Changes in / [e0de72f:69ef533] in sasmodels


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sasmodels/models
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  • sasmodels/models/core_shell_ellipsoid.c

    r5031ca3 r2222134  
    11double form_volume(double radius_equat_core, 
    2                    double polar_core, 
    3                    double equat_shell, 
    4                    double polar_shell); 
     2                   double radius_polar_core, 
     3                   double radius_equat_shell, 
     4                   double radius_polar_shell); 
    55double Iq(double q, 
    66          double radius_equat_core, 
    7           double x_core, 
    8           double thick_shell, 
    9           double x_polar_shell, 
    10           double core_sld, 
    11           double shell_sld, 
    12           double solvent_sld); 
     7          double radius_polar_core, 
     8          double radius_equat_shell, 
     9          double radius_polar_shell, 
     10          double sld_core, 
     11          double sld_shell, 
     12          double sld_solvent); 
    1313 
    1414 
    1515double Iqxy(double qx, double qy, 
    1616          double radius_equat_core, 
    17           double x_core, 
    18           double thick_shell, 
    19           double x_polar_shell, 
    20           double core_sld, 
    21           double shell_sld, 
    22           double solvent_sld, 
     17          double radius_polar_core, 
     18          double radius_equat_shell, 
     19          double radius_polar_shell, 
     20          double sld_core, 
     21          double sld_shell, 
     22          double sld_solvent, 
    2323          double theta, 
    2424          double phi); 
    … …  
    2626 
    2727double form_volume(double radius_equat_core, 
    28                    double x_core, 
    29                    double thick_shell, 
    30                    double x_polar_shell) 
     28                   double radius_polar_core, 
     29                   double radius_equat_shell, 
     30                   double radius_polar_shell) 
    3131{ 
    32     const double equat_shell = radius_equat_core + thick_shell; 
    33     const double polar_shell = radius_equat_core*x_core + thick_shell*x_polar_shell; 
    34     double vol = 4.0*M_PI/3.0*equat_shell*equat_shell*polar_shell; 
     32    double vol = 4.0*M_PI/3.0*radius_equat_shell*radius_equat_shell*radius_polar_shell; 
    3533    return vol; 
    3634} 
    3735 
    3836static double 
    39 core_shell_ellipsoid_xt_kernel(double q, 
     37core_shell_ellipsoid_kernel(double q, 
    4038          double radius_equat_core, 
    41           double x_core, 
    42           double thick_shell, 
    43           double x_polar_shell, 
    44           double core_sld, 
    45           double shell_sld, 
    46           double solvent_sld) 
     39          double radius_polar_core, 
     40          double radius_equat_shell, 
     41          double radius_polar_shell, 
     42          double sld_core, 
     43          double sld_shell, 
     44          double sld_solvent) 
    4745{ 
     46 
     47    //upper and lower integration limits 
    4848    const double lolim = 0.0; 
    4949    const double uplim = 1.0; 
    … …  
    5151    double summ = 0.0;   //initialize intergral 
    5252 
    53     const double delpc = core_sld - shell_sld; //core - shell 
    54     const double delps = shell_sld - solvent_sld; //shell - solvent 
    55  
    56  
    57     const double polar_core = radius_equat_core*x_core; 
    58     const double equat_shell = radius_equat_core + thick_shell; 
    59     const double polar_shell = radius_equat_core*x_core + thick_shell*x_polar_shell; 
     53    const double delpc = sld_core - sld_shell;    //core - shell 
     54    const double delps = sld_shell - sld_solvent; //shell - solvent 
    6055 
    6156    for(int i=0;i<N_POINTS_76;i++) { 
    … …  
    6358        double yyy = Gauss76Wt[i] * gfn4(zi, 
    6459                                  radius_equat_core, 
    65                                   polar_core, 
