Changeset 4919


Ignore:
Timestamp:
Jun 3, 2021 10:12:41 AM (2 years ago)
Author:
vondreele
Message:

change powder peak shape functions to include effect of varying step size.
Impacts scale factors & peak intensities.
New notification system invoked to let users know of change.

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIctrlGUI.py

    r4918 r4919  
    54055405        self.dlg.Destroy()
    54065406################################################################################
    5407 updateNoticeDict = {}  # example: {1234:True, 5000:False}
     5407updateNoticeDict = {4918:True}  # example: {1234:True, 5000:False}
    54085408'''A dict with versions that should be noted. The value associated with the
    54095409tag is if all older projects should show the warning, or only the first

  • trunk/GSASIImpsubs.py

    r4800 r4919  
    7575    Puts lots of junk into the global namespace in this module.
    7676    '''
    77     global x,ratio,shl,xB,xF,im,lamRatio,kRatio,xMask,Ka2
     77    global x,ratio,shl,xB,xF,im,lamRatio,kRatio,xMask,Ka2,cw
    7878    x = ma.getdata(x1)
     79    cw = np.diff(x)
     80    cw = np.append(cw,cw[-1])
    7981    ratio = ratio1
    8082    shl = shl1
    … …  
    144146        return -2
    145147    elif iBeg < iFin:
    146         yp[iBeg:iFin] = refl[11+im]*refl[9+im]*G2pwd.getFCJVoigt3(
    147             refl[5+im],refl[6+im],refl[7+im],shl,x[iBeg:iFin])
     148        fp,sumfp = G2pwd.getFCJVoigt3(refl[5+im],refl[6+im],refl[7+im],shl,x[iBeg:iFin])
     149        yp[iBeg:iFin] = 100.*refl[11+im]*refl[9+im]*fp*cw[iBeg:iFin]/sumfp
    148150        sInt = refl[11+im]*refl[9+im]
    149151        if Ka2:
    … …  
    152154            iBeg2 = max(xB,np.searchsorted(x,pos2-fmin))
    153155            iFin2 = min(np.searchsorted(x,pos2+fmax),xF)
    154             if iFin2 > iBeg2: 
    155                 yp[iBeg2:iFin2] += refl[11+im]*refl[9+im]*kRatio*G2pwd.getFCJVoigt3(
    156                     pos2,refl[6+im],refl[7+im],shl,x[iBeg2:iFin2])
     156            if iFin2 > iBeg2:
     157                fp2,sumfp2 = G2pwd.getFCJVoigt3(pos2,refl[6+im],refl[7+im],shl,x[iBeg2:iFin2])
     158                yp[iBeg2:iFin2] += 100.*refl[11+im]*refl[9+im]*kRatio*fp2*cw[iBeg2:iFin2]/sumfp2
    157159                sInt *= 1.+kRatio
    158160    refl8im = np.sum(np.where(ratio[iBeg:iFin2]>0.,yp[iBeg:iFin2]*ratio[iBeg:iFin2]/(refl[11+im]*(1.+kRatio)),0.0))
    … …  
    172174        return -2
    173175    if iBeg < iFin:
    174         yp[iBeg:iFin] = refl[11+im]*refl[9+im]*G2pwd.getEpsVoigt(
    175             refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im],x[iBeg:iFin])
     176        fp,sumfp = G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im],x[iBeg:iFin])
     177        yp[iBeg:iFin] = refl[11+im]*refl[9+im]*fp*cw[iBeg:iFin]/sumfp
    176178    refl8im = np.sum(np.where(ratio[iBeg:iFin]>0.,yp[iBeg:iFin]*ratio[iBeg:iFin]/refl[11+im],0.0))
    177179    return refl8im,refl[11+im]*refl[9+im]
    … …  
    190192        return -2
    191193    if iBeg < iFin:
    192         yp[iBeg:iFin] = refl[11+im]*refl[9+im]*G2pwd.getEpsVoigt(
    193             refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,x[iBeg:iFin])
     194        fp,sumfp = G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,x[iBeg:iFin])
     195        yp[iBeg:iFin] = refl[11+im]*refl[9+im]*fp*cw[iBeg:iFin]/sumfp
    194196    refl8im = np.sum(np.where(ratio[iBeg:iFin]>0.,yp[iBeg:iFin]*ratio[iBeg:iFin]/refl[11+im],0.0))
    195197    return refl8im,refl[11+im]*refl[9+im]
