Changeset 457


Ignore:
Timestamp:
Jan 25, 2012 9:24:20 AM (10 years ago)
Author:
vondreele
Message:

begin distance angle calcs
move gpxfile routines from GSASIIstruct.py to GSASIIIO.py
move getVCov & ValEsd? to GSASIImath.py
add some text to help/gsasII.html

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIIO.py

    r450 r457  
    2121import GSASIIpwdGUI as G2pdG
    2222import GSASIIElem as G2el
     23import os
    2324import os.path as ospath
    2425
     
    851852            wx.EndBusyCursor()
    852853        print 'project save successful'
     854
     855def GetControls(GPXfile):
     856    ''' Returns dictionary of control items found in GSASII gpx file
     857    input:
     858        GPXfile = .gpx full file name
     859    return:
     860        Controls = dictionary of control items
     861    '''
     862    Controls = {'deriv type':'analytical','min dM/M':0.0001,'shift factor':1.}
     863    file = open(GPXfile,'rb')
     864    while True:
     865        try:
     866            data = cPickle.load(file)
     867        except EOFError:
     868            break
     869        datum = data[0]
     870        if datum[0] == 'Controls':
     871            Controls.update(datum[1])
     872    file.close()
     873    return Controls
     874   
     875def GetConstraints(GPXfile):
     876    constList = []
     877    file = open(GPXfile,'rb')
     878    while True:
     879        try:
     880            data = cPickle.load(file)
     881        except EOFError:
     882            break
     883        datum = data[0]
     884        if datum[0] == 'Constraints':
     885            constDict = datum[1]
     886            for item in constDict:
     887                constList += constDict[item]
     888    file.close()
     889    constDict = []
     890    constFlag = []
     891    fixedList = []
     892    for item in constList:
     893        if item[-2]:
     894            fixedList.append(str(item[-2]))
     895        else:
     896            fixedList.append('0')
     897        if item[-1]:
     898            constFlag.append(['VARY'])
     899        else:
     900            constFlag.append([])
     901        itemDict = {}
     902        for term in item[:-2]:
     903            itemDict[term[1]] = term[0]
     904        constDict.append(itemDict)
     905    return constDict,constFlag,fixedList
     906   
     907def GetPhaseNames(GPXfile):
     908    ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
     909    input:
     910        GPXfile = gpx full file name
     911    return:
     912        PhaseNames = list of phase names
     913    '''
     914    file = open(GPXfile,'rb')
     915    PhaseNames = []
     916    while True:
     917        try:
     918            data = cPickle.load(file)
     919        except EOFError:
     920            break
     921        datum = data[0]
     922        if 'Phases' == datum[0]:
     923            for datus in data[1:]:
     924                PhaseNames.append(datus[0])
     925    file.close()
     926    return PhaseNames
     927
     928def GetAllPhaseData(GPXfile,PhaseName):
     929    ''' Returns the entire dictionary for PhaseName from GSASII gpx file
     930    input:
     931        GPXfile = gpx full file name
     932        PhaseName = phase name
     933    return:
     934        phase dictionary
     935    '''       
     936    file = open(GPXfile,'rb')
     937    General = {}
     938    Atoms = []
     939    while True:
     940        try:
     941            data = cPickle.load(file)
     942        except EOFError:
     943            break
     944        datum = data[0]
     945        if 'Phases' == datum[0]:
     946            for datus in data[1:]:
     947                if datus[0] == PhaseName:
     948                    break
     949    file.close()
     950    return datus[1]
     951   
     952def GetHistograms(GPXfile,hNames):
     953    """ Returns a dictionary of histograms found in GSASII gpx file
     954    input:
     955        GPXfile = .gpx full file name
     956        hNames = list of histogram names
     957    return:
     958        Histograms = dictionary of histograms (types = PWDR & HKLF)
     959    """
     960    file = open(GPXfile,'rb')
     961    Histograms = {}
     962    while True:
     963        try:
     964            data = cPickle.load(file)
     965        except EOFError:
     966            break
     967        datum = data[0]
     968        hist = datum[0]
     969        if hist in hNames:
     970            if 'PWDR' in hist[:4]:
     971                PWDRdata = {}
     972                PWDRdata['Data'] = datum[1][1]          #powder data arrays
     973                PWDRdata[data[2][0]] = data[2][1]       #Limits
     974                PWDRdata[data[3][0]] = data[3][1]       #Background
     975                PWDRdata[data[4][0]] = data[4][1]       #Instrument parameters
     976                PWDRdata[data[5][0]] = data[5][1]       #Sample parameters
     977                try:
     978                    PWDRdata[data[9][0]] = data[9][1]       #Reflection lists might be missing
     979                except IndexError:
     980                    PWDRdata['Reflection lists'] = {}
     981   
     982                Histograms[hist] = PWDRdata
     983            elif 'HKLF' in hist[:4]:
     984                HKLFdata = []
     985                datum = data[0]
     986                HKLFdata = datum[1:][0]
     987                Histograms[hist] = HKLFdata           
     988    file.close()
     989    return Histograms
     990   
     991def GetHistogramNames(GPXfile,hType):
     992    """ Returns a list of histogram names found in GSASII gpx file
     993    input:
     994        GPXfile = .gpx full file name
     995        hType = list ['PWDR','HKLF']
     996    return:
     997        HistogramNames = list of histogram names (types = PWDR & HKLF)
     998    """
     999    file = open(GPXfile,'rb')
     1000    HistogramNames = []
     1001    while True:
     1002        try:
     1003            data = cPickle.load(file)
     1004        except EOFError:
     1005            break
     1006        datum = data[0]
     1007        if datum[0][:4] in hType:
     1008            HistogramNames.append(datum[0])
     1009    file.close()
     1010    return HistogramNames
     1011   
     1012def GetUsedHistogramsAndPhases(GPXfile):
     1013    ''' Returns all histograms that are found in any phase
     1014    and any phase that uses a histogram
     1015    input:
     1016        GPXfile = .gpx full file name
     1017    return:
     1018        Histograms = dictionary of histograms as {name:data,...}
     1019        Phases = dictionary of phases that use histograms
     1020    '''
     1021    phaseNames = GetPhaseNames(GPXfile)
     1022    histoList = GetHistogramNames(GPXfile,['PWDR','HKLF'])
     1023    allHistograms = GetHistograms(GPXfile,histoList)
     1024    phaseData = {}
     1025    for name in phaseNames:
     1026        phaseData[name] =  GetAllPhaseData(GPXfile,name)
     1027    Histograms = {}
     1028    Phases = {}
     1029    for phase in phaseData:
     1030        Phase = phaseData[phase]
     1031        if Phase['Histograms']:
     1032            if phase not in Phases:
     1033                pId = phaseNames.index(phase)
     1034                Phase['pId'] = pId
     1035                Phases[phase] = Phase
     1036            for hist in Phase['Histograms']:
     1037                if hist not in Histograms:
     1038                    Histograms[hist] = allHistograms[hist]
     1039                    #future restraint, etc. histograms here           
     1040                    hId = histoList.index(hist)
     1041                    Histograms[hist]['hId'] = hId
     1042    return Histograms,Phases
     1043   
     1044def GPXBackup(GPXfile,makeBack=True):
     1045    import distutils.file_util as dfu
     1046    GPXpath,GPXname = ospath.split(GPXfile)
     1047    if GPXpath == '': GPXpath = '.'
     1048    Name = ospath.splitext(GPXname)[0]
     1049    files = os.listdir(GPXpath)
     1050    last = 0
     1051    for name in files:
     1052        name = name.split('.')
     1053        if len(name) == 3 and name[0] == Name and 'bak' in name[1]:
     1054            if makeBack:
     1055                last = max(last,int(name[1].strip('bak'))+1)
     1056            else:
     1057                last = max(last,int(name[1].strip('bak')))
     1058    GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx')
     1059    dfu.copy_file(GPXfile,GPXback)
     1060    return GPXback
    8531061       
     1062def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,CovData,makeBack=True):
     1063    ''' Updates gpxfile from all histograms that are found in any phase
     1064    and any phase that used a histogram
     1065    input:
     1066        GPXfile = .gpx full file name
     1067        Histograms = dictionary of histograms as {name:data,...}
     1068        Phases = dictionary of phases that use histograms
     1069        CovData = dictionary of refined variables, varyList, & covariance matrix
     1070        makeBack = True if new backup of .gpx file is to be made; else use the last one made
     1071    '''
     1072                       
     1073    GPXback = GPXBackup(GPXfile,makeBack)
     1074    print '\n',135*'-'
     1075    print 'Read from file:',GPXback
     1076    print 'Save to file  :',GPXfile
     1077    infile = open(GPXback,'rb')
     1078    outfile = open(GPXfile,'wb')
     1079    while True:
     1080        try:
     1081            data = cPickle.load(infile)
     1082        except EOFError:
     1083            break
     1084        datum = data[0]
     1085#        print 'read: ',datum[0]
     1086        if datum[0] == 'Phases':
     1087            for iphase in range(len(data)):
     1088                if data[iphase][0] in Phases:
     1089                    phaseName = data[iphase][0]
     1090                    data[iphase][1].update(Phases[phaseName])
     1091        elif datum[0] == 'Covariance':
     1092            data[0][1] = CovData
     1093        try:
     1094            histogram = Histograms[datum[0]]
     1095#            print 'found ',datum[0]
     1096            data[0][1][1] = histogram['Data']
     1097            for datus in data[1:]:
     1098#                print '    read: ',datus[0]
     1099                if datus[0] in ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']:
     1100                    datus[1] = histogram[datus[0]]
     1101        except KeyError:
     1102            pass
     1103                               
     1104        cPickle.dump(data,outfile,1)
     1105    infile.close()
     1106    outfile.close()
     1107    print 'GPX file save successful'
     1108   
     1109def SetSeqResult(GPXfile,Histograms,SeqResult):
     1110    GPXback = GPXBackup(GPXfile)
     1111    print '\n',135*'-'
     1112    print 'Read from file:',GPXback
     1113    print 'Save to file  :',GPXfile
     1114    infile = open(GPXback,'rb')
     1115    outfile = open(GPXfile,'wb')
     1116    while True:
     1117        try:
     1118            data = cPickle.load(infile)
     1119        except EOFError:
     1120            break
     1121        datum = data[0]
     1122        if datum[0] == 'Sequental results':
     1123            data[0][1] = SeqResult
     1124        try:
     1125            histogram = Histograms[datum[0]]
     1126            data[0][1][1] = histogram['Data']
     1127            for datus in data[1:]:
     1128                if datus[0] in ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']:
     1129                    datus[1] = histogram[datus[0]]
     1130        except KeyError:
     1131            pass
     1132                               
     1133        cPickle.dump(data,outfile,1)
     1134    infile.close()
     1135    outfile.close()
     1136    print 'GPX file save successful'
     1137   
     1138                   
     1139def GetPWDRdata(GPXfile,PWDRname):
     1140    ''' Returns powder data from GSASII gpx file
     1141    input:
     1142        GPXfile = .gpx full file name
     1143        PWDRname = powder histogram name as obtained from GetHistogramNames
     1144    return:
     1145        PWDRdata = powder data dictionary with:
     1146            Data - powder data arrays, Limits, Instrument Parameters, Sample Parameters
     1147       
     1148    '''
     1149    file = open(GPXfile,'rb')
     1150    PWDRdata = {}
     1151    while True:
     1152        try:
     1153            data = cPickle.load(file)
     1154        except EOFError:
     1155            break
     1156        datum = data[0]
     1157        if datum[0] == PWDRname:
     1158            PWDRdata['Data'] = datum[1][1]          #powder data arrays
     1159            PWDRdata[data[2][0]] = data[2][1]       #Limits
     1160            PWDRdata[data[3][0]] = data[3][1]       #Background
     1161            PWDRdata[data[4][0]] = data[4][1]       #Instrument parameters
     1162            PWDRdata[data[5][0]] = data[5][1]       #Sample parameters
     1163            try:
     1164                PWDRdata[data[9][0]] = data[9][1]       #Reflection lists might be missing
     1165            except IndexError:
     1166                PWDRdata['Reflection lists'] = {}
     1167    file.close()
     1168    return PWDRdata
     1169   
     1170def GetHKLFdata(GPXfile,HKLFname):
     1171    ''' Returns single crystal data from GSASII gpx file
     1172    input:
     1173        GPXfile = .gpx full file name
     1174        HKLFname = single crystal histogram name as obtained from GetHistogramNames
     1175    return:
     1176        HKLFdata = single crystal data list of reflections: for each reflection:
     1177            HKLF = [np.array([h,k,l]),FoSq,sigFoSq,FcSq,Fcp,Fcpp,phase]
     1178    '''
     1179    file = open(GPXfile,'rb')
     1180    HKLFdata = []
     1181    while True:
     1182        try:
     1183            data = cPickle.load(file)
     1184        except EOFError:
     1185            break
     1186        datum = data[0]
     1187        if datum[0] == HKLFname:
     1188            HKLFdata = datum[1:][0]
     1189    file.close()
     1190    return HKLFdata
     1191   
    8541192def SaveIntegration(self,PickId,data):
    8551193    azms = self.Integrate[1]
     
