Changeset 5430333 in sasmodels


Ignore:
Timestamp:
Mar 21, 2016 3:53:29 AM (8 years ago)
Author:
richardh
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
8e0d974
Parents:
49da079 (diff), ca3abe6 (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.
Message:

Merge branch 'master' of ​https://github.com/SasView/sasmodels

Files:
3 added
5 edited
1 moved

Legend:

Unmodified
Added
Removed

  • example/sesans_parameters_css-hs.py

    r3415f4f rca3abe6  
    2222# Initial parameter values (if other than defaults) 
    2323initial_vals = { 
    24     "sld_core" : 1.0592, 
     24    "sld_core" : 1.05, 
     25    "sld_shell" : 2.88*pen-0.05*(1-pen), 
    2526    "sld_solvent" : 2.88, 
    26     "radius" : 890, 
    27     "thickness" : 130 
     27    "radius" : 730, 
     28    "thickness" : 20, 
     29    "volfraction" : phi, 
     30    "scale" : (1-phi) 
    2831} 
    2932 

  • sasmodels/models/core_shell_sphere.py

    r3556ad7 r3f167d9  
    9191        @param thickness: shell thickness 
    9292    """ 
     93    return (1,1) 
    9394    whole = 4.0 * pi / 3.0 * pow((radius + thickness), 3) 
    9495    core = 4.0 * pi / 3.0 * radius * radius * radius 

  • sasmodels/sesans.py

    rc94577f r2684d45  
    2929 
    3030    q_min = dq = 0.1 * 2*pi / Rmax 
    31     return np.arange(q_min, Converter("1/A")(q_max[0], units=q_max[1]), dq) 
     31    return np.arange(q_min, 
     32                     Converter(q_max[1])(q_max[0], 
     33                                         units="1/A"), 
     34                     dq) 
    3235     
    3336def make_all_q(data): 
    … …  
    7578 
    7679def call_hankel(data, q_calc, Iq_calc): 
    77     return hankel(data.x, data.lam * 1e-9, 
    78                   data.sample.thickness / 10, 
     80    return hankel((data.x, data.x_unit), 
     81                  (data.lam, data.lam_unit), 
     82                  (data.sample.thickness, 
     83                   data.sample.thickness_unit), 
    7984                  q_calc, Iq_calc) 
    8085   
    … …  
    182187    *I* [cm$^{-1}$] is the value of the SANS model at *q* 
    183188    """ 
     189 
     190    from sas.sascalc.data_util.nxsunit import Converter 
     191    wavelength = Converter(wavelength[1])(wavelength[0],"A") 
     192    thickness = Converter(thickness[1])(thickness[0],"A") 
     193    Iq = Converter("1/cm")(Iq,"1/A") # All models default to inverse centimeters 
     194    SElength = Converter(SElength[1])(SElength[0],"A") 
     195 
    184196    G = np.zeros_like(SElength, 'd') 
    185197#============================================================================== 
    … …  
    192204 
    193205    # [m^-1] step size in q, needed for integration 
    194     dq = (q[1]-q[0])*1e10 
     206    dq = (q[1]-q[0]) 
    195207 
    196208    # integration step, convert q into [m**-1] and 2 pi circle integration 
    197     G *= dq*1e10*2*pi 
    198     G0 *= dq*1e10*2*pi 
     209    G *= dq*2*pi 
     210    G0 = np.sum(Iq*q)*dq*2*np.pi 
    199211 
    200212    P = exp(thickness*wavelength**2/(4*pi**2)*(G-G0)) 