    … …  
    202204    Puts lots of junk into the global namespace in this module.
    203205    '''
    204     global im,shl,x
     206    global im,shl,x,cw,yc
    205207    im = im1
    206208    shl = shl1
    207209    x = ma.getdata(x1)
    208     global cw
    209210    cw = np.diff(x)
    210211    cw = np.append(cw,cw[-1])
    211212    # create local copies of ycalc array
    212     global yc
    213213    yc = np.zeros_like(x)
    214 
    215214
    216215def ComputePwdrProfCW(profList):
    217216    'Compute the peaks profile for a set of CW peaks and add into the yc array'
    218217    for pos,refl,iBeg,iFin,kRatio in profList:
    219         yc[iBeg:iFin] += refl[11+im]*refl[9+im]*kRatio*G2pwd.getFCJVoigt3(
    220             pos,refl[6+im],refl[7+im],shl,x[iBeg:iFin])
     218        fp = G2pwd.getFCJVoigt3(pos,refl[6+im],refl[7+im],shl,x[iBeg:iFin])[0]
     219        yc[iBeg:iFin] += refl[11+im]*refl[9+im]*kRatio*fp/cw[iBeg:iFin]
    221220    return yc
    222221
    … …  
    224223    'Compute the peaks profile for a set of TOF peaks and add into the yc array'
    225224    for pos,refl,iBeg,iFin in profList:
    226         yc[iBeg:iFin] += refl[11+im]*refl[9+im]*G2pwd.getEpsVoigt(
    227             pos,refl[12+im],refl[13+im],refl[6+im],refl[7+im],x[iBeg:iFin])/cw[iBeg:iFin]
    228     return yc
     225        fp = G2pwd.getEpsVoigt(pos,refl[12+im],refl[13+im],refl[6+im],refl[7+im],x[iBeg:iFin])[0]
     226        yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp*cw[iBeg:iFin]
    229227   
    230228def ComputePwdrProfPink(profList):
    231229    'Compute the peaks profile for a set of TOF peaks and add into the yc array'
    232230    for pos,refl,iBeg,iFin in profList:
    233         yc[iBeg:iFin] += refl[11+im]*refl[9+im]*G2pwd.getEpsVoigt(
    234             pos,refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,x[iBeg:iFin])/cw[iBeg:iFin]
     231        fp = G2pwd.getEpsVoigt(pos,refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,x[iBeg:iFin])[0]
     232        yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp
    235233    return yc

  • trunk/GSASIIpwd.py

    r4915 r4919  
    718718""")
    719719   
    720    
    721 #GSASII peak fitting routine: Finger, Cox & Jephcoat model       
    722 
    723720
    724721class fcjde_gen(st.rv_continuous):
    … …  
    741738        fcj.pdf = [1/sqrt({cos(T)**2/cos(t)**2}-1) - 1/s]/|cos(T)|
    742739
    743      * if x >= 0: fcj.pdf = 0   
     740     * if x >= 0: fcj.pdf = 0   
     741     
    744742    """
    745743    def _pdf(self,x,t,s,dx):
    … …  
    759757fcjde = fcjde_gen(name='fcjde',shapes='t,s,dx')
    760758               
     759def getFCJVoigt(pos,intens,sig,gam,shl,xdata):   
