Changeset 646eeaa in sasmodels


Ignore:
Timestamp:
Nov 9, 2018 2:30:26 PM (6 years ago)
Author:
Paul Kienzle <pkienzle@…>
Children:
3b6567f
Parents:
765d025 (diff), cf3d0ce (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 remote-tracking branch 'upstream/beta_approx'

Files:
4 added
46 edited

Legend:

Unmodified
Added
Removed

  • doc/guide/scripting.rst

    rbd7630d r23df833  
    188188python kernel.  Once the kernel is in hand, we can then marshal a set of 
    189189parameters into a :class:`sasmodels.details.CallDetails` object and ship it to 
    190 the kernel using the :func:`sansmodels.direct_model.call_kernel` function.  An 
    191 example should help, *example/cylinder_eval.py*:: 
    192  
    193     from numpy import logspace 
     190the kernel using the :func:`sansmodels.direct_model.call_kernel` function.  To 
     191accesses the underlying $<F(q)>$ and $<F^2(q)>$, use 
     192:func:`sasmodels.direct_model.call_Fq` instead. 
     193 
     194The following example should 
     195help, *example/cylinder_eval.py*:: 
     196 
     197    from numpy import logspace, sqrt 
    194198    from matplotlib import pyplot as plt 
    195199    from sasmodels.core import load_model 
    196     from sasmodels.direct_model import call_kernel 
     200    from sasmodels.direct_model import call_kernel, call_Fq 
    197201 
    198202    model = load_model('cylinder') 
    199203    q = logspace(-3, -1, 200) 
    200204    kernel = model.make_kernel([q]) 
    201     Iq = call_kernel(kernel, dict(radius=200.)) 
    202     plt.loglog(q, Iq) 
     205    pars = {'radius': 200, 'radius_pd': 0.1, 'scale': 2} 
     206    Iq = call_kernel(kernel, pars) 
     207    F, Fsq, Reff, V, Vratio = call_Fq(kernel, pars) 
     208 
     209    plt.loglog(q, Iq, label='2 I(q)') 
     210    plt.loglog(q, F**2/V, label='<F(q)>^2/V') 
     211    plt.loglog(q, Fsq/V, label='<F^2(q)>/V') 
     212    plt.xlabel('q (1/A)') 
     213    plt.ylabel('I(q) (1/cm)') 
     214    plt.title('Cylinder with radius 200.') 
     215    plt.legend() 
    203216    plt.show() 
    204217 
    205 On windows, this can be called from the cmd prompt using sasview as:: 
     218.. figure:: direct_call.png 
     219 
     220    Comparison between $I(q)$, $<F(q)>$ and $<F^2(q)>$ for cylinder model. 
     221 
     222This compares $I(q)$ with $<F(q)>$ and $<F^2(q)>$ for a cylinder 
     223with *radius=200 +/- 20* and *scale=2*. Note that *call_Fq* does not 
     224include scale and background, nor does it normalize by the average volume. 
     225The definition of $F = \rho V \hat F$ scaled by the contrast and 
     226volume, compared to the canonical cylinder $\hat F$, with $\hat F(0) = 1$. 
     227Integrating over polydispersity and orientation, the returned values are 
     228$\sum_{r,w\in N(r_o, r_o/10)} \sum_\theta w F(q,r_o,\theta)\sin\theta$ and 
     229$\sum_{r,w\in N(r_o, r_o/10)} \sum_\theta w F^2(q,r_o,\theta)\sin\theta$. 
     230 
     231On windows, this example can be called from the cmd prompt using sasview as 
     232as the python interpreter:: 
    206233 
    207234    SasViewCom example/cylinder_eval.py 

  • example/cylinder_eval.py

    r2e66ef5 r23df833  
    33""" 
    44 
    5 from numpy import logspace 
     5from numpy import logspace, sqrt 
    66from matplotlib import pyplot as plt 
    77from sasmodels.core import load_model 
    8 from sasmodels.direct_model import call_kernel 
     8from sasmodels.direct_model import call_kernel, call_Fq 
    99 
    1010model = load_model('cylinder') 
    1111q = logspace(-3, -1, 200) 
    1212kernel = model.make_kernel([q]) 
    13 Iq = call_kernel(kernel, dict(radius=200.)) 
    14 plt.loglog(q, Iq) 
     13pars = {'radius': 200, 'radius_pd': 0.1, 'scale': 2} 
     14Iq = call_kernel(kernel, pars) 
     15F, Fsq, Reff, V, Vratio = call_Fq(kernel, pars) 
     16plt.loglog(q, Iq, label='2 I(q)') 
     17plt.loglog(q, F**2/V, label='<F(q)>^2/V') 
     18plt.loglog(q, Fsq/V, label='<F^2(q)>/V') 
    1519plt.xlabel('q (1/A)') 
    16 plt.ylabel('I(q)') 
     20plt.ylabel('I(q) (1/cm)') 
    1721plt.title('Cylinder with radius 200.') 
     22plt.legend() 
    1823plt.show() 

  • sasmodels/direct_model.py

    r304c775 r5024a56  
    3232from .details import make_kernel_args, dispersion_mesh 
    3333from .modelinfo import DEFAULT_BACKGROUND 
     34from .product import RADIUS_MODE_ID 
    3435 
    3536# pylint: disable=unused-import 
    … …  
    6768    # type: (Kernel, ParameterSet, float, bool) -> np.ndarray 
    6869    """ 
    69     Like :func:`call_kernel`, but returning F, F^2, R_eff, V, V_form/V_shell. 
    70     """ 
    71     R_eff_type = int(pars.pop('radius_effective_type', 1.0)) 
     70    Like :func:`call_kernel`, but returning F, F^2, R_eff, V_shell, V_form/V_shell. 
     71 
     72    For solid objects V_shell is equal to V_form and the volume ratio is 1. 
     73 
     74    Use parameter *radius_effective_mode* to select the effective radius 
     75    calculation. 
     76    """ 
     77    R_eff_type = int(pars.pop(RADIUS_MODE_ID, 1.0)) 
    7278    mesh = get_mesh(calculator.info, pars, dim=calculator.dim, mono=mono) 
    7379    #print("pars", list(zip(*mesh))[0]) 
    … …  
    7682    return calculator.Fq(call_details, values, cutoff, is_magnetic, R_eff_type) 
    7783 
    78 def call_profile(model_info, **pars): 
    79     # type: (ModelInfo, ...) -> Tuple[np.ndarray, np.ndarray, Tuple[str, str]] 
     84def call_profile(model_info, pars=None): 
     85    # type: (ModelInfo, ParameterSet) -> Tuple[np.ndarray, np.ndarray, Tuple[str, str]] 
    8086    """ 
    8187    Returns the profile *x, y, (xlabel, ylabel)* representing the model. 
    8288    """ 
     89    if pars is None: 
     90        pars = {} 
    8391    args = {} 
    8492    for p in model_info.parameters.kernel_parameters: 
    … …  
    377385        Generate a plottable profile. 
    378386        """ 
    379         return call_profile(self.model.info, **pars) 
     387        return call_profile(self.model.info, pars) 
    380388 
    381389def main(): 

  • sasmodels/model_test.py

    raa8c6e0 r5024a56  
    386386    for par in sorted(pars.keys()): 
    387387        # special handling of R_eff mode, which is not a usual parameter 
    388         if par == 'radius_effective_type': 
     388        if par == product.RADIUS_MODE_ID: 
    389389            continue 
    390390        parts = par.split('_pd') 

