source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/MultScatter_MonteCarlo_2D.ipf @ 614

Last change on this file since 614 was 614, checked in by srkline, 13 years ago

Added table of empirical incoherent cross sections in the Simultation Help file.

File size: 61.9 KB
Line 
1#pragma rtGlobals=1             // Use modern global access method.
2#pragma IgorVersion=6.1
3
4//
5// Monte Carlo simulator for SASCALC
6// October 2008 SRK
7//
8// This code simulates the scattering for a selected model based on the instrument configuration
9// This code is based directly on John Barker's code, which includes multiple scattering effects.
10// A lot of the setup, wave creation, and post-calculations are done in SASCALC->ReCalculateInten()
11//
12//
13// at the end of the procedure fils is a *very* simple example of scripting for unattended simulations
14// - not for the casual user at all.
15
16
17
18// the RNG issue is really not worth the effort. multiple copies with different RNG is as good as I need. Plus,
19// whatever XOP crashing was happining during threading is really unlikely to be from the RNG
20//
21// *** look into erand48() as the (pseudo) random number generator (it's a standard c-lib function, at least on unix)
22//     and is apparantly thread safe. drand48() returns values [0.0,1.0)
23//http://qnxcs.unomaha.edu/help/product/neutrino/lib_ref/e/erand48.html
24//
25
26
27// - Why am I off by a factor of 2.7 - 3.7 (MC too high) relative to real data?
28//   I need to include efficiency (70%?) - do I knock these off before the simulation or do I
29//    really simulate that some fraction of neutrons on the detector don't actually get counted?
30//   Is the flux estimate up-to-date? !! Flux estimates at NG3 are out-of-date....
31// - my simulated transmission is larger than what is measured, even after correcting for the quartz cell.
32//   Why? Do I need to include absorption? Just inherent problems with incoherent cross sections?
33
34// - Most importantly, this needs to be checked for correctness of the MC simulation
35// X how can I get the "data" on absolute scale? This would be a great comparison vs. the ideal model calculation
36// X why does my integrated tau not match up with John's analytical calculations? where are the assumptions?
37// X get rid of all small angle assumptions - to make sure that the calculation is correct at all angles
38
39//
40// X at the larger angles, is the "flat" detector being properly accounted for - in terms of
41//   the solid angle and how many counts fall in that pixel. Am I implicitly defining a spherical detector
42//   so that what I see is already "corrected"?
43// X the MC will, of course benefit greatly from being XOPized. Maybe think about parallel implementation
44//   by allowing the data arrays to accumulate. First pass at the XOP is done. Not pretty, not the speediest (5.8x)
45//   but it is functional. Add spinCursor() for long calculations. See WaveAccess XOP example.
46// X the background parameter for the model MUST be zero, or the integration for scattering
47//    power will be incorrect. (now the LAST point in a copy of the coef wave is set to zero, only for the rad_dev calculation
48// X fully use the SASCALC input, most importantly, flux on sample.
49// X if no MC desired, still use the selected model
50// X better display of MC results on panel
51// X settings for "count for X seconds" or "how long to 1E6 cts on detector" (but 1E6 is typically too many counts...)
52// X warn of projected simulation time
53// - add quartz window scattering to the simulation somehow
54// -?- do smeared models make any sense?? Yes, John agrees that they do, and may be used in a more realistic simulation
55//   -?- but the random deviate can't be properly calculated...
56// - make sure that the ratio of scattering coherent/incoherent is properly adjusted for the sample composition
57//   or the volume fraction of solvent.
58//
59// X add to the results the fraction of coherently scattered neutrons that are singly scattered, different than
60//   the overall fraction of singly scattered, and maybe more important to know.
61//
62// X change the fraction reaching the detector to exclude those that don't interact. These transmitted neutrons
63//   aren't counted. Is the # that interact a better number?
64//
65// - do we want to NOT offset the data by a multiplicative factor as it is "frozen" , so that the
66//   effects on the absolute scale can be seen?
67//
68// X why is "pure" incoherent scattering giving me a q^-1 slope, even with the detector all the way back?
69// -NO- can I speed up by assuming everything interacts? This would compromise the ability to calculate multiple scattering
70// X ask John how to verify what is going on
71// - a number of models are now found to be ill-behaved when q=1e-10. Then the random deviate calculation blows up.
72//   a warning has been added - but some models need a proper limiting value, and some (power-law) are simply unuseable
73//   unless something else can be done. Using a log-spacing of points doesn't seem to help, and it introduces a lot of
74//   other problems. Not the way to go.
75// - if the MC gags on a simulation, it often gets "stuck" and can't do the normal calculation from the model, which it
76//   should always default to...
77//
78//
79
80
81
82
83
84// setting the flag to 1 == 2D simulation
85// any other value for flag == 1D simulation
86//
87// must remember to close/reopen the simulation control panel to get the correct panel
88//
89Function Set_2DMonteCarlo_Flag(value)
90        Variable value
91       
92        NVAR flag=root:Packages:NIST:SAS:gDoMonteCarlo
93        flag=value
94        return(0)
95end
96
97// threaded call to the main function, adds up the individual runs, and returns what is to be displayed
98// results is calculated and sent back for display
99Function Monte_SANS_Threaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
100        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
101
102        //initialize ran1 in the XOP by passing a negative integer
103        // does nothing in the Igor code
104        Duplicate/O results retWave
105
106        Variable NNeutron=inputWave[0]
107        Variable i,nthreads= ThreadProcessorCount
108        if(nthreads>2)          //only support 2 processors until I can figure out how to properly thread the XOP and to loop it
109                nthreads=2
110        endif
111       
112//      nthreads = 1
113        NVAR mt=root:myGlobals:gThreadGroupID
114        mt = ThreadGroupCreate(nthreads)
115        NVAR gInitTime = root:Packages:NIST:SAS:gRanDateTime            //time that SASCALC was started
116//      Print "thread group ID = ",mt
117       
118        inputWave[0] = NNeutron/nthreads                //split up the number of neutrons
119       
120        for(i=0;i<nthreads;i+=1)
121                Duplicate/O nt $("nt"+num2istr(i))              //new instance for each thread
122                Duplicate/O j1 $("j1"+num2istr(i))
123                Duplicate/O j2 $("j2"+num2istr(i))
124                Duplicate/O nn $("nn"+num2istr(i))
125                Duplicate/O linear_data $("linear_data"+num2istr(i))
126                Duplicate/O retWave $("retWave"+num2istr(i))
127                Duplicate/O inputWave $("inputWave"+num2istr(i))
128                Duplicate/O ran_dev $("ran_dev"+num2istr(i))
129                               
130                // ?? I need explicit wave references?
131                // maybe I need to have everything in separate data folders - bu tI haven't tried that. seems like a reach.
132                // more likely there is something bad going on in the XOP code.
133                if(i==0)
134                        WAVE inputWave0,ran_dev0,nt0,j10,j20,nn0,linear_data0,retWave0
135                        retWave0 = 0            //clear the return wave
136                        retWave0[0] = -1*(datetime-gInitTime)           //to initialize ran3
137                        ThreadStart mt,i,Monte_SANS_W1(inputWave0,ran_dev0,nt0,j10,j20,nn0,linear_data0,retWave0)
138                        Print "started thread 0"
139                endif
140                if(i==1)
141                        WAVE inputWave1,ran_dev1,nt1,j11,j21,nn1,linear_data1,retWave1
142                        retWave1 = 0                    //clear the return wave
143                        retWave1[0] = -1*(datetime-gInitTime)           //to initialize ran1
144                        ThreadStart mt,i,Monte_SANS_W2(inputWave1,ran_dev1,nt1,j11,j21,nn1,linear_data1,retWave1)
145                        Print "started thread 1"
146                endif
147//              if(i==2)
148//                      WAVE inputWave2,ran_dev2,nt2,j12,j22,nn2,linear_data2,retWave2
149//                      retWave2[0] = -1*datetime               //to initialize ran3
150//                      ThreadStart mt,i,Monte_SANS_W(inputWave2,ran_dev2,nt2,j12,j22,nn2,linear_data2,retWave2)
151//              endif
152//              if(i==3)
153//                      WAVE inputWave3,ran_dev3,nt3,j13,j23,nn3,linear_data3,retWave3
154//                      retWave3[0] = -1*datetime               //to initialize ran3
155//                      ThreadStart mt,i,Monte_SANS_W(inputWave3,ran_dev3,nt3,j13,j23,nn3,linear_data3,retWave3)
156//              endif
157        endfor
158
159// wait until done
160        do
161                variable tgs= ThreadGroupWait(mt,100)
162        while( tgs != 0 )
163        variable dummy= ThreadGroupRelease(mt)
164        mt=0
165        Print "done with all threads"
166
167        // calculate all of the bits for the results
168        if(nthreads == 1)
169                nt = nt0                // add up each instance
170                j1 = j10
171                j2 = j20
172                nn = nn0
173                linear_data = linear_data0
174                retWave = retWave0
175        endif
176        if(nthreads == 2)
177                nt = nt0+nt1            // add up each instance
178                j1 = j10+j11
179                j2 = j20+j21
180                nn = nn0+nn1
181                linear_data = linear_data0+linear_data1
182                retWave = retWave0+retWave1
183        endif
184//      if(nthreads == 3)
185//              nt = nt0+nt1+nt2                // add up each instance
186//              j1 = j10+j11+j12
187//              j2 = j20+j21+j22
188//              nn = nn0+nn1+nn2
189//              linear_data = linear_data0+linear_data1+linear_data2
190//              retWave = retWave0+retWave1+retWave2
191//      endif
192//      if(nthreads == 4)
193//              nt = nt0+nt1+nt2+nt3            // add up each instance
194//              j1 = j10+j11+j12+j13
195//              j2 = j20+j21+j22+j23
196//              nn = nn0+nn1+nn2+nn3
197//              linear_data = linear_data0+linear_data1+linear_data2+linear_data3
198//              retWave = retWave0+retWave1+retWave2+retWave3
199//      endif
200       
201        // fill up the results wave
202        Variable xc,yc
203        xc=inputWave[3]
204        yc=inputWave[4]
205        results[0] = inputWave[9]+inputWave[10]         //total XS
206        results[1] = inputWave[10]                                              //SAS XS
207        results[2] = retWave[1]                                                 //number that interact n2
208        results[3] = retWave[2] - linear_data[xc][yc]                           //# reaching detector minus Q(0)
209        results[4] = retWave[3]/retWave[1]                              //avg# times scattered
210        results[5] = retWave[4]/retWave[7]                                              //single coherent fraction
211        results[6] = retWave[5]/retWave[7]                              //multiple coherent fraction
212        results[7] = retWave[6]/retWave[1]                              //multiple scatter fraction
213        results[8] = (retWave[0]-retWave[1])/retWave[0]                 //transmitted fraction
214       
215        return(0)
216End
217
218// worker function for threads, does nothing except switch between XOP and Igor versions
219//
220// uses ran3
221ThreadSafe Function Monte_SANS_W1(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
222        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
223       
224#if exists("Monte_SANSX")
225        Monte_SANSX(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
226#else
227        Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
228#endif
229
230        return (0)
231End
232
233// worker function for threads, does nothing except switch between XOP and Igor versions
234//
235// uses ran1
236ThreadSafe Function Monte_SANS_W2(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
237        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
238       
239#if exists("Monte_SANSX2")
240        Monte_SANSX2(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
241#else
242        Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
243#endif
244
245        return (0)
246End
247
248// NON-threaded call to the main function returns what is to be displayed
249// results is calculated and sent back for display
250Function Monte_SANS_NotThreaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
251        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
252
253        //initialize ran1 in the XOP by passing a negative integer
254        // does nothing in the Igor code, enoise is already initialized
255        Duplicate/O results retWave
256        WAVE retWave
257        retWave[0] = -1*abs(trunc(100000*enoise(1)))
258       
259#if exists("Monte_SANSX")
260        Monte_SANSX(inputWave,ran_dev,nt,j1,j2,nn,linear_data,retWave)
261#else
262        Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,retWave)
263#endif
264
265        // fill up the results wave
266        Variable xc,yc
267        xc=inputWave[3]
268        yc=inputWave[4]
269        results[0] = inputWave[9]+inputWave[10]         //total XS
270        results[1] = inputWave[10]                                              //SAS XS
271        results[2] = retWave[1]                                                 //number that interact n2
272        results[3] = retWave[2] - linear_data[xc][yc]                           //# reaching detector minus Q(0)
273        results[4] = retWave[3]/retWave[1]                              //avg# times scattered
274        results[5] = retWave[4]/retWave[7]                                              //single coherent fraction
275        results[6] = retWave[5]/retWave[7]                              //double coherent fraction
276        results[7] = retWave[6]/retWave[1]                              //multiple scatter fraction
277        results[8] = (retWave[0]-retWave[1])/retWave[0]                 //transmitted fraction
278       
279        return(0)
280End
281
282
283
284//////////
285//    PROGRAM Monte_SANS
286//    PROGRAM simulates multiple SANS.
