[fca6936] | 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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| 25 | using namespace std; |
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| 26 | |
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| 27 | extern "C" { |
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| 28 | #include "libCylinder.h" |
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[5eb9154] | 29 | #include "libStructureFactor.h" |
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[fca6936] | 30 | } |
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[0c2389e] | 31 | #include "cylinder.h" |
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[fca6936] | 32 | |
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[dbddbf5] | 33 | // Convenience parameter structure |
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| 34 | typedef struct { |
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| 35 | double scale; |
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| 36 | double radius; |
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| 37 | double length; |
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| 38 | double sldCyl; |
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| 39 | double sldSolv; |
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| 40 | double background; |
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| 41 | double cyl_theta; |
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| 42 | double cyl_phi; |
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| 43 | } CylinderParameters; |
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| 44 | |
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[af03ddd] | 45 | CylinderModel :: CylinderModel() { |
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[fca6936] | 46 | scale = Parameter(1.0); |
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| 47 | radius = Parameter(20.0, true); |
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| 48 | radius.set_min(0.0); |
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| 49 | length = Parameter(400.0, true); |
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| 50 | length.set_min(0.0); |
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[f10063e] | 51 | sldCyl = Parameter(4.e-6); |
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| 52 | sldSolv = Parameter(1.e-6); |
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[fca6936] | 53 | background = Parameter(0.0); |
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| 54 | cyl_theta = Parameter(0.0, true); |
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| 55 | cyl_phi = Parameter(0.0, true); |
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| 56 | } |
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| 57 | |
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| 58 | /** |
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| 59 | * Function to evaluate 1D scattering function |
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| 60 | * The NIST IGOR library is used for the actual calculation. |
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| 61 | * @param q: q-value |
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| 62 | * @return: function value |
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| 63 | */ |
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[af03ddd] | 64 | double CylinderModel :: operator()(double q) { |
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[f10063e] | 65 | double dp[6]; |
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[fca6936] | 66 | |
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| 67 | // Fill parameter array for IGOR library |
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| 68 | // Add the background after averaging |
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| 69 | dp[0] = scale(); |
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| 70 | dp[1] = radius(); |
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| 71 | dp[2] = length(); |
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[f10063e] | 72 | dp[3] = sldCyl(); |
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| 73 | dp[4] = sldSolv(); |
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| 74 | dp[5] = 0.0; |
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[fca6936] | 75 | |
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| 76 | // Get the dispersion points for the radius |
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| 77 | vector<WeightPoint> weights_rad; |
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| 78 | radius.get_weights(weights_rad); |
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| 79 | |
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| 80 | // Get the dispersion points for the length |
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| 81 | vector<WeightPoint> weights_len; |
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| 82 | length.get_weights(weights_len); |
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| 83 | |
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| 84 | // Perform the computation, with all weight points |
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| 85 | double sum = 0.0; |
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| 86 | double norm = 0.0; |
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[c451be9] | 87 | double vol = 0.0; |
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[fca6936] | 88 | |
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| 89 | // Loop over radius weight points |
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[34c2649] | 90 | for(size_t i=0; i<weights_rad.size(); i++) { |
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[fca6936] | 91 | dp[1] = weights_rad[i].value; |
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| 92 | |
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| 93 | // Loop over length weight points |
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[34c2649] | 94 | for(size_t j=0; j<weights_len.size(); j++) { |
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[fca6936] | 95 | dp[2] = weights_len[j].value; |
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[c451be9] | 96 | //Un-normalize by volume |
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[fca6936] | 97 | sum += weights_rad[i].weight |
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[c451be9] | 98 | * weights_len[j].weight * CylinderForm(dp, q) |
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| 99 | *pow(weights_rad[i].value,2)*weights_len[j].value; |
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| 100 | |
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| 101 | //Find average volume |
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| 102 | vol += weights_rad[i].weight |
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| 103 | * weights_len[j].weight *pow(weights_rad[i].value,2)*weights_len[j].value; |
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[fca6936] | 104 | norm += weights_rad[i].weight |
