Changeset d86967b in sasmodels


Ignore:
Timestamp:
Mar 22, 2017 11:46:49 PM (8 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
28d3067
Parents:
68dd6a9 (diff), 1aa7990 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'master' into ticket-890

Files:
17 edited

Legend:

Unmodified
Added
Removed

  • sasmodels/resolution.py

    rb397165 rb32caab  
    1717 
    1818MINIMUM_RESOLUTION = 1e-8 
    19  
    20  
    21 # When extrapolating to -q, what is the minimum positive q relative to q_min 
    22 # that we wish to calculate? 
    23 MIN_Q_SCALE_FOR_NEGATIVE_Q_EXTRAPOLATION = 0.01 
     19MINIMUM_ABSOLUTE_Q = 0.02  # relative to the minimum q in the data 
    2420 
    2521class Resolution(object): 
    … …  
    8278        self.q_calc = (pinhole_extend_q(q, q_width, nsigma=nsigma) 
    8379                       if q_calc is None else np.sort(q_calc)) 
     80 
     81        # Protect against models which are not defined for very low q.  Limit 
     82        # the smallest q value evaluated (in absolute) to 0.02*min 
     83        cutoff = MINIMUM_ABSOLUTE_Q*np.min(self.q) 
     84        self.q_calc = self.q_calc[abs(self.q_calc) >= cutoff] 
     85 
     86        # Build weight matrix from calculated q values 
    8487        self.weight_matrix = pinhole_resolution(self.q_calc, self.q, 
    8588                                np.maximum(q_width, MINIMUM_RESOLUTION)) 
     89        self.q_calc = abs(self.q_calc) 
    8690 
    8791    def apply(self, theory): 
    … …  
    123127        self.q_calc = slit_extend_q(q, qx_width, qy_width) \ 
    124128            if q_calc is None else np.sort(q_calc) 
     129 
     130        # Protect against models which are not defined for very low q.  Limit 
     131        # the smallest q value evaluated (in absolute) to 0.02*min 
     132        cutoff = MINIMUM_ABSOLUTE_Q*np.min(self.q) 
     133        self.q_calc = self.q_calc[abs(self.q_calc) >= cutoff] 
     134 
     135        # Build weight matrix from calculated q values 
    125136        self.weight_matrix = \ 
    126137            slit_resolution(self.q_calc, self.q, qx_width, qy_width) 
     138        self.q_calc = abs(self.q_calc) 
    127139 
    128140    def apply(self, theory): 
    … …  
    153165    # neither trapezoid nor Simpson's rule improved the accuracy. 
    154166    edges = bin_edges(q_calc) 
    155     edges[edges < 0.0] = 0.0 # clip edges below zero 
     167    #edges[edges < 0.0] = 0.0 # clip edges below zero 
    156168    cdf = erf((edges[:, None] - q[None, :]) / (sqrt(2.0)*q_width)[None, :]) 
    157169    weights = cdf[1:] - cdf[:-1] 
    … …  
    286298    # The current algorithm is a midpoint rectangle rule. 
    287299    q_edges = bin_edges(q_calc) # Note: requires q > 0 
    288     q_edges[q_edges < 0.0] = 0.0 # clip edges below zero 
     300    #q_edges[q_edges < 0.0] = 0.0 # clip edges below zero 
    289301    weights = np.zeros((len(q), len(q_calc)), 'd') 
    290302 
    … …  
    392404    interval. 
    393405 
    394     if *q_min* is zero or less then *q[0]/10* is used instead. 
     406    Note that extrapolated values may be negative. 
    395407    """ 
    396408    q = np.sort(q) 
    397409    if q_min + 2*MINIMUM_RESOLUTION < q[0]: 
    398         if q_min <= 0: q_min = q_min*MIN_Q_SCALE_FOR_NEGATIVE_Q_EXTRAPOLATION 
    399410        n_low = np.ceil((q[0]-q_min) / (q[1]-q[0])) if q[1] > q[0] else 15 
    400411        q_low = np.linspace(q_min, q[0], n_low+1)[:-1] 
    … …  
    448459        log_delta_q = log(10.) / points_per_decade 
    449460    if q_min < q[0]: 
    450         if q_min < 0: q_min = q[0]*MIN_Q_SCALE_FOR_NEGATIVE_Q_EXTRAPOLATION 
     461        if q_min < 0: q_min = q[0]*MINIMUM_ABSOLUTE_Q 
    451462        n_low = log_delta_q * (log(q[0])-log(q_min)) 
    452463        q_low = np.logspace(log10(q_min), log10(q[0]), np.ceil(n_low)+1)[:-1] 

  • explore/angular_pd.py

    r12eb36b r8267e0b  
    4747 
    4848def draw_mesh_new(ax, theta, dtheta, phi, dphi, flow, radius=10., dist='gauss'): 
    49     theta_center = radians(theta) 
     49    theta_center = radians(90-theta) 
    5050    phi_center = radians(phi) 
    5151    flow_center = radians(flow) 
    … …  
    137137                              radius=11., dist=dist) 
    138138        if not axis.startswith('d'): 
    139             ax.view_init(elev=theta, azim=phi) 
     139            ax.view_init(elev=90-theta if use_new else theta, azim=phi) 
    140140        plt.gcf().canvas.draw() 
    141141 

