Changes in / [48438f9:85190c2] in sasmodels


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sasmodels/models
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17 edited

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  • sasmodels/models/barbell.py

    r9b79f29 r0b56f38  
    108108              ["radius",      "Ang",         20, [0, inf],    "volume",      "Cylindrical bar radius"], 
    109109              ["length",      "Ang",        400, [0, inf],    "volume",      "Cylinder bar length"], 
    110               ["theta",       "degrees",     60, [-360, 360], "orientation", "Barbell axis to beam angle"], 
    111               ["phi",         "degrees",     60, [-360, 360], "orientation", "Rotation about beam"], 
     110              ["theta",       "degrees",     60, [-inf, inf], "orientation", "In plane angle"], 
     111              ["phi",         "degrees",     60, [-inf, inf], "orientation", "Out of plane angle"], 
    112112             ] 
    113113# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/bcc_paracrystal.py

    r9b79f29 r1f65db5  
    123123              ["sld",         "1e-6/Ang^2",  4,    [-inf, inf], "sld",         "Particle scattering length density"], 
    124124              ["sld_solvent", "1e-6/Ang^2",  1,    [-inf, inf], "sld",         "Solvent scattering length density"], 
    125               ["theta",       "degrees",    60,    [-360, 360], "orientation", "c axis to beam angle"], 
    126               ["phi",         "degrees",    60,    [-360, 360], "orientation", "rotation about beam"], 
    127               ["psi",         "degrees",    60,    [-360, 360], "orientation", "rotation about c axis"] 
     125              ["theta",       "degrees",    60,    [-inf, inf], "orientation", "In plane angle"], 
     126              ["phi",         "degrees",    60,    [-inf, inf], "orientation", "Out of plane angle"], 
     127              ["psi",         "degrees",    60,    [-inf, inf], "orientation", "Out of plane angle"] 
    128128             ] 
    129129# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/capped_cylinder.py

    r9b79f29 r0b56f38  
    129129              ["radius_cap", "Ang",     20, [0, inf],    "volume", "Cap radius"], 
    130130              ["length",     "Ang",    400, [0, inf],    "volume", "Cylinder length"], 
    131               ["theta",      "degrees", 60, [-360, 360], "orientation", "cylinder axis to beam angle"], 
    132               ["phi",        "degrees", 60, [-360, 360], "orientation", "rotation about beam"], 
     131              ["theta",      "degrees", 60, [-inf, inf], "orientation", "inclination angle"], 
     132              ["phi",        "degrees", 60, [-inf, inf], "orientation", "deflection angle"], 
    133133             ] 
    134134# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/core_shell_bicelle.py