  • sasmodels/models/barbell.c

    rd42dd4a r99658f6  
    6363 
    6464static double 
     65radius_from_excluded_volume(double radius_bell, double radius, double length) 
     66{ 
     67    const double hdist = sqrt(square(radius_bell) - square(radius)); 
     68    const double length_tot = length + 2.0*(hdist+ radius); 
     69    return 0.5*cbrt(0.75*radius_bell*(2.0*radius_bell*length_tot + (radius_bell + length_tot)*(M_PI*radius_bell + length_tot))); 
     70} 
     71 
     72static double 
    6573radius_from_volume(double radius_bell, double radius, double length) 
    6674{ 
    … …  
    8189    switch (mode) { 
    8290    default: 
    83     case 1: // equivalent sphere 
     91    case 1: // equivalent cylinder excluded volume 
     92        return radius_from_excluded_volume(radius_bell, radius , length); 
     93    case 2: // equivalent volume sphere 
    8494        return radius_from_volume(radius_bell, radius , length); 
    85     case 2: // radius 
     95    case 3: // radius 
    8696        return radius; 
    87     case 3: // half length 
     97    case 4: // half length 
    8898        return 0.5*length; 
    89     case 4: // half total length 
     99    case 5: // half total length 
    90100        return radius_from_totallength(radius_bell,radius,length); 
    91101    } 

  • sasmodels/models/barbell.py

    ree60aa7 r99658f6  
    7979.. [#] H Kaya and N R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda 
    8080   and errata) 
     81L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    8182 
    8283Authorship and Verification 
    … …  
    116117 
    117118source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "barbell.c"] 
    118 have_Fq = True 
     119have_Fq = True  
    119120effective_radius_type = [ 
    120     "equivalent sphere", "radius", "half length", "half total length", 
     121    "equivalent cylinder excluded volume","equivalent volume sphere", "radius", "half length", "half total length", 
    121122    ] 
    122123 

  • sasmodels/models/capped_cylinder.c

    rd42dd4a r99658f6  
    8585 
    8686static double 
     87radius_from_excluded_volume(double radius, double radius_cap, double length) 
     88{ 
     89    const double hc = radius_cap - sqrt(radius_cap*radius_cap - radius*radius); 
     90    const double length_tot = length + 2.0*hc; 
     91    return 0.5*cbrt(0.75*radius*(2.0*radius*length_tot + (radius + length_tot)*(M_PI*radius + length_tot))); 
     92} 
     93 
     94static double 
    8795radius_from_volume(double radius, double radius_cap, double length) 
    8896{ 
    … …  
    103111    switch (mode) { 
    104112    default: 
    105     case 1: // equivalent sphere 
     113    case 1: // equivalent cylinder excluded volume 
     114        return radius_from_excluded_volume(radius, radius_cap, length); 
     115    case 2: // equivalent volume sphere 
    106116        return radius_from_volume(radius, radius_cap, length); 
    107     case 2: // radius 
     117    case 3: // radius 
    108118        return radius; 
    109     case 3: // half length 
     119    case 4: // half length 
    110120        return 0.5*length; 
    111     case 4: // half total length 
     121    case 5: // half total length 
    112122        return radius_from_totallength(radius, radius_cap,length); 
    113123    } 

  • sasmodels/models/capped_cylinder.py

    ree60aa7 r99658f6  
    8282.. [#] H Kaya and N-R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda 
    8383   and errata) 
     84L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    8485 
    8586Authorship and Verification 
    … …  
    138139have_Fq = True 
    139140effective_radius_type = [ 
    140     "equivalent sphere", "radius", "half length", "half total length", 
     141    "equivalent cylinder excluded volume", "equivalent volume sphere", "radius", "half length", "half total length", 
    141142    ] 
    142143 

  • sasmodels/models/core_shell_bicelle.c

    rd42dd4a r99658f6  
    3737 
    3838static double 
     39radius_from_excluded_volume(double radius, double thick_rim, double thick_face, double length) 
     40{ 
     41    const double radius_tot = radius + thick_rim; 
     42    const double length_tot = length + 2.0*thick_face; 
     43    return 0.5*cbrt(0.75*radius_tot*(2.0*radius_tot*length_tot + (radius_tot + length_tot)*(M_PI*radius_tot + length_tot))); 
     44} 
     45 
     46static double 
    3947radius_from_volume(double radius, double thick_rim, double thick_face, double length) 
    4048{ 
    … …  
    5664    switch (mode) { 
    5765    default: 
    58     case 1: // equivalent sphere 
     66    case 1: // equivalent cylinder excluded volume 
     67        return radius_from_excluded_volume(radius, thick_rim, thick_face, length); 
     68    case 2: // equivalent sphere 
    5969        return radius_from_volume(radius, thick_rim, thick_face, length); 
    60     case 2: // outer rim radius 
     70    case 3: // outer rim radius 
    6171        return radius + thick_rim; 
    62     case 3: // half outer thickness 
     72    case 4: // half outer thickness 
    6373        return 0.5*length + thick_face; 
    64     case 4: // half diagonal 
     74    case 5: // half diagonal 
    6575        return radius_from_diagonal(radius,thick_rim,thick_face,length); 
    6676    } 

  • sasmodels/models/core_shell_bicelle.py

    ree60aa7 r99658f6  
    8989   from Proquest <http://search.proquest.com/docview/304915826?accountid 
    9090   =26379>`_ 
     91    
     92   L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    9193 
    9294Authorship and Verification 
    … …  
    156158have_Fq = True 
    157159effective_radius_type = [ 
    158     "equivalent sphere", "outer rim radius", 
     160    "excluded volume","equivalent volume sphere", "outer rim radius", 
    159161    "half outer thickness", "half diagonal", 
    160162    ] 

  • sasmodels/models/core_shell_bicelle_elliptical.c

    rd42dd4a r99658f6  
    88{ 
    99    return M_PI*(r_minor+thick_rim)*(r_minor*x_core+thick_rim)*(length+2.0*thick_face); 
     10} 
     11 
     12static double 
     13radius_from_excluded_volume(double r_minor, double x_core, double thick_rim, double thick_face, double length) 
     14{ 
     15    const double r_equiv     = sqrt((r_minor + thick_rim)*(r_minor*x_core + thick_rim)); 
     16    const double length_tot  = length + 2.0*thick_face; 
     17    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length_tot + (r_equiv + length_tot)*(M_PI*r_equiv + length_tot))); 
    1018} 
    1119 
    … …  
    3139    switch (mode) { 
    3240    default: 
    33     case 1: // equivalent sphere 
     41    case 1: // equivalent cylinder excluded volume 
     42        return radius_from_excluded_volume(r_minor, x_core, thick_rim, thick_face, length); 
     43    case 2: // equivalent volume sphere 
    3444        return radius_from_volume(r_minor, x_core, thick_rim, thick_face, length); 
    35     case 2: // outer rim average radius 
     45    case 3: // outer rim average radius 
    3646        return 0.5*r_minor*(1.0 + x_core) + thick_rim; 
    37     case 3: // outer rim min radius 
     47    case 4: // outer rim min radius 
    3848        return (x_core < 1.0 ? x_core*r_minor+thick_rim : r_minor+thick_rim); 
    39     case 4: // outer max radius 
     49    case 5: // outer max radius 
    4050        return (x_core > 1.0 ? x_core*r_minor+thick_rim : r_minor+thick_rim); 
    41     case 5: // half outer thickness 
     51    case 6: // half outer thickness 
    4252        return 0.5*length + thick_face; 
    43     case 6: // half diagonal 
     53    case 7: // half diagonal 
    4454        return radius_from_diagonal(r_minor,x_core,thick_rim,thick_face,length); 
    4555    } 

