribution. 
     366  The user will adjust this to trade calculation time for accuracy, but the 
     367  distribution code is free to return more or fewer, or use it for the third 
     368  parameter in a three parameter distribution. 
     369 
     370As an example, the code following wraps the Laplace distribution from scipy stats:: 
     371 
     372    import numpy as np 
     373    from scipy.stats import laplace 
     374 
     375    from sasmodels import weights 
     376 
     377    class Dispersion(weights.Dispersion): 
     378        r""" 
     379        Laplace distribution 
     380 
     381        .. math:: 
     382 
     383            w(x) = e^{-\sigma |x - \mu|} 
     384        """ 
     385        type = "laplace" 
     386        default = dict(npts=35, width=0, nsigmas=3)  # default values 
     387        def _weights(self, center, sigma, lb, ub): 
     388            x = self._linspace(center, sigma, lb, ub) 
     389            wx = laplace.pdf(x, center, sigma) 
     390            return x, wx 
     391 
     392You can plot the weights for a given value and width using the following:: 
     393 
     394    from numpy import inf 
     395    from matplotlib import pyplot as plt 
     396    from sasmodels import weights 
     397 
     398    # reload the user-defined weights 
     399    weights.load_weights() 
     400    x, wx = weights.get_weights('laplace', n=35, width=0.1, nsigmas=3, value=50, 
     401                                limits=[0, inf], relative=True) 
     402 
     403    # plot the weights 
     404    plt.interactive(True) 
     405    plt.plot(x, wx, 'x') 
     406 
     407The *self.nsigmas* and *self.npts* parameters are normally used to control 
     408the accuracy of the distribution integral. The *self._linspace* function 
     409uses them to define the *x* values (along with the *center*, *sigma*, 
     410*lb*, and *ub* which are passed as parameters).  If you repurpose npts or 
     411nsigmas you will need to generate your own *x*.  Be sure to honour the 
     412limits *lb* and *ub*, for example to disallow a negative radius or constrain 
     413the volume fraction to lie between zero and one. 
     414 
     415To activate a user-defined distribution, put it in a file such as *distname.py* 
     416in the *SAS_WEIGHTS_PATH* folder.  This is defined with an environment 
     417variable, defaulting to:: 
     418 
     419    SAS_WEIGHTS_PATH=~/.sasview/weights 
     420 
     421The weights path is loaded on startup.  To update the distribution definition 
     422in a running application you will need to enter the following python commands:: 
     423 
     424    import sasmodels.weights 
     425    sasmodels.weights.load_weights('path/to/distname.py') 
     426 
     427.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
     428 
    336429Note about DLS polydispersity 
    337430^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    338431 
    339 Several measures of polydispersity abound in Dynamic Light Scattering (DLS) and  
    340 it should not be assumed that any of the following can be simply equated with  
     432Several measures of polydispersity abound in Dynamic Light Scattering (DLS) and 
     433it should not be assumed that any of the following can be simply equated with 
    341434the polydispersity *PD* parameter used in SasView. 
    342435 
    343 The dimensionless **Polydispersity Index (PI)** is a measure of the width of the  
    344 distribution of autocorrelation function decay rates (*not* the distribution of  
    345 particle sizes itself, though the two are inversely related) and is defined by  
     436The dimensionless **Polydispersity Index (PI)** is a measure of the width of the 
     437distribution of autocorrelation function decay rates (*not* the distribution of 
     438particle sizes itself, though the two are inversely related) and is defined by 
    346439ISO 22412:2017 as 
    347440 
    … …  
    350443    PI = \mu_{2} / \bar \Gamma^2 
    351444 
    352 where $\mu_\text{2}$ is the second cumulant, and $\bar \Gamma^2$ is the  
     445where $\mu_\text{2}$ is the second cumulant, and $\bar \Gamma^2$ is the 
    353446intensity-weighted average value, of the distribution of decay rates. 
    354447 
    … …  
    359452    PI = \sigma^2 / 2\bar \Gamma^2 
    360453 
    361 where $\sigma$ is the standard deviation, allowing a **Relative Polydispersity (RP)**  
     454where $\sigma$ is the standard deviation, allowing a **Relative Polydispersity (RP)** 
    362455to be defined as 
    363456 
    … …  
    366459    RP = \sigma / \bar \Gamma = \sqrt{2 \cdot PI} 
    367460 
    368 PI values smaller than 0.05 indicate a highly monodisperse system. Values  
     461PI values smaller than 0.05 indicate a highly monodisperse system. Values 
    369462greater than 0.7 indicate significant polydispersity. 
    370463 
    371 The **size polydispersity P-parameter** is defined as the relative standard  
    372 deviation coefficient of variation   
     464The **size polydispersity P-parameter** is defined as the relative standard 
     465deviation coefficient of variation 
    373466 
    374467.. math:: 
    … …  
    377470 
    378471where $\nu$ is the variance of the distribution and $\bar R$ is the mean 
    379 value of $R$. Here, the product $P \bar R$ is *equal* to the standard  
     472value of $R$. Here, the product $P \bar R$ is *equal* to the standard 
    380473deviation of the Lognormal distribution. 
    381474 

