source: sans/Dev/trunk/NCNR_User_Procedures/Analysis/Models/ProlateCoreShell_Sq_v40.ipf @ 774

Last change on this file since 774 was 774, checked in by srkline, 12 years ago

Added the Two-Yukawa structure factor calculations to those model functions with S(Q).

Fixed the name of Vesicle_UL_Sq.ipf to be consistent.

File size: 22.1 KB
Line 
1#pragma rtGlobals=1             // Use modern global access method.
2#pragma IgorVersion=6.1
3
4// be sure to include all the necessary files...
5#include "ProlateCoreShell_v40"
6#include "EffectiveDiameter_v40"
7
8#include "HardSphereStruct_v40"
9#include "HPMSA_v40"
10#include "SquareWellStruct_v40"
11#include "StickyHardSphereStruct_v40"
12#include "Two_Yukawa_v40"
13
14Proc PlotProlate_HS(num,qmin,qmax)
15        Variable num=128,qmin=0.001,qmax=0.7
16        Prompt num "Enter number of data points for model: "
17        Prompt qmin "Enter minimum q-value (A^-1) for model: "
18        Prompt qmax "Enter maximum q-value (A^-1) for model: "
19       
20        Make/O/D/n=(num) xwave_PEF_HS,ywave_PEF_HS
21        xwave_PEF_HS =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
22        Make/O/D coef_PEF_HS = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,0.0001}
23        make/o/t parameters_PEF_HS = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","bkg (cm-1)"}
24        Edit parameters_PEF_HS,coef_PEF_HS
25       
26        Variable/G root:g_PEF_HS
27        g_PEF_HS := Prolate_HS(coef_PEF_HS,ywave_PEF_HS,xwave_PEF_HS)
28        Display ywave_PEF_HS vs xwave_PEF_HS
29        ModifyGraph log=1,marker=29,msize=2,mode=4
30        Label bottom "q (A\\S-1\\M)"
31        Label left "Intensity (cm\\S-1\\M)"
32
33        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
34       
35        AddModelToStrings("Prolate_HS","coef_PEF_HS","parameters_PEF_HS","PEF_HS")
36End
37
38// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
39Proc PlotSmearedProlate_HS(str)                                                         
40        String str
41        Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
42       
43        // if any of the resolution waves are missing => abort
44        if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
45                Abort
46        endif
47       
48        SetDataFolder $("root:"+str)
49       
50        // Setup parameter table for model function
51        Make/O/D smear_coef_PEF_HS = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,0.0001}
52        make/o/t smear_parameters_PEF_HS = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","bkg (cm-1)"}
53        Edit smear_parameters_PEF_HS,smear_coef_PEF_HS                                 
54       
55        // output smeared intensity wave, dimensions are identical to experimental QSIG values
56        // make extra copy of experimental q-values for easy plotting
57        Duplicate/O $(str+"_q") smeared_PEF_HS,smeared_qvals                           
58        SetScale d,0,0,"1/cm",smeared_PEF_HS                                                   
59                                       
60        Variable/G gs_PEF_HS=0
61        gs_PEF_HS := fSmearedProlate_HS(smear_coef_PEF_HS,smeared_PEF_HS,smeared_qvals) //this wrapper fills the STRUCT
62       
63        Display smeared_PEF_HS vs smeared_qvals                                                                 
64        ModifyGraph log=1,marker=29,msize=2,mode=4
65        Label bottom "q (A\\S-1\\M)"
66        Label left "Intensity (cm\\S-1\\M)"
67
68        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