    66                                   equat_shell, 
    67                                   polar_shell, 
     60                                  radius_polar_core, 
     61                                  radius_equat_shell, 
     62                                  radius_polar_shell, 
    6863                                  delpc, 
    6964                                  delps, 
    … …  
    7368 
    7469    double answer = (uplim-lolim)/2.0*summ; 
     70 
    7571    //convert to [cm-1] 
    7672    answer *= 1.0e-4; 
    … …  
    8076 
    8177static double 
    82 core_shell_ellipsoid_xt_kernel_2d(double q, double q_x, double q_y, 
     78core_shell_ellipsoid_kernel_2d(double q, double q_x, double q_y, 
    8379          double radius_equat_core, 
    84           double x_core, 
    85           double thick_shell, 
    86           double x_polar_shell, 
    87           double core_sld, 
    88           double shell_sld, 
    89           double solvent_sld, 
     80          double radius_polar_core, 
     81          double radius_equat_shell, 
     82          double radius_polar_shell, 
     83          double sld_core, 
     84          double sld_shell, 
     85          double sld_solvent, 
    9086          double theta, 
    9187          double phi) 
    … …  
    9591    phi = phi * M_PI_180; 
    9692 
     93 
    9794    // ellipsoid orientation, the axis of the rotation is consistent with the ploar axis. 
    9895    const double cyl_x = cos(theta) * cos(phi); 
    9996    const double cyl_y = sin(theta); 
    10097 
    101     const double sldcs = core_sld - shell_sld; 
    102     const double sldss = shell_sld- solvent_sld; 
     98    const double sldcs = sld_core - sld_shell; 
     99    const double sldss = sld_shell- sld_solvent; 
    103100 
    104101    // Compute the angle btw vector q and the 
    … …  
    106103    const double cos_val = cyl_x*q_x + cyl_y*q_y; 
    107104 
    108     const double polar_core = radius_equat_core*x_core; 
    109     const double equat_shell = radius_equat_core + thick_shell; 
    110     const double polar_shell = radius_equat_core*x_core + thick_shell*x_polar_shell; 
    111  
    112     // Call the IGOR library function to get the kernel: 
    113     // MUST use gfn4 not gf2 because of the def of params. 
     105    // Call the IGOR library function to get the kernel: MUST use gfn4 not gf2 because of the def of params. 
    114106    double answer = gfn4(cos_val, 
    115107                  radius_equat_core, 
    116                   polar_core, 
    117                   equat_shell, 
    118                   polar_shell, 
     108                  radius_polar_core, 
     109                  radius_equat_shell, 
     110                  radius_polar_shell, 
    119111                  sldcs, 
    120112                  sldss, 
    … …  
    129121double Iq(double q, 
    130122          double radius_equat_core, 
    131           double x_core, 
    132           double thick_shell, 
    133           double x_polar_shell, 
    134           double core_sld, 
    135           double shell_sld, 
    136           double solvent_sld) 
     123          double radius_polar_core, 
     124          double radius_equat_shell, 
     125          double radius_polar_shell, 
     126          double sld_core, 
     127          double sld_shell, 
     128          double sld_solvent) 
    137129{ 
    138     double intensity = core_shell_ellipsoid_xt_kernel(q, 
     130    double intensity = core_shell_ellipsoid_kernel(q, 
    139131           radius_equat_core, 
    140            x_core, 
    141            thick_shell, 
    142            x_polar_shell, 
    143            core_sld, 
    144            shell_sld, 
    145            solvent_sld); 
     132           radius_polar_core, 
     133           radius_equat_shell, 
     134           radius_polar_shell, 
     135           sld_core, 
     136           sld_shell, 
     137           sld_solvent); 
    146138 
    147139    return intensity; 
    … …  