     760    '''Compute the Finger-Cox-Jepcoat modified Voigt function for a
     761    CW powder peak by direct convolution. This version is not used.
     762    '''
     763    DX = xdata[1]-xdata[0]
     764    widths,fmin,fmax = getWidthsCW(pos,sig,gam,shl)
     765    x = np.linspace(pos-fmin,pos+fmin,256)
     766    dx = x[1]-x[0]
     767    Norm = norm.pdf(x,loc=pos,scale=widths[0])
     768    Cauchy = cauchy.pdf(x,loc=pos,scale=widths[1])
     769    arg = [pos,shl/57.2958,dx,]
     770    FCJ = fcjde.pdf(x,*arg,loc=pos)
     771    if len(np.nonzero(FCJ)[0])>5:
     772        z = np.column_stack([Norm,Cauchy,FCJ]).T
     773        Z = fft.fft(z)
     774        Df = fft.ifft(Z.prod(axis=0)).real
     775    else:
     776        z = np.column_stack([Norm,Cauchy]).T
     777        Z = fft.fft(z)
     778        Df = fft.fftshift(fft.ifft(Z.prod(axis=0))).real
     779    Df /= np.sum(Df)
     780    Df = si.interp1d(x,Df,bounds_error=False,fill_value=0.0)
     781    return intens*Df(xdata)*DX/dx
     782   
     783#### GSASII peak fitting routine: Finger, Cox & Jephcoat model       
     784
    761785def getWidthsCW(pos,sig,gam,shl):
    762786    '''Compute the peak widths used for computing the range of a peak
    763787    for constant wavelength data. On low-angle side, 50 FWHM are used,
    764     on high-angle side 75 are used, low angle side extended for axial divergence
     788    on high-angle side 75 are used, high angle side extended for axial divergence
    765789    (for peaks above 90 deg, these are reversed.)
     790   
     791    param pos: peak position; 2-theta in degrees
     792    param sig: Gaussian peak variance in centideg^2
     793    param gam: Lorentzian peak width in centidegrees
     794    param shl: axial divergence parameter (S+H)/
     795   
     796    returns: widths; [Gaussian sigma, Lornetzian gamma] in degrees
     797    returns: low angle, high angle ends of peak; 20FWHM & 50 FWHM from position
     798        reverset for 2-theta > 90 deg.
    766799    '''
    767800    widths = [np.sqrt(sig)/100.,gam/100.]
    … …  
    777810    for constant wavelength data. 50 FWHM are used on both sides each
    778811    extended by exponential coeff.
     812   
     813    param pos: peak position; TOF in musec
     814    param alp,bet: TOF peak exponential rise & decay parameters
     815    param sig: Gaussian peak variance in musec^2
     816    param gam: Lorentzian peak width in musec
     817   
     818    returns: widths; [Gaussian sigma, Lornetzian gamma] in musec
     819    returns: low TOF, high TOF ends of peak; 50FWHM from position
    779820    '''
    780821    widths = [np.sqrt(sig),gam]
    … …  
    832873    return gamFW(2.35482*s,g)   #sqrt(8ln2)*sig = FWHM(G)
    833874               
    834 def getFCJVoigt(pos,intens,sig,gam,shl,xdata):   
    835     '''Compute the Finger-Cox-Jepcoat modified Voigt function for a
    836     CW powder peak by direct convolution. This version is not used.
    837     '''
    838     DX = xdata[1]-xdata[0]
    839     widths,fmin,fmax = getWidthsCW(pos,sig,gam,shl)
    840     x = np.linspace(pos-fmin,pos+fmin,256)
    841     dx = x[1]-x[0]
    842     Norm = norm.pdf(x,loc=pos,scale=widths[0])
    843     Cauchy = cauchy.pdf(x,loc=pos,scale=widths[1])
    844     arg = [pos,shl/57.2958,dx,]
    845     FCJ = fcjde.pdf(x,*arg,loc=pos)
    846     if len(np.nonzero(FCJ)[0])>5:
    847         z = np.column_stack([Norm,Cauchy,FCJ]).T
    848         Z = fft.fft(z)
    849         Df = fft.ifft(Z.prod(axis=0)).real
    850     else:
    851         z = np.column_stack([Norm,Cauchy]).T
    852         Z = fft.fft(z)
    853         Df = fft.fftshift(fft.ifft(Z.prod(axis=0))).real
    854     Df /= np.sum(Df)
    855     Df = si.interp1d(x,Df,bounds_error=False,fill_value=0.0)
    856     return intens*Df(xdata)*DX/dx
    857 
    858875def getBackground(pfx,parmDict,bakType,dataType,xdata,fixback=None):
    859876    '''Computes the background from vars pulled from gpx file or tree.
