source: sans/Analysis/branches/ajj_23APR07/IGOR_Package_Files/Put in User Procedures/SANS_Models_v3.00/NewModels_2006/LamellarPS_HG.ipf @ 151

Last change on this file since 151 was 151, checked in by srkline, 15 years ago

(1) - cursors can now be used to select a subrange of USANS data to fit. This is done by th fit wrapper, assigning a subrange of resW to the struct

(2) all of the smeared model functions are now in the latest form of Smear_Model_N() that is NOT a pointwise calculation anymore, since the USANS matrix smearing in inherently not so.

File size: 8.2 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 includes the
8// bilayer core, headgroups, and solvent. 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_LamellarPS_HG" 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 Plot_LamellarPS_HG(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_HG, ywave_LamellarPS_HG
60        xwave_LamellarPS_HG =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
61        Make/O/D coef_LamellarPS_HG = {1,40,10,2,0.4e-6,2e-6,6e-6,30,0.001,0.001}                       //CH#2
62        make/o/t parameters_LamellarPS_HG = {"Scale","Lamellar spacing, D (A)","Tail Thick (delT) (A)","HG Thick (delH) (A)","SLD of tails (A^-2)","SLD of HG (A^-2)","SLD of solvent (A^-2)","# of Lamellar plates","Caille parameter","Incoherent Bgd (cm-1)"}        //CH#3
63        Edit parameters_LamellarPS_HG, coef_LamellarPS_HG
64        ModifyTable width(parameters_LamellarPS_HG)=160
65       
66        Variable/G root:g_LamellarPS_HG
67        g_LamellarPS_HG := LamellarPS_HG(coef_LamellarPS_HG, ywave_LamellarPS_HG,xwave_LamellarPS_HG)
68        Display ywave_LamellarPS_HG vs xwave_LamellarPS_HG
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_HG epsilon_LamellarPS_HG
76        epsilon_LamellarPS_HG = 1e-4
77        epsilon_LamellarPS_HG[7] = 1            //to make the derivative useful
78        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
79End
80
81// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
82//Proc PlotSmeared_LamellarPS_HG(str)                                                           
83//      String str
84//      Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
85//     
86//      // if any of the resolution waves are missing => abort
87//      if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
88//              Abort
89//      endif
90//     
91//      SetDataFolder $("root:"+str)
92//     
93//      // constants
94//      Variable/G root:gEuler = 0.5772156649           // Euler's constant
95//      Variable/G root:gDelQ = 0.0025          //[=] 1/A, q-resolution, default value
96//      // Setup parameter table for model function
97//      Make/O/D smear_coef_LamellarPS_HG = {1,40,10,2,0.4e-6,2e-6,6e-6,30,0.001,0.001}         //CH#4
98//      make/o/t smear_parameters_LamellarPS_HG = {"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)"}
99//      Edit smear_parameters_LamellarPS_HG,smear_coef_LamellarPS_HG                                    //display parameters in a table
100//     
101//      // output smeared intensity wave, dimensions are identical to experimental QSIG values
102//      // make extra copy of experimental q-values for easy plotting
103//      Duplicate/O $(str+"_q") smeared_LamellarPS_HG,smeared_qvals                             //
104//      SetScale d,0,0,"1/cm",smeared_LamellarPS_HG                                                     //
105//                                     
106//      Variable/G gs_LamellarPS_HG     =0
107//      gs_LamellarPS_HG         := fLamellarPS_HG_Smeared(smear_coef_LamellarPS_HG     ,smeared_LamellarPS_HG  ,smeared_qvals) //this wrapper fills the STRUCT
108//     
109//      Display smeared_LamellarPS_HG vs smeared_qvals                                                          //