  • sasmodels/models/core_shell_bicelle_elliptical.py

    r304c775 r99658f6  
    100100 
    101101.. [#] 
     102L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    102103 
    103104Authorship and Verification 
    … …  
    148149have_Fq = True 
    149150effective_radius_type = [ 
    150     "equivalent sphere", "outer rim average radius", "outer rim min radius", 
     151    "equivalent cylinder excluded volume", "equivalent volume sphere", "outer rim average radius", "outer rim min radius", 
    151152    "outer max radius", "half outer thickness", "half diagonal", 
    152153    ] 

  • sasmodels/models/core_shell_bicelle_elliptical_belt_rough.c

    rd42dd4a r99658f6  
    99    return M_PI*(  (r_minor + thick_rim)*(r_minor*x_core + thick_rim)* length + 
    1010                 square(r_minor)*x_core*2.0*thick_face  ); 
     11} 
     12 
     13static double 
     14radius_from_excluded_volume(double r_minor, double x_core, double thick_rim, double thick_face, double length) 
     15{ 
     16    const double r_equiv     = sqrt((r_minor + thick_rim)*(r_minor*x_core + thick_rim)); 
     17    const double length_tot  = length + 2.0*thick_face; 
     18    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length_tot + (r_equiv + length_tot)*(M_PI*r_equiv + length_tot))); 
    1119} 
    1220 
    … …  
    3240    switch (mode) { 
    3341    default: 
    34     case 1: // equivalent sphere 
     42    case 1: // equivalent cylinder excluded volume 
     43        return radius_from_excluded_volume(r_minor, x_core, thick_rim, thick_face, length); 
     44    case 2: // equivalent sphere 
    3545        return radius_from_volume(r_minor, x_core, thick_rim, thick_face, length); 
    36     case 2: // outer rim average radius 
     46    case 3: // outer rim average radius 
    3747        return 0.5*r_minor*(1.0 + x_core) + thick_rim; 
    38     case 3: // outer rim min radius 
     48    case 4: // outer rim min radius 
    3949        return (x_core < 1.0 ? x_core*r_minor+thick_rim : r_minor+thick_rim); 
    40     case 4: // outer max radius 
     50    case 5: // outer max radius 
    4151        return (x_core > 1.0 ? x_core*r_minor+thick_rim : r_minor+thick_rim); 
    42     case 5: // half outer thickness 
     52    case 6: // half outer thickness 
    4353        return 0.5*length + thick_face; 
    44     case 6: // half diagonal (this ignores the missing "corners", so may give unexpected answer if thick_face 
     54    case 7: // half diagonal (this ignores the missing "corners", so may give unexpected answer if thick_face 
    4555            //  or thick_rim is extremely large) 
    4656        return radius_from_diagonal(r_minor,x_core,thick_rim,thick_face,length); 

  • sasmodels/models/core_shell_bicelle_elliptical_belt_rough.py

    r304c775 r99658f6  
    112112 
    113113.. [#] 
     114L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    114115 
    115116Authorship and Verification 
    … …  
    161162have_Fq = True 
    162163effective_radius_type = [ 
    163     "equivalent sphere", "outer rim average radius", "outer rim min radius", 
     164    "equivalent cylinder excluded volume", "equivalent volume sphere", "outer rim average radius", "outer rim min radius", 
    164165    "outer max radius", "half outer thickness", "half diagonal", 
    165166    ] 

  • sasmodels/models/core_shell_cylinder.c

    rd42dd4a r99658f6  
    1111{ 
    1212    return M_PI*square(radius+thickness)*(length+2.0*thickness); 
     13} 
     14 
     15static double 
     16radius_from_excluded_volume(double radius, double thickness, double length) 
     17{ 
     18    const double radius_tot = radius + thickness; 
     19    const double length_tot = length + 2.0*thickness; 
     20    return 0.5*cbrt(0.75*radius_tot*(2.0*radius_tot*length_tot + (radius_tot + length_tot)*(M_PI*radius_tot + length_tot))); 
    1321} 
    1422 
    … …  
    3341    switch (mode) { 
    3442    default: 
    35     case 1: // equivalent sphere 
     43    case 1: //cylinder excluded volume 
     44        return radius_from_excluded_volume(radius, thickness, length); 
     45    case 2: // equivalent volume sphere 
    3646        return radius_from_volume(radius, thickness, length); 
    37     case 2: // outer radius 
     47    case 3: // outer radius 
    3848        return radius + thickness; 
    39     case 3: // half outer length 
     49    case 4: // half outer length 
    4050        return 0.5*length + thickness; 
    41     case 4: // half min outer length 
     51    case 5: // half min outer length 
    4252        return (radius < 0.5*length ? radius + thickness : 0.5*length + thickness); 
    43     case 5: // half max outer length 
     53    case 6: // half max outer length 
    4454        return (radius > 0.5*length ? radius + thickness : 0.5*length + thickness); 
    45     case 6: // half outer diagonal 
     55    case 7: // half outer diagonal 
    4656        return radius_from_diagonal(radius,thickness,length); 
    4757    } 

  • sasmodels/models/core_shell_cylinder.py

    ree60aa7 r99658f6  
    7070   1445-1452 
    7171.. [#kline] S R Kline, *J Appl. Cryst.*, 39 (2006) 895 
     72L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    7273 
    7374Authorship and Verification 
    … …  
    133134have_Fq = True 
    134135effective_radius_type = [ 
    135     "equivalent sphere", "outer radius", "half outer length", 
    136     "half min outer dimension", "half max outer dimension", 
    137     "half outer diagonal", 
     136    "excluded volume", "equivalent volume sphere", "outer radius", "half outer length", 
     137    "half min outer dimension", "half max outer dimension", "half outer diagonal", 
    138138    ] 
    139139 

  • sasmodels/models/core_shell_ellipsoid.c

    rd42dd4a r99658f6  
    7575    switch (mode) { 
    7676    default: 
    77     case 1: // equivalent sphere 
     77    case 1: // average outer curvature 
     78        return radius_from_curvature(radius_equat_core, x_core, thick_shell, x_polar_shell); 
     79    case 2: // equivalent volume sphere 
    7880        return radius_from_volume(radius_equat_core, x_core, thick_shell, x_polar_shell); 
    79     case 2: // average outer curvature 
    80         return radius_from_curvature(radius_equat_core, x_core, thick_shell, x_polar_shell); 
    8181    case 3: // min outer radius 
    8282        return (radius_polar_tot < radius_equat_tot ? radius_polar_tot : radius_equat_tot); 

  • sasmodels/models/core_shell_ellipsoid.py

    ree60aa7 r99658f6  
    147147have_Fq = True 
    148148effective_radius_type = [ 
    149     "equivalent sphere", "average outer curvature", 
     149    "average outer curvature", "equivalent volume sphere",      
    150150    "min outer radius", "max outer radius", 
    151151    ] 