69       
70        SetDataFolder root:
71        AddModelToStrings("SmearedProlate_HS","smear_coef_PEF_HS","smear_parameters_PEF_HS","PEF_HS")
72End
73       
74
75Function Prolate_HS(w,yw,xw) : FitFunc
76        Wave w,yw,xw
77       
78        Variable inten,Ras,Rbs
79        Ras = w[3]      //Ras is the rotation axis
80        Rbs = w[4]
81       
82        //setup form factor coefficient wave
83        Make/O/D/N=9 form_PEF_HS
84        form_PEF_HS[0] = 1
85        form_PEF_HS[1] = w[1]
86        form_PEF_HS[2] = w[2]
87        form_PEF_HS[3] = w[3]
88        form_PEF_HS[4] = w[4]
89        form_PEF_HS[5] = w[5]
90        form_PEF_HS[6] = w[6]
91        form_PEF_HS[7] = w[7]
92        form_PEF_HS[8] = 0
93       
94        //setup structure factor coefficient wave
95        Make/O/D/N=2 struct_PEF_HS
96        struct_PEF_HS[0] = 0.5*DiamEllip(Ras,Rbs)
97        struct_PEF_HS[1] = w[0]
98       
99        //calculate each and combine
100        Duplicate/O xw temp_PEF_HS_PQ,temp_PEF_HS_SQ            //make waves for the AAO
101        ProlateForm(form_PEF_HS,temp_PEF_HS_PQ,xw)
102        HardSphereStruct(struct_PEF_HS,temp_PEF_HS_SQ,xw)
103        yw = temp_PEF_HS_PQ *temp_PEF_HS_SQ
104        yw *= w[0]
105        yw += w[8]
106       
107        //cleanup waves
108//      Killwaves/Z form_PEF_HS,struct_PEF_HS
109       
110        return (yw)
111End
112
113Proc PlotProlate_SW(num,qmin,qmax)
114        Variable num=128,qmin=0.001,qmax=0.7
115        Prompt num "Enter number of data points for model: "
116        Prompt qmin "Enter minimum q-value (A^-1) for model: "
117        Prompt qmax "Enter maximum q-value (A^-1) for model: "
118       
119        Make/O/D/n=(num) xwave_PEF_SW,ywave_PEF_SW
120        xwave_PEF_SW =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
121        Make/O/D coef_PEF_SW = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,1.0,1.2,0.0001}
122        make/o/t parameters_PEF_SW = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","well depth (kT)","well width (diam.)","bkg (cm-1)"}
123        Edit parameters_PEF_SW,coef_PEF_SW
124       
125        Variable/G root:g_PEF_SW
126        g_PEF_SW := Prolate_SW(coef_PEF_SW,ywave_PEF_SW,xwave_PEF_SW)
127        Display ywave_PEF_SW vs xwave_PEF_SW
128        ModifyGraph log=1,marker=29,msize=2,mode=4
129        Label bottom "q (A\\S-1\\M)"
130        Label left "Intensity (cm\\S-1\\M)"
131
132        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
133       
134        AddModelToStrings("Prolate_SW","coef_PEF_SW","parameters_PEF_SW","PEF_SW")
135End
136
137// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
138Proc PlotSmearedProlate_SW(str)                                                         
139        String str
140        Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
141       
142        // if any of the resolution waves are missing => abort
143        if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
144                Abort
145        endif
146       
147        SetDataFolder $("root:"+str)
148       
149        // Setup parameter table for model function
150        Make/O/D smear_coef_PEF_SW = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,1.0,1.2,0.0001}
151        make/o/t smear_parameters_PEF_SW = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","well depth (kT)","well width (diam.)","bkg (cm-1)"}
152        Edit smear_parameters_PEF_SW,smear_coef_PEF_SW                                 
153       
154        // output smeared intensity wave, dimensions are identical to experimental QSIG values