    r9b79f29 r0b56f38  
    4747.. math:: 
    4848 
    49     \begin{align}     
     49        \begin{align}     
    5050    F(Q,\alpha) = &\bigg[  
    5151    (\rho_c - \rho_f) V_c \frac{2J_1(QRsin \alpha)}{QRsin\alpha}\frac{sin(QLcos\alpha/2)}{Q(L/2)cos\alpha} \\ 
    … …  
    6969.. figure:: img/cylinder_angle_definition.jpg 
    7070 
    71     Definition of the angles for the oriented core shell bicelle model, 
    72     note that the cylinder axis of the bicelle starts along the beam direction 
    73     when $\theta  = \phi = 0$. 
     71    Definition of the angles for the oriented core shell bicelle tmodel. 
    7472 
    7573 
    … …  
    137135    ["sld_rim",        "1e-6/Ang^2", 4, [-inf, inf], "sld",         "Cylinder rim scattering length density"], 
    138136    ["sld_solvent",    "1e-6/Ang^2", 1, [-inf, inf], "sld",         "Solvent scattering length density"], 
    139     ["theta",          "degrees",   90, [-360, 360], "orientation", "cylinder axis to beam angle"], 
    140     ["phi",            "degrees",    0, [-360, 360], "orientation", "rotation about beam"] 
     137    ["theta",          "degrees",   90, [-inf, inf], "orientation", "In plane angle"], 
     138    ["phi",            "degrees",    0, [-inf, inf], "orientation", "Out of plane angle"], 
    141139    ] 
    142140 
    … …  
    162160qy = q*sin(pi/6.0) 
    163161tests = [[{}, 0.05, 7.4883545957], 
    164         [{'theta':80., 'phi':10.}, (qx, qy), 2.81048892474 ] 
     162        [{'theta':80., 'phi':10.}, (qx, qy), 2.81048892474 ], 
    165163        ] 
    166164del qx, qy  # not necessary to delete, but cleaner 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    r9b79f29 r15a90c1  
    119119    ["radius",         "Ang",       30, [0, inf],    "volume",      "Cylinder core radius"], 
    120120    ["x_core",        "None",       3,  [0, inf],    "volume",      "axial ratio of core, X = r_polar/r_equatorial"], 
    121     ["thick_rim",  "Ang",            8, [0, inf],    "volume",      "Rim shell thickness"], 
    122     ["thick_face", "Ang",           14, [0, inf],    "volume",      "Cylinder face thickness"], 
    123     ["length",         "Ang",       50, [0, inf],    "volume",      "Cylinder length"], 
     121    ["thick_rim",  "Ang",        8, [0, inf],    "volume",      "Rim shell thickness"], 
     122    ["thick_face", "Ang",       14, [0, inf],    "volume",      "Cylinder face thickness"], 
     123    ["length",         "Ang",      50, [0, inf],    "volume",      "Cylinder length"], 
    124124    ["sld_core",       "1e-6/Ang^2", 4, [-inf, inf], "sld",         "Cylinder core scattering length density"], 
    125125    ["sld_face",       "1e-6/Ang^2", 7, [-inf, inf], "sld",         "Cylinder face scattering length density"], 
    126126    ["sld_rim",        "1e-6/Ang^2", 1, [-inf, inf], "sld",         "Cylinder rim scattering length density"], 
    127127    ["sld_solvent",    "1e-6/Ang^2", 6, [-inf, inf], "sld",         "Solvent scattering length density"], 
    128     ["theta",       "degrees",    90.0, [-360, 360], "orientation", "cylinder axis to beam angle"], 
    129     ["phi",         "degrees",    0,    [-360, 360], "orientation", "rotation about beam"], 
    130     ["psi",         "degrees",    0,    [-360, 360], "orientation", "rotation about cylinder axis"] 
     128    ["theta",          "degrees",   90, [-360, 360], "orientation", "In plane angle"], 
     129    ["phi",            "degrees",    0, [-360, 360], "orientation", "Out of plane angle"], 
     130    ["psi",            "degrees",    0, [-360, 360], "orientation", "Major axis angle relative to Q"], 
    131131    ] 
    132132 

  • sasmodels/models/core_shell_cylinder.py

    r9b79f29 r0b56f38  
    117117              ["length", "Ang", 400, [0, inf], "volume", 
    118118               "Cylinder length"], 
    119               ["theta", "degrees", 60, [-360, 360], "orientation", 
    120                "cylinder axis to beam angle"], 
    121               ["phi", "degrees",   60, [-360, 360], "orientation", 
    122                "rotation about beam"], 
     119              ["theta", "degrees", 60, [-inf, inf], "orientation", 
     120               "In plane angle"], 
     121              ["phi", "degrees", 60, [-inf, inf], "orientation", 
     122               "Out of plane angle"], 
    123123             ] 
    124124 

  • sasmodels/models/core_shell_ellipsoid.py

    r9b79f29 r8e68ea0  
    132132    ["sld_shell",     "1e-6/Ang^2", 1,   [-inf, inf], "sld",         "Shell scattering length density"], 
    133133    ["sld_solvent",   "1e-6/Ang^2", 6.3, [-inf, inf], "sld",         "Solvent scattering length density"], 
    134     ["theta",         "degrees",    0,   [-360, 360], "orientation", "elipsoid axis to beam angle"], 
    135     ["phi",           "degrees",    0,   [-360, 360], "orientation", "rotation about beam"], 
     134    ["theta",         "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation wrt incoming beam"], 
     135    ["phi",           "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation in the plane of the detector"], 
    136136    ] 
    137137# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/core_shell_parallelepiped.py

    r9b79f29 r1f65db5  
    153153              ["thick_rim_c", "Ang", 10, [0, inf], "volume", 
    154154               "Thickness of C rim"], 
    155               ["theta", "degrees", 0, [-360, 360], "orientation", 
    156                "c axis to beam angle"], 
    157               ["phi", "degrees", 0, [-360, 360], "orientation", 
    158                "rotation about beam"], 
    159               ["psi", "degrees", 0, [-360, 360], "orientation", 
    160                "rotation about c axis"], 
     155              ["theta", "degrees", 0, [-inf, inf], "orientation", 
     156               "In plane angle"], 
     157              ["phi", "degrees", 0, [-inf, inf], "orientation", 
     158               "Out of plane angle"], 
     159              ["psi", "degrees", 0, [-inf, inf], "orientation", 
     160               "Rotation angle around its own c axis against q plane"], 
    161161             ] 
    162162 