287//       revised 2/12/99  JGB
288//            added calculation of random deviate, and 2D 10/2008 SRK
289
290//    N1 = NUMBER OF INCIDENT NEUTRONS.
291//    N2 = NUMBER INTERACTED IN THE SAMPLE.
292//    N3 = NUMBER ABSORBED.
293//    THETA = SCATTERING ANGLE.
294
295//        IMON = 'Enter number of neutrons to use in simulation.'
296//        NUM_BINS = 'Enter number of THETA BINS TO use. (<5000).'
297//        R1 = 'Enter beam radius. (cm)'
298//        R2 = 'Enter sample radius. (cm)'
299//        thick = 'Enter sample thickness. (cm)'
300//        wavelength = 'Enter neutron wavelength. (A)'
301//        R0 = 'Enter sphere radius. (A)'
302//
303
304ThreadSafe Function Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,MC_linear_data,results)
305        WAVE inputWave,ran_dev,nt,j1,j2,nn,MC_linear_data,results
306
307        Variable imon,r1,r2,xCtr,yCtr,sdd,pixSize,thick,wavelength,sig_incoh,sig_sas
308        Variable NUM_BINS,N_INDEX
309        Variable RHO,SIGSAS,SIGABS_0
310        Variable ii,jj,IND,idum,INDEX,IR,NQ
311        Variable qmax,theta_max,R_DAB,R0,BOUND,I0,q0,zpow
312        Variable N1,N2,N3,DTH,zz,tt,SIG_SINGLE,xx,yy,PHI,UU,SIG
313        Variable THETA,Ran,ll,D_OMEGA,RR,Tabs,Ttot,I1_sumI
314        Variable G0,E_NT,E_NN,TRANS_th,Trans_exp,rat
315        Variable GG,GG_ED,dS_dW,ds_dw_double,ds_dw_single
316        Variable DONE,FIND_THETA,err            //used as logicals
317
318        Variable Vx,Vy,Vz,Theta_z,qq
319        Variable Sig_scat,Sig_abs,Ratio,Sig_total
320        Variable isOn=0,testQ,testPhi,xPixel,yPixel
321        Variable NSingleIncoherent,NSingleCoherent,NScatterEvents,incoherentEvent,coherentEvent
322        Variable NDoubleCoherent,NMultipleScatter,countIt,detEfficiency
323        Variable NMultipleCoherent,NCoherentEvents
324       
325        detEfficiency = 1.0             //70% counting efficiency = 0.7
326       
327        imon = inputWave[0]
328        r1 = inputWave[1]
329        r2 = inputWave[2]
330        xCtr = inputWave[3]
331        yCtr = inputWave[4]
332        sdd = inputWave[5]
333        pixSize = inputWave[6]
334        thick = inputWave[7]
335        wavelength = inputWave[8]
336        sig_incoh = inputWave[9]
337        sig_sas = inputWave[10]
338       
339//      SetRandomSeed 0.1               //to get a reproduceable sequence
340
341//scattering power and maximum qvalue to bin
342//      zpow = .1               //scattering power, calculated below
343        qmax = 4*pi/wavelength          //maximum Q to bin 1D data. (A-1) (not really used, so set to a big value)
344        sigabs_0 = 0.0          // ignore absorption cross section/wavelength [1/(cm A)]
345        N_INDEX = 50            // maximum number of scattering events per neutron
346        num_bins = 200          //number of 1-D bins (not really used)
347       
348// my additions - calculate the random deviate function as needed
349// and calculate the scattering power from the model function (passed in as a wave)
350//
351        Variable left = leftx(ran_dev)
352        Variable delta = deltax(ran_dev)
353       
354//c       total SAS cross-section
355//      SIG_SAS = zpow/thick
356        zpow = sig_sas*thick                    //since I now calculate the sig_sas from the model
357        SIG_ABS = SIGABS_0 * WAVElength
358        sig_abs = 0.0           //cm-1
359        SIG_TOTAL =SIG_ABS + SIG_SAS + sig_incoh
360//      Print "The TOTAL XSECTION. (CM-1) is ",sig_total
361//      Print "The TOTAL SAS XSECTION. (CM-1) is ",sig_sas
362//      results[0] = sig_total          //assign these after everything's done
363//      results[1] = sig_sas
364//      variable ratio1,ratio2
365//      ratio1 = sig_abs/sig_total
366//      ratio2 = sig_incoh/sig_total
367//      // 0->ratio1 = abs
368//      // ratio1 -> ratio2 = incoh
369//      // > ratio2 = coherent
370        RATIO = sig_incoh / SIG_TOTAL
371       
372//c       assuming theta = sin(theta)...OK
373        theta_max = wavelength*qmax/(2*pi)
374//C     SET Theta-STEP SIZE.
375        DTH = Theta_max/NUM_BINS
376//      Print "theta bin size = dth = ",dth
377
378//C     INITIALIZE COUNTERS.
379        N1 = 0
380        N2 = 0
381        N3 = 0
382        NSingleIncoherent = 0
383        NSingleCoherent = 0
384        NDoubleCoherent = 0
385        NMultipleScatter = 0
386        NScatterEvents = 0
387        NMultipleCoherent = 0
388        NCoherentEvents = 0
389
390//C     INITIALIZE ARRAYS.
391        j1 = 0
392        j2 = 0
393        nt = 0
394        nn=0
395       
396//C     MONITOR LOOP - looping over the number of incedent neutrons
397//note that zz, is the z-position in the sample - NOT the scattering power
398
399// NOW, start the loop, throwing neutrons at the sample.
400        do
401                Vx = 0.0                        // Initialize direction vector.
402                Vy = 0.0
403                Vz = 1.0
404               
405                Theta = 0.0             //      Initialize scattering angle.
406                Phi = 0.0                       //      Intialize azimuthal angle.
407                N1 += 1                 //      Increment total number neutrons counter.
408                DONE = 0                        //      True when neutron is scattered out of the sample.
409                INDEX = 0                       //      Set counter for number of scattering events.
410                zz = 0.0                        //      Set entering dimension of sample.
411                incoherentEvent = 0
412                coherentEvent = 0
413               
414                do                                      //      Makes sure position is within circle.
415                        ran = abs(enoise(1))            //[0,1]
416                        xx = 2.0*R1*(Ran-0.5)           //X beam position of neutron entering sample.
417                        ran = abs(enoise(1))            //[0,1]
418                        yy = 2.0*R1*(Ran-0.5)           //Y beam position ...
419                        RR = SQRT(xx*xx+yy*yy)          //Radial position of neutron in incident beam.
420                while(rr>r1)
421
422                do    //Scattering Loop, will exit when "done" == 1
423                                // keep scattering multiple times until the neutron exits the sample
424                        ran = abs(enoise(1))            //[0,1]  RANDOM NUMBER FOR DETERMINING PATH LENGTH
425                        ll = PATH_len(ran,Sig_total)
426                        //Determine new scattering direction vector.
427                        err = NewDirection(vx,vy,vz,Theta,Phi)          //vx,vy,vz is updated, theta, phi unchanged by function
428
429                        //X,Y,Z-POSITION OF SCATTERING EVENT.
430                        xx += ll*vx
431                        yy += ll*vy
432                        zz += ll*vz
433                        RR = sqrt(xx*xx+yy*yy)          //radial position of scattering event.
434
435                        //Check whether interaction occurred within sample volume.
436                        IF (((zz > 0.0) && (zz < THICK)) && (rr < r2))
437                                //NEUTRON INTERACTED.