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| 105 | * weights_len[j].weight; |
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| 106 | } |
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| 107 | } |
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[c451be9] | 108 | if (vol != 0.0 && norm != 0.0) { |
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| 109 | //Re-normalize by avg volume |
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| 110 | sum = sum/(vol/norm);} |
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| 111 | |
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[fca6936] | 112 | return sum/norm + background(); |
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| 113 | } |
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| 114 | |
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| 115 | /** |
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| 116 | * Function to evaluate 2D scattering function |
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[dbddbf5] | 117 | * @param pars: parameters of the cylinder |
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| 118 | * @param q: q-value |
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| 119 | * @param q_x: q_x / q |
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| 120 | * @param q_y: q_y / q |
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| 121 | * @return: function value |
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| 122 | */ |
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| 123 | static double cylinder_analytical_2D_scaled(CylinderParameters *pars, double q, double q_x, double q_y) { |
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| 124 | double cyl_x, cyl_y, cyl_z; |
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| 125 | double q_z; |
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| 126 | double alpha, vol, cos_val; |
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| 127 | double answer; |
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| 128 | //convert angle degree to radian |
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| 129 | double pi = 4.0*atan(1.0); |
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| 130 | double theta = pars->cyl_theta * pi/180.0; |
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| 131 | double phi = pars->cyl_phi * pi/180.0; |
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| 132 | |
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| 133 | // Cylinder orientation |
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| 134 | cyl_x = sin(theta) * cos(phi); |
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| 135 | cyl_y = sin(theta) * sin(phi); |
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| 136 | cyl_z = cos(theta); |
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| 137 | |
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| 138 | // q vector |
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| 139 | q_z = 0; |
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| 140 | |
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| 141 | // Compute the angle btw vector q and the |
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| 142 | // axis of the cylinder |
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| 143 | cos_val = cyl_x*q_x + cyl_y*q_y + cyl_z*q_z; |
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| 144 | |
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| 145 | // The following test should always pass |
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| 146 | if (fabs(cos_val)>1.0) { |
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| 147 | printf("cyl_ana_2D: Unexpected error: cos(alpha)>1\n"); |
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| 148 | return 0; |
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| 149 | } |
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| 150 | |
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| 151 | // Note: cos(alpha) = 0 and 1 will get an |
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| 152 | // undefined value from CylKernel |
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| 153 | alpha = acos( cos_val ); |
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| 154 | |
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| 155 | // Call the IGOR library function to get the kernel |
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| 156 | answer = CylKernel(q, pars->radius, pars->length/2.0, alpha) / sin(alpha); |
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| 157 | |
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| 158 | // Multiply by contrast^2 |
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| 159 | answer *= (pars->sldCyl - pars->sldSolv)*(pars->sldCyl - pars->sldSolv); |
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| 160 | |
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| 161 | //normalize by cylinder volume |
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| 162 | //NOTE that for this (Fournet) definition of the integral, one must MULTIPLY by Vcyl |
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| 163 | vol = acos(-1.0) * pars->radius * pars->radius * pars->length; |
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| 164 | answer *= vol; |
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| 165 | |
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| 166 | //convert to [cm-1] |
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| 167 | answer *= 1.0e8; |
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| 168 | |
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| 169 | //Scale |
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| 170 | answer *= pars->scale; |
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| 171 | |
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| 172 | // add in the background |
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| 173 | answer += pars->background; |
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| 174 | |
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| 175 | return answer; |
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| 176 | } |
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| 177 | |
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| 178 | /** |
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| 179 | * Function to evaluate 2D scattering function |
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| 180 | * @param pars: parameters of the cylinder |
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| 181 | * @param q: q-value |
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| 182 | * @return: function value |
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| 183 | */ |
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| 184 | static double cylinder_analytical_2DXY(CylinderParameters *pars, double qx, double qy) { |
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| 185 | double q; |
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| 186 | q = sqrt(qx*qx+qy*qy); |