  • sasmodels/models/cylinder.py

    r9b79f29 r3330bb4  
    127127              ["length", "Ang", 400, [0, inf], "volume", 
    128128               "Cylinder length"], 
    129               ["theta", "degrees", 60, [-360, 360], "orientation", 
    130                "cylinder axis to beam angle"], 
    131               ["phi", "degrees",   60, [-360, 360], "orientation", 
    132                "rotation about beam"], 
     129              ["theta", "degrees", 60, [-inf, inf], "orientation", 
     130               "latitude"], 
     131              ["phi", "degrees", 60, [-inf, inf], "orientation", 
     132               "longitude"], 
    133133             ] 
    134134 

  • sasmodels/models/ellipsoid.py

    r9b79f29 r0b56f38  
    151151              ["radius_equatorial", "Ang", 400, [0, inf], "volume", 
    152152               "Equatorial radius"], 
    153               ["theta", "degrees", 60, [-360, 360], "orientation", 
    154                "ellipsoid axis to beam angle"], 
    155               ["phi", "degrees", 60, [-360, 360], "orientation", 
    156                "rotation about beam"], 
     153              ["theta", "degrees", 60, [-inf, inf], "orientation", 
     154               "In plane angle"], 
     155              ["phi", "degrees", 60, [-inf, inf], "orientation", 
     156               "Out of plane angle"], 
    157157             ] 
    158158 

  • sasmodels/models/elliptical_cylinder.py

    r9b79f29 r15a90c1  
    126126              ["sld",         "1e-6/Ang^2", 4.0,   [-inf, inf], "sld",         "Cylinder scattering length density"], 
    127127              ["sld_solvent", "1e-6/Ang^2", 1.0,   [-inf, inf], "sld",         "Solvent scattering length density"], 
    128               ["theta",       "degrees",    90.0,  [-360, 360], "orientation", "cylinder axis to beam angle"], 
    129               ["phi",         "degrees",    0,     [-360, 360], "orientation", "rotation about beam"], 
    130               ["psi",         "degrees",    0,     [-360, 360], "orientation", "rotation about cylinder axis"]] 
     128              ["theta",       "degrees",    90.0,  [-360, 360], "orientation", "In plane angle"], 
     129              ["phi",         "degrees",    0,     [-360, 360], "orientation", "Out of plane angle"], 
     130              ["psi",         "degrees",    0,     [-360, 360], "orientation", "Major axis angle relative to Q"]] 
    131131 
    132132# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/fcc_paracrystal.py

    r9b79f29 r1f65db5  
    111111              ["sld", "1e-6/Ang^2", 4, [-inf, inf], "sld", "Particle scattering length density"], 
    112112              ["sld_solvent", "1e-6/Ang^2", 1, [-inf, inf], "sld", "Solvent scattering length density"], 
    113               ["theta",       "degrees",    60,    [-360, 360], "orientation", "c axis to beam angle"], 
    114               ["phi",         "degrees",    60,    [-360, 360], "orientation", "rotation about beam"], 
    115               ["psi",         "degrees",    60,    [-360, 360], "orientation", "rotation about c axis"] 
     113              ["theta", "degrees", 60, [-inf, inf], "orientation", "In plane angle"], 
     114              ["phi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"], 
     115              ["psi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"] 
    116116             ] 
    117117# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/hollow_cylinder.py

    r9b79f29 r0b56f38  
    8282    ["sld",         "1/Ang^2",  6.3, [-inf, inf], "sld",         "Cylinder sld"], 
    8383    ["sld_solvent", "1/Ang^2",  1,   [-inf, inf], "sld",         "Solvent sld"], 
    84     ["theta",       "degrees", 90,   [-360, 360], "orientation", "Cylinder axis to beam angle"], 
    85     ["phi",         "degrees",  0,   [-360, 360], "orientation", "Rotation about beam"], 
     84    ["theta",       "degrees", 90,   [-360, 360], "orientation", "Theta angle"], 
     85    ["phi",         "degrees",  0,   [-360, 360], "orientation", "Phi angle"], 
    8686    ] 
    8787# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/parallelepiped.py

