Changeset 430


Ignore:
Timestamp:
Nov 30, 2011 5:02:08 PM (10 years ago)
Author:
vondreele
Message:

NB: There are a few stray print statements in this version
Some work on help stuff in GSASIIgrid.py
change default sum for constraints to 1.0
get data plots to include size & preferred orientation
modify plot toolbar - eliminate subplot button & add a Help button; doesn't do anything except recognize what plot it is from
Edited gsasII.html with Word - probably messed up all the bookmarks - but added a lot of text

Location:
trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIIO.py

    r428 r430  
    439439    File = open(filename,'Ur')
    440440    cons = Bank.split()
    441     Nch = cons[2]
     441    print cons
     442    Nch = int(cons[2])
    442443    if DataType[2] == 'C':
    443444        start = float(cons[5])/100.0               #CW: from centidegrees to degrees
     
    458459            yi = max(sfloat(S[i+2:i+8]),0.0)
    459460            if yi:
    460                 ei = yi/ni
     461                vi = yi/ni
    461462            else:
    462463                yi = 0.0
    463                 ei = 1.0
     464                vi = 1.0
    464465            j += 1
    465466            if j < Nch:
    466467                x.append(xi)
    467468                y.append(yi)
    468                 w.append(1.0/ei)
     469                w.append(1.0/vi)
     470            print '%8.3f %8.0f %d %8g'%(xi,yi,ni,1./vi)
    469471        S = File.readline()
    470472    File.close()
    471473    N = len(x)
     474    print N
    472475    return [np.array(x),np.array(y),np.array(w),np.zeros(N),np.zeros(N),np.zeros(N)]
    473476   
  • trunk/GSASIIgrid.py

    r429 r430  
    128128        if helplink is None:
    129129            # no defined link to use, create a default based on key
    130             helplink = 'gsasII.html#' + self.helpType
     130            helplink = 'gsasII.html#'+self.helpType.replace(' ','_')
     131            print helplink
    131132        helplink = os.path.join(path2GSAS2,'help',helplink)
    132133        if helpMode == 'internal':
     
    276277    def _init_coll_IndexMenu(self,parent):
    277278        parent.Append(menu=self.IndexEdit, title='Cell Index/Refine')
    278         parent.Append(menu=MyHelp(self,helpType='Cell Indexing/Refine'),title='&Help')
     279        parent.Append(menu=MyHelp(self,helpType='Cell Indexing Refine'),title='&Help')
    279280       
    280281    def _init_coll_ReflMenu(self,parent):
     
    10571058            else:       #'constraint'
    10581059                constr = map(list,zip([1.0 for i in range(len(varbs))],varbs))
    1059                 return [constr+[0.0,None]]          #just one constraint
     1060                return [constr+[1.0,None]]          #just one constraint - default sum to one
    10601061        return []
    10611062             
     
    16931694        G2plt.PlotPatterns(self)
    16941695     
    1695 def OnHelp(event):
    1696     Obj = event.GetEventObject()
    1697     line = 'Help on '+Obj.GetTitle()
    1698     for child in Obj.GetChildren():
    1699         if 'NoteBook' in str(type(child)):
    1700             notebook = child.GetCurrentPage().GetParent()
    1701             line = 'Help on '+notebook.GetPageText(notebook.GetSelection())
    1702     print line
    1703     print 'Real help will come here as HTML pages'
     1696#def OnHelp(event):
     1697#    Obj = event.GetEventObject()
     1698#    line = 'Help on '+Obj.GetTitle()
     1699#    for child in Obj.GetChildren():
     1700#        if 'NoteBook' in str(type(child)):
     1701#            notebook = child.GetCurrentPage().GetParent()
     1702#            line = 'Help on '+notebook.GetPageText(notebook.GetSelection())
     1703#    print line
     1704#    print 'Real help will come here as HTML pages'
  • trunk/GSASIIphsGUI.py

    r428 r430  
    151151            generalData['Isotope'] = {}
    152152        if 'Data plot type' not in generalData:
    153             generalData['Data plot type'] = 'Microstrain'
     153            generalData['Data plot type'] = 'Mustrain'
     154        if 'POhkl' not in generalData:
     155            generalData['POhkl'] = [0,0,1]
    154156        generalData['NoAtoms'] = {}
    155157        generalData['BondRadii'] = []
     
    447449                isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
    448450                Indx[isoSel.GetId()] = elem
    449                 elemSizer.Add(isoSel,1,wx.ALIGN_CENTER_VERTICAL)
     451                elemSizer.Add(isoSel,1,wx.ALIGN_CENTER_VERTICAL|wx.EXPAND)
    450452            elemSizer.Add(wx.StaticText(dataDisplay,label='No. per cell'),0,wx.ALIGN_CENTER_VERTICAL)
    451453            for elem in generalData['AtomTypes']:
     
    19811983            else:
    19821984                try:
    1983                     hkl = [float(Saxis[i]) for i in range(3)]
     1985                    xyz = [float(Saxis[i]) for i in range(3)]
    19841986                except (ValueError,IndexError):
    1985                     hkl = textureData['PFxyz']
    1986                 if not np.any(np.array(hkl)):       #can't be all zeros!
    1987                     hkl = textureData['PFxyz']
     1987                    xyz = textureData['PFxyz']
     1988                if not np.any(np.array(xyz)):       #can't be all zeros!
     1989                    xyz = textureData['PFxyz']
    19881990                Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
    19891991                textureData['PFxyz'] = xyz
     
    21132115       
    21142116        def OnPlotSel(event):
    2115             generalData['Data plot type'] = plotSel.GetStringSelection()
     2117            Obj = event.GetEventObject()
     2118            generalData['Data plot type'] = Obj.GetStringSelection()
     2119            UpdateDData()
     2120            G2plt.PlotSizeStrainPO(self,data)
     2121           
     2122        def OnPOhkl(event):
     2123            Obj = event.GetEventObject()
     2124            Saxis = Obj.GetValue().split()
     2125            try:
     2126                hkl = [int(Saxis[i]) for i in range(3)]
     2127            except (ValueError,IndexError):
     2128                hkl = generalData['POhkl']
     2129            if not np.any(np.array(hkl)):
     2130                hkl = generalData['POhkl']
     2131            generalData['POhkl'] = hkl
     2132            h,k,l = hkl
     2133            Obj.SetValue('%3d %3d %3d'%(h,k,l))
     2134            G2plt.PlotSizeStrainPO(self,data)
    21162135       
    21172136        def OnShowData(event):
     
    21202139            UseList[hist]['Show'] = Obj.GetValue()
    21212140            UpdateDData()
    2122             G2plt.PlotStrain(self,data)
     2141            G2plt.PlotSizeStrainPO(self,data)
    21232142           
    21242143        def OnCopyData(event):
     
    22172236            UseList[hist]['Mustrain'][0] = Obj.GetValue()
    22182237            UpdateDData()
    2219             G2plt.PlotStrain(self,data)
     2238            G2plt.PlotSizeStrainPO(self,data)
    22202239           
    22212240        def OnStrainRef(event):
     
    22472266            else:
    22482267                Obj.SetValue("%.1f"%(UseList[hist]['Mustrain'][1][pid]))          #reset in case of error
    2249             G2plt.PlotStrain(self,data)
     2268            G2plt.PlotSizeStrainPO(self,data)
    22502269           
    22512270        def OnStrainAxis(event):
     
    22622281            h,k,l = hkl
    22632282            Obj.SetValue('%3d %3d %3d'%(h,k,l))
    2264             G2plt.PlotStrain(self,data)
     2283            G2plt.PlotSizeStrainPO(self,data)
    22652284           
    22662285        def OnHstrainRef(event):
     
    23552374            return axis
    23562375           
     2376        def PlotSizer():
     2377            plotSizer = wx.BoxSizer(wx.VERTICAL)
     2378            choice = ['Mustrain','Size','Preferred orientation']
     2379            plotSel = wx.RadioBox(dataDisplay,-1,'Select plot type:',choices=choice,
     2380                majorDimension=3,style=wx.RA_SPECIFY_COLS)
     2381            plotSel.SetStringSelection(generalData['Data plot type'])
     2382            plotSel.Bind(wx.EVT_RADIOBOX,OnPlotSel)   
     2383            plotSizer.Add(plotSel)
     2384            if generalData['Data plot type'] == 'Preferred orientation':
     2385                POhklSizer = wx.BoxSizer(wx.HORIZONTAL)
     2386                POhklSizer.Add(wx.StaticText(dataDisplay,-1,' Plot preferred orientation for H K L: '),0,wx.ALIGN_CENTER_VERTICAL)
     2387                h,k,l = generalData['POhkl']
     2388                poAxis = wx.TextCtrl(dataDisplay,-1,'%3d %3d %3d'%(h,k,l),style=wx.TE_PROCESS_ENTER)
     2389                poAxis.Bind(wx.EVT_TEXT_ENTER,OnPOhkl)
     2390                poAxis.Bind(wx.EVT_KILL_FOCUS,OnPOhkl)
     2391                POhklSizer.Add(poAxis,0,wx.ALIGN_CENTER_VERTICAL)
     2392                plotSizer.Add(POhklSizer)           
     2393            return plotSizer
     2394           
    23572395        def ScaleSizer():
    23582396            scaleSizer = wx.BoxSizer(wx.HORIZONTAL)
     