  • sasmodels/compare.py

    rf72d70a r01ea374  
    8383    -edit starts the parameter explorer 
    8484    -default/-demo* use demo vs default parameters 
    85     -html shows the model docs instead of running the model 
     85    -help/-html shows the model docs instead of running the model 
    8686    -title="note" adds note to the plot title, after the model name 
    8787 
    … …  
    829829    'linear', 'log', 'q4', 
    830830    'hist', 'nohist', 
    831     'edit', 'html', 
     831    'edit', 'html', 'help', 
    832832    'demo', 'default', 
    833833    ]) 
    … …  
    996996        elif arg == '-default':    opts['use_demo'] = False 
    997997        elif arg == '-html':    opts['html'] = True 
     998        elif arg == '-help':    opts['html'] = True 
    998999    # pylint: enable=bad-whitespace 
    9991000 

  • sasmodels/kernel_header.c

    rdaeef4c rb00a646  
    148148inline double sas_sinx_x(double x) { return x==0 ? 1.0 : sin(x)/x; } 
    149149 
     150// To rotate from the canonical position to theta, phi, psi, first rotate by 
     151// psi about the major axis, oriented along z, which is a rotation in the 
     152// detector plane xy. Next rotate by theta about the y axis, aligning the major 
     153// axis in the xz plane. Finally, rotate by phi in the detector plane xy. 
     154// To compute the scattering, undo these rotations in reverse order: 
     155//     rotate in xy by -phi, rotate in xz by -theta, rotate in xy by -psi 
     156// The returned q is the length of the q vector and (xhat, yhat, zhat) is a unit 
     157// vector in the q direction. 
     158// To change between counterclockwise and clockwise rotation, change the 
     159// sign of phi and psi. 
     160 
    150161#if 1 
    151162//think cos(theta) should be sin(theta) in new coords, RKH 11Jan2017 
    … …  
    166177#endif 
    167178 
     179#if 1 
     180#define ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat) do { \ 
     181    q = sqrt(qx*qx + qy*qy); \ 
     182    const double qxhat = qx/q; \ 
     183    const double qyhat = qy/q; \ 
     184    double sin_theta, cos_theta; \ 
     185    double sin_phi, cos_phi; \ 
     186    double sin_psi, cos_psi; \ 
     187    SINCOS(theta*M_PI_180, sin_theta, cos_theta); \ 
     188    SINCOS(phi*M_PI_180, sin_phi, cos_phi); \ 
     189    SINCOS(psi*M_PI_180, sin_psi, cos_psi); \ 
     190    xhat = qxhat*(-sin_phi*sin_psi + cos_theta*cos_phi*cos_psi) \ 
     191         + qyhat*( cos_phi*sin_psi + cos_theta*sin_phi*cos_psi); \ 
     192    yhat = qxhat*(-sin_phi*cos_psi - cos_theta*cos_phi*sin_psi) \ 
     193         + qyhat*( cos_phi*cos_psi - cos_theta*sin_phi*sin_psi); \ 
     194    zhat = qxhat*(-sin_theta*cos_phi) \ 
     195         + qyhat*(-sin_theta*sin_phi); \ 
     196    } while (0) 
     197#else 
     198// SasView 3.x definition of orientation 
    168199#define ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_alpha, cos_mu, cos_nu) do { \ 
    169200    q = sqrt(qx*qx + qy*qy); \ 
    … …  
    180211    cos_nu = (-cos_phi*sin_psi*sin_theta + sin_phi*cos_psi)*qxhat + sin_psi*cos_theta*qyhat; \ 
    181212    } while (0) 
     213#endif 

  • sasmodels/models/bcc_paracrystal.c

    r4962519 r50beefe  
    9090    double theta, double phi, double psi) 
    9191{ 
    92     double q, cos_a1, cos_a2, cos_a3; 
    93     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_a3, cos_a2, cos_a1); 
     92    double q, zhat, yhat, xhat; 
     93    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    9494 
    95     const double a1 = +cos_a3 - cos_a1 + cos_a2; 
    96     const double a2 = +cos_a3 + cos_a1 - cos_a2; 
    97     const double a3 = -cos_a3 + cos_a1 + cos_a2; 
     95    const double a1 = +xhat - zhat + yhat; 
     96    const double a2 = +xhat + zhat - yhat; 
     97    const double a3 = -xhat + zhat + yhat; 
    9898 
    9999    const double qd = 0.5*q*dnn; 