  • sasmodels/compare.py

    rb297ba9 rd0b0f5d  
    3939 
    4040from . import core 
     41from . import weights 
    4142from . import kerneldll 
    4243from . import kernelcl 
    … …  
    4546from .direct_model import DirectModel, get_mesh 
    4647from .generate import FLOAT_RE, set_integration_size 
    47 from .weights import plot_weights 
    4848 
    4949# pylint: disable=unused-import 
    … …  
    115115 
    116116    === environment variables === 
    117     -DSAS_MODELPATH=path sets directory containing custom models 
     117    -DSAS_MODELPATH=~/.sasmodels/custom_models sets path to custom models 
     118    -DSAS_WEIGHTS_PATH=~/.sasview/weights sets path to custom distributions 
    118119    -DSAS_OPENCL=vendor:device|cuda:device|none sets the target GPU device 
    119120    -DXDG_CACHE_HOME=~/.cache sets the pyopencl cache root (linux only) 
    120121    -DSAS_COMPILER=tinycc|msvc|mingw|unix sets the DLL compiler 
    121     -DSAS_OPENMP=1 turns on OpenMP for the DLLs 
    122     -DSAS_DLL_PATH=path sets the path to the compiled modules 
     122    -DSAS_OPENMP=0 set to 1 to turn on OpenMP for the DLLs 
     123    -DSAS_DLL_PATH=~/.sasmodels/compiled_models sets the DLL cache 
    123124 
    124125The interpretation of quad precision depends on architecture, and may 
    … …  
    784785            model_info = base._kernel.info 
    785786            dim = base._kernel.dim 
    786             plot_weights(model_info, get_mesh(model_info, base_pars, dim=dim)) 
     787            weights.plot_weights(model_info, get_mesh(model_info, base_pars, dim=dim)) 
    787788        if opts['show_profile']: 
    788789            import pylab 
    … …  
    14411442    #import pprint; pprint.pprint(model_info) 
    14421443 
     1444    # Hack to load user-defined distributions; run through all parameters 
     1445    # and make sure any pd_type parameter is a defined distribution. 
     1446    if (any(p.endswith('pd_type') and v not in weights.MODELS 
     1447            for p, v in pars.items()) or 
     1448        any(p.endswith('pd_type') and v not in weights.MODELS 
     1449            for p, v in pars2.items())): 
     1450       weights.load_weights() 
     1451 
    14431452    if opts['show_pars']: 
    14441453        if model_info.name != model_info2.name or pars != pars2: 