    151143double Iqxy(double qx, double qy, 
    152144          double radius_equat_core, 
    153           double x_core, 
    154           double thick_shell, 
    155           double x_polar_shell, 
    156           double core_sld, 
    157           double shell_sld, 
    158           double solvent_sld, 
     145          double radius_polar_core, 
     146          double radius_equat_shell, 
     147          double radius_polar_shell, 
     148          double sld_core, 
     149          double sld_shell, 
     150          double sld_solvent, 
    159151          double theta, 
    160152          double phi) 
    … …  
    162154    double q; 
    163155    q = sqrt(qx*qx+qy*qy); 
    164     double intensity = core_shell_ellipsoid_xt_kernel_2d(q, qx/q, qy/q, 
     156    double intensity = core_shell_ellipsoid_kernel_2d(q, qx/q, qy/q, 
    165157                       radius_equat_core, 
    166                        x_core, 
    167                        thick_shell, 
    168                        x_polar_shell, 
    169                        core_sld, 
    170                        shell_sld, 
    171                        solvent_sld, 
     158                       radius_polar_core, 
     159                       radius_equat_shell, 
     160                       radius_polar_shell, 
     161                       sld_core, 
     162                       sld_shell, 
     163                       sld_solvent, 
    172164                       theta, 
    173165                       phi); 

  • sasmodels/models/core_shell_ellipsoid.py

    r5031ca3 r2222134  
    11r""" 
    2 An alternative version of $P(q)$ for the core_shell_ellipsoid 
    3 having as parameters the core axial ratio X and a shell thickness, 
    4 which are more often what we would like to determine. 
     2This model provides the form factor, $P(q)$, for a core shell ellipsoid (below) 
     3where the form factor is normalized by the volume of the outer [CHECK]. 
    54 
    6 This model is also better behaved when polydispersity is applied than the four 
    7 independent radii in core_shell_ellipsoid model. 
     5.. math:: 
     6 
     7    P(q) = \text{scale} * \left<f^2\right>/V + \text{background} 
     8 
     9where the volume $V = (4/3)\pi(r_\text{major outer} r_\text{minor outer}^2)$ 
     10and the averaging $< >$ is applied over all orientations for 1D. 
     11 
     12.. figure:: img/core_shell_ellipsoid_geometry.png 
     13 
     14    The returned value is in units of |cm^-1|, on absolute scale. 
    815 
    916Definition 
    1017---------- 
    1118 
    12 .. figure:: img/core_shell_ellipsoid_geometry.png 
     19The form factor calculated is 
    1320 
    14 The geometric parameters of this model are 
     21.. math:: 
    1522 
    16 *radius_equat_core =* equatorial core radius *= R_minor_core* 
     23    P(q) &= \frac{\text{scale}}{V}\int_0^1 
     24        \left|F(q,r_\text{minor core},r_\text{major core},\alpha) 
     25        + F(q,r_\text{minor outer},r_\text{major outer},\alpha)\right|^2 
     26        d\alpha 
     27        + \text{background} 
    1728 
    18 *X_core = polar_core / radius_equat_core = Rmajor_core / Rminor_core* 
     29    \left|F(q,r_\text{minor},r_\text{major},\alpha)\right| 
     30        &=(4\pi/3)r_\text{major}r_\text{minor}^2 \Delta \rho \cdot (3j_1(u)/u) 
    1931 
    20 *Thick_shell = equat_outer - radius_equat_core = Rminor_outer - Rminor_core* 
     32    u &= q\left[ r_\text{major}^2\alpha ^2 
     33                  + r_\text{minor}^2(1-\alpha ^2)\right]^{1/2} 
    2134 
    22 *XpolarShell = Tpolar_shell / Thick_shell = (Rmajor_outer - Rmajor_core)/ 
    23 (Rminor_outer - Rminor_core)* 
     35where 
    2436 
    25 In terms of the original radii 
     37.. math:: 
    2638 
    27 *polar_core = radius_equat_core * X_core* 
     39    j_1(u)=(\sin x - x \cos x)/x^2 
    2840 
    29 *equat_shell = radius_equat_core + Thick_shell* 
     41To provide easy access to the orientation of the core-shell ellipsoid, 
     42we define the axis of the solid ellipsoid using two angles $\theta$ and $\phi$. 