  • sasmodels/models/core_shell_bicelle.c

    r592343f rb260926  
    3030 
    3131static double 
    32 bicelle_kernel(double qq, 
     32bicelle_kernel(double q, 
    3333              double rad, 
    3434              double radthick, 
    3535              double facthick, 
    36               double length, 
     36              double halflength, 
    3737              double rhoc, 
    3838              double rhoh, 
    … …  
    4242              double cos_alpha) 
    4343{ 
    44     double si1,si2,be1,be2; 
    45  
    4644    const double dr1 = rhoc-rhoh; 
    4745    const double dr2 = rhor-rhosolv; 
    4846    const double dr3 = rhoh-rhor; 
    49     const double vol1 = M_PI*rad*rad*(2.0*length); 
    50     const double vol2 = M_PI*(rad+radthick)*(rad+radthick)*2.0*(length+facthick); 
    51     const double vol3 = M_PI*rad*rad*2.0*(length+facthick); 
    52     double besarg1 = qq*rad*sin_alpha; 
    53     double besarg2 = qq*(rad+radthick)*sin_alpha; 
    54     double sinarg1 = qq*length*cos_alpha; 
    55     double sinarg2 = qq*(length+facthick)*cos_alpha; 
     47    const double vol1 = M_PI*square(rad)*2.0*(halflength); 
     48    const double vol2 = M_PI*square(rad+radthick)*2.0*(halflength+facthick); 
     49    const double vol3 = M_PI*square(rad)*2.0*(halflength+facthick); 
    5650 
    57     be1 = sas_2J1x_x(besarg1); 
    58     be2 = sas_2J1x_x(besarg2); 
    59     si1 = sas_sinx_x(sinarg1); 
    60     si2 = sas_sinx_x(sinarg2); 
     51    const double be1 = sas_2J1x_x(q*(rad)*sin_alpha); 
     52    const double be2 = sas_2J1x_x(q*(rad+radthick)*sin_alpha); 
     53    const double si1 = sas_sinx_x(q*(halflength)*cos_alpha); 
     54    const double si2 = sas_sinx_x(q*(halflength+facthick)*cos_alpha); 
    6155 
    6256    const double t = vol1*dr1*si1*be1 + 
    … …  
    6458                     vol3*dr3*si2*be1; 
    6559 
    66     const double retval = t*t*sin_alpha; 
     60    const double retval = t*t; 
    6761 
    6862    return retval; 
    … …  
    7165 
    7266static double 
    73 bicelle_integration(double qq, 
     67bicelle_integration(double q, 
    7468                   double rad, 
    7569                   double radthick, 
    … …  
    8377    // set up the integration end points 
    8478    const double uplim = M_PI_4; 
    85     const double halfheight = 0.5*length; 
     79    const double halflength = 0.5*length; 
    8680 
    8781    double summ = 0.0; 
    … …  
    9084        double sin_alpha, cos_alpha; // slots to hold sincos function output 
    9185        SINCOS(alpha, sin_alpha, cos_alpha); 
    92         double yyy = Gauss76Wt[i] * bicelle_kernel(qq, rad, radthick, facthick, 
    93                              halfheight, rhoc, rhoh, rhor, rhosolv, 
     86        double yyy = Gauss76Wt[i] * bicelle_kernel(q, rad, radthick, facthick, 
     87                             halflength, rhoc, rhoh, rhor, rhosolv, 
    9488                             sin_alpha, cos_alpha); 
    95         summ += yyy; 
     89        summ += yyy*sin_alpha; 
    9690    } 
    9791 
    … …  
    119113    double answer = bicelle_kernel(q, radius, thick_rim, thick_face, 
    120114                           0.5*length, core_sld, face_sld, rim_sld, 
    121                            solvent_sld, sin_alpha, cos_alpha) / fabs(sin_alpha); 
    122  
    123     answer *= 1.0e-4; 
    124  
    125     return answer; 
     115                           solvent_sld, sin_alpha, cos_alpha); 
     116    return 1.0e-4*answer; 
    126117} 
    127118 

  • sasmodels/models/core_shell_bicelle_elliptical.c

    r592343f rf4f85b3  
    3232} 
    3333 
    34 double  
    35                 Iq(double qq, 
    36                    double rad, 
    37                    double x_core, 
    38                    double radthick, 
    39                    double facthick, 
    40                    double length, 
    41                    double rhoc, 
    42                    double rhoh, 
    43                    double rhor, 
    44                    double rhosolv) 
     34double Iq(double q, 
     35          double rad, 
     36          double x_core, 
     37          double radthick, 
     38          double facthick, 
     39          double length, 
     40          double rhoc, 
     41          double rhoh, 
     42          double rhor, 
     43          double rhosolv) 
    4544{ 
    4645    double si1,si2,be1,be2; 
    … …  
    7473        const double sin_alpha = sqrt(1.0 - cos_alpha*cos_alpha); 
    7574        double inner_sum=0; 
    76         double sinarg1 = qq*halfheight*cos_alpha; 
    77         double sinarg2 = qq*(halfheight+facthick)*cos_alpha; 
     75        double sinarg1 = q*halfheight*cos_alpha; 
     76        double sinarg2 = q*(halfheight+facthick)*cos_alpha; 
    7877        si1 = sas_sinx_x(sinarg1); 
    7978        si2 = sas_sinx_x(sinarg2); 
    … …  
    8382            const double beta = ( Gauss76Z[j] +1.0)*M_PI_2; 
    8483            const double rr = sqrt(rA - rB*cos(beta)); 
    85             double besarg1 = qq*rr*sin_alpha; 
    86             double besarg2 = qq*(rr+radthick)*sin_alpha; 
     84            double besarg1 = q*rr*sin_alpha; 
     85            double besarg2 = q*(rr+radthick)*sin_alpha; 
    8786            be1 = sas_2J1x_x(besarg1); 
    8887            be2 = sas_2J1x_x(besarg2); 
    … …  
    114113{ 
    115114       // THIS NEEDS TESTING 
    116     double qq, cos_val, cos_mu, cos_nu; 
    117     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, qq, cos_val, cos_mu, cos_nu); 
     115    double q, xhat, yhat, zhat; 
     116    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    118117    const double dr1 = rhoc-rhoh; 
    119118    const double dr2 = rhor-rhosolv; 
    … …  
    125124    const double vol3 = M_PI*rad*radius_major*2.0*(halfheight+facthick); 
    126125 
    127     // Compute:  r = sqrt((radius_major*cos_nu)^2 + (radius_minor*cos_mu)^2) 
     126    // Compute:  r = sqrt((radius_major*zhat)^2 + (radius_minor*yhat)^2) 
    128127    // Given:    radius_major = r_ratio * radius_minor   
    129128    // ASSUME the sin_alpha is included in the separate integration over orientation of rod angle 
    130     const double r = rad*sqrt(square(x_core*cos_nu) + cos_mu*cos_mu); 
    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 ); 
     129    const double rad_minor = rad; 
     130    const double rad_major = rad*x_core; 
     131    const double r_hat = sqrt(square(rad_major*xhat) + square(rad_minor*yhat)); 
     132    const double rshell_hat = sqrt(square((rad_major+radthick)*xhat) 
     133                                   + square((rad_minor+radthick)*yhat)); 
     134    const double be1 = sas_2J1x_x( q*r_hat ); 
     135    const double be2 = sas_2J1x_x( q*rshell_hat ); 
     136    const double si1 = sas_sinx_x( q*halfheight*zhat ); 
     137    const double si2 = sas_sinx_x( q*(halfheight + facthick)*zhat ); 
    135138    const double Aq = square( vol1*dr1*si1*be1 + vol2*dr2*si2*be2 +  vol3*dr3*si2*be1); 
    136139    //const double vol = form_volume(radius_minor, r_ratio, length); 