  • sasmodels/models/core_shell_parallelepiped.c

    rd42dd4a r99658f6  
    2828 
    2929static double 
     30radius_from_excluded_volume(double length_a, double length_b, double length_c, 
     31                   double thick_rim_a, double thick_rim_b, double thick_rim_c) 
     32{ 
     33    double r_equiv, length; 
     34    double lengths[3] = {length_a+thick_rim_a, length_b+thick_rim_b, length_c+thick_rim_c}; 
     35    double lengthmax = fmax(lengths[0],fmax(lengths[1],lengths[2])); 
     36    double length_1 = lengthmax; 
     37    double length_2 = lengthmax; 
     38    double length_3 = lengthmax; 
     39 
     40    for(int ilen=0; ilen<3; ilen++) { 
     41        if (lengths[ilen] < length_1) { 
     42            length_2 = length_1; 
     43            length_1 = lengths[ilen]; 
     44            } else { 
     45                if (lengths[ilen] < length_2) { 
     46                        length_2 = lengths[ilen]; 
     47                } 
     48            } 
     49    } 
     50    if(length_2-length_1 > length_3-length_2) { 
     51        r_equiv = sqrt(length_2*length_3/M_PI); 
     52        length  = length_1; 
     53    } else  { 
     54        r_equiv = sqrt(length_1*length_2/M_PI); 
     55        length  = length_3; 
     56    } 
     57 
     58    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length + (r_equiv + length)*(M_PI*r_equiv + length))); 
     59} 
     60 
     61static double 
    3062radius_from_volume(double length_a, double length_b, double length_c, 
    3163                   double thick_rim_a, double thick_rim_b, double thick_rim_c) 
    … …  
    4880    switch (mode) { 
    4981    default: 
    50     case 1: // equivalent sphere 
     82    case 1: // equivalent cylinder excluded volume 
     83        return radius_from_excluded_volume(length_a, length_b, length_c, thick_rim_a, thick_rim_b, thick_rim_c); 
     84    case 2: // equivalent volume sphere 
    5185        return radius_from_volume(length_a, length_b, length_c, thick_rim_a, thick_rim_b, thick_rim_c); 
    52     case 2: // half outer length a 
     86    case 3: // half outer length a 
    5387        return 0.5 * length_a + thick_rim_a; 
    54     case 3: // half outer length b 
     88    case 4: // half outer length b 
    5589        return 0.5 * length_b + thick_rim_b; 
    56     case 4: // half outer length c 
     90    case 5: // half outer length c 
    5791        return 0.5 * length_c + thick_rim_c; 
    58     case 5: // equivalent circular cross-section 
     92    case 6: // equivalent circular cross-section 
    5993        return radius_from_crosssection(length_a, length_b, thick_rim_a, thick_rim_b); 
    60     case 6: // half outer ab diagonal 
     94    case 7: // half outer ab diagonal 
    6195        return 0.5*sqrt(square(length_a+ 2.0*thick_rim_a) + square(length_b+ 2.0*thick_rim_b)); 
    62     case 7: // half outer diagonal 
     96    case 8: // half outer diagonal 
    6397        return 0.5*sqrt(square(length_a+ 2.0*thick_rim_a) + square(length_b+ 2.0*thick_rim_b) + square(length_c+ 2.0*thick_rim_c)); 
    6498    } 

  • sasmodels/models/core_shell_parallelepiped.py

    ree60aa7 r99658f6  
    173173   from Proquest <http://search.proquest.com/docview/304915826?accountid 
    174174   =26379>`_ 
     175L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    175176 
    176177Authorship and Verification 
    … …  
    228229have_Fq = True 
    229230effective_radius_type = [ 
    230     "equivalent sphere", 
     231    "equivalent cylinder excluded volume",  
     232    "equivalent volume sphere", 
    231233    "half outer length_a", "half outer length_b", "half outer length_c", 
    232234    "equivalent circular cross-section", 

  • sasmodels/models/cylinder.c

    rd42dd4a r99658f6  
    1111{ 
    1212    return sas_2J1x_x(qab*radius) * sas_sinx_x(qc*0.5*length); 
     13} 
     14 
     15static double 
     16radius_from_excluded_volume(double radius, double length) 
     17{ 
     18    return 0.5*cbrt(0.75*radius*(2.0*radius*length + (radius + length)*(M_PI*radius + length))); 
    1319} 
    1420 
    … …  
    3137    default: 
    3238    case 1: 
     39        return radius_from_excluded_volume(radius, length); 
     40    case 2: 
    3341        return radius_from_volume(radius, length); 
    34     case 2: 
     42    case 3: 
    3543        return radius; 
    36     case 3: 
     44    case 4: 
    3745        return 0.5*length; 
    38     case 4: 
     46    case 5: 
    3947        return (radius < 0.5*length ? radius : 0.5*length); 
    40     case 5: 
     48    case 6: 
    4149        return (radius > 0.5*length ? radius : 0.5*length); 
    42     case 6: 
     50    case 7: 
    4351        return radius_from_diagonal(radius,length); 
    4452    } 

  • sasmodels/models/cylinder.py

    r304c775 r99658f6  
    9898J. S. Pedersen, Adv. Colloid Interface Sci. 70, 171-210 (1997). 
    9999G. Fournet, Bull. Soc. Fr. Mineral. Cristallogr. 74, 39-113 (1951). 
     100L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    100101""" 
    101102 
    … …  
    140141have_Fq = True 
    141142effective_radius_type = [ 
    142     "equivalent sphere", "radius", 
     143    "excluded volume", "equivalent volume sphere", "radius", 
    143144    "half length", "half min dimension", "half max dimension", "half diagonal", 
    144145    ] 
    … …  
    185186radius, length = parameters[2][2], parameters[3][2] 
    186187tests.extend([ 
    187     ({'radius_effective_type': 0}, 0.1, None, None, 0., pi*radius**2*length, 1.0), 
    188     ({'radius_effective_type': 1}, 0.1, None, None, (0.75*radius**2*length)**(1./3.), None, None), 
    189     ({'radius_effective_type': 2}, 0.1, None, None, radius, None, None), 
    190     ({'radius_effective_type': 3}, 0.1, None, None, length/2., None, None), 
    191     ({'radius_effective_type': 4}, 0.1, None, None, min(radius, length/2.), None, None), 
    192     ({'radius_effective_type': 5}, 0.1, None, None, max(radius, length/2.), None, None), 
    193     ({'radius_effective_type': 6}, 0.1, None, None, np.sqrt(4*radius**2 + length**2)/2., None, None), 
     188    ({'radius_effective_mode': 0}, 0.1, None, None, 0., pi*radius**2*length, 1.0),    
     189    ({'radius_effective_mode': 1}, 0.1, None, None, 0.5*(0.75*radius*(2.0*radius*length + (radius + length)*(pi*radius + length)))**(1./3.), None, None),     
     190    ({'radius_effective_mode': 2}, 0.1, None, None, (0.75*radius**2*length)**(1./3.), None, None), 
     191    ({'radius_effective_mode': 3}, 0.1, None, None, radius, None, None), 
     192    ({'radius_effective_mode': 4}, 0.1, None, None, length/2., None, None), 
     193    ({'radius_effective_mode': 5}, 0.1, None, None, min(radius, length/2.), None, None), 
     194    ({'radius_effective_mode': 6}, 0.1, None, None, max(radius, length/2.), None, None), 
     195    ({'radius_effective_mode': 7}, 0.1, None, None, np.sqrt(4*radius**2 + length**2)/2., None, None), 
    194196]) 
    195197del radius, length 

