/******************************************************************************* * * McXtrace, X-ray tracing package * Copyright, All rights reserved * DTU Physics, Kgs. Lyngby, Denmark * Synchrotron SOLEIL, Saint-Aubin, France * * Component: SasView_raspberry * * %Identification * Written by: Jose Robledo * Based on sasmodels from SasView * Origin: FZJ / DTU / ESS DMSC * * * SasView raspberry model component as sample description. * * %Description * * SasView_raspberry component, generated from raspberry.c in sasmodels. * * Example: * SasView_raspberry(sld_lg, sld_sm, sld_solvent, volfraction_lg, volfraction_sm, surface_fraction, radius_lg, radius_sm, penetration, * model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, * int target_index=1, target_x=0, target_y=0, target_z=1, * focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, * pd_radius_lg=0.0, pd_radius_sm=0.0) * * %Parameters * INPUT PARAMETERS: * sld_lg: [1e-6/Ang^2] ([-inf, inf]) large particle scattering length density. * sld_sm: [1e-6/Ang^2] ([-inf, inf]) small particle scattering length density. * sld_solvent: [1e-6/Ang^2] ([-inf, inf]) solvent scattering length density. * volfraction_lg: [] ([-inf, inf]) volume fraction of large spheres. * volfraction_sm: [] ([-inf, inf]) volume fraction of small spheres. * surface_fraction: [] ([-inf, inf]) fraction of small spheres at surface. * radius_lg: [Ang] ([0, inf]) radius of large spheres. * radius_sm: [Ang] ([0, inf]) radius of small spheres. * penetration: [Ang] ([-1, 1]) fractional penetration depth of small spheres into large sphere. * Optional parameters: * model_abs: [ ] Absorption cross section density at 2200 m/s. * model_scale: [ ] Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction. * xwidth: [m] ([-inf, inf]) Horiz. dimension of sample, as a width. * yheight: [m] ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box * zdepth: [m] ([-inf, inf]) depth of sample * R: [m] Outer radius of sample in (x,z) plane for cylinder/sphere. * target_x: [m] relative focus target position. * target_y: [m] relative focus target position. * target_z: [m] relative focus target position. * target_index: [ ] Relative index of component to focus at, e.g. next is +1. * focus_xw: [m] horiz. dimension of a rectangular area. * focus_yh: [m], vert. dimension of a rectangular area. * focus_aw: [deg], horiz. angular dimension of a rectangular area. * focus_ah: [deg], vert. angular dimension of a rectangular area. * focus_r: [m] case of circular focusing, focusing radius. * pd_radius_lg: [] (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. * pd_radius_sm: [] (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable * * %Link * %End *******************************************************************************/ DEFINE COMPONENT SasView_raspberry SETTING PARAMETERS ( sld_lg=-0.4, sld_sm=3.5, sld_solvent=6.36, volfraction_lg=0.05, volfraction_sm=0.005, surface_fraction=0.4, radius_lg=5000, radius_sm=100, penetration=0, model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, target_x=0, target_y=0, target_z=1, int target_index=1, focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, pd_radius_lg=0.0, pd_radius_sm=0.0) SHARE %{ %include "sas_kernel_header.c" /* BEGIN Required header for SASmodel raspberry */ #define HAS_Iq #define FORM_VOL #ifndef SAS_HAVE_sas_3j1x_x #define SAS_HAVE_sas_3j1x_x #line 1 "sas_3j1x_x" /** * Spherical Bessel function 3*j1(x)/x * * Used for low q to avoid cancellation error. * Note that the values differ from sasview ~ 5e-12 rather than 5e-14, but * in this case it is likely cancellation errors in the original expression * using double precision that are the source. */ double sas_3j1x_x(double q); // The choice of the number of terms in the series and the cutoff value for // switching between series and direct calculation depends on the numeric // precision. // // Point