1 | #pragma rtGlobals=1 // Use modern global access method. |
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2 | #pragma IgorVersion = 6.0 |
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3 | |
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4 | //////////////////////////////////////////////////// |
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5 | // |
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6 | // calculates the scattering from a rectangular solid |
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7 | // i.e. a parallelepiped with sides a < b < c |
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8 | // |
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9 | // - the user must make sure that the constraints are not violated |
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10 | // otherwise the calculation will not be correct |
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11 | // |
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12 | // From: Mittelbach and Porod, Acta Phys. Austriaca 14 (1961) 185-211. |
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13 | // equations (1), (13), and (14) (in German!) |
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14 | // |
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15 | // note that the equations listed in Feigin and Svergun appears |
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16 | // to be wrong - they use equation (12), which does not appear to |
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17 | // be a complete orientational average (?) |
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18 | // |
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19 | // a double integral is used, both using Gaussian quadrature |
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20 | // routines that are now included with GaussUtils |
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21 | // 20-pt quadrature appears to be enough, 76 pt is available |
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22 | // by changing the function calls |
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23 | // |
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24 | //////////////////////////////////////////////////// |
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25 | |
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26 | //this macro sets up all the necessary parameters and waves that are |
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27 | //needed to calculate the model function. |
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28 | // |
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29 | Proc PlotParallelepiped(num,qmin,qmax) |
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30 | Variable num=100, qmin=.001, qmax=.7 |
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31 | Prompt num "Enter number of data points for model: " |
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32 | Prompt qmin "Enter minimum q-value (A^1) for model: " |
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33 | Prompt qmax "Enter maximum q-value (A^1) for model: " |
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34 | // |
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35 | Make/O/D/n=(num) xwave_Parallelepiped, ywave_Parallelepiped |
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36 | xwave_Parallelepiped = alog(log(qmin) + x*((log(qmax)-log(qmin))/num)) |
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37 | Make/O/D coef_Parallelepiped = {1,35,75,400,1e-6,6.3e-6,0} //CH#2 |
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38 | make/o/t parameters_Parallelepiped = {"Scale Factor","Shortest Edge A (A)","B (A)","Longest Edge C (A)","SLD particle (A^-2)","SLD solvent (A^-2)","Incoherent Bgd (cm-1)"} //CH#3 |
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39 | Edit parameters_Parallelepiped, coef_Parallelepiped |
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40 | |
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41 | Variable/G root:g_Parallelepiped |
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42 | g_Parallelepiped := Parallelepiped(coef_Parallelepiped,ywave_Parallelepiped, xwave_Parallelepiped) |
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43 | Display ywave_Parallelepiped vs xwave_Parallelepiped |
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44 | ModifyGraph marker=29, msize=2, mode=4 |
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45 | ModifyGraph log=1 |
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46 | Label bottom "q (A\\S-1\\M) " |
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47 | Label left "I(q) (cm\\S-1\\M)" |
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48 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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49 | |
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50 | AddModelToStrings("Parallelepiped","coef_Parallelepiped","Parallelepiped") |
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51 | // |
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52 | End |
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53 | |
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54 | // - sets up a dependency to a wrapper, not the actual SmearedModelFunction |
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55 | Proc PlotSmearedParallelepiped(str) |
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56 | String str |
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57 | Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4) |
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58 | |
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59 | // if any of the resolution waves are missing => abort |
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60 | if(ResolutionWavesMissingDF(str)) //updated to NOT use global strings (in GaussUtils) |
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61 | Abort |
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62 | endif |
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63 | |
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64 | SetDataFolder $("root:"+str) |
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65 | |
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66 | // Setup parameter table for model function |
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67 | Make/O/D smear_coef_Parallelepiped = {1,35,75,400,1e-6,6.3e-6,0} //CH#4 |
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68 | make/o/t smear_parameters_Parallelepiped = {"Scale Factor","Shortest Edge A (A)","B (A)","Longest Edge C (A)","SLD particle (A^-2)","SLD solvent (A^-2)","Incoherent Bgd (cm-1)"} |
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69 | Edit smear_parameters_Parallelepiped,smear_coef_Parallelepiped //display parameters in a table |
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70 | |
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71 | // output smeared intensity wave, dimensions are identical to experimental QSIG values |
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72 | // make extra copy of experimental q-values for easy plotting |
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73 | Duplicate/O $(str+"_q") smeared_Parallelepiped,smeared_qvals // |
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74 | SetScale d,0,0,"1/cm",smeared_Parallelepiped // |
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75 | |
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76 | Variable/G gs_Parallelepiped=0 |
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77 | gs_Parallelepiped := fSmearedParallelepiped(smear_coef_Parallelepiped,smeared_Parallelepiped,smeared_qvals) //this wrapper fills the STRUCT |
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78 | |
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79 | Display smeared_Parallelepiped vs smeared_qvals // |
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80 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
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81 | Label bottom "q (A\\S-1\\M)" |
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82 | Label left "I(q) (cm\\S-1\\M)" |
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83 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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84 | |
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85 | SetDataFolder root: |
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86 | AddModelToStrings("SmearedParallelepiped","smear_coef_Parallelepiped","Parallelepiped") |
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87 | End |
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88 | |
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89 | |
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90 | |
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91 | //AAO version, uses XOP if available |
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92 | // simply calls the original single point calculation with |
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93 | // a wave assignment (this will behave nicely if given point ranges) |
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94 | Function Parallelepiped(cw,yw,xw) : FitFunc |
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95 | Wave cw,yw,xw |
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96 | |
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97 | #if exists("ParallelepipedX") |
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98 | yw = ParallelepipedX(cw,xw) |
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99 | #else |
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100 | yw = fParallelepiped(cw,xw) |
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101 | #endif |
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102 | return(0) |
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103 | End |
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104 | |
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105 | // calculates the form factor of a rectangular solid |
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106 | // - a double integral - choose points wisely |
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107 | // |