    … …  
    970987                iFin = np.searchsorted(xdata,pkP+fmax)
    971988            if 'C' in dataType:
    972                 ybi = pkI*getFCJVoigt3(pkP,pkS,pkG,0.002,xdata[iBeg:iFin])
    973                 yb[iBeg:iFin] += ybi
     989                ybi = pkI*getFCJVoigt3(pkP,pkS,pkG,0.002,xdata[iBeg:iFin])[0]
     990                yb[iBeg:iFin] += ybi/cw[iBeg:iFin]
    974991            elif 'T' in dataType:
    975                 ybi = pkI*getEpsVoigt(pkP,1.,1.,pkS,pkG,xdata[iBeg:iFin])
     992                ybi = pkI*getEpsVoigt(pkP,1.,1.,pkS,pkG,xdata[iBeg:iFin])[0]
    976993                yb[iBeg:iFin] += ybi
    977994            elif 'B' in dataType:
    978                 ybi = pkI*getEpsVoigt(pkP,1.,1.,pkS/100.,pkG/1.e4,xdata[iBeg:iFin])
     995                ybi = pkI*getEpsVoigt(pkP,1.,1.,pkS/100.,pkG/1.e4,xdata[iBeg:iFin])[0]
    979996                yb[iBeg:iFin] += ybi
    980997            sumBk[2] += np.sum(ybi)
    … …  
    11301147    '''Compute the Finger-Cox-Jepcoat modified Pseudo-Voigt function for a
    11311148    CW powder peak in external Fortran routine
     1149   
     1150    param pos: peak position in degrees
     1151    param sig: Gaussian variance in centideg^2
     1152    param gam: Lorentzian width in centideg
     1153    param shl: axial divergence parameter (S+H)/L
     1154    param xdata: array; profile points for peak to be calculated; bounded by 20FWHM to 50FWHM (or vv)
     1155   
     1156    returns: array: calculated peak function at each xdata
     1157    returns: integral of peak; nominally = 1.0
    11321158    '''
    1133     Df = pyd.pypsvfcj(len(xdata),xdata-pos,pos,sig,gam,shl)
    1134     Df /= np.sum(Df)
    1135     return Df
     1159    if len(xdata):
     1160        cw = np.diff(xdata)
     1161        cw = np.append(cw,cw[-1])
     1162        Df = pyd.pypsvfcj(len(xdata),xdata-pos,pos,sig,gam,shl)
     1163        return Df,np.sum(100.*Df*cw)
     1164    else:
     1165        return 0.,1.
