Changeset b91bb7c in sasmodels


Ignore:
Timestamp:
Jan 31, 2017 7:44:29 AM (6 years ago)
Author:
wojciech
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
4c8a5b4
Parents:
150fb81 (diff), cdcebf1 (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:

Merged with master

Files:
66 edited
2 moved

Legend:

Unmodified
Added
Removed
  • sasmodels/generate.py

    r7fcdc9f r1e7b0db0  
    139139    square(x) = x*x 
    140140    cube(x) = x*x*x 
    141     sinc(x) = sin(x)/x, with sin(0)/0 -> 1 
     141    sas_sinx_x(x) = sin(x)/x, with sin(0)/0 -> 1 
    142142    all double precision constants must include the decimal point 
    143143    all double declarations may be converted to half, float, or long double 
  • sasmodels/kernel_header.c

    rb7e8b94 rdaeef4c  
    146146inline double square(double x) { return x*x; } 
    147147inline double cube(double x) { return x*x*x; } 
    148 inline double sinc(double x) { return x==0 ? 1.0 : sin(x)/x; } 
     148inline double sas_sinx_x(double x) { return x==0 ? 1.0 : sin(x)/x; } 
    149149 
    150150#if 1 
  • sasmodels/kernel_template.c

    r0d6e865 r1e7b0db0  
    133133inline double square(double x) { return x*x; } 
    134134inline double cube(double x) { return x*x*x; } 
    135 inline double sinc(double x) { return x==0 ? 1.0 : sin(x)/x; } 
     135inline double sas_sinx_x(double x) { return x==0 ? 1.0 : sin(x)/x; } 
    136136 
    137137 
  • sasmodels/models/barbell.c

    r3a48772 r592343f  
    3333        const double t = Gauss76Z[i]*zm + zb; 
    3434        const double radical = 1.0 - t*t; 
    35         const double bj = sas_J1c(qrst*sqrt(radical)); 
     35        const double bj = sas_2J1x_x(qrst*sqrt(radical)); 
    3636        const double Fq = cos(m*t + b) * radical * bj; 
    3737        total += Gauss76Wt[i] * Fq; 
     
    4949{ 
    5050    const double bell_fq = _bell_kernel(q, h, radius_bell, half_length, sin_alpha, cos_alpha); 
    51     const double bj = sas_J1c(q*radius*sin_alpha); 
    52     const double si = sinc(q*half_length*cos_alpha); 
     51    const double bj = sas_2J1x_x(q*radius*sin_alpha); 
     52    const double si = sas_sinx_x(q*half_length*cos_alpha); 
    5353    const double cyl_fq = 2.0*M_PI*radius*radius*half_length*bj*si; 
    5454    const double Aq = bell_fq + cyl_fq; 
  • sasmodels/models/bcc_paracrystal.py

    rb0c4271 r925ad6e  
    128128# pylint: enable=bad-whitespace, line-too-long 
    129129 
    130 source = ["lib/sph_j1c.c", "lib/gauss150.c", "lib/sphere_form.c", "bcc_paracrystal.c"] 
     130source = ["lib/sas_3j1x_x.c", "lib/gauss150.c", "lib/sphere_form.c", "bcc_paracrystal.c"] 
    131131 
    132132# parameters for demo 
  • sasmodels/models/binary_hard_sphere.c

    r4f79d94 r925ad6e  
    5858    qr2 = r2*q; 
    5959 
    60     sc1 = sph_j1c(qr1); 
    61     sc2 = sph_j1c(qr2); 
     60    sc1 = sas_3j1x_x(qr1); 
     61    sc2 = sas_3j1x_x(qr2); 
    6262    b1 = r1*r1*r1*(rho1-rhos)*M_4PI_3*sc1; 
    6363    b2 = r2*r2*r2*(rho2-rhos)*M_4PI_3*sc2; 
  • sasmodels/models/binary_hard_sphere.py

    rb0c4271 r925ad6e  
    108108             ] 
    109109 
    110 source = ["lib/sph_j1c.c", "binary_hard_sphere.c"] 
     110source = ["lib/sas_3j1x_x.c", "binary_hard_sphere.c"] 
    111111 
    112112# parameters for demo and documentation 
  • sasmodels/models/capped_cylinder.c

    r3a48772 r592343f  
    3939        const double t = Gauss76Z[i]*zm + zb; 
    4040        const double radical = 1.0 - t*t; 
    41         const double bj = sas_J1c(qrst*sqrt(radical)); 
     41        const double bj = sas_2J1x_x(qrst*sqrt(radical)); 
    4242        const double Fq = cos(m*t + b) * radical * bj; 
    4343        total += Gauss76Wt[i] * Fq; 
     
    5454{ 
    5555    const double cap_Fq = _cap_kernel(q, h, radius_cap, half_length, sin_alpha, cos_alpha); 
    56     const double bj = sas_J1c(q*radius*sin_alpha); 
    57     const double si = sinc(q*half_length*cos_alpha); 
     56    const double bj = sas_2J1x_x(q*radius*sin_alpha); 
     57    const double si = sas_sinx_x(q*half_length*cos_alpha); 
    5858    const double cyl_Fq = 2.0*M_PI*radius*radius*half_length*bj*si; 
    5959    const double Aq = cap_Fq + cyl_Fq; 
  • sasmodels/models/core_multi_shell.c

    rc5ac2b2 r925ad6e  
    33f_constant(double q, double r, double sld) 
    44{ 
    5   const double bes = sph_j1c(q * r); 
     5  const double bes = sas_3j1x_x(q * r); 
    66  const double vol = M_4PI_3 * cube(r); 
    77  return sld * vol * bes; 
     
