[975ec8e] | 1 | /** |
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| 2 | This software was developed by the University of Tennessee as part of the |
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| 3 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 4 | project funded by the US National Science Foundation. |
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| 5 | |
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| 6 | If you use DANSE applications to do scientific research that leads to |
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| 7 | publication, we ask that you acknowledge the use of the software with the |
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| 8 | following sentence: |
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| 9 | |
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| 10 | "This work benefited from DANSE software developed under NSF award DMR-0520547." |
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| 11 | |
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| 12 | copyright 2008, University of Tennessee |
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| 13 | */ |
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| 14 | |
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| 15 | /** |
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| 16 | * Scattering model classes |
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| 17 | * The classes use the IGOR library found in |
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| 18 | * sansmodels/src/libigor |
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| 19 | * |
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| 20 | */ |
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| 21 | |
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| 22 | #include <math.h> |
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| 23 | #include "parameters.hh" |
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| 24 | #include <stdio.h> |
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[82c11d3] | 25 | #include <stdlib.h> |
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[975ec8e] | 26 | using namespace std; |
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[82c11d3] | 27 | #include "spheroid.h" |
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[975ec8e] | 28 | |
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| 29 | extern "C" { |
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[82c11d3] | 30 | #include "libCylinder.h" |
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| 31 | #include "libStructureFactor.h" |
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| 32 | } |
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| 33 | |
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| 34 | typedef struct { |
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| 35 | double scale; |
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| 36 | double equat_core; |
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| 37 | double polar_core; |
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| 38 | double equat_shell; |
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| 39 | double polar_shell; |
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| 40 | double sld_core; |
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| 41 | double sld_shell; |
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| 42 | double sld_solvent; |
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| 43 | double background; |
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| 44 | double axis_theta; |
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| 45 | double axis_phi; |
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| 46 | |
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| 47 | } SpheroidParameters; |
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| 48 | |
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| 49 | /** |
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| 50 | * Function to evaluate 2D scattering function |
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| 51 | * @param pars: parameters of the prolate |
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| 52 | * @param q: q-value |
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| 53 | * @param q_x: q_x / q |
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| 54 | * @param q_y: q_y / q |
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| 55 | * @return: function value |
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| 56 | */ |
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| 57 | static double spheroid_analytical_2D_scaled(SpheroidParameters *pars, double q, double q_x, double q_y) { |
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| 58 | |
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| 59 | double cyl_x, cyl_y, cyl_z; |
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| 60 | double q_z; |
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| 61 | double alpha, vol, cos_val; |
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| 62 | double answer; |
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| 63 | double Pi = 4.0*atan(1.0); |
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| 64 | double sldcs,sldss; |
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| 65 | |
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| 66 | //convert angle degree to radian |
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| 67 | double theta = pars->axis_theta * Pi/180.0; |
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| 68 | double phi = pars->axis_phi * Pi/180.0; |
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| 69 | |
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| 70 | |
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| 71 | // ellipsoid orientation, the axis of the rotation is consistent with the ploar axis. |
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| 72 | cyl_x = sin(theta) * cos(phi); |
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| 73 | cyl_y = sin(theta) * sin(phi); |
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| 74 | cyl_z = cos(theta); |
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| 75 | //del sld |
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| 76 | sldcs = pars->sld_core - pars->sld_shell; |
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| 77 | sldss = pars->sld_shell- pars->sld_solvent; |
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| 78 | |
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| 79 | // q vector |
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| 80 | q_z = 0; |
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| 81 | |
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| 82 | // Compute the angle btw vector q and the |
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| 83 | // axis of the cylinder |
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| 84 | cos_val = cyl_x*q_x + cyl_y*q_y + cyl_z*q_z; |
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| 85 | |
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| 86 | // The following test should always pass |
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| 87 | if (fabs(cos_val)>1.0) { |
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| 88 | printf("cyl_ana_2D: Unexpected error: cos(alpha)>1\n"); |
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| 89 | return 0; |
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| 90 | } |