  • sasmodels/models/ellipsoid.c

    rd42dd4a r99658f6  
    3636    switch (mode) { 
    3737    default: 
    38     case 1: // equivalent sphere 
     38    case 1: // average curvature 
     39        return radius_from_curvature(radius_polar, radius_equatorial); 
     40    case 2: // equivalent volume sphere 
    3941        return radius_from_volume(radius_polar, radius_equatorial); 
    40     case 2: // average curvature 
    41         return radius_from_curvature(radius_polar, radius_equatorial); 
    4242    case 3: // min radius 
    4343        return (radius_polar < radius_equatorial ? radius_polar : radius_equatorial); 

  • sasmodels/models/ellipsoid.py

    ree60aa7 r99658f6  
    170170have_Fq = True 
    171171effective_radius_type = [ 
    172     "equivalent sphere", "average curvature", "min radius", "max radius", 
     172    "average curvature", "equivalent volume sphere", "min radius", "max radius", 
    173173    ] 
    174174 

  • sasmodels/models/elliptical_cylinder.c

    rd42dd4a r99658f6  
    33{ 
    44    return M_PI * radius_minor * radius_minor * r_ratio * length; 
     5} 
     6 
     7static double 
     8radius_from_excluded_volume(double radius_minor, double r_ratio, double length) 
     9{ 
     10    const double r_equiv = sqrt(radius_minor*radius_minor*r_ratio); 
     11    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length + (r_equiv + length)*(M_PI*r_equiv + length))); 
    512} 
    613 
    … …  
    3845    switch (mode) { 
    3946    default: 
    40     case 1: // equivalent sphere 
     47    case 1: // equivalent cylinder excluded volume 
     48        return radius_from_excluded_volume(radius_minor, r_ratio, length); 
     49    case 2: // equivalent volume sphere 
    4150        return radius_from_volume(radius_minor, r_ratio, length); 
    42     case 2: // average radius 
     51    case 3: // average radius 
    4352        return 0.5*radius_minor*(1.0 + r_ratio); 
    44     case 3: // min radius 
     53    case 4: // min radius 
    4554        return (r_ratio > 1.0 ? radius_minor : r_ratio*radius_minor); 
    46     case 4: // max radius 
     55    case 5: // max radius 
    4756        return (r_ratio < 1.0 ? radius_minor : r_ratio*radius_minor); 
    48     case 5: // equivalent circular cross-section 
     57    case 6: // equivalent circular cross-section 
    4958        return sqrt(radius_minor*radius_minor*r_ratio); 
    50     case 6: // half length 
     59    case 7: // half length 
    5160        return 0.5*length; 
    52     case 7: // half min dimension 
     61    case 8: // half min dimension 
    5362        return radius_from_min_dimension(radius_minor,r_ratio,0.5*length); 
    54     case 8: // half max dimension 
     63    case 9: // half max dimension 
    5564        return radius_from_max_dimension(radius_minor,r_ratio,0.5*length); 
    56     case 9: // half diagonal 
     65    case 10: // half diagonal 
    5766        return radius_from_diagonal(radius_minor,r_ratio,length); 
    5867    } 

  • sasmodels/models/elliptical_cylinder.py

    ree60aa7 r99658f6  
    8888L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and 
    8989Neutron Scattering*, Plenum, New York, (1987) [see table 3.4] 
     90L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    9091 
    9192Authorship and Verification 
    … …  
    124125have_Fq = True 
    125126effective_radius_type = [ 
    126     "equivalent sphere", "average radius", "min radius", "max radius", 
     127    "equivalent cylinder excluded volume", "equivalent volume sphere", "average radius", "min radius", "max radius", 
    127128    "equivalent circular cross-section", 
    128129    "half length", "half min dimension", "half max dimension", "half diagonal", 

  • sasmodels/models/hollow_cylinder.c

    rd42dd4a r99658f6  
    1111{ 
    1212    return M_PI*length*square(radius+thickness); 
     13} 
     14 
     15static double 
     16radius_from_excluded_volume(double radius, double thickness, double length) 
     17{ 
     18    const double radius_tot = radius + thickness; 
     19    return 0.5*cbrt(0.75*radius_tot*(2.0*radius_tot*length + (radius_tot + length)*(M_PI*radius_tot + length))); 
    1320} 
    1421 
    … …  
    3138    switch (mode) { 
    3239    default: 
    33     case 1: // equivalent sphere 
     40    case 1: // excluded volume 
     41        return radius_from_excluded_volume(radius, thickness, length); 
     42    case 2: // equivalent volume sphere 
    3443        return radius_from_volume(radius, thickness, length); 
    35     case 2: // outer radius 
     44    case 3: // outer radius 
    3645        return radius + thickness; 
    37     case 3: // half length 
     46    case 4: // half length 
    3847        return 0.5*length; 
    39     case 4: // half outer min dimension 
     48    case 5: // half outer min dimension 
    4049        return (radius + thickness < 0.5*length ? radius + thickness : 0.5*length); 
    41     case 5: // half outer max dimension 
     50    case 6: // half outer max dimension 
    4251        return (radius + thickness > 0.5*length ? radius + thickness : 0.5*length); 
    43     case 6: // half outer diagonal 
     52    case 7: // half outer diagonal 
    4453        return radius_from_diagonal(radius,thickness,length); 
    4554    } 

  • sasmodels/models/hollow_cylinder.py

    r304c775 r99658f6  
    6060.. [#] L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and 
    6161   Neutron Scattering*, Plenum Press, New York, (1987) 
     62L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    6263 
    6364Authorship and Verification 
    … …  
    102103have_Fq = True 
    103104effective_radius_type = [ 
    104     "equivalent sphere", "outer radius", "half length", 
     105    "excluded volume", "equivalent outer volume sphere", "outer radius", "half length", 
    105106    "half outer min dimension", "half outer max dimension", 
    106107    "half outer diagonal", 
    … …  
    140141    [{}, 0.00005, 1764.926], 
    141142    [{}, 0.1, None, None, 
    142      (3./4*(radius+thickness)**2*length)**(1./3),  # R_eff from volume 
     143     0.5*(0.75*(radius+thickness)*(2.0*(radius+thickness)*length + ((radius+thickness) + length)*(pi*(radius+thickness) + length)))**(1./3.),  # R_eff from excluded volume 
    143144     pi*((radius+thickness)**2-radius**2)*length,  # shell volume 
    144145     (radius+thickness)**2/((radius+thickness)**2 - radius**2), # form:shell ratio 

  • sasmodels/models/hollow_rectangular_prism.c

    rd42dd4a r99658f6  
    2222 
    2323static double 
     24radius_from_excluded_volume(double length_a, double b2a_ratio, double c2a_ratio) 
     25{ 
     26    const double r_equiv = sqrt(length_a*length_a*b2a_ratio/M_PI); 
     27    const double length_c = length_a*c2a_ratio; 
     28    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length_c + (r_equiv + length_c)*(M_PI*r_equiv + length_c))); 
     29} 
     30 
     31static double 
    2432effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio, double thickness) 
    2533// NOTE length_a is external dimension! 
    … …  
    2735    switch (mode) { 
    2836    default: 
    29     case 1: // equivalent sphere 
     37    case 1: // equivalent cylinder excluded volume 
     38        return radius_from_excluded_volume(length_a, b2a_ratio, c2a_ratio); 
     39    case 2: // equivalent outer volume sphere 
    3040        return cbrt(cube(length_a)*b2a_ratio*c2a_ratio/M_4PI_3); 
    31     case 2: // half length_a 
     41    case 3: // half length_a 
    3242        return 0.5 * length_a; 
    33     case 3: // half length_b 
     43    case 4: // half length_b 
    3444        return 0.5 * length_a*b2a_ratio; 
    35     case 4: // half length_c 
     45    case 5: // half length_c 
    3646        return 0.5 * length_a*c2a_ratio; 
    37     case 5: // equivalent outer circular cross-section 
     47    case 6: // equivalent outer circular cross-section 
    3848        return length_a*sqrt(b2a_ratio/M_PI); 
    39     case 6: // half ab diagonal 
     49    case 7: // half ab diagonal 
    4050        return 0.5*sqrt(square(length_a) * (1.0 + square(b2a_ratio))); 
    41     case 7: // half diagonal 
     51    case 8: // half diagonal 
    4252        return 0.5*sqrt(square(length_a) * (1.0 + square(b2a_ratio) + square(c2a_ratio))); 
    4353    } 

