source: sans/Dev/trunk/NCNR_User_Procedures/Analysis/Models/NewModels_2009/PolyCoreBicelle_v40.ipf @ 500

#pragma rtGlobals=1             // Use modern global access method.
#pragma IgorVersion = 6.0

////////////////////////////////////////////////
// This function is for the form factor of a right circular
// cylinder with core/shell scattering length density profile. 
// Note that a different shell thickness is added on the edge of
// the particle, compared to the face.  
// Furthermore the scattering is convoluted by a log normal (or Schultz)
// distribution that creates polydispersity for the radius of the
// particle core.
// 
// 30 Apr 2003 Andrew Nelson
//  
// 17 MAY 2006 SRK - changed to normalize to total particle dimensions
//                                              (core+shell)
//  7th Jan 2007  DS  Core-shell to include varying SLD in rim and face: Model 2
//  Jan 2009  ACH - changed to run in Igor 6.03 
//
//  May 2009 AJJ - Renamed to PolyCoreBicelle_v40.ipf
/////////////////////////////////////////////////////////////////

Proc PlotPolyCoreBicelle(num,qmin,qmax)
        Variable num=100,qmin=0.001,qmax=0.7
        Prompt num "Enter number of data points for model: "
        Prompt qmin "Enter minimum q-value (A^-1) for model: "
        Prompt qmax "Enter maximum q-value (A^-1) for model: "
        
        make/o/d/n=(num) xwave_PCBicelle,ywave_PCBicelle
        xwave_PCBicelle = alog(log(qmin) + x*((log(qmax)-log(qmin))/num))
        make/o/d coef_PCBicelle = {0.01,150,0.10,10,20.,10.,4.0e-6, 1.0e-6,2.0e-6,4.0e-6,0.001}
        make/o/t parameters_PCBicelle = {"scale","mean CORE radius (A)","radial polydispersity (sigma)","CORE length (A)","radial shell thickness (A)","face shell thickness (A)","SLD core (A^-2)","SLD face (A^-2)","SLD rim(A^-2)","SLD solvent (A^-2)","incoh. bkg (cm^-1)"}
        Edit/W=(410,44,757,306)  parameters_PCBicelle,coef_PCBicelle
        ModifyTable width(parameters_PCBicelle)=162
        
        Variable/G root:g_PCBicellee
        g_PCBicelle := PolyCoreBicelle(coef_PCBicelle,ywave_PCBicelle,xwave_PCBicelle)
        Display ywave_PCBicelle vs xwave_PCBicelle
        ModifyGraph log=1, marker=29,msize=2,mode=4
        Label bottom "q (A\\S-1\\M)"
        Label left "Intensity (cm\\S-1\\M)"
        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
        
        AddModelToStrings("PolyCoreBicelle","coef_PCBicelle","Bicelle")
End


Proc PlotSmearedPolyCoreBicelle(str)
        String str
        Prompt str,"Pick the data folder containing the resolution you want",popup,getAList(4)                                                  
        //no input parameters necessary, it MUST use the experimental q-values
        // from the experimental data read in from an AVE/QSIG data file
        
        // if no gQvals wave, data must not have been loaded => abort
        if(ResolutionWavesMissingDF(str))               //updated to NOT use global strings (in GaussUtils)
                Abort
        endif
        
        SetDataFolder $("root:"+str)
        
        // Setup parameter table for model function
        make/o/d smear_coef_PCBicelle = {0.01,150,0.10,10,20.,10.,4.0e-6,1.0e-6,2.0e-6,4.0e-6,0.001}
        make/o/t smear_parameters_PCBicelle = {"scale","mean CORE radius (A)","radial polydispersity (sigma)","CORE length (A)","radial shell thickness (A)","face shell thickness (A)","SLD core (A^-2)","SLD face (A^-2)","SLD rim(A^-2)","SLD solvent (A^-2)","incoh. bkg (cm^-1)"}
        Edit smear_parameters_PCBicelle,smear_coef_PCBicelle
        
        // output smeared intensity wave, dimensions are identical to experimental QSIG values
        // make extra copy of experimental q-values for easy plotting
        
        Duplicate/O $(str+"_q") smeared_PCBicelle,smeared_qvals                         
        SetScale d,0,0,"1/cm",smeared_PCBicelle                                                 
                                        
        Variable/G gs_PCBicelle=0
        gs_PCBicelle := fSmearedPolyCoreBicelle(smear_coef_PCBicelle,smeared_PCBicelle,smeared_qvals)
                
        Display smeared_PCBicelle vs smeared_qvals                                                                      
        ModifyGraph log=1,marker=29,msize=2,mode=4
        Label bottom "q (A\\S-1\\M)"
        Label left "Intensity (cm\\S-1\\M)"
        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
        
