Changeset 9b79f29 in sasmodels


Ignore:
Timestamp:
Apr 8, 2017 7:48:49 AM (7 years ago)
Author:
richardh
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
48438f9
Parents:
737679d
Message:

more docs change for new rotation angles

Location:
sasmodels/models
Files:
17 edited

Legend:

Unmodified
Added
Removed

  • sasmodels/models/barbell.py

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

  • sasmodels/models/bcc_paracrystal.py

    r1f65db5 r9b79f29  
    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,    [-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"] 
     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"] 
    128128             ] 
    129129# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/capped_cylinder.py

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

  • sasmodels/models/core_shell_bicelle.py

    r0b56f38 r9b79f29  
    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 tmodel. 
     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 $\theta  = \phi = 0$. 
    7274 
    7375 
    … …  
    135137    ["sld_rim",        "1e-6/Ang^2", 4, [-inf, inf], "sld",         "Cylinder rim scattering length density"], 
    136138    ["sld_solvent",    "1e-6/Ang^2", 1, [-inf, inf], "sld",         "Solvent scattering length density"], 
    137     ["theta",          "degrees",   90, [-inf, inf], "orientation", "In plane angle"], 
    138     ["phi",            "degrees",    0, [-inf, inf], "orientation", "Out of plane angle"], 
     139    ["theta",          "degrees",   90, [-360, 360], "orientation", "cylinder axis to beam angle"], 
     140    ["phi",            "degrees",    0, [-360, 360], "orientation", "rotation about beam"] 
    139141    ] 
    140142 
    … …  
    160162qy = q*sin(pi/6.0) 
    161163tests = [[{}, 0.05, 7.4883545957], 
    162         [{'theta':80., 'phi':10.}, (qx, qy), 2.81048892474 ], 
     164        [{'theta':80., 'phi':10.}, (qx, qy), 2.81048892474 ] 
    163165        ] 
    164166del qx, qy  # not necessary to delete, but cleaner 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    r16a8c63 r9b79f29  
    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, [-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"], 
     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"] 
    131131    ] 
    132132 

  • sasmodels/models/core_shell_cylinder.py

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

  • sasmodels/models/core_shell_ellipsoid.py

    rdaeef4c r9b79f29  
    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,   [-inf, inf], "orientation", "Oblate orientation wrt incoming beam"], 
    135     ["phi",           "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation in the plane of the detector"], 
     134    ["theta",         "degrees",    0,   [-360, 360], "orientation", "elipsoid axis to beam angle"], 
     135    ["phi",           "degrees",    0,   [-360, 360], "orientation", "rotation about beam"], 
    136136    ] 
    137137# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/core_shell_parallelepiped.py

    r1f65db5 r9b79f29  
    153153              ["thick_rim_c", "Ang", 10, [0, inf], "volume", 
    154154               "Thickness of C rim"], 
    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"], 
     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"], 
    161161             ] 
    162162 

  • sasmodels/models/cylinder.py

    r3fd0499 r9b79f29  
    127127              ["length", "Ang", 400, [0, inf], "volume", 
    128128               "Cylinder length"], 
    129               ["theta", "degrees", 60, [-inf, inf], "orientation", 
    130                "latitude"], 
    131               ["phi", "degrees", 60, [-inf, inf], "orientation", 
    132                "longitude"], 
     129              ["theta", "degrees", 60, [-360, 360], "orientation", 
     130               "cylinder axis to beam angle"], 
     131              ["phi", "degrees",   60, [-360, 360], "orientation", 
     132               "rotation about beam"], 
    133133             ] 
    134134 

  • sasmodels/models/ellipsoid.py

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

  • sasmodels/models/elliptical_cylinder.py

    r16a8c63 r9b79f29  
    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", "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"]] 
     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"]] 
    131131 
    132132# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/fcc_paracrystal.py

    r1f65db5 r9b79f29  
    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, [-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"] 
     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"] 
    116116             ] 
    117117# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/hollow_cylinder.py

    r0b56f38 r9b79f29  
    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", "Theta angle"], 
    85     ["phi",         "degrees",  0,   [-360, 360], "orientation", "Phi angle"], 
     84    ["theta",       "degrees", 90,   [-360, 360], "orientation", "Cylinder axis to beam angle"], 
     85    ["phi",         "degrees",  0,   [-360, 360], "orientation", "Rotation about beam"], 
    8686    ] 
    8787# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/parallelepiped.py

    r3fd0499 r9b79f29  
    205205              ["length_c", "Ang", 400, [0, inf], "volume", 
    206206               "Larger side of the parallelepiped"], 
    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"], 
     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"], 
    213213             ] 
    214214 

  • sasmodels/models/sc_paracrystal.py

    r737679d r9b79f29  
    8383model computation. 
    8484 
    85 <<<<<<< HEAD 
    8685.. figure:: img/parallelepiped_angle_definition.png 
    8786 
    8887    Orientation of the crystal with respect to the scattering plane, when  
    8988    $\theta = \phi = 0$ the $c$ axis is along the beam direction (the $z$ axis). 
    90 ======= 
    91 .. figure:: img/sc_crystal_angle_definition.jpg 
    92 >>>>>>> 3fd04991e2575b02401723d8534c376cd9b66305 
    9389 
    9490Reference 
    … …  
    134130              ["sld",  "1e-6/Ang^2",         3.0, [0.0, inf],  "sld",         "Sphere scattering length density"], 
    135131              ["sld_solvent", "1e-6/Ang^2",  6.3, [0.0, inf],  "sld",         "Solvent scattering length density"], 
    136               ["theta",       "degrees",     0.0, [-inf, inf], "orientation", "Orientation of the a1 axis w/respect incoming beam"], 
    137               ["phi",         "degrees",     0.0, [-inf, inf], "orientation", "Orientation of the a2 in the plane of the detector"], 
    138               ["psi",         "degrees",     0.0, [-inf, inf], "orientation", "Orientation of the a3 in the plane of the detector"], 
     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"] 
    139135             ] 
    140136# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/stacked_disks.py

    r0b56f38 r9b79f29  
    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,   [-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"], 
     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"], 
    135135    ] 
    136136# pylint: enable=bad-whitespace, line-too-long 

  • sasmodels/models/triaxial_ellipsoid.py

    r737679d r9b79f29  
    113113* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
    114114* **Last Modified by:** Paul Kienzle (improved calculation) **Date:** April 4, 2017 
    115 <<<<<<< HEAD 
    116 * **Last Reviewed by:** Paul Kienzle &Richard Heenan **Date:**  April 4, 2017 
    117 ======= 
    118115* **Last Reviewed by:** Paul Kienzle & Richard Heenan **Date:**  April 4, 2017 
    119 >>>>>>> 3fd04991e2575b02401723d8534c376cd9b66305 
    120116 
    121117""" 
    … …  
    144140              ["radius_polar", "Ang", 10, [0, inf], "volume", 
    145141               "Polar radius, Rc"], 
    146               ["theta", "degrees", 60, [-inf, inf], "orientation", 
    147                "In plane angle"], 
    148               ["phi", "degrees", 60, [-inf, inf], "orientation", 
    149                "Out of plane angle"], 
    150               ["psi", "degrees", 60, [-inf, inf], "orientation", 
    151                "Out of plane angle"], 
     142              ["theta", "degrees", 60, [-360, 360], "orientation", 
     143               "polar axis to beam angle"], 
     144              ["phi", "degrees", 60, [-360, 360], "orientation", 
     145               "rotation about beam"], 
     146              ["psi", "degrees", 60, [-360, 360], "orientation", 
     147               "rotation about polar axis"], 
    152148             ] 
    153149 
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