where direct calculation reaches machine precision: // // single machine precision eps 3e-8 at qr=1.1 ** // double machine precision eps 4e-16 at qr=1.1 // // Point where Taylor series reaches machine precision (eps), where taylor // series matches direct calculation (cross) and the error at that point: // // prec n eps cross error // single 3 0.28 0.4 6.2e-7 // single 4 0.68 0.7 2.3e-7 // single 5 1.18 1.2 7.5e-8 // double 3 0.01 0.03 2.3e-13 // double 4 0.06 0.1 3.1e-14 // double 5 0.16 0.2 5.0e-15 // // ** Note: relative error on single precision starts increase on the direct // method at qr=1.1, rising from 3e-8 to 5e-5 by qr=1e3. This should be // safe for the sans range, with objects of 100 nm supported to a q of 0.1 // while maintaining 5 digits of precision. For usans/sesans, the objects // are larger but the q is smaller, so again it should be fine. // // See explore/sph_j1c.py for code to explore these ranges. // Use 4th order series #if FLOAT_SIZE>4 #define SPH_J1C_CUTOFF 0.1 #else #define SPH_J1C_CUTOFF 0.7 #endif #pragma acc routine seq double sas_3j1x_x(double q) { // 2017-05-18 PAK - support negative q if (fabs(q) < SPH_J1C_CUTOFF) { const double q2 = q*q; return (1.0 + q2*(-3./30. + q2*(3./840. + q2*(-3./45360.))));// + q2*(3./3991680.))))); } else { double sin_q, cos_q; SINCOS(q, sin_q, cos_q); return 3.0*(sin_q/q - cos_q)/(q*q); } } #endif // SAS_HAVE_sas_3j1x_x #ifndef SAS_HAVE_raspberry #define SAS_HAVE_raspberry #line 1 "raspberry" double form_volume_raspberry(double radius_lg, double radius_sm, double penetration); double Iq_raspberry(double q, double sld_lg, double sld_sm, double sld_solvent, double volfraction_lg, double volfraction_sm, double surf_fraction, double radius_lg, double radius_sm, double penetration); double form_volume_raspberry(double radius_lg, double radius_sm, double penetration) { //Because of the complex structure, volume normalization must //happen in the Iq code below. Thus the form volume is set to 1.0 here double volume=1.0; return volume; } static double radius_effective_raspberry(int mode, double radius_lg, double radius_sm, double penetration) { switch (mode) { default: case 1: // radius_large return radius_lg; case 2: // radius_outer return radius_lg + 2.0*radius_sm - penetration; } } double Iq_raspberry(double q, double sld_lg, double sld_sm, double sld_solvent, double volfraction_lg, double volfraction_sm, double surface_fraction, double radius_lg, double radius_sm, double penetration) { // Ref: J. coll. inter. sci. (2010) vol. 343 (1) pp. 36-41. double vfL, rL, sldL, vfS, rS, sldS, deltaS, delrhoL, delrhoS, sldSolv; double VL, VS, Np, f2, fSs; double psiL,psiS; double sfLS,sfSS; double slT; vfL = volfraction_lg; rL = radius_lg; sldL = sld_lg; vfS = volfraction_sm; fSs = surface_fraction; rS = radius_sm; sldS = sld_sm; deltaS = penetration; sldSolv = sld_solvent; delrhoL = fabs(sldL - sldSolv); delrhoS = fabs(sldS - sldSolv); VL = M_4PI_3*rL*rL*rL; VS = M_4PI_3*rS*rS*rS; //Number of small particles per large particle Np = vfS*fSs*VL/vfL/VS; //Total scattering length difference slT = delrhoL*VL + Np*delrhoS*VS; //Form factors for each particle psiL = sas_3j1x_x(q*rL); psiS = sas_3j1x_x(q*rS); //Cross term between large and small particles sfLS = psiL*psiS*sas_sinx_x(q*(rL+deltaS*rS)); //Cross term between small particles at the surface sfSS = psiS*psiS*sas_sinx_x(q*(rL+deltaS*rS))*sas_sinx_x(q*(rL+deltaS*rS)); //Large sphere form factor term f2 = delrhoL*delrhoL*VL*VL*psiL*psiL; //Small sphere form factor term f2 += Np*delrhoS*delrhoS*VS*VS*psiS*psiS; //Small particle - small particle cross term f2 += Np*(Np-1)*delrhoS*delrhoS*VS*VS*sfSS; //Large-small particle cross term f2 += 2*Np*delrhoL*delrhoS*VL*VS*sfLS; //Normalise by total scattering length difference if (f2 != 0.0){ f2 = f2/slT/slT; } //I(q) for large-small composite particles f2 = f2*(vfL*delrhoL*delrhoL*VL + vfS*fSs*Np*delrhoS*delrhoS*VS); //I(q) for free small particles f2+= vfS*(1.0-fSs)*delrhoS*delrhoS*VS*psiS*psiS; // normalize to single particle volume and convert to 1/cm f2 *= 1.0e8; // [=] 1/cm f2 *= 1.0e-12; // convert for (1/A^-6)^2 to (1/A)^2 return f2; } #endif // SAS_HAVE_raspberry /* END Required header for SASmodel raspberry */ %} DECLARE %{ double shape; double my_a_k; %} INITIALIZE %{ shape = -1; /* -1:no shape, 0:cyl, 1:box, 2:sphere */ if (xwidth && yheight && zdepth) shape = 1; else if (R > 0 && yheight) shape = 0; else if (R > 0 && !yheight) shape = 2; if (shape < 0) exit (fprintf (stderr, "SasView_model: %s: sample has invalid dimensions.\n" "ERROR Please check parameter values.\n", NAME_CURRENT_COMP)); /* now compute target coords if a component index is supplied */ if (!target_index && !target_x && !target_y && !target_z) target_index = 1; if (target_index) { Coords ToTarget; ToTarget = coords_sub (POS_A_COMP_INDEX (INDEX_CURRENT_COMP + target_index), POS_A_CURRENT_COMP); ToTarget = rot_apply (ROT_A_CURRENT_COMP, ToTarget); coords_get (ToTarget, &target_x, &target_y, &target_z); } if (!(target_x || target_y || target_z)) { printf ("SasView_model: %s: The target is not defined. Using direct beam (Z-axis).\n", NAME_CURRENT_COMP); target_z = 1; } /*TODO fix absorption*/ my_a_k = model_abs; /* assume absorption is given in 1/m */ %} TRACE %{ double l0, l1, k, l_full, l, dl, d_Phi; double aim_x = 0, aim_y = 0, aim_z = 1, axis_x, axis_y, axis_z; double f, solid_angle, kx_i, ky_i, kz_i, q, qx, qy, qz; char intersect = 0; /* Intersection photon trajectory / sample (sample surface) */ if (shape == 0) { intersect = cylinder_intersect (&l0, &l1, x, y, z, kx, ky, kz, R, yheight); } else if (shape == 1) { intersect = box_intersect (&l0, &l1, x, y, z, kx, ky, kz, xwidth, yheight, zdepth); } else if (shape == 2) { intersect = sphere_intersect (&l0, &l1, x, y, z, kx, ky, kz, R); } if (intersect) { if (l0 < 0) ABSORB; /* Photon enters at l0. */ k = sqrt (kx * kx + ky * ky + kz * kz); l_full = (l1 - l0); /* Length of full path through sample */ dl = rand01 () * (l1 - l0) + l0; /* Point of scattering */ PROP_DL (dl); /* Point of scattering */ l = (dl - l0); /* Penetration in sample */ kx_i = kx; ky_i = ky; kz_i = kz; if ((target_x || target_y || target_z)) { aim_x = target_x - x; /* Vector pointing at target (anal./det.) */ aim_y = target_y - y; aim_z = target_z - z; } if (focus_aw && focus_ah) { randvec_target_rect_angular (&kx, &ky, &kz, &solid_angle, aim_x, aim_y, aim_z, focus_aw, focus_ah, ROT_A_CURRENT_COMP); } else if (focus_xw && focus_yh) { randvec_target_rect (&kx, &ky, &kz, &solid_angle, aim_x, aim_y, aim_z, focus_xw, focus_yh, ROT_A_CURRENT_COMP); } else { randvec_target_circle (&kx, &ky, &kz, &solid_angle, aim_x, aim_y, aim_z, focus_r); } NORM (kx, ky, kz); kx *= k; ky *= k; kz *= k; qx = (kx_i - kx); qy = (ky_i - ky); qz = (kz_i - kz); q = sqrt (qx * qx + qy * qy + qz * qz); double trace_radius_lg = radius_lg; double trace_radius_sm = radius_sm; if (pd_radius_lg != 0.0 || pd_radius_sm != 0.0) { trace_radius_lg = (randnorm () * pd_radius_lg + 1.0) * radius_lg; trace_radius_sm = (randnorm () * pd_radius_sm + 1.0) * radius_sm; } // Sample dependent. Retrieved from SasView.///////////////////// float Iq_out; Iq_out = 1; Iq_out = Iq_raspberry (q, sld_lg, sld_sm, sld_solvent, volfraction_lg, volfraction_sm, surface_fraction, trace_radius_lg, trace_radius_sm, penetration); float vol; vol = 1; // Scale by 1.0E2 [SasView: 1/cm -> McXtrace: 1/m] Iq_out = model_scale * Iq_out / vol * 1.0E2; p *= l_full * solid_angle / (4 * PI) * Iq_out * exp (-my_a_k * (l + l1)); SCATTER; } %} MCDISPLAY %{ if (shape == 0) { /* cylinder */ cylinder (0, 0, 0, R, yheight, 0, 0, 1, 0); } else if (shape == 1) { /* box */ box (0, 0, 0, xwidth, yheight, zdepth, 0, 0, 1, 0); } else if (shape == 2) { /* sphere */ sphere (0, 0, 0, R); } %} END