        SetDataFolder root:
        AddModelToStrings("SmearedPolyCoreBicelle","smear_coef_PCBicelle","Bicelle")
End
///////////////////////////////////////////////////////////////////////////////
// unsmeared model calculation: function integrates for a polydisperse radius.
//  Relies on the following two functions to return the monodisperse form factor.
///////////////////////////////////////////////////////////////////////////////
Function PolyCoreBicelle(cw,yw,xw) : FitFunc
        Wave cw,yw,xw
        
#if exists("PolyCoreBicelleX")
        yw = PolyCoreBicelleX(cw,xw)
#else
        yw = fPolyCoreBicelle(cw,xw)
#endif
        return(0)
End

Function  fPolyCoreBicelle(w,x) : FitFunc
        Wave w
        Variable x

//The input variables are (and output)
        //[0] scale
        //[1] cylinder CORE RADIUS (A)
        //[2] radial polydispersity (sigma)
        //[3] cylinder CORE LENGTH (A)
        //[4] radial shell Thickness (A)
        //[5] face shell Thickness (A)
        //[6] core SLD (A^-2)
        //[7] face SLD (A^-2)
        //[8] rim SLD (A^-2)
        //[9] solvent SLD (A^-2)
        //[10] background (cm^-1)
        Variable scale,length,sigma,bkg,radius,radthick,facthick,rhoc,rhoh, rhor, rhosolv
        Variable fc, vcyl,qq
        Variable nord,ii,va,vb,summ,yyy,rad,AR,lgAR,zed,Rsqr,lgRsqr,Rsqrsumm,Rsqryyy,tot
        String weightStr,zStr
        scale = w[0]
        radius = w[1]
        sigma = w[2]                            //sigma is the standard mean deviation
        length = w[3]
        radthick = w[4]
        facthick= w[5]
        rhoc = w[6]
        rhoh = w[7]
        rhor=w[8]
        rhosolv = w[9]
        bkg = w[10]
        
        weightStr = "gauss20wt"
        zStr = "gauss20z"
        
//      if wt,z waves don't exist, create them
        
        if (WaveExists($weightStr) == 0)                // wave reference is not valid, 
                Make/D/N=20 $weightStr,$zStr
                Wave w20 = $weightStr
                Wave z20 = $zStr                                // wave references to pass
                Make20GaussPoints(w20,z20)      
        else
                if(exists(weightStr) > 1) 
                         Abort "wave name is already in use"            // execute if condition is false
                endif
                Wave w20 = $weightStr
                Wave z20 = $zStr                        
        endif

/////////////////////////////////////////////////////////////////////////
// This integration loop is for the radial polydispersity.
//  The loop uses values from cylintegration to average
// the scattering over a radial size distribution.
/////////////////////////////////////////////////////////////////////////

        nord = 20
        va = exp(ln(radius)-(4.*sigma))
        if (va<0)
                va=0                                    //to avoid numerical error when  va<0 (-ve r value)
        endif
        vb = exp(ln(radius)+(4.*sigma))

// evaluate at Gauss points 
// remember to index from 0,size-1
        qq = x          
        summ = 0.0                      // initialize integral
        Rsqrsumm = 0.0
        
        ii=0
        do
                // Using 20 Gauss points
                rad = ( z20[ii]*(vb-va) + vb + va )/2.0                 //make distribution points
                
                AR=(1/(rad*sigma*sqrt(2*Pi)))*exp(-(0.5*((ln(radius/rad))/sigma)*((ln(radius/rad))/sigma)))

                yyy = w20[ii] * AR * BicelleIntegration(qq,rad,radthick,facthick,rhoc,rhoh,rhor,rhosolv,length)
                Rsqryyy= w20[ii] * AR * (rad+radthick)*(rad+radthick)           //SRK normalize to total dimensions
                
                summ += yyy
                Rsqrsumm +=  Rsqryyy
                ii+=1
        while (ii<nord)         // end of loop over quadrature points

// calculate value of integral to return
        fc = (vb-va)/2.0*summ
        Rsqr=(vb-va)/2.0*Rsqrsumm

//NOTE that for absolute intensity scaling you need to multiply by the
// number density of particles. This is the vol frac of core particles
// divided by the core volume.
        vcyl=Pi*Rsqr*(length+2*facthick)                //SRK normalize to total dimensions
        fc /= vcyl

//convert to [cm-1]
        fc *= 1.0e8
//Scale
        fc *= scale                     //scale will be the volume fraction of core particles.
// add in the  incoherent background
        fc += bkg