  • sasmodels/models/hollow_rectangular_prism.py

    ree60aa7 r99658f6  
    9898 
    9999.. [#Nayuk2012] R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854 
     100L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    100101 
    101102 
    … …  
    150151have_Fq = True 
    151152effective_radius_type = [ 
    152     "equivalent sphere", "half length_a", "half length_b", "half length_c", 
     153    "equivalent cylinder excluded volume", "equivalent outer volume sphere",  
     154    "half length_a", "half length_b", "half length_c", 
    153155    "equivalent outer circular cross-section", 
    154156    "half ab diagonal", "half diagonal", 

  • sasmodels/models/hollow_rectangular_prism_thin_walls.c

    rd42dd4a r99658f6  
    1818 
    1919static double 
     20radius_from_excluded_volume(double length_a, double b2a_ratio, double c2a_ratio) 
     21{ 
     22    const double r_equiv = sqrt(length_a*length_a*b2a_ratio/M_PI); 
     23    const double length_c = length_a*c2a_ratio; 
     24    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length_c + (r_equiv + length_c)*(M_PI*r_equiv + length_c))); 
     25} 
     26 
     27static double 
    2028effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio) 
    2129{ 
    2230    switch (mode) { 
    2331    default: 
    24     case 1: // equivalent sphere 
     32    case 1: // equivalent cylinder excluded volume 
     33        return radius_from_excluded_volume(length_a, b2a_ratio, c2a_ratio); 
     34    case 2: // equivalent outer volume sphere 
    2535        return cbrt(cube(length_a)*b2a_ratio*c2a_ratio/M_4PI_3); 
    26     case 2: // half length_a 
     36    case 3: // half length_a 
    2737        return 0.5 * length_a; 
    28     case 3: // half length_b 
     38    case 4: // half length_b 
    2939        return 0.5 * length_a*b2a_ratio; 
    30     case 4: // half length_c 
     40    case 5: // half length_c 
    3141        return 0.5 * length_a*c2a_ratio; 
    32     case 5: // equivalent outer circular cross-section 
     42    case 6: // equivalent outer circular cross-section 
    3343        return length_a*sqrt(b2a_ratio/M_PI); 
    34     case 6: // half ab diagonal 
     44    case 7: // half ab diagonal 
    3545        return 0.5*sqrt(square(length_a) * (1.0 + square(b2a_ratio))); 
    36     case 7: // half diagonal 
     46    case 8: // half diagonal 
    3747        return 0.5*sqrt(square(length_a) * (1.0 + square(b2a_ratio) + square(c2a_ratio))); 
    3848    } 

  • sasmodels/models/hollow_rectangular_prism_thin_walls.py

    ree60aa7 r99658f6  
    7272 
    7373.. [#Nayuk2012] R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854 
     74L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    7475 
    7576 
    … …  
    110111have_Fq = True 
    111112effective_radius_type = [ 
    112     "equivalent sphere", "half length_a", "half length_b", "half length_c", 
     113    "equivalent cylinder excluded volume", "equivalent outer volume sphere",  
     114    "half length_a", "half length_b", "half length_c", 
    113115    "equivalent outer circular cross-section", 
    114116    "half ab diagonal", "half diagonal", 

  • sasmodels/models/parallelepiped.c

    rd42dd4a r99658f6  
    66 
    77static double 
     8radius_from_excluded_volume(double length_a, double length_b, double length_c) 
     9{ 
     10    double r_equiv, length; 
     11    double lengths[3] = {length_a, length_b, length_c}; 
     12    double lengthmax = fmax(lengths[0],fmax(lengths[1],lengths[2])); 
     13    double length_1 = lengthmax; 
     14    double length_2 = lengthmax; 
     15    double length_3 = lengthmax; 
     16 
     17    for(int ilen=0; ilen<3; ilen++) { 
     18        if (lengths[ilen] < length_1) { 
     19            length_2 = length_1; 
     20            length_1 = lengths[ilen]; 
     21            } else { 
     22                if (lengths[ilen] < length_2) { 
     23                        length_2 = lengths[ilen]; 
     24                } 
     25            } 
     26    } 
     27    if(length_2-length_1 > length_3-length_2) { 
     28        r_equiv = sqrt(length_2*length_3/M_PI); 
     29        length  = length_1; 
     30    } else  { 
     31        r_equiv = sqrt(length_1*length_2/M_PI); 
     32        length  = length_3; 
     33    } 
     34 
     35    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length + (r_equiv + length)*(M_PI*r_equiv + length))); 
     36} 
     37 
     38static double 
    839effective_radius(int mode, double length_a, double length_b, double length_c) 
    940{ 
    1041    switch (mode) { 
    1142    default: 
    12     case 1: // equivalent sphere 
     43    case 1: // equivalent cylinder excluded volume 
     44        return radius_from_excluded_volume(length_a,length_b,length_c); 
     45    case 2: // equivalent volume sphere 
    1346        return cbrt(length_a*length_b*length_c/M_4PI_3); 
    14     case 2: // half length_a 
     47    case 3: // half length_a 
    1548        return 0.5 * length_a; 
    16     case 3: // half length_b 
     49    case 4: // half length_b 
    1750        return 0.5 * length_b; 
    18     case 4: // half length_c 
     51    case 5: // half length_c 
    1952        return 0.5 * length_c; 
    20     case 5: // equivalent circular cross-section 
     53    case 6: // equivalent circular cross-section 
    2154        return sqrt(length_a*length_b/M_PI); 
    22     case 6: // half ab diagonal 
     55    case 7: // half ab diagonal 
    2356        return 0.5*sqrt(length_a*length_a + length_b*length_b); 
    24     case 7: // half diagonal 
     57    case 8: // half diagonal 
    2558        return 0.5*sqrt(length_a*length_a + length_b*length_b + length_c*length_c); 
    2659    } 

  • sasmodels/models/parallelepiped.py

    ree60aa7 r99658f6  
    180180   14 (1961) 185-211 
    181181.. [#] R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854 
     182L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    182183 
    183184Authorship and Verification 
    … …  
    232233have_Fq = True 
    233234effective_radius_type = [ 
    234     "equivalent sphere", "half length_a", "half length_b", "half length_c", 
     235    "equivalent cylinder excluded volume", "equivalent volume sphere",  
     236    "half length_a", "half length_b", "half length_c", 
    235237    "equivalent circular cross-section", "half ab diagonal", "half diagonal", 
    236238    ] 

