/******************************************************************************* * * McStas, neutron ray-tracing package * Copyright (C) 1997-2008, All rights reserved * Risoe National Laboratory, Roskilde, Denmark * Institut Laue Langevin, Grenoble, France * * Component: SasView_polymer_micelle * * %Identification * Written by: Jose Robledo * Based on sasmodels from SasView * Origin: FZJ / DTU / ESS DMSC * * * SasView polymer_micelle model component as sample description. * * %Description * * SasView_polymer_micelle component, generated from polymer_micelle.c in sasmodels. * * Example: * SasView_polymer_micelle(ndensity, v_core, v_corona, sld_solvent, sld_core, sld_corona, radius_core, rg, d_penetration, n_aggreg, * 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_core=0.0, pd_rg=0.0) * * %Parameters * INPUT PARAMETERS: * ndensity: [1e15/cm^3] ([0.0, inf]) Number density of micelles. * v_core: [Ang^3] ([0.0, inf]) Core volume . * v_corona: [Ang^3] ([0.0, inf]) Corona volume. * sld_solvent: [1e-6/Ang^2] ([0.0, inf]) Solvent scattering length density. * sld_core: [1e-6/Ang^2] ([0.0, inf]) Core scattering length density. * sld_corona: [1e-6/Ang^2] ([0.0, inf]) Corona scattering length density. * radius_core: [Ang] ([0.0, inf]) Radius of core ( must be >> rg ). * rg: [Ang] ([0.0, inf]) Radius of gyration of chains in corona. * d_penetration: [] ([-inf, inf]) Factor to mimic non-penetration of Gaussian chains. * n_aggreg: [] ([-inf, inf]) Aggregation number of the micelle. * 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_core: [] (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable. * pd_rg: [] (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_polymer_micelle SETTING PARAMETERS ( ndensity=8.94, v_core=62624.0, v_corona=61940.0, sld_solvent=6.4, sld_core=0.34, sld_corona=0.8, radius_core=45.0, rg=20.0, d_penetration=1.0, n_aggreg=6.0, 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_core=0.0, pd_rg=0.0) SHARE %{ %include "sas_kernel_header.c" /* BEGIN Required header for SASmodel polymer_micelle */ #define HAS_Iq #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_polymer_micelle #define SAS_HAVE_polymer_micelle #line 1 "polymer_micelle" double Iq_polymer_micelle(double q, double ndensity, double v_core, double v_corona, double solvent_sld, double core_sld, double corona_sld, double radius_core, double rg, double d_penetration, double n_aggreg); static double micelle_spherical_kernel(double q, double ndensity, double v_core, double v_corona, double solvent_sld, double core_sld, double corona_sld, double radius_core, double rg, double d_penetration, double n_aggreg) { const double rho_solv = solvent_sld; // sld of solvent [1/A^2] const double rho_core = core_sld; // sld of core [1/A^2] const double rho_corona = corona_sld; // sld of corona [1/A^2] const double beta_core = v_core * (rho_core - rho_solv); const double beta_corona = v_corona * (rho_corona - rho_solv); // Self-correlation term of the core const double bes_core = sas_3j1x_x(q*radius_core); const double term1 = square(n_aggreg*beta_core*bes_core); // Self-correlation term of the chains const double qrg2 = square(q*rg); const double debye_chain = (qrg2 == 0.0) ? 1.0 : 2.0*(expm1(-qrg2)+qrg2)/(qrg2*qrg2); const double term2 = n_aggreg * beta_corona * beta_corona * debye_chain; // Interference cross-term between core and chains const double chain_ampl = (qrg2 == 0.0) ? 