    3333  f = 0.; 
    3434  for (int i=0; i<n; i++) { 
    35     f += M_4PI_3 * cube(r) * (sld[i] - last_sld) * sph_j1c(q*r); 
     35    f += M_4PI_3 * cube(r) * (sld[i] - last_sld) * sas_3j1x_x(q*r); 
    3636    last_sld = sld[i]; 
    3737    r += thickness[i]; 
    3838  } 
    39   f += M_4PI_3 * cube(r) * (solvent_sld - last_sld) * sph_j1c(q*r); 
     39  f += M_4PI_3 * cube(r) * (solvent_sld - last_sld) * sas_3j1x_x(q*r); 
    4040  return f * f * 1.0e-4; 
    4141} 
  • sasmodels/models/core_multi_shell.py

    r2d73a53 r925ad6e  
    101101             ] 
    102102 
    103 source = ["lib/sph_j1c.c", "core_multi_shell.c"] 
     103source = ["lib/sas_3j1x_x.c", "core_multi_shell.c"] 
    104104 
    105105def profile(sld_core, radius, sld_solvent, n, sld, thickness): 
  • sasmodels/models/core_shell_bicelle.c

    r5bddd89 r592343f  
    5555    double sinarg2 = qq*(length+facthick)*cos_alpha; 
    5656 
    57     be1 = sas_J1c(besarg1); 
    58     be2 = sas_J1c(besarg2); 
    59     si1 = sinc(sinarg1); 
    60     si2 = sinc(sinarg2); 
     57    be1 = sas_2J1x_x(besarg1); 
     58    be2 = sas_2J1x_x(besarg2); 
     59    si1 = sas_sinx_x(sinarg1); 
     60    si2 = sas_sinx_x(sinarg2); 
    6161 
    6262    const double t = vol1*dr1*si1*be1 + 
  • sasmodels/models/core_shell_bicelle.py

    rfcb33e4 r3b9a526  
    141141# pylint: enable=bad-whitespace, line-too-long 
    142142 
    143 source = ["lib/Si.c", "lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", 
     143source = ["lib/sas_Si.c", "lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", 
    144144          "core_shell_bicelle.c"] 
    145145 
     
    156156            phi=0) 
    157157 
    158 qx, qy = 0.4 * cos(90), 0.5 * sin(0) 
     158#qx, qy = 0.4 * cos(pi/2.0), 0.5 * sin(0) 
  • sasmodels/models/core_shell_bicelle_elliptical.c

    rfcb33e4 r592343f  
    7676        double sinarg1 = qq*halfheight*cos_alpha; 
    7777        double sinarg2 = qq*(halfheight+facthick)*cos_alpha; 
    78         si1 = sinc(sinarg1); 
    79         si2 = sinc(sinarg2); 
     78        si1 = sas_sinx_x(sinarg1); 
     79        si2 = sas_sinx_x(sinarg2); 
    8080        for(int j=0;j<76;j++) { 
    8181            //76 gauss points for the inner integral (WAS 20 points,so this may make unecessarily slow, but playing safe) 
     
    8585            double besarg1 = qq*rr*sin_alpha; 
    8686            double besarg2 = qq*(rr+radthick)*sin_alpha; 
    87             be1 = sas_J1c(besarg1); 
    88             be2 = sas_J1c(besarg2); 
     87            be1 = sas_2J1x_x(besarg1); 
     88            be2 = sas_2J1x_x(besarg2); 
    8989            inner_sum += Gauss76Wt[j] *square(dr1*si1*be1 + 
    9090                                              dr2*si2*be2 + 
     
    129129    // ASSUME the sin_alpha is included in the separate integration over orientation of rod angle 
    130130    const double r = rad*sqrt(square(x_core*cos_nu) + cos_mu*cos_mu); 
    131     const double be1 = sas_J1c(qq*r); 
    132     const double be2 = sas_J1c( qq*(r + radthick ) ); 
    133     const double si1 = sinc( qq*halfheight*cos_val ); 
    134     const double si2 = sinc( qq*(halfheight + facthick)*cos_val ); 
     131    const double be1 = sas_2J1x_x( qq*r ); 
     132    const double be2 = sas_2J1x_x( qq*(r + radthick ) ); 
     133    const double si1 = sas_sinx_x( qq*halfheight*cos_val ); 
     134    const double si2 = sas_sinx_x( qq*(halfheight + facthick)*cos_val ); 
    135135    const double Aq = square( vol1*dr1*si1*be1 + vol2*dr2*si2*be2 +  vol3*dr3*si2*be1); 
    136136    //const double vol = form_volume(radius_minor, r_ratio, length); 
  • sasmodels/models/core_shell_bicelle_elliptical.py

    rfcb33e4 r3b9a526  
    8383 
    8484    Definition of the angles for the oriented core_shell_bicelle_elliptical model. 
     85    Note that *theta* and *phi* are currently defined differently to those for the core_shell_bicelle model. 
    8586 
    8687 
     
    132133# pylint: enable=bad-whitespace, line-too-long 
    133134 
    134 source = ["lib/Si.c", "lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c","core_shell_bicelle_elliptical.c"] 
     135source = ["lib/sas_Si.c", "lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", 
     136          "core_shell_bicelle_elliptical.c"] 
    135137 
    136138demo = dict(scale=1, background=0, 
     
    148150            psi=0) 
    149151 
    150 qx, qy = 0.4 * cos(90), 0.5 * sin(0) 
     152#qx, qy = 0.4 * cos(pi/2.0), 0.5 * sin(0) 
    151153 
    152154tests = [ 
  • sasmodels/models/core_shell_cylinder.c

    r9aa4881 r592343f  
    1111double _cyl(double vd, double besarg, double siarg) 
    1212{ 
    13     return vd * sinc(siarg) * sas_J1c(besarg); 
     13    return vd * sas_sinx_x(siarg) * sas_2J1x_x(besarg); 
    1414} 
    1515 
  • sasmodels/models/core_shell_ellipsoid.py

    rb7e8b94 rdaeef4c  
    137137# pylint: enable=bad-whitespace, line-too-long 
    138138 
    139 source = ["lib/sph_j1c.c", "lib/gfn.c", "lib/gauss76.c", 
     139source = ["lib/sas_3j1x_x.c", "lib/gfn.c", "lib/gauss76.c", 
    140140          "core_shell_ellipsoid.c"] 
    141141 
     
    165165qx = q*cos(pi/6.0) 
    166166qy = q*sin(pi/6.0) 
    167 phi = 0.0 
    168167# 11Jan2017 RKH sorted tests after redefinition of angles 
    169168tests = [ 
     
    193192      'scale': 1.0, 
    194193     }, 0.01, 8688.53], 
    195 # why does it need theta setting here, not globally above? 
    196    [{'background': 0.001, 'theta':90.0}, (0.4, 0.5), 0.00690673], 
     194 
     195   # 2D tests 
     196   [{'background': 0.001, 
     197     'theta': 90.0, 
     198     'phi': 0.0, 
     199     }, (0.4, 0.5), 0.00690673], 
    197200 
    198201   [{'radius_equat_core': 20.0, 
     
