Changeset 1475

Timestamp:

Aug 22, 2014 1:09:47 PM (9 years ago)

Author:

vondreele

Message:

add MCSA tutorial to main gsasII.html web page
change difB tern from d3 to 1/d - works much better
make all TOF/2-theta to dsp & vv conversions with G2lat.Pos2dsp & Dsp2pos routines.

Location:

trunk

Files:

• GSASIIlattice.py (modified) (3 diffs)
• GSASIIplot.py (modified) (12 diffs)
• GSASIIpwdGUI.py (modified) (1 diff)
• GSASIIstrIO.py (modified) (1 diff)
• GSASIIstrMath.py (modified) (2 diffs)
• help/MCSA in GSAS.htm (modified) (42 diffs)
• help/MCSA in GSAS_files/filelist.xml (modified) (1 diff)
• help/MCSA in GSAS_files/props061.xml (modified) (1 diff)
• help/gsasII.html (modified) (45 diffs)

trunk/GSASIIlattice.py

@@ -417 +417 @@
 def Pos2dsp(Inst,pos):
     ''' convert powder pattern position (2-theta or TOF, musec) to d-spacing
-    ignores secondary effects (e.g. difA,difB in TOF)
+    ignores secondary effects (e.g. difB in TOF)
     '''
     if 'C' in Inst['Type'][0]:
         wave = G2mth.getWave(Inst)
-        dsp = wave/(2.0*sind((pos-Inst['Zero'][1])/2.0))
-    else:   #'T'OF - ignore difA, difB
-        dsp = (pos-Inst['Zero'][1])/Inst['difC'][1]
-    return dsp
+        return wave/(2.0*sind((pos-Inst.get('Zero',[0,0])[1])/2.0))
+    else:   #'T'OF - ignore difB
+        T = pos-Inst['Zero'][1]
+        T1 = Inst['difC'][1]**2-4.*Inst['difA'][1]*T
+        return 2.*T/(Inst['difC'][1]+np.sqrt(T1))
     
 def Dsp2pos(Inst,dsp):
@@ -431 +432 @@
     if 'C' in Inst['Type'][0]:
         wave = G2mth.getWave(Inst)
-        pos = 2.0*asind(wave/(2.*dsp))+Inst['Zero'][1]             
+        pos = 2.0*asind(wave/(2.*dsp))+Inst.get('Zero',[0,0])[1]             
     else:   #'T'OF
-        pos = Inst['difC'][1]*dsp+Inst['Zero'][1]+Inst['difA'][1]*dsp**2+Inst.get('difB',[0,0,False])[1]*dsp**3
+        pos = Inst['difC'][1]*dsp+Inst['Zero'][1]+Inst['difA'][1]*dsp**2+Inst.get('difB',[0,0,False])[1]/dsp
     return pos
     
@@ -442 +443 @@
         pos = 2.0*asind(parmdict['Lam']/(2.*dsp))+parmdict['Zero']
     else:   #'T'OF
-        pos = parmdict['difC']*dsp+parmdict['difA']*dsp**2+parmdict['difB']*dsp**3+parmdict['Zero']
+        pos = parmdict['difC']*dsp+parmdict['difA']*dsp**2+parmdict['difB']/dsp+parmdict['Zero']
     return pos
                    