    13431681    return Phase
    13441682
    1345 def ValEsd(value,esd=0,nTZ=False):                  #NOT complete - don't use
    1346     # returns value(esd) string; nTZ=True for no trailing zeros
    1347     # use esd < 0 for level of precision shown e.g. esd=-0.01 gives 2 places beyond decimal
    1348     #get the 2 significant digits in the esd
    1349     edig = lambda esd: int(round(10**(math.log10(esd) % 1+1)))
    1350     #get the number of digits to represent them
    1351     epl = lambda esd: 2+int(1.545-math.log10(10*edig(esd)))
    1352    
    1353     mdec = lambda esd: -int(math.log10(abs(esd)))
    1354     ndec = lambda esd: int(1.545-math.log10(abs(esd)))
    1355     if esd > 0:
    1356         fmt = '"%.'+str(ndec(esd))+'f(%d)"'
    1357         print fmt,ndec(esd),esd*10**(mdec(esd)+1)
    1358         return fmt%(value,int(esd*10**(mdec(esd)+1)))
    1359     elif esd < 0:
    1360          return str(round(value,mdec(esd)))
    1361     else:
    1362         text = "%F"%(value)
    1363         if nTZ:
    1364             return text.rstrip('0')
    1365         else:
    1366             return text
    1367 
    1368 def Fesd(value,esd=0,nTZ=False):
    1369 #pythonized version of fortran routine in GSAS cifsubs directory - doesn't work correctly
    1370     nint = lambda x: int(round(x))
    1371     iExp = 0
    1372     if value == 0. and esd == 0.:
    1373         iDec = 1
    1374         iFld = 5
    1375     elif value == 0.:
    1376         iDec = max(0.,1.545-math.log10(abs(esd)))
    1377         iFld = 4+iDec
    1378     elif esd == 0.:
    1379         iDec = 5
    1380         iFld = max(1.,math.log10(abs(value)))+3+iDec
    1381     else:
    1382         iFld = math.log10(max(abs(esd),abs(value)))
    1383         if iFld < -4:
    1384             iExp = 1-iFld
    1385             iFld -= iExp
    1386         elif iFld > 8:
    1387             iExp = -iFld
    1388             iFld += iExp
    1389         if iExp:
    1390             value *= 10.**iExp
    1391             esd *= 10.**iExp
    1392         iDec = min(7,int(max(0.,1.545-math.log10(max(0.000001*abs(value),abs(esd))))))
    1393         iFld = max(1,iFld)+3+iDec
    1394     if esd <= 0.:
    1395         iSigw = 0
    1396     else:
    1397         iSig = nint(esd*(10.**iDec))
    1398         iSigw = 1
    1399         if iSig > 0:
    1400             iSigw = int(1.+math.log10(1.*iSig))
    1401     if iSigw > 2:
    1402         xmult = 10.**(iSigw-2)
    1403         value = xmult*nint(value/xmult)
    1404         iSig = xmult*nint(iSig/xmult)           
    1405         iSigw = int(1.+math.log10(1.*iSig))
    1406     if iSigw == 0:
    1407         fmt = '%.'+str(iDec)+'f'
    1408         string = fmt%(value)
    1409     elif iDec > 0:
    1410         fmt = '%.'+str(iDec)+'f(%d)'
    1411         string = fmt%(value,iSig)
    1412     else:
    1413         fmt = '%'+str(iFld)+'d(%d)'
    1414         string = fmt%(nint(value),iSig)
    1415     if iExp:
    1416         iDig = 1+math.log10(abs(1.*iExp))
    1417         if iExp > 0:
    1418             iDig += 1
    1419             string += str(-iExp)
    1420     return string
    1421    
    1422 
  • trunk/GSASIIgrid.py

    r453 r457  
    726726    'mapType':'Fobs','d-max':100.,'d-min':0.2,'histograms':[],
    727727    'stepSize':[0.5,0.5,0.5],'minX':[0.,0.,0.],'maxX':[1.0,1.0,1.0],
    728     #distance/angle controls
    729     'distMax':0.0,'angleMax':0.0,'useMapPeaks':False}
    730728    '''
    731729    def SeqSizer():
     
    842840    mainSizer.Add(wx.StaticText(self.dataDisplay,label=' Density Map Controls:'),0,wx.ALIGN_CENTER_VERTICAL)
    843841
    844     mainSizer.Add((5,5),0)
    845     mainSizer.Add(wx.StaticText(self.dataDisplay,label=' Distance/angle Controls:'),0,wx.ALIGN_CENTER_VERTICAL)
    846        
    847842    mainSizer.Layout()   
    848843    self.dataDisplay.SetSizer(mainSizer)
  • trunk/GSASIImath.py

    r453 r457  
    133133        return [x0,None,{'num cyc':icycle,'fvec':M,'nfev':nfev,'lamMax':lamMax,'psing':psing}]
    134134   
     135def getVCov(varyNames,varyList,covMatrix):
     136    vcov = np.zeros((len(varyNames),len(varyNames)))
     137    for i1,name1 in enumerate(varyNames):
     138        for i2,name2 in enumerate(varyNames):
     139            try:
     140                vcov[i1][i2] = covMatrix[varyList.index(name1)][varyList.index(name2)]
     141            except ValueError:
     142                vcov[i1][i2] = 0.0
     143    return vcov
     144   
     145def ValEsd(value,esd=0,nTZ=False):                  #NOT complete - don't use
     146    # returns value(esd) string; nTZ=True for no trailing zeros
     147    # use esd < 0 for level of precision shown e.g. esd=-0.01 gives 2 places beyond decimal
     148    #get the 2 significant digits in the esd
     149    edig = lambda esd: int(round(10**(math.log10(esd) % 1+1)))
     150    #get the number of digits to represent them
     151    epl = lambda esd: 2+int(1.545-math.log10(10*edig(esd)))
     152   
     153    mdec = lambda esd: -int(round(math.log10(abs(esd))))+1
     154    ndec = lambda esd: int(1.545-math.log10(abs(esd)))
     155    if esd > 0:
     156        fmt = '"%.'+str(ndec(esd))+'f(%d)"'
     157        return str(fmt%(value,int(round(esd*10**(mdec(esd)))))).strip('"')
     158    elif esd < 0:
     159         return str(round(value,mdec(esd)))
     160    else:
     161        text = str("%f"%(value))
     162        if nTZ:
     163            return text.rstrip('0')
     164        else:
     165            return text
     166
     167   
  • trunk/GSASIIphsGUI.py

    r445 r457  
    2323import GSASIIgrid as G2gd
    2424import GSASIIIO as G2IO
     25import GSASIIstruct as G2str
    2526import numpy as np
    2627import numpy.linalg as nl
     
    132133        self.Destroy()
    133134
     135class DisAglDialog(wx.Dialog):
     136    def __init__(self,parent,data):
     137        wx.Dialog.__init__(self,parent,-1,'Distance Angle Controls',
     138            pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
     139        self.data = data
     140        panel = wx.Panel(self)
     141        mainSizer = wx.BoxSizer(wx.VERTICAL)
     142        mainSizer.Add(wx.StaticText(panel,-1,'Controls for phase '+data['Name']),
     143            0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10)
     144        mainSizer.Add((10,10),1)
     145       
     146        radiiSizer = wx.FlexGridSizer(2,3,5,5)
     147        radiiSizer.Add(wx.StaticText(panel,-1,' Type'),0,wx.ALIGN_CENTER_VERTICAL)
     148        radiiSizer.Add(wx.StaticText(panel,-1,'Bond radii'),0,wx.ALIGN_CENTER_VERTICAL)
     149        radiiSizer.Add(wx.StaticText(panel,-1,'Angle radii'),0,wx.ALIGN_CENTER_VERTICAL)
     150        self.objList = {}
     151        for id,item in enumerate(self.data['AtomTypes']):
     152            radiiSizer.Add(wx.StaticText(panel,-1,' '+item),0,wx.ALIGN_CENTER_VERTICAL)
     153            bRadii = wx.TextCtrl(panel,-1,value='%.3f'%(data['BondRadii'][id]),style=wx.TE_PROCESS_ENTER)
     154            self.objList[bRadii.GetId()] = ['BondRadii',id]
     155            bRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
     156            bRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
     157            radiiSizer.Add(bRadii,0,wx.ALIGN_CENTER_VERTICAL)
     158            aRadii = wx.TextCtrl(panel,-1,value='%.3f'%(data['AngleRadii'][id]),style=wx.TE_PROCESS_ENTER)
     159            self.objList[aRadii.GetId()] = ['AngleRadii',id]
     160            aRadii.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
     161            aRadii.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
     162            radiiSizer.Add(aRadii,0,wx.ALIGN_CENTER_VERTICAL)
     163        mainSizer.Add(radiiSizer,0,wx.EXPAND)
     164        factorSizer = wx.FlexGridSizer(2,2,5,5)
     165        Names = ['Bond','Angle']
     166        for i,name in enumerate(Names):
     167            factorSizer.Add(wx.StaticText(panel,-1,name+' search factor'),0,wx.ALIGN_CENTER_VERTICAL)
     168            bondFact = wx.TextCtrl(panel,-1,value='%.3f'%(data['Factors'][i]),style=wx.TE_PROCESS_ENTER)
     169            self.objList[bondFact.GetId()] = ['Factors',i]
     170            bondFact.Bind(wx.EVT_TEXT_ENTER,self.OnRadiiVal)
     171            bondFact.Bind(wx.EVT_KILL_FOCUS,self.OnRadiiVal)
     172            factorSizer.Add(bondFact)
     173        mainSizer.Add(factorSizer,0,wx.EXPAND)
     174       
     175        OkBtn = wx.Button(panel,-1,"Ok")
     176        OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
     177        btnSizer = wx.BoxSizer(wx.HORIZONTAL)
     178        btnSizer.Add((20,20),1)
     179        btnSizer.Add(OkBtn)
     180        btnSizer.Add((20,20),1)       
     181        mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
     182        panel.SetSizer(mainSizer)
     183        panel.Fit()
     184        self.Fit()
     185   
     186    def OnRadiiVal(self,event):
     187        Obj = event.GetEventObject()
     188        item = self.objList[Obj.GetId()]
     189        try:
     190            self.data[item[0]][item[1]] = float(Obj.GetValue())
     191        except ValueError:
     192            pass
     193        Obj.SetValue("%.3f"%(self.data[item[0]][item[1]]))          #reset in case of error
     194       
     195    def OnOk(self,event):
     196        parent = self.GetParent()
     197        parent.Raise()
     198        self.EndModal(wx.ID_OK)             
     199        self.Destroy()
     200       
    134201def UpdatePhaseData(self,Item,data,oldPage):
    135202
     