    11361166
    11371167def getdFCJVoigt3(pos,sig,gam,shl,xdata):
    11381168    '''Compute analytic derivatives the Finger-Cox-Jepcoat modified Pseudo-Voigt
    11391169    function for a CW powder peak
     1170   
     1171    param pos: peak position in degrees
     1172    param sig: Gaussian variance in centideg^2
     1173    param gam: Lorentzian width in centideg
     1174    param shl: axial divergence parameter (S+H)/L
     1175    param xdata: array; profile points for peak to be calculated; bounded by 20FWHM to 50FWHM (or vv)
     1176   
     1177    returns: arrays: function and derivatives of pos, sig, gam, & shl
    11401178    '''
    11411179    Df,dFdp,dFds,dFdg,dFdsh = pyd.pydpsvfcj(len(xdata),xdata-pos,pos,sig,gam,shl)
    … …  
    11451183    '''Compute the simple Pseudo-Voigt function for a
    11461184    small angle Bragg peak in external Fortran routine
     1185   
     1186    param pos: peak position in degrees
     1187    param sig: Gaussian variance in centideg^2
     1188    param gam: Lorentzian width in centideg
     1189   
     1190    returns: array: calculated peak function at each xdata
     1191    returns: integral of peak; nominally = 1.0
    11471192    '''
    11481193   
     1194    cw = np.diff(xdata)
     1195    cw = np.append(cw,cw[-1])
    11491196    Df = pyd.pypsvoigt(len(xdata),xdata-pos,sig,gam)
    1150     Df /= np.sum(Df)
    1151     return Df
     1197    return Df,np.sum(100.*Df*cw)
    11521198
    11531199def getdPsVoigt(pos,sig,gam,xdata):
    11541200    '''Compute the simple Pseudo-Voigt function derivatives for a
    11551201    small angle Bragg peak peak in external Fortran routine
     1202   
     1203    param pos: peak position in degrees
     1204    param sig: Gaussian variance in centideg^2
     1205    param gam: Lorentzian width in centideg
     1206
     1207    returns: arrays: function and derivatives of pos, sig, gam, & shl
    11561208    '''
    11571209   
    … …  
    11641216    '''
    11651217   
     1218    cw = np.diff(xdata)
     1219    cw = np.append(cw,cw[-1])
    11661220    Df = pyd.pyepsvoigt(len(xdata),xdata-pos,alp,bet,sig,gam)
    1167     Df /= np.sum(Df)
    1168     return Df 
     1221    return Df,np.sum(Df*cw) 
    11691222   
    11701223def getdEpsVoigt(pos,alp,bet,sig,gam,xdata):
    … …  
    13161369
    13171370def getPeakProfile(dataType,parmDict,xdata,fixback,varyList,bakType):
    1318     'Computes the profile for a powder pattern'
     1371    '''Computes the profile for a powder pattern for single peak fitting
     1372    NB: not used for Rietveld refinement
     1373    '''
    13191374   
    13201375    yb = getBackground('',parmDict,bakType,dataType,xdata,fixback)[0]
    13211376    yc = np.zeros_like(yb)
    1322     cw = np.diff(xdata)
    1323     cw = np.append(cw,cw[-1])
     1377    # cw = np.diff(xdata)
     1378    # cw = np.append(cw,cw[-1])
    13241379    if 'C' in dataType:
    13251380        shl = max(parmDict['SH/L'],0.002)
    … …  
    13551410                elif not iBeg-iFin:     #peak above high limit
    13561411                    return yb+yc
    1357                 yc[iBeg:iFin] += intens*getFCJVoigt3(pos,sig,gam,shl,xdata[iBeg:iFin])
     1412                fp = getFCJVoigt3(pos,sig,gam,shl,xdata[iBeg:iFin])[0]
     1413                yc[iBeg:iFin] += intens*fp
    13581414                if Ka2:
    13591415                    pos2 = pos+lamRatio*tand(pos/2.0)       # + 360/pi * Dlam/lam * tan(th)
    … …  
    13611417                    iFin = np.searchsorted(xdata,pos2+fmin)
    13621418                    if iBeg-iFin:
    1363                         yc[iBeg:iFin] += intens*kRatio*getFCJVoigt3(pos2,sig,gam,shl,xdata[iBeg:iFin])
     1419                        fp2 = getFCJVoigt3(pos2,sig,gam,shl,xdata[iBeg:iFin])[0]