    25672605        mainSizer = wx.BoxSizer(wx.VERTICAL)
    25682606        mainSizer.Add(wx.StaticText(dataDisplay,-1,'Histogram data for '+PhaseName+':'),0,wx.ALIGN_CENTER_VERTICAL)
    2569         plotSizer = wx.BoxSizer(wx.HORIZONTAL)
    2570         choice = ['Microstrain','Size','Preferred orientation']
    2571         plotSel = wx.RadioBox(dataDisplay,-1,'Select plot type:',choices=choice,
    2572             majorDimension=3,style=wx.RA_SPECIFY_COLS)
    2573         plotSel.SetStringSelection(generalData['Data plot type'])
    2574         plotSel.Bind(wx.EVT_RADIOBOX,OnPlotSel)   
    2575         plotSizer.Add(plotSel)
    2576         mainSizer.Add(plotSizer)
     2607        mainSizer.Add(PlotSizer())           
     2608           
    25772609        for item in keyList:
    25782610            histData = UseList[item]
     
    28942926            self.dataFrame.Bind(wx.EVT_MENU, OnDataDelete, id=G2gd.wxID_DATADELETE)
    28952927            UpdateDData()
    2896             G2plt.PlotStrain(self,data)
     2928            G2plt.PlotSizeStrainPO(self,data,Start=True)
    28972929        elif text == 'Draw Options':
    28982930            self.dataFrame.SetMenuBar(self.dataFrame.BlankMenu)
  • trunk/GSASIIplot.py

    r428 r430  
    3333from OpenGL.GLUT import *
    3434from OpenGL.GLE import *
     35from matplotlib.backends.backend_wx import _load_bitmap
    3536from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as Canvas
    3637from matplotlib.backends.backend_wxagg import NavigationToolbar2Wx as Toolbar
     
    5859        self.figure = mpl.figure.Figure(dpi=dpi,figsize=(5,7))
    5960        self.canvas = Canvas(self,-1,self.figure)
    60         self.toolbar = Toolbar(self.canvas)
     61        self.toolbar = GSASIItoolbar(self.canvas)
    6162
    6263        self.toolbar.Realize()
     
    8182        self.figure = mpl.figure.Figure(dpi=dpi,figsize=(6,6))
    8283        self.canvas = Canvas(self,-1,self.figure)
    83         self.toolbar = Toolbar(self.canvas)
     84        self.toolbar = GSASIItoolbar(self.canvas)
    8485
    8586        self.toolbar.Realize()
     
    156157            self.status.SetStatusText('Better to select this from GSAS-II data tree',1)
    157158        self.status.DestroyChildren()                           #get rid of special stuff on status bar
     159       
     160class GSASIItoolbar(Toolbar):
     161    ON_MPL_HELP = wx.NewId()
     162    def __init__(self,plotCanvas):
     163        Toolbar.__init__(self,plotCanvas)
     164        POSITION_OF_CONFIGURE_SUBPLOTS_BTN = 6
     165        self.DeleteToolByPos(POSITION_OF_CONFIGURE_SUBPLOTS_BTN)
     166        help = os.path.join(os.path.split(sys.argv[0])[0],'help.ico')
     167        self.AddSimpleTool(self.ON_MPL_HELP,_load_bitmap(help),'Help on','Show help on')
     168        wx.EVT_TOOL(self,self.ON_MPL_HELP,self.OnHelp)
     169    def OnHelp(self,event):
     170        Page = self.GetParent().GetParent()
     171        pageNo = Page.GetSelection()
     172       
     173        print 'Matplotlib help on '+Page.GetPageText(pageNo)
    158174       
    159175def PlotSngl(self,newPlot=False):
     
    11371153    Page.canvas.draw()
    11381154   
    1139 def PlotStrain(self,data):
    1140     '''Plot 3D microstrain figure. In this instance data is for a phase
     1155def PlotSizeStrainPO(self,data,Start=False):
     1156    '''Plot 3D mustrain/size/preferred orientation figure. In this instance data is for a phase
    11411157    '''
     1158   
    11421159    PatternId = self.PatternId
    11431160    generalData = data['General']
    11441161    SGData = generalData['SGData']
     1162    SGLaue = SGData['SGLaue']
     1163    if Start:                   #initialize the spherical harmonics qlmn arrays
     1164        ptx.pyqlmninit()
     1165        Start = False
    11451166    MuStrKeys = G2spc.MustrainNames(SGData)
    11461167    cell = generalData['Cell'][1:]
     
    11481169    Vol = cell[6]
    11491170    useList = data['Histograms']
     1171    phase = generalData['Name']
     1172    plotType = generalData['Data plot type']
     1173    plotDict = {'Mustrain':'Mustrain','Size':'Size','Preferred orientation':'Pref.Ori.'}
     1174    for ptype in plotDict:
     1175        self.G2plotNB.Delete(ptype)       
     1176
    11501177    for item in useList:
    11511178        if useList[item]['Show']:
    11521179            break
    11531180    else:
    1154         self.G2plotNB.Delete('Microstrain')
    11551181        return            #nothing to show!!
    11561182   
    11571183    numPlots = len(useList)
    1158    
    1159     try:
    1160         plotNum = self.G2plotNB.plotList.index('Microstrain')
    1161         Page = self.G2plotNB.nb.GetPage(plotNum)
    1162         Page.figure.clf()
    1163         Plot = mp3d.Axes3D(Page.figure)
    1164         if not Page.IsShown():
    1165             Page.Show()
    1166     except ValueError:
    1167         Plot = mp3d.Axes3D(self.G2plotNB.add3D('Microstrain'))
    1168         plotNum = self.G2plotNB.plotList.index('Microstrain')
    1169         Page = self.G2plotNB.nb.GetPage(plotNum)
     1184
     1185    if plotType in ['Mustrain','Size']:
     1186        Plot = mp3d.Axes3D(self.G2plotNB.add3D(plotType))
     1187    else:
     1188        Plot = self.G2plotNB.addMpl(plotType).gca()       
     1189    plotNum = self.G2plotNB.plotList.index(plotType)
     1190    Page = self.G2plotNB.nb.GetPage(plotNum)
    11701191    Page.SetFocus()
    11711192    self.G2plotNB.status.SetStatusText('Adjust frame size to get desired aspect ratio',1)
     1193    if not Page.IsShown():
     1194        Page.Show()
    11721195   
    11731196    for item in useList:
    11741197        if useList[item]['Show']:
    1175             muStrain = useList[item]['Mustrain']
    11761198            PHI = np.linspace(0.,360.,30,True)
    11771199            PSI = np.linspace(0.,180.,30,True)
     