155        // make extra copy of experimental q-values for easy plotting
156        Duplicate/O $(str+"_q") smeared_PEF_SW,smeared_qvals                           
157        SetScale d,0,0,"1/cm",smeared_PEF_SW                                                   
158                                       
159        Variable/G gs_PEF_SW=0
160        gs_PEF_SW := fSmearedProlate_SW(smear_coef_PEF_SW,smeared_PEF_SW,smeared_qvals) //this wrapper fills the STRUCT
161       
162        Display smeared_PEF_SW vs smeared_qvals                                                                 
163        ModifyGraph log=1,marker=29,msize=2,mode=4
164        Label bottom "q (A\\S-1\\M)"
165        Label left "Intensity (cm\\S-1\\M)"
166
167        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
168       
169        SetDataFolder root:
170        AddModelToStrings("SmearedProlate_SW","smear_coef_PEF_SW","smear_parameters_PEF_SW","PEF_SW")
171End
172       
173
174Function Prolate_SW(w,yw,xw) : FitFunc
175        Wave w,yw,xw
176       
177        Variable inten,Ras,Rbs
178        Ras = w[3]      //Ras is the rotation axis
179        Rbs = w[4]
180       
181        //setup form factor coefficient wave
182        Make/O/D/N=9 form_PEF_SW
183        form_PEF_SW[0] = 1
184        form_PEF_SW[1] = w[1]
185        form_PEF_SW[2] = w[2]
186        form_PEF_SW[3] = w[3]
187        form_PEF_SW[4] = w[4]
188        form_PEF_SW[5] = w[5]
189        form_PEF_SW[6] = w[6]
190        form_PEF_SW[7] = w[7]
191        form_PEF_SW[8] = 0
192       
193        //setup structure factor coefficient wave
194        Make/O/D/N=4 struct_PEF_SW
195        struct_PEF_SW[0] = 0.5*DiamEllip(Ras,Rbs)
196        struct_PEF_SW[1] = w[0]
197        struct_PEF_SW[2] = w[8]
198        struct_PEF_SW[3] = w[9]
199       
200        //calculate each and combine
201        Duplicate/O xw temp_PEF_SW_PQ,temp_PEF_SW_SQ            //make waves for the AAO
202        ProlateForm(form_PEF_SW,temp_PEF_SW_PQ,xw)
203        SquareWellStruct(struct_PEF_SW,temp_PEF_SW_SQ,xw)
204        yw = temp_PEF_SW_PQ * temp_PEF_SW_SQ
205        yw *= w[0]
206        yw += w[10]
207       
208        //cleanup waves
209//      Killwaves/Z form_PEF_SW,struct_PEF_SW
210       
211        return (0)
212End
213
214Proc PlotProlate_SC(num,qmin,qmax)
215        Variable num=128,qmin=0.001,qmax=0.7
216        Prompt num "Enter number of data points for model: "
217        Prompt qmin "Enter minimum q-value (A^-1) for model: "
218        Prompt qmax "Enter maximum q-value (A^-1) for model: "
219       
220        if(!DataFolderExists(":HayPenMSA"))
221                NewDataFolder :HayPenMSA
222        endif
223        Make/O/D/N=17 :HayPenMSA:gMSAWave
224       
225        Make/O/D/n=(num) xwave_PEF_SC,ywave_PEF_SC
226        xwave_PEF_SC =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
227        Make/O/D coef_PEF_SC = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,20,0,298,78,0.0001}
228        make/o/t parameters_PEF_SC = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","charge","movalent salt(M)","Temperature (K)","dielectric const","bkg (cm-1)"}
229        Edit parameters_PEF_SC,coef_PEF_SC
230       
231        Variable/G root:g_PEF_SC
232        g_PEF_SC := Prolate_SC(coef_PEF_SC,ywave_PEF_SC,xwave_PEF_SC)
233        Display ywave_PEF_SC vs xwave_PEF_SC
234        ModifyGraph log=1,marker=29,msize=2,mode=4
235        Label bottom "q (A\\S-1\\M)"
236        Label left "Intensity (cm\\S-1\\M)"
237