  • sasmodels/models/core_shell_parallelepiped.c

    r1e7b0db0 r92dfe0c  
    134134    double psi) 
    135135{ 
    136     double q, cos_val_a, cos_val_b, cos_val_c; 
    137     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_val_c, cos_val_b, cos_val_a); 
     136    double q, zhat, yhat, xhat; 
     137    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    138138 
    139139    // cspkernel in csparallelepiped recoded here 
    … …  
    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 = 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); 
     162    double siA = sas_sinx_x(0.5*q*length_a*xhat); 
     163    double siB = sas_sinx_x(0.5*q*length_b*yhat); 
     164    double siC = sas_sinx_x(0.5*q*length_c*zhat); 
     165    double siAt = sas_sinx_x(0.5*q*ta*xhat); 
     166    double siBt = sas_sinx_x(0.5*q*tb*yhat); 
     167    double siCt = sas_sinx_x(0.5*q*tc*zhat); 
    168168     
    169169 

  • sasmodels/models/core_shell_parallelepiped.py

    r797a8e3 r92dfe0c  
    4444 
    4545    F_{a}(Q,\alpha,\beta)= 
    46     \Bigg(\frac{sin(Q(L_A+2t_A)/2sin\alpha sin\beta)}{Q(L_A+2t_A)/2sin\alpha 
    47     sin\beta)} 
    48     - \frac{sin(QL_A/2sin\alpha sin\beta)}{QL_A/2sin\alpha sin\beta)} \Bigg) 
    49     + \frac{sin(QL_B/2sin\alpha sin\beta)}{QL_B/2sin\alpha sin\beta)} 
    50     + \frac{sin(QL_C/2sin\alpha sin\beta)}{QL_C/2sin\alpha sin\beta)} 
     46    \left[\frac{\sin(Q(L_A+2t_A)/2\sin\alpha \sin\beta)}{Q(L_A+2t_A)/2\sin\alpha\sin\beta} 
     47    - \frac{\sin(QL_A/2\sin\alpha \sin\beta)}{QL_A/2\sin\alpha \sin\beta} \right] 
     48    \left[\frac{\sin(QL_B/2\sin\alpha \sin\beta)}{QL_B/2\sin\alpha \sin\beta} \right] 
     49    \left[\frac{\sin(QL_C/2\sin\alpha \sin\beta)}{QL_C/2\sin\alpha \sin\beta} \right] 
    5150 
    5251.. note:: 
    … …  
    5857 
    5958FITTING NOTES 
    60 If the scale is set equal to the particle volume fraction, |phi|, the returned 
     59If the scale is set equal to the particle volume fraction, $\phi$, the returned 
    6160value is the scattered intensity per unit volume, $I(q) = \phi P(q)$. 
    6261However, **no interparticle interference effects are included in this 