110//      ModifyGraph log=1,marker=29,msize=2,mode=4
111//      Label bottom "q (\\S-1\\M)"
112//      Label left "I(q) (cm\\S-1\\M)"
113//     
114//      SetDataFolder root:
115//End
116       
117
118
119//AAO version, uses XOP if available
120// simply calls the original single point calculation with
121// a wave assignment (this will behave nicely if given point ranges)
122Function LamellarPS_HG(cw,yw,xw) : FitFunc
123        Wave cw,yw,xw
124       
125#if exists("LamellarPS_HGX")
126        yw = LamellarPS_HGX(cw,xw)
127#else
128        yw = fLamellarPS_HG(cw,xw)
129#endif
130        return(0)
131End
132
133//
134Function fLamellarPS_HG(w,x) : FitFunc
135        Wave w
136        Variable x
137//       Input (fitting) variables are:
138//[0]Scale
139//[1]repeat spacing, D
140//[2]Tail Thickness (delT)
141//[3]HG thickness (delH)
142//[4]SLD tails
143//[5]SLD HG
144//[6]SLD solvent
145//[7]# of Lam plates
146//[8]Caille parameter
147//[9]Incoherent Bgd (cm-1)
148       
149//      give them nice names
150        Variable scale,dd,delT,delH,SLD_T,SLD_H,SLD_S,NN,Cp,bkg
151        scale = w[0]
152        dd = w[1]
153        delT = w[2]
154        delH = w[3]
155        SLD_T = w[4]
156        SLD_H = w[5]
157        SLD_S = w[6]
158        NN = trunc(w[7])                //be sure that NN is an integer
159        Cp = w[8]
160        bkg = w[9]
161       
162//      local variables
163        Variable inten, qval,Pq,Sq,ii,alpha,temp,t1,t2,t3,dQ,drh,drt
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        drh = SLD_H - SLD_S
189//      drt = SLD_T - SLD_H             //original
190        drt = SLD_T - SLD_S             //matches Lionel's changes in the Lamellar_HG model
191       
192        Pq = drh*(sin(qval*(delH+delT))-sin(qval*delT)) + drt*sin(qval*delT)
193        Pq *= Pq
194        Pq *= 4/(qval^2)
195       
196        ii=0
197        Sq = 0
198        for(ii=1;ii<(NN-1);ii+=1)
199                temp = 0
200                alpha = Cp/4/pi/pi*(ln(pi*ii) + Euler)
201                t1 = 2*dQ*dQ*dd*dd*alpha
202                t2 = 2*qval*qval*dd*dd*alpha
203                t3 = dQ*dQ*dd*dd*ii*ii
204               
205                temp = 1-ii/NN
206                temp *= cos(dd*qval*ii/(1+t1))
207                temp *= exp(-1*(t2 + t3)/(2*(1+t1)) )
208                temp /= sqrt(1+t1)
209               
210                Sq += temp
211        endfor
212        Sq *= 2
213        Sq += 1
214       
215        inten = 2*Pi*scale*Pq*Sq/(dd*Qval^2)
216       
217        inten *= 1e8            // 1/A to 1/cm
218        //inten = Sq
219        Return (inten+bkg)
220End
221
222//wrapper to calculate the smeared model as an AAO-Struct
223// fills the struct and calls the ususal function with the STRUCT parameter
224//
225// used only for the dependency, not for fitting
226//
227//Function fLamellarPS_HG_Smeared(coefW,yW,xW)
228//      Wave coefW,yW,xW
229//     
230//      String str = getWavesDataFolder(yW,0)
231//      String DF="root:"+str+":"
232//     
233//      WAVE resW = $(DF+str+"_res")
234//     
235//      STRUCT ResSmearAAOStruct fs
236//      WAVE fs.coefW = coefW   
237//      WAVE fs.yW = yW
238//      WAVE fs.xW = xW
239//      WAVE fs.resW = resW
240//     
241//      Variable err
242//      err = LamellarPS_HG_Smeared(fs)
243//     
244//      return (0)
245//End
246
247//////the smeared model calculation
248//Function LamellarPS_HG_Smeared(s) :FitFunc
249//      Struct ResSmearAAOStruct &s
250//
251////    the name of your unsmeared model (AAO) is the first argument
252//      Smear_Model_20(LamellarPS_HG,s.coefW,s.xW,s.yW,s.resW)
253//
254//      return(0)
255//End
256       
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