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| 91 | |
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| 92 | // Note: cos(alpha) = 0 and 1 will get an |
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| 93 | // undefined value from CylKernel |
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| 94 | alpha = acos( cos_val ); |
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| 95 | |
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| 96 | // Call the IGOR library function to get the kernel: MUST use gfn4 not gf2 because of the def of params. |
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| 97 | answer = gfn4(cos_val,pars->equat_core,pars->polar_core,pars->equat_shell,pars->polar_shell,sldcs,sldss,q); |
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| 98 | //It seems that it should be normalized somehow. How??? |
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| 99 | |
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| 100 | //normalize by cylinder volume |
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| 101 | //NOTE that for this (Fournet) definition of the integral, one must MULTIPLY by Vcyl |
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| 102 | vol = 4.0*Pi/3.0*pars->equat_shell*pars->equat_shell*pars->polar_shell; |
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| 103 | answer /= vol; |
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| 104 | |
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| 105 | //convert to [cm-1] |
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| 106 | answer *= 1.0e8; |
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| 107 | |
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| 108 | //Scale |
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| 109 | answer *= pars->scale; |
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| 110 | |
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| 111 | // add in the background |
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| 112 | answer += pars->background; |
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| 113 | |
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| 114 | return answer; |
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[975ec8e] | 115 | } |
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| 116 | |
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[eddff027] | 117 | CoreShellEllipsoidModel :: CoreShellEllipsoidModel() { |
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[82c11d3] | 118 | scale = Parameter(1.0); |
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| 119 | equat_core = Parameter(200.0, true); |
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| 120 | equat_core.set_min(0.0); |
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| 121 | polar_core = Parameter(20.0, true); |
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| 122 | polar_core.set_min(0.0); |
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| 123 | equat_shell = Parameter(250.0, true); |
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| 124 | equat_shell.set_min(0.0); |
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| 125 | polar_shell = Parameter(30.0, true); |
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| 126 | polar_shell.set_min(0.0); |
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| 127 | sld_core = Parameter(2e-6); |
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| 128 | sld_shell = Parameter(1e-6); |
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| 129 | sld_solvent = Parameter(6.3e-6); |
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| 130 | background = Parameter(0.0); |
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| 131 | axis_theta = Parameter(0.0, true); |
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| 132 | axis_phi = Parameter(0.0, true); |
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[975ec8e] | 133 | |
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| 134 | } |
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| 135 | |
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[82c11d3] | 136 | |
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| 137 | /** |
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| 138 | * Function to evaluate 2D scattering function |
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| 139 | * @param pars: parameters of the prolate |
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| 140 | * @param q: q-value |
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| 141 | * @return: function value |
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| 142 | */ |
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| 143 | static double spheroid_analytical_2DXY(SpheroidParameters *pars, double qx, double qy) { |
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| 144 | double q; |
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| 145 | q = sqrt(qx*qx+qy*qy); |
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| 146 | return spheroid_analytical_2D_scaled(pars, q, qx/q, qy/q); |
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| 147 | } |
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| 148 | |
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[975ec8e] | 149 | /** |
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| 150 | * Function to evaluate 1D scattering function |
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| 151 | * The NIST IGOR library is used for the actual calculation. |
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| 152 | * @param q: q-value |
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| 153 | * @return: function value |
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| 154 | */ |
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[eddff027] | 155 | double CoreShellEllipsoidModel :: operator()(double q) { |
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[82c11d3] | 156 | double dp[9]; |
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| 157 | |
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| 158 | // Fill parameter array for IGOR library |
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| 159 | // Add the background after averaging |
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| 160 | dp[0] = scale(); |
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| 161 | dp[1] = equat_core(); |
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| 162 | dp[2] = polar_core(); |
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| 163 | dp[3] = equat_shell(); |
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| 164 | dp[4] = polar_shell(); |
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| 165 | dp[5] = sld_core(); |
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| 166 | dp[6] = sld_shell(); |
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| 167 | dp[7] = sld_solvent(); |
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| 168 | dp[8] = 0.0; |
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| 169 | |
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| 170 | // Get the dispersion points for the major core |
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| 171 | vector<WeightPoint> weights_equat_core; |
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| 172 | equat_core.get_weights(weights_equat_core); |
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| 173 | |
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| 174 | // Get the dispersion points for the minor core |