238        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
239       
240        AddModelToStrings("Prolate_SC","coef_PEF_SC","parameters_PEF_SC","PEF_SC")
241End
242
243// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
244Proc PlotSmearedProlate_SC(str)                                                         
245        String str
246        Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
247       
248        // if any of the resolution waves are missing => abort
249        if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
250                Abort
251        endif
252       
253        SetDataFolder $("root:"+str)
254       
255        if(!DataFolderExists(":HayPenMSA"))
256                NewDataFolder :HayPenMSA
257        endif
258        Make/O/D/N=17 :HayPenMSA:gMSAWave
259       
260        // Setup parameter table for model function
261        Make/O/D smear_coef_PEF_SC = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,20,0,298,78,0.0001}
262        make/o/t smear_parameters_PEF_SC = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","charge","movalent salt(M)","Temperature (K)","dielectric const","bkg (cm-1)"}
263        Edit smear_parameters_PEF_SC,smear_coef_PEF_SC                                 
264       
265        // output smeared intensity wave, dimensions are identical to experimental QSIG values
266        // make extra copy of experimental q-values for easy plotting
267        Duplicate/O $(str+"_q") smeared_PEF_SC,smeared_qvals                           
268        SetScale d,0,0,"1/cm",smeared_PEF_SC                                                   
269                                       
270        Variable/G gs_PEF_SC=0
271        gs_PEF_SC := fSmearedProlate_SC(smear_coef_PEF_SC,smeared_PEF_SC,smeared_qvals) //this wrapper fills the STRUCT
272       
273        Display smeared_PEF_SC vs smeared_qvals                                                                 
274        ModifyGraph log=1,marker=29,msize=2,mode=4
275        Label bottom "q (A\\S-1\\M)"
276        Label left "Intensity (cm\\S-1\\M)"
277
278        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
279       
280        SetDataFolder root:
281        AddModelToStrings("SmearedProlate_SC","smear_coef_PEF_SC","smear_parameters_PEF_SC","PEF_SC")
282End
283
284
285Function Prolate_SC(w,yw,xw) : FitFunc
286        Wave w,yw,xw
287       
288        Variable inten,Ras,Rbs
289        Ras = w[3]      //Ras is the rotation axis
290        Rbs = w[4]
291       
292        //setup form factor coefficient wave
293        Make/O/D/N=9 form_PEF_SC
294        form_PEF_SC[0] = 1
295        form_PEF_SC[1] = w[1]
296        form_PEF_SC[2] = w[2]
297        form_PEF_SC[3] = w[3]
298        form_PEF_SC[4] = w[4]
299        form_PEF_SC[5] = w[5]
300        form_PEF_SC[6] = w[6]
301        form_PEF_SC[7] = w[7]
302        form_PEF_SC[8] = 0
303       
304        //setup structure factor coefficient wave
305        Make/O/D/N=6 struct_PEF_SC
306        struct_PEF_SC[0] = DiamEllip(Ras,Rbs)
307        struct_PEF_SC[1] = w[8]
308        struct_PEF_SC[2] = w[0]
309        struct_PEF_SC[3] = w[10]
310        struct_PEF_SC[4] = w[9]
311        struct_PEF_SC[5] = w[11]
312       
313        //calculate each and combine
314        Duplicate/O xw temp_PEF_SC_PQ,temp_PEF_SC_SQ            //make waves for the AAO
315        ProlateForm(form_PEF_SC,temp_PEF_SC_PQ,xw)
316        HayterPenfoldMSA(struct_PEF_SC,temp_PEF_SC_SQ,xw)
317        yw = temp_PEF_SC_PQ * temp_PEF_SC_SQ
318        yw *= w[0]
319        yw += w[12]
320       