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| 187 | return cylinder_analytical_2D_scaled(pars, q, qx/q, qy/q); |
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| 188 | } |
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| 189 | |
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| 190 | /** |
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| 191 | * Function to evaluate 2D scattering function |
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[fca6936] | 192 | * @param q_x: value of Q along x |
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| 193 | * @param q_y: value of Q along y |
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| 194 | * @return: function value |
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| 195 | */ |
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[af03ddd] | 196 | double CylinderModel :: operator()(double qx, double qy) { |
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[fca6936] | 197 | CylinderParameters dp; |
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| 198 | // Fill parameter array |
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| 199 | dp.scale = scale(); |
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| 200 | dp.radius = radius(); |
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| 201 | dp.length = length(); |
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[f10063e] | 202 | dp.sldCyl = sldCyl(); |
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| 203 | dp.sldSolv = sldSolv(); |
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[fca6936] | 204 | dp.background = 0.0; |
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| 205 | dp.cyl_theta = cyl_theta(); |
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| 206 | dp.cyl_phi = cyl_phi(); |
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| 207 | |
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| 208 | // Get the dispersion points for the radius |
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| 209 | vector<WeightPoint> weights_rad; |
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| 210 | radius.get_weights(weights_rad); |
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| 211 | |
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| 212 | // Get the dispersion points for the length |
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| 213 | vector<WeightPoint> weights_len; |
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| 214 | length.get_weights(weights_len); |
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| 215 | |
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| 216 | // Get angular averaging for theta |
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| 217 | vector<WeightPoint> weights_theta; |
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| 218 | cyl_theta.get_weights(weights_theta); |
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| 219 | |
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| 220 | // Get angular averaging for phi |
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| 221 | vector<WeightPoint> weights_phi; |
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| 222 | cyl_phi.get_weights(weights_phi); |
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| 223 | |
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| 224 | // Perform the computation, with all weight points |
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| 225 | double sum = 0.0; |
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| 226 | double norm = 0.0; |
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[c451be9] | 227 | double norm_vol = 0.0; |
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| 228 | double vol = 0.0; |
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[4628e31] | 229 | double pi = 4.0*atan(1.0); |
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[fca6936] | 230 | // Loop over radius weight points |
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[34c2649] | 231 | for(size_t i=0; i<weights_rad.size(); i++) { |
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[fca6936] | 232 | dp.radius = weights_rad[i].value; |
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| 233 | |
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| 234 | |
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| 235 | // Loop over length weight points |
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[34c2649] | 236 | for(size_t j=0; j<weights_len.size(); j++) { |
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[fca6936] | 237 | dp.length = weights_len[j].value; |
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| 238 | |
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| 239 | // Average over theta distribution |
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[34c2649] | 240 | for(size_t k=0; k<weights_theta.size(); k++) { |
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[fca6936] | 241 | dp.cyl_theta = weights_theta[k].value; |
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| 242 | |
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| 243 | // Average over phi distribution |
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[34c2649] | 244 | for(size_t l=0; l<weights_phi.size(); l++) { |
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[fca6936] | 245 | dp.cyl_phi = weights_phi[l].value; |
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[c451be9] | 246 | //Un-normalize by volume |
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[fca6936] | 247 | double _ptvalue = weights_rad[i].weight |
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| 248 | * weights_len[j].weight |
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| 249 | * weights_theta[k].weight |
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| 250 | * weights_phi[l].weight |
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[c451be9] | 251 | * cylinder_analytical_2DXY(&dp, qx, qy) |
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| 252 | *pow(weights_rad[i].value,2)*weights_len[j].value; |
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[fca6936] | 253 | if (weights_theta.size()>1) { |
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[4628e31] | 254 | _ptvalue *= fabs(sin(weights_theta[k].value*pi/180.0)); |
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[fca6936] | 255 | } |
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| 256 | sum += _ptvalue; |
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[c451be9] | 257 | //Find average volume |
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| 258 | vol += weights_rad[i].weight |
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| 259 | * weights_len[j].weight |
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| 260 | * pow(weights_rad[i].value,2)*weights_len[j].value; |
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| 261 | //Find norm for volume |
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| 262 | norm_vol += weights_rad[i].weight |
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| 263 | * weights_len[j].weight; |