     1420                        yc[iBeg:iFin] += intens*kRatio*fp2
    13641421                iPeak += 1
    13651422            except KeyError:        #no more peaks to process
    … …  
    14051462                elif not iBeg-iFin:     #peak above high limit
    14061463                    return yb+yc
    1407                 yc[iBeg:iFin] += intens*getEpsVoigt(pos,alp,bet,sig/1.e4,gam/100.,xdata[iBeg:iFin])
     1464                yc[iBeg:iFin] += intens*getEpsVoigt(pos,alp,bet,sig/1.e4,gam/100.,xdata[iBeg:iFin])[0]
    14081465                iPeak += 1
    14091466            except KeyError:        #no more peaks to process
    … …  
    14631520                elif not iBeg-iFin:     #peak above high limit
    14641521                    return yb+yc
    1465                 yc[iBeg:iFin] += intens*getEpsVoigt(pos,alp,bet,sig,gam,xdata[iBeg:iFin])
     1522                yc[iBeg:iFin] += intens*getEpsVoigt(pos,alp,bet,sig,gam,xdata[iBeg:iFin])[0]
    14661523                iPeak += 1
    14671524            except KeyError:        #no more peaks to process
    … …  
    14691526           
    14701527def getPeakProfileDerv(dataType,parmDict,xdata,fixback,varyList,bakType):
    1471     'needs a doc string'
    1472 # needs to return np.array([dMdx1,dMdx2,...]) in same order as varylist = backVary,insVary,peakVary order
     1528    '''Computes the profile derivatives for a powder pattern for single peak fitting
     1529   
     1530    return: np.array([dMdx1,dMdx2,...]) in same order as varylist = backVary,insVary,peakVary order
     1531   
     1532    NB: not used for Rietveld refinement
     1533    '''
    14731534    dMdv = np.zeros(shape=(len(varyList),len(xdata)))
    14741535    dMdb,dMddb,dMdpk,dMdfb = getBackgroundDerv('',parmDict,bakType,dataType,xdata,fixback)
    … …  
    15291590                dMdipk = getdFCJVoigt3(pos,sig,gam,shl,xdata[iBeg:iFin])
    15301591                for i in range(1,5):
    1531                     dMdpk[i][iBeg:iFin] += 100.*cw[iBeg:iFin]*intens*dMdipk[i]
    1532                 dMdpk[0][iBeg:iFin] += 100.*cw[iBeg:iFin]*dMdipk[0]
     1592                    dMdpk[i][iBeg:iFin] += intens*dMdipk[i]
     1593                dMdpk[0][iBeg:iFin] += dMdipk[0]
    15331594                dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'sig':dMdpk[2],'gam':dMdpk[3],'shl':dMdpk[4]}
    15341595                if Ka2:
    … …  
    15391600                        dMdipk2 = getdFCJVoigt3(pos2,sig,gam,shl,xdata[iBeg:iFin])
    15401601                        for i in range(1,5):
    1541                             dMdpk[i][iBeg:iFin] += 100.*cw[iBeg:iFin]*intens*kRatio*dMdipk2[i]
    1542                         dMdpk[0][iBeg:iFin] += 100.*cw[iBeg:iFin]*kRatio*dMdipk2[0]
    1543                         dMdpk[5][iBeg:iFin] += 100.*cw[iBeg:iFin]*dMdipk2[0]
     1602                            dMdpk[i][iBeg:iFin] += intens*kRatio*dMdipk2[i]
     1603                        dMdpk[0][iBeg:iFin] += kRatio*dMdipk2[0]
     1604                        dMdpk[5][iBeg:iFin] += dMdipk2[0]
    15441605                        dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'sig':dMdpk[2],'gam':dMdpk[3],'shl':dMdpk[4],'L1/L2':dMdpk[5]*intens}
    15451606                for parmName in ['pos','int','sig','gam']:
    … …  
    21942255    yb *= 0.
    21952256    yd *= 0.
    2196     cw = x[1:]-x[:-1]
    21972257    xBeg = np.searchsorted(x,Limits[0])
    21982258    xFin = np.searchsorted(x,Limits[1])+1
    … …  
    22662326        FWHM = getFWHM(peak[0],Inst)
    22672327        try:
    2268             binsperFWHM.append(FWHM/cw[x.searchsorted(peak[0])])
     2328            xpk = x.searchsorted(peak[0])
     2329            cw = x[xpk]-x[xpk-1]
     2330            binsperFWHM.append(FWHM/cw)
    22692331        except IndexError:
    22702332            binsperFWHM.append(0.)
