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 | #include "flexcyl_ellipX.h" |
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27 | |
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28 | extern "C" { |
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29 | #include "libCylinder.h" |
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30 | #include "libStructureFactor.h" |
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31 | } |
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32 | |
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33 | typedef struct { |
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34 | double scale; |
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35 | double length; |
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36 | double kuhn_length; |
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37 | double radius; |
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38 | double axis_ratio; |
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39 | double sldCyl; |
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40 | double sldSolv; |
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41 | double background; |
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42 | } FlexCylEXParameters; |
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43 | |
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44 | FlexCylEllipXModel :: FlexCylEllipXModel() { |
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45 | scale = Parameter(1.0); |
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46 | length = Parameter(1000.0, true); |
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47 | length.set_min(0.0); |
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48 | kuhn_length = Parameter(100.0, true); |
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49 | kuhn_length.set_min(0.0); |
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50 | radius = Parameter(20.0, true); |
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51 | radius.set_min(0.0); |
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52 | axis_ratio = Parameter(1.5); |
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53 | axis_ratio.set_min(0.0); |
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54 | sldCyl = Parameter(1.0e-6); |
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55 | sldSolv = Parameter(6.3e-6); |
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56 | background = Parameter(0.0001); |
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57 | } |
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58 | |
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59 | /** |
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60 | * Function to evaluate 1D scattering function |
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61 | * The NIST IGOR library is used for the actual calculation. |
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62 | * @param q: q-value |
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63 | * @return: function value |
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64 | */ |
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65 | double FlexCylEllipXModel :: operator()(double q) { |
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66 | double dp[8]; |
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67 | |
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68 | // Fill parameter array for IGOR library |
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69 | // Add the background after averaging |
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70 | dp[0] = scale(); |
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71 | dp[1] = length(); |
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72 | dp[2] = kuhn_length(); |
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73 | dp[3] = radius(); |
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74 | dp[4] = axis_ratio(); |
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75 | dp[5] = sldCyl(); |
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76 | dp[6] = sldSolv(); |
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77 | dp[7] = 0.0; |
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78 | |
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79 | // Get the dispersion points for the length |
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80 | vector<WeightPoint> weights_len; |
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81 | length.get_weights(weights_len); |
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82 | |
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83 | // Get the dispersion points for the kuhn_length |
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84 | vector<WeightPoint> weights_kuhn; |
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85 | kuhn_length.get_weights(weights_kuhn); |
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86 | |
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87 | // Get the dispersion points for the radius |
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88 | vector<WeightPoint> weights_rad; |
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89 | radius.get_weights(weights_rad); |
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90 | |
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91 | // Get the dispersion points for the axis_ratio |
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92 | vector<WeightPoint> weights_ratio; |
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93 | axis_ratio.get_weights(weights_ratio); |
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94 | |
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95 | // Perform the computation, with all weight points |
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96 | double sum = 0.0; |
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97 | double norm = 0.0; |
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98 | double vol = 0.0; |
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99 | |
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100 | // Loop over length weight points |
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101 | for(int i=0; i< (int)weights_len.size(); i++) { |
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102 | dp[1] = weights_len[i].value; |
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103 | |
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104 | // Loop over kuhn_length weight points |
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105 | for(int j=0; j< (int)weights_kuhn.size(); j++) { |
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106 | dp[2] = weights_kuhn[j].value; |
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107 | |
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108 | // Loop over radius weight points |
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109 | for(int k=0; k< (int)weights_rad.size(); k++) { |
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110 | dp[3] = weights_rad[k].value; |
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111 | // Loop over axis_ratio weight points |
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112 | for(int l=0; l< (int)weights_ratio.size(); l++) { |
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113 | dp[4] = weights_ratio[l].value; |
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114 | |
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115 | //Un-normalize by volume |
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116 | sum += weights_len[i].weight * weights_kuhn[j].weight*weights_rad[k].weight |
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117 | * weights_ratio[l].weight * FlexCyl_Ellip(dp, q) |
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118 | * (pow(weights_rad[k].value,2.0) * weights_ratio[l].value * weights_len[i].value); |
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119 | //Find weighted volume |
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120 | vol += weights_rad[k].weight * weights_kuhn[j].weight |
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121 | * weights_len[i].weight * weights_ratio[l].weight |
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122 | *pow(weights_rad[k].value,2.0)* weights_ratio[l].weight*weights_len[i].value; |