trunk/GSASIIplot.py

@@ -943 +943 @@
             try:
                 Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
-                if 'C' in Parms['Type'][0]:
-                    wave = G2mth.getWave(Parms)
-                    if G2frame.qPlot and 'PWDR' in plottype:
-                        try:
-                            xpos = 2.0*asind(xpos*wave/(4*math.pi))
-                        except ValueError:      #avoid bad value in asin beyond upper limit
-                            pass
-                    elif G2frame.dPlot:
-                        dsp = xpos
-                        q = 2.*np.pi/dsp
-                        xpos = 2.0*asind(wave/(2.*dsp))
-                    dsp = 0.0
-                    if abs(xpos) > 0.:                  #avoid possible singularity at beam center
-                        if 'PWDR' in plottype:
-                            dsp = wave/(2.*sind(abs(xpos)/2.0))
-                            q = 2.*np.pi/dsp
-                        elif 'SASD' in plottype:
-                            dsp = 2*np.pi/xpos
-                            q = xpos
-                    if G2frame.Contour:
-                        if 'PWDR' in plottype:
-                            G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
-                        elif 'SASD' in plottype:
-                            G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f pattern ID =%5d'%(dsp,q,int(ypos)),1)
+                if G2frame.qPlot and 'PWDR' in plottype:
+                    q = xpos
+                    dsp = 2.*np.pi/q
+                    try:
+                        xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos)
+                    except ValueError:      #avoid bad value in asin beyond upper limit
+                        pass
+                elif 'SASD' in plottype:
+                    q = xpos
+                    dsp = 2.*np.pi/q
+                elif G2frame.dPlot:
+                    dsp = xpos
+                    q = 2.*np.pi/dsp
+                    xpos = G2lat.Dsp2pos(Parms,xpos)
+                else:
+                    dsp = G2lat.Pos2dsp(Parms,xpos)
+                    q = 2.*np.pi/dsp
+                if G2frame.Contour: #PWDR only
+                    if 'C' in Parms['Type'][0]:
+                        G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
                     else:
+                        G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
+                else:
+                    if 'C' in Parms['Type'][0]:
                         if 'PWDR' in plottype:
                             if G2frame.SqrtPlot:
@@ -974 +973 @@
                                 G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
                         elif 'SASD' in plottype:
-                            G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f Intensity =%12.5g'%(dsp,q,ypos),1)
-                else:       #TOF neutrons
-                    dsp = 0.0
-                    difC = Parms['difC'][1]
-                    if G2frame.dPlot:
-                        dsp = xpos
-                        xpos = difC*dsp
-                    elif G2frame.qPlot and 'PWDR' in plottype:
-                        dsp = 2.*np.pi/xpos
-                        xpos = difC*dsp
-                    else:
-                        dsp = xpos/difC             #rough approx.!
-                    q = 2.*np.pi/dsp
-                    if G2frame.Contour:
-                        G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
+                            G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1)
                     else:
                         if G2frame.SqrtPlot:
-                            G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
+                            G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
                         else:
-                            G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
+                            G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
                 if G2frame.itemPicked:
                     Page.canvas.SetToolTipString('%9.5f'%(xpos))
@@ -1023 +1008 @@
         except TypeError:
             return
-        if 'C' in Parms['Type'][0]:
-            wave = G2mth.getWave(Parms)
-        else:
-            difC = Parms['difC'][1]
         PickId = G2frame.PickId
         pick = event.artist
@@ -1037 +1018 @@
             if ind.all() != [0] and ObsLine[0].get_label() in str(pick):                                    #picked a data point
                 data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
-                if 'C' in Parms['Type'][0]:
-                    if G2frame.qPlot:                              #qplot - convert back to 2-theta
-                        xy[0] = 2.0*asind(xy[0]*wave/(4*math.pi))
-                    elif G2frame.dPlot:                            #dplot - convert back to 2-theta
-                        xy[0] = 2.0*asind(wave/(2.*xy[0]))
-                elif 'T' in Parms['Type'][0]:
-                    if G2frame.qPlot:                              #qplot - convert back to TOF
-                        xy[0] = 2.0*math.pi*difC/xy[0]
-                    elif G2frame.dPlot:                            #dplot - convert back to TOF
-                        xy[0] *= difC                    
+                if G2frame.qPlot:                              #qplot - convert back to 2-theta
+                    xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
+                elif G2frame.dPlot:                            #dplot - convert back to 2-theta
+                    xy[0] = G2lat.Dsp2pos(Parms,xy[0])
                 XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
                 data['peaks'].append(XY)
@@ -1058 +1033 @@
                 LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
                 data = G2frame.PatternTree.GetItemPyData(LimitId)
-                if 'C' in Parms['Type'][0]:                            #CW data - TOF later in an elif
-                    if G2frame.qPlot and 'PWDR' in plottype:                              #qplot - convert back to 2-theta
-                        xy[0] = 2.0*asind(xy[0]*wave/(4*math.pi))
-                    elif G2frame.dPlot:                            #dplot - convert back to 2-theta
-                        xy[0] = 2.0*asind(wave/(2.*xy[0]))
-                elif 'T' in Parms['Type'][0]:
-                    if G2frame.qPlot:                              #qplot - convert back to TOF
-                        xy[0] = 2.0*math.pi*difC/xy[0]
-                    elif G2frame.dPlot:                            #dplot - convert back to TOF
-                        xy[0] *= difC                    
+                if G2frame.qPlot:                              #qplot - convert back to 2-theta
+                    xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
+                elif G2frame.dPlot:                            #dplot - convert back to 2-theta
+                    xy[0] = G2lat.Dsp2pos(Parms,xy[0])
                 if G2frame.ifGetExclude:
                     excl = [0,0]
@@ -1110 +1079 @@
             return
         Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
-        if 'C' in Parms['Type'][0]:
-            wave = G2mth.getWave(Parms)
-        else:
-            difC = Parms['difC'][1]
         xpos = event.xdata
         PickId = G2frame.PickId
@@ -1130 +1095 @@
                 id2 = lineNo%2
                 if G2frame.qPlot and 'PWDR' in plottype:
-                    if 'C' in Parms['Type'][0]:
-                        data[id][id2] = 2.0*asind(wave*xpos/(4*math.pi))
-                    else:
-                        data[id][id2] = 2*math.pi*Parms['difC'][1]/xpos
+                    data[id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
                 elif G2frame.dPlot and 'PWDR' in plottype:
-                    if 'C' in Parms['Type'][0]:
-                        data[id][id2] = 2.0*asind(wave/(2*xpos))
-                    else:
-                        data[id][id2] *= Parms['difC'][1]
+                    data[id][id2] = G2lat.Dsp2pos(Parms,xpos)
                 else:
                     data[id][id2] = xpos
@@ -1155 +1114 @@
                 else:
                     if G2frame.qPlot:
-                        if 'C' in Parms['Type'][0]: 
-                            data['peaks'][lineNo-2][0] = 2.0*asind(wave*xpos/(4*math.pi))
-                        else:
-                            data['peaks'][lineNo-2][0] = 2*math.pi*Parms['difC'][1]/xpos
+                        data['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
                     elif G2frame.dPlot:
-                        if 'C' in Parms['Type'][0]:
-                            data['peaks'][lineNo-2][0] = 2.0*asind(wave/(2*xpos))
-                        else:
-                            data['peaks'][lineNo-2][0] *= Parms['difC'][1]
+                        data['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,xpos)
                     else:
                         data['peaks'][lineNo-2][0] = xpos
@@ -1381 +1334 @@
         if G2frame.qPlot and 'PWDR' in plottype:
             Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
-            if 'C' in Parms['Type'][0]:
-                X = 4*np.pi*npsind((xye[0]-Zero)/2.0)/wave
-            else:
-                X = 2*np.pi*Parms['difC'][1]/(xye[0]-Zero)
+            X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye[0])
         elif G2frame.dPlot and 'PWDR' in plottype:
             Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
-            if 'C' in Parms['Type'][0]:
-                X = wave/(2.*npsind(xye[0]-Zero)/2.0)
-            else:
-                X = (xye[0]-Zero)/Parms['difC'][1]
+            X = G2lat.Pos2dsp(Parms,xye[0])
         else:
-            X = xye[0]-Zero
+            X = xye[0]
         if not lenX:
             lenX = len(X)
@@ -1410 +1357 @@
         if LimitId and ifpicked:
             limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
+            lims = limits[1]
             if G2frame.qPlot and 'PWDR' in plottype:
-                if 'C' in Parms['Type'][0]:
-                    limits = 4*np.pi*npsind(limits/2.0)/wave
-                else:
-                    limits = 2*np.pi*difC/limits
+                lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims)
             elif G2frame.dPlot and 'PWDR' in plottype:
-                if 'C' in Parms['Type'][0]:
-                    limits = wave/(2*npsind(limits/2.0))
-                else:
-                    limits /= difC                
-            Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))    
-            Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
+                lims = G2lat.Pos2dsp(Parms,lims)
+            Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.))    
+            Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.))
             for i,item in enumerate(limits[2:]):
                 Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))    
@@ -1535 +1477 @@
                     for item in data['peaks']:
                         if G2frame.qPlot:
-                            if 'C' in Parms['Type'][0]:
-                                Lines.append(Plot.axvline(4*math.pi*sind(item[0]/2.)/wave,color=colors[N%6],picker=2.))
-                            else:
-                                Lines.append(Plot.axvline(2*math.pi*difC/item[0],color=colors[N%6],picker=2.))                                
-                        if G2frame.dPlot:
-                            if 'C' in Parms['Type'][0]:
-                                Lines.append(Plot.axvline(wave/(2*sind(item[0]/2.)),color=colors[N%6],picker=2.))
-                            else:
-                                Lines.append(Plot.axvline(item[0]/difC,color=colors[N%6],picker=2.))                                
+                            Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
+                        elif G2frame.dPlot:
+                            Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
                         else:
                             Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
@@ -1568 +1504 @@
     if PickId and not G2frame.Contour:
         Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
-        if 'C' in Parms['Type'][0]:
-            wave = G2mth.getWave(Parms)
-        else:
-            difC = Parms['difC'][1]
         if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
             peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))[0]
             for peak in peaks:
                 if G2frame.qPlot:
-                    if 'C' in Parms['Type'][0]:
-                        Plot.axvline(4*np.pi*sind(peak[0]/2.0)/wave,color='b')
-                    else:
-                        Plot.axvline(2*np.pi*Parms['difC'][1]/peak[0],color='b')
+                    Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b')
                 if G2frame.dPlot:
-                    if 'C' in Parms['Type'][0]:
-                        Plot.axvline(wave/(2*sind(peak[0]/2.0)),color='b')
-                    else:
-                        Plot.avline(peak[0]/Parms['difC'][1],color='b')
+                    Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b')
                 else:
                     Plot.axvline(peak[0],color='b')
             for hkl in G2frame.HKL:
                 if G2frame.qPlot:
-                    if 'C' in Parms['Type'][0]:
-                        Plot.axvline(4*np.pi*sind(hkl[5]/2.0)/wave,color='b')
-                    else:
-                        Plot.axvline(2*np.pi*Parms['difC'][1]/hkl[5],color='b')
+                    Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[5]),color='r',dashes=(5,5))
                 if G2frame.dPlot:
-                    if 'C' in Parms['Type'][0]:
-                        Plot.axvline(wave/(2*sind(hkl[5]/2.0)),color='b')
-                    else:
-                        Plot.avline(hkl[5]/Parms['difC'][1],color='b')
+                    Plot.axvline(G2lat.Pos2dsp(Parms,hkl[5]),color='r',dashes=(5,5))
                 else:
                     Plot.axvline(hkl[5],color='r',dashes=(5,5))