  • sasmodels/models/__init__.py

    r2d81cfe rd827c5e  
    11""" 
    2 1D Modeling for SAS 
     2Model definition files 
     3---------------------- 
     4 
     5The models below are grouped by type.  The list is a snapshot at a particular 
     6time and may be out of date. 
     7 
     8Models with pure form factor (all of which define *F(Q)*): 
     9 
     10    :mod:`barbell` 
     11    :mod:`capped_cylinder` 
     12    :mod:`core_multi_shell` 
     13    :mod:`core_shell_bicelle` 
     14    :mod:`core_shell_bicelle_elliptical` 
     15    :mod:`core_shell_bicelle_elliptical_belt_rough` 
     16    :mod:`core_shell_cylinder` 
     17    :mod:`core_shell_ellipsoid` 
     18    :mod:`core_shell_parallelepipied` 
     19    :mod:`core_shell_sphere` 
     20    :mod:`cylinder` [limiting conditions (long rods, thin disks) not implemented] 
     21    :mod:`ellipsoid` 
     22    :mod:`elliptical_cylinder` 
     23    :mod:`fuzzy_sphere` 
     24    :mod:`hollow_cylinder` 
     25    :mod:`hollow_rectangular_prism` 
     26    :mod:`hollow_rectangular_prism_thin_walls` 
     27    :mod:`multilayer_vesicle` 
     28    :mod:`onion` 
     29    :mod:`parallelepiped` 
     30    :mod:`rectangular_prism` 
     31    :mod:`sphere` 
     32    :mod:`spherical_sld` 
     33    :mod:`triaxial_ellipsoid` 
     34    :mod:`vesicle` 
     35 
     36Models with local structure factor: 
     37 
     38    :mod:`flexible_cylinder` 
     39    :mod:`flexible_cylinder_elliptical` 
     40    :mod:`linear_pearls` 
     41    :mod:`mono_gauss_coil` 
     42    :mod:`pearl_necklace` 
     43    :mod:`poly_gauss_coil` 
     44    :mod:`polymer_micelle` 
     45    :mod:`pringle` 
     46    :mod:`raspberry` 
     47    :mod:`stacked_disks` 
     48    :mod:`star_polymer` 
     49 
     50Models with long range structure factor: 
     51 
     52    :mod:`binary_hard_sphere` 
     53    :mod:`bcc_paracrystal` 
     54    :mod:`fcc_paracrystal` 
     55    :mod:`fractal` 
     56    :mod:`fractal_core_shell` 
     57    :mod:`lamellar` 
     58    :mod:`lamellar_hg` 
     59    :mod:`lamellar_hg_stack_caille` 
     60    :mod:`lamellar_stack_caille` 
     61    :mod:`lamellar_stack_paracrystal` 
     62    :mod:`mass_fractal` 
     63    :mod:`mass_surface_fractal` 
     64    :mod:`rpa` 
     65    :mod:`sc_paracrystal` 
     66    :mod:`surface_fractal` 
     67 
     68Models which are pure structure factors:: 
     69 
     70    :mod:`hardsphere` 
     71    :mod:`hayter_msa` 
     72    :mod:`squarewell` 
     73    :mod:`stickyhardsphere` 
     74 
     75Other models: 
     76 
     77    :mod:`adsorbed_layer` 
     78    :mod:`be_polyelectrolyte` 
     79    :mod:`broad_peak` 
     80    :mod:`correlation_length` 
     81    :mod:`dab` 
     82    :mod:`gauss_lorentz_gel` 
     83    :mod:`gaussian_peak` 
     84    :mod:`gel_fit` 
     85    :mod:`guinier_porod` 
     86    :mod:`guinier` 
     87    :mod:`line` 
     88    :mod:`lorentz` 
     89    :mod:`peak_lorentz` 
     90    :mod:`polymer_excl_volume` 
     91    :mod:`porod` 
     92    :mod:`power_law` 
     93    :mod:`spinodal` 
     94    :mod:`teubner_strey` 
     95    :mod:`two_lorentzian` 
     96    :mod:`unified_power_Rg` 
     97 
    398""" 

  • sasmodels/sasview_model.py

    ra34b811 rd0b0f5d  
    3131from . import modelinfo 
    3232from .details import make_kernel_args, dispersion_mesh 
     33 
     34# Hack: load in any custom distributions 
     35# Uses ~/.sasview/weights/*.py unless SASMODELS_WEIGHTS is set in the environ. 
     36# Override with weights.load_weights(pattern="<weights_path>/*.py") 
     37weights.load_weights() 
    3338 
    3439# pylint: disable=unused-import 

  • sasmodels/weights.py

    rb297ba9 rd0b0f5d  
    230230)) 
    231231 
     232SAS_WEIGHTS_PATH = "~/.sasview/weights" 
     233def load_weights(pattern=None): 
     234    # type: (str) -> None 
     235    """ 
     236    Load dispersion distributions matching the given glob pattern 
     237    """ 
     238    import logging 
     239    import os 
     240    import os.path 
     241    import glob 
     242    import traceback 
     243    from .custom import load_custom_kernel_module 
     244    if pattern is None: 
     245        path = os.environ.get("SAS_WEIGHTS_PATH", SAS_WEIGHTS_PATH) 
     246        pattern = os.path.join(path, "*.py") 
     247    for filename in sorted(glob.glob(os.path.expanduser(pattern))): 
     248        try: 
     249            #print("loading weights from", filename) 
     250            module = load_custom_kernel_module(filename) 
     251            MODELS[module.Dispersion.type] = module.Dispersion 
     252        except Exception as exc: 
     253            logging.error(traceback.format_exc(exc)) 
    232254 
    233255def get_weights(disperser, n, width, nsigmas, value, limits, relative): 
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