1 | #pragma rtGlobals=1 // Use modern global access method. |
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2 | #pragma IgorVersion=6.1 |
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3 | |
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4 | //////////////////////////////////////////////////// |
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5 | // |
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6 | // model function that calculates the scattering from |
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7 | // lamellar surfactant structures. contrast is from the solvent, |
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8 | // surfactant headgroups, and surfactant tails |
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9 | // |
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10 | // The system is considered to be DILUTE - Interference (S(Q)) |
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11 | // effects are NOT taken into account. |
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12 | // ONLY the form factor is calculated |
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13 | // |
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14 | // REFERENCE: Nallet, Laversanne, and Roux, J. Phys. II France, 3, (1993) 487-502. |
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15 | // also in J. Phys. Chem. B, 105, (2001) 11081-11088. |
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16 | // |
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17 | // 16 JULY 2003 SRK |
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18 | // 13 FEB 06 correct normalization (L.Porcar) |
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19 | // |
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20 | //////////////////////////////////////////////////// |
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21 | |
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22 | //this macro sets up all the necessary parameters and waves that are |
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23 | //needed to calculate the model function. |
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24 | // |
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25 | Proc PlotLamellarFF_HG(num,qmin,qmax) |
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26 | Variable num=128, qmin=.001, qmax=.5 |
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27 | Prompt num "Enter number of data points for model: " |
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28 | Prompt qmin "Enter minimum q-value (A^1) for model: " |
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29 | Prompt qmax "Enter maximum q-value (A^1) for model: " |
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30 | // |
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31 | Make/O/D/n=(num) xwave_LamellarFF_HG, ywave_LamellarFF_HG |
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32 | xwave_LamellarFF_HG = alog(log(qmin) + x*((log(qmax)-log(qmin))/num)) |
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33 | Make/O/D coef_LamellarFF_HG = {1,15,10,4e-7,3e-6,6e-6,0} //CH#2 |
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34 | make/o/t parameters_LamellarFF_HG = {"Scale","Tail length (A)","Headgroup thickness (A)","SLD Tails (A^-2)","SLD Headgroup (A^-2)","SLD Solvent (A^-2)","Incoherent Bgd (cm-1)"} //CH#3 |
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35 | Edit parameters_LamellarFF_HG, coef_LamellarFF_HG |
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36 | ModifyTable width(parameters_LamellarFF_HG)=160 |
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37 | |
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38 | Variable/G root:g_LamellarFF_HG |
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39 | g_LamellarFF_HG := LamellarFF_HG(coef_LamellarFF_HG, ywave_LamellarFF_HG, xwave_LamellarFF_HG) |
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40 | Display ywave_LamellarFF_HG vs xwave_LamellarFF_HG |
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41 | ModifyGraph marker=29, msize=2, mode=4 |
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42 | ModifyGraph log=1 |
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43 | Label bottom "q (A\\S-1\\M) " |
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44 | Label left "I(q) (cm\\S-1\\M)" |
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45 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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46 | |
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47 | AddModelToStrings("LamellarFF_HG","coef_LamellarFF_HG","parameters_LamellarFF_HG","LamellarFF_HG") |
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48 | // |
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49 | End |
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50 | |
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51 | // - sets up a dependency to a wrapper, not the actual SmearedModelFunction |
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52 | Proc PlotSmearedLamellarFF_HG(str) |
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53 | String str |
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54 | Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4) |
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55 | |
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56 | // if any of the resolution waves are missing => abort |
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57 | if(ResolutionWavesMissingDF(str)) //updated to NOT use global strings (in GaussUtils) |
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58 | Abort |
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59 | endif |
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60 | |
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61 | SetDataFolder $("root:"+str) |
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62 | |
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63 | // Setup parameter table for model function |
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64 | Make/O/D smear_coef_LamellarFF_HG = {1,15,10,4e-7,3e-6,6e-6,0} //CH#4 |
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65 | make/o/t smear_parameters_LamellarFF_HG = {"Scale","Tail length (A)","Headgroup thickness (A)","SLD Tails (A^-2)","SLD Headgroup (A^-2)","SLD Solvent (A^-2)","Incoherent Bgd (cm-1)"} |
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66 | Edit smear_parameters_LamellarFF_HG,smear_coef_LamellarFF_HG //display parameters in a table |
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67 | |
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68 | // output smeared intensity wave, dimensions are identical to experimental QSIG values |
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69 | // make extra copy of experimental q-values for easy plotting |
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70 | Duplicate/O $(str+"_q") smeared_LamellarFF_HG,smeared_qvals // |
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71 | SetScale d,0,0,"1/cm",smeared_LamellarFF_HG // |
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72 | |
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73 | Variable/G gs_LamellarFF_HG=0 |
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74 | gs_LamellarFF_HG := fSmearedLamellarFF_HG(smear_coef_LamellarFF_HG,smeared_LamellarFF_HG,smeared_qvals) //this wrapper fills the STRUCT |
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75 | |
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76 | Display smeared_LamellarFF_HG vs smeared_qvals // |
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77 | ModifyGraph log=1,marker=29,msize=2,mode=4 |
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78 | Label bottom "q (A\\S-1\\M)" |
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79 | Label left "I(q) (cm\\S-1\\M)" |
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80 | AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2) |
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81 | |
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82 | SetDataFolder root: |