    206209      'scale': 0.01, 
    207210      'theta': 90.0, 
     211      'phi': 0.0, 
    208212     }, (qx, qy), 0.01000025], 
    209213    ] 
  • sasmodels/models/core_shell_parallelepiped.c

    r14838a3 r1e7b0db0  
    8787            double sin_uu, cos_uu; 
    8888            SINCOS(M_PI_2*uu, sin_uu, cos_uu); 
    89             const double si1 = sinc(mu_proj * sin_uu * a_scaled); 
    90             const double si2 = sinc(mu_proj * cos_uu); 
    91             const double si3 = sinc(mu_proj * sin_uu * ta); 
    92             const double si4 = sinc(mu_proj * cos_uu * tb); 
     89            const double si1 = sas_sinx_x(mu_proj * sin_uu * a_scaled); 
     90            const double si2 = sas_sinx_x(mu_proj * cos_uu); 
     91            const double si3 = sas_sinx_x(mu_proj * sin_uu * ta); 
     92            const double si4 = sas_sinx_x(mu_proj * cos_uu * tb); 
    9393 
    9494            // Expression in libCylinder.c (neither drC nor Vot are used) 
     
    109109 
    110110        // now sum up the outer integral 
    111         const double si = sinc(mu * c_scaled * sigma); 
     111        const double si = sas_sinx_x(mu * c_scaled * sigma); 
    112112        outer_total += Gauss76Wt[i] * inner_total * si * si; 
    113113    } 
     
    160160    double tc = length_a + 2.0*thick_rim_c; 
    161161    //handle arg=0 separately, as sin(t)/t -> 1 as t->0 
    162     double siA = sinc(0.5*q*length_a*cos_val_a); 
    163     double siB = sinc(0.5*q*length_b*cos_val_b); 
    164     double siC = sinc(0.5*q*length_c*cos_val_c); 
    165     double siAt = sinc(0.5*q*ta*cos_val_a); 
    166     double siBt = sinc(0.5*q*tb*cos_val_b); 
    167     double siCt = sinc(0.5*q*tc*cos_val_c); 
     162    double siA = sas_sinx_x(0.5*q*length_a*cos_val_a); 
     163    double siB = sas_sinx_x(0.5*q*length_b*cos_val_b); 
     164    double siC = sas_sinx_x(0.5*q*length_c*cos_val_c); 
     165    double siAt = sas_sinx_x(0.5*q*ta*cos_val_a); 
     166    double siBt = sas_sinx_x(0.5*q*tb*cos_val_b); 
     167    double siCt = sas_sinx_x(0.5*q*tc*cos_val_c); 
    168168     
    169169 
  • sasmodels/models/core_shell_sphere.py

    r4962519 r925ad6e  
    7575# pylint: enable=bad-whitespace, line-too-long 
    7676 
    77 source = ["lib/sph_j1c.c", "lib/core_shell.c", "core_shell_sphere.c"] 
     77source = ["lib/sas_3j1x_x.c", "lib/core_shell.c", "core_shell_sphere.c"] 
    7878 
    7979demo = dict(scale=1, background=0, radius=60, thickness=10, 
  • sasmodels/models/cylinder.c

    rb829b16 r592343f  
    1818    const double qr = q*radius; 
    1919    const double qh = q*0.5*length;  
    20     return sas_J1c(qr*sn) * sinc(qh*cn); 
     20    return sas_2J1x_x(qr*sn) * sas_sinx_x(qh*cn); 
    2121} 
    2222 
  • sasmodels/models/ellipsoid.c

    r73e08ae r925ad6e  
    1818    const double r = radius_equatorial 
    1919                     * sqrt(1.0 + sin_alpha*sin_alpha*(ratio*ratio - 1.0)); 
    20     const double f = sph_j1c(q*r); 
     20    const double f = sas_3j1x_x(q*r); 
    2121 
    2222    return f*f; 
  • sasmodels/models/ellipsoid.py

    r0d6e865 r925ad6e  
    135135             ] 
    136136 
    137 source = ["lib/sph_j1c.c", "lib/gauss76.c", "ellipsoid.c"] 
     137source = ["lib/sas_3j1x_x.c", "lib/gauss76.c", "ellipsoid.c"] 
    138138 
    139139def ER(radius_polar, radius_equatorial): 
  • sasmodels/models/elliptical_cylinder.c

    r251f54b r592343f  
    3939            const double theta = ( Gauss20Z[j]*(vbj-vaj) + vaj + vbj )/2.0; 
    4040            const double r = sin_val*sqrt(rA - rB*cos(theta)); 
    41             const double be = sas_J1c(q*r); 
     41            const double be = sas_2J1x_x(q*r); 
    4242            inner_sum += Gauss20Wt[j] * be * be; 
    4343        } 
     
    4646 
    4747        //now calculate outer integral 
    48         const double si = sinc(q*0.5*length*cos_val); 
     48        const double si = sas_sinx_x(q*0.5*length*cos_val); 
    4949        outer_sum += Gauss76Wt[i] * inner_sum * si * si; 
    5050    } 
     
    7373    // Given:    radius_major = r_ratio * radius_minor 
    7474    const double r = radius_minor*sqrt(square(r_ratio*cos_nu) + cos_mu*cos_mu); 
    75     const double be = sas_J1c(q*r); 
    76     const double si = sinc(q*0.5*length*cos_val); 
     75    const double be = sas_2J1x_x(q*r); 
     76    const double si = sas_sinx_x(q*0.5*length*cos_val); 
    7777    const double Aq = be * si; 
    7878    const double delrho = sld - solvent_sld; 
  • sasmodels/models/fcc_paracrystal.py

    r0bef47b r925ad6e  
    116116# pylint: enable=bad-whitespace, line-too-long 
    117117 
    118 source = ["lib/sph_j1c.c", "lib/gauss150.c", "lib/sphere_form.c", "fcc_paracrystal.c"] 
     118source = ["lib/sas_3j1x_x.c", "lib/gauss150.c", "lib/sphere_form.c", "fcc_paracrystal.c"] 
    119119 
    120120# parameters for demo 
  • sasmodels/models/flexible_cylinder.c