    r9b79f29 rafd4692  
    205205              ["length_c", "Ang", 400, [0, inf], "volume", 
    206206               "Larger side of the parallelepiped"], 
    207               ["theta", "degrees", 60, [-360, 360], "orientation", 
    208                "c axis to beam angle"], 
    209               ["phi", "degrees", 60, [-360, 360], "orientation", 
    210                "rotation about beam"], 
    211               ["psi", "degrees", 60, [-360, 360], "orientation", 
    212                "rotation about c axis"], 
     207              ["theta", "degrees", 60, [-inf, inf], "orientation", 
     208               "In plane angle"], 
     209              ["phi", "degrees", 60, [-inf, inf], "orientation", 
     210               "Out of plane angle"], 
     211              ["psi", "degrees", 60, [-inf, inf], "orientation", 
     212               "Rotation angle around its own c axis against q plane"], 
    213213             ] 
    214214 

  • sasmodels/models/sc_paracrystal.py

    r9b79f29 r0881f4e  
    130130              ["sld",  "1e-6/Ang^2",         3.0, [0.0, inf],  "sld",         "Sphere scattering length density"], 
    131131              ["sld_solvent", "1e-6/Ang^2",  6.3, [0.0, inf],  "sld",         "Solvent scattering length density"], 
    132               ["theta",       "degrees",    0,    [-360, 360], "orientation", "c axis to beam angle"], 
    133               ["phi",         "degrees",    0,    [-360, 360], "orientation", "rotation about beam"], 
    134               ["psi",         "degrees",    0,    [-360, 360], "orientation", "rotation about c axis"] 
     132              ["theta",       "degrees",     0.0, [-inf, inf], "orientation", "Orientation of the a1 axis w/respect incoming beam"], 
     133              ["phi",         "degrees",     0.0, [-inf, inf], "orientation", "Orientation of the a2 in the plane of the detector"], 
     134              ["psi",         "degrees",     0.0, [-inf, inf], "orientation", "Orientation of the a3 in the plane of the detector"], 
    135135             ] 
    136136# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/stacked_disks.py

    r9b79f29 rf3073b0  
    131131    ["sld_layer",   "1e-6/Ang^2",  0.0, [-inf, inf], "sld",         "Layer scattering length density"], 
    132132    ["sld_solvent", "1e-6/Ang^2",  5.0, [-inf, inf], "sld",         "Solvent scattering length density"], 
    133     ["theta",       "degrees",     0,   [-360, 360], "orientation", "Orientation of the stacked disk axis w/respect incoming beam"], 
    134     ["phi",         "degrees",     0,   [-360, 360], "orientation", "Rotation about beam"], 
     133    ["theta",       "degrees",     0,   [-inf, inf], "orientation", "Orientation of the stacked disk axis w/respect incoming beam"], 
     134    ["phi",         "degrees",     0,   [-inf, inf], "orientation", "Orientation of the stacked disk in the plane of the detector"], 
    135135    ] 
    136136# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/triaxial_ellipsoid.py

    r9b79f29 r0881f4e  
    118118* **Last Modified by:** Paul Kienzle (improved calculation) **Date:** April 4, 2017 
    119119* **Last Reviewed by:** Paul Kienzle & Richard Heenan **Date:**  April 4, 2017 
     120""" 
    120121 
    121122from numpy import inf, sin, cos, pi 
    … …  
    142143              ["radius_polar", "Ang", 10, [0, inf], "volume", 
    143144               "Polar radius, Rc"], 
    144               ["theta", "degrees", 60, [-360, 360], "orientation", 
    145                "polar axis to beam angle"], 
    146               ["phi", "degrees", 60, [-360, 360], "orientation", 
    147                "rotation about beam"], 
    148               ["psi", "degrees", 60, [-360, 360], "orientation", 
    149                "rotation about polar axis"], 
     145              ["theta", "degrees", 60, [-inf, inf], "orientation", 
     146               "In plane angle"], 
     147              ["phi", "degrees", 60, [-inf, inf], "orientation", 
     148               "Out of plane angle"], 
     149              ["psi", "degrees", 60, [-inf, inf], "orientation", 
     150               "Out of plane angle"], 
    150151             ] 
    151152 
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