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123 | norm += weights_len[i].weight * weights_kuhn[j].weight |
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124 | *weights_rad[k].weight* weights_ratio[l].weight; |
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125 | } |
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126 | } |
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127 | } |
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128 | } |
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129 | if (vol != 0.0 && norm != 0.0) { |
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130 | //Re-normalize by avg volume |
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131 | sum = sum/(vol/norm);} |
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132 | |
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133 | return sum/norm + background(); |
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134 | } |
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135 | |
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136 | /** |
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137 | * Function to evaluate 2D scattering function |
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138 | * @param q_x: value of Q along x |
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139 | * @param q_y: value of Q along y |
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140 | * @return: function value |
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141 | */ |
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142 | double FlexCylEllipXModel :: operator()(double qx, double qy) { |
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143 | double q = sqrt(qx*qx + qy*qy); |
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144 | return (*this).operator()(q); |
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145 | } |
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146 | |
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147 | /** |
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148 | * Function to evaluate 2D scattering function |
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149 | * @param pars: parameters of the triaxial ellipsoid |
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150 | * @param q: q-value |
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151 | * @param phi: angle phi |
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152 | * @return: function value |
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153 | */ |
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154 | double FlexCylEllipXModel :: evaluate_rphi(double q, double phi) { |
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155 | //double qx = q*cos(phi); |
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156 | //double qy = q*sin(phi); |
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157 | return (*this).operator()(q); |
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158 | } |
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159 | /** |
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160 | * Function to calculate effective radius |
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161 | * @return: effective radius value |
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162 | */ |
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163 | double FlexCylEllipXModel :: calculate_ER() { |
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164 | FlexCylEXParameters dp; |
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165 | |
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166 | dp.radius = radius(); |
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167 | dp.length = length(); |
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168 | dp.axis_ratio = axis_ratio(); |
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169 | |
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170 | double rad_out = 0.0; |
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171 | double suf_rad = sqrt(dp.radius*dp.radius*dp.axis_ratio ); |
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172 | // Perform the computation, with all weight points |
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173 | double sum = 0.0; |
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174 | double norm = 0.0; |
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175 | |
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176 | // Get the dispersion points for the total length |
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177 | vector<WeightPoint> weights_length; |
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178 | length.get_weights(weights_length); |
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179 | |
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180 | // Get the dispersion points for minor radius |
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181 | vector<WeightPoint> weights_radius ; |
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182 | radius.get_weights(weights_radius); |
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183 | |
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184 | // Get the dispersion points for axis ratio = major_radius/minor_radius |
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185 | vector<WeightPoint> weights_ratio ; |
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186 | axis_ratio.get_weights(weights_ratio); |
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187 | |
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188 | // Loop over major shell weight points |
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189 | for(int i=0; i< (int)weights_length.size(); i++) { |
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190 | dp.length = weights_length[i].value; |
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191 | for(int k=0; k< (int)weights_radius.size(); k++) { |
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192 | dp.radius = weights_radius[k].value; |
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193 | // Loop over axis_ratio weight points |
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194 | for(int l=0; l< (int)weights_ratio.size(); l++) { |
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195 | dp.axis_ratio = weights_ratio[l].value; |
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196 | suf_rad = sqrt(dp.radius * dp.radius * dp.axis_ratio); |
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197 | //Note: output of "DiamCyl(dp.length,dp.radius)" is DIAMETER. |
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198 | sum +=weights_length[i].weight * weights_radius[k].weight |
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199 | * weights_ratio[l].weight *DiamCyl(dp.length,suf_rad)/2.0; |
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200 | norm += weights_length[i].weight* weights_radius[k].weight* weights_ratio[l].weight; |
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201 | } |
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202 | } |
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203 | } |
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204 | if (norm != 0){ |
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205 | //return the averaged value |
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206 | rad_out = sum/norm;} |
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207 | else{ |
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208 | //return normal value |
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209 | //Note: output of "DiamCyl(dp.length,dp.radius)" is DIAMETER. |
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210 | rad_out = DiamCyl(dp.length,suf_rad)/2.0;} |
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211 | |
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212 | return rad_out; |
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213 | } |
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214 | double FlexCylEllipXModel :: calculate_VR() { |
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215 | return 1.0; |
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216 | } |
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