    r4937980 r592343f  
    1414{ 
    1515    const double contrast = sld - solvent_sld; 
    16     const double cross_section = sas_J1c(q*radius); 
     16    const double cross_section = sas_2J1x_x(q*radius); 
    1717    const double volume = M_PI*radius*radius*length; 
    1818    const double flex = Sk_WR(q, length, kuhn_length); 
  • sasmodels/models/flexible_cylinder_elliptical.c

    r92ce163 r592343f  
    2222        SINCOS(zi, sn, cn); 
    2323        const double arg = q*sqrt(a*a*sn*sn + b*b*cn*cn); 
    24         const double yyy = sas_J1c(arg); 
     24        const double yyy = sas_2J1x_x(arg); 
    2525        sum += Gauss76Wt[i] * yyy * yyy; 
    2626    } 
  • sasmodels/models/fractal.c

    r217590b r925ad6e  
    1414    //calculate P(q) for the spherical subunits 
    1515    const double V = M_4PI_3*cube(radius); 
    16     const double pq = V * square((sld_block-sld_solvent)*sph_j1c(q*radius)); 
     16    const double pq = V * square((sld_block-sld_solvent)*sas_3j1x_x(q*radius)); 
    1717 
    1818    // scale to units cm-1 sr-1 (assuming data on absolute scale) 
  • sasmodels/models/fractal.py

    rfef353f r925ad6e  
    9797# pylint: enable=bad-whitespace, line-too-long 
    9898 
    99 source = ["lib/sph_j1c.c", "lib/sas_gamma.c", "lib/fractal_sq.c", "fractal.c"] 
     99source = ["lib/sas_3j1x_x.c", "lib/sas_gamma.c", "lib/fractal_sq.c", "fractal.c"] 
    100100 
    101101demo = dict(volfraction=0.05, 
  • sasmodels/models/fractal_core_shell.py

    rd6f60c3 r925ad6e  
    9595# pylint: enable=bad-whitespace, line-too-long 
    9696 
    97 source = ["lib/sph_j1c.c", "lib/sas_gamma.c", "lib/core_shell.c", 
     97source = ["lib/sas_3j1x_x.c", "lib/sas_gamma.c", "lib/core_shell.c", 
    9898          "lib/fractal_sq.c", "fractal_core_shell.c"] 
    9999 
  • sasmodels/models/fuzzy_sphere.py

    r3a48772 r925ad6e  
    8181# pylint: enable=bad-whitespace,line-too-long 
    8282 
    83 source = ["lib/sph_j1c.c"] 
     83source = ["lib/sas_3j1x_x.c"] 
    8484 
    8585# No volume normalization despite having a volume parameter 
     
    9191Iq = """ 
    9292    const double qr = q*radius; 
    93     const double bes = sph_j1c(qr); 
     93    const double bes = sas_3j1x_x(qr); 
    9494    const double qf = q*fuzziness; 
    9595    const double fq = bes * (sld - sld_solvent) * form_volume(radius) * exp(-0.5*qf*qf); 
  • sasmodels/models/guinier_porod.py

    ra807206 rcdcebf1  
    44and dimensionality of scattering objects, including asymmetric objects 
    55such as rods or platelets, and shapes intermediate between spheres 
    6 and rods or between rods and platelets. 
     6and rods or between rods and platelets, and overcomes some of the  
     7deficiencies of the (Beaucage) Unified_Power_Rg model (see Hammouda, 2010). 
    78 
    89Definition 
     
    5960--------- 
    6061 
    61 A Guinier, G Fournet, *Small-Angle Scattering of X-Rays*, 
    62 John Wiley and Sons, New York, (1955) 
     62B Hammouda, *A new Guinier-Porod model, J. Appl. Cryst.*, (2010), 43, 716-719 
    6363 
    64 O Glatter, O Kratky, *Small-Angle X-Ray Scattering*, Academic Press (1982) 
    65 Check out Chapter 4 on Data Treatment, pages 155-156. 
     64B Hammouda, *Analysis of the Beaucage model, J. Appl. Cryst.*, (2010), 43, 1474-1478 
     65 
    6666""" 
    6767 
  • sasmodels/models/hollow_cylinder.c

    rf8f0991 r592343f  
    2020{ 
    2121    const double qs = q*sin_val; 
    22     const double lam1 = sas_J1c((radius+thickness)*qs); 
    23     const double lam2 = sas_J1c(radius*qs); 
     22    const double lam1 = sas_2J1x_x((radius+thickness)*qs); 
     23    const double lam2 = sas_2J1x_x(radius*qs); 
    2424    const double gamma_sq = square(radius/(radius+thickness)); 
    25     //Note: lim_{thickness -> 0} psi = J0(radius*qs) 
    26     //Note: lim_{radius -> 0} psi = sas_J1c(thickness*qs) 
     25    //Note: lim_{thickness -> 0} psi = sas_J0(radius*qs) 
     26    //Note: lim_{radius -> 0} psi = sas_2J1x_x(thickness*qs) 
    2727    const double psi = (lam1 - gamma_sq*lam2)/(1.0 - gamma_sq); //SRK 10/19/00 
    28     const double t2 = sinc(0.5*q*length*cos_val); 
     28    const double t2 = sas_sinx_x(0.5*q*length*cos_val); 
    2929    return psi*t2; 
    3030} 
  • sasmodels/models/hollow_rectangular_prism.c

    r6f676fb r1e7b0db0  
    4545        SINCOS(theta, sin_theta, cos_theta); 
    4646 
    47         const double termC1 = sinc(q * c_half * cos(theta)); 
    48         const double termC2 = sinc(q * (c_half-thickness)*cos(theta)); 
     47        const double termC1 = sas_sinx_x(q * c_half * cos(theta)); 
     48        const double termC2 = sas_sinx_x(q * (c_half-thickness)*cos(theta)); 
    4949 
    5050        double inner_sum = 0.0; 
     