  • sasmodels/models/_spherepy.py

    raa2edb2 r49da079  
    1717where *scale* is a volume fraction, $V$ is the volume of the scatterer, 
    1818$r$ is the radius of the sphere, *background* is the background level and 
    19 *sld* and *solvent_sld* are the scattering length densities (SLDs) of the 
     19*sld* and *sld_solvent* are the scattering length densities (SLDs) of the 
    2020scatterer and the solvent respectively. 
    2121 
    … …  
    4747from numpy import pi, inf, sin, cos, sqrt, log 
    4848 
    49 name = "sphere (python)" 
    50 title = "Spheres with uniform scattering length density" 
     49name = " _sphere (python)" 
     50title = "PAK testing ideas for Spheres with uniform scattering length density" 
    5151description = """\ 
    52 P(q)=(scale/V)*[3V(sld-solvent_sld)*(sin(qr)-qr cos(qr)) 
     52P(q)=(scale/V)*[3V(sld-sld_solvent)*(sin(qr)-qr cos(qr)) 
    5353                /(qr)^3]^2 + background 
    5454    r: radius of sphere 
    5555    V: The volume of the scatter 
    5656    sld: the SLD of the sphere 
    57     solvent_sld: the SLD of the solvent 
     57    sld_solvent: the SLD of the solvent 
    5858""" 
    5959category = "shape:sphere" 
    … …  
    6262parameters = [["sld", "1e-6/Ang^2", 1, [-inf, inf], "", 
    6363               "Layer scattering length density"], 
    64               ["solvent_sld", "1e-6/Ang^2", 6, [-inf, inf], "", 
     64              ["sld_solvent", "1e-6/Ang^2", 6, [-inf, inf], "", 
    6565               "Solvent scattering length density"], 
    6666              ["radius", "Ang", 50, [0, inf], "volume", 
    … …  
    7272    return 1.333333333333333 * pi * radius ** 3 
    7373 
    74 def Iq(q, sld, solvent_sld, radius): 
     74def Iq(q, sld, sld_solvent, radius): 
    7575    #print "q",q 
    76     #print "sld,r",sld,solvent_sld,radius 
     76    #print "sld,r",sld,sld_solvent,radius 
    7777    qr = q * radius 
    7878    sn, cn = sin(qr), cos(qr) 
    … …  
    8585    bes = 3 * (sn - qr * cn) / qr ** 3 # may be 0/0 but we fix that next line 
    8686    bes[qr == 0] = 1 
    87     fq = bes * (sld - solvent_sld) * form_volume(radius) 
     87    fq = bes * (sld - sld_solvent) * form_volume(radius) 
    8888    return 1.0e-4 * fq ** 2 
    8989Iq.vectorized = True  # Iq accepts an array of q values 
    9090 
    91 def Iqxy(qx, qy, sld, solvent_sld, radius): 
    92     return Iq(sqrt(qx ** 2 + qy ** 2), sld, solvent_sld, radius) 
     91def Iqxy(qx, qy, sld, sld_solvent, radius): 
     92    return Iq(sqrt(qx ** 2 + qy ** 2), sld, sld_solvent, radius) 
    9393Iqxy.vectorized = True  # Iqxy accepts arrays of qx, qy values 
    9494 
    95 def sesans(z, sld, solvent_sld, radius): 
     95def sesans(z, sld, sld_solvent, radius): 
    9696    """ 
    9797    Calculate SESANS-correlation function for a solid sphere. 
    … …  
    115115 
    116116demo = dict(scale=1, background=0, 
    117             sld=6, solvent_sld=1, 
     117            sld=6, sld_solvent=1, 
    118118            radius=120, 
    119119            radius_pd=.2, radius_pd_n=45) 
    120120oldname = "SphereModel" 
    121 oldpars = dict(sld='sldSph', solvent_sld='sldSolv', radius='radius') 
     121oldpars = dict(sld='sldSph', sld_solvent='sldSolv', radius='radius') 

  • sasmodels/models/sphere.py

    raa2edb2 r49da079  
    1717where *scale* is a volume fraction, $V$ is the volume of the scatterer, 
    1818$r$ is the radius of the sphere, *background* is the background level and 
    19 *sld* and *solvent_sld* are the scattering length densities (SLDs) of the 
     19*sld* and *sld_solvent* are the scattering length densities (SLDs) of the 
    2020scatterer and the solvent respectively. 
    2121 
    … …  
    4949title = "Spheres with uniform scattering length density" 
    5050description = """\ 
    51 P(q)=(scale/V)*[3V(sld-solvent_sld)*(sin(qr)-qr cos(qr)) 
     51P(q)=(scale/V)*[3V(sld-sld_solvent)*(sin(qr)-qr cos(qr)) 
    5252                /(qr)^3]^2 + background 
    5353    r: radius of sphere 
    5454    V: The volume of the scatter 
    5555    sld: the SLD of the sphere 
    56     solvent_sld: the SLD of the solvent 
     56    sld_solvent: the SLD of the solvent 
    5757""" 
    5858category = "shape:sphere" 
    … …  
    6161parameters = [["sld", "1e-6/Ang^2", 1, [-inf, inf], "", 
    6262               "Layer scattering length density"], 
    63               ["solvent_sld", "1e-6/Ang^2", 6, [-inf, inf], "", 
     63              ["sld_solvent", "1e-6/Ang^2", 6, [-inf, inf], "", 
    6464               "Solvent scattering length density"], 
    6565              ["radius", "Ang", 50, [0, inf], "volume", 
    … …  
    7676 
    7777Iq = """ 
    78     return sphere_form(q, radius, sld, solvent_sld); 
     78    return sphere_form(q, radius, sld, sld_solvent); 
    7979    """ 
    8080 
    … …  
    8282    // never called since no orientation or magnetic parameters. 
    8383    //return -1.0; 
    84     return Iq(sqrt(qx*qx + qy*qy), sld, solvent_sld, radius); 
     84    return Iq(sqrt(qx*qx + qy*qy), sld, sld_solvent, radius); 
    8585    """ 
    8686 
    … …  
    9494 
    9595demo = dict(scale=1, background=0, 
    96             sld=6, solvent_sld=1, 
     96            sld=6, sld_solvent=1, 
    9797            radius=120, 
    9898            radius_pd=.2, radius_pd_n=45) 
    9999oldname = "SphereModel" 
    100 oldpars = dict(sld='sldSph', solvent_sld='sldSolv', radius='radius') 
     100oldpars = dict(sld='sldSph', sld_solvent='sldSolv', radius='radius') 

  • sasmodels/models/triaxial_ellipsoid.py

    r6ef4293 r49da079  
    9191               "Solvent scattering length density"], 
    9292              ["req_minor", "Ang", 20, [0, inf], "volume", 
    93                "Minor equitorial radius"], 
     93               "Minor equatorial radius"], 
    9494              ["req_major", "Ang", 400, [0, inf], "volume", 
    9595               "Major equatorial radius"], 
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