     43These angles are defined as for 
     44:ref:`cylinder orientation <cylinder-angle-definition>`. 
     45The contrast is defined as SLD(core) - SLD(shell) and SLD(shell) - SLD(solvent). 
    3046 
    31 *polar_shell = radius_equat_core * X_core + Thick_shell * XpolarShell* 
     47Note: It is the users' responsibility to ensure that shell radii are larger than 
     48the core radii, especially if both are polydisperse, in which case the 
     49core_shell_ellipsoid_xt model may be much better. 
    3250 
    33 (where we note that "shell" perhaps confusingly, relates to the outer radius) 
    34 When *X_core < 1* the core is oblate; when *X_core > 1* it is prolate. 
    35 *X_core = 1* is a spherical core. 
    3651 
    37 For a fixed shell thickness *XpolarShell = 1*, to scale the shell thickness 
    38 pro-rata with the radius *XpolarShell = X_core*. 
     52.. note:: 
     53    The 2nd virial coefficient of the solid ellipsoid is calculated based on 
     54    the *radius_a* (= *radius_polar_shell)* and *radius_b (= radius_equat_shell)* values, 
     55    and used as the effective radius for *S(Q)* when $P(Q) * S(Q)$ is applied. 
    3956 
    40 When including an $S(q)$, the radius in $S(q)$ is calculated to be that of 
    41 a sphere with the same 2nd virial coefficient of the outer surface of the 
    42 ellipsoid. This may have some undesirable effects if the aspect ratio of the 
    43 ellipsoid is large (ie, if $X << 1$ or $X >> 1$ ), when the $S(q)$ 
    44 - which assumes spheres - will not in any case be valid. 
     57.. figure:: img/core_shell_ellipsoid_angle_projection.jpg 
    4558 
    46 If SAS data are in absolute units, and the SLDs are correct, then scale should 
    47 be the total volume fraction of the "outer particle". When $S(q)$ is introduced 
    48 this moves to the $S(q)$ volume fraction, and scale should then be 1.0, 
    49 or contain some other units conversion factor (for example, if you have SAXS data). 
     59    The angles for oriented core_shell_ellipsoid. 
     60 
     61Our model uses the form factor calculations implemented in a c-library provided 
     62by the NIST Center for Neutron Research (Kline, 2006). 
    5063 
    5164References 
    5265---------- 
    5366 
    54 R K Heenan, 2015, reparametrised the core_shell_ellipsoid model 
     67M Kotlarchyk, S H Chen, *J. Chem. Phys.*, 79 (1983) 2461 
    5568 
     69S J Berr, *Phys. Chem.*, 91 (1987) 4760 
    5670""" 
    5771 
    5872from numpy import inf, sin, cos, pi 
    5973 
    60 name = "core_shell_ellipsoid_xt" 
     74name = "core_shell_ellipsoid" 
    6175title = "Form factor for an spheroid ellipsoid particle with a core shell structure." 
    6276description = """ 
    63         [core_shell_ellipsoid_xt] Calculates the form factor for an spheroid 
    64         ellipsoid particle with a core_shell structure. 
    65         The form factor is averaged over all possible 
    66         orientations of the ellipsoid such that P(q) 
    67         = scale*<f^2>/Vol + bkg, where f is the 
    68         single particle scattering amplitude. 
    69         [Parameters]: 
    70         radius_equat_core = equatorial radius of core, 
    71         x_core = ratio of core polar/equatorial radii, 
    72         thick_shell = equatorial radius of outer surface, 
    73         x_polar_shell = ratio of polar shell thickness to equatorial shell thickness, 
    74         sld_core = SLD_core 
    75         sld_shell = SLD_shell 
    76         sld_solvent = SLD_solvent 
    77         background = Incoherent bkg 
    78         scale =scale 
    79         Note:It is the users' responsibility to ensure 
    80         that shell radii are larger than core radii. 