    11791201            Y = np.outer(npcosd(PHI),npsind(PSI))
    11801202            Z = np.outer(np.ones(np.size(PHI)),npcosd(PSI))
    1181             if muStrain[0] == 'isotropic':
    1182 #                muiso = muStrain[1][0]*math.pi/0.018      #centidegrees to radians!
    1183                 muiso = muStrain[1][0]
    1184                 X *= muiso
    1185                 Y *= muiso
    1186                 Z *= muiso               
    1187                
    1188             elif muStrain[0] == 'uniaxial':
    1189                 def uniaxMustrain(xyz,muiso,muaniso,axes):
    1190                     Z = np.array(axes)
    1191                     cp = abs(np.dot(xyz,Z))
    1192                     sp = np.sqrt(1.-cp**2)
    1193                     R = muiso*muaniso/np.sqrt((muiso*cp)**2+(muaniso*sp)**2)
    1194 #                    S = muiso+muaniso*cp           #old GSAS - wrong math!!
    1195 #                    return R*xyz*math.pi/0.018      #centidegrees to radians!
    1196                     return R*xyz
    1197                 muiso,muaniso = muStrain[1][:2]
    1198                 axes = np.inner(A,np.array(muStrain[3]))
    1199                 axes /= nl.norm(axes)
    1200                 Shkl = np.array(muStrain[1])
    1201                 Shape = X.shape[0]
    1202                 XYZ = np.dstack((X,Y,Z))
    1203                 XYZ = np.nan_to_num(np.apply_along_axis(uniaxMustrain,2,XYZ,muiso,muaniso,axes))
    1204                 X,Y,Z = np.dsplit(XYZ,3)
    1205                 X = X[:,:,0]
    1206                 Y = Y[:,:,0]
    1207                 Z = Z[:,:,0]
    1208                
    1209             elif muStrain[0] == 'generalized':
    1210                 def genMustrain(xyz,SGData,A,Shkl):
    1211                     uvw = np.inner(A.T,xyz)
    1212                     Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
    1213                     sum = np.sum(np.multiply(Shkl,Strm))
    1214                     sum = np.where(sum > 0.01,sum,0.01)
    1215                     sum = np.sqrt(sum)*math.pi/0.018      #centidegrees to radians!
    1216                     return sum*xyz
    1217                 Shkl = np.array(muStrain[4])
    1218                 if np.any(Shkl):
     1203            coeff = useList[item][plotDict[plotType]]
     1204            if plotType in ['Mustrain','Size']:
     1205                if coeff[0] == 'isotropic':
     1206                    X *= coeff[1][0]
     1207                    Y *= coeff[1][0]
     1208                    Z *= coeff[1][0]                               
     1209                elif coeff[0] == 'uniaxial':
     1210                   
     1211                    def uniaxCalc(xyz,iso,aniso,axes):
     1212                        Z = np.array(axes)
     1213                        cp = abs(np.dot(xyz,Z))
     1214                        sp = np.sqrt(1.-cp**2)
     1215                        R = iso*aniso/np.sqrt((iso*cp)**2+(aniso*sp)**2)
     1216                        return R*xyz
     1217                       
     1218                    iso,aniso = coeff[1][:2]
     1219                    axes = np.inner(A,np.array(coeff[3]))
     1220                    axes /= nl.norm(axes)
     1221                    Shkl = np.array(coeff[1])
    12191222                    Shape = X.shape[0]
    12201223                    XYZ = np.dstack((X,Y,Z))
    1221                     XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
     1224                    XYZ = np.nan_to_num(np.apply_along_axis(uniaxCalc,2,XYZ,iso,aniso,axes))
    12221225                    X,Y,Z = np.dsplit(XYZ,3)
    12231226                    X = X[:,:,0]
    12241227                    Y = Y[:,:,0]
    12251228                    Z = Z[:,:,0]
     1229               
     1230                elif coeff[0] == 'generalized':
    12261231                   
    1227             if np.any(X) and np.any(Y) and np.any(Z):
    1228                 Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
     1232                    def genMustrain(xyz,SGData,A,Shkl):
     1233                        uvw = np.inner(A.T,xyz)
     1234                        Strm = np.array(G2spc.MustrainCoeff(uvw,SGData))
     1235                        sum = np.sum(np.multiply(Shkl,Strm))
     1236                        sum = np.where(sum > 0.01,sum,0.01)
     1237                        sum = np.sqrt(sum)*math.pi/0.018      #centidegrees to radians!
     1238                        return sum*xyz
     1239                       
     1240                    Shkl = np.array(coeff[4])
     1241                    if np.any(Shkl):
     1242                        Shape = X.shape[0]
     1243                        XYZ = np.dstack((X,Y,Z))
     1244                        XYZ = np.nan_to_num(np.apply_along_axis(genMustrain,2,XYZ,SGData,A,Shkl))
     1245                        X,Y,Z = np.dsplit(XYZ,3)
     1246                        X = X[:,:,0]
     1247                        Y = Y[:,:,0]
     1248                        Z = Z[:,:,0]
     1249                           
     1250                elif coeff[0] == 'ellipsoidal':
     1251                    print 'ellipsoid plot'
     1252                   
     1253                if np.any(X) and np.any(Y) and np.any(Z):
     1254                    Plot.plot_surface(X,Y,Z,rstride=1,cstride=1,color='g',linewidth=1)
     1255                if plotType == 'Size':
     1256                    Plot.set_title('Crystallite size for '+phase)
     1257                    Plot.set_xlabel(r'X, $\mu$m')
     1258                    Plot.set_ylabel(r'Y, $\mu$m')
     1259                    Plot.set_zlabel(r'Z, $\mu$m')
     1260                else:   
     1261                    Plot.set_title(r'$\mu$strain for '+phase)
     1262                    Plot.set_xlabel(r'X, $\mu$strain')
     1263                    Plot.set_ylabel(r'Y, $\mu$strain')
     1264                    Plot.set_zlabel(r'Z, $\mu$strain')
     1265            else:
     1266                h,k,l = generalData['POhkl']
     1267                if coeff[0] == 'MD':
     1268                    print 'March-Dollase preferred orientation plot'
    12291269               
    1230             Plot.set_xlabel('X')
    1231             Plot.set_ylabel('Y')
    1232             Plot.set_zlabel('Z')
     1270                else:
     1271                    PH = np.array(generalData['POhkl'])
     1272                    phi,beta = G2lat.CrsAng(PH,cell[:6],SGData)
     1273                    SHCoef = {}
     1274                    for item in coeff[5]:
     1275                        L,N = eval(item.strip('C'))
     1276                        SHCoef['C%d,0,%d'%(L,N)] = coeff[5][item]                       
     1277                    ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData)
     1278                    X = np.linspace(0,90.0,26)
     1279                    Y = G2lat.polfcal(ODFln,'0',X,0.0)
     1280                    Plot.plot(X,Y,color='k',label=str(PH))
     1281                    Plot.legend(loc='best')
     1282                    Plot.set_title('Axial distribution for HKL='+str(PH)+' in '+phase)
     1283                    Plot.set_xlabel(r'$\psi$',fontsize=16)
     1284                    Plot.set_ylabel('MRD',fontsize=14)
    12331285    Page.canvas.draw()
    12341286   
     
    12461298    SGData = generalData['SGData']
    12471299    textureData = generalData['SH Texture']
     1300    self.G2plotNB.Delete('Texture')
    12481301    if not textureData['Order']:
    1249         self.G2plotNB.Delete('Texture')
    12501302        return                  #no plot!!
    12511303    SHData = generalData['SH Texture']
     
    12771329                   
    12781330                    self.G2plotNB.status.SetFields(['',
    1279                         'psi =%9.3f, beta =%9.3f, MRD =%9.3f xyz=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
     1331                        'psi =%9.3f, beta =%9.3f, MRD =%9.3f hkl=%5.2f,%5.2f,%5.2f'%(r,p,ipf,x,y,z)])
    12801332                                   
    12811333            elif 'Axial' in SHData['PlotType']:
     
    12931345                    self.G2plotNB.status.SetFields(['','phi =%9.3f, gam =%9.3f, MRD =%9.3f'%(r,p,pf)])
    12941346                   
    1295     try:
    1296         plotNum = self.G2plotNB.plotList.index('Texture')
    1297         Page = self.G2plotNB.nb.GetPage(plotNum)
    1298         Page.figure.clf()
    1299         Plot = Page.figure.gca()
    1300         if not Page.IsShown():
    1301             Page.Show()
    1302     except ValueError:
    1303         Plot = self.G2plotNB.addMpl('Texture').gca()
    1304         plotNum = self.G2plotNB.plotList.index('Texture')
    1305         Page = self.G2plotNB.nb.GetPage(plotNum)
    1306         Page.canvas.mpl_connect('motion_notify_event', OnMotion)
     1347    Plot = self.G2plotNB.addMpl('Texture').gca()
     1348    plotNum = self.G2plotNB.plotList.index('Texture')
     1349    Page = self.G2plotNB.nb.GetPage(plotNum)
     1350    Page.canvas.mpl_connect('motion_notify_event', OnMotion)
    13071351
    13081352    Page.SetFocus()
  • trunk/help/gsasII.html