438                                ran = abs(enoise(1))            //[0,1]
439                               
440//                              if(ran<ratio1)
441//                                      //absorption event
442//                                      n3 +=1
443//                                      done=1
444//                              else
445
446                                INDEX += 1                      //Increment counter of scattering events.
447                                IF(INDEX == 1)
448                                        N2 += 1                 //Increment # of scat. neutrons
449                                Endif
450                                //Split neutron interactions into scattering and absorption events
451//                              IF(ran > (ratio1+ratio2) )              //C             NEUTRON SCATTERED coherently
452                                IF(ran > ratio)         //C             NEUTRON SCATTERED coherently
453                                        coherentEvent += 1
454                                        FIND_THETA = 0                  //false
455                                        DO
456                                                //ran = abs(enoise(1))          //[0,1]
457                                                //theta = Scat_angle(Ran,R_DAB,wavelength)      // CHOOSE DAB ANGLE -- this is 2Theta
458                                                //Q0 = 2*PI*THETA/WAVElength                                    // John chose theta, calculated Q
459
460                                                // pick a q-value from the deviate function
461                                                // pnt2x truncates the point to an integer before returning the x
462                                                // so get it from the wave scaling instead
463                                                Q0 =left + binarysearchinterp(ran_dev,abs(enoise(1)))*delta
464                                                theta = Q0/2/Pi*wavelength              //SAS approximation. 1% error at theta=30 deg (theta/2=15deg)
465                                               
466                                                //Print "q0, theta = ",q0,theta
467                                               
468                                                FIND_THETA = 1          //always accept
469
470                                        while(!find_theta)
471                                        ran = abs(enoise(1))            //[0,1]
472                                        PHI = 2.0*PI*Ran                        //Chooses azimuthal scattering angle.
473                                ELSE
474                                        //NEUTRON scattered incoherently
475                   // N3 += 1
476                  // DONE = 1
477                  // phi and theta are random over the entire sphere of scattering
478                  // !can't just choose random theta and phi, won't be random over sphere solid angle
479                        incoherentEvent += 1
480                       
481                        ran = abs(enoise(1))            //[0,1]
482                                        theta = acos(2*ran-1)           
483                       
484                        ran = abs(enoise(1))            //[0,1]
485                                        PHI = 2.0*PI*Ran                        //Chooses azimuthal scattering angle.
486                                ENDIF           //(ran > ratio)
487//                              endif           // event was absorption
488                        ELSE
489                                //NEUTRON ESCAPES FROM SAMPLE -- bin it somewhere
490                                DONE = 1                //done = true, will exit from loop
491                               
492//                              countIt = 1
493//                              if(abs(enoise(1)) > detEfficiency)              //efficiency of 70% wired @top
494//                                      countIt = 0                                     //detector does not register
495//                              endif
496                               
497                                //Increment #scattering events array
498                                If (index <= N_Index)
499                                        NN[INDEX] += 1
500                                Endif
501                               
502                                if(index != 0)          //the neutron interacted at least once, figure out where it ends up
503
504                                        Theta_z = acos(Vz)              // Angle WITH respect to z axis.
505                                        testQ = 2*pi*sin(theta_z)/wavelength
506                                       
507                                        // pick a random phi angle, and see if it lands on the detector
508                                        // since the scattering is isotropic, I can safely pick a new, random value
509                                        // this would not be true if simulating anisotropic scattering.
510                                        //testPhi = abs(enoise(1))*2*Pi
511                                        testPhi = MC_FindPhi(Vx,Vy)             //use the exiting phi value as defined by Vx and Vy
512                                       
513                                        // is it on the detector?       
514                                        FindPixel(testQ,testPhi,wavelength,sdd,pixSize,xCtr,yCtr,xPixel,yPixel)
515                                       
516                                        if(xPixel != -1 && yPixel != -1)
517                                                //if(index==1)  // only the single scattering events
518                                                        MC_linear_data[xPixel][yPixel] += 1             //this is the total scattering, including multiple scattering
519                                                //endif
520                                                        isOn += 1               // neutron that lands on detector
521                                        endif
522       
523                                        If(theta_z < theta_max)
524                                                //Choose index for scattering angle array.
525                                                //IND = NINT(THETA_z/DTH + 0.4999999)
526                                                ind = round(THETA_z/DTH + 0.4999999)            //round is eqivalent to nint()
527                                                NT[ind] += 1                    //Increment bin for angle.
528                                                //Increment angle array for single scattering events.
529                                                IF(INDEX == 1)
530                                                        j1[ind] += 1
531                                                Endif
532                                                //Increment angle array for double scattering events.
533                                                IF (INDEX == 2)
534                                                        j2[ind] += 1
535                                                Endif
536                                        EndIf
537                                       
538                                        // increment all of the counters now since done==1 here and I'm sure to exit and get another neutron
539                                        NScatterEvents += index         //total number of scattering events
540                                        if(index == 1 && incoherentEvent == 1)
541                                                NSingleIncoherent += 1
542                                        endif
543                                        if(index == 1 && coherentEvent == 1)
544                                                NSingleCoherent += 1
545                                        endif
546                                        if(index == 2 && coherentEvent == 1 && incoherentEvent == 0)
547                                                NDoubleCoherent += 1
548                                        endif
549                                        if(index > 1)
550                                                NMultipleScatter += 1
551                                        endif
552                                        if(coherentEvent >= 1 && incoherentEvent == 0)
553                                                NCoherentEvents += 1
554                                        endif
555                                        if(coherentEvent > 1 && incoherentEvent == 0)
556                                                NMultipleCoherent += 1
557                                        endif
558                                       
559                                       
560                                        //Print "n1,index (x,y) = ",n1,index, xpixel,ypixel
561                                       
562                                else    // if neutron escaped without interacting
563                               
564                                        // then it must be a transmitted neutron
565                                        // don't need to calculate, just increment the proper counters
566                                       
567                                        MC_linear_data[xCtr+xx/pixsize][yCtr+yy/pixsize] += 1
568                                        isOn += 1
569                                        nt[0] += 1
570                                       
571                                endif           //if interacted
572                        ENDIF
573                while (!done)
574        while(n1 < imon)
575
576//      Print "Monte Carlo Done"
577        results[0] = n1
578        results[1] = n2
579        results[2] = isOn
580        results[3] = NScatterEvents             //sum of # of times that neutrons scattered (coh+incoh)
581        results[4] = NSingleCoherent            //# of events that are single, coherent
582        results[5] = NMultipleCoherent  //# of scattered neutrons that are coherently scattered more than once
583        results[6] = NMultipleScatter           //# of scattered neutrons that are scattered more than once (coh and/or incoh)
584        results[7] = NCoherentEvents            //# of scattered neutrons that are scattered coherently one or more times
585       
586//      Print "# absorbed = ",n3
587
588//      trans_th = exp(-sig_total*thick)
589//      TRANS_exp = (N1-N2) / N1                        // Transmission
590        // dsigma/domega assuming isotropic scattering, with no absorption.
591//      Print "trans_exp = ",trans_exp
592//      Print "total # of neutrons reaching 2D detector",isOn
593//      Print "fraction of incident neutrons reaching detector ",isOn/iMon
594       
595//      Print "Total number of neutrons = ",N1
596//      Print "Total number of neutrons that interact = ",N2
597//      Print "Fraction of singly scattered neutrons = ",sum(j1,-inf,inf)/N2
598//      results[2] = N2                                         //number that scatter
599//      results[3] = isOn - MC_linear_data[xCtr][yCtr]                  //# scattered reaching detector minus zero angle
600
601       
602//      Tabs = (N1-N3)/N1
603//      Ttot = (N1-N2)/N1
604//      I1_sumI = NN[0]/(N2-N3)
605//      Print "Tabs = ",Tabs
606//      Print "Transmitted neutrons = ",Ttot
607//      results[8] = Ttot
608//      Print "I1 / all I1 = ", I1_sumI
609
610End
611////////        end of main function for calculating multiple scattering
612
613
614// returns the random deviate as a wave
615// and the total SAS cross-section [1/cm] sig_sas
616Function CalculateRandomDeviate(func,coef,lam,outWave,SASxs)
617        FUNCREF SANSModelAAO_MCproto func
618        WAVE coef
619        Variable lam
620        String outWave
621        Variable &SASxs
622
623        Variable nPts_ran=10000,qu
624        qu = 4*pi/lam           
625       
626// hard-wired into the Simulation directory rather than the SAS folder.
627// plotting resolution-smeared models won't work any other way
628        Make/O/N=(nPts_ran)/D root:Simulation:Gq,root:Simulation:xw             // if these waves are 1000 pts, the results are "pixelated"
629        WAVE Gq = root:Simulation:gQ
630        WAVE xw = root:Simulation:xw
631        SetScale/I x (0+1e-4),qu*(1-1e-10),"", Gq,xw                    //don't start at zero or run up all the way to qu to avoid numerical errors
632
633/// if all of the coefficients are well-behaved, then the last point is the background
634// and I can set it to zero here (only for the calculation)
635        Duplicate/O coef,tmp_coef
636        Variable num=numpnts(coef)
637        tmp_coef[num-1] = 0
638       
639        xw=x                                                                                            //for the AAO
640        func(tmp_coef,Gq,xw)                                                                    //call as AAO
641
642//      Gq = x*Gq                                                                                                       // SAS approximation
643        Gq = Gq*sin(2*asin(x/qu))/sqrt(1-(x/qu))                        // exact
644        //
645        //
646        Integrate/METH=1 Gq/D=Gq_INT
647       
648//      SASxs = lam*lam/2/pi*Gq_INT[nPts_ran-1]                 //if the approximation is used
649        SASxs = lam*Gq_INT[nPts_ran-1]
650       
651        Gq_INT /= Gq_INT[nPts_ran-1]
652       
653        Duplicate/O Gq_INT $outWave
654
655        return(0)
656End
657
658// returns the random deviate as a wave
659// and the total SAS cross-section [1/cm] sig_sas
660//
661// uses a log spacing of x for better coverage
662// downside is that it doesn't use built-in integrate, which is automatically cumulative
663//
664// --- Currently does not work - since the usage of the random deviate in the MC routine is based on the
665// wave properties of ran_dev, that is it must have the proper scaling and be equally spaced.
666//
667// -- not really sure that this will solve any of the problems with some functions (notably those with power-laws)
668// giving unreasonably large SAS cross sections. (>>10)
669//
670Function CalculateRandomDeviate_log(func,coef,lam,outWave,SASxs)
671        FUNCREF SANSModelAAO_MCproto func
672        WAVE coef
673        Variable lam
674        String outWave
675        Variable &SASxs
676
677        Variable nPts_ran=1000,qu,qmin,ii
678        qmin=1e-5
679        qu = 4*pi/lam           
680
681// hard-wired into the Simulation directory rather than the SAS folder.