  • sasmodels/models/ellipsoid.c

    r130d4c7 r3b571ae  
    33double Iqxy(double qx, double qy, double sld, double sld_solvent, 
    44    double radius_polar, double radius_equatorial, double theta, double phi); 
    5  
    6 static double 
    7 _ellipsoid_kernel(double q, double radius_polar, double radius_equatorial, double cos_alpha) 
    8 { 
    9     double ratio = radius_polar/radius_equatorial; 
    10     // Using ratio v = Rp/Re, we can expand the following to match the 
    11     // form given in Guinier (1955) 
    12     //     r = Re * sqrt(1 + cos^2(T) (v^2 - 1)) 
    13     //       = Re * sqrt( (1 - cos^2(T)) + v^2 cos^2(T) ) 
    14     //       = Re * sqrt( sin^2(T) + v^2 cos^2(T) ) 
    15     //       = sqrt( Re^2 sin^2(T) + Rp^2 cos^2(T) ) 
    16     // 
    17     // Instead of using pythagoras we could pass in sin and cos; this may be 
    18     // slightly better for 2D which has already computed it, but it introduces 
    19     // an extra sqrt and square for 1-D not required by the current form, so 
    20     // leave it as is. 
    21     const double r = radius_equatorial 
    22                      * sqrt(1.0 + cos_alpha*cos_alpha*(ratio*ratio - 1.0)); 
    23     const double f = sas_3j1x_x(q*r); 
    24  
    25     return f*f; 
    26 } 
    275 
    286double form_volume(double radius_polar, double radius_equatorial) 
    … …  
    3715    double radius_equatorial) 
    3816{ 
     17    // Using ratio v = Rp/Re, we can implement the form given in Guinier (1955) 
     18    //     i(h) = int_0^pi/2 Phi^2(h a sqrt(cos^2 + v^2 sin^2) cos dT 
     19    //          = int_0^pi/2 Phi^2(h a sqrt((1-sin^2) + v^2 sin^2) cos dT 
     20    //          = int_0^pi/2 Phi^2(h a sqrt(1 + sin^2(v^2-1)) cos dT 
     21    // u-substitution of 
     22    //     u = sin, du = cos dT 
     23    //     i(h) = int_0^1 Phi^2(h a sqrt(1 + u^2(v^2-1)) du 
     24    const double v_square_minus_one = square(radius_polar/radius_equatorial) - 1.0; 
     25 
    3926    // translate a point in [-1,1] to a point in [0, 1] 
     27    // const double u = Gauss76Z[i]*(upper-lower)/2 + (upper+lower)/2; 
    4028    const double zm = 0.5; 
    4129    const double zb = 0.5; 
    4230    double total = 0.0; 
    4331    for (int i=0;i<76;i++) { 
    44         //const double cos_alpha = (Gauss76Z[i]*(upper-lower) + upper + lower)/2; 
    45         const double cos_alpha = Gauss76Z[i]*zm + zb; 
    46         total += Gauss76Wt[i] * _ellipsoid_kernel(q, radius_polar, radius_equatorial, cos_alpha); 
     32        const double u = Gauss76Z[i]*zm + zb; 
     33        const double r = radius_equatorial*sqrt(1.0 + u*u*v_square_minus_one); 
     34        const double f = sas_3j1x_x(q*r); 
     35        total += Gauss76Wt[i] * f * f; 
    4736    } 
    4837    // translate dx in [-1,1] to dx in [lower,upper] 
    … …  
    6251    double q, sin_alpha, cos_alpha; 
    6352    ORIENT_SYMMETRIC(qx, qy, theta, phi, q, sin_alpha, cos_alpha); 
    64     const double form = _ellipsoid_kernel(q, radius_polar, radius_equatorial, cos_alpha); 
     53    const double r = sqrt(square(radius_equatorial*sin_alpha) 
     54                          + square(radius_polar*cos_alpha)); 
     55    const double f = sas_3j1x_x(q*r); 
    6556    const double s = (sld - sld_solvent) * form_volume(radius_polar, radius_equatorial); 
    6657 
    67     return 1.0e-4 * form * s * s; 
     58    return 1.0e-4 * square(f * s); 
    6859} 
    6960 