    r427 r430  
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    322<title>Help for GSAS-II</title>
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     25  <o:Author>Von Dreele</o:Author>
     26  <o:LastAuthor>Von Dreele</o:LastAuthor>
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     34  <o:Company>Argonne National Laboratory</o:Company>
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     227   UnhideWhenUsed="false" Name="Medium Shading 1 Accent 3"/>
     228  <w:LsdException Locked="false" Priority="64" SemiHidden="false"
     229   UnhideWhenUsed="false" Name="Medium Shading 2 Accent 3"/>
     230  <w:LsdException Locked="false" Priority="65" SemiHidden="false"
     231   UnhideWhenUsed="false" Name="Medium List 1 Accent 3"/>
     232  <w:LsdException Locked="false" Priority="66" SemiHidden="false"
     233   UnhideWhenUsed="false" Name="Medium List 2 Accent 3"/>
     234  <w:LsdException Locked="false" Priority="67" SemiHidden="false"
     235   UnhideWhenUsed="false" Name="Medium Grid 1 Accent 3"/>
     236  <w:LsdException Locked="false" Priority="68" SemiHidden="false"
     237   UnhideWhenUsed="false" Name="Medium Grid 2 Accent 3"/>
     238  <w:LsdException Locked="false" Priority="69" SemiHidden="false"
     239   UnhideWhenUsed="false" Name="Medium Grid 3 Accent 3"/>
     240  <w:LsdException Locked="false" Priority="70" SemiHidden="false"
     241   UnhideWhenUsed="false" Name="Dark List Accent 3"/>
     242  <w:LsdException Locked="false" Priority="71" SemiHidden="false"
     243   UnhideWhenUsed="false" Name="Colorful Shading Accent 3"/>
     244  <w:LsdException Locked="false" Priority="72" SemiHidden="false"
     245   UnhideWhenUsed="false" Name="Colorful List Accent 3"/>
     246  <w:LsdException Locked="false" Priority="73" SemiHidden="false"
     247   UnhideWhenUsed="false" Name="Colorful Grid Accent 3"/>
     248  <w:LsdException Locked="false" Priority="60" SemiHidden="false"
     249   UnhideWhenUsed="false" Name="Light Shading Accent 4"/>
     250  <w:LsdException Locked="false" Priority="61" SemiHidden="false"
     251   UnhideWhenUsed="false" Name="Light List Accent 4"/>
     252  <w:LsdException Locked="false" Priority="62" SemiHidden="false"
     253   UnhideWhenUsed="false" Name="Light Grid Accent 4"/>
     254  <w:LsdException Locked="false" Priority="63" SemiHidden="false"
     255   UnhideWhenUsed="false" Name="Medium Shading 1 Accent 4"/>
     256  <w:LsdException Locked="false" Priority="64" SemiHidden="false"
     257   UnhideWhenUsed="false" Name="Medium Shading 2 Accent 4"/>
     258  <w:LsdException Locked="false" Priority="65" SemiHidden="false"
     259   UnhideWhenUsed="false" Name="Medium List 1 Accent 4"/>
     260  <w:LsdException Locked="false" Priority="66" SemiHidden="false"
     261   UnhideWhenUsed="false" Name="Medium List 2 Accent 4"/>
     262  <w:LsdException Locked="false" Priority="67" SemiHidden="false"
     263   UnhideWhenUsed="false" Name="Medium Grid 1 Accent 4"/>
     264  <w:LsdException Locked="false" Priority="68" SemiHidden="false"
     265   UnhideWhenUsed="false" Name="Medium Grid 2 Accent 4"/>
     266  <w:LsdException Locked="false" Priority="69" SemiHidden="false"
     267   UnhideWhenUsed="false" Name="Medium Grid 3 Accent 4"/>
     268  <w:LsdException Locked="false" Priority="70" SemiHidden="false"
     269   UnhideWhenUsed="false" Name="Dark List Accent 4"/>
     270  <w:LsdException Locked="false" Priority="71" SemiHidden="false"
     271   UnhideWhenUsed="false" Name="Colorful Shading Accent 4"/>
     272  <w:LsdException Locked="false" Priority="72" SemiHidden="false"
     273   UnhideWhenUsed="false" Name="Colorful List Accent 4"/>
     274  <w:LsdException Locked="false" Priority="73" SemiHidden="false"
     275   UnhideWhenUsed="false" Name="Colorful Grid Accent 4"/>
     276  <w:LsdException Locked="false" Priority="60" SemiHidden="false"
     277   UnhideWhenUsed="false" Name="Light Shading Accent 5"/>
     278  <w:LsdException Locked="false" Priority="61" SemiHidden="false"
     279   UnhideWhenUsed="false" Name="Light List Accent 5"/>
     280  <w:LsdException Locked="false" Priority="62" SemiHidden="false"
     281   UnhideWhenUsed="false" Name="Light Grid Accent 5"/>
     282  <w:LsdException Locked="false" Priority="63" SemiHidden="false"
     283   UnhideWhenUsed="false" Name="Medium Shading 1 Accent 5"/>
     284  <w:LsdException Locked="false" Priority="64" SemiHidden="false"
     285   UnhideWhenUsed="false" Name="Medium Shading 2 Accent 5"/>
     286  <w:LsdException Locked="false" Priority="65" SemiHidden="false"
     287   UnhideWhenUsed="false" Name="Medium List 1 Accent 5"/>
     288  <w:LsdException Locked="false" Priority="66" SemiHidden="false"
     289   UnhideWhenUsed="false" Name="Medium List 2 Accent 5"/>
     290  <w:LsdException Locked="false" Priority="67" SemiHidden="false"
     291   UnhideWhenUsed="false" Name="Medium Grid 1 Accent 5"/>
     292  <w:LsdException Locked="false" Priority="68" SemiHidden="false"
     293   UnhideWhenUsed="false" Name="Medium Grid 2 Accent 5"/>
     294  <w:LsdException Locked="false" Priority="69" SemiHidden="false"
     295   UnhideWhenUsed="false" Name="Medium Grid 3 Accent 5"/>
     296  <w:LsdException Locked="false" Priority="70" SemiHidden="false"
     297   UnhideWhenUsed="false" Name="Dark List Accent 5"/>
     298  <w:LsdException Locked="false" Priority="71" SemiHidden="false"
     299   UnhideWhenUsed="false" Name="Colorful Shading Accent 5"/>
     300  <w:LsdException Locked="false" Priority="72" SemiHidden="false"
     301   UnhideWhenUsed="false" Name="Colorful List Accent 5"/>
     302  <w:LsdException Locked="false" Priority="73" SemiHidden="false"
     303   UnhideWhenUsed="false" Name="Colorful Grid Accent 5"/>
     304  <w:LsdException Locked="false" Priority="60" SemiHidden="false"
     305   UnhideWhenUsed="false" Name="Light Shading Accent 6"/>
     306  <w:LsdException Locked="false" Priority="61" SemiHidden="false"
     307   UnhideWhenUsed="false" Name="Light List Accent 6"/>
     308  <w:LsdException Locked="false" Priority="62" SemiHidden="false"
     309   UnhideWhenUsed="false" Name="Light Grid Accent 6"/>
     310  <w:LsdException Locked="false" Priority="63" SemiHidden="false"
     311   UnhideWhenUsed="false" Name="Medium Shading 1 Accent 6"/>
     312  <w:LsdException Locked="false" Priority="64" SemiHidden="false"
     313   UnhideWhenUsed="false" Name="Medium Shading 2 Accent 6"/>
     314  <w:LsdException Locked="false" Priority="65" SemiHidden="false"
     315   UnhideWhenUsed="false" Name="Medium List 1 Accent 6"/>
     316  <w:LsdException Locked="false" Priority="66" SemiHidden="false"
     317   UnhideWhenUsed="false" Name="Medium List 2 Accent 6"/>
     318  <w:LsdException Locked="false" Priority="67" SemiHidden="false"
     319   UnhideWhenUsed="false" Name="Medium Grid 1 Accent 6"/>
     320  <w:LsdException Locked="false" Priority="68" SemiHidden="false"
     321   UnhideWhenUsed="false" Name="Medium Grid 2 Accent 6"/>
     322  <w:LsdException Locked="false" Priority="69" SemiHidden="false"
     323   UnhideWhenUsed="false" Name="Medium Grid 3 Accent 6"/>
     324  <w:LsdException Locked="false" Priority="70" SemiHidden="false"
     325   UnhideWhenUsed="false" Name="Dark List Accent 6"/>
     326  <w:LsdException Locked="false" Priority="71" SemiHidden="false"
     327   UnhideWhenUsed="false" Name="Colorful Shading Accent 6"/>
     328  <w:LsdException Locked="false" Priority="72" SemiHidden="false"
     329   UnhideWhenUsed="false" Name="Colorful List Accent 6"/>
     330  <w:LsdException Locked="false" Priority="73" SemiHidden="false"
     331   UnhideWhenUsed="false" Name="Colorful Grid Accent 6"/>
     332  <w:LsdException Locked="false" Priority="19" SemiHidden="false"
     333   UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis"/>
     334  <w:LsdException Locked="false" Priority="21" SemiHidden="false"
     335   UnhideWhenUsed="false" QFormat="true" Name="Intense Emphasis"/>
     336  <w:LsdException Locked="false" Priority="31" SemiHidden="false"
     337   UnhideWhenUsed="false" QFormat="true" Name="Subtle Reference"/>
     338  <w:LsdException Locked="false" Priority="32" SemiHidden="false"
     339   UnhideWhenUsed="false" QFormat="true" Name="Intense Reference"/>
     340  <w:LsdException Locked="false" Priority="33" SemiHidden="false"
     341   UnhideWhenUsed="false" QFormat="true" Name="Book Title"/>
     342  <w:LsdException Locked="false" Priority="37" Name="Bibliography"/>
     343  <w:LsdException Locked="false" Priority="39" QFormat="true" Name="TOC Heading"/>
     344 </w:LatentStyles>
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     350        {font-family:"Cambria Math";
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     354        mso-font-format:other;
     355        mso-font-pitch:variable;
     356        mso-font-signature:0 0 0 0 0 0;}
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     362        mso-font-pitch:variable;
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     369        mso-font-pitch:variable;
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     374        mso-style-qformat:yes;
     375        mso-style-parent:"";
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     382        mso-fareast-theme-font:minor-fareast;}
     383h1
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     386        mso-style-qformat:yes;
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     399h2
     400        {mso-style-priority:9;
     401        mso-style-unhide:no;
     402        mso-style-qformat:yes;
     403        mso-style-link:"Heading 2 Char";
     404        mso-margin-top-alt:auto;
     405        margin-right:0in;
     406        mso-margin-bottom-alt:auto;
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     411        font-family:"Times New Roman","serif";
     412        mso-fareast-font-family:"Times New Roman";
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     414        font-weight:bold;}
     415h3
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     417        mso-style-unhide:no;
     418        mso-style-qformat:yes;
     419        mso-style-link:"Heading 3 Char";
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     421        margin-right:0in;
     422        mso-margin-bottom-alt:auto;
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     424        mso-pagination:widow-orphan;
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     426        font-size:13.5pt;
     427        font-family:"Times New Roman","serif";
     428        mso-fareast-font-family:"Times New Roman";
     429        mso-fareast-theme-font:minor-fareast;
     430        font-weight:bold;}
     431h4
     432        {mso-style-noshow:yes;
     433        mso-style-priority:9;
     434        mso-style-qformat:yes;
     435        mso-style-link:"Heading 4 Char";
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     438        margin-right:0in;
     439        margin-bottom:0in;
     440        margin-left:0in;
     441        margin-bottom:.0001pt;
     442        mso-pagination:widow-orphan lines-together;
     443        page-break-after:avoid;
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     446        font-family:"Cambria","serif";
     447        mso-ascii-font-family:Cambria;
     448        mso-ascii-theme-font:major-latin;
     449        mso-fareast-font-family:"Times New Roman";
     450        mso-fareast-theme-font:major-fareast;
     451        mso-hansi-font-family:Cambria;
     452        mso-hansi-theme-font:major-latin;
     453        mso-bidi-font-family:"Times New Roman";
     454        mso-bidi-theme-font:major-bidi;
     455        color:#4F81BD;
     456        mso-themecolor:accent1;
     457        font-weight:bold;
     458        font-style:italic;}
     459a:link, span.MsoHyperlink
     460        {mso-style-priority:99;
     461        color:blue;
     462        text-decoration:underline;
     463        text-underline:single;}
     464a:visited, span.MsoHyperlinkFollowed
     465        {mso-style-noshow:yes;
     466        mso-style-priority:99;
     467        color:purple;
     468        text-decoration:underline;
     469        text-underline:single;}
     470p
     471        {mso-style-noshow:yes;
     472        mso-style-priority:99;
     473        mso-margin-top-alt:auto;
     474        margin-right:0in;
     475        mso-margin-bottom-alt:auto;
     476        margin-left:0in;
     477        mso-pagination:widow-orphan;
     478        font-size:12.0pt;
     479        font-family:"Times New Roman","serif";
     480        mso-fareast-font-family:"Times New Roman";
     481        mso-fareast-theme-font:minor-fareast;}
     482pre
     483        {mso-style-noshow:yes;
     484        mso-style-priority:99;
     485        mso-style-link:"HTML Preformatted Char";
     486        margin:0in;
     487        margin-bottom:.0001pt;
     488        mso-pagination:widow-orphan;
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     491        font-family:"Courier New";
     492        mso-fareast-font-family:"Times New Roman";}
     493p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
     494        {mso-style-noshow:yes;
     495        mso-style-priority:99;
     496        mso-style-link:"Balloon Text Char";
     497        margin:0in;