321        //cleanup waves
322//      Killwaves/Z form_PEF_SC,struct_PEF_SC
323       
324        return (0)
325End
326
327
328Proc PlotProlate_SHS(num,qmin,qmax)
329        Variable num=128,qmin=0.001,qmax=0.7
330        Prompt num "Enter number of data points for model: "
331        Prompt qmin "Enter minimum q-value (A^-1) for model: "
332        Prompt qmax "Enter maximum q-value (A^-1) for model: "
333       
334        Make/O/D/n=(num) xwave_PEF_SHS,ywave_PEF_SHS
335        xwave_PEF_SHS =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
336        Make/O/D coef_PEF_SHS = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,0.05,0.2,0.0001}
337        make/o/t parameters_PEF_SHS = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","perturbation parameter (0.1)","stickiness, tau","bkg (cm-1)"}
338        Edit parameters_PEF_SHS,coef_PEF_SHS
339       
340        Variable/G root:g_PEF_SHS
341        g_PEF_SHS := Prolate_SHS(coef_PEF_SHS,ywave_PEF_SHS,xwave_PEF_SHS)
342        Display ywave_PEF_SHS vs xwave_PEF_SHS
343        ModifyGraph log=1,marker=29,msize=2,mode=4
344        Label bottom "q (A\\S-1\\M)"
345        Label left "Intensity (cm\\S-1\\M)"
346
347        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
348       
349        AddModelToStrings("Prolate_SHS","coef_PEF_SHS","parameters_PEF_SHS","PEF_SHS")
350End
351
352// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
353Proc PlotSmearedProlate_SHS(str)                                                               
354        String str
355        Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
356       
357        // if any of the resolution waves are missing => abort
358        if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
359                Abort
360        endif
361       
362        SetDataFolder $("root:"+str)
363       
364        // Setup parameter table for model function
365        Make/O/D smear_coef_PEF_SHS = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,0.05,0.2,0.0001}
366        make/o/t smear_parameters_PEF_SHS = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","perturbation parameter (0.1)","stickiness, tau","bkg (cm-1)"}
367        Edit smear_parameters_PEF_SHS,smear_coef_PEF_SHS                                       
368       
369        // output smeared intensity wave, dimensions are identical to experimental QSIG values
370        // make extra copy of experimental q-values for easy plotting
371        Duplicate/O $(str+"_q") smeared_PEF_SHS,smeared_qvals                           
372        SetScale d,0,0,"1/cm",smeared_PEF_SHS                                                   
373                                       
374        Variable/G gs_PEF_SHS=0
375        gs_PEF_SHS := fSmearedProlate_SHS(smear_coef_PEF_SHS,smeared_PEF_SHS,smeared_qvals)     //this wrapper fills the STRUCT
376       
377        Display smeared_PEF_SHS vs smeared_qvals                                                                       
378        ModifyGraph log=1,marker=29,msize=2,mode=4
379        Label bottom "q (A\\S-1\\M)"
380        Label left "Intensity (cm\\S-1\\M)"
381
382        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
383       
384        SetDataFolder root:
385        AddModelToStrings("SmearedProlate_SHS","smear_coef_PEF_SHS","smear_parameters_PEF_SHS","PEF_SHS")
386End
387       
388
389Function Prolate_SHS(w,yw,xw) : FitFunc
390        Wave w,yw,xw
391       
392        Variable inten,Ras,Rbs
393        Ras = w[3]      //Ras is the rotation axis
394        Rbs = w[4]
395       