  • sasmodels/models/ellipsoid.py

    r925ad6e r3b571ae  
    1818.. math:: 
    1919 
    20     F(q,\alpha) = \frac{3 \Delta \rho V (\sin[qr(R_p,R_e,\alpha)] 
    21                 - \cos[qr(R_p,R_e,\alpha)])} 
    22                 {[qr(R_p,R_e,\alpha)]^3} 
     20    F(q,\alpha) = \Delta \rho V \frac{3(\sin qr  - qr \cos qr)}{(qr)^3} 
    2321 
    24 and 
     22for 
    2523 
    2624.. math:: 
    2725 
    28     r(R_p,R_e,\alpha) = \left[ R_e^2 \sin^2 \alpha 
    29         + R_p^2 \cos^2 \alpha \right]^{1/2} 
     26    r = \left[ R_e^2 \sin^2 \alpha + R_p^2 \cos^2 \alpha \right]^{1/2} 
    3027 
    3128 
    3229$\alpha$ is the angle between the axis of the ellipsoid and $\vec q$, 
    33 $V = (4/3)\pi R_pR_e^2$ is the volume of the ellipsoid , $R_p$ is the polar radius along the 
    34 rotational axis of the ellipsoid, $R_e$ is the equatorial radius perpendicular 
    35 to the rotational axis of the ellipsoid and $\Delta \rho$ (contrast) is the 
    36 scattering length density difference between the scatterer and the solvent. 
     30$V = (4/3)\pi R_pR_e^2$ is the volume of the ellipsoid, $R_p$ is the polar 
     31radius along the rotational axis of the ellipsoid, $R_e$ is the equatorial 
     32radius perpendicular to the rotational axis of the ellipsoid and 
     33$\Delta \rho$ (contrast) is the scattering length density difference between 
     34the scatterer and the solvent. 
    3735 
    38 For randomly oriented particles: 
     36For randomly oriented particles use the orientational average, 
    3937 
    4038.. math:: 
    4139 
    42    F^2(q)=\int_{0}^{\pi/2}{F^2(q,\alpha)\sin(\alpha)d\alpha} 
     40   \langle F^2(q) \rangle = \int_{0}^{\pi/2}{F^2(q,\alpha)\sin(\alpha)\,d\alpha} 
    4341 
     42 
     43computed via substitution of $u=\sin(\alpha)$, $du=\cos(\alpha)\,d\alpha$ as 
     44 
     45.. math:: 
     46 
     47    \langle F^2(q) \rangle = \int_0^1{F^2(q, u)\,du} 
     48 
     49with 
     50 
     51.. math:: 
     52 
     53    r = R_e \left[ 1 + u^2\left(R_p^2/R_e^2 - 1\right)\right]^{1/2} 
    4454 
    4555To provide easy access to the orientation of the ellipsoid, we define 
    … …  
    4858:ref:`cylinder orientation figure <cylinder-angle-definition>`. 
    4959For the ellipsoid, $\theta$ is the angle between the rotational axis 
    50 and the $z$ -axis. 
     60and the $z$ -axis in the $xz$ plane followed by a rotation by $\phi$ 
     61in the $xy$ plane. 
    5162 
    5263NB: The 2nd virial coefficient of the solid ellipsoid is calculated based 
    … …  
    90101than 500. 
    91102 
     103Model was also tested against the triaxial ellipsoid model with equal major 
     104and minor equatorial radii.  It is also consistent with the cyclinder model 
     105with polar radius equal to length and equatorial radius equal to radius. 
     106 
    92107References 
    93108---------- 
    … …  
    96111*Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, 
    97112Plenum Press, New York, 1987. 
     113 
     114Authorship and Verification 
     115---------------------------- 
     116 
     117* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     118* **Converted to sasmodels by:** Helen Park **Date:** July 9, 2014 
     119* **Last Modified by:** Paul Kienzle **Date:** March 22, 2017 
    98120""" 
    99121 

  • sasmodels/models/elliptical_cylinder.c

    r592343f r61104c8  
    6767     double theta, double phi, double psi) 
    6868{ 
    69     double q, cos_val, cos_mu, cos_nu; 
    70     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_val, cos_mu, cos_nu); 
     69    double q, xhat, yhat, zhat; 
     70    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    7171 
    7272    // Compute:  r = sqrt((radius_major*cos_nu)^2 + (radius_minor*cos_mu)^2) 
    7373    // Given:    radius_major = r_ratio * radius_minor 
    74     const double r = radius_minor*sqrt(square(r_ratio*cos_nu) + cos_mu*cos_mu); 
     74    const double r = radius_minor*sqrt(square(r_ratio*xhat) + square(yhat)); 
    7575    const double be = sas_2J1x_x(q*r); 
    76     const double si = sas_sinx_x(q*0.5*length*cos_val); 
     76    const double si = sas_sinx_x(q*zhat*0.5*length); 
    7777    const double Aq = be * si; 
    7878    const double delrho = sld - solvent_sld; 

  • sasmodels/models/fcc_paracrystal.c

    r4962519 r50beefe  
    9090    double theta, double phi, double psi) 
    9191{ 
    92     double q, cos_a1, cos_a2, cos_a3; 
    93     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_a3, cos_a2, cos_a1); 
     92    double q, zhat, yhat, xhat; 
     93    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    9494 
    95     const double a1 = cos_a2 + cos_a3; 
    96     const double a2 = cos_a3 + cos_a1; 
    97     const double a3 = cos_a2 + cos_a1; 
     95    const double a1 = yhat + xhat; 
     96    const double a2 = xhat + zhat; 
     97    const double a3 = yhat + zhat; 
    9898    const double qd = 0.5*q*dnn; 
    9999    const double arg = 0.5*square(qd*d_factor)*(a1*a1 + a2*a2 + a3*a3); 

  • sasmodels/models/parallelepiped.c

    r1e7b0db0 rd605080  
    6767    double psi) 
    6868{ 
    69     double q, cos_val_a, cos_val_b, cos_val_c; 
    70     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_val_c, cos_val_b, cos_val_a); 
     69    double q, xhat, yhat, zhat; 
     70    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    7171 
    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); 
     72    const double siA = sas_sinx_x(0.5*length_a*q*xhat); 
     73    const double siB = sas_sinx_x(0.5*length_b*q*yhat); 
     74    const double siC = sas_sinx_x(0.5*length_c*q*zhat); 
    7575    const double V = form_volume(length_a, length_b, length_c); 
    7676    const double drho = (sld - solvent_sld); 