    81         oblate: polar radius < equatorial radius 
    82         prolate :  polar radius > equatorial radius - this new model will make this easier 
    83         and polydispersity integrals more logical (as previously the shell could disappear). 
     77    [SpheroidCoreShellModel] Calculates the form factor for an spheroid 
     78    ellipsoid particle with a core_shell structure. 
     79    The form factor is averaged over all possible 
     80    orientations of the ellipsoid such that P(q) 
     81    = scale*<f^2>/Vol + bkg, where f is the 
     82    single particle scattering amplitude. 
     83    [Parameters]: 
     84    radius_equat_core = equatorial radius of core, Rminor_core, 
     85    radius_polar_core = polar radius of core, Rmajor_core, 
     86    radius_equat_shell = equatorial radius of shell, Rminor_outer, 
     87    radius_polar_shell = polar radius of shell, Rmajor_outer, 
     88    sld_core = scattering length density of core, 
     89    sld_shell = scattering length density of shell, 
     90    sld_solvent = scattering length density of solvent, 
     91    background = Incoherent bkg 
     92    scale =scale 
     93    Note:It is the users' responsibility to ensure 
     94    that shell radii are larger than core radii, 
     95    especially if both are polydisperse. 
     96    oblate: polar radius < equatorial radius 
     97    prolate :  polar radius > equatorial radius 
    8498    """ 
    8599category = "shape:ellipsoid" 
    86100 
    87101# pylint: disable=bad-whitespace, line-too-long 
    88 #             ["name", "units", default, [lower, upper], "type", "description"], 
     102#   ["name", "units", default, [lower, upper], "type", "description"], 
    89103parameters = [ 
    90     ["radius_equat_core","Ang",     20,   [0, inf],    "volume",      "Equatorial radius of core"], 
    91     ["x_core",        "None",       3,   [0, inf],    "volume",      "axial ratio of core, X = r_polar/r_equatorial"], 
    92     ["thick_shell",   "Ang",       30,   [0, inf],    "volume",      "thickness of shell at equator"], 
    93     ["x_polar_shell", "",           1,   [0, inf],    "volume",      "ratio of thickness of shell at pole to that at equator"], 
    94     ["sld_core",      "1e-6/Ang^2", 2,   [-inf, inf], "sld",         "Core scattering length density"], 
    95     ["sld_shell",     "1e-6/Ang^2", 1,   [-inf, inf], "sld",         "Shell scattering length density"], 
    96     ["sld_solvent",   "1e-6/Ang^2", 6.3, [-inf, inf], "sld",         "Solvent scattering length density"], 
    97     ["theta",         "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation wrt incoming beam"], 
    98     ["phi",           "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation in the plane of the detector"], 
     104    ["radius_equat_core",  "Ang",      200,   [0, inf],    "volume",      "Equatorial radius of core, r minor core"], 
     105    ["radius_polar_core",  "Ang",       10,   [0, inf],    "volume",      "Polar radius of core, r major core"], 
     106    ["radius_equat_shell", "Ang",      250,   [0, inf],    "volume",      "Equatorial radius of shell, r minor outer"], 
     107    ["radius_polar_shell", "Ang",       30,   [0, inf],    "volume",      "Polar radius of shell, r major outer"], 
     108    ["sld_core",    "1e-6/Ang^2", 2,   [-inf, inf], "sld",         "Core scattering length density"], 
     109    ["sld_shell",   "1e-6/Ang^2", 1,   [-inf, inf], "sld",         "Shell scattering length density"], 
     110    ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "sld",         "Solvent scattering length density"], 
