1 | //Headers |
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2 | static double form_volume(double thick_inter[], |
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3 | double thick_flat_[], |
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4 | double core_radius, |
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5 | int n_shells); |
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6 | |
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7 | static double Iq(double q, |
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8 | int n_shells, |
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9 | double thick_inter[], |
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10 | double func_inter[], |
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11 | double sld_core, |
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12 | double sld_solvent, |
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13 | double sld_flat[], |
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14 | double thick_flat[], |
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15 | double nu_inter[], |
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16 | int npts_inter, |
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17 | double core_radius); |
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18 | |
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19 | static double Iqxy(double qx, double qy, |
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20 | int n_shells, |
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21 | double thick_inter[], |
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22 | double func_inter[], |
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23 | double sld_core, |
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24 | double sld_solvent, |
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25 | double sld_flat[], |
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26 | double thick_flat[], |
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27 | double nu_inter[], |
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28 | int npts_inter, |
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29 | double core_radius); |
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30 | |
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31 | //Main code |
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32 | static double form_volume(double thick_inter[], |
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33 | double thick_flat_[], |
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34 | double core_radius, |
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35 | int n) |
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36 | { |
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37 | double radius = 0.0; |
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38 | int i; |
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39 | double r = core_radius; |
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40 | for (i=0; i < n; i++) { |
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41 | r += thick_inter[i]; |
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42 | r += thick_flat[i]; |
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43 | } |
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44 | return M_4PI_3*cube(r); |
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45 | } |
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46 | |
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47 | |
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48 | static double sphere_sld_kernel(double dp[], double q) { |
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49 | int n = dp[0]; |
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50 | int i,j,k; |
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51 | |
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52 | double scale = dp[1]; |
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53 | double thick_inter_core = dp[2]; |
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54 | double sld_core = dp[4]; |
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55 | double sld_solv = dp[5]; |
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56 | double background = dp[6]; |
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57 | double npts = dp[57]; //number of sub_layers in each interface |
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58 | double nsl=npts;//21.0; //nsl = Num_sub_layer: must be ODD double number |
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59 | int n_s; |
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60 | |
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61 | double sld_i,sld_f,dz,bes,fun,f,vol,qr,r,contr,f2; |
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62 | double sign,slope=0.0; |
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63 | double pi; |
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64 | |
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65 | double total_thick=0.0; |
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66 | |
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67 | int fun_type[12]; |
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68 | double sld[12]; |
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69 | double thick_inter[12]; |
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70 | double thick[12]; |
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71 | double fun_coef[12]; |
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72 | |
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73 | fun_type[0] = dp[3]; |
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74 | fun_coef[0] = fabs(dp[58]); |
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75 | for (i =1; i<=n; i++){ |
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76 | sld[i] = dp[i+6]; |
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77 | thick_inter[i]= dp[i+16]; |
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78 | thick[i] = dp[i+26]; |
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79 | fun_type[i] = dp[i+36]; |
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80 | fun_coef[i] = fabs(dp[i+46]); |
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81 | total_thick += thick[i]; |
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82 | total_thick += thick_inter[i]; |
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83 | } |
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84 | sld[0] = sld_core; |
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85 | sld[n+1] = sld_solv; |
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86 | thick[0] = dp[59]; |
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87 | thick[n+1] = total_thick/5.0; |
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88 | thick_inter[0] = thick_inter_core; |
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89 | thick_inter[n+1] = 0.0; |
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90 | fun_coef[n+1] = 0.0; |
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91 | pi = 4.0*atan(1.0); |
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92 | f = 0.0; |
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93 | r = 0.0; |
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94 | vol = 0.0; |
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95 | //vol_pre = 0.0; |
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96 | //vol_sub = 0.0; |
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97 | sld_f = sld_core; |
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98 | |
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99 | //floor_nsl = floor(nsl/2.0); |
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100 | |
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101 | dz = 0.0; |
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102 | // iteration for # of shells + core + solvent |
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103 | for (i=0;i<=n+1; i++){ |
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104 | //iteration for N sub-layers |
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105 | //if (fabs(thick[i]) <= 1e-24){ |
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106 | // continue; |
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107 | //} |
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108 | // iteration for flat and interface |
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109 | for (j=0;j<2;j++){ |
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110 | // iteration for sub_shells in the interface |
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111 | // starts from #1 sub-layer |
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112 | for (n_s=1;n_s<=nsl; n_s++){ |
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113 | // for solvent, it doesn't have an interface |
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114 | if (i==n+1 && j==1) |
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115 | break; |
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116 | // for flat layers |
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117 | if (j==0){ |
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118 | dz = thick[i]; |
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119 | sld_i = sld[i]; |
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120 | slope = 0.0; |
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121 | } |
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122 | // for interfacial sub_shells |
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123 | else{ |
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124 | dz = thick_inter[i]/nsl; |
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125 | // find sld_i at the outer boundary of sub-layer #n_s |
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126 | sld_i = intersldfunc(fun_type[i],nsl, n_s, fun_coef[i], sld[i], sld[i+1]); |
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127 | // calculate slope |
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128 | slope= (sld_i -sld_f)/dz; |
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129 | } |
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130 | contr = sld_f-slope*r; |
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131 | // iteration for the left and right boundary of the shells(or sub_shells) |
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132 | for (k=0; k<2; k++){ |
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133 | // At r=0, the contribution to I is zero, so skip it. |
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134 | if ( i == 0 && j == 0 && k == 0){ |
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135 | continue; |
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136 | } |
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137 | // On the top of slovent there is no interface; skip it. |
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138 | if (i == n+1 && k == 1){ |
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139 | continue; |