     498        margin-bottom:.0001pt;
     499        mso-pagination:widow-orphan;
     500        font-size:8.0pt;
     501        font-family:"Tahoma","sans-serif";
     502        mso-fareast-font-family:"Times New Roman";
     503        mso-fareast-theme-font:minor-fareast;}
     504span.MsoPlaceholderText
     505        {mso-style-noshow:yes;
     506        mso-style-priority:99;
     507        mso-style-unhide:no;
     508        color:gray;}
     509p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
     510        {mso-style-noshow:yes;
     511        mso-style-priority:34;
     512        mso-style-unhide:no;
     513        mso-style-qformat:yes;
     514        margin-top:0in;
     515        margin-right:0in;
     516        margin-bottom:0in;
     517        margin-left:.5in;
     518        margin-bottom:.0001pt;
     519        mso-add-space:auto;
     520        mso-pagination:widow-orphan;
     521        font-size:12.0pt;
     522        font-family:"Times New Roman","serif";
     523        mso-fareast-font-family:"Times New Roman";
     524        mso-fareast-theme-font:minor-fareast;}
     525p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
     526        {mso-style-noshow:yes;
     527        mso-style-priority:34;
     528        mso-style-unhide:no;
     529        mso-style-qformat:yes;
     530        mso-style-type:export-only;
     531        margin-top:0in;
     532        margin-right:0in;
     533        margin-bottom:0in;
     534        margin-left:.5in;
     535        margin-bottom:.0001pt;
     536        mso-add-space:auto;
     537        mso-pagination:widow-orphan;
     538        font-size:12.0pt;
     539        font-family:"Times New Roman","serif";
     540        mso-fareast-font-family:"Times New Roman";
     541        mso-fareast-theme-font:minor-fareast;}
     542p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
     543        {mso-style-noshow:yes;
     544        mso-style-priority:34;
     545        mso-style-unhide:no;
     546        mso-style-qformat:yes;
     547        mso-style-type:export-only;
     548        margin-top:0in;
     549        margin-right:0in;
     550        margin-bottom:0in;
     551        margin-left:.5in;
     552        margin-bottom:.0001pt;
     553        mso-add-space:auto;
     554        mso-pagination:widow-orphan;
     555        font-size:12.0pt;
     556        font-family:"Times New Roman","serif";
     557        mso-fareast-font-family:"Times New Roman";
     558        mso-fareast-theme-font:minor-fareast;}
     559p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
     560        {mso-style-noshow:yes;
     561        mso-style-priority:34;
     562        mso-style-unhide:no;
     563        mso-style-qformat:yes;
     564        mso-style-type:export-only;
     565        margin-top:0in;
     566        margin-right:0in;
     567        margin-bottom:0in;
     568        margin-left:.5in;
     569        margin-bottom:.0001pt;
     570        mso-add-space:auto;
     571        mso-pagination:widow-orphan;
     572        font-size:12.0pt;
     573        font-family:"Times New Roman","serif";
     574        mso-fareast-font-family:"Times New Roman";
     575        mso-fareast-theme-font:minor-fareast;}
     576span.Heading1Char
     577        {mso-style-name:"Heading 1 Char";
     578        mso-style-priority:9;
     579        mso-style-unhide:no;
     580        mso-style-locked:yes;
     581        mso-style-link:"Heading 1";
     582        mso-ansi-font-size:14.0pt;
     583        mso-bidi-font-size:14.0pt;
     584        font-family:"Cambria","serif";
     585        mso-ascii-font-family:Cambria;
     586        mso-ascii-theme-font:major-latin;
     587        mso-fareast-font-family:"Times New Roman";
     588        mso-fareast-theme-font:major-fareast;
     589        mso-hansi-font-family:Cambria;
     590        mso-hansi-theme-font:major-latin;
     591        mso-bidi-font-family:"Times New Roman";
     592        mso-bidi-theme-font:major-bidi;
     593        color:#365F91;
     594        mso-themecolor:accent1;
     595        mso-themeshade:191;
     596        font-weight:bold;}
     597span.Heading2Char
     598        {mso-style-name:"Heading 2 Char";
     599        mso-style-noshow:yes;
     600        mso-style-priority:9;
     601        mso-style-unhide:no;
     602        mso-style-locked:yes;
     603        mso-style-link:"Heading 2";
     604        mso-ansi-font-size:13.0pt;
     605        mso-bidi-font-size:13.0pt;
     606        font-family:"Cambria","serif";
     607        mso-ascii-font-family:Cambria;
     608        mso-ascii-theme-font:major-latin;
     609        mso-fareast-font-family:"Times New Roman";
     610        mso-fareast-theme-font:major-fareast;
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     982@list l6:level8
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     990ol
     991        {margin-bottom:0in;}
     992ul
     993        {margin-bottom:0in;}
     994-->
     995</style>
     996<!--[if gte mso 10]>
     997<style>
     998 /* Style Definitions */
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     1002        mso-tstyle-colband-size:0;
     1003        mso-style-noshow:yes;
     1004        mso-style-priority:99;
     1005        mso-style-qformat:yes;
     1006        mso-style-parent:"";
     1007        mso-padding-alt:0in 5.4pt 0in 5.4pt;
     1008        mso-para-margin:0in;
     1009        mso-para-margin-bottom:.0001pt;
     1010        mso-pagination:widow-orphan;
     1011        font-size:10.0pt;
     1012        font-family:"Times New Roman","serif";}
     1013</style>
     1014<![endif]--><!--[if gte mso 9]><xml>
     1015 <o:shapedefaults v:ext="edit" spidmax="6146"/>
     1016</xml><![endif]--><!--[if gte mso 9]><xml>
     1017 <o:shapelayout v:ext="edit">
     1018  <o:idmap v:ext="edit" data="1"/>
     1019 </o:shapelayout></xml><![endif]-->
    41020</head>
    51021
    6 <body>
    7 <P align="RIGHT"><IMG SRC="gsas2logo.png" alt="GSAS-II logo" align="RIGHT"></P>
    8 <h1>Help for GSAS-II</h1>
    9 
    10 This is where to find help on various GSAS-II windows.
    11 <A name="Data tree"><h2>GSAS-II data tree</h2></A>
    12 This is a hierarchical view of the data items in the current
    13 project. Clicking on any item in the window opens a view where
    14 information in that item can be viewed or edited. For example, the
    15 <a href="#Sample Parameters">"Sample Parameters"</A>
    16 item contains information about how data were
    17 collected, such as the sample temperature
    18 <a href="#Sample Parameters">(see below)</A>.
    19 
    20 
    21 <A name="Atoms"><h3>Atoms Control Window</H3></A>
    22 This window...
    23 <A name="Constraints"><h3>Constraints Control Window</H3></A>
    24 This window...
    25 <A name="Restraints"><h3>Restraints Control Window</H3></A>
    26 This window...
    27 <A name="Data"><h3>DiffractionData Control Window</H3></A>
    28 This window...
    29 <A name="Draw Atoms"><h3>Draw Atoms Control Window</H3></A>
    30 This window...
    31 <A name="Pawley"><h3>Pawley Control Window</H3></A>
    32 This window...
    33 <A name="Index Peaks"><h3>Index Peaks Control Window</H3></A>
    34 This window...
    35 <A name="Images"><h3>Images Control Window</H3></A>
    36 This window...
    37 <A name="Background"><h3>Background Control Window</H3></A>
    38 This window...
    39 <A name="Limits"><h3>Limits Control Window</H3></A>
    40 This window...
    41 <A name="Instrument Parameters"><h3>Instrument Parameters Control Window</H3></A>
    42 This window...
    43 <A name="Image Masks"><h3>Image Masks Control Window</H3></A>
    44 This window...
    45 <A name="Sample Parameters"><h3>Sample Parameters Control Window</H3></A>
    46 This window...
    47 <A name="Powder Peaks"><h3>Powder Peaks Control Window</H3></A>
    48 This window...
    49 <A name="Cell Indexing/Refine"><h3>Cell Indexing/Refine Control Window</H3></A>
    50 This window...
    51 <A name="Reflection List"><h3>Reflection List Control Window</H3></A>
    52 This window...
    53 <A name="Texture"><h3>Texture Control Window</H3></A>
    54 This window...
    55 <A name="PDF Controls"><h3>PDF Controls Control Window</H3></A>
    56 This window...
    57 
    58 <hr>
    59 <!-- hhmts start --> Last modified: Tue Nov 22 13:19:47 CST 2011 <!-- hhmts end -->
    60 </body> </html>
     1022<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
     1023
     1024<div class=WordSection1>
     1025
     1026<h1><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600"
     1027 o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f"
     1028 stroked="f">
     1029 <v:stroke joinstyle="miter"/>
     1030 <v:formulas>
     1031  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
     1032  <v:f eqn="sum @0 1 0"/>
     1033  <v:f eqn="sum 0 0 @1"/>
     1034  <v:f eqn="prod @2 1 2"/>
     1035  <v:f eqn="prod @3 21600 pixelWidth"/>
     1036  <v:f eqn="prod @3 21600 pixelHeight"/>
     1037  <v:f eqn="sum @0 0 1"/>
     1038  <v:f eqn="prod @6 1 2"/>
     1039  <v:f eqn="prod @7 21600 pixelWidth"/>
     1040  <v:f eqn="sum @8 21600 0"/>
     1041  <v:f eqn="prod @7 21600 pixelHeight"/>
     1042  <v:f eqn="sum @10 21600 0"/>
     1043 </v:formulas>
     1044 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
     1045 <o:lock v:ext="edit" aspectratio="t"/>
     1046</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1035" type="#_x0000_t75"
     1047 alt="GSAS-II logo" style='position:absolute;margin-left:56pt;margin-top:0;
     1048 width:96pt;height:96pt;z-index:1;visibility:visible;mso-wrap-style:square;
     1049 mso-wrap-distance-left:0;mso-wrap-distance-top:0;mso-wrap-distance-right:0;
     1050 mso-wrap-distance-bottom:0;mso-position-horizontal:right;
     1051 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
     1052 mso-position-vertical-relative:line' o:allowoverlap="f">
     1053 <v:imagedata src="gsas2logo.png"/>
     1054 <w:wrap type="square" anchory="line"/>
     1055</v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
     1056align=right alt="GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
     1057style='mso-fareast-font-family:"Times New Roman"'>Help for GSAS-II<o:p></o:p></span></h1>
     1058
     1059<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1060is where to find help on various GSAS-II windows and plots. <o:p></o:p></span></p>
     1061
     1062<h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times New Roman"'>GSAS-II
     1063data tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
     1064
     1065<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1066is a hierarchical view of the data items in your GSAS-II project (name.gpx). Clicking
     1067on any item in the window opens a view where information in that item can be
     1068viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
     1069Parameters&quot;</a> item contains information about how data were collected,
     1070such as the sample temperature <a href="#Sample_Parameters">(see below)</a>. <o:p></o:p></span></p>
     1071
     1072<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1073
     1074<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1075style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1076style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     1077&#8216;<b style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211;</p>
     1078
     1079<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1080auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1081style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1082style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1083style='mso-bidi-font-weight:normal'>Open project&#8230;</b> - Open a previously
     1084saved GSAS-II project file (name.gpx). If you currently have a project file
     1085open, you are asked if it is OK to over write it; Cancel will cancel the
     1086process.</p>
     1087
     1088<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1089auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1090style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1091style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1092style='mso-bidi-font-weight:normal'>Save project</b> &#8211; Save the current
     1093project. If a file name is shown after &#8216;Loaded <span class=GramE>Data:&#8217;<span
     1094style='mso-fareast-font-family:"Times New Roman"'>,</span></span><span
     1095style='mso-fareast-font-family:"Times New Roman"'> it will be saved there.
     1096Otherwise, you will be prompted for a new name in a file dialog (you may change
     1097directory as well). If the file exists, you will be asked if it OK to
     1098overwrite.</span></p>
     1099
     1100<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1101auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1102style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     1103style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1104style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Save
     1105As&#8230;</span></b><span style='mso-fareast-font-family:"Times New Roman"'> -
     1106Save the current project to a new file. A file dialog will be shown to enter
     1107the name (and change directory if desired). If the file exists, you will be