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83 | AddModelToStrings("SmearedLamellarFF_HG","smear_coef_LamellarFF_HG","smear_parameters_LamellarFF_HG","LamellarFF_HG") |
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84 | End |
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85 | |
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86 | |
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87 | |
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88 | //AAO version, uses XOP if available |
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89 | // simply calls the original single point calculation with |
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90 | // a wave assignment (this will behave nicely if given point ranges) |
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91 | Function LamellarFF_HG(cw,yw,xw) : FitFunc |
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92 | Wave cw,yw,xw |
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93 | |
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94 | #if exists("LamellarFF_HGX") |
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95 | yw = LamellarFF_HGX(cw,xw) |
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96 | #else |
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97 | yw = fLamellarFF_HG(cw,xw) |
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98 | #endif |
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99 | return(0) |
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100 | End |
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101 | |
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102 | //CH#1 |
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103 | // you should write your function to calculate the intensity |
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104 | // for a single q-value (that's the input parameter x) |
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105 | // based on the wave (array) of parameters that you send it (w) |
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106 | // |
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107 | Function fLamellarFF_HG(w,x) : FitFunc |
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108 | Wave w |
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109 | Variable x |
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110 | // Input (fitting) variables are: |
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111 | //[0]Scale |
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112 | //[1]tail length |
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113 | //[2]hg thickness |
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114 | //[3]sld tail |
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115 | //[4]sld HG |
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116 | //[5]sld solvent |
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117 | //[6]Incoherent Bgd (cm-1) |
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118 | |
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119 | // give them nice names |
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120 | Variable scale,delT,delH,slds,sldh,sldt,sig,contr,NN,Cp,bkg |
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121 | scale = w[0] |
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122 | delT = w[1] |
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123 | delH = w[2] |
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124 | sldt = w[3] |
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125 | sldh = w[4] |
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126 | slds = w[5] |
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127 | bkg = w[6] |
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128 | |
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129 | // local variables |
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130 | Variable inten, qval,Pq,drh,drt |
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131 | |
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132 | // x is the q-value for the calculation |
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133 | qval = x |
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134 | drh = sldh - slds |
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135 | drt = sldt - slds //correction 13FEB06 by L.Porcar |
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136 | |
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137 | Pq = drh*(sin(qval*(delH+delT))-sin(qval*delT)) + drt*sin(qval*delT) |
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138 | Pq *= Pq |
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139 | Pq *= 4/(qval^2) |
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140 | |
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141 | inten = 2*Pi*scale*Pq/Qval^2 //dimensionless... |
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142 | |
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143 | inten /= 2*(delT+delH) //normalize by the bilayer thickness |
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144 | |
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145 | inten *= 1e8 // 1/A to 1/cm |
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146 | Return (inten+bkg) |
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147 | End |
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148 | |
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149 | //wrapper to calculate the smeared model as an AAO-Struct |
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150 | // fills the struct and calls the ususal function with the STRUCT parameter |
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151 | // |
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152 | // used only for the dependency, not for fitting |
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153 | // |
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154 | Function fSmearedLamellarFF_HG(coefW,yW,xW) |
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155 | Wave coefW,yW,xW |
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156 | |
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157 | String str = getWavesDataFolder(yW,0) |
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158 | String DF="root:"+str+":" |
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159 | |
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160 | WAVE resW = $(DF+str+"_res") |
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161 | |
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162 | STRUCT ResSmearAAOStruct fs |
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163 | WAVE fs.coefW = coefW |
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164 | WAVE fs.yW = yW |
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165 | WAVE fs.xW = xW |
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166 | WAVE fs.resW = resW |
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167 | |
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168 | Variable err |
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169 | err = SmearedLamellarFF_HG(fs) |
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170 | |
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171 | return (0) |
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172 | End |
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173 | |
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174 | //the smeared model calculation |
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175 | Function SmearedLamellarFF_HG(s) :FitFunc |
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176 | Struct ResSmearAAOStruct &s |
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177 | |
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178 | // the name of your unsmeared model (AAO) is the first argument |
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179 | Smear_Model_20(LamellarFF_HG,s.coefW,s.xW,s.yW,s.resW) |
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180 | |
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181 | return(0) |
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182 | End |
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