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| 175 | vector<WeightPoint> weights_polar_core; |
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| 176 | polar_core.get_weights(weights_polar_core); |
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| 177 | |
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| 178 | // Get the dispersion points for the major shell |
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| 179 | vector<WeightPoint> weights_equat_shell; |
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| 180 | equat_shell.get_weights(weights_equat_shell); |
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| 181 | |
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| 182 | // Get the dispersion points for the minor_shell |
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| 183 | vector<WeightPoint> weights_polar_shell; |
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| 184 | polar_shell.get_weights(weights_polar_shell); |
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| 185 | |
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| 186 | |
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| 187 | // Perform the computation, with all weight points |
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| 188 | double sum = 0.0; |
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| 189 | double norm = 0.0; |
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| 190 | double vol = 0.0; |
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| 191 | |
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| 192 | // Loop over major core weight points |
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| 193 | for(int i=0; i<(int)weights_equat_core.size(); i++) { |
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| 194 | dp[1] = weights_equat_core[i].value; |
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| 195 | |
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| 196 | // Loop over minor core weight points |
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| 197 | for(int j=0; j<(int)weights_polar_core.size(); j++) { |
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| 198 | dp[2] = weights_polar_core[j].value; |
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| 199 | |
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| 200 | // Loop over major shell weight points |
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| 201 | for(int k=0; k<(int)weights_equat_shell.size(); k++) { |
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| 202 | dp[3] = weights_equat_shell[k].value; |
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| 203 | |
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| 204 | // Loop over minor shell weight points |
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| 205 | for(int l=0; l<(int)weights_polar_shell.size(); l++) { |
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| 206 | dp[4] = weights_polar_shell[l].value; |
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| 207 | //Un-normalize by volume |
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| 208 | sum += weights_equat_core[i].weight* weights_polar_core[j].weight * weights_equat_shell[k].weight |
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| 209 | * weights_polar_shell[l].weight * OblateForm(dp, q) |
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| 210 | * pow(weights_equat_shell[k].value,2)*weights_polar_shell[l].value; |
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| 211 | //Find average volume |
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| 212 | vol += weights_equat_core[i].weight* weights_polar_core[j].weight |
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| 213 | * weights_equat_shell[k].weight |
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| 214 | * weights_polar_shell[l].weight |
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| 215 | * pow(weights_equat_shell[k].value,2)*weights_polar_shell[l].value; |
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| 216 | norm += weights_equat_core[i].weight* weights_polar_core[j].weight * weights_equat_shell[k].weight |
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| 217 | * weights_polar_shell[l].weight; |
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| 218 | } |
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| 219 | } |
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| 220 | } |
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| 221 | } |
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| 222 | if (vol != 0.0 && norm != 0.0) { |
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| 223 | //Re-normalize by avg volume |
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| 224 | sum = sum/(vol/norm);} |
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| 225 | return sum/norm + background(); |
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[975ec8e] | 226 | } |
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| 227 | |
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| 228 | /** |
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| 229 | * Function to evaluate 2D scattering function |
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| 230 | * @param q_x: value of Q along x |
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| 231 | * @param q_y: value of Q along y |
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| 232 | * @return: function value |
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| 233 | */ |
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| 234 | /* |
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| 235 | double OblateModel :: operator()(double qx, double qy) { |
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| 236 | double q = sqrt(qx*qx + qy*qy); |
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| 237 | |
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| 238 | return (*this).operator()(q); |
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| 239 | } |
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[82c11d3] | 240 | */ |
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[975ec8e] | 241 | |
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| 242 | /** |
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| 243 | * Function to evaluate 2D scattering function |
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| 244 | * @param pars: parameters of the oblate |
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| 245 | * @param q: q-value |
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| 246 | * @param phi: angle phi |
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| 247 | * @return: function value |
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| 248 | */ |
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[eddff027] | 249 | double CoreShellEllipsoidModel :: evaluate_rphi(double q, double phi) { |
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[82c11d3] | 250 | double qx = q*cos(phi); |
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| 251 | double qy = q*sin(phi); |
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| 252 | return (*this).operator()(qx, qy); |
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[975ec8e] | 253 | } |
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| 254 | |
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[5eb9154] | 255 | /** |
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| 256 | * Function to evaluate 2D scattering function |