     1108asked if it OK to overwrite.</span></p>
     1109
     1110<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1111auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1112style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     1113style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1114style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Close
     1115project</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     1116&#8211; Close the current project; you will be asked if you want to save it
     1117first.</span></p>
     1118
     1119<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1120auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1121style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
     1122style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1123style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Exit</span></b><span
     1124style='mso-fareast-font-family:"Times New Roman"'> &#8211; Exit the GSAS-II
     1125program; if there is a current project you will be asked if you want to save it
     1126first. Pressing the red X in the upper right (Windows) also exits (no save
     1127option) GSAS-II; useful for escaping from GSAS-II if needed.</span></p>
     1128
     1129<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1130style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1131style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     1132&#8216;<b style='mso-bidi-font-weight:normal'>Data</b>&#8217; &#8211; </p>
     1133
     1134<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1135auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1136style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1137style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1138style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in
     1139powder diffraction patterns (multiple patterns can be selected). GSAS-II can
     1140read most of the old GSAS powder format files with the position in <span
     1141class=SpellE>centidegrees</span> 2-theta. It can also read &#8220;<span
     1142class=SpellE>xye</span>&#8221; format files used by <span class=SpellE>topas</span>
     1143where the position is in degrees 2-theta. As each file is read, an old GSAS
     1144style &#8220;instrument parameter file&#8221; is searched for; if not found a <span
     1145class=SpellE>CuK</span><span style='font-family:Symbol'>a</span> laboratory
     1146data set is assumed. </p>
     1147
     1148<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1149auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1150style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1151style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1152style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - </p>
     1153
     1154<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1155auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1156style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     1157style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1158style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks&#8230;</b> - </p>
     1159
     1160<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1161auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1162style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     1163style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1164style='mso-bidi-font-weight:normal'>Read single crystal data&#8230;</b> - </p>
     1165
     1166<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1167auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1168style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
     1169style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1170style='mso-bidi-font-weight:normal'>Sum powder data</b> - </p>
     1171
     1172<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1173auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1174style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
     1175style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1176style='mso-bidi-font-weight:normal'>Sum image data</b> - </p>
     1177
     1178<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1179auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1180style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
     1181style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1182style='mso-bidi-font-weight:normal'>Add phase</b> - </p>
     1183
     1184<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1185auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1186style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
     1187style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1188style='mso-bidi-font-weight:normal'>Delete phase</b> - </p>
     1189
     1190<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1191auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1192style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
     1193style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1194</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Rename
     1195data</b> - </p>
     1196
     1197<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1198auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1199style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
     1200style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1201</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete
     1202data</b> - </p>
     1203
     1204<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1205style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     1206style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     1207&#8216;<b style='mso-bidi-font-weight:normal'>Calculate</b>&#8217; &#8211; </p>
     1208
     1209<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1210auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1211style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1212style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1213style='mso-bidi-font-weight:normal'>Make new PDFs</b> - </p>
     1214
     1215<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1216auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1217style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1218style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1219style='mso-bidi-font-weight:normal'>View LS <span class=SpellE>parms</span></b>
     1220- </p>
     1221
     1222<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1223auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1224style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     1225style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1226style='mso-bidi-font-weight:normal'>Refine</b> - </p>
     1227
     1228<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1229auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1230style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     1231style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1232style='mso-bidi-font-weight:normal'>Sequential refine</b> - </p>
     1233
     1234<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1235auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1236style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
     1237style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1238style='mso-bidi-font-weight:normal'>Solve</b> - </p>
     1239
     1240<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1241style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1242style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     1243&#8216;<b style='mso-bidi-font-weight:normal'>Import</b>&#8217; &#8211; </p>
     1244
     1245<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1246auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1247style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1248style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1249style='mso-bidi-font-weight:normal'>Import GSAS Exp phase&#8230;</b> - </p>
     1250
     1251<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1252auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1253style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1254style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1255style='mso-bidi-font-weight:normal'>Import PDB phase&#8230;</b> - </p>
     1256
     1257<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1258auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1259style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     1260style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1261style='mso-bidi-font-weight:normal'>Import CIF phase&#8230;</b> - </p>
     1262
     1263<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1264auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1265style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     1266style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1267style='mso-bidi-font-weight:normal'>Import HKLs&#8230;</b> - </p>
     1268
     1269<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1270style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
     1271style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
     1272&#8216;<b style='mso-bidi-font-weight:normal'>Export</b>&#8217; &#8211;</p>
     1273
     1274<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1275auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1276style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1277style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1278style='mso-bidi-font-weight:normal'>Export Powder Patterns&#8230;</b> - </p>
     1279
     1280<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1281auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1282style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1283style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1284style='mso-bidi-font-weight:normal'>Export All Peak Lists&#8230;</b> - </p>
     1285
     1286<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1287auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1288style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     1289style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1290style='mso-bidi-font-weight:normal'>Export HKLs&#8230;</b> - </p>
     1291
     1292<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1293auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1294style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     1295style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1296style='mso-bidi-font-weight:normal'>Export PDF&#8230;</b> - </p>
     1297
     1298<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1299auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1300style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
     1301style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1302style='mso-bidi-font-weight:normal'>Export Phase&#8230;</b> - </p>
     1303
     1304<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
     1305text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1306style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
     1307style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1308style='mso-bidi-font-weight:normal'>Export CIF&#8230;</b> - </p>
     1309
     1310<h3><a name=Notebook><span style='mso-fareast-font-family:"Times New Roman"'>Notebook</span></a><span
     1311style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1312
     1313<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1314window provides a place for you to enter whatever text commentary you wish.
     1315Each time you enter this window, a date/time entry is provided for you. A
     1316possibly useful technique is to select a portion of the console window after a
     1317refinement completes (it will contain refinement results with residuals, new
     1318values &amp; <span class=SpellE>esds</span>) and paste it into this Notebook
     1319window so it becomes a part of your project file.<o:p></o:p></span></p>
     1320
     1321<h3><a name=Controls><span style='mso-fareast-font-family:"Times New Roman"'>Controls</span></a><span
     1322style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1323
     1324<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1325window provides the main controls for the major calculations in GSAS-II. At
     1326present only Refinement Controls are presented.<o:p></o:p></span></p>
     1327
     1328<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     1329main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
     1330MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
     1331algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
     1332package. Their purpose is to </span>minimize the sum of the squares of M<span
     1333style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
     1334variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
     1335algorithm as written by </span>Burton S. <span class=SpellE>Garbow</span>,
     1336Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
     1337J. <span class=GramE>More (Argonne National Laboratory, 1980).</span></p>
     1338
     1339<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1340
     1341<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1342style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1343style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1344style='mso-fareast-font-family:"Times New Roman"'>Select whether the refinement