trunk/GSASIIpwdGUI.py

@@ -2093 +2093 @@
         G2indx.IndexPeaks(peaks,G2frame.HKL)
         for hkl in G2frame.HKL:
-            hkl.append(G2lat.Dsp2pos(Inst,hkl[3])++controls[1])
+            hkl.append(G2lat.Dsp2pos(Inst,hkl[3])+controls[1])
         if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
             G2plt.PlotPowderLines(G2frame)

trunk/GSASIIstrIO.py

@@ -1818 +1818 @@
                                 Phi.append(phi)
                         elif 'T' in inst['Type'][0]:
-                            pos = inst['difC'][1]*d+inst['difA'][1]*d**2+inst['difB'][1]*d**3+Zero
+                            pos = inst['difC'][1]*d+inst['difA'][1]*d**2+inst['difB'][1]/d+Zero
                             if limits[0] < pos < limits[1]:
                                 wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0])

trunk/GSASIIstrMath.py

@@ -1390 +1390 @@
             pos -= const*(parmDict[hfx+'DisplaceX']*cosd(pos)+parmDict[hfx+'DisplaceY']*sind(pos))
     elif 'T' in calcControls[hfx+'histType']:
-        pos = parmDict[hfx+'difC']*d+parmDict[hfx+'difA']*d**2+parmDict[hfx+'difB']*d**3+parmDict[hfx+'Zero']
+        pos = parmDict[hfx+'difC']*d+parmDict[hfx+'difA']*d**2+parmDict[hfx+'difB']/d+parmDict[hfx+'Zero']
         #do I need sample position effects - maybe?
     return pos
@@ -1422 +1422 @@
         dpdDC = dsp
         dpdDA = dsp**2
-        dpdDB = dsp**3
+        dpdDB = 1./dsp
         return dpdA,dpdZ,dpdDC,dpdDA,dpdDB
             

trunk/help/MCSA in GSAS.htm

@@ -23 +23 @@
   <o:Author>vondreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>13</o:Revision>
-  <o:TotalTime>572</o:TotalTime>
+  <o:Revision>14</o:Revision>
+  <o:TotalTime>579</o:TotalTime>
   <o:Created>2014-08-19T14:01:00Z</o:Created>
-  <o:LastSaved>2014-08-20T21:24:00Z</o:LastSaved>
+  <o:LastSaved>2014-08-22T13:42:00Z</o:LastSaved>
   <o:Pages>9</o:Pages>
-  <o:Words>2417</o:Words>
-  <o:Characters>13779</o:Characters>
+  <o:Words>2418</o:Words>
+  <o:Characters>13784</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
   <o:Lines>114</o:Lines>
   <o:Paragraphs>32</o:Paragraphs>
-  <o:CharactersWithSpaces>16164</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>16170</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -477 +477 @@
         letter-spacing:.25pt;}
 a:link, span.MsoHyperlink
-        {mso-style-priority:99;
+        {mso-style-noshow:yes;
+        mso-style-priority:99;
         color:blue;
         text-decoration:underline;
@@ -799 +800 @@
         mso-ansi-font-size:10.0pt;
         mso-bidi-font-size:10.0pt;
+        font-family:"Calibri","sans-serif";
         mso-ascii-font-family:Calibri;
         mso-hansi-font-family:Calibri;
@@ -953 +955 @@
 <p class=MsoNormal>In these exercises you will use GSAS-II to solve the
 structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
-diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
-were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
+diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
+kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
 and were originally collected on NSLS beam line X17b. The MC/SA technique is
 needed in these cases because as you will see the data does not extend very far
@@ -1049 +1051 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image031.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
 