682// plotting resolution-smeared models won't work any other way
683        Make/O/N=(nPts_ran)/D root:Simulation:Gq,root:Simulation:xw             // if these waves are 1000 pts, the results are "pixelated"
684        WAVE Gq = root:Simulation:gQ
685        WAVE xw = root:Simulation:xw
686//      SetScale/I x (0+1e-4),qu*(1-1e-10),"", Gq,xw                    //don't start at zero or run up all the way to qu to avoid numerical errors
687        xw =  alog(log(qmin) + x*((log(qu)-log(qmin))/nPts_ran))
688
689/// if all of the coefficients are well-behaved, then the last point is the background
690// and I can set it to zero here (only for the calculation)
691        Duplicate/O coef,tmp_coef
692        Variable num=numpnts(coef)
693        tmp_coef[num-1] = 0
694       
695        func(tmp_coef,Gq,xw)                                                                    //call as AAO
696        Gq = Gq*sin(2*asin(xw/qu))/sqrt(1-(xw/qu))                      // exact
697
698       
699        Duplicate/O Gq Gq_INT
700        Gq_INT = 0
701        for(ii=0;ii<nPts_ran;ii+=1)
702                Gq_INT[ii] = AreaXY(xw,Gq,qmin,xw[ii])
703        endfor
704       
705        SASxs = lam*Gq_INT[nPts_ran-1]
706       
707        Gq_INT /= Gq_INT[nPts_ran-1]
708       
709        Duplicate/O Gq_INT $outWave
710
711        return(0)
712End
713
714ThreadSafe Function FindPixel(testQ,testPhi,lam,sdd,pixSize,xCtr,yCtr,xPixel,yPixel)
715        Variable testQ,testPhi,lam,sdd,pixSize,xCtr,yCtr,&xPixel,&yPixel
716
717        Variable theta,dy,dx,qx,qy
718        //decompose to qx,qy
719        qx = testQ*cos(testPhi)
720        qy = testQ*sin(testPhi)
721
722        //convert qx,qy to pixel locations relative to # of pixels x, y from center
723        theta = 2*asin(qy*lam/4/pi)
724        dy = sdd*tan(theta)
725        yPixel = round(yCtr + dy/pixSize)
726       
727        theta = 2*asin(qx*lam/4/pi)
728        dx = sdd*tan(theta)
729        xPixel = round(xCtr + dx/pixSize)
730
731        NVAR pixelsX = root:myGlobals:gNPixelsX
732        NVAR pixelsY = root:myGlobals:gNPixelsY
733       
734        //if on detector, return xPix and yPix values, otherwise -1
735        if(yPixel > pixelsY || yPixel < 0)
736                yPixel = -1
737        endif
738        if(xPixel > pixelsX || xPixel < 0)
739                xPixel = -1
740        endif
741       
742        return(0)
743End
744
745Function MC_CheckFunctionAndCoef(funcStr,coefStr)
746        String funcStr,coefStr
747       
748        SVAR/Z listStr=root:Packages:NIST:coefKWStr
749        if(SVAR_Exists(listStr) == 1)
750                String properCoefStr = StringByKey(funcStr, listStr  ,"=",";",0)
751                if(cmpstr("",properCoefStr)==0)
752                        return(0)               //false, no match found, so properCoefStr is returned null
753                endif
754                if(cmpstr(coefStr,properCoefStr)==0)
755                        return(1)               //true, the coef is the correct match
756                endif
757        endif
758        return(0)                       //false, wrong coef
759End
760
761Function/S MC_getFunctionCoef(funcStr)
762        String funcStr
763
764        SVAR/Z listStr=root:Packages:NIST:coefKWStr
765        String coefStr=""
766        if(SVAR_Exists(listStr) == 1)
767                coefStr = StringByKey(funcStr, listStr  ,"=",";",0)
768        endif
769        return(coefStr)
770End
771
772Function SANSModelAAO_MCproto(w,yw,xw)
773        Wave w,yw,xw
774       
775        Print "in SANSModelAAO_MCproto function"
776        return(1)
777end
778
779Function/S MC_FunctionPopupList()
780        String list,tmp
781        list = User_FunctionPopupList()
782       
783        //simplify the display, forcing smeared calculations behind the scenes
784        tmp = FunctionList("Smear*",";","NPARAMS:1")            //smeared dependency calculations
785        list = RemoveFromList(tmp, list,";")
786
787
788        if(strlen(list)==0)
789                list = "No functions plotted"
790        endif
791       
792        list = SortList(list)
793       
794        return(list)
795End             
796
797
798//Function Scat_Angle(Ran,R_DAB,wavelength)
799//      Variable Ran,r_dab,wavelength
800//
801//      Variable qq,arg,theta
802//      qq = 1. / ( R_DAB*sqrt(1.0/Ran - 1.0) )
803//      arg = qq*wavelength/(4*pi)
804//      If (arg < 1.0)
805//              theta = 2.*asin(arg)
806//      else
807//              theta = pi
808//      endif
809//      Return (theta)
810//End
811
812//calculates new direction (xyz) from an old direction
813//theta and phi don't change
814ThreadSafe Function NewDirection(vx,vy,vz,theta,phi)
815        Variable &vx,&vy,&vz
816        Variable theta,phi
817       
818        Variable err=0,vx0,vy0,vz0
819        Variable nx,ny,mag_xy,tx,ty,tz
820       
821        //store old direction vector
822        vx0 = vx
823        vy0 = vy
824        vz0 = vz
825       
826        mag_xy = sqrt(vx0*vx0 + vy0*vy0)
827        if(mag_xy < 1e-12)
828                //old vector lies along beam direction
829                nx = 0
830                ny = 1
831                tx = 1
832                ty = 0
833                tz = 0
834        else
835                Nx = -Vy0 / Mag_XY
836                Ny = Vx0 / Mag_XY
837                Tx = -Vz0*Vx0 / Mag_XY
838                Ty = -Vz0*Vy0 / Mag_XY
839                Tz = Mag_XY
840        endif
841       
842        //new scattered direction vector
843        Vx = cos(phi)*sin(theta)*Tx + sin(phi)*sin(theta)*Nx + cos(theta)*Vx0
844        Vy = cos(phi)*sin(theta)*Ty + sin(phi)*sin(theta)*Ny + cos(theta)*Vy0
845        Vz = cos(phi)*sin(theta)*Tz + cos(theta)*Vz0
846       
847        Return(err)
848End
849
850ThreadSafe Function path_len(aval,sig_tot)
851        Variable aval,sig_tot
852       
853        Variable retval
854       
855        retval = -1*ln(1-aval)/sig_tot
856       
857        return(retval)
858End
859
860// globals are initialized in SASCALC.ipf
861// coordinates if I make this part of the panel - but this breaks other things...
862//
863//Proc MC_SASCALC()
864////    PauseUpdate; Silent 1           // building window...
865//
866////    NewPanel /W=(92,556,390,1028)/K=1 as "SANS Simulator"
867//      SetVariable MC_setvar0,pos={491,73},size={144,15},bodyWidth=80,title="# of neutrons"
868//      SetVariable MC_setvar0,format="%5.4g"
869//      SetVariable MC_setvar0,limits={-inf,inf,100},value= root:Packages:NIST:SAS:gImon
870//      SetVariable MC_setvar0_1,pos={491,119},size={131,15},bodyWidth=60,title="Thickness (cm)"
871//      SetVariable MC_setvar0_1,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gThick
872//      SetVariable MC_setvar0_2,pos={491,96},size={149,15},bodyWidth=60,title="Incoherent XS (cm)"
873//      SetVariable MC_setvar0_2,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gSig_incoh
874//      SetVariable MC_setvar0_3,pos={491,142},size={150,15},bodyWidth=60,title="Sample Radius (cm)"
875//      SetVariable MC_setvar0_3,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gR2
876//      PopupMenu MC_popup0,pos={476,13},size={165,20},proc=MC_ModelPopMenuProc,title="Model Function"
877//      PopupMenu MC_popup0,mode=1,value= #"MC_FunctionPopupList()"
878//      Button MC_button0,pos={480,181},size={130,20},proc=MC_DoItButtonProc,title="Do MC Simulation"
879//      Button MC_button1,pos={644,181},size={80,20},proc=MC_Display2DButtonProc,title="Show 2D"
880//      SetVariable setvar0_3,pos={568,484},size={50,20},disable=1
881//      GroupBox group0,pos={478,42},size={267,130},title="Monte Carlo"
882//      SetVariable cntVar,pos={653,73},size={80,15},proc=CountTimeSetVarProc,title="time(s)"
883//      SetVariable cntVar,format="%d"
884//      SetVariable cntVar,limits={1,10,1},value= root:Packages:NIST:SAS:gCntTime
885//     
886//      String fldrSav0= GetDataFolder(1)
887//      SetDataFolder root:Packages:NIST:SAS:
888//      Edit/W=(476,217,746,450)/HOST=#  results_desc,results
889//      ModifyTable format(Point)=1,width(Point)=0,width(results_desc)=150
890//      SetDataFolder fldrSav0
891//      RenameWindow #,T_results
892//      SetActiveSubwindow ##
893//EndMacro
894
895// as a stand-alone panel, extra control bar  (right) and subwindow implementations don't work right
896// for various reasons...
897Proc MC_SASCALC()