    … …  
    42444306    hplot = plotter.add('derivatives test for '+name).gca()
    42454307    hplot.plot(xdata,100.*dx*getdFCJVoigt3(myDict['pos'],myDict['sig'],myDict['gam'],myDict['shl'],xdata)[idx+1])
    4246     y0 = getFCJVoigt3(myDict['pos'],myDict['sig'],myDict['gam'],myDict['shl'],xdata)
     4308    y0 = getFCJVoigt3(myDict['pos'],myDict['sig'],myDict['gam'],myDict['shl'],xdata)[0]
    42474309    myDict[name] += delt
    4248     y1 = getFCJVoigt3(myDict['pos'],myDict['sig'],myDict['gam'],myDict['shl'],xdata)
     4310    y1 = getFCJVoigt3(myDict['pos'],myDict['sig'],myDict['gam'],myDict['shl'],xdata)[0]
    42494311    hplot.plot(xdata,(y1-y0)/delt,'r+')
    42504312

  • trunk/GSASIIsasd.py

    r4095 r4919  
    13351335            elif 'Bragg' in Type:
    13361336                Ic += parmDict[cid+'PkInt']*G2pwd.getPsVoigt(parmDict[cid+'PkPos'],
    1337                     parmDict[cid+'PkSig'],parmDict[cid+'PkGam'],Q)
     1337                    parmDict[cid+'PkSig'],parmDict[cid+'PkGam'],Q)[0]
    13381338        Ic += parmDict['Back']  #/parmDict['Scale']
    13391339        slitLen = Sample['SlitLen']

  • trunk/GSASIIstrMath.py

    r4915 r4919  
    32063206    yb,Histogram['sumBk'] = G2pwd.getBackground(hfx,parmDict,bakType,calcControls[hfx+'histType'],x,fixback)
    32073207    yc = np.zeros_like(yb)
    3208     cw = np.diff(ma.getdata(x))
    3209     cw = np.append(cw,cw[-1])
     3208    # cw = np.diff(ma.getdata(x))
     3209    # cw = np.append(cw,cw[-1])
    32103210       
    32113211    if 'C' in calcControls[hfx+'histType']:   
    … …  
    33113311                    profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin,1.))
    33123312                else:
    3313                     yc[iBeg:iFin] += refl[11+im]*refl[9+im]*G2pwd.getFCJVoigt3(refl[5+im],refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))    #>90% of time spent here
     3313                    fp = G2pwd.getFCJVoigt3(refl[5+im],refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))[0]
     3314                    yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp   #>90% of time spent here
    33143315                if Ka2:
    33153316                    pos2 = refl[5+im]+lamRatio*tand(refl[5+im]/2.0)       # + 360/pi * Dlam/lam * tan(th)
    … …  
    33263327                        profArgs[iref%ncores].append((pos2,refl,iBeg,iFin,kRatio))
    33273328                    else:
    3328                         yc[iBeg:iFin] += refl[11+im]*refl[9+im]*kRatio*G2pwd.getFCJVoigt3(pos2,refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))        #and here
     3329                        fp2 = G2pwd.getFCJVoigt3(pos2,refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))[0]
     3330                        yc[iBeg:iFin] += refl[11+im]*refl[9+im]*kRatio*fp2       #and here
    33293331        elif 'B' in calcControls[hfx+'histType']:
    33303332            for iref,refl in enumerate(refDict['RefList']):
    … …  
    33643366                    profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin,1.))
    33653367                else:
    3366                     yc[iBeg:iFin] += refl[11+im]*refl[9+im]*G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,ma.getdata(x[iBeg:iFin]))
     3368                    fp = G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,ma.getdata(x[iBeg:iFin]))[0]
     3369                    yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp          #*cw[iBeg:iFin]
    33673370        elif 'T' in calcControls[hfx+'histType']:
    33683371            for iref,refl in enumerate(refDict['RefList']):
    … …  
    34023405                    profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin))
    34033406                else:
    3404                     yc[iBeg:iFin] += refl[11+im]*refl[9+im]*G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im],ma.getdata(x[iBeg:iFin]))/cw[iBeg:iFin]
     3407                    fp = G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im],ma.getdata(x[iBeg:iFin]))[0]
     3408                    yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp
    34053409#        print 'profile calc time: %.3fs'%(time.time()-time0)
    34063410        if useMP and 'C' in calcControls[hfx+'histType']:
    … …  
    34343438    if len(args) >= 11: tprc=args[10]
    34353439    if len(args) >= 12: histogram=args[11]
     3440   
    34363441    def cellVaryDerv(pfx,SGData,dpdA):
    34373442        if SGData['SGLaue'] in ['-1',]:
    … …  
    34883493    if hfx+'BF mult' in varylist:
    34893494        dMdv[varylist.index(hfx+'BF mult')] += dMdfb
    3490     cw = np.diff(ma.getdata(x))
    3491     cw = np.append(cw,cw[-1])
     3495    # cw = np.diff(ma.getdata(x))
     3496    # cw = np.append(cw,cw[-1])