 <p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
@@ -1170 +1172 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>
-and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
+Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
 
 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
@@ -1195 +1197 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;height:375pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;
+ height:375pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
-src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="_x0000_i1050"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1212 +1214 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;height:252pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_3" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;
+ height:252pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
-src="MCSA%20in%20GSAS_files/image033.gif" v:shapes="_x0000_i1049"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1231 +1233 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
-src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1259 +1261 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;height:225pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_5" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
+ height:225pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
-src="MCSA%20in%20GSAS_files/image035.gif" v:shapes="_x0000_i1047"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1288 +1290 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1046" type="#_x0000_t75" style='width:525pt;height:450pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image036.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1331 +1333 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1045" type="#_x0000_t75" style='width:402pt;height:197.25pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_7" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
+ height:197.25pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
-src="MCSA%20in%20GSAS_files/image037.gif" v:shapes="_x0000_i1045"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1369 +1371 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1378 +1380 @@
 <h2><span class=GramE>Step 6.</span> Setup for Monte Carlo/Simulated Annealing</h2>
 
-<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic rings
-with one N-substituted position and an amino side group</p>
+<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
+rings with one N-substituted position and an amino side group</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1387 +1389 @@
   cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
-src="MCSA%20in%20GSAS_files/image039.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
 
 <p class=MsoNormal>MC/SA structure solution consists of optimizing the position
@@ -1421 +1423 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
-src="MCSA%20in%20GSAS_files/image040.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1436 +1438 @@
   cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
-src="MCSA%20in%20GSAS_files/image041.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1452 +1454 @@
   cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
-src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1460 +1462 @@
 necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something meaningful,
-I used <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
+mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
+meaningful, I used <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
 
 <p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
@@ -1481 +1484 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
-src="MCSA%20in%20GSAS_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1488 +1491 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1038" type="#_x0000_t75" style='width:4in;height:232.5pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
+ height:232.5pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="MCSA%20in%20GSAS_files/image044.png" o:title="" croptop="17592f"
   cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
-src="MCSA%20in%20GSAS_files/image045.jpg" v:shapes="_x0000_i1038"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image027.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1541 +1544 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
-src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
+src="MCSA%20in%20GSAS_files/image028.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
@@ -1615 +1618 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
-src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image047.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1637 +1640 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image048.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
-src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image049.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1650 +1653 @@
   cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
-src="MCSA%20in%20GSAS_files/image060.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image051.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1656 +1659 @@
 <p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
 good solution with a very low Residual (~4.8%). This problem typically gives
-suitable solutions with Residuals of 4-5%. If no good solution appears (e.g. molecules
-clashing), then you should just rerun MC/SA perhaps using more runs or more
-trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
+suitable solutions with Residuals of 4-5%. If no good solution appears (e.g.
+molecules clashing), then you should just rerun MC/SA perhaps using more runs
+or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
-want to retain; the others will be cleared before the next MC/SA run starts. When
-you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
+want to retain; the others will be cleared before the next MC/SA run starts.
+When you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the
@@ -1671 +1674 @@
 mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
 
-<p class=MsoNormal>MC/SA refinement of a solution is achieved by narrowing the
-search ranges and rerunning the MC/SA calculations. This is done by checking
-the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
+and rerunning the MC/SA calculations. This is done by checking the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
 box. Using 10% of the ranges reduces the search volume in this case by ~6
-orders of magnitude so that the true minimum is much easier to find. Now rerun
-Compute/MC/SA; be sure to select the best one before starting. The residual
-should drop to a much lower level. This refinement can be repeated with tighter
-restriction on the ranges; I used 5% for a final run and got</p>
+orders of magnitude so that the true minimum is much easier to find. Now rerun <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
+be sure to select the best one before starting. The residual should drop to a
+much lower level. This refinement can be repeated with tighter restriction on
+the ranges; I used 5% for a final run and got</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1686 +1691 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
-src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image053.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1699 +1704 @@
   cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
-src="MCSA%20in%20GSAS_files/image062.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image055.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1711 +1716 @@
   cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
-src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image057.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
 
 <p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
@@ -1721 +1726 @@
 mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move <span class=SpellE>Mc</span>/SA
-solution</span></b>; the drawing will show the new atom positions</p>
+minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
+the drawing will show the new atom positions</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1730 +1735 @@
   cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
-src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image072.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
 
 <p class=MsoNormal>And they will be listed in the Atoms table.</p>
@@ -1739 +1744 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
-src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image076.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
 
 <p class=MsoNormal>It is now ready for <span class=SpellE>Rietveld</span>
@@ -1749 +1754 @@
 
 <p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
-be ready for the first <span class=SpellE>Rietveld</span> refinement: 1)
-Uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
+be ready for the first <span class=SpellE>Rietveld</span> refinement: 1) On the
+<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
+tab uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
 minor-latin'>Do Pawley refinement?</span></b> box, 2) check the <b
@@ -1775 +1782 @@
 window and in the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the uniaxial
+mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
 model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
@@ -1810 +1819 @@
 Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin'>RB Models</span></b> tab; it will be empty. Do Edit/Assign atoms
-to rigid body; then select amino in the Select rigid body model <span
-class=SpellE>pulldown</span> (the only choice). The RB Models window will show</p>
+minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
+atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
+body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
+show</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1819 +1837 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
-src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image077.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -1832 +1850 @@
 minor-latin'>Ready</span></b></span> when done; the structure will be drawn
 with yellow bonds indicating that it is now a rigid body and not independent
-atoms. The RB Models window shows the new rigid body</p>
+atoms. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>RB Models</span></b> window shows the new rigid body</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1839 +1859 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
-src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image078.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
 