  • sasmodels/models/sc_paracrystal.c

    r4962519 r50beefe  
    111111          double psi) 
    112112{ 
    113     double q, cos_a1, cos_a2, cos_a3; 
    114     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, cos_a3, cos_a2, cos_a1); 
     113    double q, zhat, yhat, xhat; 
     114    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    115115 
    116116    const double qd = q*dnn; 
    … …  
    118118    const double tanh_qd = tanh(arg); 
    119119    const double cosh_qd = cosh(arg); 
    120     const double Zq = tanh_qd/(1. - cos(qd*cos_a1)/cosh_qd) 
    121                     * tanh_qd/(1. - cos(qd*cos_a2)/cosh_qd) 
    122                     * tanh_qd/(1. - cos(qd*cos_a3)/cosh_qd); 
     120    const double Zq = tanh_qd/(1. - cos(qd*zhat)/cosh_qd) 
     121                    * tanh_qd/(1. - cos(qd*yhat)/cosh_qd) 
     122                    * tanh_qd/(1. - cos(qd*xhat)/cosh_qd); 
    123123 
    124124    const double Fq = sphere_form(q, radius, sphere_sld, solvent_sld)*Zq; 

  • sasmodels/models/triaxial_ellipsoid.c

    r925ad6e r68dd6a9  
    2020    double radius_polar) 
    2121{ 
    22     double sn, cn; 
    23     // translate a point in [-1,1] to a point in [0, 1] 
    24     const double zm = 0.5; 
    25     const double zb = 0.5; 
     22    const double pa = square(radius_equat_minor/radius_equat_major) - 1.0; 
     23    const double pc = square(radius_polar/radius_equat_major) - 1.0; 
     24    // translate a point in [-1,1] to a point in [0, pi/2] 
     25    const double zm = M_PI_4; 
     26    const double zb = M_PI_4; 
    2627    double outer = 0.0; 
    2728    for (int i=0;i<76;i++) { 
    28         //const double cos_alpha = (Gauss76Z[i]*(upper-lower) + upper + lower)/2; 
    29         const double x = 0.5*(Gauss76Z[i] + 1.0); 
    30         SINCOS(M_PI_2*x, sn, cn); 
    31         const double acosx2 = radius_equat_minor*radius_equat_minor*cn*cn; 
    32         const double bsinx2 = radius_equat_major*radius_equat_major*sn*sn; 
    33         const double c2 = radius_polar*radius_polar; 
     29        //const double u = Gauss76Z[i]*(upper-lower)/2 + (upper + lower)/2; 
     30        const double phi = Gauss76Z[i]*zm + zb; 
     31        const double pa_sinsq_phi = pa*square(sin(phi)); 
    3432 
    3533        double inner = 0.0; 
     34        const double um = 0.5; 
     35        const double ub = 0.5; 
    3636        for (int j=0;j<76;j++) { 
    37             const double ysq = square(Gauss76Z[j]*zm + zb); 
    38             const double t = q*sqrt(acosx2 + bsinx2*(1.0-ysq) + c2*ysq); 
    39             const double fq = sas_3j1x_x(t); 
    40             inner += Gauss76Wt[j] * fq * fq ; 
     37            // translate a point in [-1,1] to a point in [0, 1] 
     38            const double usq = square(Gauss76Z[j]*um + ub); 
     39            const double r = radius_equat_major*sqrt(pa_sinsq_phi*(1.0-usq) + 1.0 + pc*usq); 
     40            const double fq = sas_3j1x_x(q*r); 
     41            inner += Gauss76Wt[j] * fq * fq; 
    4142        } 
    42         outer += Gauss76Wt[i] * 0.5 * inner; 
     43        outer += Gauss76Wt[i] * inner;  // correcting for dx later 
    4344    } 
    44     // translate dx in [-1,1] to dx in [lower,upper] 
    45     const double fqsq = outer*zm; 
     45    // translate integration ranges from [-1,1] to [lower,upper] and normalize by 4 pi 
     46    const double fqsq = outer/4.0;  // = outer*um*zm*8.0/(4.0*M_PI); 
    4647    const double s = (sld - sld_solvent) * form_volume(radius_equat_minor, radius_equat_major, radius_polar); 
    4748    return 1.0e-4 * s * s * fqsq; 
    … …  
    5859    double psi) 
    5960{ 
    60     double q, calpha, cmu, cnu; 
    61     ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, calpha, cmu, cnu); 
     61    double q, xhat, yhat, zhat; 
     62    ORIENT_ASYMMETRIC(qx, qy, theta, phi, psi, q, xhat, yhat, zhat); 
    6263 
    63     const double t = q*sqrt(radius_equat_minor*radius_equat_minor*cnu*cnu 
    64                           + radius_equat_major*radius_equat_major*cmu*cmu 
    65                           + radius_polar*radius_polar*calpha*calpha); 
    66     const double fq = sas_3j1x_x(t); 
     64    const double r = sqrt(square(radius_equat_minor*xhat) 
     65                          + square(radius_equat_major*yhat) 
     66                          + square(radius_polar*zhat)); 
     67    const double fq = sas_3j1x_x(q*r); 
    6768    const double s = (sld - sld_solvent) * form_volume(radius_equat_minor, radius_equat_major, radius_polar); 
    6869 

