#define INVALID(v) (v.radius_bell < v.radius) //barbell kernel - same as dumbell static double _bell_kernel(double qab, double qc, double h, double radius_bell, double half_length) { // translate a point in [-1,1] to a point in [lower,upper] const double upper = 1.0; const double lower = h/radius_bell; const double zm = 0.5*(upper-lower); const double zb = 0.5*(upper+lower); // cos term in integral is: // cos (q (R t - h + L/2) cos(alpha)) // so turn it into: // cos (m t + b) // where: // m = q R cos(alpha) // b = q(L/2-h) cos(alpha) const double m = radius_bell*qc; // cos argument slope const double b = (half_length-h)*qc; // cos argument intercept const double qab_r = radius_bell*qab; // Q*R*sin(theta) double total = 0.0; for (int i = 0; i < GAUSS_N; i++){ const double t = GAUSS_Z[i]*zm + zb; const double radical = 1.0 - t*t; const double bj = sas_2J1x_x(qab_r*sqrt(radical)); const double Fq = cos(m*t + b) * radical * bj; total += GAUSS_W[i] * Fq; } // translate dx in [-1,1] to dx in [lower,upper] const double integral = total*zm; const double bell_fq = 2.0*M_PI*cube(radius_bell)*integral; return bell_fq; } static double _fq(double qab, double qc, double h, double radius_bell, double radius, double half_length) { const double bell_fq = _bell_kernel(qab, qc, h, radius_bell, half_length); const double bj = sas_2J1x_x(radius*qab); const double si = sas_sinx_x(half_length*qc); const double cyl_fq = 2.0*M_PI*radius*radius*half_length*bj*si; const double Aq = bell_fq + cyl_fq; return Aq; } static double form_volume(double radius_bell, double radius, double length) { // bell radius should never be less than radius when this is called const double hdist = sqrt(square(radius_bell) - square(radius)); const double p1 = 2.0/3.0*cube(radius_bell); const double p2 = square(radius_bell)*hdist; const double p3 = cube(hdist)/3.0; return M_PI*square(radius)*length + 2.0*M_PI*(p1+p2-p3); } static double radius_from_excluded_volume(double radius_bell, double radius, double length) { const double hdist = sqrt(square(radius_bell) - square(radius)); const double length_tot = length + 2.0*(hdist+ radius); return 0.5*cbrt(0.75*radius_bell*(2.0*radius_bell*length_tot + (radius_bell + length_tot)*(M_PI*radius_bell + length_tot))); } static double radius_from_volume(double radius_bell, double radius, double length) { const double vol_barbell = form_volume(radius_bell,radius,length); return cbrt(vol_barbell/M_4PI_3); } static double radius_from_totallength(double radius_bell, double radius, double length) { const double hdist = sqrt(square(radius_bell) - square(radius)); return 0.5*length + hdist + radius_bell; } static double effective_radius(int mode, double radius_bell, double radius, double length) { switch (mode) { default: case 1: // equivalent cylinder excluded volume return radius_from_excluded_volume(radius_bell, radius , length); case 2: // equivalent volume sphere return radius_from_volume(radius_bell, radius , length); case 3: // radius return radius; case 4: // half length return 0.5*length; case 5: // half total length return radius_from_totallength(radius_bell,radius,length); } } static void Fq(double q,double *F1, double *F2, double sld, double solvent_sld, double radius_bell, double radius, double length) { const double h = -sqrt(radius_bell*radius_bell - radius*radius); const double half_length = 0.5*length; // translate a point in [-1,1] to a point in [0, pi/2] const double zm = M_PI_4; const double zb = M_PI_4; double total_F1 = 0.0; double total_F2 = 0.0; for (int i = 0; i < GAUSS_N; i++){ const double alpha= GAUSS_Z[i]*zm + zb; double sin_alpha, cos_alpha; // slots to hold sincos function output SINCOS(alpha, sin_alpha, cos_alpha); const double Aq = _fq(q*sin_alpha, q*cos_alpha, h, radius_bell, radius, half_length); total_F1 += GAUSS_W[i] * Aq * sin_alpha; total_F2 += GAUSS_W[i] * Aq * Aq * sin_alpha; } // translate dx in [-1,1] to dx in [lower,upper] const double form_avg = total_F1*zm; const double form_squared_avg = total_F2*zm; //Contrast const double s = (sld - solvent_sld); *F1 = 1.0e-2 * s * form_avg; *F2 = 1.0e-4 * s * s * form_squared_avg; } static double Iqac(double qab, double qc, double sld, double solvent_sld, double radius_bell, double radius, double length) { const double h = -sqrt(square(radius_bell) - square(radius)); const double Aq = _fq(qab, qc, h, radius_bell, radius, 0.5*length); // Multiply by contrast^2 and convert to cm-1 const double s = (sld - solvent_sld); return 1.0e-4 * square(s * Aq); }