source: sans/Analysis/branches/ajj_23APR07/IGOR_Package_Files/Put in User Procedures/SANS_Models_v3.00/NewModels_2006/LamellarPS.ipf @ 166

Last change on this file since 166 was 166, checked in by srkline, 15 years ago

Modified all procedure files to add to the keyword=value strings to identify the function, coefficients, and suffix once the model is plotted (and the objects will exist)

a one-liner in the Plot and PlotSmeared? macros.

  • necessary for smoother functioning of the wrapper panel.
File size: 7.9 KB
Line 
1#pragma rtGlobals=1             // Use modern global access method.
2#pragma IgorVersion = 6.0
3
4////////////////////////////////////////////////////
5//
6// model function that calculates the scattering from
7// lamellar surfactant structures. contrast is two-phase,
8// from the solvent and uniform bilayer. Integer numbers of
9// repeating bilayers (at a repeat spacing) leads to the
10// familiar lamellar peaks. Bending constant information
11// can be extracted from the Caille parameter with moderate
12// success. A number of the parameters should be held
13// fixed during the fitting procedure, as they should be well
14// known:
15//              repeat spacing D = 2*pi/Qo
16//              contrast = calculated value
17//              polydispersity should be close to 0.1-0.3
18//   Caille parameter <0.8 or 1.0
19//
20// NOTES for Curve Fitting:
21// the epsilon wave "epsilon_Lamellar" should be used to force a
22// larger derivative step for the # of repeat units, which is an integer.
23// a singular matix error will always result if you don't follow this.
24// Also, the # of repeats should be constrained to ~3<N<200, otherwise
25// the optimization can pick a VERY large N, and waste lots of time
26// in the summation loop
27//
28// instrumental resolution is taken into account in the REGULAR
29// model calculation. resolution of ONLY the S(Q) peaks are
30// included. performing the typical smearing calculation would
31// be "double smearing", so is not done.
32//
33// the delta Q parameter "gDelQ" or "dQ" is taken from the q-dependent
34// instrument resolution "abssq" column as this is the identical definition
35// as in the original reference. If the real resolution function cannot be
36// found, a default value, typical of a "medium" q-range on the NG3 SANS is
37// used, although the real values are highly preferred
38//
39// REFERENCE:   Nallet, Laversanne, and Roux, J. Phys. II France, 3, (1993) 487-502.
40//              also in J. Phys. Chem. B, 105, (2001) 11081-11088.
41//
42// 14 JULY 2003 SRK
43//
44////////////////////////////////////////////////////
45
46//this macro sets up all the necessary parameters and waves that are
47//needed to calculate the model function.
48//
49Proc PlotLamellarPS(num,qmin,qmax)
50        Variable num=128, qmin=.001, qmax=.5
51        Prompt num "Enter number of data points for model: "
52        Prompt qmin "Enter minimum q-value (^1) for model: "
53        Prompt qmax "Enter maximum q-value (^1) for model: "
54//
55        // constants
56        Variable/G root:gEuler = 0.5772156649           // Euler's constant
57        Variable/G root:gDelQ = 0.0025          //[=] 1/A, q-resolution, default value
58       
59        Make/O/D/n=(num) xwave_LamellarPS, ywave_LamellarPS
60        xwave_LamellarPS =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
61        Make/O/D coef_LamellarPS = {1,400,30,0.15,6e-6,20,0.1,0}                        //CH#2
62        make/o/t parameters_LamellarPS = {"Scale","Lamellar spacing, D (A)","Bilayer Thick (delta) (A)","polydisp of Bilayer Thickness","contrast (A^-2)","# of Lamellar plates","Caille parameter","Incoherent Bgd (cm-1)"}    //CH#3
63        Edit parameters_LamellarPS, coef_LamellarPS
64        ModifyTable width(parameters_LamellarPS)=160
65       
66        Variable/G root:g_LamellarPS
67        g_LamellarPS := LamellarPS(coef_LamellarPS, ywave_LamellarPS, xwave_LamellarPS)
68        Display ywave_LamellarPS vs xwave_LamellarPS
69        ModifyGraph marker=29, msize=2, mode=4
70        ModifyGraph log=1
71        Label bottom "q (\\S-1\\M) "
72        Label left "I(q) (cm\\S-1\\M)"
73        //
74        // make epsilon wave appropriate for integer number of lamellar repeats
75        Duplicate/O coef_LamellarPS epsilon_LamellarPS
76        epsilon_LamellarPS = 1e-4
77        epsilon_LamellarPS[5] = 1               //to make the derivative useful
78        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
79       
80        AddModelToStrings("LamellarPS","coef_LamellarPS","LamellarPS")
81End
82
83// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
84//Proc PlotSmeared_LamellarPS(str)                                                             
85//      String str
86//      Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
87//     
88//      // if any of the resolution waves are missing => abort
89//      if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
90//              Abort
91//      endif
92//     
93//      SetDataFolder $("root:"+str)
94//     
95//      // constants
96//      Variable/G root:gEuler = 0.5772156649           // Euler's constant
97//      Variable/G root:gDelQ = 0.0025          //[=] 1/A, q-resolution, default value
98//      // Setup parameter table for model function
99//      Make/O/D smear_coef_LamellarPS = {1,400,30,0.15,6e-6,20,0.1,0}          //CH#4