  • sasmodels/models/triaxial_ellipsoid.py

    r925ad6e r67595af  
    22# Note: model title and parameter table are inserted automatically 
    33r""" 
    4 All three axes are of different lengths with $R_a \leq R_b \leq R_c$ 
    5 **Users should maintain this inequality for all calculations**. 
     4Definition 
     5---------- 
     6 
     7.. figure:: img/triaxial_ellipsoid_geometry.jpg 
     8 
     9    Ellipsoid with $R_a$ as *radius_equat_minor*, $R_b$ as *radius_equat_major* 
     10    and $R_c$ as *radius_polar*.  For highest accuracy in the orientational 
     11    average, prefer $R_c > R_b > R_a$. 
     12 
     13Given an ellipsoid 
    614 
    715.. math:: 
    816 
    9     P(q) = \text{scale} V \left< F^2(q) \right> + \text{background} 
     17    \frac{X^2}{R_a^2} + \frac{Y^2}{R_b^2} + \frac{Z^2}{R_c^2} = 1 
    1018 
    11 where the volume $V = 4/3 \pi R_a R_b R_c$, and the averaging 
    12 $\left<\ldots\right>$ is applied over all orientations for 1D. 
    13  
    14 .. figure:: img/triaxial_ellipsoid_geometry.jpg 
    15  
    16     Ellipsoid schematic. 
    17  
    18 Definition 
    19 ---------- 
    20  
    21 The form factor calculated is 
     19the scattering is defined by the average over all orientations $\Omega$, 
    2220 
    2321.. math:: 
    2422 
    25     P(q) = \frac{\text{scale}}{V}\int_0^1\int_0^1 
    26         \Phi^2(qR_a^2\cos^2( \pi x/2) + qR_b^2\sin^2(\pi y/2)(1-y^2) + R_c^2y^2) 
    27         dx dy 
     23    P(q) = \text{scale}\frac{V}{4 \pi}\int_\Omega \Phi^2(qr) d\Omega + \text{background} 
    2824 
    2925where 
    … …  
    3127.. math:: 
    3228 
    33     \Phi(u) = 3 u^{-3} (\sin u - u \cos u) 
     29    \Phi(qr) &= 3 j_1(qr)/qr = 3 (\sin qr - qr \cos qr)/(qr)^3 \\ 
     30    r^2 &= R_a^2e^2 + R_b^2f^2 + R_c^2g^2 \\ 
     31    V &= \tfrac{4}{3} \pi R_a R_b R_c 
     32 
     33The $e$, $f$ and $g$ terms are the projections of the orientation vector on $X$, 
     34$Y$ and $Z$ respectively.  Keeping the orientation fixed at the canonical 
     35axes, we can integrate over the incident direction using polar angle 
     36$-\pi/2 \le \gamma \le \pi/2$ and equatorial angle $0 \le \phi \le 2\pi$ 
     37(as defined in ref [1]), 
     38 
     39 .. math:: 
     40 
     41     \langle\Phi^2\rangle = \int_0^{2\pi} \int_{-\pi/2}^{\pi/2} \Phi^2(qr) \cos \gamma\,d\gamma d\phi 
     42 
     43with $e = \cos\gamma \sin\phi$, $f = \cos\gamma \cos\phi$ and $g = \sin\gamma$. 
     44A little algebra yields 
     45 
     46.. math:: 
     47 
     48    r^2 = b^2(p_a \sin^2 \phi \cos^2 \gamma + 1 + p_c \sin^2 \gamma) 
     49 
     50for 
     51 
     52.. math:: 
     53 
     54    p_a = \frac{a^2}{b^2} - 1 \text{ and } p_c = \frac{c^2}{b^2} - 1 
     55 
     56Due to symmetry, the ranges can be restricted to a single quadrant 
     57$0 \le \gamma \le \pi/2$ and $0 \le \phi \le \pi/2$, scaling the resulting 
     58integral by 8. The computation is done using the substitution $u = \sin\gamma$, 
     59$du = \cos\gamma\,d\gamma$, giving 
     60 
     61.. math:: 
     62 
     63    \langle\Phi^2\rangle &= 8 \int_0^{\pi/2} \int_0^1 \Phi^2(qr) du d\phi \\ 
     64    r^2 &= b^2(p_a \sin^2(\phi)(1 - u^2) + 1 + p_c u^2) 
    3465 
    3566To provide easy access to the orientation of the triaxial ellipsoid, 
    … …  
    69100---------- 
    70101 
    71 L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray 
    72 and Neutron Scattering*, Plenum, New York, 1987. 
     102[1] Finnigan, J.A., Jacobs, D.J., 1971. 
     103*Light scattering by ellipsoidal particles in solution*, 
     104J. Phys. D: Appl. Phys. 4, 72-77. doi:10.1088/0022-3727/4/1/310 
     105 
    73106""" 
    74107 
    … …  
    91124               "Solvent scattering length density"], 
    92125              ["radius_equat_minor", "Ang", 20, [0, inf], "volume", 
    93                "Minor equatorial radius"], 
     126               "Minor equatorial radius, Ra"], 
    94127              ["radius_equat_major", "Ang", 400, [0, inf], "volume", 
    95                "Major equatorial radius"], 
     128               "Major equatorial radius, Rb"], 
    96129              ["radius_polar", "Ang", 10, [0, inf], "volume", 
    97                "Polar radius"], 
     130               "Polar radius, Rc"], 
    98131              ["theta", "degrees", 60, [-inf, inf], "orientation", 
    99132               "In plane angle"], 
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