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| 257 | * @param q_x: value of Q along x |
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| 258 | * @param q_y: value of Q along y |
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| 259 | * @return: function value |
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| 260 | */ |
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[eddff027] | 261 | double CoreShellEllipsoidModel :: operator()(double qx, double qy) { |
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[82c11d3] | 262 | SpheroidParameters dp; |
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| 263 | // Fill parameter array |
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| 264 | dp.scale = scale(); |
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| 265 | dp.equat_core = equat_core(); |
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| 266 | dp.polar_core = polar_core(); |
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| 267 | dp.equat_shell = equat_shell(); |
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| 268 | dp.polar_shell = polar_shell(); |
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| 269 | dp.sld_core = sld_core(); |
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| 270 | dp.sld_shell = sld_shell(); |
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| 271 | dp.sld_solvent = sld_solvent(); |
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| 272 | dp.background = 0.0; |
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| 273 | dp.axis_theta = axis_theta(); |
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| 274 | dp.axis_phi = axis_phi(); |
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| 275 | |
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| 276 | // Get the dispersion points for the major core |
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| 277 | vector<WeightPoint> weights_equat_core; |
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| 278 | equat_core.get_weights(weights_equat_core); |
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| 279 | |
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| 280 | // Get the dispersion points for the minor core |
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| 281 | vector<WeightPoint> weights_polar_core; |
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| 282 | polar_core.get_weights(weights_polar_core); |
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| 283 | |
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| 284 | // Get the dispersion points for the major shell |
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| 285 | vector<WeightPoint> weights_equat_shell; |
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| 286 | equat_shell.get_weights(weights_equat_shell); |
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| 287 | |
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| 288 | // Get the dispersion points for the minor shell |
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| 289 | vector<WeightPoint> weights_polar_shell; |
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| 290 | polar_shell.get_weights(weights_polar_shell); |
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| 291 | |
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| 292 | |
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| 293 | // Get angular averaging for theta |
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| 294 | vector<WeightPoint> weights_theta; |
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| 295 | axis_theta.get_weights(weights_theta); |
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| 296 | |
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| 297 | // Get angular averaging for phi |
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| 298 | vector<WeightPoint> weights_phi; |
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| 299 | axis_phi.get_weights(weights_phi); |
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| 300 | |
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| 301 | // Perform the computation, with all weight points |
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| 302 | double sum = 0.0; |
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| 303 | double norm = 0.0; |
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| 304 | double norm_vol = 0.0; |
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| 305 | double vol = 0.0; |
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| 306 | double pi = 4.0*atan(1.0); |
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| 307 | // Loop over major core weight points |
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| 308 | for(int i=0; i< (int)weights_equat_core.size(); i++) { |
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| 309 | dp.equat_core = weights_equat_core[i].value; |
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| 310 | |
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| 311 | // Loop over minor core weight points |
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| 312 | for(int j=0; j< (int)weights_polar_core.size(); j++) { |
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| 313 | dp.polar_core = weights_polar_core[j].value; |
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| 314 | |
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| 315 | // Loop over major shell weight points |
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| 316 | for(int k=0; k< (int)weights_equat_shell.size(); k++) { |
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| 317 | dp.equat_shell = weights_equat_shell[i].value; |
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| 318 | |
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| 319 | // Loop over minor shell weight points |
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| 320 | for(int l=0; l< (int)weights_polar_shell.size(); l++) { |
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| 321 | dp.polar_shell = weights_polar_shell[l].value; |
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| 322 | |
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| 323 | // Average over theta distribution |
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| 324 | for(int m=0; m< (int)weights_theta.size(); m++) { |
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| 325 | dp.axis_theta = weights_theta[m].value; |
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| 326 | |
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| 327 | // Average over phi distribution |
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| 328 | for(int n=0; n< (int)weights_phi.size(); n++) { |
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| 329 | dp.axis_phi = weights_phi[n].value; |
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| 330 | //Un-normalize by volume |
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| 331 | double _ptvalue = weights_equat_core[i].weight *weights_polar_core[j].weight |
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| 332 | * weights_equat_shell[k].weight * weights_polar_shell[l].weight |
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| 333 | * weights_theta[m].weight |
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| 334 | * weights_phi[n].weight |
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| 335 | * spheroid_analytical_2DXY(&dp, qx, qy) |