 <p class=MsoNormal>To refine the rigid body parameters check the <b
@@ -1855 +1875 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
-of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and the
-<span class=SpellE>RBModels</span> window shows the new parameters</p>
+of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
+the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
+new parameters</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1863 +1886 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image073.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
-src="MCSA%20in%20GSAS_files/image075.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image079.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
 
 <p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
@@ -1872 +1895 @@
  <v:imagedata src="MCSA%20in%20GSAS_files/image074.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="MCSA%20in%20GSAS_files/image082.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
+src="MCSA%20in%20GSAS_files/image080.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
 
 <p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.

trunk/help/MCSA in GSAS_files/filelist.xml

@@ -6 +6 @@
  <o:File HRef="colorschememapping.xml"/>
  <o:File HRef="image001.png"/>
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- <o:File HRef="image082.gif"/>
+ <o:File HRef="image080.gif"/>
  <o:File HRef="filelist.xml"/>
 </xml>

trunk/help/MCSA in GSAS_files/props061.xml

@@ -1 +1 @@
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trunk/help/gsasII.html

@@ -25 +25 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>144</o:Revision>
-  <o:TotalTime>3995</o:TotalTime>
+  <o:Revision>145</o:Revision>
+  <o:TotalTime>3997</o:TotalTime>
   <o:Created>2011-11-28T16:49:00Z</o:Created>
-  <o:LastSaved>2014-05-15T15:02:00Z</o:LastSaved>
-  <o:Pages>2</o:Pages>
-  <o:Words>10871</o:Words>
-  <o:Characters>61971</o:Characters>
+  <o:LastSaved>2014-08-22T13:28:00Z</o:LastSaved>
+  <o:Pages>28</o:Pages>
+  <o:Words>10888</o:Words>
+  <o:Characters>62064</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>516</o:Lines>
+  <o:Lines>517</o:Lines>
   <o:Paragraphs>145</o:Paragraphs>
-  <o:CharactersWithSpaces>72697</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>72807</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -2358 +2358 @@
 href="Charge%20Flipping%20-%20sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p>
 
+<p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight:
+bold'>Monte Carlo/Simulated Annealing structure solution – <o:p></o:p></span></strong></p>
+
+<p class=MsoNormal style='text-indent:.5in'><strong><span style='font-weight:
+normal'><a href="MCSA%20in%20GSAS.htm">MCSA in GSAS-II<o:p></o:p></a></span></strong></p>
+
 <p class=MsoNormal><strong><a href="Small%20Angle%20Image%20Processing.htm"><span
 style='font-weight:normal'>Small angle image processing</span></a><o:p></o:p></strong></p>
@@ -2400 +2406 @@
 
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
-is a hierarchical view of the data items in your GSAS-II project (name.gpx).
-Clicking on any item in the tree opens a window where information in that item
-can be viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
+is a hierarchical view of the data items in your GSAS-II project (name.gpx). Clicking
+on any item in the tree opens a window where information in that item can be
+viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
 Parameters&quot;</a> item under a ‘PWDR’ entry contains information about how
 data were collected, such as the sample temperature <a href="#Sample_Parameters">(see
@@ -2430 +2436 @@
 class=SpellE>gpx</span> file (e.g. name.bak3.gpx) to recover a previous version
 of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b>…
-to e.g. name.gpx to overwrite the current version. Otherwise you will get
-backups of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p>
+to e.g. name.gpx to overwrite the current version. Otherwise you will get backups
+of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2441 +2447 @@
 style='mso-fareast-font-family:"Times New Roman"'>, it will be saved there.
 Otherwise, you will be prompted for a new name in a file dialog (you may change
-directory as well). If the file exists, you will be asked if it OK to overwrite.</span></p>
+directory as well). If the file exists, you will be asked if it OK to
+overwrite.</span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2503 +2510 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of previously
-read powder patterns; each with a multiplier. Can be used to accumulate data,
-subtract background or empty container patterns, etc. Patterns used to form the
-sum must be of identical range and step size. Result is a new PWDR entry in the
-GSAS-II data tree.</p>
+style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of
+previously read powder patterns; each with a multiplier. Can be used to
+accumulate data, subtract background or empty container patterns, etc. Patterns
+used to form the sum must be of identical range and step size. Result is a new
+PWDR entry in the GSAS-II data tree.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2527 +2534 @@
 box for a name to be assigned to the new phase. Then the <b style='mso-bidi-font-weight:
 normal'><a href="#General">General</a></b> tab is opened for this phase; you
-should first select the phase type, enter the space group symbol and then
-lattice parameters. Note that nonstandard space group symbols are permitted; there
-must be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).</p>
+should first select the phase type, enter the space group symbol and then lattice
+parameters. Note that nonstandard space group symbols are permitted; there must
+be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2543 +2550 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad idea!!
-Don’t use this unless the data to be renamed has not been used anywhere in
-GSAS-II, e.g. only rename freshly read data.</p>
+style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad
+idea!! Don’t use this unless the data to be renamed has not been used anywhere
+in GSAS-II, e.g. only rename freshly read data.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -2639 +2646 @@
 style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the
 macromolecular phase information from a Protein Data Base file (name.PDB or
-name.ENT). The file name is found in a directory dialog; you can change
-directories as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT
-(or .<span class=SpellE>ent</span>) file names are shown. Be careful that the
-space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
-conventions (e.g. with spaces between axial fields). A dialog box is shown with
-the proposed phase name. You can change it if desired.</p>
+name.ENT). The file name is found in a directory dialog; you can change directories
+as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT (or .<span
+class=SpellE>ent</span>) file names are shown. Be careful that the space group
+symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions
+(e.g. with spaces between axial fields). A dialog box is shown with the
+proposed phase name. You can change it if desired.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
@@ -2781 +2788 @@
 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight:
-normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b> This
-reads structure factors (as F) and sig(F) from a SHELX format .<span
+normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b>
+This reads structure factors (as F) and sig(F) from a SHELX format .<span
 class=SpellE>hkl</span> file. The file names are found in a directory dialog;
 you can change directories as needed. You must know this is the content of this
@@ -2888 +2895 @@
 