396        //setup form factor coefficient wave
397        Make/O/D/N=9 form_PEF_SHS
398        form_PEF_SHS[0] = 1
399        form_PEF_SHS[1] = w[1]
400        form_PEF_SHS[2] = w[2]
401        form_PEF_SHS[3] = w[3]
402        form_PEF_SHS[4] = w[4]
403        form_PEF_SHS[5] = w[5]
404        form_PEF_SHS[6] = w[6]
405        form_PEF_SHS[7] = w[7]
406        form_PEF_SHS[8] = 0
407       
408        //setup structure factor coefficient wave
409        Make/O/D/N=4 struct_PEF_SHS
410        struct_PEF_SHS[0] = 0.5*DiamEllip(Ras,Rbs)
411        struct_PEF_SHS[1] = w[0]
412        struct_PEF_SHS[2] = w[8]
413        struct_PEF_SHS[3] = w[9]
414       
415        //calculate each and combine
416        Duplicate/O xw temp_PEF_SHS_PQ,temp_PEF_SHS_SQ          //make waves for the AAO
417        ProlateForm(form_PEF_SHS,temp_PEF_SHS_PQ,xw)
418        StickyHS_Struct(struct_PEF_SHS,temp_PEF_SHS_SQ,xw)
419        yw = temp_PEF_SHS_PQ * temp_PEF_SHS_SQ
420        yw *= w[0]
421        yw += w[10]
422       
423        //cleanup waves
424//      Killwaves/Z form_PEF_SHS,struct_PEF_SHS
425       
426        return (0)
427End
428
429// two yukawa
430Proc PlotProlate_2Y(num,qmin,qmax)
431        Variable num=128,qmin=0.001,qmax=0.7
432        Prompt num "Enter number of data points for model: "
433        Prompt qmin "Enter minimum q-value (A^-1) for model: "
434        Prompt qmax "Enter maximum q-value (A^-1) for model: "
435       
436        Make/O/D/n=(num) xwave_PEF_2Y,ywave_PEF_2Y
437        xwave_PEF_2Y =  alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
438        Make/O/D coef_PEF_2Y = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,6,10,-1,2,0.0001}
439        make/o/t parameters_PEF_2Y = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","scale, K1","charge, Z1","scale, K2","charge, Z2","bkg (cm-1)"}
440        Edit parameters_PEF_2Y,coef_PEF_2Y
441       
442        Variable/G root:g_PEF_2Y
443        g_PEF_2Y := Prolate_2Y(coef_PEF_2Y,ywave_PEF_2Y,xwave_PEF_2Y)
444        Display ywave_PEF_2Y vs xwave_PEF_2Y
445        ModifyGraph log=1,marker=29,msize=2,mode=4
446        Label bottom "q (A\\S-1\\M)"
447        Label left "Intensity (cm\\S-1\\M)"
448
449        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
450       
451        AddModelToStrings("Prolate_2Y","coef_PEF_2Y","parameters_PEF_2Y","PEF_2Y")
452End
453
454// - sets up a dependency to a wrapper, not the actual SmearedModelFunction
455Proc PlotSmearedProlate_2Y(str)                                                         
456        String str
457        Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)
458       
459        // if any of the resolution waves are missing => abort
460        if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
461                Abort
462        endif
463       
464        SetDataFolder $("root:"+str)
465       
466        // Setup parameter table for model function
467        Make/O/D smear_coef_PEF_2Y = {0.01,100,50,110,60,1e-6,2e-6,6.3e-6,6,10,-1,2,0.0001}
468        make/o/t smear_parameters_PEF_2Y = {"volume fraction","major core radius (A)","minor core radius (A)","major shell radius (A)","minor shell radius (A)","SLD core (A-2)","SLD shell (A-2)","SLD solvent (A-2)","scale, K1","charge, Z1","scale, K2","charge, Z2","bkg (cm-1)"}
469        Edit smear_parameters_PEF_2Y,smear_coef_PEF_2Y                                 
470       
471        // output smeared intensity wave, dimensions are identical to experimental QSIG values
472        // make extra copy of experimental q-values for easy plotting