    5757            // Amplitude AP from eqn. (13), rewritten to avoid round-off effects when arg=0 
    5858 
    59             const double termA1 = sinc(q * a_half * sin_theta * sin_phi); 
    60             const double termA2 = sinc(q * (a_half-thickness) * sin_theta * sin_phi); 
     59            const double termA1 = sas_sinx_x(q * a_half * sin_theta * sin_phi); 
     60            const double termA2 = sas_sinx_x(q * (a_half-thickness) * sin_theta * sin_phi); 
    6161 
    62             const double termB1 = sinc(q * b_half * sin_theta * cos_phi); 
    63             const double termB2 = sinc(q * (b_half-thickness) * sin_theta * cos_phi); 
     62            const double termB1 = sas_sinx_x(q * b_half * sin_theta * cos_phi); 
     63            const double termB2 = sas_sinx_x(q * (b_half-thickness) * sin_theta * cos_phi); 
    6464 
    6565            const double AP1 = vol_total * termA1 * termB1 * termC1; 
  • sasmodels/models/lib/core_shell.c

    r3a48772 r925ad6e  
    1616    const double core_qr = q * radius; 
    1717    const double core_contrast = core_sld - shell_sld; 
    18     const double core_bes = sph_j1c(core_qr); 
     18    const double core_bes = sas_3j1x_x(core_qr); 
    1919    const double core_volume = M_4PI_3 * cube(radius); 
    2020    double f = core_volume * core_bes * core_contrast; 
     
    2323    const double shell_qr = q * (radius + thickness); 
    2424    const double shell_contrast = shell_sld - solvent_sld; 
    25     const double shell_bes = sph_j1c(shell_qr); 
     25    const double shell_bes = sas_3j1x_x(shell_qr); 
    2626    const double shell_volume = M_4PI_3 * cube(radius + thickness); 
    2727    f += shell_volume * shell_bes * shell_contrast; 
  • sasmodels/models/lib/gfn.c

    r3a48772 r925ad6e  
    1818    // changing to more accurate sph_j1c since the following inexplicably fails on Radeon Nano. 
    1919    //const double siq = (uq == 0.0 ? 1.0 : 3.0*(sin(uq)/uq/uq - cos(uq)/uq)/uq); 
    20     const double siq = sph_j1c(uq); 
     20    const double siq = sas_3j1x_x(uq); 
    2121    const double vc = M_4PI_3*aa*aa*bb; 
    2222    const double gfnc = siq*vc*delpc; 
     
    2626    const double vt = M_4PI_3*trmaj*trmaj*trmin; 
    2727    //const double sit = (ut == 0.0 ? 1.0 : 3.0*(sin(ut)/ut/ut - cos(ut)/ut)/ut); 
    28     const double sit = sph_j1c(ut); 
     28    const double sit = sas_3j1x_x(ut); 
    2929    const double gfnt = sit*vt*delps; 
    3030 
  • sasmodels/models/lib/sas_3j1x_x.c

    rba32cdd r473a9f1  
    77* using double precision that are the source. 
    88*/ 
    9 double sph_j1c(double q); 
     9double sas_3j1x_x(double q); 
    1010 
    1111// The choice of the number of terms in the series and the cutoff value for 
     
    4444#endif 
    4545 
    46 double sph_j1c(double q) 
     46double sas_3j1x_x(double q) 
    4747{ 
    4848    if (q < SPH_J1C_CUTOFF) { 
  • sasmodels/models/lib/sas_J1.c

    rc8902ac r473a9f1  
    217217 
    218218//Finally J1c function that equals 2*J1(x)/x 
    219 double sas_J1c(double x); 
    220 double sas_J1c(double x) 
     219double sas_2J1x_x(double x); 
     220double sas_2J1x_x(double x) 
    221221{ 
    222222    return (x != 0.0 ) ? 2.0*sas_J1(x)/x : 1.0; 
  • sasmodels/models/lib/sas_Si.c

    rf719764 r473a9f1  
    11// integral of sin(x)/x Taylor series approximated to w/i 0.1% 
    2 double Si(double x); 
    3 double Si(double x) 
     2double sas_Si(double x); 
     3double sas_Si(double x) 
    44{ 
    55    if (x >= M_PI*6.2/4.0) { 
  • sasmodels/models/lib/sphere_form.c

    rba32cdd r925ad6e  
    99double sphere_form(double q, double radius, double sld, double solvent_sld) 
    1010{ 
    11     const double fq = sphere_volume(radius) * sph_j1c(q*radius); 
     11    const double fq = sphere_volume(radius) * sas_3j1x_x(q*radius); 
    1212    const double contrast = (sld - solvent_sld); 
    1313    return 1.0e-4*square(contrast * fq); 
  • sasmodels/models/linear_pearls.c

    r4962519 r925ad6e  
    4444 
    4545    //sine functions of a pearl 
    46     double psi = sph_j1c(q * radius); 
     46    double psi = sas_3j1x_x(q * radius); 
    4747 
    4848    // N pearls contribution 
     
    5050    n_contrib = num_pearls; 
    5151    for(int num=1; num<=n_max; num++) { 
    52         n_contrib += (2.0*(num_pearls-num)*sinc(q*separation*num)); 
     52        n_contrib += (2.0*(num_pearls-num)*sas_sinx_x(q*separation*num)); 
    5353    } 
    5454    // form factor for num_pearls 
  • sasmodels/models/linear_pearls.py

    r4962519 r925ad6e  
    6363single = False 
    6464 
    65 source = ["lib/sph_j1c.c", "linear_pearls.c"] 
     65source = ["lib/sas_3j1x_x.c", "linear_pearls.c"] 
    6666 
    6767demo = dict(scale=1.0, background=0.0, 
  • sasmodels/models/mass_fractal.c

    r6d96b66 r925ad6e  
    55{ 
    66    //calculate P(q) 
    7     const double pq = square(sph_j1c(q*radius)); 
     7    const double pq = square(sas_3j1x_x(q*radius)); 
    88 
    99    //calculate S(q) 
  • sasmodels/models/mass_fractal.py

    r6d96b66 r925ad6e  
    8686# pylint: enable=bad-whitespace, line-too-long 
    8787 
    88 source = ["lib/sph_j1c.c", "lib/sas_gamma.c", "mass_fractal.c"] 
     88source = ["lib/sas_3j1x_x.c", "lib/sas_gamma.c", "mass_fractal.c"] 
    8989 
    9090demo = dict(scale=1, background=0, 
  • sasmodels/models/multilayer_vesicle.c

    r3a48772 r925ad6e  
    2020        // layer 1 
    2121        voli = M_4PI_3*ri*ri*ri; 
    22         fval += voli*sldi*sph_j1c(ri*q); 
     22        fval += voli*sldi*sas_3j1x_x(ri*q); 
    2323 
    2424        ri += thick_shell; 
     