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
-window provides a place for you to enter whatever text commentary you wish.
-Each time you enter this window, a date/time entry is provided for you. A
-possibly useful technique is to select a portion of the <span class=SpellE>project.lst</span>
+window provides a place for you to enter whatever text commentary you wish. Each
+time you enter this window, a date/time entry is provided for you. A possibly
+useful technique is to select a portion of the <span class=SpellE>project.lst</span>
 file after a refinement completes (it will contain refinement results with
 residuals, new values &amp; <span class=SpellE>esds</span>) and paste it into
@@ -2932 +2939 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
-style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for convergence;
-the refinement will stop when the change in the minimization function is less
-than this value. Set Min delta-M/M = 1.0 to force just a single cycle to be
-performed. A value less than 10<sup>-4</sup> (the default) generally gives no
-better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
+style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for
+convergence; the refinement will stop when the change in the minimization
+function is less than this value. Set Min delta-M/M = 1.0 to force just a
+single cycle to be performed. A value less than 10<sup>-4</sup> (the default)
+generally gives no better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span
@@ -3034 +3041 @@
 will cancel the operation. The equivalenced parameters will show as an equation
 of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
-M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword
-‘EQUIV’ marks it as <span class=GramE>an equivalence</span>. A Delete button
-can be used to remove it.<o:p></o:p></span></p>
+M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword ‘EQUIV’
+marks it as <span class=GramE>an equivalence</span>. A Delete button can be
+used to remove it.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -3110 +3117 @@
 style='mso-fareast-font-family:"Times New Roman"'>You can examine the table of
 restraints and change individual values; grayed out regions cannot be changed.
-The ‘<span class=SpellE>calc</span>’ values are determined from the atom
-positions in your structure, ‘<span class=SpellE>obs</span>’ values are the
-target values for the restraint and ‘<span class=SpellE>esd</span>’ is the
-uncertainty used to weight the restraint in the refinement (multiplied by the
-weight factor).<o:p></o:p></span></p>
+The ‘<span class=SpellE>calc</span>’ values are determined from the atom positions
+in your structure, ‘<span class=SpellE>obs</span>’ values are the target values
+for the restraint and ‘<span class=SpellE>esd</span>’ is the uncertainty used
+to weight the restraint in the refinement (multiplied by the weight factor).<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span
@@ -3181 +3187 @@
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change
 value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – this
-changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a dialog
-box will appear asking for the new value. <o:p></o:p></span></p>
+changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a
+dialog box will appear asking for the new value. <o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -3337 +3343 @@
 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
 normal;mso-bidi-font-weight:bold'> – this will create a text file of selected
-columns with values and corresponding <span class=SpellE>esds</span>. A file dialog
-box will appear; give a suitable file name; you may change directory if
+columns with values and corresponding <span class=SpellE>esds</span>. A file
+dialog box will appear; give a suitable file name; you may change directory if
 desired.<o:p></o:p></span></h5>
 
@@ -3399 +3405 @@
 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
 window shows the limits in position to be used in any fitting for this powder
-pattern. The ‘original’ values are obtained from the minimum &amp; maximum
-values in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p>
+pattern. The ‘original’ values are obtained from the minimum &amp; maximum values
+in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
@@ -3783 +3789 @@
 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Save</span></span><span
 style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves the
-sample parameters to a file with the extension ’.samprm’. A file dialog box
+color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves
+the sample parameters to a file with the extension ’.samprm’. A file dialog box
 will appear to ask for the file name.<span class=MsoHyperlink><span
 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
@@ -4048 +4054 @@
 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’
-– <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak
-positions &amp; intensities from the </span><a href="#Peak_List"><span
-style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
-none;text-underline:none'>Peak List</span></a><span style='mso-fareast-font-family:
-"Times New Roman"'> to make them available for the indexing routine. The d-obs is
-obtained from Bragg’s Law after applying the Zero correction shown on the </span><a
+– <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak positions
+&amp; intensities from the </span><a href="#Peak_List"><span style='mso-fareast-font-family:
+"Times New Roman";color:windowtext;text-decoration:none;text-underline:none'>Peak
+List</span></a><span style='mso-fareast-font-family:"Times New Roman"'> to make
+them available for the indexing routine. The d-obs is obtained from Bragg’s Law
+after applying the Zero correction shown on the </span><a
 href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman";
 color:windowtext;text-decoration:none;text-underline:none'>Instrument
@@ -4172 +4178 @@
 style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
-"Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell Index/Refine’
-</b>– <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
-none;text-underline:none'><o:p></o:p></span></span></span></span></p>
+"Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell
+Index/Refine’ </b>– <span class=MsoHyperlink><span style='color:windowtext;
+text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
@@ -4335 +4341 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
-the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – select
-between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
+the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
+select between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span
@@ -4474 +4480 @@
 style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
 style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
-map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
-procedure; they will be printed on the console and will be shown in the ‘<a
+map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this procedure;
+they will be printed on the console and will be shown in the ‘<a
 name="Map_peaks"></a><a href="gsasII.html"><span style='mso-bookmark:Map_peaks'><span
 style='color:windowtext;text-decoration:none;text-underline:none'>Map peaks</span></span></a><span
@@ -4492 +4498 @@
 style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
-using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You will
-need to select a source for the reflection set and perhaps select an element
-for normalization by its form factor, a resolution limit (usually 0.5A) and a
-charge flip threshold (usually 0.1); these are found at the bottom of the <b
-style='mso-bidi-font-weight:normal'>General</b> window. A progress bar showing
-the charge flip residual is shown while the charge flip is in operation. When
-the residual is no longer decreasing (be patient – it doesn’t necessarily fall
-continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
+using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
+will need to select a source for the reflection set and perhaps select an
+element for normalization by its form factor, a resolution limit (usually 0.5A)
+and a charge flip threshold (usually 0.1); these are found at the bottom of the
+<b style='mso-bidi-font-weight:normal'>General</b> window. A progress bar
+showing the charge flip residual is shown while the charge flip is in
+operation. When the residual is no longer decreasing (be patient – it doesn’t
+necessarily fall continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
 button to stop the charge flipping. The resulting map will be positioned to
 properly place symmetry operators (NB: depends on the quality of the resulting
@@ -4546 +4552 @@
 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
 style='mso-fareast-font-family:"Times New Roman"'>Phase type – </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>this can only be set when
-there are no atoms in the Atoms page for this phase. Select it when the phase
-is initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
+style='mso-fareast-font-family:"Times New Roman"'>this can only be set when there
+are no atoms in the Atoms page for this phase. Select it when the phase is
+initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -4773 +4779 @@
 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
 style='mso-fareast-font-family:"Times New Roman"'>Reflection set from</span></b><span
-style='mso-fareast-font-family:"Times New Roman"'> – This is the source of structure
-factors to be used in a charge flip calculation. These may be either a single
-crystal data set, or structure factors extracted from a powder pattern via a
-Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
+style='mso-fareast-font-family:"Times New Roman"'> – This is the source of
+structure factors to be used in a charge flip calculation. These may be either
+a single crystal data set, or structure factors extracted from a powder pattern
+via a Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
 