898
899        // when opening the panel, set the raw counts check to 1
900        root:Packages:NIST:SAS:gRawCounts = 1
901       
902        PauseUpdate; Silent 1           // building window...
903        NewPanel /W=(92,556,713,818)/K=1 as "SANS Simulator"
904        DoWindow/C MC_SASCALC
905       
906        SetVariable MC_setvar0,pos={28,73},size={144,15},bodyWidth=80,title="# of neutrons"
907        SetVariable MC_setvar0,format="%5.4g"
908        SetVariable MC_setvar0,limits={0,inf,100},value= root:Packages:NIST:SAS:gImon
909        SetVariable MC_setvar0_1,pos={28,119},size={131,15},bodyWidth=60,title="Thickness (cm)"
910        SetVariable MC_setvar0_1,limits={0,inf,0.1},value= root:Packages:NIST:SAS:gThick
911        SetVariable MC_setvar0_2,pos={28,96},size={149,15},bodyWidth=60,title="Incoherent XS (1/cm)"
912        SetVariable MC_setvar0_2,limits={0,inf,0.1},value= root:Packages:NIST:SAS:gSig_incoh
913        SetVariable MC_setvar0_3,pos={28,142},size={150,15},bodyWidth=60,title="Sample Radius (cm)"
914        SetVariable MC_setvar0_3,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gR2
915        PopupMenu MC_popup0,pos={13,13},size={165,20},proc=MC_ModelPopMenuProc,title="Model Function"
916        PopupMenu MC_popup0,mode=1,value= #"MC_FunctionPopupList()"
917        Button MC_button0,pos={17,181},size={130,20},proc=MC_DoItButtonProc,title="Do MC Simulation"
918        Button MC_button0,fColor=(3,52428,1)
919        Button MC_button1,pos={17,208},size={80,20},proc=MC_Display2DButtonProc,title="Show 2D"
920        SetVariable setvar0_3,pos={105,484},size={50,20},disable=1
921        GroupBox group0,pos={15,42},size={267,130},title="Monte Carlo"
922        SetVariable cntVar,pos={185,73},size={90,15},proc=CountTimeSetVarProc,title="time(s)"
923        SetVariable cntVar,format="%d"
924        SetVariable cntVar,limits={1,3600,1},value= root:Packages:NIST:SAS:gCntTime
925        Button MC_button2,pos={17,234},size={100,20},proc=SaveAsVAXButtonProc,title="Save 2D VAX"
926        CheckBox check0,pos={216,180},size={68,14},title="Raw counts",variable = root:Packages:NIST:SAS:gRawCounts
927        CheckBox check0_1,pos={216,199},size={60,14},title="Yes Offset",variable= root:Packages:NIST:SAS:gDoTraceOffset
928        CheckBox check0_2,pos={216,199+19},size={60,14},title="Beam Stop in",variable= root:Packages:NIST:SAS:gBeamStopIn
929        CheckBox check0_3,pos={216,199+2*19},size={60,14},title="use XOP",variable= root:Packages:NIST:SAS:gUse_MC_XOP
930       
931        String fldrSav0= GetDataFolder(1)
932        SetDataFolder root:Packages:NIST:SAS:
933        Edit/W=(344,23,606,248)/HOST=#  results_desc,results
934        ModifyTable format(Point)=1,width(Point)=0,width(results_desc)=150
935        SetDataFolder fldrSav0
936        RenameWindow #,T_results
937        SetActiveSubwindow ##
938EndMacro
939
940Function CountTimeSetVarProc(sva) : SetVariableControl
941        STRUCT WMSetVariableAction &sva
942
943        switch( sva.eventCode )
944                case 1: // mouse up
945                case 2: // Enter key
946                case 3: // Live update
947                        Variable dval = sva.dval
948
949                        // get the neutron flux, multiply, and reset the global for # neutrons
950                        NVAR imon=root:Packages:NIST:SAS:gImon
951                        imon = dval*beamIntensity()
952                       
953                        break
954        endswitch
955
956        return 0
957End
958
959
960Function MC_ModelPopMenuProc(pa) : PopupMenuControl
961        STRUCT WMPopupAction &pa
962
963        switch( pa.eventCode )
964                case 2: // mouse up
965                        Variable popNum = pa.popNum
966                        String popStr = pa.popStr
967                        SVAR gStr = root:Packages:NIST:SAS:gFuncStr
968                        gStr = popStr
969                       
970                        break
971        endswitch
972
973        return 0
974End
975
976Function MC_DoItButtonProc(ba) : ButtonControl
977        STRUCT WMButtonAction &ba
978
979        switch( ba.eventCode )
980                case 2: // mouse up
981                        // click code here
982                        NVAR doMC = root:Packages:NIST:SAS:gDoMonteCarlo
983                        doMC = 1
984                        ReCalculateInten(1)
985                        doMC = 0                //so the next time won't be MC
986                        break
987        endswitch
988
989        return 0
990End
991
992
993Function MC_Display2DButtonProc(ba) : ButtonControl
994        STRUCT WMButtonAction &ba
995
996        switch( ba.eventCode )
997                case 2: // mouse up
998                        // click code here
999                        Execute "ChangeDisplay(\"SAS\")"
1000                        break
1001        endswitch
1002
1003        return 0
1004End
1005
1006// after a 2d data image is averaged in the usual way, take the waves and generate a "fake" folder of the 1d
1007// data, to appear as if it was loaded from a real data file.
1008//
1009// ---- use FakeUSANSDataFolder() if you want to fake a 1D USANS data set ----
1010//
1011Function        Fake1DDataFolder(qval,aveint,sigave,sigmaQ,qbar,fSubs,dataFolder)
1012        WAVE qval,aveint,sigave,sigmaQ,qbar,fSubs
1013        String dataFolder
1014
1015        String baseStr=dataFolder
1016        if(DataFolderExists("root:"+baseStr))
1017                SetDataFolder $("root:"+baseStr)
1018        else
1019                NewDataFolder/S $("root:"+baseStr)
1020        endif
1021
1022        ////overwrite the existing data, if it exists
1023        Duplicate/O qval, $(baseStr+"_q")
1024        Duplicate/O aveint, $(baseStr+"_i")
1025        Duplicate/O sigave, $(baseStr+"_s")
1026
1027
1028        // make a resolution matrix for SANS data
1029        Variable np=numpnts(qval)
1030        Make/D/O/N=(np,4) $(baseStr+"_res")
1031        Wave res=$(baseStr+"_res")
1032       
1033        res[][0] = sigmaQ[p]            //sigQ
1034        res[][1] = qBar[p]              //qBar
1035        res[][2] = fSubS[p]             //fShad
1036        res[][3] = qval[p]              //Qvalues
1037       
1038        // keep a copy of everything in SAS too... the smearing wrapper function looks for
1039        // data in folders based on waves it is passed - an I lose control of that
1040        Duplicate/O res, $("root:Packages:NIST:SAS:"+baseStr+"_res")
1041        Duplicate/O qval,  $("root:Packages:NIST:SAS:"+baseStr+"_q")
1042        Duplicate/O aveint,  $("root:Packages:NIST:SAS:"+baseStr+"_i")
1043        Duplicate/O sigave,  $("root:Packages:NIST:SAS:"+baseStr+"_s")
1044       
1045        //clean up             
1046        SetDataFolder root:
1047       
1048End
1049
1050// writes out a VAX binary data file
1051// automatically generates a name
1052// will prompt for the sample label
1053//
1054// currently hard-wired for SAS data folder
1055//
1056Function SaveAsVAXButtonProc(ctrlName,[runIndex,simLabel])
1057        String ctrlName
1058        Variable runIndex
1059        String simLabel
1060
1061       
1062        // if default parameters were passed in, use them
1063        // if not, set them to "bad" values so that the user will be prompted later     
1064        NVAR autoSaveIndex = root:Packages:NIST:SAS:gAutoSaveIndex
1065        SVAR autoSaveLabel = root:Packages:NIST:SAS:gAutoSaveLabel
1066       
1067        // Determine if the optional parameters were supplied
1068        if( ParamIsDefault(runIndex))           //==1 if parameter was NOT specified
1069                print "runIndex not specified"
1070                autoSaveIndex=0                                 // 0 == bad value, test for this later
1071        else
1072                autoSaveIndex=runIndex
1073        endif
1074       
1075        if( ParamIsDefault(simLabel))           //==1 if parameter was NOT specified
1076                print "simLabel not specified"
1077                autoSaveLabel=""                                        // "" == bad value, test for this later
1078        else
1079                autoSaveLabel=simLabel
1080        endif
1081       
1082        String fullpath="",destStr=""
1083        Variable refnum
1084       
1085        fullpath = Write_RawData_File("SAS","",0)
1086       
1087        // write out the results into a text file
1088        destStr = "root:Packages:NIST:SAS:"
1089        SetDataFolder $destStr
1090
1091        WAVE results=results
1092        WAVE/T results_desc=results_desc
1093       
1094        //check each wave
1095        If(!(WaveExists(results)))
1096                Abort "results DNExist WriteVAXData()"
1097        Endif
1098        If(!(WaveExists(results_desc)))
1099                Abort "results_desc DNExist WriteVAXData()"
1100        Endif
1101       
1102        NVAR actSimTime = root:Packages:NIST:SAS:g_actSimTime
1103        String str = ""
1104        sprintf str,"%30s\t\t%g seconds\r","MonteCarlo Simulation time = ",actSimTime
1105               
1106        Open refNum as fullpath+".txt"
1107                wfprintf refNum, "%30s\t\t%g\r",results_desc,results
1108                FBinWrite refNum,str
1109                FStatus refNum
1110                FSetPos refNum,V_logEOF
1111        Close refNum
1112       
1113        ///////////////////////////////
1114       
1115        // could also automatically do the average here, but probably not worth the the effort...
1116       
1117        SetDataFolder root:
1118       
1119        return(0)
1120End
1121
1122// calculates the fraction of the scattering that reaches the detector, given the random deviate function
1123// and qmin and qmax
1124//
1125//
1126// still some question of the corners and number of pixels per q-bin
1127Function FractionReachingDetector(ran_dev,Qmin,Qmax)
1128        wave ran_dev
1129        Variable Qmin,Qmax
1130       
1131        Variable r1,r2,frac
1132        r1=x2pnt(ran_dev,Qmin)
1133        r2=x2pnt(ran_dev,Qmax)
1134       
1135        // no normalization needed - the full q-range is defined as [0,1]
1136        frac = ran_dev[r2] - ran_dev[r1]
1137       
1138        return frac
1139End
1140
1141
1142/// called in SASCALC:ReCalculateInten()
1143Function        Simulate_2D_MC(funcStr,aveint,qval,sigave,sigmaq,qbar,fsubs)
1144        String funcStr
1145        WAVE aveint,qval,sigave,sigmaq,qbar,fsubs
1146
1147        NVAR doMonteCarlo = root:Packages:NIST:SAS:gDoMonteCarlo                // == 1 if 2D MonteCarlo set by hidden flag
1148        WAVE rw=root:Packages:NIST:SAS:realsRead
1149       
1150// Try to nicely exit from a threading error, if possible
1151        Variable err=0
1152        if(!exists("root:myGlobals:gThreadGroupID"))
1153                Variable/G root:myGlobals:gThreadGroupID=0
1154        endif
1155        NVAR mt=root:myGlobals:gThreadGroupID
1156
1157        if(mt!=0)       //there was an error with the stopping of the threads, possibly user abort
1158                err = ThreadGroupRelease(mt)
1159                Print "threading err = ",err
1160                if(err == 0)
1161                        // all *should* be OK
1162                else
1163                        return(0)
1164                endif
1165        endif
1166
1167        NVAR imon = root:Packages:NIST:SAS:gImon
1168        NVAR thick = root:Packages:NIST:SAS:gThick
1169        NVAR sig_incoh = root:Packages:NIST:SAS:gSig_incoh
1170        NVAR r2 = root:Packages:NIST:SAS:gR2
1171
1172        // do the simulation here, or not
1173        Variable r1,xCtr,yCtr,sdd,pixSize,wavelength
1174        String coefStr,abortStr,str
1175
1176        r1 = rw[24]/2/10                // sample diameter convert diam in [mm] to radius in cm
1177        xCtr = rw[16]
1178        yCtr = rw[17]
1179        sdd = rw[18]*100                //conver header of [m] to [cm]
1180        pixSize = rw[10]/10             // convert pix size in mm to cm
1181        wavelength = rw[26]
1182        coefStr = MC_getFunctionCoef(funcStr)
1183       
1184        if(!MC_CheckFunctionAndCoef(funcStr,coefStr))
1185                doMonteCarlo = 0                //we're getting out now, reset the flag so we don't continually end up here
1186                Abort "The coefficients and function type do not match. Please correct the selections in the popup menus."