    2626        // layer 2 
    2727        voli = M_4PI_3*ri*ri*ri; 
    28         fval -= voli*sldi*sph_j1c(ri*q); 
     28        fval -= voli*sldi*sas_3j1x_x(ri*q); 
    2929 
    3030        //do 2 layers at a time 
  • sasmodels/models/multilayer_vesicle.py

    r041bc75 r925ad6e  
    107107# pylint: enable=bad-whitespace, line-too-long 
    108108 
    109 source = ["lib/sph_j1c.c", "multilayer_vesicle.c"] 
     109source = ["lib/sas_3j1x_x.c", "multilayer_vesicle.c"] 
    110110 
    111111polydispersity = ["radius", "n_pairs"] 
  • sasmodels/models/onion.c

    r9762341 r925ad6e  
    66  const double vol = M_4PI_3 * cube(r); 
    77  const double qr = q * r; 
    8   const double bes = sph_j1c(qr); 
     8  const double bes = sas_3j1x_x(qr); 
    99  const double alpha = A * r/thickness; 
    1010  double result; 
  • sasmodels/models/onion.py

    r9762341 r925ad6e  
    314314# pylint: enable=bad-whitespace, line-too-long 
    315315 
    316 source = ["lib/sph_j1c.c", "onion.c"] 
     316source = ["lib/sas_3j1x_x.c", "onion.c"] 
    317317single = False 
    318318 
  • sasmodels/models/parallelepiped.c

    r14838a3 r1e7b0db0  
    3939            double sin_uu, cos_uu; 
    4040            SINCOS(M_PI_2*uu, sin_uu, cos_uu); 
    41             const double si1 = sinc(mu_proj * sin_uu * a_scaled); 
    42             const double si2 = sinc(mu_proj * cos_uu); 
     41            const double si1 = sas_sinx_x(mu_proj * sin_uu * a_scaled); 
     42            const double si2 = sas_sinx_x(mu_proj * cos_uu); 
    4343            inner_total += Gauss76Wt[j] * square(si1 * si2); 
    4444        } 
    4545        inner_total *= 0.5; 
    4646 
    47         const double si = sinc(mu * c_scaled * sigma); 
     47        const double si = sas_sinx_x(mu * c_scaled * sigma); 
    4848        outer_total += Gauss76Wt[i] * inner_total * si * si; 
    4949    } 
     
    7070    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_val_c, cos_val_b, cos_val_a); 
    7171 
    72     const double siA = sinc(0.5*q*length_a*cos_val_a); 
    73     const double siB = sinc(0.5*q*length_b*cos_val_b); 
    74     const double siC = sinc(0.5*q*length_c*cos_val_c); 
     72    const double siA = sas_sinx_x(0.5*q*length_a*cos_val_a); 
     73    const double siB = sas_sinx_x(0.5*q*length_b*cos_val_b); 
     74    const double siC = sas_sinx_x(0.5*q*length_c*cos_val_c); 
    7575    const double V = form_volume(length_a, length_b, length_c); 
    7676    const double drho = (sld - solvent_sld); 
  • sasmodels/models/pearl_necklace.c

    r2126131 r4b541ac  
    3434    // But there is a 1/(1-sinc) term below which blows up so don't bother 
    3535    const double q_edge = q * edge_sep; 
    36     const double beta = (Si(q*(A_s-radius)) - Si(q*radius)) / q_edge; 
    37     const double gamma = Si(q_edge) / q_edge; 
    38     const double psi = sph_j1c(q*radius); 
     36    const double beta = (sas_Si(q*(A_s-radius)) - sas_Si(q*radius)) / q_edge; 
     37    const double gamma = sas_Si(q_edge) / q_edge; 
     38    const double psi = sas_3j1x_x(q*radius); 
    3939 
    4040    // Precomputed sinc terms 
    41     const double si = sinc(q*A_s); 
     41    const double si = sas_sinx_x(q*A_s); 
    4242    const double omsi = 1.0 - si; 
    4343    const double pow_si = pow(si, num_pearls); 
     
    5454        - 2.0 * (1.0 - pow_si/si)*beta*beta / (omsi*omsi) 
    5555        + 2.0 * num_strings*beta*beta / omsi 
    56         + num_strings * (2.0*gamma - square(sinc(q_edge/2.0))) 
     56        + num_strings * (2.0*gamma - square(sas_sinx_x(q_edge/2.0))) 
    5757        ); 
    5858 
  • sasmodels/models/pearl_necklace.py

    r2126131 r4b541ac  
    9292             ] 
    9393 
    94 source = ["lib/Si.c", "lib/sph_j1c.c", "pearl_necklace.c"] 
     94source = ["lib/sas_Si.c", "lib/sas_3j1x_x.c", "pearl_necklace.c"] 
    9595single = False  # use double precision unless told otherwise 
    9696 
  • sasmodels/models/polymer_micelle.c

    rc3ebc71 r925ad6e  
    3131 
    3232    // Self-correlation term of the core 
    33     const double bes_core = sph_j1c(q*radius_core); 
     33    const double bes_core = sas_3j1x_x(q*radius_core); 
    3434    const double term1 = square(n_aggreg*beta_core*bes_core); 
    3535 
     