@@ -4786 +4792 @@
 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
 style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor
-chosen to normalize the structure factors before charge flipping. <b
+style='mso-fareast-font-family:"Times New Roman"'>– This is an element form
+factor chosen to normalize the structure factors before charge flipping. <b
 style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
 the lower right of the Periodic Table display shown when this is selected.<span
@@ -4829 +4835 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
-style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated Annealing
-controls are at the bottom of the window. (Future capability &amp; under
-development).<o:p></o:p></span></p>
+style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated
+Annealing controls are at the bottom of the window. (Future capability &amp;
+under development).<o:p></o:p></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -4840 +4846 @@
 set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
 This is the source of structure factors to be used in a charge flip
-calculation. These may be either a single crystal data set, or structure factors
-extracted from a powder pattern via a Pawley refinement or a Rietveld
+calculation. These may be either a single crystal data set, or structure
+factors extracted from a powder pattern via a Pawley refinement or a Rietveld
 refinement.<o:p></o:p></span></p>
 
@@ -4910 +4916 @@
 text-underline:none'><o:p></o:p></span></span></h4>
 
-<p class=MsoNormal>This is the table of parameters for the atoms in this
-crystal structure model. The menu controls allow manipulation of the values,
-refinement flags as well as initiate calculations of geometrical values
-(distances &amp; angles) among the atoms.</p>
+<p class=MsoNormal>This is the table of parameters for the atoms in this crystal
+structure model. The menu controls allow manipulation of the values, refinement
+flags as well as initiate calculations of geometrical values (distances &amp;
+angles) among the atoms.</p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
@@ -4960 +4966 @@
 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
 style='mso-fareast-font-family:"Times New Roman"'>Ctrl LMB</span></b><span
-style='mso-fareast-font-family:"Times New Roman"'> – on a row number
-selects/deselects the atom.<span class=MsoHyperlink><span style='color:windowtext;
-text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
+style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects/deselects
+the atom.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
+none;text-underline:none'><o:p></o:p></span></span></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -4985 +4991 @@
 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double
-left click a Type column heading</b>: a dialog box is shown that allows you to select
-all atoms with that type. <span class=MsoHyperlink><span style='mso-fareast-font-family:
-"Times New Roman";color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
+left click a Type column heading</b>: a dialog box is shown that allows you to
+select all atoms with that type. <span class=MsoHyperlink><span
+style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
+none;text-underline:none'><o:p></o:p></span></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo21'><![if !supportLists]><span
@@ -5160 +5167 @@
 be applied to the parameter for all selected atoms. <span class=SpellE><b
 style='mso-bidi-font-weight:normal'>Uiso</b></span> and <span class=SpellE><b
-style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new
-value to be used for all selected atoms. </p>
+style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new value
+to be used for all selected atoms. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -5190 +5197 @@
 style='mso-bidi-font-weight:normal'>Distances &amp; Angles – </b>compute
 distances and angles with esds (if possible) for selected atoms. A popup dialog
-box will appear with distance angle controls. NB: if atoms have been added or
-their type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
+box will appear with distance angle controls. NB: if atoms have been added or their
+type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
 of this dialog box before proceeding.</p>
 
@@ -5204 +5211 @@
 
 <p class=MsoNormal>This gives a list of the atoms and bonds that are to be
-rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks,
-ellipsoids &amp; sticks or polyhedra. There are two menus for this tab; Edit
-allows modification of the list of atoms to be rendered and Compute gives some
-options for geometric characterization of selected atoms.</p>
+rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks, ellipsoids
+&amp; sticks or polyhedra. There are two menus for this tab; Edit allows
+modification of the list of atoms to be rendered and Compute gives some options
+for geometric characterization of selected atoms.</p>
 