    714781                if 'Atoms' in data['Drawing']:
    715782                    DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
    716                     FindBonds()
     783                    FindBondsDraw()
    717784                   
    718785        def AtomTypeSelect(event):
     
    929996        indx = Atoms.GetSelectedRows()
    930997        if indx:
     998            generalData = data['General']
    931999            colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
    9321000            cx = colLabels.index('x')
     
    9711039            else:
    9721040                Atoms.ForceRefresh()
     1041
     1042    def OnDistAngle(event):
     1043        indx = Atoms.GetSelectedRows()
     1044        Oxyz = []
     1045        xyz = []
     1046        DisAglData = {}
     1047        if indx:
     1048            generalData = data['General']
     1049            DisAglData['OrigIndx'] = indx
     1050            DisAglData['Name'] = generalData['Name']
     1051            DisAglData['Factors'] = [0.85,0.85]
     1052            DisAglData['AtomTypes'] = generalData['AtomTypes']
     1053            DisAglData['BondRadii'] = generalData['BondRadii']
     1054            DisAglData['AngleRadii'] = generalData['AngleRadii']
     1055            DisAglDialog(self,DisAglData).ShowModal()
     1056            atomData = data['Atoms']
     1057            colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
     1058            cx = colLabels.index('x')
     1059            cn = colLabels.index('Name')
     1060            for i,atom in enumerate(atomData):
     1061                xyz.append(atom[cn:cn+2]+atom[cx:cx+3])
     1062                if i in indx:
     1063                    Oxyz.append(atom[cn:cn+2]+atom[cx:cx+3])
     1064            DisAglData['OrigAtoms'] = Oxyz
     1065            DisAglData['TargAtoms'] = xyz
     1066            generalData = data['General']
     1067            DisAglData['SGData'] = generalData['SGData']
     1068            DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
     1069            if 'pId' in data:
     1070                DisAglData['pId'] = data['pId']
     1071                DisAglData['covData'] = self.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(self,self.root, 'Covariance'))
     1072            G2str.DistAngle(DisAglData)
    9731073               
    9741074#Structure drawing GUI stuff               
     
    11351235                            atomData[r][c] = parms
    11361236                            drawAtoms.SetCellValue(r,c,parms)
    1137                         FindBonds()
     1237                        FindBondsDraw()
    11381238                        G2plt.PlotStructure(self,data)
    11391239                    dlg.Destroy()
     
    11771277                if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
    11781278                    atomData[r][c] = drawAtoms.GetCellValue(r,c)
    1179                     FindBonds()
     1279                    FindBondsDraw()
    11801280                elif drawAtoms.GetColLabelValue(c) == 'Color':
    11811281                    color = atomData[r][c]
     
    12551355        self.dataFrame.setSizePosLeft([600,300])
    12561356       
    1257         FindBonds()
     1357        FindBondsDraw()
    12581358        drawAtoms.ClearSelection()
    12591359        G2plt.PlotStructure(self,data)
     
    12771377                    drawAtoms.SetCellValue(r,cs,parms)
    12781378            dlg.Destroy()
    1279             FindBonds()
     1379            FindBondsDraw()
    12801380            drawAtoms.ClearSelection()
    12811381            G2plt.PlotStructure(self,data)
     
    15841684                            atomData[j][-1].append(-Dx*atomB[3]/sumR)
    15851685                   
    1586     def FindBonds():                    #uses numpy & masks - very fast even for proteins!
     1686    def FindBondsDraw():                    #uses numpy & masks - very fast even for proteins!
    15871687        import numpy.ma as ma
    15881688        cx,ct,cs = data['Drawing']['atomPtrs']
     
    17511851        def OnShowHyd(event):
    17521852            drawingData['showHydrogen'] = showHydrogen.GetValue()
    1753             FindBonds()
     1853            FindBondsDraw()
    17541854            G2plt.PlotStructure(self,data)
    17551855
     
    17701870            drawingData['radiusFactor'] = value
    17711871            radFactor.SetValue("%.2f"%(value))
    1772             FindBonds()
     1872            FindBondsDraw()
    17731873            G2plt.PlotStructure(self,data)
    17741874
     
    29243024            self.dataFrame.Bind(wx.EVT_MENU, AtomTransform, id=G2gd.wxID_ATOMSTRANSFORM)
    29253025            self.dataFrame.Bind(wx.EVT_MENU, OnReloadDrawAtoms, id=G2gd.wxID_RELOADDRAWATOMS)
     3026            self.dataFrame.Bind(wx.EVT_MENU, OnDistAngle, id=G2gd.wxID_ATOMSDISAGL)
    29263027            FillAtomsGrid()
    29273028        elif text == 'General':
  • trunk/GSASIIstruct.py

    r453 r457  
    88########### SVN repository information ###################
    99import sys
    10 import os
    11 import os.path as ospath
    1210import numpy as np
    1311import numpy.linalg as nl
    14 import cPickle
    1512import time
    1613import math
    1714import GSASIIpath
     15import GSASIIIO as G2IO
    1816import GSASIIElem as G2el
    1917import GSASIIlattice as G2lat
     
    3937    print 80*'*','\n'
    4038
    41 def GetControls(GPXfile):
    42     ''' Returns dictionary of control items found in GSASII gpx file
    43     input:
    44         GPXfile = .gpx full file name
    45     return:
    46         Controls = dictionary of control items
    47     '''
    48     Controls = {'deriv type':'analytical','min dM/M':0.0001,'shift factor':1.}
    49     file = open(GPXfile,'rb')
    50     while True:
    51         try:
    52             data = cPickle.load(file)
    53         except EOFError:
    54             break
    55         datum = data[0]
    56         if datum[0] == 'Controls':
    57             Controls.update(datum[1])
    58     file.close()
    59     return Controls
    60    
    6139def ShowControls(Controls):
    6240    print ' Least squares controls:'
     
    6442    print ' Minimum delta-M/M for convergence: ','%.2g'%(Controls['min dM/M'])
    6543    print ' Initial shift factor: ','%.3f'%(Controls['shift factor'])
    66    
    67 def GetConstraints(GPXfile):
    68     constList = []
    69     file = open(GPXfile,'rb')
    70     while True:
    71         try:
    72             data = cPickle.load(file)
    73         except EOFError:
    74             break
    75         datum = data[0]
    76         if datum[0] == 'Constraints':
    77             constDict = datum[1]
    78             for item in constDict:
    79                 constList += constDict[item]
    80     file.close()
    81     constDict = []
    82     constFlag = []
    83     fixedList = []
    84     for item in constList:
    85         if item[-2]:
    86             fixedList.append(str(item[-2]))
    87         else:
    88             fixedList.append('0')
    89         if item[-1]:
    90             constFlag.append(['VARY'])
    91         else:
    92             constFlag.append([])
    93         itemDict = {}
    94         for term in item[:-2]:
    95             itemDict[term[1]] = term[0]
    96         constDict.append(itemDict)
    97     return constDict,constFlag,fixedList
    98    
    99 def GetPhaseNames(GPXfile):
    100     ''' Returns a list of phase names found under 'Phases' in GSASII gpx file
    101     input:
    102         GPXfile = gpx full file name
    103     return:
    104         PhaseNames = list of phase names
    105     '''
    106     file = open(GPXfile,'rb')
    107     PhaseNames = []
    108     while True:
    109         try:
    110             data = cPickle.load(file)
    111         except EOFError:
    112             break
    113         datum = data[0]
    114         if 'Phases' == datum[0]:
    115             for datus in data[1:]:
    116                 PhaseNames.append(datus[0])
    117     file.close()
    118     return PhaseNames
    119 
    120 def GetAllPhaseData(GPXfile,PhaseName):
    121     ''' Returns the entire dictionary for PhaseName from GSASII gpx file
    122     input:
    123         GPXfile = gpx full file name
    124         PhaseName = phase name
    125     return:
    126         phase dictionary
    127     '''       
    128     file = open(GPXfile,'rb')
    129     General = {}
    130     Atoms = []
    131     while True:
    132         try:
    133             data = cPickle.load(file)
    134         except EOFError:
    135             break
    136         datum = data[0]
    137         if 'Phases' == datum[0]:
    138             for datus in data[1:]:
    139                 if datus[0] == PhaseName:
    140                     break
    141     file.close()
    142     return datus[1]
    143    
    144 def GetHistograms(GPXfile,hNames):
    145     """ Returns a dictionary of histograms found in GSASII gpx file
    146     input:
    147         GPXfile = .gpx full file name
    148         hNames = list of histogram names
    149     return:
    150         Histograms = dictionary of histograms (types = PWDR & HKLF)
    151     """
    152     file = open(GPXfile,'rb')
    153     Histograms = {}
    154     while True:
    155         try:
    156             data = cPickle.load(file)
    157         except EOFError:
    158             break
    159         datum = data[0]
    160         hist = datum[0]
    161         if hist in hNames:
    162             if 'PWDR' in hist[:4]:
    163                 PWDRdata = {}
    164                 PWDRdata['Data'] = datum[1][1]          #powder data arrays
    165                 PWDRdata[data[2][0]] = data[2][1]       #Limits
    166                 PWDRdata[data[3][0]] = data[3][1]       #Background
    167                 PWDRdata[data[4][0]] = data[4][1]       #Instrument parameters
    168                 PWDRdata[data[5][0]] = data[5][1]       #Sample parameters
    169                 try:
    170                     PWDRdata[data[9][0]] = data[9][1]       #Reflection lists might be missing
    171                 except IndexError:
    172                     PWDRdata['Reflection lists'] = {}
    173    
    174                 Histograms[hist] = PWDRdata
    175             elif 'HKLF' in hist[:4]:
    176                 HKLFdata = []
    177                 datum = data[0]
    178                 HKLFdata = datum[1:][0]
    179                 Histograms[hist] = HKLFdata           
    180     file.close()
    181     return Histograms
    182    
    183 def GetHistogramNames(GPXfile,hType):
    184     """ Returns a list of histogram names found in GSASII gpx file
    185     input:
    186         GPXfile = .gpx full file name
    187         hType = list ['PWDR','HKLF']
    188     return:
    189         HistogramNames = list of histogram names (types = PWDR & HKLF)
    190     """
    191     file = open(GPXfile,'rb')
    192     HistogramNames = []
    193     while True:
    194         try:
    195             data = cPickle.load(file)
    196         except EOFError:
    197             break
    198         datum = data[0]
    199         if datum[0][:4] in hType:
    200             HistogramNames.append(datum[0])
    201     file.close()
    202     return HistogramNames
    203    
    204 def GetUsedHistogramsAndPhases(GPXfile):
    205     ''' Returns all histograms that are found in any phase
    206     and any phase that uses a histogram
    207     input:
    208         GPXfile = .gpx full file name
    209     return:
    210         Histograms = dictionary of histograms as {name:data,...}
    211         Phases = dictionary of phases that use histograms
    212     '''
    213     phaseNames = GetPhaseNames(GPXfile)
    214     histoList = GetHistogramNames(GPXfile,['PWDR','HKLF'])
    215     allHistograms = GetHistograms(GPXfile,histoList)
    216     phaseData = {}
    217     for name in phaseNames:
    218         phaseData[name] =  GetAllPhaseData(GPXfile,name)
    219     Histograms = {}
    220     Phases = {}
    221     for phase in phaseData:
    222         Phase = phaseData[phase]
    223         if Phase['Histograms']:
    224             if phase not in Phases:
    225                 pId = phaseNames.index(phase)
    226                 Phase['pId'] = pId
    227                 Phases[phase] = Phase
    228             for hist in Phase['Histograms']:
    229                 if hist not in Histograms:
    230                     Histograms[hist] = allHistograms[hist]
    231                     #future restraint, etc. histograms here           
    232                     hId = histoList.index(hist)
    233                     Histograms[hist]['hId'] = hId
    234     return Histograms,Phases
    235    
    236 def GPXBackup(GPXfile,makeBack=True):
    237     import distutils.file_util as dfu
    238     GPXpath,GPXname = ospath.split(GPXfile)
    239     if GPXpath == '': GPXpath = '.'
    240     Name = ospath.splitext(GPXname)[0]
    241     files = os.listdir(GPXpath)
    242     last = 0
    243     for name in files:
    244         name = name.split('.')
    245         if len(name) == 3 and name[0] == Name and 'bak' in name[1]:
    246             if makeBack:
    247                 last = max(last,int(name[1].strip('bak'))+1)
    248             else:
    249                 last = max(last,int(name[1].strip('bak')))
    250     GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx')
    251     dfu.copy_file(GPXfile,GPXback)
    252     return GPXback
    253        
    254 def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,CovData,makeBack=True):
    255     ''' Updates gpxfile from all histograms that are found in any phase
    256     and any phase that used a histogram
    257     input:
    258         GPXfile = .gpx full file name
    259         Histograms = dictionary of histograms as {name:data,...}
    260         Phases = dictionary of phases that use histograms
    261         CovData = dictionary of refined variables, varyList, & covariance matrix
    262         makeBack = True if new backup of .gpx file is to be made; else use the last one made
    263     '''
    264                        
    265     GPXback = GPXBackup(GPXfile,makeBack)
    266     print '\n',135*'-'
    267     print 'Read from file:',GPXback
    268     print 'Save to file  :',GPXfile
    269     infile = open(GPXback,'rb')
    270     outfile = open(GPXfile,'wb')
    271     while True:
    272         try:
    273             data = cPickle.load(infile)
    274         except EOFError:
    275             break
    276         datum = data[0]
    277 #        print 'read: ',datum[0]
    278         if datum[0] == 'Phases':
    279             for iphase in range(len(data)):
    280                 if data[iphase][0] in Phases:
    281                     phaseName = data[iphase][0]
    282                     data[iphase][1].update(Phases[phaseName])
    283         elif datum[0] == 'Covariance':
    284             data[0][1] = CovData
    285         try:
    286             histogram = Histograms[datum[0]]
    287 #            print 'found ',datum[0]
    288             data[0][1][1] = histogram['Data']
    289             for datus in data[1:]:
    290 #                print '    read: ',datus[0]
    291                 if datus[0] in ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']:
    292                     datus[1] = histogram[datus[0]]
    293         except KeyError:
    294             pass
    295                                
    296         cPickle.dump(data,outfile,1)
    297     infile.close()
    298     outfile.close()
    299     print 'refinement save successful'
    300    
    301 def SetSeqResult(GPXfile,Histograms,SeqResult):
    302     GPXback = GPXBackup(GPXfile)
    303     print '\n',135*'-'
    304     print 'Read from file:',GPXback
    305     print 'Save to file  :',GPXfile
    306     infile = open(GPXback,'rb')
    307     outfile = open(GPXfile,'wb')
    308     while True:
    309         try:
    310             data = cPickle.load(infile)
    311         except EOFError:
    312             break
    313         datum = data[0]
    314         if datum[0] == 'Sequental results':
    315             data[0][1] = SeqResult
    316         try:
    317             histogram = Histograms[datum[0]]
    318             data[0][1][1] = histogram['Data']
    319             for datus in data[1:]:
    320                 if datus[0] in ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']:
    321                     datus[1] = histogram[datus[0]]
    322         except KeyError:
    323             pass
    324                                
    325         cPickle.dump(data,outfile,1)
    326     infile.close()
    327     outfile.close()
    328     print 'refinement save successful'
    329    
    330                    
    331 def GetPWDRdata(GPXfile,PWDRname):
    332     ''' Returns powder data from GSASII gpx file
    333     input:
    334         GPXfile = .gpx full file name
    335         PWDRname = powder histogram name as obtained from GetHistogramNames
    336     return:
    337         PWDRdata = powder data dictionary with:
    338             Data - powder data arrays, Limits, Instrument Parameters, Sample Parameters
    339        
    340     '''
    341     file = open(GPXfile,'rb')
    342     PWDRdata = {}
    343     while True:
    344         try:
    345             data = cPickle.load(file)
    346         except EOFError:
    347             break
    348         datum = data[0]
    349         if datum[0] == PWDRname:
    350             PWDRdata['Data'] = datum[1][1]          #powder data arrays
    351             PWDRdata[data[2][0]] = data[2][1]       #Limits
    352             PWDRdata[data[3][0]] = data[3][1]       #Background
    353             PWDRdata[data[4][0]] = data[4][1]       #Instrument parameters
    354             PWDRdata[data[5][0]] = data[5][1]       #Sample parameters
    355             try:
    356                 PWDRdata[data[9][0]] = data[9][1]       #Reflection lists might be missing
    357             except IndexError:
    358                 PWDRdata['Reflection lists'] = {}
    359     file.close()
    360     return PWDRdata
    361    
    362 def GetHKLFdata(GPXfile,HKLFname):
    363     ''' Returns single crystal data from GSASII gpx file
    364     input:
    365         GPXfile = .gpx full file name
    366         HKLFname = single crystal histogram name as obtained from GetHistogramNames
    367     return:
    368         HKLFdata = single crystal data list of reflections: for each reflection:
    369             HKLF = [np.array([h,k,l]),FoSq,sigFoSq,FcSq,Fcp,Fcpp,phase]
    370     '''
    371     file = open(GPXfile,'rb')
    372     HKLFdata = []
    373     while True:
    374         try:
    375             data = cPickle.load(file)
    376         except EOFError:
    377             break
    378         datum = data[0]
    379         if datum[0] == HKLFname:
    380             HKLFdata = datum[1:][0]
    381     file.close()
    382     return HKLFdata
    38344   
    38445def GetFFtable(General):
     
    465126    elif SGData['SGLaue'] in ['m3m','m3']:
    466127        return [pfx+'A0',]
    467        
    468            
     128                   
    469129def GetPhaseData(PhaseData,Print=True):
    470130           
     
    655315    return Natoms,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables
    656316   
    657 def getVCov(varyNames,varyList,covMatrix):
    658     vcov = np.zeros((len(varyNames),len(varyNames)))
    659     for i1,name1 in enumerate(varyNames):
    660         for i2,name2 in enumerate(varyNames):
    661             try:
    662                 vcov[i1][i2] = covMatrix[varyList.index(name1)][varyList.index(name2)]
    663             except ValueError:
    664                 vcov[i1][i2] = 0.0
    665     return vcov
    666    
    667317def cellFill(pfx,SGData,parmDict,sigDict):
    668318    if SGData['SGLaue'] in ['-1',]:
     
    721371    varyList = covData['varyList']
    722372    covMatrix = covData['covMatrix']
    723     vcov = getVCov(RMnames,varyList,covMatrix)
     373    vcov = G2mth.getVCov(RMnames,varyList,covMatrix)
    724374    Ax = np.array(A)
    725375    Ax[3:] /= 2.
     
    26172267                   
    26182268def Refine(GPXfile,dlg):
    2619     import cPickle
    26202269    import pytexture as ptx
    26212270    ptx.pyqlmninit()            #initialize fortran arrays for spherical harmonics
     
    26262275    calcControls = {}
    26272276    G2mv.InitVars()   
    2628     Controls = GetControls(GPXfile)
     2277    Controls = G2IO.GetControls(GPXfile)
    26292278    ShowControls(Controls)           
    2630     constrDict,constrFlag,fixedList = GetConstraints(GPXfile)
    2631     Histograms,Phases = GetUsedHistogramsAndPhases(GPXfile)
     2279    constrDict,constrFlag,fixedList = G2IO.GetConstraints(GPXfile)
     2280    Histograms,Phases = G2IO.GetUsedHistogramsAndPhases(GPXfile)
    26322281    if not Phases:
    26332282        print ' *** ERROR - you have no histograms to refine! ***'
     
    27412390    SetHistogramData(parmDict,sigDict,Histograms)
    27422391    G2mv.PrintIndependentVars(parmDict,varyList,sigDict)
    2743     SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,covData)
     2392    G2IO.SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,covData)
     2393   
    27442394#for testing purposes!!!
     2395#    import cPickle
    27452396#    file = open('structTestdata.dat','wb')
    27462397#    cPickle.dump(parmDict,file,1)
     
    27542405#    cPickle.dump(pawleyLookup,file,1)
    27552406#    file.close()
     2407
    27562408    if dlg:
    27572409        return Rwp
    27582410
    27592411def SeqRefine(GPXfile,dlg):
    2760     import cPickle
    27612412    import pytexture as ptx
    27622413    ptx.pyqlmninit()            #initialize fortran arrays for spherical harmonics
     
    27652416    print ' Sequential Refinement'
    27662417    G2mv.InitVars()   
    2767     Controls = GetControls(GPXfile)
     2418    Controls = G2IO.GetControls(GPXfile)
    27682419    ShowControls(Controls)           
    2769     constrDict,constrFlag,fixedList = GetConstraints(GPXfile)
    2770     Histograms,Phases = GetUsedHistogramsAndPhases(GPXfile)
     2420    constrDict,constrFlag,fixedList = G2IO.GetConstraints(GPXfile)
     2421    Histograms,Phases = G2IO.GetUsedHistogramsAndPhases(GPXfile)
    27712422    if not Phases:
    27722423        print ' *** ERROR - you have no histograms to refine! ***'
     
    27812432        histNames = Controls['Seq Data']
    27822433    else:
    2783         histNames = GetHistogramNames(GPXfile,['PWDR',])
     2434        histNames = G2IO.GetHistogramNames(GPXfile,['PWDR',])
    27842435    if 'Reverse Seq' in Controls:
    27852436        if Controls['Reverse Seq']:
     
    28992550        SetHistogramData(parmDict,sigDict,Histo,ifPrint)
    29002551        SeqResult[histogram] = covData
    2901         SetUsedHistogramsAndPhases(GPXfile,Histo,Phases,covData,makeBack)
     2552        G2IO.SetUsedHistogramsAndPhases(GPXfile,Histo,Phases,covData,makeBack)
    29022553        makeBack = False
    2903     SetSeqResult(GPXfile,Histograms,SeqResult)
    2904 
     2554    G2IO.SetSeqResult(GPXfile,Histograms,SeqResult)
     2555
     2556def DistAngle(DisAglData):
     2557    import numpy.ma as ma
     2558   
     2559    def ShowBanner(name):
     2560        print 80*'*'
     2561        print '   Interatomic Distances and Angles for phase '+name
     2562        print 80*'*','\n'
     2563
     2564    ShowBanner(DisAglData['Name'])
     2565    SGData = DisAglData['SGData']
     2566    SGtext = G2spc.SGPrint(SGData)
     2567    for line in SGtext: print line
     2568    Cell = DisAglData['Cell']
     2569   
     2570    Amat,Bmat = G2lat.cell2AB(Cell[:6])
     2571    if 'covData' in DisAglData:   
     2572        covData = DisAglData['covData']
     2573        pfx = str(DisAglData['pId'])+'::'
     2574        A = G2lat.cell2A(Cell[:6])
     2575        cellSig = getCellEsd(pfx,SGData,A,covData)
     2576        names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
     2577        valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
     2578        line = '\n Unit cell:'
     2579        for name,vals in zip(names,valEsd):
     2580            line += name+vals 
     2581        print line
     2582    else:
     2583        print '\n Unit cell: a = ','%.5f'%(Cell[0]),' b = ','%.5f'%(Cell[1]),' c = ','%.5f'%(Cell[2]), \
     2584            ' alpha = ','%.3f'%(Cell[3]),' beta = ','%.3f'%(Cell[4]),' gamma = ', \
     2585            '%.3f'%(Cell[5]),' volume = ','%.3f'%(Cell[6])
     2586    Factor = DisAglData['Factors']
     2587    Radii = dict(zip(DisAglData['AtomTypes'],zip(DisAglData['BondRadii'],DisAglData['AngleRadii'])))
     2588    Units = np.array([                   #is there a nicer way to make this?
     2589        [-1,-1,-1],[-1,-1,0],[-1,-1,1],[-1,0,-1],[-1,0,0],[-1,0,1],[-1,1,-1],[-1,1,0],[-1,1,1],
     2590        [0,-1,-1],[0,-1,0],[0,-1,1],[0,0,-1],[0,0,0],[0,0,1],[0,1,-1],[0,1,0],[0,1,1],
     2591        [1,-1,-1],[1,-1,0],[1,-1,1],[1,0,-1],[1,0,0],[1,0,1],[1,1,-1],[1,1,0],[1,1,1]])
     2592    origAtoms = zip(DisAglData['OrigIndx'],DisAglData['OrigAtoms'])
     2593    targAtoms = DisAglData['TargAtoms']
     2594    for Oatom in origAtoms:
     2595        Dist = []
     2596        Vect = []
     2597        for Tatom in targAtoms:
     2598            result = G2spc.GenAtom(Tatom[2:5],SGData,False)
     2599            BsumR = (Radii[Oatom[1][1]][0]+Radii[Tatom[1]][0])*Factor[0]
     2600            AsumR = (Radii[Oatom[1][1]][1]+Radii[Tatom[1]][1])*Factor[1]
     2601            for Txyz,Top,Tunit in result:
     2602                Dx = (Txyz-np.array(Oatom[1][2:5]))+Units
     2603                dx = np.inner(Amat,Dx)
     2604                dist = ma.masked_less(np.sqrt(np.sum(dx**2,axis=0)),0.5)
     2605                IndB = ma.nonzero(ma.masked_greater(dist-BsumR,0.))
     2606                IndA = ma.nonzero(ma.masked_greater(dist-AsumR,0.))
     2607                if np.any(IndB):
     2608                    for indb in IndB:
     2609                        Dist.append([Oatom[1][0],Tatom[0],Tunit,Top,ma.getdata(dist[indb])])
     2610                        Vect += dx.T[indb]
     2611       
     2612        for dist in Dist:
     2613            print dist
     2614           
     2615        for vect in Vect:
     2616            print vect
     2617           
     2618                 
     2619
     2620#    def FindBonds():                    #uses numpy & masks - very fast even for proteins!
     2621#        import numpy.ma as ma
     2622#        atomData = data['Atoms']
     2623#        generalData = data['General']
     2624#        Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
     2625#        radii = generalData['BondRadii']
     2626#        atomTypes = generalData['AtomTypes']
     2627#        try:
     2628#            indH = atomTypes.index('H')
     2629#            radii[indH] = 0.5
     2630#        except:
     2631#            pass           
     2632#        for atom in atomData:
     2633#            atom[-2] = []               #clear out old bond/angle tables
     2634#            atom[-1] = []
     2635#        Indx = range(len(atomData))
     2636#        Atoms = []
     2637#        Radii = []
     2638#        for atom in atomData:
     2639#            Atoms.append(np.array(atom[cx:cx+3]))
     2640#            try:
     2641#                if not hydro and atom[ct] == 'H':
     2642#                    Radii.append(0.0)
     2643#                else:
     2644#                    Radii.append(radii[atomTypes.index(atom[ct])])
     2645#            except ValueError:          #changed atom type!
     2646#                Radii.append(0.20)
     2647#        Atoms = np.array(Atoms)
     2648#        Radii = np.array(Radii)
     2649#        IASR = zip(Indx,Atoms,Radii)
     2650#        for atomA in IASR:
     2651#                Dx = Atoms-atomA[1]
     2652#                dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5) #gets rid of self & disorder "bonds" < 0.5A
     2653#                sumR = atomA[3]+Radii
     2654#                IndB = ma.nonzero(ma.masked_greater(dist-radiusFactor*sumR,0.))                 #get indices of bonded atoms
     2655#                i = atomA[0]
     2656#                for j in IndB[0]:
     2657#                    if j > i:
     2658#                        atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
     2659#                        atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
     2660#                       
    29052661
    29062662def main():
  • trunk/help/gsasII.html

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    10301068        font-family:"Times New Roman","serif";}
    10311069</style>
    1032 <![endif]--><!--[if gte mso 9]><xml>
    1033  <o:shapedefaults v:ext="edit" spidmax="6146"/>
     1070<![endif]-->
     1071<link href=gsasIIfav.png rel="SHORTCUT ICON">
     1072<!--[if gte mso 9]><xml>
     1073 <o:shapedefaults v:ext="edit" spidmax="7170"/>
    10341074</xml><![endif]--><!--[if gte mso 9]><xml>
    10351075 <o:shapelayout v:ext="edit">
     
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    10631103 <o:lock v:ext="edit" aspectratio="t"/>
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     1104</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1036" type="#_x0000_t75"
    10651105 alt="GSAS-II logo" style='position:absolute;margin-left:56pt;margin-top:0;
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    10761116
    10771117<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1078 is where to find help on various GSAS-II windows and plots.
    1079 Note that GSAS-II operates with three windows: the main <a href="#Data_tree">
    1080 GSAS-II data tree</A> window, which provides a hierarchical view of
    1081   the current project; the <a href="#Data_Frame">
    1082 GSAS-II data editing</A> window, which shows the contents of a
    1083   particular section of the project, where values can be examined and
    1084 changed; and the <a href="#Plots">
    1085 GSAS-II Plots</A> window, which shows graphical representations of the results.
    1086   <o:p></o:p></span></p>
    1087 
    1088 <P><hr><hr>
    1089   <h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times
    1090   New Roman"'>1. GSAS-II
    1091 data tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    1092 
    1093 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1094 is a hierarchical view of the data items in your GSAS-II project (name.gpx). Clicking
    1095 on any item in the window opens a view where information in that item can be
    1096 viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
     1118is where to find help on various GSAS-II windows and plots. Note that GSAS-II
     1119operates with three windows: the main <a href="#Data_tree">GSAS-II data tree</a>
     1120window, which provides a hierarchical view of the current project; the <a
     1121href="#Data_Frame">GSAS-II data editing</a> window, which shows the contents of
     1122a particular section of the project, where values can be examined and changed;
     1123and the <a href="#Plots">GSAS-II Plots</a> window, which shows graphical
     1124representations of the results. <o:p></o:p></span></p>
     1125
     1126<div class=MsoNormal align=center style='text-align:center'><span
     1127style='mso-fareast-font-family:"Times New Roman"'>
     1128
     1129<hr size=2 width="100%" align=center>
     1130
     1131</span></div>
     1132
     1133<div class=MsoNormal align=center style='text-align:center'><span
     1134style='mso-fareast-font-family:"Times New Roman"'>
     1135
     1136<hr size=2 width="100%" align=center>
     1137
     1138</span></div>
     1139
     1140<h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times New Roman"'>1.
     1141GSAS-II data tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
     1142
     1143<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1144is a hierarchical view of the data items in your GSAS-II project (name.gpx).
     1145Clicking on any item in the window opens a view where information in that item
     1146can be viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
    10971147Parameters&quot;</a> item contains information about how data were collected,
    10981148such as the sample temperature <a href="#Sample_Parameters">(see below)</a>. <o:p></o:p></span></p>
    10991149
    11001150<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1101 The menus associated with this window provide access to many features
    1102 of GSAS-II, as outlined below:
    1103 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1151
     1152<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     1153menus associated with this window provide access to many features of GSAS-II,
     1154as outlined below: <o:p></o:p></span></p>
     1155
     1156<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    11041157style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    11051158style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    11071160
    11081161<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1109 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1162auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11101163style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    11111164style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11161169
    11171170<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1118 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1171auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11191172style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    11201173style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11281181
    11291182<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1130 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1183auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11311184style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    11321185style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11381191
    11391192<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1140 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1193auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11411194style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    11421195style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11471200
    11481201<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1149 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1202auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11501203style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    11511204style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11561209option) GSAS-II; useful for escaping from GSAS-II if needed.</span></p>
    11571210
    1158 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1211<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    11591212style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    11601213style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    11621215
    11631216<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1164 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1217auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11651218style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    11661219style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11761229
    11771230<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1178 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1231auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11791232style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    11801233style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    1181 style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - </p>
    1182 
    1183 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1184 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1234style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - Read in 2-D
     1235powder diffraction images (multiple patterns can be selected). GSAS-II can read
     1236many different image file formats including MAR345 files, Quantum ADSC files,
     1237and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these
     1238formats have data fields that should contain relevant information for the
     1239exposure (e.g. wavelength), these are rarely filled in correctly by the data
     1240acquisition software. Thus, you should have separately noted this information
     1241as it will be needed</p>
     1242
     1243<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1244auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11851245style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    11861246style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    1187 style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks&#8230;</b> - </p>
    1188 
    1189 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1190 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1247style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks&#8230;</b> - Read
     1248in a list of powder pattern peak positions as either a d-spacing table or a set
     1249of 2<span style='font-family:Symbol'>Q</span> positions; these can be used in
     1250GSAS-II powder pattern indexing. </p>
     1251
     1252<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1253auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11911254style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    11921255style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    11941257
    11951258<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1196 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1259auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11971260style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    11981261style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12001263
    12011264<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1202 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1265auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12031266style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    12041267style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12061269
    12071270<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1208 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1271auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12091272style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    12101273style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12121275
    12131276<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1214 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1277auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12151278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
    12161279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12181281
    12191282<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1220 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1283auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12211284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
    12221285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    12251288
    12261289<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1227 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1290auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12281291style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
    12291292style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     
    12311294data</b> - </p>
    12321295
    1233 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1296<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    12341297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    12351298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    12371300
    12381301<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1239 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1302auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12401303style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    12411304style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12431306
    12441307<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1245 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1308auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12461309style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    12471310style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12501313
    12511314<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1252 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1315auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12531316style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    12541317style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12561319
    12571320<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1258 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1321auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12591322style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    12601323style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12621325
    12631326<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1264 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1327auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12651328style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    12661329style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    12671330style='mso-bidi-font-weight:normal'>Solve</b> - </p>
    12681331
    1269 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1332<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    12701333style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    12711334style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    12731336
    12741337<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1275 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1338auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12761339style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    12771340style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12791342
    12801343<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1281 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1344auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12821345style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    12831346style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12851348
    12861349<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1287 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1350auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12881351style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    12891352style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    12911354
    12921355<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1293 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1356auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12941357style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    12951358style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    12961359style='mso-bidi-font-weight:normal'>Import HKLs&#8230;</b> - </p>
    12971360
    1298 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1361<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    12991362style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    13001363style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     
    13021365
    13031366<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1304 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1367auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13051368style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    13061369style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    13081371
    13091372<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1310 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1373auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13111374style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    13121375style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    13141377
    13151378<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1316 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1379auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13171380style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    13181381style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    13201383
    13211384<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1322 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1385auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13231386style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    13241387style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    13261389
    13271390<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1328 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1391auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13291392style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    13301393style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    13321395
    13331396<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    1334 text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1397text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13351398style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    13361399style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    13371400style='mso-bidi-font-weight:normal'>Export CIF&#8230;</b> - </p>
    13381401
    1339 <P><hr><hr>
    1340 <h2><a name="Data_Frame"><span style='mso-fareast-font-family:"Times
    1341 New Roman"'>2. GSAS-II
    1342 Data Editing Window</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    1343 Different information is displayed in the Data Editing Window,
    1344 depending on which section of the <a href="#Data_tree">data tree</A>
    1345 is selected. For example, clicking on the "Notebook" entry of the tree
    1346 brings up the Notebook editing window described below.
     1402<div class=MsoNormal align=center style='text-align:center'><span
     1403style='mso-fareast-font-family:"Times New Roman"'>
     1404
     1405<hr size=2 width="100%" align=center>
     1406
     1407</span></div>
     1408
     1409<div class=MsoNormal align=center style='text-align:center'><span
     1410style='mso-fareast-font-family:"Times New Roman"'>
     1411
     1412<hr size=2 width="100%" align=center>
     1413
     1414</span></div>
     1415
     1416<h2><a name="Data_Frame"><span style='mso-fareast-font-family:"Times New Roman"'>2.
     1417GSAS-II Data Editing Window</span></a><span style='mso-fareast-font-family:
     1418"Times New Roman"'><o:p></o:p></span></h2>
     1419
     1420<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Different
     1421information is displayed in the Data Editing Window, depending on which section
     1422of the <a href="#Data_tree">data tree</a> is selected. For example, clicking on
     1423the &quot;Notebook&quot; entry of the tree brings up the Notebook editing
     1424window described below. <o:p></o:p></span></p>
    13471425
    13481426<h4><a name=Notebook><span style='mso-fareast-font-family:"Times New Roman"'>Notebook</span></a><span
     
    13621440<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    13631441window provides the main controls for the major calculations in GSAS-II. At
    1364 present only Refinement Controls are presented.<o:p></o:p></span></p>
    1365 
    1366 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1367 main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
     1442present only Refinement Controls are presented. <o:p></o:p></span></p>
     1443
     1444<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Two
     1445of the main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
    13681446MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
    13691447algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
    1370 package. Their purpose is to </span>minimize the sum of the squares of M<span
    1371 style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
    1372 variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
    1373 algorithm as written by </span>Burton S. <span class=SpellE>Garbow</span>,
     1448package and a third one is a python version utilizing only the <span
     1449class=SpellE>numpy</span> package. The purpose is to </span>minimize the sum of
     1450the squares of M<span style='mso-fareast-font-family:"Times New Roman"'>
     1451nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
     1452algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
     1453routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
    13741454Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
    1375 J. <span class=GramE>More (Argonne National Laboratory, 1980).</span></p>
     1455J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The
     1456python/numpy version was developed by us based on the material in Numerical
     1457Recipes (Press, Flannery, <span class=SpellE><span class=GramE>Teulosky</span></span>
     1458&amp; <span class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt
     1459algorithm.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    13761460
    13771461<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    13781462
    1379 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1463<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    13801464style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    13811465style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    13821466style='mso-fareast-font-family:"Times New Roman"'>Select whether the refinement
    1383 uses &#8216;analytic&#8217; or &#8216;numeric&#8217; derivatives. The latter is
    1384 slower and perhaps a bit less accurate, but may be needed if the analytic
    1385 functions are not fully developed. Generally use &#8216;analytic&#8217; for
    1386 routine work.<o:p></o:p></span></p>
    1387 
    1388 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1467uses &#8216;analytic <span class=SpellE>Jacobian</span>&#8217;, &#8216;analytic
     1468Hessian&#8217; or &#8216;numeric&#8217; derivatives. The latter is slower and
     1469perhaps a bit less accurate, but may be needed if the analytic functions are
     1470not fully developed. The <span class=SpellE>Jacobian</span> matrix is shaped N x
     1471M (parameters x observations) and is much larger than the Hessian matrix which
     1472is shaped M x M (parameters x parameters). Generally use &#8216;analytic
     1473Hessian&#8217; for routine work.<o:p></o:p></span></p>
     1474
     1475<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    13891476style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    13901477style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     
    13961483to 1.0.<o:p></o:p></span></p>
    13971484
    1398 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1485<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    13991486style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    14001487style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1401 style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Initial shift
    1402 factor&#8217; for the first cycle of refinement. This value is modified by the
    1403 least squares routine. The allowed range is 10<sup>-5</sup> to 100. Smaller
    1404 values may be needed if your initial <span class=GramE>refinement</span> trials
    1405 immediately diverge, however make sure your starting parameter values are
    1406 &#8216;reasonable&#8217;. The selected default (=1.0) normally gives good
    1407 performance.<o:p></o:p></span></p>
    1408 
    1409 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1488style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic Jacobean&#8217;
     1489is chosen then select &#8216;Initial shift factor&#8217; for the first cycle of
     1490refinement. This value is modified by the least squares routine. The allowed
     1491range is 10<sup>-5</sup> to 100. Smaller values may be needed if your initial <span
     1492class=GramE>refinement</span> trials immediately diverge, however make sure
     1493your starting parameter values are &#8216;reasonable&#8217;. The selected
     1494default (=1.0) normally gives good performance.<o:p></o:p></span></p>
     1495
     1496<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    14101497style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1498style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1499style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic Hessian&#8217;
     1500is chosen then select &#8216;Max cycles&#8217;, the maximum number of least
     1501squares cycles to be performed. Choices are given in the pull down selection;
     1502the default is 3 cycles.<o:p></o:p></span></p>
     1503
     1504<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
     1505style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    14111506style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    14121507style='mso-fareast-font-family:"Times New Roman"'>Select data for sequential
     
    14381533<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    14391534
    1440 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo6'><![if !supportLists]><span
     1535<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo6'><![if !supportLists]><span
    14411536style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    14421537style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1443 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the parameter
    1444 types you wish to constrain. Each will have the same possibilities in the
    1445 &#8216;Edit menu.<o:p></o:p></span></p>
    1446 
    1447 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo6'><![if !supportLists]><span
     1538style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the
     1539parameter types you wish to constrain. Each will have the same possibilities in
     1540the &#8216;Edit menu.<o:p></o:p></span></p>
     1541
     1542<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo6'><![if !supportLists]><span
    14481543style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    14491544style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     
    14521547
    14531548<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1454 auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1549auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    14551550style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    14561551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     
    14701565
    14711566<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1472 auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1567auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    14731568style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    14741569style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    14891584
    14901585<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1491 auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1586auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    14921587style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    14931588style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    15011596the first one. Choose those and press OK. Cancel in either dialog will cancel
    15021597the operation. The equivalenced parameters will show as an equation of the form
    1503 M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the
    1504 multipliers M1, <span class=GramE>M2, &#8230;</span> and C can be changed via
    1505 the &#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
     1598M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the multipliers
     1599M1, <span class=GramE>M2, &#8230;</span> and C can be changed via the
     1600&#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
    15061601constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
    15071602
    15081603<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    1509 text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1604text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    15101605style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    15111606style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     
    15351630<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    15361631
    1537 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo8'><![if !supportLists]><span
     1632<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo8'><![if !supportLists]><span
    15381633style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    15391634style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     
    15471642operation.<o:p></o:p></span></p>
    15481643
    1549 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo8'><![if !supportLists]><span
     1644<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo8'><![if !supportLists]><span
    15501645style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    15511646style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     
    15581653new value.<o:p></o:p></span></p>
    15591654
    1560 
    15611655<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture Control
    15621656Window<o:p></o:p></span></h4>
     
    16101704<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
    16111705
    1612 <H3>Phase Windows</H3>
    1613 When a phase is selected from the <a href="#Data_tree">data tree</A>,
    1614 parameters are show from that selected phase in a tabbed
    1615 window. Clicking on the tab raises the windows listed below.
    1616 <blockquote>
    1617 <A name="General"><H4><U>General</U> Phase Parameters</H4></A>
    1618 This is used for overall parameters describing the phase such as the
    1619 space group, the unit cell parameters and overall parameters for
    1620 the atom present in the phase.
    1621 <A name="Data"><H4>Sample <U>Data</U></H4></A>
    1622 <A name="Texture"><H4><U>Texture</U> Parameters</H4></A>
    1623 <A name="Atoms"><H4><U>Atom</U> Parameter<U>s</U></H4></A>
    1624 <A name="Draw_Options"><H4><U>Draw Options</U></H4></A>
    1625 <A name="Draw_Atoms"><H4><U>Draw Atoms</U></H4></A>
    1626 
    1627 </blockquote>
    1628 
    1629 <H3>Powder Histogram Windows</H3>
    1630 When a powder diffraction data set (histogram) is selected from the
    1631 <a href="#Data_tree">data tree</A>, a variety of subcategories in the
    1632 tree are shown. The items that are shown depend on the data set type.
    1633 Selecting a subcategory raises the window listed below.
    1634 <blockquote>
    1635 <A name=""><H4><U></U></H4></A>
    1636 <A name="Comments"><H4><U>Comments</U></H4></A>
    1637 
    1638 <h4><a name=Background><span style='mso-fareast-font-family:"Times New Roman"'>Background</span></a><span
    1639 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1640 
    1641 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1642 window shows the choice of background function and coefficients to be used in
    1643 fitting this powder pattern.<o:p></o:p></span></p>
    1644 
    1645 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1646 
    1647 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1648 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1649 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1650 style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
    1651 style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
     1706<h3>Phase Windows</h3>
     1707
     1708<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>When
     1709a phase is selected from the <a href="#Data_tree">data tree</a>, parameters are
     1710show from that selected phase in a tabbed window. Clicking on the tab raises
     1711the windows listed below. <o:p></o:p></span></p>
     1712
     1713<h4><a name=General><u>General</u> Phase Parameters</a></h4>
     1714
     1715<span style='mso-bookmark:General'></span>
     1716
     1717<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1718is used for overall parameters describing the phase such as the space group,
     1719the unit cell parameters and overall parameters for the atom present in the
     1720phase. <a name=Data><o:p></o:p></a></span></p>
     1721
     1722<h4><span style='mso-bookmark:Data'>Sample <u>Data</u></span></h4>
     1723
     1724<span style='mso-bookmark:Data'></span>
     1725
     1726<h4><a name=Texture><u>Texture</u> Parameters</a></h4>
     1727
     1728<h4><span style='mso-bookmark:Texture'><a name=Atoms><u>Atom</u> Parameter<u>s</u></a></span></h4>
     1729
     1730<span style='mso-bookmark:Atoms'></span>
     1731
     1732<h4><span style='mso-bookmark:Texture'><a name="Draw_Options"><u>Draw Options</u></a></span></h4>
     1733
     1734<span style='mso-bookmark:Draw_Options'></span>
     1735
     1736<h4><span style='mso-bookmark:Texture'><a name="Draw_Atoms"><u>Draw Atoms</u></a></span></h4>
     1737
     1738<span style='mso-bookmark:Draw_Atoms'></span>
     1739
     1740<h3><span style='mso-bookmark:Texture'>Powder Histogram Windows</span></h3>
     1741
     1742<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1743"Times New Roman"'>When a powder diffraction data set (histogram) is selected
     1744from the </span></span><a href="#Data_tree"><span style='mso-bookmark:Texture'><span
     1745style='mso-fareast-font-family:"Times New Roman"'>data tree</span></span><span
     1746style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
     1747style='mso-fareast-font-family:"Times New Roman"'>, a variety of subcategories
     1748in the tree are shown. The items that are shown depend on the data set type.
     1749Selecting a subcategory raises the window listed below. <o:p></o:p></span></span></p>
     1750
     1751<h4><span style='mso-bookmark:Texture'><a name=Comments></a><a name=""></a><span
     1752style='mso-bookmark:Comments'><u>Comments</u></span></span></h4>
     1753
     1754<span style='mso-bookmark:Comments'></span>
     1755
     1756<h4><span style='mso-bookmark:Texture'><a name=Background><span
     1757style='mso-fareast-font-family:"Times New Roman"'>Background</span></a></span><span
     1758style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1759
     1760<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1761"Times New Roman"'>This window shows the choice of background function and
     1762coefficients to be used in fitting this powder pattern.<o:p></o:p></span></span></p>
     1763
     1764<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1765"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     1766
     1767<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1768style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1769"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1770</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu
     1771&#8216;<b style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
    16521772style='mso-bidi-font-weight:normal'>Copy</b> &#8211; this copies the background
    16531773parameters shown to other selected powder patterns. If used, a dialog box (Copy
     
    16551775copy the background parameters to any or all of them; select &#8216;All&#8217;
    16561776to copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
    1657 &#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
    1658 
    1659 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1660 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1661 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1662 style='mso-fareast-font-family:"Times New Roman"'>You can select a different
    1663 Background function from the pull down tab.<o:p></o:p></span></p>
    1664 
    1665 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1666 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    1667 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1668 style='mso-fareast-font-family:"Times New Roman"'>You can choose to refine/not
    1669 refine the background coefficients.<o:p></o:p></span></p>
    1670 
    1671 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1672 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    1673 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1674 style='mso-fareast-font-family:"Times New Roman"'>You can select the number of
    1675 background coefficients to be used (1-36).<o:p></o:p></span></p>
    1676 
    1677 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1678 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    1679 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1680 style='mso-fareast-font-family:"Times New Roman"'>You can change individual
    1681 background coefficient values. Enter the value then press Enter or click the
    1682 mouse elsewhere in the Background window. This will set the new value.<o:p></o:p></span></p>
    1683 
    1684 <h4><a name="Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
    1685 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1686 
    1687 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1688 window... <o:p></o:p></span></p>
    1689 
    1690 <h4><a name="Sample_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Sample
    1691 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1692 
    1693 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1694 window... <o:p></o:p></span></p>
    1695 
    1696 <h4><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
    1697 Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></a><span
    1698 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1699 
    1700 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1701 window shows the list of peaks that will be used by the peak fitting refinement.
    1702 It is filled by picking peaks in the powder pattern displayed in the GSASII
    1703 Plots window as a sequence of &#8216;+&#8217; marks. See <a
    1704 href="#Powder_Patterns">Powder Patterns</a> below for details for what can be
    1705 done on this plot.<o:p></o:p></span></p>
    1706 
    1707 <h4><a name="Index_Peaks"><span style='mso-fareast-font-family:"Times New Roman"'>Index
    1708 Peak List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1709 
    1710 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1711 window shows the list of peaks that will be used for indexing (see </span><a
    1712 href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
    1713 Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'>).
     1777&#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></span></p>
     1778
     1779<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1780style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1781"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1782</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1783can select a different Background function from the pull down tab.<o:p></o:p></span></span></p>
     1784
     1785<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1786style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1787"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1788</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1789can choose to refine/not refine the background coefficients.<o:p></o:p></span></span></p>
     1790
     1791<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1792style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1793"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1794</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1795can select the number of background coefficients to be used (1-36).<o:p></o:p></span></span></p>
     1796
     1797<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1798style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1799"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1800</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1801can change individual background coefficient values. Enter the value then press
     1802Enter or click the mouse elsewhere in the Background window. This will set the
     1803new value.<o:p></o:p></span></span></p>
     1804
     1805<h4><span style='mso-bookmark:Texture'><a name="Instrument_Parameters"><span
     1806style='mso-fareast-font-family:"Times New Roman"'>Instrument Parameters</span></a></span><span
     1807style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1808
     1809<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1810"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1811
     1812<h4><span style='mso-bookmark:Texture'><a name="Sample_Parameters"><span
     1813style='mso-fareast-font-family:"Times New Roman"'>Sample Parameters</span></a></span><span
     1814style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1815
     1816<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1817"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1818
     1819<h4><span style='mso-bookmark:Texture'><a name="Peak_List"></a><a
     1820name="Powder_Peaks"><span style='mso-bookmark:Peak_List'><span
     1821style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></a></span><span
     1822style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1823
     1824<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1825"Times New Roman"'>This window shows the list of peaks that will be used by the
     1826peak fitting refinement. It is filled by picking peaks in the powder pattern
     1827displayed in the GSASII Plots window as a sequence of &#8216;+&#8217; marks.
     1828See </span></span><a href="#Powder_Patterns"><span style='mso-bookmark:Texture'><span
     1829style='mso-fareast-font-family:"Times New Roman"'>Powder Patterns</span></span><span
     1830style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
     1831style='mso-fareast-font-family:"Times New Roman"'> below for details for what
     1832can be done on this plot.<o:p></o:p></span></span></p>
     1833
     1834<h4><span style='mso-bookmark:Texture'><a name="Index_Peaks"><span
     1835style='mso-fareast-font-family:"Times New Roman"'>Index Peak List</span></a></span><span
     1836style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1837
     1838<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1839"Times New Roman"'>This window shows the list of peaks that will be used for
     1840indexing (see </span></span><a href="#Unit_Cells_List"><span style='mso-bookmark:
     1841Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Unit Cells
     1842List</span></span><span style='mso-bookmark:Texture'></span></a><span
     1843style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>).
    17141844It must be filled before indexing can proceed. When indexing is completed, this
    17151845display will show the resulting <span class=SpellE>hkl</span> values for every
    17161846indexed reflection along with the calculated d-spacing (&#8216;d-<span
    1717 class=SpellE>calc</span>&#8217;) for the selected unit cell in </span><a
    1718 href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
    1719 Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
     1847class=SpellE>calc</span>&#8217;) for the selected unit cell in </span></span><a
     1848href="#Unit_Cells_List"><span style='mso-bookmark:Texture'><span
     1849style='mso-fareast-font-family:"Times New Roman"'>Unit Cells List</span></span><span
     1850style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
     1851style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></span></p>
     1852
     1853<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1854"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     1855
     1856<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo12'><span
     1857style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1858"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1859</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu
     1860&#8216;<b style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
     1861style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
     1862positions &amp; intensities from the </span></span><a href="#Peak_List"><span
     1863style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Peak
     1864List</span></span><span style='mso-bookmark:Texture'></span></a><span
     1865style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1866to make them available for the indexing routine. The d-<span class=SpellE>obs</span>
     1867is obtained from Bragg&#8217;s Law after applying the Zero correction shown on
     1868the </span></span><a href="#Instrument_Parameters"><span style='mso-bookmark:
     1869Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
     1870Parameters</span></span><span style='mso-bookmark:Texture'></span></a><span
     1871style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1872table to the position shown here.<o:p></o:p></span></span></p>
     1873
     1874<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l3 level1 lfo12'><span
     1875style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1876"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1877</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1878may deselect individual peaks from indexing by <span class=SpellE>unchecking</span>
     1879the corresponding &#8216;use&#8217; box.<o:p></o:p></span></span></p>
     1880
     1881<h4><span style='mso-bookmark:Texture'><a name="Cell_Indexing_Refine"><span
     1882style='mso-fareast-font-family:"Times New Roman"'>Unit Cells List</span></a></span><span
     1883style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1884
     1885<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1886"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1887
     1888<h4><span style='mso-bookmark:Texture'><a name="Reflection_List"><span
     1889style='mso-fareast-font-family:"Times New Roman"'>Reflection List</span></a></span><span
     1890style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1891
     1892<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1893"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1894
     1895<div class=MsoNormal align=center style='text-align:center'><span
     1896style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1897
     1898<hr size=2 width="100%" align=center>
     1899
     1900</span></span></div>
     1901
     1902<div class=MsoNormal align=center style='text-align:center'><span
     1903style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1904
     1905<hr size=2 width="100%" align=center>
     1906
     1907</span></span></div>
     1908
     1909<h2><span style='mso-bookmark:Texture'><a name=Plots><span style='mso-fareast-font-family:
     1910"Times New Roman"'>3. GSAS-II Plots Window</span></a></span><span
     1911style='mso-bookmark:Plots'></span><span style='mso-bookmark:Texture'><span
     1912style='mso-fareast-font-family:"Times New Roman";font-weight:normal'> </span></span><span
     1913style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h2>
     1914
     1915<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1916"Times New Roman"'>This window presents all the graphical material as a
     1917multipage tabbed set of plots utilizing the <span class=SpellE>matplotlib</span>
     1918python package. Each page has a tool bar (at bottom in Windows) with the
     1919controls<o:p></o:p></span></span></p>
     1920
     1921<p class=MsoNormal><span style='mso-bookmark:Texture'></span><span
     1922style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman";
     1923mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
     1924src=graphbar.jpg></span></span><span style='mso-bookmark:Texture'><span
     1925style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></p>
     1926
     1927<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1928"Times New Roman"'>These are Home, Back, Forward, Pan, Zoom, Save and Help,
     1929respectively. <o:p></o:p></span></span></p>
     1930
     1931<ul type=disc>
     1932 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1933     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1934     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Home:
     1935     returns the plot to the initial scaling <o:p></o:p></span></span></li>
     1936 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1937     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1938     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Back:
     1939     returns the plot to the previous scaling <o:p></o:p></span></span></li>
     1940 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1941     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1942     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Forward:
     1943     reverses the action in the previous press(es) of the Back button <o:p></o:p></span></span></li>
     1944 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1945     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1946     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Pan:
     1947     allows you to control panning across the plot (press left mouse button)
     1948     and zooming (press right mouse button), <o:p></o:p></span></span></li>
     1949 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1950     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1951     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Zoom:
     1952     allows you to select a portion of the plot (press right mouse button &amp;
     1953     drag for zoom box) for the next plot. <o:p></o:p></span></span></li>
     1954 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1955     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1956     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Save:
     1957     allows you to save the currently displayed plot in one of several
     1958     graphical formats suitable for printing or insertion in a document. The <o:p></o:p></span></span></li>
     1959 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1960     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1961     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Help:
     1962     accesses GSASII help on the specific plot type. <o:p></o:p></span></span></li>
     1963</ul>
     1964
     1965<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1966"Times New Roman"'><o:p>&nbsp;</o:p></span></span></p>
     1967
     1968<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1969"Times New Roman"'>Below the toolbar may be a status bar that on the left may
     1970show either an instruction for a keyed input or a pull down selection of keyed
     1971input; on the right may be displayed position dependent information that is
     1972updated as the mouse is moved over the plot region.<o:p></o:p></span></span></p>
     1973
     1974<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1975"Times New Roman"'><o:p>&nbsp;</o:p></span></span></p>
     1976
     1977<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1978"Times New Roman"'>The specific types of plots that are pages in the GSASII
     1979Plots windows are next.<o:p></o:p></span></span></p>
     1980
     1981<h4><span style='mso-bookmark:Texture'><a name="Powder_Patterns"><span
     1982style='mso-fareast-font-family:"Times New Roman"'>Powder Patterns</span></a></span><span
     1983style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1984