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[fca6936] | 264 | |
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| 265 | norm += weights_rad[i].weight |
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| 266 | * weights_len[j].weight |
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| 267 | * weights_theta[k].weight |
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| 268 | * weights_phi[l].weight; |
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| 269 | |
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| 270 | } |
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| 271 | } |
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| 272 | } |
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| 273 | } |
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| 274 | // Averaging in theta needs an extra normalization |
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| 275 | // factor to account for the sin(theta) term in the |
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| 276 | // integration (see documentation). |
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| 277 | if (weights_theta.size()>1) norm = norm / asin(1.0); |
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[c451be9] | 278 | if (vol != 0.0 && norm_vol != 0.0) { |
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| 279 | //Re-normalize by avg volume |
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| 280 | sum = sum/(vol/norm_vol);} |
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| 281 | |
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[fca6936] | 282 | return sum/norm + background(); |
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| 283 | } |
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| 284 | |
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| 285 | /** |
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| 286 | * Function to evaluate 2D scattering function |
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| 287 | * @param pars: parameters of the cylinder |
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| 288 | * @param q: q-value |
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| 289 | * @param phi: angle phi |
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| 290 | * @return: function value |
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| 291 | */ |
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[af03ddd] | 292 | double CylinderModel :: evaluate_rphi(double q, double phi) { |
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[fca6936] | 293 | double qx = q*cos(phi); |
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| 294 | double qy = q*sin(phi); |
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| 295 | return (*this).operator()(qx, qy); |
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| 296 | } |
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[f9bf661] | 297 | /** |
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| 298 | * Function to calculate effective radius |
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| 299 | * @return: effective radius value |
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| 300 | */ |
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| 301 | double CylinderModel :: calculate_ER() { |
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| 302 | CylinderParameters dp; |
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| 303 | |
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| 304 | dp.radius = radius(); |
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| 305 | dp.length = length(); |
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| 306 | double rad_out = 0.0; |
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| 307 | |
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| 308 | // Perform the computation, with all weight points |
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| 309 | double sum = 0.0; |
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| 310 | double norm = 0.0; |
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| 311 | |
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| 312 | // Get the dispersion points for the major shell |
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| 313 | vector<WeightPoint> weights_length; |
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| 314 | length.get_weights(weights_length); |
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| 315 | |
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| 316 | // Get the dispersion points for the minor shell |
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| 317 | vector<WeightPoint> weights_radius ; |
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| 318 | radius.get_weights(weights_radius); |
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[fca6936] | 319 | |
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[f9bf661] | 320 | // Loop over major shell weight points |
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| 321 | for(int i=0; i< (int)weights_length.size(); i++) { |
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| 322 | dp.length = weights_length[i].value; |
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| 323 | for(int k=0; k< (int)weights_radius.size(); k++) { |
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| 324 | dp.radius = weights_radius[k].value; |
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| 325 | //Note: output of "DiamCyl(dp.length,dp.radius)" is DIAMETER. |
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| 326 | sum +=weights_length[i].weight |
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| 327 | * weights_radius[k].weight*DiamCyl(dp.length,dp.radius)/2.0; |
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| 328 | norm += weights_length[i].weight* weights_radius[k].weight; |
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| 329 | } |
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| 330 | } |
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| 331 | if (norm != 0){ |
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| 332 | //return the averaged value |
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| 333 | rad_out = sum/norm;} |
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| 334 | else{ |
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| 335 | //return normal value |
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| 336 | //Note: output of "DiamCyl(dp.length,dp.radius)" is DIAMETER. |
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| 337 | rad_out = DiamCyl(dp.length,dp.radius)/2.0;} |
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| 338 | |
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| 339 | return rad_out; |
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| 340 | } |
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[e08bd5b] | 341 | double CylinderModel :: calculate_VR() { |
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| 342 | return 1.0; |
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| 343 | } |
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