1187        endif
1188       
1189        Variable sig_sas
1190//              FUNCREF SANSModelAAO_MCproto func=$("fSmeared"+funcStr)         //a wrapper for the structure version
1191        FUNCREF SANSModelAAO_MCproto func=$(funcStr)            //unsmeared
1192        WAVE results = root:Packages:NIST:SAS:results
1193        WAVE linear_data = root:Packages:NIST:SAS:linear_data
1194        WAVE data = root:Packages:NIST:SAS:data
1195
1196        results = 0
1197        linear_data = 0
1198       
1199        CalculateRandomDeviate(func,$coefStr,wavelength,"root:Packages:NIST:SAS:ran_dev",SIG_SAS)
1200        if(sig_sas > 100)
1201                sprintf abortStr,"sig_sas = %g. Please check that the model coefficients have a zero background, or the low q is well-behaved.",sig_sas
1202                Abort abortStr
1203        endif
1204       
1205        WAVE ran_dev=$"root:Packages:NIST:SAS:ran_dev"
1206       
1207        Make/O/D/N=5000 root:Packages:NIST:SAS:nt=0,root:Packages:NIST:SAS:j1=0,root:Packages:NIST:SAS:j2=0
1208        Make/O/D/N=100 root:Packages:NIST:SAS:nn=0
1209        Make/O/D/N=11 root:Packages:NIST:SAS:inputWave=0
1210       
1211        WAVE nt = root:Packages:NIST:SAS:nt
1212        WAVE j1 = root:Packages:NIST:SAS:j1
1213        WAVE j2 = root:Packages:NIST:SAS:j2
1214        WAVE nn = root:Packages:NIST:SAS:nn
1215        WAVE inputWave = root:Packages:NIST:SAS:inputWave
1216
1217        inputWave[0] = imon
1218        inputWave[1] = r1
1219        inputWave[2] = r2
1220        inputWave[3] = xCtr
1221        inputWave[4] = yCtr
1222        inputWave[5] = sdd
1223        inputWave[6] = pixSize
1224        inputWave[7] = thick
1225        inputWave[8] = wavelength
1226        inputWave[9] = sig_incoh
1227        inputWave[10] = sig_sas
1228
1229        linear_data = 0         //initialize
1230
1231        Variable t0,trans
1232       
1233        // get a time estimate, and give the user a chance to exit if they're unsure.
1234        t0 = stopMStimer(-2)
1235        inputWave[0] = 1000
1236        NVAR useXOP = root:Packages:NIST:SAS:gUse_MC_XOP                //if zero, will use non-threaded Igor code
1237       
1238        if(useXOP)
1239                //use a single thread, otherwise time is dominated by overhead
1240                Monte_SANS_NotThreaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1241        else
1242                Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1243        endif
1244       
1245        t0 = (stopMSTimer(-2) - t0)*1e-6
1246        t0 *= imon/1000/ThreadProcessorCount                    //projected time, in seconds (using threads for the calculation)
1247
1248        Print "Estimated Simulation time (s) = ",t0
1249       
1250// to correct for detector efficiency, send only the fraction of neutrons that are actually counted     
1251        NVAR detectorEff = root:Packages:NIST:SAS:g_detectorEff
1252        NVAR actSimTime = root:Packages:NIST:SAS:g_actSimTime
1253        NVAR SimTimeWarn = root:Packages:NIST:SAS:g_SimTimeWarn
1254
1255        inputWave[0] = imon     * detectorEff                   //reset number of input neutrons before full simulation
1256       
1257        if(t0>SimTimeWarn)
1258                sprintf str,"The simulation will take approximately %d seconds.\r- Proceed?",t0
1259                DoAlert 1,str
1260                if(V_flag == 2)
1261                        doMonteCarlo = 0
1262                        reCalculateInten(1)             //come back in and do the smeared calculation
1263                        return(0)
1264                endif
1265        endif
1266       
1267        linear_data = 0         //initialize
1268// threading crashes!! - there must be some operation in the XOP that is not threadSafe. What, I don't know...
1269// I think it's the ran() calls, being "non-reentrant". So the XOP now defines two separate functions, that each
1270// use a different rng. This works. 1.75x speedup.     
1271        t0 = stopMStimer(-2)
1272
1273        if(useXOP)
1274                Monte_SANS_Threaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1275        else
1276                Monte_SANS_NotThreaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1277        endif
1278       
1279        t0 = (stopMSTimer(-2) - t0)*1e-6
1280        Printf  "MC sim time = %g seconds\r",t0
1281        actSimTime = t0
1282       
1283        trans = results[8]                      //(n1-n2)/n1
1284        if(trans == 0)
1285                trans = 1
1286        endif
1287
1288        Print "counts on detector, including transmitted = ",sum(linear_data,-inf,inf)
1289       
1290//              linear_data[xCtr][yCtr] = 0                     //snip out the transmitted spike
1291//              Print "counts on detector not transmitted = ",sum(linear_data,-inf,inf)
1292
1293        // or simulate a beamstop
1294        NVAR MC_BS_in = root:Packages:NIST:SAS:gBeamStopIn              //if zero, beam stop is "out", as in a transmission measurement
1295       
1296        Variable rad=beamstopDiam()/2           //beamstop radius in cm
1297        if(MC_BS_in)
1298                rad /= 0.5                              //convert cm to pixels
1299                rad += 0.                                       // (no - it cuts off the low Q artificially) add an extra pixel to each side to account for edge
1300                Duplicate/O linear_data,root:Packages:NIST:SAS:tmp_mask//,root:Packages:NIST:SAS:MC_linear_data
1301                WAVE tmp_mask = root:Packages:NIST:SAS:tmp_mask
1302                tmp_mask = (sqrt((p-xCtr)^2+(q-yCtr)^2) < rad) ? 0 : 1          //behind beamstop = 0, away = 1
1303               
1304                linear_data *= tmp_mask
1305        endif
1306       
1307        results[9] = sum(linear_data,-inf,inf)
1308        //              Print "counts on detector not behind beamstop = ",results[9]
1309       
1310        // convert to absolute scale
1311        Variable kappa          //,beaminten = beamIntensity()
1312//              kappa = beamInten*pi*r1*r1*thick*(pixSize/sdd)^2*trans*(iMon/beaminten)
1313        kappa = thick*(pixSize/sdd)^2*trans*iMon
1314       
1315        //use kappa to get back to counts => linear_data = round(linear_data*kappa)
1316        Note/K linear_data ,"KAPPA="+num2str(kappa)+";"
1317       
1318        NVAR rawCts = root:Packages:NIST:SAS:gRawCounts
1319        if(!rawCts)                     //go ahead and do the linear scaling
1320                linear_data = linear_data / kappa
1321                linear_data /= detectorEff
1322        endif           
1323        data = linear_data
1324       
1325        // re-average the 2D data
1326        S_CircularAverageTo1D("SAS")
1327       
1328        // put the new result into the simulation folder
1329        Fake1DDataFolder(qval,aveint,sigave,sigmaQ,qbar,fSubs,"Simulation")     
1330                               
1331
1332        return(0)
1333end
1334
1335//phi is defined from +x axis, proceeding CCW around [0,2Pi]
1336ThreadSafe Function MC_FindPhi(vx,vy)
1337        variable vx,vy
1338       
1339        variable phi
1340       
1341        phi = atan(vy/vx)               //returns a value from -pi/2 to pi/2
1342       
1343        // special cases
1344        if(vx==0 && vy > 0)
1345                return(pi/2)
1346        endif
1347        if(vx==0 && vy < 0)
1348                return(3*pi/2)
1349        endif
1350        if(vx >= 0 && vy == 0)
1351                return(0)
1352        endif
1353        if(vx < 0 && vy == 0)
1354                return(pi)
1355        endif
1356       
1357       
1358        if(vx > 0 && vy > 0)
1359                return(phi)
1360        endif
1361        if(vx < 0 && vy > 0)
1362                return(phi + pi)
1363        endif
1364        if(vx < 0 && vy < 0)
1365                return(phi + pi)
1366        endif
1367        if( vx > 0 && vy < 0)
1368                return(phi + 2*pi)
1369        endif
1370       
1371        return(phi)
1372end
1373
1374
1375
1376
1377
1378Proc Sim_1D_Panel()