  • sasmodels/models/pearl_necklace.c

    r3f853beb r99658f6  
    6767} 
    6868 
    69 double form_volume(double radius, double edge_sep, 
    70     double thick_string, double fp_num_pearls) 
     69double form_volume(double radius, double edge_sep, double thick_string, double fp_num_pearls) 
    7170{ 
    7271    const int num_pearls = (int)(fp_num_pearls + 0.5); //Force integer number of pearls 
    … …  
    7776 
    7877    return volume; 
     78} 
     79 
     80static double 
     81radius_from_volume(double radius, double edge_sep, double thick_string, double fp_num_pearls) 
     82{ 
     83    const int num_pearls = (int) fp_num_pearls +0.5; 
     84    const double vol_tot = form_volume(radius, edge_sep, thick_string, fp_num_pearls); 
     85    return cbrt(vol_tot/M_4PI_3); 
     86} 
     87 
     88static double 
     89effective_radius(int mode, double radius, double edge_sep, double thick_string, double fp_num_pearls) 
     90{ 
     91    switch (mode) { 
     92    default: 
     93    case 1: 
     94        return radius_from_volume(radius, edge_sep, thick_string, fp_num_pearls); 
     95    } 
    7996} 
    8097 

  • sasmodels/models/pearl_necklace.py

    r2cc8aa2 rcf3d0ce  
    5353R Schweins and K Huber, *Particle Scattering Factor of Pearl Necklace Chains*, 
    5454*Macromol. Symp.* 211 (2004) 25-42 2004 
     55L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
    5556""" 
    5657 
    … …  
    9596source = ["lib/sas_Si.c", "lib/sas_3j1x_x.c", "pearl_necklace.c"] 
    9697single = False  # use double precision unless told otherwise 
    97  
    98 def volume(radius, edge_sep, thick_string, num_pearls): 
    99     """ 
    100     Calculates the total particle volume of the necklace. 
    101     Redundant with form_volume. 
    102     """ 
    103     num_pearls = int(num_pearls + 0.5) 
    104     number_of_strings = num_pearls - 1.0 
    105     string_vol = edge_sep * pi * pow((thick_string / 2.0), 2.0) 
    106     pearl_vol = 4.0 /3.0 * pi * pow(radius, 3.0) 
    107     total_vol = number_of_strings * string_vol 
    108     total_vol += num_pearls * pearl_vol 
    109     return total_vol 
    110  
    111 def ER(radius, edge_sep, thick_string, num_pearls): 
    112     """ 
    113     Calculation for effective radius. 
    114     """ 
    115     num_pearls = int(num_pearls + 0.5) 
    116     tot_vol = volume(radius, edge_sep, thick_string, num_pearls) 
    117     rad_out = (tot_vol/(4.0/3.0*pi)) ** (1./3.) 
    118     return rad_out 
    119  
     98effective_radius_type = [ 
     99    "equivalent volume sphere",  
     100    ] 
     101     
    120102def random(): 
    121103    radius = 10**np.random.uniform(1, 3) # 1 - 1000 

  • sasmodels/models/pringle.c

    rd42dd4a r99658f6  
    105105 
    106106static double 
     107radius_from_excluded_volume(double radius, double thickness) 
     108{ 
     109    return 0.5*cbrt(0.75*radius*(2.0*radius*thickness + (radius + thickness)*(M_PI*radius + thickness))); 
     110} 
     111 
     112static double 
    107113effective_radius(int mode, double radius, double thickness, double alpha, double beta) 
    108114{ 
    109115    switch (mode) { 
    110116    default: 
    111     case 1: // equivalent sphere 
     117    case 1: // equivalent cylinder excluded volume 
     118        return radius_from_excluded_volume(radius, thickness); 
     119    case 2: // equivalent volume sphere 
    112120        return cbrt(M_PI*radius*radius*thickness/M_4PI_3); 
    113     case 2: // radius 
     121    case 3: // radius 
    114122        return radius; 
    115123    } 

  • sasmodels/models/pringle.py

    ree60aa7 r99658f6  
    4242Karen Edler, Universtiy of Bath, Private Communication. 2012. 
    4343Derivation by Stefan Alexandru Rautu. 
     44L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949). 
    4445 
    4546* **Author:** Andrew Jackson **Date:** 2008 
    … …  
    7475source = ["lib/polevl.c", "lib/sas_J0.c", "lib/sas_J1.c", 
    7576          "lib/sas_JN.c", "lib/gauss76.c", "pringle.c"] 
    76 effective_radius_type = ["equivalent sphere", "radius"] 
     77effective_radius_type = ["equivalent cylinder excluded volume", "equivalent volume sphere", "radius"] 
    7778 
    7879def random(): 

  • sasmodels/models/rectangular_prism.c

    rd42dd4a r99658f6  
    66 
    77static double 
     8radius_from_excluded_volume(double length_a, double b2a_ratio, double c2a_ratio) 
     9{ 
     10    double const r_equiv   = sqrt(length_a*length_a*b2a_ratio/M_PI); 
     11    double const length_c  = c2a_ratio*length_a; 
     12    return 0.5*cbrt(0.75*r_equiv*(2.0*r_equiv*length_c + (r_equiv + length_c)*(M_PI*r_equiv + length_c))); 
     13} 
     14 
     15static double 
    816effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio) 
    917{ 
    1018    switch (mode) { 
    1119    default: 
    12     case 1: // equivalent sphere 
     20    case 1: // equivalent cylinder excluded volume 
     21        return radius_from_excluded_volume(length_a,b2a_ratio,c2a_ratio); 
     22    case 2: // equivalent volume sphere 
    1323        return cbrt(cube(length_a)*b2a_ratio*c2a_ratio/M_4PI_3); 
    14     case 2: // half length_a 
     24    case 3: // half length_a 
    1525        return 0.5 * length_a; 
    16     case 3: // half length_b 
     26    case 4: // half length_b 
    1727        return 0.5 * length_a*b2a_ratio; 
    18     case 4: // half length_c 
     28    case 5: // half length_c 
    1929        return 0.5 * length_a*c2a_ratio; 
    20     case 5: // equivalent circular cross-section 
     30    case 6: // equivalent circular cross-section 
    2131        return length_a*sqrt(b2a_ratio/M_PI); 
    22     case 6: // half ab diagonal 
     32    case 7: // half ab diagonal 
    2333        return 0.5*sqrt(square(length_a) * (1.0 + square(b2a_ratio))); 
    24     case 7: // half diagonal 
     34    case 8: // half diagonal 
    2535        return 0.5*sqrt(square(length_a) * (1.0 + square(b2a_ratio) + square(c2a_ratio))); 
    2636    } 

  • sasmodels/models/rectangular_prism.py

    ree60aa7 r99658f6  
    9999 
    100100R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854 
     101 
     102L. Onsager, Ann. New York Acad. Sci. 51, 627-659 (1949).  
     103 
    101104""" 
    102105 
    … …  
    137140have_Fq = True 
    138141effective_radius_type = [ 
    139     "equivalent sphere", "half length_a", "half length_b", "half length_c", 
     142    "equivalent cylinder excluded volume", "equivalent volume sphere",  
     143    "half length_a", "half length_b", "half length_c", 
    140144    "equivalent circular cross-section", "half ab diagonal", "half diagonal", 
    141145    ] 