100//      make/o/t smear_parameters_LamellarPS = {"Scale","Lamellar spacing, D (A)","Bilayer Thick (delta) (A)","polydisp of Bilayer Thickness","contrast (A^-2)","# of Lamellar plates","Caille parameter","Incoherent Bgd (cm-1)"}
101//      Edit smear_parameters_LamellarPS,smear_coef_LamellarPS                                  //display parameters in a table
102//     
103//      // output smeared intensity wave, dimensions are identical to experimental QSIG values
104//      // make extra copy of experimental q-values for easy plotting
105//      Duplicate/O $(str+"_q") smeared_LamellarPS,smeared_qvals                                //
106//      SetScale d,0,0,"1/cm",smeared_LamellarPS                                                        //
107//                                     
108//      Variable/G gs_LamellarPS=0
109//      gs_LamellarPS := fLamellarPS_Smeared(smear_coef_LamellarPS,smeared_LamellarPS,smeared_qvals)    //this wrapper fills the STRUCT
110//     
111//      Display smeared_LamellarPS vs smeared_qvals                                                                     //
112//      ModifyGraph log=1,marker=29,msize=2,mode=4
113//      Label bottom "q (\\S-1\\M)"
114//      Label left "I(q) (cm\\S-1\\M)"
115//     
116//      SetDataFolder root:
117//End
118
119
120
121
122
123//AAO version, uses XOP if available
124// simply calls the original single point calculation with
125// a wave assignment (this will behave nicely if given point ranges)
126Function LamellarPS(cw,yw,xw) : FitFunc
127        Wave cw,yw,xw
128       
129#if exists("LamellarPSX")
130        yw = LamellarPSX(cw,xw)
131#else
132        yw = fLamellarPS(cw,xw)
133#endif
134        return(0)
135End
136
137// instrument resolution IS included here in S(Q)
138Function fLamellarPS(w,x) : FitFunc
139        Wave w
140        Variable x
141//       Input (fitting) variables are:
142//[0]Scale
143//[1]Lam spacing, D
144//[2]Bilay Thick (delta)
145//[3]polydisp of the bilayer thickness
146//[4]contrast
147//[5]# of Lam plates
148//[6]Caille parameter
149//[7]Incoherent Bgd (cm-1)
150       
151//      give them nice names
152        Variable scale,dd,del,sig,contr,NN,Cp,bkg
153        scale = w[0]
154        dd = w[1]
155        del = w[2]
156        sig = w[3]*del
157        contr = w[4]
158        NN = trunc(w[5])                //be sure that NN is an integer
159        Cp = w[6]
160        bkg = w[7]
161       
162//      local variables
163        Variable inten, qval,Pq,Sq,ii,alpha,temp,t1,t2,t3,dQ
164       
165        NVAR Euler = root:gEuler
166        NVAR dQDefault = root:gDelQ
167        //      x is the q-value for the calculation
168        qval = x
169        //get the instrument resolution
170        SVAR/Z sigQ = gSig_Q
171        SVAR/Z qStr = gQVals
172       
173        if(SVAR_Exists(sigQ) && SVAR_Exists(qStr))
174                Wave/Z sigWave=$sigQ
175                Wave/Z sig_Qwave = $qStr
176                if(waveexists(sigWave)&&waveexists(sig_qwave))
177                        dQ = interp(qval, sig_Qwave, sigWave )
178                else
179//                      if(qval>0.01 && qval<0.012)
180//                              print "using default resolution"
181//                      endif
182                        dQ = dQDefault
183                endif
184        else
185                dQ = dQDefault
186        endif
187       
188        Pq = 2*contr^2/qval/qval*(1-cos(qval*del)*exp(-0.5*qval^2*sig^2))
189       
190        ii=0
191        Sq = 0
192        for(ii=1;ii<(NN-1);ii+=1)
193                temp = 0
194                alpha = Cp/4/pi/pi*(ln(pi*ii) + Euler)
195                t1 = 2*dQ*dQ*dd*dd*alpha
196                t2 = 2*qval*qval*dd*dd*alpha
197                t3 = dQ*dQ*dd*dd*ii*ii
198               
199                temp = 1-ii/NN
200                temp *= cos(dd*qval*ii/(1+t1))
201                temp *= exp(-1*(t2 + t3)/(2*(1+t1)) )
202                temp /= sqrt(1+t1)
203               
204                Sq += temp
205        endfor
206        Sq *= 2
207        Sq += 1
208       
209        inten = 2*Pi*scale*Pq*Sq/(dd*Qval^2)
210       
211        inten *= 1e8            // 1/A to 1/cm
212        //inten = Sq
213        Return (inten+bkg)
214End
215
216//wrapper to calculate the smeared model as an AAO-Struct
217// fills the struct and calls the ususal function with the STRUCT parameter
218//
219// used only for the dependency, not for fitting
220//
221//Function fLamellarPS_Smeared(coefW,yW,xW)
222//      Wave coefW,yW,xW
223//     
224//      String str = getWavesDataFolder(yW,0)
225//      String DF="root:"+str+":"
226//     
227//      WAVE resW = $(DF+str+"_res")
228//     
229//      STRUCT ResSmearAAOStruct fs
230//      WAVE fs.coefW = coefW   
231//      WAVE fs.yW = yW
232//      WAVE fs.xW = xW
233//      WAVE fs.resW = resW
234//     
235//      Variable err
236//      err = LamellarPS_Smeared(fs)
237//     
238//      return (0)
239//End
240
241//the smeared model calculation
242//Function LamellarPS_Smeared(s) :FitFunc
243//      Struct ResSmearAAOStruct &s
244//
245////    the name of your unsmeared model (AAO) is the first argument
246//      Smear_Model_20(LamellarPS,s.coefW,s.xW,s.yW,s.resW)
247//
248//      return(0)
249//End
250////
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