 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
@@ -5236 +5243 @@
 the selection list. <b style='mso-bidi-font-weight:normal'>NB</b>: beware of
 atoms that are hiding behind the one you are trying to select, they may be
-selected inadvertently. You can rotate the structure anytime during the selection
-process.</p>
+selected inadvertently. You can rotate the structure anytime during the
+selection process.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span
@@ -5327 +5334 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms
-currently in the draw atom table, find all atoms that belong in the
-coordination sphere around the selected atoms via unit cell translations. NB:
-symmetry operations are not used in this search.</p>
+style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms currently
+in the draw atom table, find all atoms that belong in the coordination sphere
+around the selected atoms via unit cell translations. NB: symmetry operations
+are not used in this search.</p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
@@ -5383 +5390 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
-style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are
-selected, a best plane is determined for them. The result is shown on the
-console window; it may be cut &amp; pasted to another application (e.g. Microsoft
-Word). Shown are the atom coordinates transformed to Cartesian best plane
-coordinates where the largest range is over the X-axis and the smallest is over
-the Z-axis with the origin at the unweighted center of the selection. Root mean
-square displacements along each axis for the best plane are also listed. The
-Z-axis RMS value indicates the flatness of the proposed plane. <b
-style='mso-bidi-font-weight:normal'>NB</b>: if you select (e.g. all) atoms then
-Best plane will give Cartesian coordinates for these atoms with respect to a
-coordinate system where the X-axis is along the longest axis of the atom
-grouping and the Z-axis is along the shortest distance. The origin is at the
-unweighted center of the selected atoms.</p>
+style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are selected,
+a best plane is determined for them. The result is shown on the console window;
+it may be cut &amp; pasted to another application (e.g. Microsoft Word). Shown
+are the atom coordinates transformed to Cartesian best plane coordinates where
+the largest range is over the X-axis and the smallest is over the Z-axis with
+the origin at the unweighted center of the selection. Root mean square
+displacements along each axis for the best plane are also listed. The Z-axis
+RMS value indicates the flatness of the proposed plane. <b style='mso-bidi-font-weight:
+normal'>NB</b>: if you select (e.g. all) atoms then Best plane will give
+Cartesian coordinates for these atoms with respect to a coordinate system where
+the X-axis is along the longest axis of the atom grouping and the Z-axis is
+along the shortest distance. The origin is at the unweighted center of the
+selected atoms.</p>
 
 <h4>RB Models</h4>
@@ -5596 +5603 @@
 style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
 "Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>You can change the refine flags either by clicking
-on the box or by selecting one and then selecting the column (a single click on
-the column heading). Then type ‘y’ to set the refine flags or ‘n’ to clear the
-flags. You should deselect those reflections that fall below the lower limit or
-above the upper limit of the powder pattern otherwise you may have a singular
-matrix error in your Pawley refinement.</span></p>
+</span></span></span><![endif]>You can change the refine flags either by
+clicking on the box or by selecting one and then selecting the column (a single
+click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
+clear the flags. You should deselect those reflections that fall below the
+lower limit or above the upper limit of the powder pattern otherwise you may
+have a singular matrix error in your Pawley refinement.</span></p>
 
 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo25'><span
@@ -5657 +5664 @@
 
 <p class=MsoNormal align=center style='text-align:center'><span
+style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
+
+<p class=MsoNormal align=center style='text-align:center'><span
 style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='color:windowtext;
 text-decoration:none;text-underline:none'><o:p>&nbsp;</o:p></span></span></span></p>
@@ -5673 +5683 @@
 
 </span></span></a></div>
+
+<p class=MsoNormal align=center style='text-align:center'><span
+style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
 
 <p class=MsoNormal align=center style='text-align:center'><span
@@ -6022 +6035 @@
 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>:
 contour off/on</span></b></span><span style='mso-bookmark:Pawley'><span
-style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring
-and returns to a waterfall plot with any offsets applied.<span
-class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
-text-underline:none'><o:p></o:p></span></span></span></span></p>
+style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring and
+returns to a waterfall plot with any offsets applied.<span class=MsoHyperlink><span
+style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo28'><span
@@ -6061 +6073 @@
 <p class=MsoNormal><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
 "Times New Roman"'>The variance-covariance matrix as a color coded array is
-shown on this page. The color bar to the right shows the range of covariances (-1
-to 1) and corresponding colors. The parameter names are to the right and the
-parameter numbers are below the plot.<span class=MsoHyperlink><span
+shown on this page. The color bar to the right shows the range of covariances
+(-1 to 1) and corresponding colors. The parameter names are to the right and
+the parameter numbers are below the plot.<span class=MsoHyperlink><span
 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
 
@@ -6075 +6087 @@
 </span></span></span><![endif]>Move the mouse cursor across the plot. If on a
 diagonal cell, the parameter name, value and esd is shown both as a tool tip
-and in the right hand portion of the status bar. If the cursor is off the
-diagonal, the two parameter names and their covariance are shown in the tool
-tip and the status bar.</span></p>
+and in the right hand portion of the status bar. If the cursor is off the diagonal,
+the two parameter names and their covariance are shown in the tool tip and the
+status bar.</span></p>
 
 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo29'><span
@@ -6138 +6150 @@
 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span></span><span
 style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:"Times New Roman"'>/d)
-from the Gaussian and Lorentzian parts of the profile function. The computed
-curves are based on the values of U, V, W, X and Y shown in the Instrument
-Parameters window in parentheses. These are the values for the instrument
-contribution that were set when the powder pattern was first read in to
-GSAS-II. If individual peak fitting has been performed, the values of ‘sig’
-&amp; ‘gam’ for the peaks are plotted as ‘+’; these are computed from the
-fitted values of U, V, W, X and Y as well as any sig or gam individually
-refined.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
-none;text-underline:none'><o:p></o:p></span></span></span></span></p>
+from the Gaussian and Lorentzian parts of the profile function. The computed curves
+are based on the values of U, V, W, X and Y shown in the Instrument Parameters
+window in parentheses. These are the values for the instrument contribution
+that were set when the powder pattern was first read in to GSAS-II. If
+individual peak fitting has been performed, the values of ‘sig’ &amp; ‘gam’ for
+the peaks are plotted as ‘+’; these are computed from the fitted values of U,
+V, W, X and Y as well as any sig or gam individually refined.<span
+class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
+text-underline:none'><o:p></o:p></span></span></span></span></p>
 
 <h4><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
@@ -6299 +6311 @@
 style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
 
+<p class=MsoNormal align=center style='text-align:center'><span
+style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
+
 <p class=MsoNormal><span style='mso-bookmark:Pawley'><!-- hhmts start --></span><a
 href="gsasII.html"><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family: