Changeset 1475


Ignore:
Timestamp:
Aug 22, 2014 1:09:47 PM (8 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:
9 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIlattice.py

    r1452 r1475  
    417417def Pos2dsp(Inst,pos):
    418418    ''' convert powder pattern position (2-theta or TOF, musec) to d-spacing
    419     ignores secondary effects (e.g. difA,difB in TOF)
     419    ignores secondary effects (e.g. difB in TOF)
    420420    '''
    421421    if 'C' in Inst['Type'][0]:
    422422        wave = G2mth.getWave(Inst)
    423         dsp = wave/(2.0*sind((pos-Inst['Zero'][1])/2.0))
    424     else:   #'T'OF - ignore difA, difB
    425         dsp = (pos-Inst['Zero'][1])/Inst['difC'][1]
    426     return dsp
     423        return wave/(2.0*sind((pos-Inst.get('Zero',[0,0])[1])/2.0))
     424    else:   #'T'OF - ignore difB
     425        T = pos-Inst['Zero'][1]
     426        T1 = Inst['difC'][1]**2-4.*Inst['difA'][1]*T
     427        return 2.*T/(Inst['difC'][1]+np.sqrt(T1))
    427428   
    428429def Dsp2pos(Inst,dsp):
     
    431432    if 'C' in Inst['Type'][0]:
    432433        wave = G2mth.getWave(Inst)
    433         pos = 2.0*asind(wave/(2.*dsp))+Inst['Zero'][1]             
     434        pos = 2.0*asind(wave/(2.*dsp))+Inst.get('Zero',[0,0])[1]             
    434435    else:   #'T'OF
    435         pos = Inst['difC'][1]*dsp+Inst['Zero'][1]+Inst['difA'][1]*dsp**2+Inst.get('difB',[0,0,False])[1]*dsp**3
     436        pos = Inst['difC'][1]*dsp+Inst['Zero'][1]+Inst['difA'][1]*dsp**2+Inst.get('difB',[0,0,False])[1]/dsp
    436437    return pos
    437438   
     
    442443        pos = 2.0*asind(parmdict['Lam']/(2.*dsp))+parmdict['Zero']
    443444    else:   #'T'OF
    444         pos = parmdict['difC']*dsp+parmdict['difA']*dsp**2+parmdict['difB']*dsp**3+parmdict['Zero']
     445        pos = parmdict['difC']*dsp+parmdict['difA']*dsp**2+parmdict['difB']/dsp+parmdict['Zero']
    445446    return pos
    446447                   
  • trunk/GSASIIplot.py

    r1474 r1475  
    943943            try:
    944944                Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
    945                 if 'C' in Parms['Type'][0]:
    946                     wave = G2mth.getWave(Parms)
    947                     if G2frame.qPlot and 'PWDR' in plottype:
    948                         try:
    949                             xpos = 2.0*asind(xpos*wave/(4*math.pi))
    950                         except ValueError:      #avoid bad value in asin beyond upper limit
    951                             pass
    952                     elif G2frame.dPlot:
    953                         dsp = xpos
    954                         q = 2.*np.pi/dsp
    955                         xpos = 2.0*asind(wave/(2.*dsp))
    956                     dsp = 0.0
    957                     if abs(xpos) > 0.:                  #avoid possible singularity at beam center
    958                         if 'PWDR' in plottype:
    959                             dsp = wave/(2.*sind(abs(xpos)/2.0))
    960                             q = 2.*np.pi/dsp
    961                         elif 'SASD' in plottype:
    962                             dsp = 2*np.pi/xpos
    963                             q = xpos
    964                     if G2frame.Contour:
    965                         if 'PWDR' in plottype:
    966                             G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
    967                         elif 'SASD' in plottype:
    968                             G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f pattern ID =%5d'%(dsp,q,int(ypos)),1)
     945                if G2frame.qPlot and 'PWDR' in plottype:
     946                    q = xpos
     947                    dsp = 2.*np.pi/q
     948                    try:
     949                        xpos = G2lat.Dsp2pos(Parms,2.0*np.pi/xpos)
     950                    except ValueError:      #avoid bad value in asin beyond upper limit
     951                        pass
     952                elif 'SASD' in plottype:
     953                    q = xpos
     954                    dsp = 2.*np.pi/q
     955                elif G2frame.dPlot:
     956                    dsp = xpos
     957                    q = 2.*np.pi/dsp
     958                    xpos = G2lat.Dsp2pos(Parms,xpos)
     959                else:
     960                    dsp = G2lat.Pos2dsp(Parms,xpos)
     961                    q = 2.*np.pi/dsp
     962                if G2frame.Contour: #PWDR only
     963                    if 'C' in Parms['Type'][0]:
     964                        G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
    969965                    else:
     966                        G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
     967                else:
     968                    if 'C' in Parms['Type'][0]:
    970969                        if 'PWDR' in plottype:
    971970                            if G2frame.SqrtPlot:
     
    974973                                G2frame.G2plotNB.status.SetStatusText('2-theta =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
    975974                        elif 'SASD' in plottype:
    976                             G2frame.G2plotNB.status.SetStatusText('d =%9.5f q = %9.5f Intensity =%12.5g'%(dsp,q,ypos),1)
    977                 else:       #TOF neutrons
    978                     dsp = 0.0
    979                     difC = Parms['difC'][1]
    980                     if G2frame.dPlot:
    981                         dsp = xpos
    982                         xpos = difC*dsp
    983                     elif G2frame.qPlot and 'PWDR' in plottype:
    984                         dsp = 2.*np.pi/xpos
    985                         xpos = difC*dsp
    986                     else:
    987                         dsp = xpos/difC             #rough approx.!
    988                     q = 2.*np.pi/dsp
    989                     if G2frame.Contour:
    990                         G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f pattern ID =%5d'%(xpos,dsp,q,int(ypos)),1)
     975                            G2frame.G2plotNB.status.SetStatusText('q =%12.5g Intensity =%12.5g d =%9.1f'%(q,ypos,dsp),1)
    991976                    else:
    992977                        if G2frame.SqrtPlot:
    993                             G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
     978                            G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f sqrt(Intensity) =%9.2f'%(xpos,dsp,q,ypos),1)
    994979                        else:
    995                             G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q = %9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
     980                            G2frame.G2plotNB.status.SetStatusText('TOF =%9.3f d =%9.5f q =%9.5f Intensity =%9.2f'%(xpos,dsp,q,ypos),1)
    996981                if G2frame.itemPicked:
    997982                    Page.canvas.SetToolTipString('%9.5f'%(xpos))
     
    10231008        except TypeError:
    10241009            return
    1025         if 'C' in Parms['Type'][0]:
    1026             wave = G2mth.getWave(Parms)
    1027         else:
    1028             difC = Parms['difC'][1]
    10291010        PickId = G2frame.PickId
    10301011        pick = event.artist
     
    10371018            if ind.all() != [0] and ObsLine[0].get_label() in str(pick):                                    #picked a data point
    10381019                data = G2frame.PatternTree.GetItemPyData(G2frame.PickId)
    1039                 if 'C' in Parms['Type'][0]:
    1040                     if G2frame.qPlot:                              #qplot - convert back to 2-theta
    1041                         xy[0] = 2.0*asind(xy[0]*wave/(4*math.pi))
    1042                     elif G2frame.dPlot:                            #dplot - convert back to 2-theta
    1043                         xy[0] = 2.0*asind(wave/(2.*xy[0]))
    1044                 elif 'T' in Parms['Type'][0]:
    1045                     if G2frame.qPlot:                              #qplot - convert back to TOF
    1046                         xy[0] = 2.0*math.pi*difC/xy[0]
    1047                     elif G2frame.dPlot:                            #dplot - convert back to TOF
    1048                         xy[0] *= difC                   
     1020                if G2frame.qPlot:                              #qplot - convert back to 2-theta
     1021                    xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
     1022                elif G2frame.dPlot:                            #dplot - convert back to 2-theta
     1023                    xy[0] = G2lat.Dsp2pos(Parms,xy[0])
    10491024                XY = G2mth.setPeakparms(Parms,Parms2,xy[0],xy[1])
    10501025                data['peaks'].append(XY)
     
    10581033                LimitId = G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Limits')
    10591034                data = G2frame.PatternTree.GetItemPyData(LimitId)
    1060                 if 'C' in Parms['Type'][0]:                            #CW data - TOF later in an elif
    1061                     if G2frame.qPlot and 'PWDR' in plottype:                              #qplot - convert back to 2-theta
    1062                         xy[0] = 2.0*asind(xy[0]*wave/(4*math.pi))
    1063                     elif G2frame.dPlot:                            #dplot - convert back to 2-theta
    1064                         xy[0] = 2.0*asind(wave/(2.*xy[0]))
    1065                 elif 'T' in Parms['Type'][0]:
    1066                     if G2frame.qPlot:                              #qplot - convert back to TOF
    1067                         xy[0] = 2.0*math.pi*difC/xy[0]
    1068                     elif G2frame.dPlot:                            #dplot - convert back to TOF
    1069                         xy[0] *= difC                   
     1035                if G2frame.qPlot:                              #qplot - convert back to 2-theta
     1036                    xy[0] = G2lat.Dsp2pos(Parms,2*np.pi/xy[0])
     1037                elif G2frame.dPlot:                            #dplot - convert back to 2-theta
     1038                    xy[0] = G2lat.Dsp2pos(Parms,xy[0])
    10701039                if G2frame.ifGetExclude:
    10711040                    excl = [0,0]
     
    11101079            return
    11111080        Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
    1112         if 'C' in Parms['Type'][0]:
    1113             wave = G2mth.getWave(Parms)
    1114         else:
    1115             difC = Parms['difC'][1]
    11161081        xpos = event.xdata
    11171082        PickId = G2frame.PickId
     
    11301095                id2 = lineNo%2
    11311096                if G2frame.qPlot and 'PWDR' in plottype:
    1132                     if 'C' in Parms['Type'][0]:
    1133                         data[id][id2] = 2.0*asind(wave*xpos/(4*math.pi))
    1134                     else:
    1135                         data[id][id2] = 2*math.pi*Parms['difC'][1]/xpos
     1097                    data[id][id2] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
    11361098                elif G2frame.dPlot and 'PWDR' in plottype:
    1137                     if 'C' in Parms['Type'][0]:
    1138                         data[id][id2] = 2.0*asind(wave/(2*xpos))
    1139                     else:
    1140                         data[id][id2] *= Parms['difC'][1]
     1099                    data[id][id2] = G2lat.Dsp2pos(Parms,xpos)
    11411100                else:
    11421101                    data[id][id2] = xpos
     
    11551114                else:
    11561115                    if G2frame.qPlot:
    1157                         if 'C' in Parms['Type'][0]:
    1158                             data['peaks'][lineNo-2][0] = 2.0*asind(wave*xpos/(4*math.pi))
    1159                         else:
    1160                             data['peaks'][lineNo-2][0] = 2*math.pi*Parms['difC'][1]/xpos
     1116                        data['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,2.*np.pi/xpos)
    11611117                    elif G2frame.dPlot:
    1162                         if 'C' in Parms['Type'][0]:
    1163                             data['peaks'][lineNo-2][0] = 2.0*asind(wave/(2*xpos))
    1164                         else:
    1165                             data['peaks'][lineNo-2][0] *= Parms['difC'][1]
     1118                        data['peaks'][lineNo-2][0] = G2lat.Dsp2pos(Parms,xpos)
    11661119                    else:
    11671120                        data['peaks'][lineNo-2][0] = xpos
     
    13811334        if G2frame.qPlot and 'PWDR' in plottype:
    13821335            Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
    1383             if 'C' in Parms['Type'][0]:
    1384                 X = 4*np.pi*npsind((xye[0]-Zero)/2.0)/wave
    1385             else:
    1386                 X = 2*np.pi*Parms['difC'][1]/(xye[0]-Zero)
     1336            X = 2.*np.pi/G2lat.Pos2dsp(Parms,xye[0])
    13871337        elif G2frame.dPlot and 'PWDR' in plottype:
    13881338            Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root, Pattern[2])
    1389             if 'C' in Parms['Type'][0]:
    1390                 X = wave/(2.*npsind(xye[0]-Zero)/2.0)
    1391             else:
    1392                 X = (xye[0]-Zero)/Parms['difC'][1]
     1339            X = G2lat.Pos2dsp(Parms,xye[0])
    13931340        else:
    1394             X = xye[0]-Zero
     1341            X = xye[0]
    13951342        if not lenX:
    13961343            lenX = len(X)
     
    14101357        if LimitId and ifpicked:
    14111358            limits = np.array(G2frame.PatternTree.GetItemPyData(LimitId))
     1359            lims = limits[1]
    14121360            if G2frame.qPlot and 'PWDR' in plottype:
    1413                 if 'C' in Parms['Type'][0]:
    1414                     limits = 4*np.pi*npsind(limits/2.0)/wave
    1415                 else:
    1416                     limits = 2*np.pi*difC/limits
     1361                lims = 2.*np.pi/G2lat.Pos2dsp(Parms,lims)
    14171362            elif G2frame.dPlot and 'PWDR' in plottype:
    1418                 if 'C' in Parms['Type'][0]:
    1419                     limits = wave/(2*npsind(limits/2.0))
    1420                 else:
    1421                     limits /= difC               
    1422             Lines.append(Plot.axvline(limits[1][0],color='g',dashes=(5,5),picker=3.))   
    1423             Lines.append(Plot.axvline(limits[1][1],color='r',dashes=(5,5),picker=3.))
     1363                lims = G2lat.Pos2dsp(Parms,lims)
     1364            Lines.append(Plot.axvline(lims[0],color='g',dashes=(5,5),picker=3.))   
     1365            Lines.append(Plot.axvline(lims[1],color='r',dashes=(5,5),picker=3.))
    14241366            for i,item in enumerate(limits[2:]):
    14251367                Lines.append(Plot.axvline(item[0],color='m',dashes=(5,5),picker=3.))   
     
    15351477                    for item in data['peaks']:
    15361478                        if G2frame.qPlot:
    1537                             if 'C' in Parms['Type'][0]:
    1538                                 Lines.append(Plot.axvline(4*math.pi*sind(item[0]/2.)/wave,color=colors[N%6],picker=2.))
    1539                             else:
    1540                                 Lines.append(Plot.axvline(2*math.pi*difC/item[0],color=colors[N%6],picker=2.))                               
    1541                         if G2frame.dPlot:
    1542                             if 'C' in Parms['Type'][0]:
    1543                                 Lines.append(Plot.axvline(wave/(2*sind(item[0]/2.)),color=colors[N%6],picker=2.))
    1544                             else:
    1545                                 Lines.append(Plot.axvline(item[0]/difC,color=colors[N%6],picker=2.))                               
     1479                            Lines.append(Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
     1480                        elif G2frame.dPlot:
     1481                            Lines.append(Plot.axvline(G2lat.Pos2dsp(Parms,item[0]),color=colors[N%6],picker=2.))
    15461482                        else:
    15471483                            Lines.append(Plot.axvline(item[0],color=colors[N%6],picker=2.))
     
    15681504    if PickId and not G2frame.Contour:
    15691505        Parms,Parms2 = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Instrument Parameters'))
    1570         if 'C' in Parms['Type'][0]:
    1571             wave = G2mth.getWave(Parms)
    1572         else:
    1573             difC = Parms['difC'][1]
    15741506        if G2frame.PatternTree.GetItemText(PickId) in ['Index Peak List','Unit Cells List']:
    15751507            peaks = np.array((G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,PatternId, 'Index Peak List'))))[0]
    15761508            for peak in peaks:
    15771509                if G2frame.qPlot:
    1578                     if 'C' in Parms['Type'][0]:
    1579                         Plot.axvline(4*np.pi*sind(peak[0]/2.0)/wave,color='b')
    1580                     else:
    1581                         Plot.axvline(2*np.pi*Parms['difC'][1]/peak[0],color='b')
     1510                    Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,peak[0]),color='b')
    15821511                if G2frame.dPlot:
    1583                     if 'C' in Parms['Type'][0]:
    1584                         Plot.axvline(wave/(2*sind(peak[0]/2.0)),color='b')
    1585                     else:
    1586                         Plot.avline(peak[0]/Parms['difC'][1],color='b')
     1512                    Plot.axvline(G2lat.Pos2dsp(Parms,peak[0]),color='b')
    15871513                else:
    15881514                    Plot.axvline(peak[0],color='b')
    15891515            for hkl in G2frame.HKL:
    15901516                if G2frame.qPlot:
    1591                     if 'C' in Parms['Type'][0]:
    1592                         Plot.axvline(4*np.pi*sind(hkl[5]/2.0)/wave,color='b')
    1593                     else:
    1594                         Plot.axvline(2*np.pi*Parms['difC'][1]/hkl[5],color='b')
     1517                    Plot.axvline(2.*np.pi/G2lat.Pos2dsp(Parms,hkl[5]),color='r',dashes=(5,5))
    15951518                if G2frame.dPlot:
    1596                     if 'C' in Parms['Type'][0]:
    1597                         Plot.axvline(wave/(2*sind(hkl[5]/2.0)),color='b')
    1598                     else:
    1599                         Plot.avline(hkl[5]/Parms['difC'][1],color='b')
     1519                    Plot.axvline(G2lat.Pos2dsp(Parms,hkl[5]),color='r',dashes=(5,5))
    16001520                else:
    16011521                    Plot.axvline(hkl[5],color='r',dashes=(5,5))
  • trunk/GSASIIpwdGUI.py

    r1466 r1475  
    20932093        G2indx.IndexPeaks(peaks,G2frame.HKL)
    20942094        for hkl in G2frame.HKL:
    2095             hkl.append(G2lat.Dsp2pos(Inst,hkl[3])++controls[1])
     2095            hkl.append(G2lat.Dsp2pos(Inst,hkl[3])+controls[1])
    20962096        if 'PKS' in G2frame.PatternTree.GetItemText(G2frame.PatternId):
    20972097            G2plt.PlotPowderLines(G2frame)
  • trunk/GSASIIstrIO.py

    r1460 r1475  
    18181818                                Phi.append(phi)
    18191819                        elif 'T' in inst['Type'][0]:
    1820                             pos = inst['difC'][1]*d+inst['difA'][1]*d**2+inst['difB'][1]*d**3+Zero
     1820                            pos = inst['difC'][1]*d+inst['difA'][1]*d**2+inst['difB'][1]/d+Zero
    18211821                            if limits[0] < pos < limits[1]:
    18221822                                wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0])
  • trunk/GSASIIstrMath.py

    r1474 r1475  
    13901390            pos -= const*(parmDict[hfx+'DisplaceX']*cosd(pos)+parmDict[hfx+'DisplaceY']*sind(pos))
    13911391    elif 'T' in calcControls[hfx+'histType']:
    1392         pos = parmDict[hfx+'difC']*d+parmDict[hfx+'difA']*d**2+parmDict[hfx+'difB']*d**3+parmDict[hfx+'Zero']
     1392        pos = parmDict[hfx+'difC']*d+parmDict[hfx+'difA']*d**2+parmDict[hfx+'difB']/d+parmDict[hfx+'Zero']
    13931393        #do I need sample position effects - maybe?
    13941394    return pos
     
    14221422        dpdDC = dsp
    14231423        dpdDA = dsp**2
    1424         dpdDB = dsp**3
     1424        dpdDB = 1./dsp
    14251425        return dpdA,dpdZ,dpdDC,dpdDA,dpdDB
    14261426           
  • trunk/help/MCSA in GSAS.htm

    r1474 r1475  
    2323  <o:Author>vondreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>13</o:Revision>
    26   <o:TotalTime>572</o:TotalTime>
     25  <o:Revision>14</o:Revision>
     26  <o:TotalTime>579</o:TotalTime>
    2727  <o:Created>2014-08-19T14:01:00Z</o:Created>
    28   <o:LastSaved>2014-08-20T21:24:00Z</o:LastSaved>
     28  <o:LastSaved>2014-08-22T13:42:00Z</o:LastSaved>
    2929  <o:Pages>9</o:Pages>
    30   <o:Words>2417</o:Words>
    31   <o:Characters>13779</o:Characters>
     30  <o:Words>2418</o:Words>
     31  <o:Characters>13784</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>114</o:Lines>
    3434  <o:Paragraphs>32</o:Paragraphs>
    35   <o:CharactersWithSpaces>16164</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>16170</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    477477        letter-spacing:.25pt;}
    478478a:link, span.MsoHyperlink
    479         {mso-style-priority:99;
     479        {mso-style-noshow:yes;
     480        mso-style-priority:99;
    480481        color:blue;
    481482        text-decoration:underline;
     
    799800        mso-ansi-font-size:10.0pt;
    800801        mso-bidi-font-size:10.0pt;
     802        font-family:"Calibri","sans-serif";
    801803        mso-ascii-font-family:Calibri;
    802804        mso-hansi-font-family:Calibri;
     
    953955<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
    954956structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
    955 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
    956 were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
     957diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
     958kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
    957959and were originally collected on NSLS beam line X17b. The MC/SA technique is
    958960needed in these cases because as you will see the data does not extend very far
     
    10491051 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
    10501052</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1051 src="MCSA%20in%20GSAS_files/image031.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
     1053src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
    10521054
    10531055<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    11701172style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    11711173<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1172 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>
    1173 and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
    1174 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1175 mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
     1174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
     1175Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
     1176normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1177minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
    11761178
    11771179<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
     
    11951197
    11961198<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1197  id="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;height:375pt;
    1198  visibility:visible;mso-wrap-style:square'>
     1199 id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;
     1200 height:375pt;visibility:visible;mso-wrap-style:square'>
    11991201 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
    12001202</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
    1201 src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="_x0000_i1050"><![endif]></span></p>
     1203src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
    12021204
    12031205<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12121214
    12131215<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1214  id="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;height:252pt;
    1215  visibility:visible;mso-wrap-style:square'>
     1216 id="Picture_x0020_3" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;
     1217 height:252pt;visibility:visible;mso-wrap-style:square'>
    12161218 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
    12171219</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
    1218 src="MCSA%20in%20GSAS_files/image033.gif" v:shapes="_x0000_i1049"><![endif]></span></p>
     1220src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
    12191221
    12201222<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12311233 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
    12321234</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
    1233 src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1235src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    12341236
    12351237<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12591261
    12601262<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1261  id="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;height:225pt;
    1262  visibility:visible;mso-wrap-style:square'>
     1263 id="Picture_x0020_5" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
     1264 height:225pt;visibility:visible;mso-wrap-style:square'>
    12631265 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
    12641266</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
    1265 src="MCSA%20in%20GSAS_files/image035.gif" v:shapes="_x0000_i1047"><![endif]></span></p>
     1267src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
    12661268
    12671269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12881290
    12891291<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1290  id="_x0000_i1046" type="#_x0000_t75" style='width:525pt;height:450pt;
    1291  visibility:visible;mso-wrap-style:square'>
     1292 id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
     1293 height:450pt;visibility:visible;mso-wrap-style:square'>
    12921294 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
    12931295</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1294 src="MCSA%20in%20GSAS_files/image036.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
     1296src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
    12951297
    12961298<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    13311333
    13321334<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1333  id="_x0000_i1045" type="#_x0000_t75" style='width:402pt;height:197.25pt;
    1334  visibility:visible;mso-wrap-style:square'>
     1335 id="Picture_x0020_7" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
     1336 height:197.25pt;visibility:visible;mso-wrap-style:square'>
    13351337 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
    13361338</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
    1337 src="MCSA%20in%20GSAS_files/image037.gif" v:shapes="_x0000_i1045"><![endif]></span></p>
     1339src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    13381340
    13391341<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    13691371 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
    13701372</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1371 src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1373src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    13721374
    13731375<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    13781380<h2><span class=GramE>Step 6.</span> Setup for Monte Carlo/Simulated Annealing</h2>
    13791381
    1380 <p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic rings
    1381 with one N-substituted position and an amino side group</p>
     1382<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
     1383rings with one N-substituted position and an amino side group</p>
    13821384
    13831385<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    13871389  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
    13881390</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
    1389 src="MCSA%20in%20GSAS_files/image039.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
     1391src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
    13901392
    13911393<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
     
    14211423 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
    14221424</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
    1423 src="MCSA%20in%20GSAS_files/image040.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
     1425src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
    14241426
    14251427<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14361438  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
    14371439</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
    1438 src="MCSA%20in%20GSAS_files/image041.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1440src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
    14391441
    14401442<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14521454  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
    14531455</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
    1454 src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     1456src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    14551457
    14561458<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14601462necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
    14611463style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1462 mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something meaningful,
    1463 I used <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1464 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
     1464mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
     1465meaningful, I used <b style='mso-bidi-font-weight:normal'><span
     1466style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1467mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
    14651468
    14661469<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
     
    14811484 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
    14821485</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
    1483 src="MCSA%20in%20GSAS_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
     1486src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
    14841487
    14851488<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14881491
    14891492<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1490  id="_x0000_i1038" type="#_x0000_t75" style='width:4in;height:232.5pt;
    1491  visibility:visible;mso-wrap-style:square'>
     1493 id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
     1494 height:232.5pt;visibility:visible;mso-wrap-style:square'>
    14921495 <v:imagedata src="MCSA%20in%20GSAS_files/image044.png" o:title="" croptop="17592f"
    14931496  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
    14941497</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
    1495 src="MCSA%20in%20GSAS_files/image045.jpg" v:shapes="_x0000_i1038"><![endif]></span></p>
     1498src="MCSA%20in%20GSAS_files/image027.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    14961499
    14971500<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15411544 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
    15421545</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
    1543 src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
     1546src="MCSA%20in%20GSAS_files/image028.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
    15441547style='mso-spacerun:yes'> </span></p>
    15451548
     
    16151618 <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
    16161619</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
    1617 src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1620src="MCSA%20in%20GSAS_files/image047.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
    16181621
    16191622<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16371640 <v:imagedata src="MCSA%20in%20GSAS_files/image048.png" o:title=""/>
    16381641</v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
    1639 src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1642src="MCSA%20in%20GSAS_files/image049.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
    16401643
    16411644<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16501653  cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
    16511654</v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
    1652 src="MCSA%20in%20GSAS_files/image060.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1655src="MCSA%20in%20GSAS_files/image051.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    16531656
    16541657<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16561659<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
    16571660good solution with a very low Residual (~4.8%). This problem typically gives
    1658 suitable solutions with Residuals of 4-5%. If no good solution appears (e.g. molecules
    1659 clashing), then you should just rerun MC/SA perhaps using more runs or more
    1660 trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
     1661suitable solutions with Residuals of 4-5%. If no good solution appears (e.g.
     1662molecules clashing), then you should just rerun MC/SA perhaps using more runs
     1663or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
    16611664style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    16621665mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
    1663 want to retain; the others will be cleared before the next MC/SA run starts. When
    1664 you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
     1666want to retain; the others will be cleared before the next MC/SA run starts.
     1667When you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
    16651668normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    16661669minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the
     
    16711674mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
    16721675
    1673 <p class=MsoNormal>MC/SA refinement of a solution is achieved by narrowing the
    1674 search ranges and rerunning the MC/SA calculations. This is done by checking
    1675 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1676<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
     1677and rerunning the MC/SA calculations. This is done by checking the <b
     1678style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16761679mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
    16771680box. Using 10% of the ranges reduces the search volume in this case by ~6
    1678 orders of magnitude so that the true minimum is much easier to find. Now rerun
    1679 Compute/MC/SA; be sure to select the best one before starting. The residual
    1680 should drop to a much lower level. This refinement can be repeated with tighter
    1681 restriction on the ranges; I used 5% for a final run and got</p>
     1681orders of magnitude so that the true minimum is much easier to find. Now rerun <b
     1682style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
     1684be sure to select the best one before starting. The residual should drop to a
     1685much lower level. This refinement can be repeated with tighter restriction on
     1686the ranges; I used 5% for a final run and got</p>
    16821687
    16831688<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16861691 <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
    16871692</v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
    1688 src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
     1693src="MCSA%20in%20GSAS_files/image053.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
    16891694
    16901695<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16991704  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
    17001705</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
    1701 src="MCSA%20in%20GSAS_files/image062.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
     1706src="MCSA%20in%20GSAS_files/image055.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
    17021707
    17031708<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17111716  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
    17121717</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
    1713 src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
     1718src="MCSA%20in%20GSAS_files/image057.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    17141719
    17151720<p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
     
    17211726mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
    17221727normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1723 minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move <span class=SpellE>Mc</span>/SA
    1724 solution</span></b>; the drawing will show the new atom positions</p>
     1728minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
     1729the drawing will show the new atom positions</p>
    17251730
    17261731<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17301735  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
    17311736</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
    1732 src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1737src="MCSA%20in%20GSAS_files/image072.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
    17331738
    17341739<p class=MsoNormal>And they will be listed in the Atoms table.</p>
     
    17391744 <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
    17401745</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    1741 src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     1746src="MCSA%20in%20GSAS_files/image076.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    17421747
    17431748<p class=MsoNormal>It is now ready for <span class=SpellE>Rietveld</span>
     
    17491754
    17501755<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
    1751 be ready for the first <span class=SpellE>Rietveld</span> refinement: 1)
    1752 Uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1756be ready for the first <span class=SpellE>Rietveld</span> refinement: 1) On the
     1757<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1758mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     1759tab uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    17531760"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    17541761minor-latin'>Do Pawley refinement?</span></b> box, 2) check the <b
     
    17751782window and in the <b style='mso-bidi-font-weight:normal'><span
    17761783style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1777 mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the uniaxial
     1784mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
     1785style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1786mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
    17781787model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
    17791788style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    18101819Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    18111820"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1812 minor-latin'>RB Models</span></b> tab; it will be empty. Do Edit/Assign atoms
    1813 to rigid body; then select amino in the Select rigid body model <span
    1814 class=SpellE>pulldown</span> (the only choice). The RB Models window will show</p>
     1821minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
     1822style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1823mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
     1824atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
     1825normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1826minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
     1827style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
     1829body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
     1830normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1831minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
     1832show</p>
    18151833
    18161834<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18191837 <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
    18201838</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
    1821 src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     1839src="MCSA%20in%20GSAS_files/image077.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    18221840
    18231841<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    18321850minor-latin'>Ready</span></b></span> when done; the structure will be drawn
    18331851with yellow bonds indicating that it is now a rigid body and not independent
    1834 atoms. The RB Models window shows the new rigid body</p>
     1852atoms. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1853"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1854minor-latin'>RB Models</span></b> window shows the new rigid body</p>
    18351855
    18361856<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18391859 <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
    18401860</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
    1841 src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1861src="MCSA%20in%20GSAS_files/image078.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    18421862
    18431863<p class=MsoNormal>To refine the rigid body parameters check the <b
     
    18551875style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    18561876mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
    1857 of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and the
    1858 <span class=SpellE>RBModels</span> window shows the new parameters</p>
     1877of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
     1878the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1879style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1880mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
     1881new parameters</p>
    18591882
    18601883<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18631886 <v:imagedata src="MCSA%20in%20GSAS_files/image073.png" o:title=""/>
    18641887</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
    1865 src="MCSA%20in%20GSAS_files/image075.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
     1888src="MCSA%20in%20GSAS_files/image079.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    18661889
    18671890<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
     
    18721895 <v:imagedata src="MCSA%20in%20GSAS_files/image074.png" o:title=""/>
    18731896</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1874 src="MCSA%20in%20GSAS_files/image082.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
     1897src="MCSA%20in%20GSAS_files/image080.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    18751898
    18761899<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
  • trunk/help/MCSA in GSAS_files/filelist.xml

    r1474 r1475  
    66 <o:File HRef="colorschememapping.xml"/>
    77 <o:File HRef="image001.png"/>
    8  <o:File HRef="image031.gif"/>
     8 <o:File HRef="image002.gif"/>
    99 <o:File HRef="image003.png"/>
    10  <o:File HRef="image032.gif"/>
     10 <o:File HRef="image004.gif"/>
    1111 <o:File HRef="image005.png"/>
    12  <o:File HRef="image033.gif"/>
     12 <o:File HRef="image006.gif"/>
    1313 <o:File HRef="image007.png"/>
    14  <o:File HRef="image034.gif"/>
     14 <o:File HRef="image008.gif"/>
    1515 <o:File HRef="image009.png"/>
    16  <o:File HRef="image035.gif"/>
     16 <o:File HRef="image010.gif"/>
    1717 <o:File HRef="image011.png"/>
    18  <o:File HRef="image036.gif"/>
     18 <o:File HRef="image012.gif"/>
    1919 <o:File HRef="image013.png"/>
    20  <o:File HRef="image037.gif"/>
     20 <o:File HRef="image014.gif"/>
    2121 <o:File HRef="image015.png"/>
    22  <o:File HRef="image038.gif"/>
     22 <o:File HRef="image016.gif"/>
    2323 <o:File HRef="image017.png"/>
    24  <o:File HRef="image039.jpg"/>
     24 <o:File HRef="image018.jpg"/>
    2525 <o:File HRef="image019.png"/>
    26  <o:File HRef="image040.gif"/>
     26 <o:File HRef="image020.gif"/>
    2727 <o:File HRef="image021.png"/>
    28  <o:File HRef="image041.jpg"/>
     28 <o:File HRef="image022.jpg"/>
    2929 <o:File HRef="image023.png"/>
    30  <o:File HRef="image042.jpg"/>
     30 <o:File HRef="image024.jpg"/>
    3131 <o:File HRef="image025.png"/>
    32  <o:File HRef="image043.gif"/>
     32 <o:File HRef="image026.gif"/>
    3333 <o:File HRef="image044.png"/>
    34  <o:File HRef="image045.jpg"/>
     34 <o:File HRef="image027.jpg"/>
    3535 <o:File HRef="image029.png"/>
    36  <o:File HRef="image046.gif"/>
     36 <o:File HRef="image028.gif"/>
    3737 <o:File HRef="image030.png"/>
    38  <o:File HRef="image058.gif"/>
     38 <o:File HRef="image047.gif"/>
    3939 <o:File HRef="image048.png"/>
    40  <o:File HRef="image059.gif"/>
     40 <o:File HRef="image049.gif"/>
    4141 <o:File HRef="image050.png"/>
    42  <o:File HRef="image060.jpg"/>
     42 <o:File HRef="image051.jpg"/>
    4343 <o:File HRef="image052.png"/>
    44  <o:File HRef="image061.gif"/>
     44 <o:File HRef="image053.gif"/>
    4545 <o:File HRef="image054.png"/>
    46  <o:File HRef="image062.jpg"/>
     46 <o:File HRef="image055.jpg"/>
    4747 <o:File HRef="image056.png"/>
    48  <o:File HRef="image063.jpg"/>
     48 <o:File HRef="image057.jpg"/>
    4949 <o:File HRef="image064.png"/>
    50  <o:File HRef="image065.jpg"/>
     50 <o:File HRef="image072.jpg"/>
    5151 <o:File HRef="image066.png"/>
    52  <o:File HRef="image067.gif"/>
     52 <o:File HRef="image076.gif"/>
    5353 <o:File HRef="image068.png"/>
    54  <o:File HRef="image069.gif"/>
     54 <o:File HRef="image077.gif"/>
    5555 <o:File HRef="image070.png"/>
    56  <o:File HRef="image071.gif"/>
     56 <o:File HRef="image078.gif"/>
    5757 <o:File HRef="image073.png"/>
    58  <o:File HRef="image075.gif"/>
     58 <o:File HRef="image079.gif"/>
    5959 <o:File HRef="image074.png"/>
    60  <o:File HRef="image082.gif"/>
     60 <o:File HRef="image080.gif"/>
    6161 <o:File HRef="filelist.xml"/>
    6262</xml>
  • trunk/help/MCSA in GSAS_files/props061.xml

    r1474 r1475  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
    2 <ds:datastoreItem ds:itemID="{61455713-2E19-452C-BAB9-F2B10658DF75}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
     2<ds:datastoreItem ds:itemID="{79E00A83-53B5-4915-9D04-0FD6C141C6DA}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
  • trunk/help/gsasII.html

    r1347 r1475  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>144</o:Revision>
    28   <o:TotalTime>3995</o:TotalTime>
     27  <o:Revision>145</o:Revision>
     28  <o:TotalTime>3997</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2014-05-15T15:02:00Z</o:LastSaved>
    31   <o:Pages>2</o:Pages>
    32   <o:Words>10871</o:Words>
    33   <o:Characters>61971</o:Characters>
     30  <o:LastSaved>2014-08-22T13:28:00Z</o:LastSaved>
     31  <o:Pages>28</o:Pages>
     32  <o:Words>10888</o:Words>
     33  <o:Characters>62064</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>516</o:Lines>
     35  <o:Lines>517</o:Lines>
    3636  <o:Paragraphs>145</o:Paragraphs>
    37   <o:CharactersWithSpaces>72697</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>72807</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    23582358href="Charge%20Flipping%20-%20sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p>
    23592359
     2360<p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight:
     2361bold'>Monte Carlo/Simulated Annealing structure solution – <o:p></o:p></span></strong></p>
     2362
     2363<p class=MsoNormal style='text-indent:.5in'><strong><span style='font-weight:
     2364normal'><a href="MCSA%20in%20GSAS.htm">MCSA in GSAS-II<o:p></o:p></a></span></strong></p>
     2365
    23602366<p class=MsoNormal><strong><a href="Small%20Angle%20Image%20Processing.htm"><span
    23612367style='font-weight:normal'>Small angle image processing</span></a><o:p></o:p></strong></p>
     
    24002406
    24012407<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    2402 is a hierarchical view of the data items in your GSAS-II project (name.gpx).
    2403 Clicking on any item in the tree opens a window where information in that item
    2404 can be viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
     2408is a hierarchical view of the data items in your GSAS-II project (name.gpx). Clicking
     2409on any item in the tree opens a window where information in that item can be
     2410viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
    24052411Parameters&quot;</a> item under a ‘PWDR’ entry contains information about how
    24062412data were collected, such as the sample temperature <a href="#Sample_Parameters">(see
     
    24302436class=SpellE>gpx</span> file (e.g. name.bak3.gpx) to recover a previous version
    24312437of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b>…
    2432 to e.g. name.gpx to overwrite the current version. Otherwise you will get
    2433 backups of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p>
     2438to e.g. name.gpx to overwrite the current version. Otherwise you will get backups
     2439of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p>
    24342440
    24352441<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    24412447style='mso-fareast-font-family:"Times New Roman"'>, it will be saved there.
    24422448Otherwise, you will be prompted for a new name in a file dialog (you may change
    2443 directory as well). If the file exists, you will be asked if it OK to overwrite.</span></p>
     2449directory as well). If the file exists, you will be asked if it OK to
     2450overwrite.</span></p>
    24442451
    24452452<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25032510style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    25042511style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2505 style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of previously
    2506 read powder patterns; each with a multiplier. Can be used to accumulate data,
    2507 subtract background or empty container patterns, etc. Patterns used to form the
    2508 sum must be of identical range and step size. Result is a new PWDR entry in the
    2509 GSAS-II data tree.</p>
     2512style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of
     2513previously read powder patterns; each with a multiplier. Can be used to
     2514accumulate data, subtract background or empty container patterns, etc. Patterns
     2515used to form the sum must be of identical range and step size. Result is a new
     2516PWDR entry in the GSAS-II data tree.</p>
    25102517
    25112518<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25272534box for a name to be assigned to the new phase. Then the <b style='mso-bidi-font-weight:
    25282535normal'><a href="#General">General</a></b> tab is opened for this phase; you
    2529 should first select the phase type, enter the space group symbol and then
    2530 lattice parameters. Note that nonstandard space group symbols are permitted; there
    2531 must be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).</p>
     2536should first select the phase type, enter the space group symbol and then lattice
     2537parameters. Note that nonstandard space group symbols are permitted; there must
     2538be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).</p>
    25322539
    25332540<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25432550style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    25442551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2545 style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad idea!!
    2546 Don’t use this unless the data to be renamed has not been used anywhere in
    2547 GSAS-II, e.g. only rename freshly read data.</p>
     2552style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad
     2553idea!! Don’t use this unless the data to be renamed has not been used anywhere
     2554in GSAS-II, e.g. only rename freshly read data.</p>
    25482555
    25492556<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    26392646style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the
    26402647macromolecular phase information from a Protein Data Base file (name.PDB or
    2641 name.ENT). The file name is found in a directory dialog; you can change
    2642 directories as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT
    2643 (or .<span class=SpellE>ent</span>) file names are shown. Be careful that the
    2644 space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
    2645 conventions (e.g. with spaces between axial fields). A dialog box is shown with
    2646 the proposed phase name. You can change it if desired.</p>
     2648name.ENT). The file name is found in a directory dialog; you can change directories
     2649as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT (or .<span
     2650class=SpellE>ent</span>) file names are shown. Be careful that the space group
     2651symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions
     2652(e.g. with spaces between axial fields). A dialog box is shown with the
     2653proposed phase name. You can change it if desired.</p>
    26472654
    26482655<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     
    27812788style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    27822789</span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    2783 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b> This
    2784 reads structure factors (as F) and sig(F) from a SHELX format .<span
     2790normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b>
     2791This reads structure factors (as F) and sig(F) from a SHELX format .<span
    27852792class=SpellE>hkl</span> file. The file names are found in a directory dialog;
    27862793you can change directories as needed. You must know this is the content of this
     
    28882895
    28892896<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    2890 window provides a place for you to enter whatever text commentary you wish.
    2891 Each time you enter this window, a date/time entry is provided for you. A
    2892 possibly useful technique is to select a portion of the <span class=SpellE>project.lst</span>
     2897window provides a place for you to enter whatever text commentary you wish. Each
     2898time you enter this window, a date/time entry is provided for you. A possibly
     2899useful technique is to select a portion of the <span class=SpellE>project.lst</span>
    28932900file after a refinement completes (it will contain refinement results with
    28942901residuals, new values &amp; <span class=SpellE>esds</span>) and paste it into
     
    29322939style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    29332940style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    2934 style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for convergence;
    2935 the refinement will stop when the change in the minimization function is less
    2936 than this value. Set Min delta-M/M = 1.0 to force just a single cycle to be
    2937 performed. A value less than 10<sup>-4</sup> (the default) generally gives no
    2938 better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
     2941style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for
     2942convergence; the refinement will stop when the change in the minimization
     2943function is less than this value. Set Min delta-M/M = 1.0 to force just a
     2944single cycle to be performed. A value less than 10<sup>-4</sup> (the default)
     2945generally gives no better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
    29392946
    29402947<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span
     
    30343041will cancel the operation. The equivalenced parameters will show as an equation
    30353042of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
    3036 M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword
    3037 ‘EQUIV’ marks it as <span class=GramE>an equivalence</span>. A Delete button
    3038 can be used to remove it.<o:p></o:p></span></p>
     3043M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword ‘EQUIV’
     3044marks it as <span class=GramE>an equivalence</span>. A Delete button can be
     3045used to remove it.<o:p></o:p></span></p>
    30393046
    30403047<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    31103117style='mso-fareast-font-family:"Times New Roman"'>You can examine the table of
    31113118restraints and change individual values; grayed out regions cannot be changed.
    3112 The ‘<span class=SpellE>calc</span>’ values are determined from the atom
    3113 positions in your structure, ‘<span class=SpellE>obs</span>’ values are the
    3114 target values for the restraint and ‘<span class=SpellE>esd</span>’ is the
    3115 uncertainty used to weight the restraint in the refinement (multiplied by the
    3116 weight factor).<o:p></o:p></span></p>
     3119The ‘<span class=SpellE>calc</span>’ values are determined from the atom positions
     3120in your structure, ‘<span class=SpellE>obs</span>’ values are the target values
     3121for the restraint and ‘<span class=SpellE>esd</span>’ is the uncertainty used
     3122to weight the restraint in the refinement (multiplied by the weight factor).<o:p></o:p></span></p>
    31173123
    31183124<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span
     
    31813187style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change
    31823188value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – this
    3183 changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a dialog
    3184 box will appear asking for the new value. <o:p></o:p></span></p>
     3189changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a
     3190dialog box will appear asking for the new value. <o:p></o:p></span></p>
    31853191
    31863192<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    33373343style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    33383344normal;mso-bidi-font-weight:bold'> – this will create a text file of selected
    3339 columns with values and corresponding <span class=SpellE>esds</span>. A file dialog
    3340 box will appear; give a suitable file name; you may change directory if
     3345columns with values and corresponding <span class=SpellE>esds</span>. A file
     3346dialog box will appear; give a suitable file name; you may change directory if
    33413347desired.<o:p></o:p></span></h5>
    33423348
     
    33993405<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    34003406window shows the limits in position to be used in any fitting for this powder
    3401 pattern. The ‘original’ values are obtained from the minimum &amp; maximum
    3402 values in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p>
     3407pattern. The ‘original’ values are obtained from the minimum &amp; maximum values
     3408in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p>
    34033409
    34043410<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    37833789style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Save</span></span><span
    37843790style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    3785 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves the
    3786 sample parameters to a file with the extension ’.samprm’. A file dialog box
     3791color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves
     3792the sample parameters to a file with the extension ’.samprm’. A file dialog box
    37873793will appear to ask for the file name.<span class=MsoHyperlink><span
    37883794style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
     
    40484054</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    40494055"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’
    4050 – <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak
    4051 positions &amp; intensities from the </span><a href="#Peak_List"><span
    4052 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    4053 none;text-underline:none'>Peak List</span></a><span style='mso-fareast-font-family:
    4054 "Times New Roman"'> to make them available for the indexing routine. The d-obs is
    4055 obtained from Bragg’s Law after applying the Zero correction shown on the </span><a
     4056– <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak positions
     4057&amp; intensities from the </span><a href="#Peak_List"><span style='mso-fareast-font-family:
     4058"Times New Roman";color:windowtext;text-decoration:none;text-underline:none'>Peak
     4059List</span></a><span style='mso-fareast-font-family:"Times New Roman"'> to make
     4060them available for the indexing routine. The d-obs is obtained from Bragg’s Law
     4061after applying the Zero correction shown on the </span><a
    40564062href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman";
    40574063color:windowtext;text-decoration:none;text-underline:none'>Instrument
     
    41724178style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    41734179</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    4174 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell Index/Refine’
    4175 </b>– <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    4176 none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     4180"Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell
     4181Index/Refine’ </b>– <span class=MsoHyperlink><span style='color:windowtext;
     4182text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    41774183
    41784184<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     
    43354341style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    43364342style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
    4337 the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – select
    4338 between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
     4343the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
     4344select between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
    43394345
    43404346<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span
     
    44744480style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
    44754481style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
    4476 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
    4477 procedure; they will be printed on the console and will be shown in the ‘<a
     4482map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this procedure;
     4483they will be printed on the console and will be shown in the ‘<a
    44784484name="Map_peaks"></a><a href="gsasII.html"><span style='mso-bookmark:Map_peaks'><span
    44794485style='color:windowtext;text-decoration:none;text-underline:none'>Map peaks</span></span></a><span
     
    44924498style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
    44934499flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    4494 using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You will
    4495 need to select a source for the reflection set and perhaps select an element
    4496 for normalization by its form factor, a resolution limit (usually 0.5A) and a
    4497 charge flip threshold (usually 0.1); these are found at the bottom of the <b
    4498 style='mso-bidi-font-weight:normal'>General</b> window. A progress bar showing
    4499 the charge flip residual is shown while the charge flip is in operation. When
    4500 the residual is no longer decreasing (be patient – it doesn’t necessarily fall
    4501 continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
     4500using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
     4501will need to select a source for the reflection set and perhaps select an
     4502element for normalization by its form factor, a resolution limit (usually 0.5A)
     4503and a charge flip threshold (usually 0.1); these are found at the bottom of the
     4504<b style='mso-bidi-font-weight:normal'>General</b> window. A progress bar
     4505showing the charge flip residual is shown while the charge flip is in
     4506operation. When the residual is no longer decreasing (be patient – it doesn’t
     4507necessarily fall continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
    45024508button to stop the charge flipping. The resulting map will be positioned to
    45034509properly place symmetry operators (NB: depends on the quality of the resulting
     
    45464552</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    45474553style='mso-fareast-font-family:"Times New Roman"'>Phase type – </span></b><span
    4548 style='mso-fareast-font-family:"Times New Roman"'>this can only be set when
    4549 there are no atoms in the Atoms page for this phase. Select it when the phase
    4550 is initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
     4554style='mso-fareast-font-family:"Times New Roman"'>this can only be set when there
     4555are no atoms in the Atoms page for this phase. Select it when the phase is
     4556initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    45514557
    45524558<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    47734779</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    47744780style='mso-fareast-font-family:"Times New Roman"'>Reflection set from</span></b><span
    4775 style='mso-fareast-font-family:"Times New Roman"'> – This is the source of structure
    4776 factors to be used in a charge flip calculation. These may be either a single
    4777 crystal data set, or structure factors extracted from a powder pattern via a
    4778 Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
     4781style='mso-fareast-font-family:"Times New Roman"'> – This is the source of
     4782structure factors to be used in a charge flip calculation. These may be either
     4783a single crystal data set, or structure factors extracted from a powder pattern
     4784via a Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
    47794785style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    47804786
     
    47864792</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    47874793style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span
    4788 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor
    4789 chosen to normalize the structure factors before charge flipping. <b
     4794style='mso-fareast-font-family:"Times New Roman"'>– This is an element form
     4795factor chosen to normalize the structure factors before charge flipping. <b
    47904796style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
    47914797the lower right of the Periodic Table display shown when this is selected.<span
     
    48294835style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
    48304836style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4831 style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated Annealing
    4832 controls are at the bottom of the window. (Future capability &amp; under
    4833 development).<o:p></o:p></span></p>
     4837style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated
     4838Annealing controls are at the bottom of the window. (Future capability &amp;
     4839under development).<o:p></o:p></span></p>
    48344840
    48354841<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    48404846set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    48414847This is the source of structure factors to be used in a charge flip
    4842 calculation. These may be either a single crystal data set, or structure factors
    4843 extracted from a powder pattern via a Pawley refinement or a Rietveld
     4848calculation. These may be either a single crystal data set, or structure
     4849factors extracted from a powder pattern via a Pawley refinement or a Rietveld
    48444850refinement.<o:p></o:p></span></p>
    48454851
     
    49104916text-underline:none'><o:p></o:p></span></span></h4>
    49114917
    4912 <p class=MsoNormal>This is the table of parameters for the atoms in this
    4913 crystal structure model. The menu controls allow manipulation of the values,
    4914 refinement flags as well as initiate calculations of geometrical values
    4915 (distances &amp; angles) among the atoms.</p>
     4918<p class=MsoNormal>This is the table of parameters for the atoms in this crystal
     4919structure model. The menu controls allow manipulation of the values, refinement
     4920flags as well as initiate calculations of geometrical values (distances &amp;
     4921angles) among the atoms.</p>
    49164922
    49174923<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
     
    49604966</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    49614967style='mso-fareast-font-family:"Times New Roman"'>Ctrl LMB</span></b><span
    4962 style='mso-fareast-font-family:"Times New Roman"'> – on a row number
    4963 selects/deselects the atom.<span class=MsoHyperlink><span style='color:windowtext;
    4964 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     4968style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects/deselects
     4969the atom.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     4970none;text-underline:none'><o:p></o:p></span></span></span></p>
    49654971
    49664972<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    49854991style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    49864992</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double
    4987 left click a Type column heading</b>: a dialog box is shown that allows you to select
    4988 all atoms with that type. <span class=MsoHyperlink><span style='mso-fareast-font-family:
    4989 "Times New Roman";color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
     4993left click a Type column heading</b>: a dialog box is shown that allows you to
     4994select all atoms with that type. <span class=MsoHyperlink><span
     4995style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
     4996none;text-underline:none'><o:p></o:p></span></span></p>
    49904997
    49914998<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo21'><![if !supportLists]><span
     
    51605167be applied to the parameter for all selected atoms. <span class=SpellE><b
    51615168style='mso-bidi-font-weight:normal'>Uiso</b></span> and <span class=SpellE><b
    5162 style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new
    5163 value to be used for all selected atoms. </p>
     5169style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new value
     5170to be used for all selected atoms. </p>
    51645171
    51655172<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    51905197style='mso-bidi-font-weight:normal'>Distances &amp; Angles – </b>compute
    51915198distances and angles with esds (if possible) for selected atoms. A popup dialog
    5192 box will appear with distance angle controls. NB: if atoms have been added or
    5193 their type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
     5199box will appear with distance angle controls. NB: if atoms have been added or their
     5200type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
    51945201of this dialog box before proceeding.</p>
    51955202
     
    52045211
    52055212<p class=MsoNormal>This gives a list of the atoms and bonds that are to be
    5206 rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks,
    5207 ellipsoids &amp; sticks or polyhedra. There are two menus for this tab; Edit
    5208 allows modification of the list of atoms to be rendered and Compute gives some
    5209 options for geometric characterization of selected atoms.</p>
     5213rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks, ellipsoids
     5214&amp; sticks or polyhedra. There are two menus for this tab; Edit allows
     5215modification of the list of atoms to be rendered and Compute gives some options
     5216for geometric characterization of selected atoms.</p>
    52105217
    52115218<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
     
    52365243the selection list. <b style='mso-bidi-font-weight:normal'>NB</b>: beware of
    52375244atoms that are hiding behind the one you are trying to select, they may be
    5238 selected inadvertently. You can rotate the structure anytime during the selection
    5239 process.</p>
     5245selected inadvertently. You can rotate the structure anytime during the
     5246selection process.</p>
    52405247
    52415248<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span
     
    53275334style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
    53285335style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5329 style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms
    5330 currently in the draw atom table, find all atoms that belong in the
    5331 coordination sphere around the selected atoms via unit cell translations. NB:
    5332 symmetry operations are not used in this search.</p>
     5336style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms currently
     5337in the draw atom table, find all atoms that belong in the coordination sphere
     5338around the selected atoms via unit cell translations. NB: symmetry operations
     5339are not used in this search.</p>
    53335340
    53345341<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    53835390style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    53845391style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5385 style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are
    5386 selected, a best plane is determined for them. The result is shown on the
    5387 console window; it may be cut &amp; pasted to another application (e.g. Microsoft
    5388 Word). Shown are the atom coordinates transformed to Cartesian best plane
    5389 coordinates where the largest range is over the X-axis and the smallest is over
    5390 the Z-axis with the origin at the unweighted center of the selection. Root mean
    5391 square displacements along each axis for the best plane are also listed. The
    5392 Z-axis RMS value indicates the flatness of the proposed plane. <b
    5393 style='mso-bidi-font-weight:normal'>NB</b>: if you select (e.g. all) atoms then
    5394 Best plane will give Cartesian coordinates for these atoms with respect to a
    5395 coordinate system where the X-axis is along the longest axis of the atom
    5396 grouping and the Z-axis is along the shortest distance. The origin is at the
    5397 unweighted center of the selected atoms.</p>
     5392style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are selected,
     5393a best plane is determined for them. The result is shown on the console window;
     5394it may be cut &amp; pasted to another application (e.g. Microsoft Word). Shown
     5395are the atom coordinates transformed to Cartesian best plane coordinates where
     5396the largest range is over the X-axis and the smallest is over the Z-axis with
     5397the origin at the unweighted center of the selection. Root mean square
     5398displacements along each axis for the best plane are also listed. The Z-axis
     5399RMS value indicates the flatness of the proposed plane. <b style='mso-bidi-font-weight:
     5400normal'>NB</b>: if you select (e.g. all) atoms then Best plane will give
     5401Cartesian coordinates for these atoms with respect to a coordinate system where
     5402the X-axis is along the longest axis of the atom grouping and the Z-axis is
     5403along the shortest distance. The origin is at the unweighted center of the
     5404selected atoms.</p>
    53985405
    53995406<h4>RB Models</h4>
     
    55965603style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    55975604"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5598 </span></span></span><![endif]>You can change the refine flags either by clicking
    5599 on the box or by selecting one and then selecting the column (a single click on
    5600 the column heading). Then type ‘y’ to set the refine flags or ‘n’ to clear the
    5601 flags. You should deselect those reflections that fall below the lower limit or
    5602 above the upper limit of the powder pattern otherwise you may have a singular
    5603 matrix error in your Pawley refinement.</span></p>
     5605</span></span></span><![endif]>You can change the refine flags either by
     5606clicking on the box or by selecting one and then selecting the column (a single
     5607click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
     5608clear the flags. You should deselect those reflections that fall below the
     5609lower limit or above the upper limit of the powder pattern otherwise you may
     5610have a singular matrix error in your Pawley refinement.</span></p>
    56045611
    56055612<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo25'><span
     
    56575664
    56585665<p class=MsoNormal align=center style='text-align:center'><span
     5666style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     5667
     5668<p class=MsoNormal align=center style='text-align:center'><span
    56595669style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='color:windowtext;
    56605670text-decoration:none;text-underline:none'><o:p>&nbsp;</o:p></span></span></span></p>
     
    56735683
    56745684</span></span></a></div>
     5685
     5686<p class=MsoNormal align=center style='text-align:center'><span
     5687style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    56755688
    56765689<p class=MsoNormal align=center style='text-align:center'><span
     
    60226035style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>:
    60236036contour off/on</span></b></span><span style='mso-bookmark:Pawley'><span
    6024 style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring
    6025 and returns to a waterfall plot with any offsets applied.<span
    6026 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6027 text-underline:none'><o:p></o:p></span></span></span></span></p>
     6037style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring and
     6038returns to a waterfall plot with any offsets applied.<span class=MsoHyperlink><span
     6039style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60286040
    60296041<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo28'><span
     
    60616073<p class=MsoNormal><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
    60626074"Times New Roman"'>The variance-covariance matrix as a color coded array is
    6063 shown on this page. The color bar to the right shows the range of covariances (-1
    6064 to 1) and corresponding colors. The parameter names are to the right and the
    6065 parameter numbers are below the plot.<span class=MsoHyperlink><span
     6075shown on this page. The color bar to the right shows the range of covariances
     6076(-1 to 1) and corresponding colors. The parameter names are to the right and
     6077the parameter numbers are below the plot.<span class=MsoHyperlink><span
    60666078style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60676079
     
    60756087</span></span></span><![endif]>Move the mouse cursor across the plot. If on a
    60766088diagonal cell, the parameter name, value and esd is shown both as a tool tip
    6077 and in the right hand portion of the status bar. If the cursor is off the
    6078 diagonal, the two parameter names and their covariance are shown in the tool
    6079 tip and the status bar.</span></p>
     6089and in the right hand portion of the status bar. If the cursor is off the diagonal,
     6090the two parameter names and their covariance are shown in the tool tip and the
     6091status bar.</span></p>
    60806092
    60816093<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo29'><span
     
    61386150style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span></span><span
    61396151style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:"Times New Roman"'>/d)
    6140 from the Gaussian and Lorentzian parts of the profile function. The computed
    6141 curves are based on the values of U, V, W, X and Y shown in the Instrument
    6142 Parameters window in parentheses. These are the values for the instrument
    6143 contribution that were set when the powder pattern was first read in to
    6144 GSAS-II. If individual peak fitting has been performed, the values of ‘sig’
    6145 &amp; ‘gam’ for the peaks are plotted as ‘+’; these are computed from the
    6146 fitted values of U, V, W, X and Y as well as any sig or gam individually
    6147 refined.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    6148 none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     6152from the Gaussian and Lorentzian parts of the profile function. The computed curves
     6153are based on the values of U, V, W, X and Y shown in the Instrument Parameters
     6154window in parentheses. These are the values for the instrument contribution
     6155that were set when the powder pattern was first read in to GSAS-II. If
     6156individual peak fitting has been performed, the values of ‘sig’ &amp; ‘gam’ for
     6157the peaks are plotted as ‘+’; these are computed from the fitted values of U,
     6158V, W, X and Y as well as any sig or gam individually refined.<span
     6159class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     6160text-underline:none'><o:p></o:p></span></span></span></span></p>
    61496161
    61506162<h4><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
     
    62996311style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    63006312
     6313<p class=MsoNormal align=center style='text-align:center'><span
     6314style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     6315
    63016316<p class=MsoNormal><span style='mso-bookmark:Pawley'><!-- hhmts start --></span><a
    63026317href="gsasII.html"><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
Note: See TracChangeset for help on using the changeset viewer.