    4141    // Interference cross-term between core and chains 
    4242    const double chain_ampl = (qrg2 == 0.0) ? 1.0 : -expm1(-qrg2)/qrg2; 
    43     const double bes_corona = sinc(q*(radius_core + d_penetration * rg)); 
     43    const double bes_corona = sas_sinx_x(q*(radius_core + d_penetration * rg)); 
    4444    const double term3 = 2.0 * n_aggreg * n_aggreg * beta_core * beta_corona * 
    4545                 bes_core * chain_ampl * bes_corona; 
  • sasmodels/models/polymer_micelle.py

    rbba9361 r925ad6e  
    104104single = False 
    105105 
    106 source = ["lib/sph_j1c.c", "polymer_micelle.c"] 
     106source = ["lib/sas_3j1x_x.c", "polymer_micelle.c"] 
    107107 
    108108demo = dict(scale=1, background=0, 
  • sasmodels/models/pringle.c

    r30fbe2e r1e7b0db0  
    9191        SINCOS(psi, sin_psi, cos_psi); 
    9292        double bessel_term = _sum_bessel_orders(radius, alpha, beta, q*sin_psi, q*cos_psi); 
    93         double sinc_term = square(sinc(q * thickness * cos_psi / 2.0)); 
     93        double sinc_term = square(sas_sinx_x(q * thickness * cos_psi / 2.0)); 
    9494        double pringle_kernel = 4.0 * sin_psi * bessel_term * sinc_term; 
    9595        sum += Gauss76Wt[i] * pringle_kernel; 
  • sasmodels/models/raspberry.c

    r2c74c11 r925ad6e  
    5151 
    5252    //Form factors for each particle 
    53     psiL = sph_j1c(q*rL); 
    54     psiS = sph_j1c(q*rS); 
     53    psiL = sas_3j1x_x(q*rL); 
     54    psiS = sas_3j1x_x(q*rS); 
    5555 
    5656    //Cross term between large and small particles 
    57     sfLS = psiL*psiS*sinc(q*(rL+deltaS*rS)); 
     57    sfLS = psiL*psiS*sas_sinx_x(q*(rL+deltaS*rS)); 
    5858    //Cross term between small particles at the surface 
    59     sfSS = psiS*psiS*sinc(q*(rL+deltaS*rS))*sinc(q*(rL+deltaS*rS)); 
     59    sfSS = psiS*psiS*sas_sinx_x(q*(rL+deltaS*rS))*sas_sinx_x(q*(rL+deltaS*rS)); 
    6060 
    6161    //Large sphere form factor term 
  • sasmodels/models/raspberry.py

    r40a87fa r8e68ea0  
    129129            Ref: J. coll. inter. sci. (2010) vol. 343 (1) pp. 36-41.""" 
    130130category = "shape:sphere" 
    131 #single = False 
     131 
    132132 
    133133#             [ "name", "units", default, [lower, upper], "type", "description"], 
     
    152152             ] 
    153153 
    154 source = ["lib/sph_j1c.c", "raspberry.c"] 
     154source = ["lib/sas_3j1x_x.c", "raspberry.c"] 
    155155 
    156156# parameters for demo 
  • sasmodels/models/rectangular_prism.c

    rab2aea8 r1e7b0db0  
    3333        SINCOS(theta, sin_theta, cos_theta); 
    3434 
    35         const double termC = sinc(q * c_half * cos_theta); 
     35        const double termC = sas_sinx_x(q * c_half * cos_theta); 
    3636 
    3737        double inner_sum = 0.0; 
     
    4242 
    4343            // Amplitude AP from eqn. (12), rewritten to avoid round-off effects when arg=0 
    44             const double termA = sinc(q * a_half * sin_theta * sin_phi); 
    45             const double termB = sinc(q * b_half * sin_theta * cos_phi); 
     44            const double termA = sas_sinx_x(q * a_half * sin_theta * sin_phi); 
     45            const double termB = sas_sinx_x(q * b_half * sin_theta * cos_phi); 
    4646            const double AP = termA * termB * termC; 
    4747            inner_sum += Gauss76Wt[j] * AP * AP; 
  • sasmodels/models/sc_paracrystal.py

    r0bef47b r925ad6e  
    133133# pylint: enable=bad-whitespace, line-too-long 
    134134 
    135 source = ["lib/sph_j1c.c", "lib/sphere_form.c", "lib/gauss150.c", "sc_paracrystal.c"] 
     135source = ["lib/sas_3j1x_x.c", "lib/sphere_form.c", "lib/gauss150.c", "sc_paracrystal.c"] 
    136136 
    137137demo = dict(scale=1, background=0, 
  • sasmodels/models/sphere.py

    r7e6bea81 r925ad6e  
    6666             ] 
    6767 
    68 source = ["lib/sph_j1c.c", "lib/sphere_form.c"] 
     68source = ["lib/sas_3j1x_x.c", "lib/sphere_form.c"] 
    6969 
    7070# No volume normalization despite having a volume parameter 
  • sasmodels/models/spherical_sld.c

    r54bcd4a r925ad6e  
    3434    const double qr = q * r; 
    3535    const double qrsq = qr * qr; 
    36     const double bes = sph_j1c(qr); 
     36    const double bes = sas_3j1x_x(qr); 
    3737    double sinqr, cosqr; 
    3838    SINCOS(qr, sinqr, cosqr); 
     
    6060 
    6161        // uniform shell; r=0 => r^3=0 => f=0, so works for core as well. 
    62         f -= M_4PI_3 * cube(r) * sld_l * sph_j1c(q*r); 
     62        f -= M_4PI_3 * cube(r) * sld_l * sas_3j1x_x(q*r); 
    6363        r += thickness[shell]; 
    64         f += M_4PI_3 * cube(r) * sld_l * sph_j1c(q*r); 
     64        f += M_4PI_3 * cube(r) * sld_l * sas_3j1x_x(q*r); 
    6565 
    6666        // iterate over sub_shells in the interface 
     
    9292    } 
    9393    // add in solvent effect 
    94     f -= M_4PI_3 * cube(r) * sld_solvent * sph_j1c(q*r); 
     94    f -= M_4PI_3 * cube(r) * sld_solvent * sas_3j1x_x(q*r); 
    9595 
    9696    const double f2 = f * f * 1.0e-4; 
  • sasmodels/models/spherical_sld.py

    r2d65d51 r925ad6e  
    214214             ] 
    215215# pylint: enable=bad-whitespace, line-too-long 
    216 source = ["lib/polevl.c", "lib/sas_erf.c", "lib/sph_j1c.c", "spherical_sld.c"] 
     216source = ["lib/polevl.c", "lib/sas_erf.c", "lib/sas_3j1x_x.c", "spherical_sld.c"] 
    217217single = False  # TODO: fix low q behaviour 
    218218 
  • sasmodels/models/stacked_disks.c