     1985<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1986"Times New Roman"'>The powder patterns that are part of your project are shown
     1987on this page. They can be displayed as a stack of powder patterns, just a
     1988single pattern or as a contour image of the peak intensities. What can be done
     1989here will depend on which is displayed and on which item in the GSAS-II data
     1990tree you have selected.<o:p></o:p></span></span></p>
     1991
     1992<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1993"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     1994
     1995<h4><span style='mso-bookmark:Texture'><a name=Covariance><span
     1996style='mso-fareast-font-family:"Times New Roman"'>Covariance</span></a></span><span
     1997style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1998
     1999<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2000"Times New Roman"'>The variance-covariance matrix as a color coded array is
     2001shown on this page. The color bar to the right shows the range of <span
     2002class=SpellE>covariances</span> (-1 to 1) and corresponding colors. The
     2003parameter names are to the right and the parameter numbers are below the plot.<o:p></o:p></span></span></p>
     2004
     2005<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2006"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2007
     2008<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo15'><span
     2009style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     2010"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     2011</span></span></span><![endif]>Move the mouse cursor across the plot. If on a
     2012diagonal cell, the parameter name, value and <span class=SpellE>esd</span> is
     2013shown both as a tool tip and in the right hand portion of the status bar. If
     2014the cursor is off the diagonal, the two parameter names and their covariance
     2015are shown in the tool tip and the status bar.</span></p>
     2016
     2017<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo15'><span
     2018style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     2019"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     2020</span></span></span><![endif]><span class=GramE>Type &#8216;s&#8217;</span>
     2021&#8211; A color scheme selection dialog is shown. Select a color scheme and
     2022press <span class=GramE>OK,</span> the new color scheme will be plotted. The
     2023default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</span></p>
     2024
     2025<h4><span style='mso-bookmark:Texture'><a name="Structure_Factors"><span
     2026style='mso-fareast-font-family:"Times New Roman"'>Structure Factors </span></a></span></h4>
     2027
     2028<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2029"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
     2030
     2031<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2032"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2033
     2034<h4><span style='mso-bookmark:Texture'><a name="Powder_Lines"><span
     2035style='mso-fareast-font-family:"Times New Roman"'>Powder Lines </span></a></span></h4>
     2036
     2037<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2038"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
     2039
     2040<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2041"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2042
     2043<h4><span style='mso-bookmark:Texture'><a name="Peak_Widths"><span
     2044style='mso-fareast-font-family:"Times New Roman"'>Peak Widths </span></a></span></h4>
     2045
     2046<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2047"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
     2048
     2049<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2050"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2051
     2052<h4><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2053"Times New Roman"'>Texture </span></span></h4>
     2054
     2055<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2056plot shows... <o:p></o:p></span></p>
    17202057
    17212058<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    17222059
    1723 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo12'><![if !supportLists]><span
    1724 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1725 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1726 style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
    1727 style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
    1728 style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
    1729 positions &amp; intensities from the </span><a href="#Peak_List"><span
    1730 style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></a><span
    1731 style='mso-fareast-font-family:"Times New Roman"'> to make them available for
    1732 the indexing routine. The d-<span class=SpellE>obs</span> is obtained from
    1733 Bragg&#8217;s Law after applying the Zero correction shown on the </span><a
    1734 href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
    1735 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'>
    1736 table to the position shown here.<o:p></o:p></span></p>
    1737 
    1738 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo12'><![if !supportLists]><span
    1739 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1740 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1741 style='mso-fareast-font-family:"Times New Roman"'>You may deselect individual
    1742 peaks from indexing by <span class=SpellE>unchecking</span> the corresponding
    1743 &#8216;use&#8217; box.<o:p></o:p></span></p>
    1744 
    1745 <h4><a name="Cell_Indexing_Refine"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
    1746 Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1747 
    1748 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1749 window... <o:p></o:p></span></p>
    1750 
    1751 <h4><a name="Reflection_List"><span style='mso-fareast-font-family:"Times New Roman"'>Reflection
    1752 List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1753 
    1754 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1755 window... <o:p></o:p></span></p>
    1756 
    1757 </blockquote>
    1758 
    1759 <P><hr><hr>
    1760 <h2><a name=Plots><span style='mso-fareast-font-family:"Times New
    1761 Roman"'>3. GSAS-II
    1762 Plots Window</span></a><span style='mso-bookmark:Plots'></span><span style='mso-fareast-font-family:
    1763 "Times New Roman";font-weight:normal'> </span><span style='mso-fareast-font-family:
    1764 "Times New Roman"'><o:p></o:p></span></h2>
    1765 
    1766 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1767 window presents all the graphical material as a multipage tabbed set of plots
    1768 utilizing the <span class=SpellE>matplotlib</span> python package. Each page
    1769 has a tool bar (at bottom in Windows) with the controls<o:p></o:p></span></p>
    1770 
    1771 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    1772 mso-no-proof:yes'><img border=0 width=225 height=31
    1773 src="graphbar.jpg" align="middle"></span><span
    1774 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    1775 
    1776 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
    1777 are Home, Back, Forward, Pan, Zoom, Save and Help, respectively.
    1778 <UL>
    1779   <LI>Home: returns the plot to the initial scaling
    1780   <LI>Back: returns the plot to the previous scaling
    1781   <LI>Forward: reverses the action in the previous press(es)
    1782   of the Back button
    1783   <LI>Pan: allows you to control panning across the plot (press left mouse button) and
    1784 zooming (press right mouse button),
    1785   <LI>Zoom: allows you to select a
    1786 portion of the plot (press right mouse button &amp; drag for zoom box) for the
    1787 next plot.
    1788   <LI>Save: allows you to save the currently displayed plot in one of
    1789 several graphical formats suitable for printing or insertion in a document. The
    1790   <LI>Help: accesses GSASII help on the specific plot type.
    1791 </UL>
    1792   <o:p></o:p></span></p>
    1793 
    1794 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Below
    1795 the toolbar may be a status bar that on the left may show either an instruction
    1796 for a keyed input or a pull down selection of keyed input; on the right may be
    1797 displayed position dependent information that is updated as the mouse is moved
    1798 over the plot region.<o:p></o:p></span></p>
    1799 
    1800 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
    1801 
    1802 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1803 specific types of plots that are pages in the GSASII Plots windows are next.<o:p></o:p></span></p>
    1804 
    1805 <h4><a name="Powder_Patterns"><span style='mso-fareast-font-family:"Times New Roman"'>Powder
    1806 Patterns</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1807 
    1808 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1809 powder patterns that are part of your project are shown on this page. They can
    1810 be displayed as a stack of powder patterns, just a single pattern or as a
    1811 contour image of the peak intensities. What can be done here will depend on
    1812 which is displayed and on which item in the GSAS-II data tree you have
    1813 selected.<o:p></o:p></span></p>
     2060<h4><a name="Sequential_refinement"><span style='mso-fareast-font-family:"Times New Roman"'>Sequential
     2061refinement </span></a></h4>
     2062
     2063<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2064plot shows... <o:p></o:p></span></p>
     2065
    18142066<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18152067
    1816 <h4><a name=Covariance><span style='mso-fareast-font-family:"Times New Roman"'>Covariance</span></a><span
    1817 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1818 
    1819 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1820 variance-covariance matrix as a color coded array is shown on this page. The
    1821 color bar to the right shows the range of <span class=SpellE>covariances</span>
    1822 (-1 to 1) and corresponding colors. The parameter names are to the right and
    1823 the parameter numbers are below the plot.<o:p></o:p></span></p>
     2068<h4><a name="2D_Powder_Image"><span style='mso-fareast-font-family:"Times New Roman"'>2D
     2069Powder Image </span></a></h4>
     2070
     2071<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2072plot shows... <o:p></o:p></span></p>
    18242073
    18252074<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18262075
    1827 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo14'><![if !supportLists]><span
    1828 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1829 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
    1830 the mouse cursor across the plot. If on a diagonal cell, the parameter name,
    1831 value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
    1832 right hand portion of the status bar. If the cursor is off the diagonal, the
    1833 two parameter names and their covariance are shown in the tool tip and the
    1834 status bar.</p>
    1835 
    1836 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo14'><![if !supportLists]><span
    1837 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1838 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1839 class=GramE>Type &#8216;s&#8217;</span> &#8211; A color scheme selection dialog
    1840 is shown. Select a color scheme and press <span class=GramE>OK,</span> the new
    1841 color scheme will be plotted. The default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
    1842 
    1843 <h4><a name="Structure_Factors">
    1844 <span style='mso-fareast-font-family:"Times New Roman"'>
    1845 Structure Factors
     2076<h4><a name="2D_Integration"><span style='mso-fareast-font-family:"Times New Roman"'>2D
     2077Integration </span></a></h4>
     2078
     2079<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2080plot shows... <o:p></o:p></span></p>
     2081
     2082<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     2083
     2084<h4><a name="2D_Transformed_Powder_Image"><span style='mso-fareast-font-family:
     2085"Times New Roman"'>2D Transformed Powder Image </span></a></h4>
     2086
     2087<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2088plot shows... <o:p></o:p></span></p>
     2089
     2090<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     2091
     2092<h4><a name=Mustrain><span style='mso-fareast-font-family:"Times New Roman"'>Mustrain
    18462093</span></a></h4>
    1847 This plot shows...
     2094
     2095<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2096plot shows... <o:p></o:p></span></p>
     2097
    18482098<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18492099
    1850 <h4><a name="Powder_Lines">
    1851 <span style='mso-fareast-font-family:"Times New Roman"'>
    1852 Powder Lines
    1853 </span></a></h4>
    1854 This plot shows...
     2100<h4><a name=Size><span style='mso-fareast-font-family:"Times New Roman"'>Size </span></a></h4>
     2101
     2102<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2103plot shows... <o:p></o:p></span></p>
     2104
    18552105<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18562106
    1857 
    1858 <h4><a name="Peak_Widths">
    1859 <span style='mso-fareast-font-family:"Times New Roman"'>
    1860 Peak Widths
    1861 </span></a></h4>
    1862 This plot shows...
     2107<h4><a name="Preferred_orientation"><span style='mso-fareast-font-family:"Times New Roman"'>Preferred
     2108Orientation </span></a></h4>
     2109
     2110<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2111plot shows... <o:p></o:p></span></p>
     2112
    18632113<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1864 
    1865 
    1866 <h4><a name="Texture">
    1867 <span style='mso-fareast-font-family:"Times New Roman"'>
    1868 Texture
    1869 </span></a></h4>
    1870 This plot shows...
    1871 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1872 
    1873 
    1874 <h4><a name="Sequential_refinement">
    1875 <span style='mso-fareast-font-family:"Times New Roman"'>
    1876 Sequential refinement
    1877 </span></a></h4>
    1878 This plot shows...
    1879 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1880 
    1881 
    1882 <h4><a name="2D_Powder_Image">
    1883 <span style='mso-fareast-font-family:"Times New Roman"'>
    1884 2D Powder Image
    1885 </span></a></h4>
    1886 This plot shows...
    1887 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1888 
    1889 
    1890 <h4><a name="2D_Integration">
    1891 <span style='mso-fareast-font-family:"Times New Roman"'>
    1892 2D Integration
    1893 </span></a></h4>
    1894 This plot shows...
    1895 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1896 
    1897 
    1898 <h4><a name="2D_Transformed_Powder_Image">
    1899 <span style='mso-fareast-font-family:"Times New Roman"'>
    1900 2D Transformed Powder Image
    1901 </span></a></h4>
    1902 This plot shows...
    1903 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1904 
    1905 
    1906 <h4><a name="Mustrain">
    1907 <span style='mso-fareast-font-family:"Times New Roman"'>
    1908 Mustrain
    1909 </span></a></h4>
    1910 This plot shows...
    1911 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1912 
    1913 
    1914 <h4><a name="Size">
    1915 <span style='mso-fareast-font-family:"Times New Roman"'>
    1916 Size
    1917 </span></a></h4>
    1918 This plot shows...
    1919 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1920 
    1921 <h4><a name="Preferred_orientation">
    1922 <span style='mso-fareast-font-family:"Times New Roman"'>
    1923 Preferred Orientation
    1924 </span></a></h4>
    1925 This plot shows...
    1926 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1927 
    1928 
    19292114
    19302115<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
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