  • sasmodels/models/triaxial_ellipsoid.c

    rd42dd4a r99658f6  
    55{ 
    66    return M_4PI_3*radius_equat_minor*radius_equat_major*radius_polar; 
     7} 
     8 
     9static double 
     10radius_from_curvature(double radius_equat_minor, double radius_equat_major, double radius_polar) 
     11{ 
     12    // Trivial cases 
     13    if (radius_equat_minor == radius_equat_major == radius_polar) return radius_polar; 
     14    if (radius_equat_minor * radius_equat_major * radius_polar == 0.)  return 0.; 
     15 
     16 
     17    double r_equat_equiv, r_polar_equiv; 
     18    double radii[3] = {radius_equat_minor, radius_equat_major, radius_polar}; 
     19    double radmax = fmax(radii[0],fmax(radii[1],radii[2])); 
     20 
     21    double radius_1 = radmax; 
     22    double radius_2 = radmax; 
     23    double radius_3 = radmax; 
     24 
     25    for(int irad=0; irad<3; irad++) { 
     26        if (radii[irad] < radius_1) { 
     27            radius_3 = radius_2; 
     28            radius_2 = radius_1; 
     29            radius_1 = radii[irad]; 
     30            } else { 
     31                if (radii[irad] < radius_2) { 
     32                        radius_2 = radii[irad]; 
     33                } 
     34            } 
     35    } 
     36    if(radius_2-radius_1 > radius_3-radius_2) { 
     37        r_equat_equiv = sqrt(radius_2*radius_3); 
     38        r_polar_equiv = radius_1; 
     39    } else  { 
     40        r_equat_equiv = sqrt(radius_1*radius_2); 
     41        r_polar_equiv = radius_3; 
     42    } 
     43 
     44    // see equation (26) in A.Isihara, J.Chem.Phys. 18(1950)1446-1449 
     45    const double ratio = (r_polar_equiv < r_equat_equiv 
     46                          ? r_polar_equiv / r_equat_equiv 
     47                          : r_equat_equiv / r_polar_equiv); 
     48    const double e1 = sqrt(1.0 - ratio*ratio); 
     49    const double b1 = 1.0 + asin(e1) / (e1 * ratio); 
     50    const double bL = (1.0 + e1) / (1.0 - e1); 
     51    const double b2 = 1.0 + 0.5 * ratio * ratio / e1 * log(bL); 
     52    const double delta = 0.75 * b1 * b2; 
     53    const double ddd = 2.0 * (delta + 1.0) * r_polar_equiv * r_equat_equiv * r_equat_equiv; 
     54    return 0.5 * cbrt(ddd); 
    755} 
    856 
    … …  
    3280    switch (mode) { 
    3381    default: 
    34     case 1: // equivalent sphere 
     82    case 1: // equivalent biaxial ellipsoid average curvature 
     83        return radius_from_curvature(radius_equat_minor,radius_equat_major, radius_polar); 
     84    case 2: // equivalent volume sphere 
    3585        return radius_from_volume(radius_equat_minor,radius_equat_major, radius_polar); 
    36     case 2: // min radius 
     86    case 3: // min radius 
    3787        return radius_from_min_dimension(radius_equat_minor,radius_equat_major, radius_polar); 
    38     case 3: // max radius 
     88    case 4: // max radius 
    3989        return radius_from_max_dimension(radius_equat_minor,radius_equat_major, radius_polar); 
    4090    } 

  • sasmodels/models/triaxial_ellipsoid.py

    ree60aa7 r99658f6  
    158158source = ["lib/sas_3j1x_x.c", "lib/gauss76.c", "triaxial_ellipsoid.c"] 
    159159have_Fq = True 
    160 effective_radius_type = ["equivalent sphere", "min radius", "max radius"] 
     160effective_radius_type = ["equivalent biaxial ellipsoid average curvature", "equivalent volume sphere", "min radius", "max radius"] 
    161161 
    162162def random(): 

  • sasmodels/product.py

    r39a06c9 r99658f6  
    3737#] 
    3838 
     39STRUCTURE_MODE_ID = "structure_factor_mode" 
     40RADIUS_MODE_ID = "radius_effective_mode" 
    3941RADIUS_ID = "radius_effective" 
    4042VOLFRAC_ID = "volfraction" 
    … …  
    4345    if p_info.have_Fq: 
    4446        par = parse_parameter( 
    45                 "structure_factor_mode", 
     47                STRUCTURE_MODE_ID, 
    4648                "", 
    4749                0, 
    … …  
    5254    if p_info.effective_radius_type is not None: 
    5355        par = parse_parameter( 
    54                 "radius_effective_mode", 
     56                RADIUS_MODE_ID, 
    5557                "", 
    56                 0, 
     58                1, 
    5759                [["unconstrained"] + p_info.effective_radius_type], 
    5860                "", 

  • sasmodels/sasview_model.py

    raa8c6e0 r5024a56  
    859859    P = _make_standard_model('cylinder')() 
    860860    model = MultiplicationModel(P, S) 
    861     model.setParam('radius_effective_mode', 1.0) 
     861    model.setParam(product.RADIUS_MODE_ID, 1.0) 
    862862    value = model.evalDistribution([0.1, 0.1]) 
    863863    if np.isnan(value): 

  • .gitignore

    re9ed2de r6ceca44  
    88*.so 
    99*.obj 
     10*.o 
    1011/doc/_build/ 
    1112/doc/api/ 
    … …  
    1920/.pydevproject 
    2021/.idea 
     22.vscode 
    2123/sasmodels.egg-info/ 
    2224/example/Fit_*/ 

  • sasmodels/modelinfo.py

    r39a06c9 r765d025  
    1212from os.path import abspath, basename, splitext 
    1313import inspect 
     14import logging 
    1415 
    1516import numpy as np  # type: ignore 
     17 
     18from . import autoc 
    1619 
    1720# Optional typing 
    … …  
    3235    TestCondition = Tuple[ParameterSetUser, TestInput, TestValue] 
    3336# pylint: enable=unused-import 
     37 
     38logger = logging.getLogger(__name__) 
    3439 
    3540# If MAX_PD changes, need to change the loop macros in kernel_iq.c 
    … …  
    810815    info.profile = getattr(kernel_module, 'profile', None) # type: ignore 
    811816    info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore 
    812     # Default single and opencl to True for C models.  Python models have callable Iq. 
    813     info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq)) 
    814     info.single = getattr(kernel_module, 'single', not callable(info.Iq)) 
    815817    info.random = getattr(kernel_module, 'random', None) 
    816818 
    … …  
    821823    info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore 
    822824 
     825    info.lineno = {} 
     826    _find_source_lines(info, kernel_module) 
     827    if getattr(kernel_module, 'py2c', False): 
     828        try: 
     829            warnings = autoc.convert(info, kernel_module) 
     830        except Exception as exc: 
     831            warnings = [str(exc)] 
     832        if warnings: 
     833            warnings.append("while converting %s from C to python"%name) 
     834            if len(warnings) > 2: 
     835                warnings = "\n".join(warnings) 
     836            else: 
     837                warnings = " ".join(warnings) 
     838            logger.warn(warnings) 
     839 
     840    # Default single and opencl to True for C models.  Python models have callable Iq. 
     841    # Needs to come after autoc.convert since the Iq symbol may have been 
     842    # converted from python to C 
     843    info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq)) 
     844    info.single = getattr(kernel_module, 'single', not callable(info.Iq)) 
     845 
    823846    if callable(info.Iq) and parameters.has_2d: 
    824847        raise ValueError("oriented python models not supported") 
    825848 
    826     info.lineno = {} 
    827     _find_source_lines(info, kernel_module) 
    828849    return info 
    829850 
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