    r98ce141 r6c3e266  
    5353    const double sinarg2 = q*(halfheight+thick_layer)*cos_alpha; 
    5454 
    55     const double be1 = sas_J1c(besarg1); 
    56     //const double be2 = sas_J1c(besarg2); 
     55    const double be1 = sas_2J1x_x(besarg1); 
     56    //const double be2 = sas_2J1x_x(besarg2); 
    5757    const double be2 = be1; 
    58     const double si1 = sinc(sinarg1); 
    59     const double si2 = sinc(sinarg2); 
     58    const double si1 = sas_sinx_x(sinarg1); 
     59    const double si2 = sas_sinx_x(sinarg2); 
    6060 
    6161    const double dr1 = core_sld - solvent_sld; 
  • sasmodels/models/surface_fractal.c

    rb716cc6 r925ad6e  
    1515{ 
    1616    // calculate P(q) 
    17     const double pq = square(sph_j1c(q*radius)); 
     17    const double pq = square(sas_3j1x_x(q*radius)); 
    1818 
    1919    // calculate S(q) 
  • sasmodels/models/surface_fractal.py

    r5c94f41 r925ad6e  
    7272# pylint: enable=bad-whitespace, line-too-long 
    7373 
    74 source = ["lib/sph_j1c.c", "lib/sas_gamma.c", "surface_fractal.c"] 
     74source = ["lib/sas_3j1x_x.c", "lib/sas_gamma.c", "surface_fractal.c"] 
    7575 
    7676demo = dict(scale=1, background=1e-5, 
  • sasmodels/models/triaxial_ellipsoid.c

    r3a48772 r925ad6e  
    3737            const double ysq = square(Gauss76Z[j]*zm + zb); 
    3838            const double t = q*sqrt(acosx2 + bsinx2*(1.0-ysq) + c2*ysq); 
    39             const double fq = sph_j1c(t); 
     39            const double fq = sas_3j1x_x(t); 
    4040            inner += Gauss76Wt[j] * fq * fq ; 
    4141        } 
     
    6464                          + radius_equat_major*radius_equat_major*cmu*cmu 
    6565                          + radius_polar*radius_polar*calpha*calpha); 
    66     const double fq = sph_j1c(t); 
     66    const double fq = sas_3j1x_x(t); 
    6767    const double s = (sld - sld_solvent) * form_volume(radius_equat_minor, radius_equat_major, radius_polar); 
    6868 
  • sasmodels/models/triaxial_ellipsoid.py

    r416f5c7 r925ad6e  
    104104             ] 
    105105 
    106 source = ["lib/sph_j1c.c", "lib/gauss76.c", "triaxial_ellipsoid.c"] 
     106source = ["lib/sas_3j1x_x.c", "lib/gauss76.c", "triaxial_ellipsoid.c"] 
    107107 
    108108def ER(radius_equat_minor, radius_equat_major, radius_polar): 
  • sasmodels/models/unified_power_Rg.py

    rb3f2a24 rcdcebf1  
    33---------- 
    44 
    5 The Beaucage model employs the empirical multiple level unified 
    6 Exponential/Power-law fit method developed by G. Beaucage. Four functions 
    7 are included so that 1, 2, 3, or 4 levels can be used. In addition a 0 level 
    8 has been added which simply calculates 
     5This model employs the empirical multiple level unified Exponential/Power-law  
     6fit method developed by Beaucage. Four functions are included so that 1, 2, 3,  
     7or 4 levels can be used. In addition a 0 level has been added which simply  
     8calculates 
    99 
    1010.. math:: 
     
    1515many different types of particles, including fractal clusters, random coils 
    1616(Debye equation), ellipsoidal particles, etc. 
     17 
     18The model works best for mass fractal systems characterized by Porod exponents  
     19between 5/3 and 3. It should not be used for surface fractal systems. Hammouda  
     20(2010) has pointed out a deficiency in the way this model handles the  
     21transitioning between the Guinier and Porod regimes and which can create  
     22artefacts that appear as kinks in the fitted model function. 
     23 
     24Also see the Guinier_Porod model. 
    1725 
    1826The empirical fit function is: 
     
    5664 
    5765G Beaucage, *J. Appl. Cryst.*, 29 (1996) 134-146 
     66 
     67B Hammouda, *Analysis of the Beaucage model, J. Appl. Cryst.*, (2010), 43, 1474-1478 
    5868 
    5969""" 
  • sasmodels/models/vesicle.c

    r3a48772 r925ad6e  
    3030    contrast = sld_solvent-sld; 
    3131    vol = M_4PI_3*cube(radius); 
    32     f = vol * sph_j1c(q*radius) * contrast; 
     32    f = vol * sas_3j1x_x(q*radius) * contrast; 
    3333  
    3434    //now the shell. No volume normalization as this is done by the caller 
    3535    contrast = sld-sld_solvent; 
    3636    vol = M_4PI_3*cube(radius+thickness); 
    37     f += vol * sph_j1c(q*(radius+thickness)) * contrast; 
     37    f += vol * sas_3j1x_x(q*(radius+thickness)) * contrast; 
    3838 
    3939    //rescale to [cm-1].  
  • sasmodels/models/vesicle.py

    r3a48772 r925ad6e  
    9494             ] 
    9595 
    96 source = ["lib/sph_j1c.c", "vesicle.c"] 
     96source = ["lib/sas_3j1x_x.c", "vesicle.c"] 
    9797 
    9898def ER(radius, thickness): 
  • doc/ref/gpu/gpu_computations.rst

    r3f5a566 r7e74ed5  
    3131from available OpenCL platforms. 
    3232 
     33OpenCL devices can be set from OpenCL options dialog in Fitting menu or as 
     34enviromental variables. 
     35 
     36**If you don't want to use OpenCL, you can select "No OpenCL" option from** 
     37**GUI dialog or set *SAS_OPENCL=None* in your environment settings** 
     38**This will only use normal programs.** 
     39 
    3340SasView prefers AMD or NVIDIA drivers for GPU, and prefers Intel or 
    3441Apple drivers for CPU. Both GPU and CPU are included on the assumption that CPU  
     
    3946chose to run the model. 
    4047 
    41 **If you don't want to use OpenCL, you can set** *SAS_OPENCL=None* 
    42 **in your environment settings, and it will only use normal programs.** 
    43  
    44 If you want to use one of the other devices, you can run the following 
    45 from the python console in SasView:: 
     48If you want to use one of the other devices, you can select it from OpenCL 
     49options dialog (accessible from Fitting menu) or run the following from 
     50the python console in SasView:: 
    4651 
    4752    import pyopencl as cl 
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