1.0 : -expm1(-qrg2)/qrg2; const double bes_corona = sas_sinx_x(q*(radius_core + d_penetration * rg)); const double term3 = 2.0 * n_aggreg * n_aggreg * beta_core * beta_corona * bes_core * chain_ampl * bes_corona; // Interference cross-term between chains const double term4 = n_aggreg * (n_aggreg - 1.0) * square(beta_corona * chain_ampl * bes_corona); // I(q)_micelle : Sum of 4 terms computed above double i_micelle = term1 + term2 + term3 + term4; // rescale from [A^2] to [cm^2] i_micelle *= 1.0e-13; // "normalize" by number density --> intensity in [cm-1] i_micelle *= ndensity; return(i_micelle); } double Iq_polymer_micelle(double q, double ndensity, double v_core, double v_corona, double solvent_sld, double core_sld, double corona_sld, double radius_core, double rg, double d_penetration, double n_aggreg) { return micelle_spherical_kernel(q, ndensity, v_core, v_corona, solvent_sld, core_sld, corona_sld, radius_core, rg, d_penetration, n_aggreg); } #endif // SAS_HAVE_polymer_micelle /* END Required header for SASmodel polymer_micelle */ %} DECLARE %{ double shape; double my_a_v; %} 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; } my_a_v = model_abs * 2200 * 100; /* Is not yet divided by v. 100: Convert barns -> fm^2 */ %} TRACE %{ double t0, t1, v, l_full, l, l_1, dt, d_phi, my_s; double aim_x = 0, aim_y = 0, aim_z = 1, axis_x, axis_y, axis_z; double arg, tmp_vx, tmp_vy, tmp_vz, vout_x, vout_y, vout_z; double f, solid_angle, vx_i, vy_i, vz_i, q, qx, qy, qz; char intersect = 0; /* Intersection neutron trajectory / sample (sample surface) */ if (shape == 0) { intersect = cylinder_intersect (&t0, &t1, x, y, z, vx, vy, vz, R, yheight); } else if (shape == 1) { intersect = box_intersect (&t0, &t1, x, y, z, vx, vy, vz, xwidth, yheight, zdepth); } else if (shape == 2) { intersect = sphere_intersect (&t0, &t1, x, y, z, vx, vy, vz, R); } if (intersect) { if (t0 < 0) ABSORB; /* Neutron enters at t=t0. */ v = sqrt (vx * vx + vy * vy + vz * vz); l_full = v * (t1 - t0); /* Length of full path through sample */ dt = rand01 () * (t1 - t0) + t0; /* Time of scattering */ PROP_DT (dt); /* Point of scattering */ l = v * (dt - t0); /* Penetration in sample */ vx_i = vx; vy_i = vy; vz_i = vz; 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 (&vx, &vy, &vz, &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 (&vx, &vy, &vz, &solid_angle, aim_x, aim_y, aim_z, focus_xw, focus_yh, ROT_A_CURRENT_COMP); } else { randvec_target_circle (&vx, &vy, &vz, &solid_angle, aim_x, aim_y, aim_z, focus_r); } NORM (vx, vy, vz); vx *= v; vy *= v; vz *= v; qx = V2K * (vx_i - vx); qy = V2K * (vy_i - vy); qz = V2K * (vz_i - vz); q = sqrt (qx * qx + qy * qy + qz * qz); double trace_radius_core = radius_core; double trace_rg = rg; if (pd_radius_core != 0.0 || pd_rg != 0.0) { trace_radius_core = (randnorm () * pd_radius_core + 1.0) * radius_core; trace_rg = (randnorm () * pd_rg + 1.0) * rg; } // Sample dependent. Retrieved from SasView.///////////////////// float Iq_out; Iq_out = 1; Iq_out = Iq_polymer_micelle (q, ndensity, v_core, v_corona, sld_solvent, sld_core, sld_corona, trace_radius_core, trace_rg, d_penetration, n_aggreg); float vol; vol = 1; // Scale by 1.0E2 [SasView: 1/cm -> McStas: 1/m] Iq_out = model_scale * Iq_out / vol * 1.0E2; l_1 = v * t1; p *= l_full * solid_angle / (4 * PI) * Iq_out * exp (-my_a_v * (l + l_1) / v); SCATTER; } %} MCDISPLAY %{ if (shape == 0) { /* cylinder */ circle ("xz", 0, yheight / 2.0, 0, R); circle ("xz", 0, -yheight / 2.0, 0, R); line (-R, -yheight / 2.0, 0, -R, +yheight / 2.0, 0); line (+R, -yheight / 2.0, 0, +R, +yheight / 2.0, 0); line (0, -yheight / 2.0, -R, 0, +yheight / 2.0, -R); line (0, -yheight / 2.0, +R, 0, +yheight / 2.0, +R); } else if (shape == 1) { /* box */ double xmin = -0.5 * xwidth; double xmax = 0.5 * xwidth; double ymin = -0.5 * yheight; double ymax = 0.5 * yheight; double zmin = -0.5 * zdepth; double zmax = 0.5 * zdepth; multiline (5, xmin, ymin, zmin, xmax, ymin, zmin, xmax, ymax, zmin, xmin, ymax, zmin, xmin, ymin, zmin); multiline (5, xmin, ymin, zmax, xmax, ymin, zmax, xmax, ymax, zmax, xmin, ymax, zmax, xmin, ymin, zmax); line (xmin, ymin, zmin, xmin, ymin, zmax); line (xmax, ymin, zmin, xmax, ymin, zmax); line (xmin, ymax, zmin, xmin, ymax, zmax); line (xmax, ymax, zmin, xmax, ymax, zmax); } else if (shape == 2) { /* sphere */ circle ("xy", 0, 0.0, 0, R); circle ("xz", 0, 0.0, 0, R); circle ("yz", 0, 0.0, 0, R); } %} END