473        Duplicate/O $(str+"_q") smeared_PEF_2Y,smeared_qvals                           
474        SetScale d,0,0,"1/cm",smeared_PEF_2Y                                                   
475                                       
476        Variable/G gs_PEF_2Y=0
477        gs_PEF_2Y := fSmearedProlate_2Y(smear_coef_PEF_2Y,smeared_PEF_2Y,smeared_qvals) //this wrapper fills the STRUCT
478       
479        Display smeared_PEF_2Y vs smeared_qvals                                                                 
480        ModifyGraph log=1,marker=29,msize=2,mode=4
481        Label bottom "q (A\\S-1\\M)"
482        Label left "Intensity (cm\\S-1\\M)"
483
484        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
485       
486        SetDataFolder root:
487        AddModelToStrings("SmearedProlate_2Y","smear_coef_PEF_2Y","smear_parameters_PEF_2Y","PEF_2Y")
488End
489       
490
491Function Prolate_2Y(w,yw,xw) : FitFunc
492        Wave w,yw,xw
493       
494        Variable inten,Ras,Rbs
495        Ras = w[3]      //Ras is the rotation axis
496        Rbs = w[4]
497       
498        //setup form factor coefficient wave
499        Make/O/D/N=9 form_PEF_2Y
500        form_PEF_2Y[0] = 1
501        form_PEF_2Y[1] = w[1]
502        form_PEF_2Y[2] = w[2]
503        form_PEF_2Y[3] = w[3]
504        form_PEF_2Y[4] = w[4]
505        form_PEF_2Y[5] = w[5]
506        form_PEF_2Y[6] = w[6]
507        form_PEF_2Y[7] = w[7]
508        form_PEF_2Y[8] = 0
509       
510        //setup structure factor coefficient wave
511        Make/O/D/N=6 struct_PEF_2Y
512        struct_PEF_2Y[0] = w[0]
513        struct_PEF_2Y[1] = 0.5*DiamEllip(Ras,Rbs)
514        struct_PEF_2Y[2] = w[8]
515        struct_PEF_2Y[3] = w[9]
516        struct_PEF_2Y[4] = w[10]
517        struct_PEF_2Y[5] = w[11]
518       
519        //calculate each and combine
520        Duplicate/O xw temp_PEF_2Y_PQ,temp_PEF_2Y_SQ            //make waves for the AAO
521        ProlateForm(form_PEF_2Y,temp_PEF_2Y_PQ,xw)
522        TwoYukawa(struct_PEF_2Y,temp_PEF_2Y_SQ,xw)
523        yw = temp_PEF_2Y_PQ *temp_PEF_2Y_SQ
524        yw *= w[0]
525        yw += w[12]
526       
527        //cleanup waves
528//      Killwaves/Z form_PEF_2Y,struct_PEF_2Y
529       
530        return (yw)
531End
532
533// this is all there is to the smeared calculation!
534Function SmearedProlate_HS(s) :FitFunc
535        Struct ResSmearAAOStruct &s
536
537//      the name of your unsmeared model is the first argument
538        Smear_Model_20(Prolate_HS,s.coefW,s.xW,s.yW,s.resW)
539
540        return(0)
541End
542
543// this is all there is to the smeared calculation!
544Function SmearedProlate_SW(s) :FitFunc
545        Struct ResSmearAAOStruct &s
546
547//      the name of your unsmeared model is the first argument
548        Smear_Model_20(Prolate_Sw,s.coefW,s.xW,s.yW,s.resW)
549
550        return(0)
551End
552
553// this is all there is to the smeared calculation!
554Function SmearedProlate_SC(s) :FitFunc
555        Struct ResSmearAAOStruct &s
556
557//      the name of your unsmeared model is the first argument
558        Smear_Model_20(Prolate_SC,s.coefW,s.xW,s.yW,s.resW)
559
560        return(0)
561End
562
563// this is all there is to the smeared calculation!
564Function SmearedProlate_SHS(s) :FitFunc
565        Struct ResSmearAAOStruct &s
566
567//      the name of your unsmeared model is the first argument
568        Smear_Model_20(Prolate_SHS,s.coefW,s.xW,s.yW,s.resW)
569
570        return(0)
571End
572
573// this is all there is to the smeared calculation!