     1345uses &#8216;analytic&#8217; or &#8216;numeric&#8217; derivatives. The latter is
     1346slower and perhaps a bit less accurate, but may be needed if the analytic
     1347functions are not fully developed. Generally use &#8216;analytic&#8217; for
     1348routine work.<o:p></o:p></span></p>
     1349
     1350<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1351style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1352style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1353style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Min
     1354delta-M/M&#8217; for convergence; the refinement will stop when the change in
     1355the minimization function is less than this value. Set Min delta-M/M = 1.0 to
     1356force just a single cycle to be performed. A value less than 10<sup>-4</sup>
     1357(the default) generally gives no better result. The allowed range is 10<sup>-9</sup>
     1358to 1.0.<o:p></o:p></span></p>
     1359
     1360<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1361style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     1362style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1363style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Initial shift
     1364factor&#8217; for the first cycle of refinement. This value is modified by the
     1365least squares routine. The allowed range is 10<sup>-5</sup> to 100. Smaller
     1366values may be needed if your initial <span class=GramE>refinement</span> trials
     1367immediately diverge, however make sure your starting parameter values are
     1368&#8216;reasonable&#8217;. The selected default (=1.0) normally gives good
     1369performance.<o:p></o:p></span></p>
     1370
     1371<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1372style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1373style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1374style='mso-fareast-font-family:"Times New Roman"'>Select data for sequential
     1375refinement; the data sets may be done in &#8216;reverse order&#8217;. <o:p></o:p></span></p>
     1376
     1377<h3><span style='mso-fareast-font-family:"Times New Roman"'>Covariance<o:p></o:p></span></h3>
     1378
     1379<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1380window is blank; the GSASII Plots window &#8216;<a href="#Covariance">Covariance&#8217;</a>
     1381shows a graphical representation of the variance-covariance matrix <o:p></o:p></span></p>
     1382
     1383<h3><a name=Constraints><span style='mso-fareast-font-family:"Times New Roman"'>Constraints<o:p></o:p></span></a></h3>
     1384
     1385<span style='mso-bookmark:Constraints'></span>
     1386
     1387<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1388window shows the constraints to be used in a refinement. It is organized into
     1389three tabbed pages. &#8216;Phase constraints&#8217; contain those involving
     1390parameters that describe aspects of the crystalline phases to be used in the
     1391refinement (e.g. atom coordinates, thermal motion and site fraction
     1392parameters). &#8216;Histogram/Phase constraints&#8217; are those which describe
     1393aspects of the pattern that depend on both the phase and the data set used in
     1394the refinement (e.g. </span><span style='font-family:Symbol;mso-fareast-font-family:
     1395"Times New Roman"'>m</span><span style='mso-fareast-font-family:"Times New Roman"'>strain
     1396and crystallite size parameters). &#8216;Histogram constraints&#8217; are those
     1397that depend only on the data set (e.g. profile coefficients U<span class=GramE>,V,W,X</span>
     1398and Y).<o:p></o:p></span></p>
     1399
     1400<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1401
     1402<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo6'><![if !supportLists]><span
     1403style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1404style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1405style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the parameter
     1406types you wish to constrain. Each will have the same possibilities in the
     1407&#8216;Edit menu.<o:p></o:p></span></p>
     1408
     1409<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo6'><![if !supportLists]><span
     1410style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1411style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1412style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
     1413style='mso-bidi-font-weight:normal'>Edit</b>&#8217; &#8211; <o:p></o:p></span></p>
     1414
     1415<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1416auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1417style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
     1418style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1419class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
     1420"Times New Roman"'>Add</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1421style='mso-fareast-font-family:"Times New Roman"'> Hold</span></b><span
     1422style='mso-fareast-font-family:"Times New Roman"'> &#8211; select a parameter
     1423that you wish to remain fixed although other parameters of the same type may be
     1424selected as a group for refinement. For example, if the space group for a phase
     1425has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom y-parameter
     1426is arbitrary and should be selected for a Hold to keep the structure from
     1427drifting up or down the y-axis during refinement. If selected, a dialog box
     1428will appear showing the list of available parameters; select one and then OK to
     1429implement it, Cancel will cancel the operation. The held parameter will be
     1430shown in the constraint window with the keyword &#8216;FIXED&#8217;. A Delete
     1431button can be used to remove it.<o:p></o:p></span></p>
     1432
     1433<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1434auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1435style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
     1436style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1437style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
     1438equivalence</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     1439&#8211; select a list of parameters that should have the same value (possibly
     1440with a non-unitary multiplier for some). Examples are a list of atoms with the
     1441same thermal motion <span class=SpellE>Uiso</span>, sets of profile
     1442coefficients U<span class=GramE>,V,W</span> across multiple data sets. If
     1443selected, a dialog box will appear with a list of the available parameters.
     1444Select one and press OK; a second dialog box will appear with only those
     1445parameters that can be made equivalent to the first one. Choose those and press
     1446OK. Cancel in either dialog will cancel the operation. The equivalenced
     1447parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
     1448usually M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217;
     1449button. The keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an
     1450equivalence</span>. A Delete button can be used to remove it.<o:p></o:p></span></p>
     1451
     1452<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1453auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1454style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
     1455style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1456style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
     1457constraint</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     1458&#8211; select a list of parameters whose sum (with possible non-unitary
     1459multipliers) is fixed. For example, the sum of site fractions for atoms on the
     1460same site could be fixed to unity. If selected, a dialog box will appear with a
     1461list of the available parameters. Select one and press OK; a second dialog box
     1462will appear with only those parameters that can be used in a constraint with
     1463the first one. Choose those and press OK. Cancel in either dialog will cancel
     1464the operation. The equivalenced parameters will show as an equation of the form
     1465M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the
     1466multipliers M1, <span class=GramE>M2, &#8230;</span> and C can be changed via
     1467the &#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
     1468constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
     1469
     1470<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
     1471text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1472style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
     1473style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
     1474style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
     1475function</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
     1476&#8211; this is very similar the &#8220;Add constraint&#8221; type except that
     1477the result of the sum can be varied in the refinement. The keyword
     1478&#8216;FUNCT&#8217; marks it as a function; the &#8216;Refine?&#8217; box
     1479indicates your choice to refine the result of the sum. A Delete button can be
     1480used to remove it.<o:p></o:p></span></p>
     1481
     1482<h3><a name=Restraints><span style='mso-fareast-font-family:"Times New Roman"'>Restraints</span></a><span
     1483style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1484
     1485<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1486window... <o:p></o:p></span></p>
     1487
     1488<h3><a name=Limits><span style='mso-fareast-font-family:"Times New Roman"'>Limits</span></a><span
     1489style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1490
     1491<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1492window shows the limits in position to be used in any fitting for this powder
     1493pattern. The &#8216;original&#8217; values are obtained from the minimum &amp;
     1494maximum values in the powder pattern. You can modify &#8216;changed&#8217; as
     1495needed.<o:p></o:p></span></p>
     1496
     1497<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1498
     1499<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo8'><![if !supportLists]><span
     1500style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1501style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1502style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
     1503style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
     1504style='mso-bidi-font-weight:normal'>Copy</b> - this copies the limits shown to
     1505other selected powder patterns. If used, a dialog box (Copy Limits) will appear
     1506showing the list of available powder patterns, you can copy the limits to any
     1507or all of them; select &#8216;All&#8217; to copy them to all patterns. Then
     1508select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to cancel the
     1509operation.<o:p></o:p></span></p>
     1510
     1511<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo8'><![if !supportLists]><span
     1512style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1513style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1514style='mso-fareast-font-family:"Times New Roman"'>You can change <span
     1515class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the
     1516&#8216;changed&#8217; row as needed. Use the mouse to select the value to be
     1517changed (the background on the box will be blue or have a black border or a
     1518vertical bar will appear in the value), then enter the new value and press
     1519Enter or click the mouse elsewhere in the Background window. This will set the
     1520new value.<o:p></o:p></span></p>
     1521
     1522<h3><a name=Background><span style='mso-fareast-font-family:"Times New Roman"'>Background</span></a><span
     1523style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1524
     1525<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1526window shows the choice of background function and coefficients to be used in
     1527fitting this powder pattern.<o:p></o:p></span></p>
     1528
     1529<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1530
     1531<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
     1532style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1533style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1534style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
     1535style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
     1536style='mso-bidi-font-weight:normal'>Copy</b> &#8211; this copies the background
     1537parameters shown to other selected powder patterns. If used, a dialog box (Copy
     1538Parameters) will appear showing the list of available powder patterns, you can
     1539copy the background parameters to any or all of them; select &#8216;All&#8217;
     1540to copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
     1541&#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
     1542
     1543<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