    34923497    Ka2 = False #also for TOF!
    34933498    if 'C' in calcControls[hfx+'histType']:   
    … …  
    35873592                dMdipk = G2pwd.getdFCJVoigt3(refl[5+im],refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))
    35883593                for i in range(5):
    3589                     dMdpk[i] += 100.*cw[iBeg:iFin]*refl[11+im]*refl[9+im]*dMdipk[i]
     3594                    dMdpk[i] += refl[11+im]*refl[9+im]*dMdipk[i]
    35903595                dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'sig':dMdpk[2],'gam':dMdpk[3],'shl':dMdpk[4],'L1/L2':np.zeros_like(dMdpk[0])}
    35913596                if Ka2:
    … …  
    35983603                        dMdipk2 = G2pwd.getdFCJVoigt3(pos2,refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg2:iFin2]))
    35993604                        for i in range(5):
    3600                             dMdpk2[i] = 100.*cw[iBeg2:iFin2]*refl[11+im]*refl[9+im]*kRatio*dMdipk2[i]
    3601                         dMdpk2[5] = 100.*cw[iBeg2:iFin2]*refl[11+im]*dMdipk2[0]
     3605                            dMdpk2[i] = refl[11+im]*refl[9+im]*kRatio*dMdipk2[i]
     3606                        dMdpk2[5] = refl[11+im]*dMdipk2[0]
    36023607                        dervDict2 = {'int':dMdpk2[0],'pos':dMdpk2[1],'sig':dMdpk2[2],'gam':dMdpk2[3],'shl':dMdpk2[4],'L1/L2':dMdpk2[5]*refl[9]}
    36033608            elif 'T' in calcControls[hfx+'histType']:
    … …  
    36193624                dMdipk = G2pwd.getdEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,ma.getdata(x[iBeg:iFin]))
    36203625                for i in range(6):
    3621                     dMdpk[i] = cw[iBeg:iFin]*refl[11+im]*refl[9+im]*dMdipk[i]
     3626                    dMdpk[i] = refl[11+im]*refl[9+im]*dMdipk[i]
    36223627                dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'alp':dMdpk[2],'bet':dMdpk[3],'sig':dMdpk[4]/1.e4,'gam':dMdpk[5]/100.}           
    36233628            if Phase['General'].get('doPawley'):

  • trunk/versioninfo.txt

    r4918 r4919  
    1111# 1234: This is text for version 1234. The second colon here (:) is ignored.
    1212
     134918: With this version of GSAS-II, the profile functions have been changed to account for possible variation in the powder
     14pattern step size across the scan. This will likely change the histogram scale factor (see Sample Parameters), peak
     15intensities (see Peak List) and background peak intensities (see Background). For Constant Wavelength data, they will change
     16by a factor related to the pattern step size, e.g. for 11BM data with a step size of 0.001 deg 2-theta the new scale factor will be
     17~0.1 times the old one. If you choose to repeat the refinement for this project, you may need to be sure that parameters affecting
     18peak shape are turned off for the initial refinement. It should converge quickly to the new scale factor.
     19%%For TOF data there may be similar changes to the scale factor && peak intensities as noted above. Significant improvement in profile
     20residuals have been observed in some cases with these new functions.
     21This change is of no consequence for single crystal, small angle or reflectometry data in GSAS-II.
     22
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