1379        PauseUpdate; Silent 1           // building window...
1380        NewPanel /W=(92,556,713,818)/K=1 as "1D SANS Simulator"
1381        DoWindow/C Sim_1D_Panel
1382       
1383        SetVariable cntVar,pos={26,68},size={160,15},title="Counting time(s)",format="%d"
1384        SetVariable cntVar,limits={1,36000,10},value= root:Packages:NIST:SAS:gCntTime
1385        SetVariable cntVar, proc=Sim_1D_CountTimeSetVarProc
1386        SetVariable MC_setvar0_1,pos={26,91},size={160,15},title="Thickness (cm)"
1387        SetVariable MC_setvar0_1,limits={0,inf,0.1},value= root:Packages:NIST:SAS:gThick
1388        SetVariable MC_setvar0_1, proc=Sim_1D_SamThickSetVarProc
1389
1390        SetVariable MC_setvar0_3,pos={26,114},size={160,15},title="Sample Transmission"
1391        SetVariable MC_setvar0_3,limits={0,1,0.01},value= root:Packages:NIST:SAS:gSamTrans
1392        SetVariable MC_setvar0_3, proc=Sim_1D_SamTransSetVarProc
1393
1394        PopupMenu MC_popup0,pos={13,13},size={165,20},proc=Sim_1D_ModelPopMenuProc,title="Model Function"
1395        PopupMenu MC_popup0,mode=1,value= #"MC_FunctionPopupList()"
1396        Button MC_button0,pos={17,181},size={130,20},proc=Sim_1D_DoItButtonProc,title="Do 1D Simulation"
1397        Button MC_button0,fColor=(3,52428,1)
1398        Button MC_button1,pos={17,211},size={150,20},proc=Save_1DSimData,title="Save Simulated Data"
1399        GroupBox group0,pos={15,42},size={280,130},title="Sample Setup"
1400        CheckBox check0_1,pos={216,179},size={60,14},title="Yes Offset",variable= root:Packages:NIST:SAS:gDoTraceOffset
1401        CheckBox check0_2,pos={216,199},size={60,14},title="Abs scale?",variable= root:Packages:NIST:SAS:g_1D_DoABS
1402        CheckBox check0_3,pos={216,219},size={60,14},title="Noise?",variable= root:Packages:NIST:SAS:g_1D_AddNoise
1403       
1404// a box for the results
1405        GroupBox group1,pos={314,23},size={277,163},title="Simulation Results"
1406        ValDisplay valdisp0,pos={326,48},size={220,13},title="Total detector counts"
1407        ValDisplay valdisp0,limits={0,0,0},barmisc={0,1000},value= root:Packages:NIST:SAS:g_1DTotCts
1408        ValDisplay valdisp0_1,pos={326,72},size={220,13},title="Estimated count rate (1/s)"
1409        ValDisplay valdisp0_1,limits={0,0,0},barmisc={0,1000},value=root:Packages:NIST:SAS:g_1DEstDetCR
1410        ValDisplay valdisp0_2,pos={326,96},size={220,13},title="Fraction of beam scattered"
1411        ValDisplay valdisp0_2,limits={0,0,0},barmisc={0,1000},value= root:Packages:NIST:SAS:g_1DFracScatt
1412        ValDisplay valdisp0_3,pos={326,121},size={220,13},title="Estimated transmission"
1413        ValDisplay valdisp0_3,limits={0,0,0},barmisc={0,1000},value=root:Packages:NIST:SAS:g_1DEstTrans
1414        ValDisplay valdisp0_4,pos={326,145},size={220,13},title="Multiple Coherent Scattering"
1415        ValDisplay valdisp0_4,limits={0,0,0},barmisc={0,1000},value=root:Packages:NIST:SAS:g_MultScattFraction
1416        // set the flags here -- do the simulation, but not 2D
1417       
1418        root:Packages:NIST:SAS:doSimulation     = 1     // == 1 if 1D simulated data, 0 if other from the checkbox
1419        root:Packages:NIST:SAS:gDoMonteCarlo     = 0  // == 1 if 2D MonteCarlo set by hidden flag
1420
1421       
1422EndMacro
1423
1424Function Sim_1D_CountTimeSetVarProc(sva) : SetVariableControl
1425        STRUCT WMSetVariableAction &sva
1426
1427        switch( sva.eventCode )
1428                case 1: // mouse up
1429                case 2: // Enter key
1430                case 3: // Live update
1431                        Variable dval = sva.dval
1432
1433                        ReCalculateInten(1)
1434                       
1435                        break
1436        endswitch
1437
1438        return 0
1439End
1440
1441Function Sim_1D_SamThickSetVarProc(sva) : SetVariableControl
1442        STRUCT WMSetVariableAction &sva
1443
1444        switch( sva.eventCode )
1445                case 1: // mouse up
1446                case 2: // Enter key
1447                case 3: // Live update
1448                        Variable dval = sva.dval
1449
1450                        ReCalculateInten(1)
1451                       
1452                        break
1453        endswitch
1454
1455        return 0
1456End
1457
1458Function Sim_1D_SamTransSetVarProc(sva) : SetVariableControl
1459        STRUCT WMSetVariableAction &sva
1460
1461        switch( sva.eventCode )
1462                case 1: // mouse up
1463                case 2: // Enter key
1464                case 3: // Live update
1465                        Variable dval = sva.dval
1466
1467                        ReCalculateInten(1)
1468                       
1469                        break
1470        endswitch
1471
1472        return 0
1473End
1474
1475
1476Function Sim_1D_ModelPopMenuProc(pa) : PopupMenuControl
1477        STRUCT WMPopupAction &pa
1478
1479        switch( pa.eventCode )
1480                case 2: // mouse up
1481                        Variable popNum = pa.popNum
1482                        String popStr = pa.popStr
1483                        SVAR gStr = root:Packages:NIST:SAS:gFuncStr
1484                        gStr = popStr
1485                       
1486                        break
1487        endswitch
1488
1489        return 0
1490End
1491
1492
1493Function Sim_1D_DoItButtonProc(ba) : ButtonControl
1494        STRUCT WMButtonAction &ba
1495
1496        switch( ba.eventCode )
1497                case 2: // mouse up
1498               
1499                        ReCalculateInten(1)
1500                       
1501                        break
1502        endswitch
1503
1504        return 0
1505End
1506
1507
1508//
1509//
1510//
1511Function Save_1DSimData(ctrlName) : ButtonControl
1512        String ctrlName
1513
1514        String type="SAS",fullpath=""
1515        Variable dialog=1               //=1 will present dialog for name
1516       
1517        String destStr=""
1518        destStr = "root:Packages:NIST:"+type
1519       
1520        Variable refNum
1521        String formatStr = "%15.4g %15.4g %15.4g %15.4g %15.4g %15.4g\r\n"
1522        String fname,ave="C",hdrStr1="",hdrStr2=""
1523        Variable step=1
1524       
1525        If(1)
1526                //setup a "fake protocol" wave, sice I have no idea of the current state of the data
1527                Make/O/T/N=8 root:myGlobals:Protocols:SIMProtocol
1528                Wave/T SIMProtocol = $"root:myGlobals:Protocols:SIMProtocol"
1529                String junk="****SIMULATED DATA****"
1530                //stick in the fake protocol...
1531                NVAR ctTime = root:Packages:NIST:SAS:gCntTime
1532                NVAR totalCts = root:Packages:NIST:SAS:g_1DTotCts                       //summed counts (simulated)
1533                NVAR detCR = root:Packages:NIST:SAS:g_1DEstDetCR                // estimated detector count rate
1534                NVAR fractScat = root:Packages:NIST:SAS:g_1DFracScatt
1535                NVAR mScat = root:Packages:NIST:SAS:g_MultScattFraction
1536       
1537                SIMProtocol[0] = junk
1538                SIMProtocol[1] = "\tCounting time (s) = "+num2str(ctTime)
1539                SIMProtocol[2] = "\tTotal detector counts = "+num2str(totalCts)
1540                SIMProtocol[3] = "\tDetector countrate (1/s) = "+num2str(detCR)
1541                SIMProtocol[4] = "\tFraction of beam scattered coherently = "+num2str(fractScat)
1542                SIMProtocol[5] = "\tFraction of multiple coherent scattering = "+num2str(mScat)
1543                SIMProtocol[6] = ""
1544                SIMProtocol[7] = ""
1545                //set the global
1546                String/G root:myGlobals:Protocols:gProtoStr = "SIMProtocol"
1547        Endif
1548       
1549       
1550        //*****these waves MUST EXIST, or IGOR Pro will crash, with a type 2 error****
1551        WAVE intw=$(destStr + ":integersRead")
1552        WAVE rw=$(destStr + ":realsRead")
1553        WAVE/T textw=$(destStr + ":textRead")
1554        WAVE qvals =$(destStr + ":qval")
1555        WAVE inten=$(destStr + ":aveint")
1556        WAVE sig=$(destStr + ":sigave")
1557        WAVE qbar = $(destStr + ":QBar")
1558        WAVE sigmaq = $(destStr + ":SigmaQ")
1559        WAVE fsubs = $(destStr + ":fSubS")
1560
1561        SVAR gProtoStr = root:myGlobals:Protocols:gProtoStr
1562        Wave/T proto=$("root:myGlobals:Protocols:"+gProtoStr)
1563       
1564        //check each wave
1565        If(!(WaveExists(intw)))
1566                Abort "intw DNExist Save_1DSimData()"
1567        Endif
1568        If(!(WaveExists(rw)))
1569                Abort "rw DNExist Save_1DSimData()"
1570        Endif
1571        If(!(WaveExists(textw)))
1572                Abort "textw DNExist Save_1DSimData()"
1573        Endif
1574        If(!(WaveExists(qvals)))
1575                Abort "qvals DNExist Save_1DSimData()"
1576        Endif
1577        If(!(WaveExists(inten)))
1578                Abort "inten DNExist Save_1DSimData()"
1579        Endif
1580        If(!(WaveExists(sig)))
1581                Abort "sig DNExist Save_1DSimData()"
1582        Endif
1583        If(!(WaveExists(qbar)))
1584                Abort "qbar DNExist Save_1DSimData()"
1585        Endif
1586        If(!(WaveExists(sigmaq)))
1587                Abort "sigmaq DNExist Save_1DSimData()"
1588        Endif
1589        If(!(WaveExists(fsubs)))
1590                Abort "fsubs DNExist Save_1DSimData()"
1591        Endif
1592        If(!(WaveExists(proto)))
1593                Abort "current protocol wave DNExist Save_1DSimData()"
1594        Endif
1595
1596        //strings can be too long to print-- must trim to 255 chars
1597        Variable ii,num=8
1598        Make/O/T/N=(num) tempShortProto
1599        for(ii=0;ii<num;ii+=1)
1600                tempShortProto[ii] = (proto[ii])[0,240]
1601        endfor
1602       
1603        if(dialog)
1604                PathInfo/S catPathName
1605                fullPath = DoSaveFileDialog("Save data as")
1606                If(cmpstr(fullPath,"")==0)
1607                        //user cancel, don't write out a file
1608                        Close/A
1609                        Abort "no data file was written"
1610                Endif
1611                //Print "dialog fullpath = ",fullpath
1612        Endif
1613       
1614        NVAR monCt = root:Packages:NIST:SAS:gImon
1615        NVAR thick = root:Packages:NIST:SAS:gThick
1616        NVAR trans = root:Packages:NIST:SAS:gSamTrans                   //for 1D, default value
1617       
1618
1619       
1620        hdrStr1 = num2str(monCt)+"  "+num2str(rw[26])+"       "+num2str(rw[19])+"     "+num2str(rw[18])
1621        hdrStr1 += "     "+num2str(trans)+"     "+num2str(thick) + ave +"   "+num2str(step) + "\r\n"
1622
1623        hdrStr2 = num2str(rw[16])+"  "+num2str(rw[17])+"  "+num2str(rw[23])+"    "+num2str(rw[24])+"    "
1624        hdrStr2 += num2str(rw[25])+"    "+num2str(rw[27])+"    "+num2str(rw[21])+"    "+"ORNL  " + "\r\n"
1625       
1626        //actually open the file here
1627        Open refNum as fullpath
1628       
1629        //write out the standard header information
1630        fprintf refnum,"FILE: %s\t\t CREATED: %s\r\n","SIMULATED DATA",(date() +"  "+ time())
1631        fprintf refnum,"LABEL: %s\r\n","SIMULATED DATA"
1632        fprintf refnum,"MON CNT   LAMBDA   DET ANG   DET DIST   TRANS   THICK   AVE   STEP\r\n"
1633        fprintf refnum,hdrStr1
1634        fprintf refnum,"BCENT(X,Y)   A1(mm)   A2(mm)   A1A2DIST(m)   DL/L   BSTOP(mm)   DET_TYP \r\n"
1635        fprintf refnum,hdrStr2
1636//      fprintf refnum,headerFormat,rw[0],rw[26],rw[19],rw[18],rw[4],rw[5],ave,step
1637
1638        //insert protocol information here
1639        //-1 list of sample files
1640        //0 - bkg
1641        //1 - emp
1642        //2 - div
1643        //3 - mask
1644        //4 - abs params c2-c5
1645        //5 - average params
1646        fprintf refnum, "SAM: %s\r\n",tempShortProto[0]
1647        fprintf refnum, "BGD: %s\r\n",tempShortProto[1]
1648        fprintf refnum, "EMP: %s\r\n",tempShortProto[2]
1649        fprintf refnum, "DIV: %s\r\n",tempShortProto[3]
1650        fprintf refnum, "MASK: %s\r\n",tempShortProto[4]
1651        fprintf refnum, "ABS: %s\r\n",tempShortProto[5]
1652        fprintf refnum, "Average Choices: %s\r\n",tempShortProto[6]
1653       
1654        //write out the data columns
1655        fprintf refnum,"The 6 columns are | Q (1/A) | I(Q) (1/cm) | std. dev. I(Q) (1/cm) | sigmaQ | meanQ | ShadowFactor|\r\n"
1656        wfprintf refnum, formatStr, qvals,inten,sig,sigmaq,qbar,fsubs
1657       
1658        Close refnum
1659       
1660        SetDataFolder root:             //(redundant)
1661       
1662        //write confirmation of write operation to history area
1663        Print "Averaged File written: ", GetFileNameFromPathNoSemi(fullPath)
1664        KillWaves/Z tempShortProto
1665
1666        //clear the stuff that was created for case of saving files
1667        If(1)
1668                Killwaves/Z root:myGlobals:Protocols:SIMProtocol
1669                String/G root:myGlobals:Protocols:gProtoStr = ""
1670        Endif
1671       
1672       
1673        return(0)
1674       
1675End
1676
1677
1678/// called in SASCALC:ReCalculateInten()
1679Function Simulate_1D(funcStr,aveint,qval,sigave,sigmaq,qbar,fsubs)
1680        String funcStr
1681        WAVE aveint,qval,sigave,sigmaq,qbar,fsubs
1682
1683        Variable r1,xCtr,yCtr,sdd,pixSize,wavelength
1684        String coefStr,abortStr,str     
1685
1686        FUNCREF SANSModelAAO_MCproto func=$("fSmeared"+funcStr)                 //a wrapper for the structure version
1687        FUNCREF SANSModelAAO_MCproto funcUnsmeared=$(funcStr)           //unsmeared
1688        coefStr = MC_getFunctionCoef(funcStr)
1689       
1690        if(!MC_CheckFunctionAndCoef(funcStr,coefStr))
1691                Abort "Function and coefficients do not match. You must plot the unsmeared function before simulation."