     111    ["theta",       "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation wrt incoming beam"], 
     112    ["phi",         "degrees",    0,   [-inf, inf], "orientation", "Oblate orientation in the plane of the detector"], 
    99113    ] 
    100114# pylint: enable=bad-whitespace, line-too-long 
    101115 
    102 source = ["lib/sph_j1c.c", "lib/gfn.c", "lib/gauss76.c", 
    103           "core_shell_ellipsoid_xt.c"] 
     116source = ["lib/sph_j1c.c", "lib/gfn.c", "lib/gauss76.c", "core_shell_ellipsoid.c"] 
    104117 
    105 def ER(radius_equat_core, x_core, thick_shell, x_polar_shell): 
     118def ER(radius_equat_core, radius_polar_core, radius_equat_shell, radius_polar_shell): 
    106119    """ 
    107120        Returns the effective radius used in the S*P calculation 
    108121    """ 
    109122    from .ellipsoid import ER as ellipsoid_ER 
    110     polar_outer = radius_equat_core*x_core + thick_shell*x_polar_shell 
    111     equat_outer = radius_equat_core + thick_shell 
    112     return ellipsoid_ER(polar_outer, equat_outer) 
     123    return ellipsoid_ER(radius_polar_shell, radius_equat_shell) 
    113124 
    114125 
    115 demo = dict(scale=0.05, background=0.001, 
    116             radius_equat_core=20.0, 
    117             x_core=3.0, 
    118             thick_shell=30.0, 
    119             x_polar_shell=1.0, 
     126demo = dict(scale=1, background=0.001, 
     127            radius_equat_core=200.0, 
     128            radius_polar_core=10.0, 
     129            radius_equat_shell=250.0, 
     130            radius_polar_shell=30.0, 
    120131            sld_core=2.0, 
    121132            sld_shell=1.0, 
    … …  
    130141 
    131142tests = [ 
    132     # Accuracy tests based on content in test/utest_coreshellellipsoidXTmodel.py 
     143    # Accuracy tests based on content in test/utest_other_models.py 
    133144    [{'radius_equat_core': 200.0, 
    134       'x_core': 0.1, 
    135       'thick_shell': 50.0, 
    136       'x_polar_shell': 0.2, 
     145      'radius_polar_core': 20.0, 
     146      'radius_equat_shell': 250.0, 
     147      'radius_polar_shell': 30.0, 
    137148      'sld_core': 2.0, 
    138149      'sld_shell': 1.0, 
    … …  
    143154 
    144155    # Additional tests with larger range of parameters 
    145     [{'background': 0.01}, 0.1, 11.6915], 
     156    [{'background': 0.01}, 0.1, 8.86741], 
    146157 
    147158    [{'radius_equat_core': 20.0, 
    148       'x_core': 200.0, 
    149       'thick_shell': 54.0, 
    150       'x_polar_shell': 3.0, 
     159      'radius_polar_core': 200.0, 
     160      'radius_equat_shell': 54.0, 
     161      'radius_polar_shell': 3.0, 
    151162      'sld_core': 20.0, 
    152163      'sld_shell': 10.0, 
    … …  
    154165      'background': 0.0, 
    155166      'scale': 1.0, 
    156      }, 0.01, 8688.53], 
     167     }, 0.01, 26150.4], 
    157168 
    158     [{'background': 0.001}, (0.4, 0.5), 0.00690673], 
     169    [{'background': 0.001}, (0.4, 0.5), 0.00170471], 
    159170 
    160171    [{'radius_equat_core': 20.0, 
    161       'x_core': 200.0, 
    162       'thick_shell': 54.0, 
    163       'x_polar_shell': 3.0, 
     172      'radius_polar_core': 200.0, 
     173      'radius_equat_shell': 54.0, 
     174      'radius_polar_shell': 3.0, 
    164175      'sld_core': 20.0, 
    165176      'sld_shell': 10.0, 
    … …  
    167178      'background': 0.01, 
    168179      'scale': 0.01, 
    169      }, (qx, qy), 0.0100002], 
     180     }, (qx, qy), 0.105764], 
    170181    ] 
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