        Return (fc)
End

////////////////////////////////////////////////////////////////////////////
//BicelleIntegration calculates the Form factor for the Bicelle core shell cylinder
////////////////////////////////////////////////////////////////////////////
Function  BicelleIntegration(qq,rad,radthick,facthick,rhoc, rhoh, rhor, rhosolv, length)
        Variable  qq,rad,radthick,facthick,rhoc,rhoh,rhor,rhosolv,length
        Variable  answer,halfheight
        Variable nord,ii,va,vb,summ,yyy,zi
        String weightStr,zStr
        
        weightStr = "gauss76wt"
        zStr = "gauss76z"

//      if wt,z waves don't exist, create them
//     20 Gauss points is not enough for cylinder calculation
        
        if (WaveExists($weightStr) == 0)                                // wave reference is not valid, 
                Make/D/N=76 $weightStr,$zStr
                Wave w76 = $weightStr
                Wave z76 = $zStr                                                        // wave references to pass
                Make76GaussPoints(w76,z76)      
        else
                if(exists(weightStr) > 1) 
                         Abort "wave name is already in use"    
                endif
                Wave w76 = $weightStr
                Wave z76 = $zStr        
        endif

// set up the integration end points 
        nord = 76
        va = 0
        vb = Pi/2
        halfheight = length/2.0

// evaluate at Gauss points 
// remember to index from 0,size-1

        summ = 0.0                              // initialize integral
        ii=0
        do
                // Using 76 Gauss points
                zi = ( z76[ii]*(vb-va) + vb + va )/2.0          
                yyy = w76[ii] * BicelleKernel(qq, rad, radthick, facthick, rhoc,rhoh, rhor,rhosolv, halfheight, zi)
                summ += yyy 
     ii+=1
        while(ii<nord)          // end of loop over quadrature points

// calculate value of integral to return
  answer = (vb-va)/2.0*summ
        Return (answer)

End                             //End of function cylintegration

////////////////////////////////////////////////////////////////////////
// F(qq, rcore, thick, rhoc,rhos,rhosolv, length, zi)  This returns the
// arguments used for the integration over theta for orientational average
////////////////////////////////////////////////////////////////////////
Function BicelleKernel(qq, rad, radthick, facthick, rhoc,rhoh, rhor,rhosolv, length, dum)
        Variable qq, rad, radthick, facthick, rhoc,rhoh,rhor,rhosolv, length, dum
        
// qq is the q-value for the calculation (1/A)
// radius is the core radius of the cylinder (A)
//  radthick and facthick are the radial and face layer thicknesses
// rho(n) are the respective SLD's
// length is the *Half* CORE-LENGTH of the cylinder 
// dum is the dummy variable for the integration (theta)

        Variable dr1,dr2, dr3, besarg1,besarg2, vol1,vol2, vol3,sinarg1,sinarg2,t1,t2,t3, retval                //Local variables 

        dr1 = rhoc-rhoh
        dr2 = rhor-rhosolv
        dr3=  rhoh-rhor
        vol1 = Pi*rad*rad*(2*length)
        vol2 = Pi*(rad+radthick)*(rad+radthick)*(2*length+2*facthick)
        vol3= Pi*(rad)*(rad)*(2*length+2*facthick)
        besarg1 = qq*rad*sin(dum)
        besarg2 = qq*(rad+radthick)*sin(dum)
        sinarg1 = qq*length*cos(dum)
        sinarg2 = qq*(length+facthick)*cos(dum)
        
        t1 = 2*vol1*dr1*sin(sinarg1)/sinarg1*bessJ(1,besarg1)/besarg1
        t2 = 2*vol2*dr2*sin(sinarg2)/sinarg2*bessJ(1,besarg2)/besarg2
        t3 = 2*vol3*dr3*sin(sinarg2)/sinarg2*bessJ(1,besarg1)/besarg1
        
        retval = ((t1+t2+t3)^2)*sin(dum)
        return retval
    
End 

// this is all there is to the smeared calculation!
Function fSmearedPolyCoreBicelle(coefW,yW,xW)
        Wave coefW,yW,xW
        
        String str = getWavesDataFolder(yW,0)
        String DF="root:"+str+":"
        
        WAVE resW = $(DF+str+"_res")
        
        STRUCT ResSmearAAOStruct fs
        WAVE fs.coefW = coefW   
        WAVE fs.yW = yW
        WAVE fs.xW = xW
        WAVE fs.resW = resW
        
        Variable err
        err = SmearedPolyCoreBicelle(fs)
         
        return (0)
End

// this is all there is to the smeared calculation!
Function SmearedPolyCoreBicelle(s) :FitFunc
        Struct ResSmearAAOStruct &s

//      the name of your unsmeared model (AAO) is the first argument
        Smear_Model_20(PolyCoreBicelle,s.coefW,s.xW,s.yW,s.resW)

        return(0)
End