1692        endif
1693       
1694        Wave inten=$"root:Simulation:Simulation_i"              // this will exist and send the smeared calculation to the corect DF
1695       
1696        // the resolution-smeared intensity is calculated, including the incoherent background
1697        func($coefStr,inten,qval)
1698
1699        NVAR imon = root:Packages:NIST:SAS:gImon
1700        NVAR ctTime = root:Packages:NIST:SAS:gCntTime
1701        NVAR thick = root:Packages:NIST:SAS:gThick
1702        NVAR trans = root:Packages:NIST:SAS:gSamTrans
1703        NVAR SimDetCts = root:Packages:NIST:SAS:g_1DTotCts                      //summed counts (simulated)
1704        NVAR estDetCR = root:Packages:NIST:SAS:g_1DEstDetCR                     // estimated detector count rate
1705        NVAR fracScat = root:Packages:NIST:SAS:g_1DFracScatt            // fraction of beam captured on detector
1706        NVAR estTrans = root:Packages:NIST:SAS:g_1DEstTrans             // estimated transmission of sample
1707        NVAR mScat = root:Packages:NIST:SAS:g_MultScattFraction
1708        NVAR detectorEff = root:Packages:NIST:SAS:g_detectorEff
1709       
1710        WAVE rw=root:Packages:NIST:SAS:realsRead
1711        WAVE nCells=root:Packages:NIST:SAS:nCells                               
1712                                       
1713        pixSize = rw[10]/10             // convert pix size in mm to cm
1714        sdd = rw[18]*100                //convert header of [m] to [cm]
1715        wavelength = rw[26]             // in 1/A
1716       
1717        imon = beamIntensity()*ctTime
1718       
1719        // calculate the scattering cross section simply to be able to estimate the transmission
1720        Variable sig_sas=0
1721       
1722        // remember that the random deviate is the coherent portion ONLY - the incoherent background is
1723        // subtracted before the calculation.
1724        CalculateRandomDeviate(funcUnsmeared,$coefStr,wavelength,"root:Packages:NIST:SAS:ran_dev",sig_sas)
1725       
1726//                              if(sig_sas > 100)
1727//                                      sprintf abortStr,"sig_sas = %g. Please check that the model coefficients have a zero background, or the low q is well-behaved.",sig_sas
1728//                              endif
1729
1730        // calculate the multiple scattering fraction for display (10/2009)
1731        Variable ii,nMax=10,tau
1732        mScat=0
1733        tau = thick*sig_sas
1734        // this sums the normalized scattering P', so the result is the fraction of multiply coherently scattered
1735        // neutrons out of those that were scattered
1736        for(ii=2;ii<nMax;ii+=1)
1737                mScat += tau^(ii)/factorial(ii)
1738//              print tau^(ii)/factorial(ii)
1739        endfor
1740        estTrans = exp(-1*thick*sig_sas)                //thickness and sigma both in units of cm
1741        mscat *= (estTrans)/(1-estTrans)
1742
1743        if(mScat > 0.1)         //  /Z to supress error if this was a 1D calc with the 2D panel open
1744                ValDisplay/Z valdisp0_4 win=Sim_1D_Panel,labelBack=(65535,32768,32768)
1745        else
1746                ValDisplay/Z valdisp0_4 win=Sim_1D_Panel,labelBack=0
1747        endif
1748
1749
1750        Print "Sig_sas = ",sig_sas
1751       
1752        Duplicate/O qval prob_i,countsInAnnulus
1753       
1754        // not needed - nCells takes care of this when the error is correctly calculated
1755//                              Duplicate/O qval circle_fraction,rval,nCells_expected
1756//                              rval = sdd*tan(2*asin(qval*wavelength/4/pi))            //radial distance in cm
1757//                              nCells_expected = 2*pi*rval/pixSize                                     //does this need to be an integer?
1758//                              circle_fraction = nCells / nCells_expected
1759       
1760                               
1761//                              prob_i = trans*thick*nCells*(pixSize/sdd)^2*inten                       //probability of a neutron in q-bin(i) that has nCells
1762        prob_i = trans*thick*(pixSize/sdd)^2*inten                      //probability of a neutron in q-bin(i)
1763       
1764        Variable P_on = sum(prob_i,-inf,inf)
1765        Print "P_on = ",P_on
1766       
1767//                              fracScat = P_on
1768        fracScat = 1-estTrans
1769       
1770//                              aveint = (Imon)*prob_i / circle_fraction / nCells_expected
1771// added correction for detector efficiency, since SASCALC is flux on sample
1772        aveint = (Imon)*prob_i*detectorEff
1773
1774        countsInAnnulus = aveint*nCells
1775        SimDetCts = sum(countsInAnnulus,-inf,inf)
1776        estDetCR = SimDetCts/ctTime
1777       
1778       
1779        NVAR doABS = root:Packages:NIST:SAS:g_1D_DoABS
1780        NVAR addNoise = root:Packages:NIST:SAS:g_1D_AddNoise
1781       
1782        // this is where the number of cells comes in - the calculation of the error bars
1783        // sigma[i] = SUM(sigma[ij]^2) / nCells^2
1784        // and since in the simulation, SUM(sigma[ij]^2) = nCells*sigma[ij]^2 = nCells*Inten
1785        // then...
1786        sigave = sqrt(aveint/nCells)            // corrected based on John's memo, from 8/9/99
1787       
1788        // add in random error in aveint based on the sigave
1789        if(addNoise)
1790                aveint += gnoise(sigave)
1791        endif
1792
1793        // signature in the standard deviation, do this after the noise is added
1794        // start at 10 to be out of the beamstop (makes for nicer plotting)
1795        // end at 50 to leave the natural statistics at the end of the set (may have a total of 80+ points if no offset)
1796        sigave[10,50;10] = 10*sigave[p]
1797
1798        // convert to absolute scale, remembering to un-correct for the detector efficiency
1799        if(doABS)
1800                Variable kappa = thick*(pixSize/sdd)^2*trans*iMon
1801                aveint /= kappa
1802                sigave /= kappa
1803                aveint /= detectorEff
1804                sigave /= detectorEff
1805        endif
1806                               
1807                               
1808        return(0)
1809End
1810
1811/// for testing only
1812Function testProbability(sas,thick)
1813        Variable sas,thick
1814       
1815        Variable tau,trans,p2p,p3p,p4p
1816       
1817        tau = sas*thick
1818        trans = exp(-tau)
1819       
1820        Print "tau = ",tau
1821        Print "trans = ",trans
1822       
1823        p2p = tau^2/factorial(2)*trans/(1-trans)
1824        p3p = tau^3/factorial(3)*trans/(1-trans)
1825        p4p = tau^4/factorial(4)*trans/(1-trans)
1826       
1827        Print "double scattering = ",p2p
1828        Print "triple scattering = ",p3p
1829        Print "quadruple scattering = ",p4p
1830       
1831        Variable ii,nMax=10,mScat=0
1832        for(ii=2;ii<nMax;ii+=1)
1833                mScat += tau^(ii)/factorial(ii)
1834//              print tau^(ii)/factorial(ii)
1835        endfor
1836        mscat *= (Trans)/(1-Trans)
1837
1838        Print "Total fraction of multiple scattering = ",mScat
1839
1840        return(mScat)
1841End
1842
1843
1844//// this is a very simple example of how to script the MC simulation to run unattended
1845//
1846//  you need to supply for each "run":  the run index (you increment manually)
1847//                                                                                              the sample label (as a string)
1848//
1849// changing the various configuration paramters will have to be done on a case-by-case basis
1850// looking into SASCALC to see what is really changed,
1851// or the configuration parameters of the MC_SASCALC panel
1852//
1853//
1854//Function Script_2DMC()
1855//
1856//
1857//      NVAR SimTimeWarn = root:Packages:NIST:SAS:g_SimTimeWarn
1858//      SimTimeWarn = 36000                     //sets the threshold for the warning dialog to 10 hours
1859//      STRUCT WMButtonAction ba
1860//      ba.eventCode = 2                        //fake mouse click on button
1861//     
1862//      NVAR detDist = root:Packages:NIST:SAS:gDetDist
1863//
1864//      detDist = 200           //set directly in cm
1865//      MC_DoItButtonProc(ba)
1866//      SaveAsVAXButtonProc("",runIndex=105,simLabel="this is run 105, SDD = 200")
1867//     
1868//      detDist = 300           //set directly in cm
1869//      MC_DoItButtonProc(ba)
1870//      SaveAsVAXButtonProc("",runIndex=106,simLabel="this is run 106, SDD = 300")
1871//
1872//      detDist = 400           //set directly in cm
1873//      MC_DoItButtonProc(ba)
1874//      SaveAsVAXButtonProc("",runIndex=107,simLabel="this is run 107, SDD = 400")
1875//     
1876//
1877// SimTimeWarn = 10             //back to 10 seconds for manual operation
1878//      return(0)
1879//end
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