     1544style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1545style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1546style='mso-fareast-font-family:"Times New Roman"'>You can select a different
     1547Background function from the pull down tab.<o:p></o:p></span></p>
     1548
     1549<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
     1550style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
     1551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1552style='mso-fareast-font-family:"Times New Roman"'>You can choose to refine/not
     1553refine the background coefficients.<o:p></o:p></span></p>
     1554
     1555<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
     1556style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1557style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1558style='mso-fareast-font-family:"Times New Roman"'>You can select the number of
     1559background coefficients to be used (1-36).<o:p></o:p></span></p>
     1560
     1561<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
     1562style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
     1563style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1564style='mso-fareast-font-family:"Times New Roman"'>You can change individual
     1565background coefficient values. Enter the value then press Enter or click the
     1566mouse elsewhere in the Background window. This will set the new value.<o:p></o:p></span></p>
     1567
     1568<h3><a name="Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
     1569Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1570
     1571<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1572window... <o:p></o:p></span></p>
     1573
     1574<h3><a name="Sample_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Sample
     1575Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1576
     1577<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1578window... <o:p></o:p></span></p>
     1579
     1580<h3><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
     1581Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></a><span
     1582style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1583
     1584<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1585window shows the list of peaks that will be used by the peak fitting refinement.
     1586It is filled by picking peaks in the powder pattern displayed in the GSASII
     1587Plots window as a sequence of &#8216;+&#8217; marks. See <a
     1588href="#Powder_Patterns">Powder Patterns</a> below for details for what can be
     1589done on this plot.<o:p></o:p></span></p>
     1590
     1591<h3><a name="Index_Peaks"><span style='mso-fareast-font-family:"Times New Roman"'>Index
     1592Peak List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1593
     1594<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1595window shows the list of peaks that will be used for indexing (see </span><a
     1596href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
     1597Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'>).
     1598It must be filled before indexing can proceed. When indexing is completed, this
     1599display will show the resulting <span class=SpellE>hkl</span> values for every
     1600indexed reflection along with the calculated d-spacing (&#8216;d-<span
     1601class=SpellE>calc</span>&#8217;) for the selected unit cell in </span><a
     1602href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
     1603Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
     1604
     1605<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1606
     1607<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo12'><![if !supportLists]><span
     1608style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1609style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1610style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
     1611style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
     1612style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
     1613positions &amp; intensities from the </span><a href="#Peak_List"><span
     1614style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></a><span
     1615style='mso-fareast-font-family:"Times New Roman"'> to make them available for
     1616the indexing routine. The d-<span class=SpellE>obs</span> is obtained from
     1617Bragg&#8217;s Law after applying the Zero correction shown on the </span><a
     1618href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
     1619Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'>
     1620table to the position shown here.<o:p></o:p></span></p>
     1621
     1622<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo12'><![if !supportLists]><span
     1623style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1624style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1625style='mso-fareast-font-family:"Times New Roman"'>You may deselect individual
     1626peaks from indexing by <span class=SpellE>unchecking</span> the corresponding
     1627&#8216;use&#8217; box.<o:p></o:p></span></p>
     1628
     1629<h3><a name="Cell_Indexing_Refine"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
     1630Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1631
     1632<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1633window... <o:p></o:p></span></p>
     1634
     1635<h3><a name="Reflection_List"><span style='mso-fareast-font-family:"Times New Roman"'>Reflection
     1636List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1637
     1638<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1639window... <o:p></o:p></span></p>
     1640
     1641<h3><span style='mso-fareast-font-family:"Times New Roman"'>Texture Control
     1642Window<o:p></o:p></span></h3>
     1643
     1644<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1645window... <o:p></o:p></span></p>
     1646
     1647<h3><span style='mso-fareast-font-family:"Times New Roman"'>Image Masks<o:p></o:p></span></h3>
     1648
     1649<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1650window... <o:p></o:p></span></p>
     1651
     1652<h3><span style='mso-fareast-font-family:"Times New Roman"'>Atoms Control
     1653Window<o:p></o:p></span></h3>
     1654
     1655<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1656window... <o:p></o:p></span></p>
     1657
     1658<h3><span style='mso-fareast-font-family:"Times New Roman"'>Diffraction Data
     1659Control Window<o:p></o:p></span></h3>
     1660
     1661<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1662window... <o:p></o:p></span></p>
     1663
     1664<h3><span style='mso-fareast-font-family:"Times New Roman"'>Draw Atoms Control
     1665Window<o:p></o:p></span></h3>
     1666
     1667<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1668window... <o:p></o:p></span></p>
     1669
     1670<h3><span style='mso-fareast-font-family:"Times New Roman"'>Pawley Control
     1671Window<o:p></o:p></span></h3>
     1672
     1673<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1674window... <o:p></o:p></span></p>
     1675
     1676<h3><a name=Images><span style='mso-fareast-font-family:"Times New Roman"'>Images
     1677Control<o:p></o:p></span></a></h3>
     1678
     1679<span style='mso-bookmark:Images'></span>
     1680
     1681<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1682window... <o:p></o:p></span></p>
     1683
     1684<h3><span style='mso-fareast-font-family:"Times New Roman"'>PDF Controls
     1685Control Window<o:p></o:p></span></h3>
     1686
     1687<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1688window... <o:p></o:p></span></p>
     1689
     1690<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     1691
     1692<h2><a name=Plots><span style='mso-fareast-font-family:"Times New Roman"'>GSASII
     1693Plots</span></a><span style='mso-bookmark:Plots'></span><span style='mso-fareast-font-family:
     1694"Times New Roman";font-weight:normal'> </span><span style='mso-fareast-font-family:
     1695"Times New Roman"'><o:p></o:p></span></h2>
     1696
     1697<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1698window presents all the graphical material as a multipage tabbed set of plots
     1699utilizing the <span class=SpellE>matplotlib</span> python package. Each page
     1700has a tool bar (at bottom in Windows) with the controls<o:p></o:p></span></p>
     1701
     1702<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     1703mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_3" o:spid="_x0000_i1026"
     1704 type="#_x0000_t75" style='width:168.75pt;height:23.25pt;visibility:visible;
     1705 mso-wrap-style:square'>
     1706 <v:imagedata src="gsasII_files/image001.png" o:title="" croptop="44118f"
     1707  cropbottom="18773f" cropleft="22405f" cropright="32288f"/>
     1708</v:shape><![endif]--><![if !vml]><img border=0 width=225 height=31
     1709src="gsasII_files/image002.jpg" v:shapes="Picture_x0020_3"><![endif]></span><span
     1710style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     1711
     1712<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
     1713are Home, Back, Forward, Pan, Zoom, Save and Help, respectively. The Pan option
     1714allows you to control panning across the plot (press left mouse button) and
     1715zooming (press right mouse button), the Zoom option allows you to select a
     1716portion of the plot (press right mouse button &amp; drag for zoom box) for the
     1717next plot. The Save allows you to save the currently displayed plot in one of
     1718several graphical formats suitable for printing or insertion in a document. The
     1719Help icon is for access to this GSASII help.<o:p></o:p></span></p>
     1720
     1721<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Below
     1722the toolbar may be a status bar that on the left may show either an instruction
     1723for a keyed input or a pull down selection of keyed input; on the right may be
     1724displayed position dependent information that is updated as the mouse is moved
     1725over the plot region.<o:p></o:p></span></p>
     1726
     1727<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     1728
     1729<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     1730specific types of plots that are pages in the GSASII Plots windows are next.<o:p></o:p></span></p>
     1731
     1732<h3><a name="Powder_Patterns"><span style='mso-fareast-font-family:"Times New Roman"'>Powder
     1733Patterns</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1734
     1735<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     1736powder patterns that are part of your project are shown on this page. They can
     1737be displayed as a stack of powder patterns, just a single pattern or as a
     1738contour image of the peak intensities. What can be done here will depend on
     1739which is displayed and on which item in the GSAS-II data tree you have
     1740selected.<o:p></o:p></span></p>
     1741
     1742<h3><a name=Covariance><span style='mso-fareast-font-family:"Times New Roman"'>Covariance</span></a><span
     1743style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h3>
     1744
     1745<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     1746variance-covariance matrix as a color coded array is shown on this page. The
     1747color bar to the right shows the range of <span class=SpellE>covariances</span>
     1748(-1 to 1) and corresponding colors. The parameter names are to the right and
     1749the parameter numbers are below the plot.<o:p></o:p></span></p>
     1750
     1751<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     1752
     1753<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo14'><![if !supportLists]><span
     1754style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
     1755style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
     1756the mouse cursor across the plot. If on a diagonal cell, the parameter name,
     1757value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
     1758right hand portion of the status bar. If the cursor is off the diagonal, the
     1759two parameter names and their covariance are shown in the tool tip and the
     1760status bar.</p>
     1761
     1762<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo14'><![if !supportLists]><span
     1763style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
     1764style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1765class=GramE>Type &#8216;s&#8217;</span> &#8211; A color scheme selection dialog
     1766is shown. Select a color scheme and press <span class=GramE>OK,</span> the new
     1767color scheme will be plotted. The default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
     1768
     1769<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     1770
     1771<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     1772
     1773<div class=MsoNormal align=center style='text-align:center'><span
     1774style='mso-fareast-font-family:"Times New Roman"'>
     1775
     1776<hr size=2 width="100%" align=center>
     1777
     1778</span></div>
     1779
     1780<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last
     1781modified: Tue Nov 22 13:19:47 CST 2011 <o:p></o:p></span></p>
     1782
     1783<!-- hhmts end --></div>
     1784
     1785</body>
     1786
     1787</html>
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