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| 336 | * pow(weights_equat_shell[k].value,2)*weights_polar_shell[l].value; |
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| 337 | if (weights_theta.size()>1) { |
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| 338 | _ptvalue *= fabs(sin(weights_theta[m].value*pi/180.0)); |
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| 339 | } |
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| 340 | sum += _ptvalue; |
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| 341 | //Find average volume |
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| 342 | vol += weights_equat_shell[k].weight |
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| 343 | * weights_polar_shell[l].weight |
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| 344 | * pow(weights_equat_shell[k].value,2)*weights_polar_shell[l].value; |
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| 345 | //Find norm for volume |
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| 346 | norm_vol += weights_equat_shell[k].weight |
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| 347 | * weights_polar_shell[l].weight; |
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| 348 | |
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| 349 | norm += weights_equat_core[i].weight *weights_polar_core[j].weight |
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| 350 | * weights_equat_shell[k].weight * weights_polar_shell[l].weight |
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| 351 | * weights_theta[m].weight * weights_phi[n].weight; |
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| 352 | } |
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| 353 | } |
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| 354 | } |
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| 355 | } |
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| 356 | } |
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| 357 | } |
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| 358 | // Averaging in theta needs an extra normalization |
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| 359 | // factor to account for the sin(theta) term in the |
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| 360 | // integration (see documentation). |
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| 361 | if (weights_theta.size()>1) norm = norm / asin(1.0); |
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| 362 | |
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| 363 | if (vol != 0.0 && norm_vol != 0.0) { |
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| 364 | //Re-normalize by avg volume |
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| 365 | sum = sum/(vol/norm_vol);} |
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| 366 | |
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| 367 | return sum/norm + background(); |
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[975ec8e] | 368 | } |
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| 369 | |
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[5eb9154] | 370 | /** |
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| 371 | * Function to calculate effective radius |
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| 372 | * @return: effective radius value |
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| 373 | */ |
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| 374 | double CoreShellEllipsoidModel :: calculate_ER() { |
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[82c11d3] | 375 | SpheroidParameters dp; |
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| 376 | |
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| 377 | dp.equat_shell = equat_shell(); |
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| 378 | dp.polar_shell = polar_shell(); |
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| 379 | |
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| 380 | double rad_out = 0.0; |
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| 381 | |
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| 382 | // Perform the computation, with all weight points |
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| 383 | double sum = 0.0; |
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| 384 | double norm = 0.0; |
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| 385 | |
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| 386 | // Get the dispersion points for the major shell |
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| 387 | vector<WeightPoint> weights_equat_shell; |
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| 388 | equat_shell.get_weights(weights_equat_shell); |
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| 389 | |
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| 390 | // Get the dispersion points for the minor shell |
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| 391 | vector<WeightPoint> weights_polar_shell; |
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| 392 | polar_shell.get_weights(weights_polar_shell); |
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| 393 | |
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| 394 | // Loop over major shell weight points |
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| 395 | for(int i=0; i< (int)weights_equat_shell.size(); i++) { |
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| 396 | dp.equat_shell = weights_equat_shell[i].value; |
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| 397 | for(int k=0; k< (int)weights_polar_shell.size(); k++) { |
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| 398 | dp.polar_shell = weights_polar_shell[k].value; |
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| 399 | //Note: output of "DiamEllip(dp.polar_shell,dp.equat_shell)" is DIAMETER. |
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| 400 | sum +=weights_equat_shell[i].weight |
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| 401 | * weights_polar_shell[k].weight*DiamEllip(dp.polar_shell,dp.equat_shell)/2.0; |
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| 402 | norm += weights_equat_shell[i].weight* weights_polar_shell[k].weight; |
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| 403 | } |
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| 404 | } |
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| 405 | if (norm != 0){ |
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| 406 | //return the averaged value |
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| 407 | rad_out = sum/norm;} |
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| 408 | else{ |
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| 409 | //return normal value |
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| 410 | //Note: output of "DiamEllip(dp.polar_shell,dp.equat_shell)" is DIAMETER. |
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| 411 | rad_out = DiamEllip(dp.polar_shell,dp.equat_shell)/2.0;} |
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| 412 | |
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| 413 | return rad_out; |
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[5eb9154] | 414 | } |
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[e08bd5b] | 415 | double CoreShellEllipsoidModel :: calculate_VR() { |
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| 416 | return 1.0; |
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| 417 | } |
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