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108 | Function fParallelepiped(w,x) : FitFunc |
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109 | Wave w |
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110 | Variable x |
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111 | // Input (fitting) variables are: |
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112 | //[0] scale factor |
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113 | //[1] Edge A (A) |
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114 | //[2] Edge B (A) |
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115 | //[3] Edge C (A) |
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116 | //[4] contrast (A^-2) |
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117 | //[5] incoherent background (cm^-1) |
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118 | // give them nice names |
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119 | Variable scale,aa,bb,cc,contr,bkg,inten,qq,ii,arg,mu,sldp,slds |
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120 | scale = w[0] |
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121 | aa = w[1] |
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122 | bb = w[2] |
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123 | cc = w[3] |
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124 | sldp = w[4] |
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125 | slds = w[5] |
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126 | bkg = w[6] |
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127 | |
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128 | contr = sldp - slds |
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129 | // mu = bb*x //scale in terms of B |
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130 | // aa = aa/bb |
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131 | // cc = cc/bb |
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132 | |
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133 | inten = IntegrateFn20(PP_Outer,0,1,w,x) |
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134 | // inten = IntegrateFn76(PP_Outer,0,1,w,x) |
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135 | |
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136 | inten *= aa*cc*bb //multiply by volume |
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137 | inten *= 1e8 //convert to cm^-1 |
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138 | inten *= contr*contr |
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139 | inten *= scale |
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140 | inten += bkg |
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141 | |
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142 | Return (inten) |
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143 | End |
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144 | |
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145 | // outer integral |
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146 | |
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147 | // x is the q-value - remember that "mu" in the notation = B*Q |
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148 | Function PP_Outer(w,x,dum) |
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149 | Wave w |
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150 | Variable x,dum |
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151 | |
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152 | Variable retVal,mu,aa,bb,cc,mudum,arg |
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153 | aa = w[1] |
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154 | bb = w[2] |
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155 | cc = w[3] |
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156 | mu = bb*x |
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157 | |
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158 | mudum = mu*sqrt(1-dum^2) |
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159 | retval = IntegrateFn20(PP_inner,0,1,w,mudum) |
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160 | // retval = IntegrateFn76(PP_inner,0,1,w,mudum) |
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161 | |
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162 | cc = cc/bb |
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163 | arg = mu*cc*dum/2 |
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164 | if(arg==0) |
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165 | retval *= 1 |
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166 | else |
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167 | retval *= sin(arg)*sin(arg)/arg/arg |
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168 | endif |
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169 | |
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170 | return(retVal) |
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171 | End |
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172 | |
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173 | //returns the integrand of the inner integral |
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174 | Function PP_Inner(w,mu,uu) |
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175 | Wave w |
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176 | Variable mu,uu |
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177 | |
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178 | Variable aa,bb,retVal,arg1,arg2,tmp1,tmp2 |
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179 | |
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180 | //NVAR mu = root:gEvalQval //already has been converted to S=2*pi*q |
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181 | aa = w[1] |
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182 | bb = w[2] |
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183 | aa = aa/bb |
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184 | |
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185 | //Mu*(1-x^2)^(0.5) |
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186 | |
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187 | //handle arg=0 separately, as sin(t)/t -> 1 as t->0 |
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188 | arg1 = (mu/2)*cos(Pi*uu/2) |
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189 | arg2 = (mu*aa/2)*sin(Pi*uu/2) |
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190 | if(arg1==0) |
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191 | tmp1 = 1 |
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192 | else |
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193 | tmp1 = sin(arg1)*sin(arg1)/arg1/arg1 |
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194 | endif |
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195 | if(arg2==0) |
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196 | tmp2 = 1 |
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197 | else |
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198 | tmp2 = sin(arg2)*sin(arg2)/arg2/arg2 |
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199 | endif |
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200 | retval = tmp1*tmp2 |
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201 | |
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202 | return(retVal) |
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203 | End |
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204 | |
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205 | //wrapper to calculate the smeared model as an AAO-Struct |
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206 | // fills the struct and calls the ususal function with the STRUCT parameter |
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207 | // |
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208 | // used only for the dependency, not for fitting |
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209 | // |
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210 | Function fSmearedParallelepiped(coefW,yW,xW) |
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211 | Wave coefW,yW,xW |
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212 | |
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213 | String str = getWavesDataFolder(yW,0) |
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214 | String DF="root:"+str+":" |
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215 | |
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216 | WAVE resW = $(DF+str+"_res") |
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217 | |
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218 | STRUCT ResSmearAAOStruct fs |
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219 | WAVE fs.coefW = coefW |
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220 | WAVE fs.yW = yW |
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221 | WAVE fs.xW = xW |
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222 | WAVE fs.resW = resW |
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223 | |
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224 | Variable err |
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225 | err = SmearedParallelepiped(fs) |
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226 | |
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227 | return (0) |
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228 | End |
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229 | |
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230 | // this is all there is to the smeared calculation! |
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231 | Function SmearedParallelepiped(s) :FitFunc |
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232 | Struct ResSmearAAOStruct &s |
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233 | |
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234 | // the name of your unsmeared model (AAO) is the first argument |
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235 | Smear_Model_20(Parallelepiped,s.coefW,s.xW,s.yW,s.resW) |
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236 | |
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237 | return(0) |
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238 | End |
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