574Function SmearedProlate_2Y(s) :FitFunc
575        Struct ResSmearAAOStruct &s
576
577//      the name of your unsmeared model is the first argument
578        Smear_Model_20(Prolate_2Y,s.coefW,s.xW,s.yW,s.resW)
579
580        return(0)
581End
582
583//wrapper to calculate the smeared model as an AAO-Struct
584// fills the struct and calls the ususal function with the STRUCT parameter
585//
586// used only for the dependency, not for fitting
587//
588Function fSmearedProlate_HS(coefW,yW,xW)
589        Wave coefW,yW,xW
590       
591        String str = getWavesDataFolder(yW,0)
592        String DF="root:"+str+":"
593       
594        WAVE resW = $(DF+str+"_res")
595       
596        STRUCT ResSmearAAOStruct fs
597        WAVE fs.coefW = coefW   
598        WAVE fs.yW = yW
599        WAVE fs.xW = xW
600        WAVE fs.resW = resW
601       
602        Variable err
603        err = SmearedProlate_HS(fs)
604       
605        return (0)
606End
607
608//wrapper to calculate the smeared model as an AAO-Struct
609// fills the struct and calls the ususal function with the STRUCT parameter
610//
611// used only for the dependency, not for fitting
612//
613Function fSmearedProlate_SW(coefW,yW,xW)
614        Wave coefW,yW,xW
615       
616        String str = getWavesDataFolder(yW,0)
617        String DF="root:"+str+":"
618       
619        WAVE resW = $(DF+str+"_res")
620       
621        STRUCT ResSmearAAOStruct fs
622        WAVE fs.coefW = coefW   
623        WAVE fs.yW = yW
624        WAVE fs.xW = xW
625        WAVE fs.resW = resW
626       
627        Variable err
628        err = SmearedProlate_SW(fs)
629       
630        return (0)
631End
632
633//wrapper to calculate the smeared model as an AAO-Struct
634// fills the struct and calls the ususal function with the STRUCT parameter
635//
636// used only for the dependency, not for fitting
637//
638Function fSmearedProlate_SC(coefW,yW,xW)
639        Wave coefW,yW,xW
640       
641        String str = getWavesDataFolder(yW,0)
642        String DF="root:"+str+":"
643       
644        WAVE resW = $(DF+str+"_res")
645       
646        STRUCT ResSmearAAOStruct fs
647        WAVE fs.coefW = coefW   
648        WAVE fs.yW = yW
649        WAVE fs.xW = xW
650        WAVE fs.resW = resW
651       
652        Variable err
653        err = SmearedProlate_SC(fs)
654       
655        return (0)
656End
657
658//wrapper to calculate the smeared model as an AAO-Struct
659// fills the struct and calls the ususal function with the STRUCT parameter
660//
661// used only for the dependency, not for fitting
662//
663Function fSmearedProlate_SHS(coefW,yW,xW)
664        Wave coefW,yW,xW
665       
666        String str = getWavesDataFolder(yW,0)
667        String DF="root:"+str+":"
668       
669        WAVE resW = $(DF+str+"_res")
670       
671        STRUCT ResSmearAAOStruct fs
672        WAVE fs.coefW = coefW   
673        WAVE fs.yW = yW
674        WAVE fs.xW = xW
675        WAVE fs.resW = resW
676       
677        Variable err
678        err = SmearedProlate_SHS(fs)
679       
680        return (0)
681End
682
683//wrapper to calculate the smeared model as an AAO-Struct
684// fills the struct and calls the ususal function with the STRUCT parameter
685//
686// used only for the dependency, not for fitting
687//
688Function fSmearedProlate_2Y(coefW,yW,xW)
689        Wave coefW,yW,xW
690       
691        String str = getWavesDataFolder(yW,0)
692        String DF="root:"+str+":"
693       
694        WAVE resW = $(DF+str+"_res")
695       
696        STRUCT ResSmearAAOStruct fs
697        WAVE fs.coefW = coefW   
698        WAVE fs.yW = yW
699        WAVE fs.xW = xW
700        WAVE fs.resW = resW
701       
702        Variable err
703        err = SmearedProlate_2Y(fs)
704       
705        return (0)
706End
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