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140 | } |
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141 | // At the right side (outer) boundary |
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142 | if ( k == 1){ |
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143 | sign = 1.0; |
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144 | r += dz; |
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145 | } |
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146 | // At the left side (inner) boundary |
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147 | else{ |
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148 | sign = -1.0; |
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149 | } |
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150 | qr = q * r; |
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151 | fun = 0.0; |
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152 | |
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153 | if(qr == 0.0){ |
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154 | // sigular point |
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155 | bes = sign * 1.0; |
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156 | } |
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157 | else{ |
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158 | // for flat sub-layer |
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159 | //TODO: Single precision calculation most likely fails here |
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160 | //bes = sign * 3.0 * (sin(qr) - qr * cos(qr)) / (qr * qr * qr); |
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161 | bes = sign * sph_j1c(qr); |
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162 | if (fabs(slope) > 0.0 ){ |
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163 | //fun = sign * 3.0 * r * (2.0*qr*sin(qr)-((qr*qr)-2.0)*cos(qr))/(qr * qr * qr * qr); |
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164 | fun = sign * r * sph_j1c(qr) + sign * 3.0 * sin(qr)/(qr * qr * q ) |
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165 | + sign * 6.0 * cos(qr)/(qr * qr * qr * q); |
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166 | } |
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167 | } |
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168 | |
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169 | //Some initial optimization tries |
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170 | /*bes = (qr == 0.0 ? sign * 1.0 : sign * 3.0 * (sin(qr) - qr * cos(qr)) / (qr * qr * qr)); |
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171 | //TODO: Will have to chnage this function |
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172 | if (qr!= 0.0 && fabs(slope) > 0.0 ){ |
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173 | fun = sign * 3.0 * r * (2.0*qr*sin(qr)-((qr*qr)-2.0)*cos(qr))/(qr * qr * qr * qr); |
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174 | }*/ |
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175 | |
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176 | // update total volume |
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177 | vol = 4.0 * pi / 3.0 * r * r * r; |
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178 | // we won't do the following volume correction for now. |
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179 | // substrate empty area of volume |
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180 | //if (k == 1 && fabs(sld_in[i]-sld_solv) < 1e-04*fabs(sld_solv) && fun_type[i]==0){ |
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181 | // vol_sub += (vol_pre - vol); |
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182 | //} |
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183 | f += vol * (bes * contr + fun * slope); |
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184 | } |
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185 | // remember this sld as sld_f |
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186 | sld_f = sld_i; |
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187 | // no sub-layer iteration (n_s loop) for the flat layer |
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188 | if (j==0) |
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189 | break; |
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190 | } |
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191 | } |
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192 | } |
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193 | //vol += vol_sub; |
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194 | f2 = f * f / vol; |
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195 | //f2 *= scale; |
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196 | //f2 += background; |
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197 | //free(fun_type); |
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198 | //free(sld); |
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199 | //free(thick_inter); |
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200 | //free(thick); |
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201 | //free(fun_coef); |
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202 | |
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203 | return (f2); |
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204 | } |
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205 | |
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206 | |
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207 | /** |
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208 | * Function to evaluate 1D SphereSLD function |
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209 | * @param q: q-value |
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210 | * @return: function value |
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211 | */ |
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212 | double Iq(double q, |
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213 | int n_shells, |
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214 | double thick_inter[], |
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215 | double func_inter[], |
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216 | double sld_core, |
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217 | double sld_solvent, |
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218 | double sld_flat[], |
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219 | double thick_flat[], |
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220 | double nu_inter[], |
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221 | int npts_inter, |
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222 | double core_radius |
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223 | ) { |
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224 | |
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225 | //printf("Number of points %d\n",npts_inter); |
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226 | double intensity; |
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227 | //TODO: Remove this container at later stage. It is only kept to minimize stupid errors now |
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228 | double dp[60]; |
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229 | dp[0] = n_shells; |
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230 | //This is scale will also have to be removed at some stage |
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231 | dp[1] = 1.0; |
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232 | dp[2] = thick_inter_0; |
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233 | dp[3] = func_inter_0; |
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234 | dp[4] = sld_core; |
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235 | dp[5] = sld_solvent; |
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236 | dp[6] = 0.0; |
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237 | |
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238 | for (i=0; i<n; i++){ |
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239 | dp[i+7] = sld_flat[i]; |
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240 | dp[i+17] = thick_inter[i]; |
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241 | dp[i+27] = thick_flat[i]; |
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242 | dp[i+37] = func_inter[i]; |
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243 | dp[i+47] = nu_inter[i]; |
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244 | } |
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245 | |
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246 | dp[57] = npts_inter; |
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247 | dp[58] = nu_inter_0; |
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248 | dp[59] = rad_core_0; |
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249 | |
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250 | intensity = 1.0e-4*sphere_sld_kernel(dp,q); |
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251 | //printf("%10d\n",intensity); |
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252 | return intensity; |
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253 | } |
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254 | |
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255 | /** |
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256 | * Function to evaluate 2D SphereSLD 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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261 | double Iqxy(double qx, double qy, |
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262 | int n_shells, |
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263 | double thick_inter[], |
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264 | double func_inter[], |
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265 | double sld_core, |
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266 | double sld_solvent, |
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267 | double sld_flat[], |
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268 | double thick_flat[], |
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269 | double nu_inter[], |
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270 | int npts_inter, |
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271 | double core_radius |
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272 | ) { |
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273 | |
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274 | double q = sqrt(qx*qx + qy*qy); |
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275 | return Iq(q, n_shells, thick_inter[], func_inter[], sld_core, sld_solvent, |
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276 | sld_flat[], thick_flat[],nu_inter[], npts_inter, core_radius) |
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277 | |
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278 | } |
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279 | |
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