Changeset 710


Ignore:
Timestamp:
Aug 15, 2012 10:06:27 AM (10 years ago)
Author:
vondreele
Message:

update garnet tutorial to reflect new options
fix backbone plotting for multichain proteins
finish 1st attempt at strain tensor refinement - but not right

Location:
trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIimage.py

    r706 r710  
    1313import numpy as np
    1414import numpy.linalg as nl
     15from scipy.optimize import leastsq
    1516import copy
    1617import GSASIIpath
     
    128129   
    129130def FitDetector(rings,p0,wave):
    130     from scipy.optimize import leastsq
    131131       
    132132    def CalibPrint(ValSig):
     
    752752#    print 'Masks:',Masks
    753753    StaControls = copy.deepcopy(Controls)
    754     StaControls['distance'] += StrSta['Sample z']*cosd(StrSta['Sample phi'])
     754    phi = StrSta['Sample phi']
     755    wave = Controls['wavelength']
     756    StaControls['distance'] += StrSta['Sample z']*cosd(phi)
    755757    pixSize = StaControls['pixelSize']
    756758    scalex = 1000./pixSize[0]
     
    769771        else:
    770772            rings = np.array(Ring)
    771        
    772        
     773    E = StrSta['strain']
     774    p0 = [E[0][0],E[1][1],E[2][2],E[0][1],E[0][2],E[1][2]]
     775    E = FitStrain(rings,p0,wave,phi)
     776    StrSta['strain'] = E
    773777
    774778def calcFij(omg,phi,azm,th):
    775     ''' Uses parameters as defined by Bob He & Kingsley Smity, Adv. in X-Ray Anal. 41, 501 (1997)
     779    ''' Uses parameters as defined by Bob He & Kingsley Smith, Adv. in X-Ray Anal. 41, 501 (1997)
    776780    omg: his omega = sample omega rotation; 0 when incident beam || sample surface, 90
    777781            when perp. to sample surface
     
    791795    return -Fij*nptand(th)
    792796
    793 def FitStrain(rings,p0,wave):
    794     from scipy.optimize import leastsq
     797def FitStrain(rings,p0,wave,phi):
    795798
    796799    def StrainPrint(ValSig):
     
    810813        print sigstr
    811814       
    812     def strainCalc(E,xyd,wave,phi):
     815    def strainCalc(p,xyd,wave,phi):
     816#        E = np.array([[p[0],p[3],p[4]],[p[3],p[1],p[5]],[p[4],p[5],p[2]]])
     817        E = np.array([[p[0],0,0],[0,p[1],0],[0,0,0]])
    813818        th,azm,dsp = xyd
    814819        th0 = npasind(wave/(2.*dsp))
    815         dth = 180.*np.sum(StrSta['strain']*calcFij(phi,0.,azm,th))/(np.pi*1.e6) #in degrees
    816        
     820        dth = 180.*np.sum(E*calcFij(phi,0.,azm,th).T)/(np.pi*1.e6) #in degrees & microstrain units
     821        th0 += dth
     822        return (th-th0)**2
     823       
     824    names = ['e11','e22','e33','e12','e13','e23']
     825    fmt = ['%12.2f','%12.2f','%12.2f','%12.2f','%12.2f','%12.5f']
     826    p1 = [p0[0],p0[1]]   
     827    result = leastsq(strainCalc,p1,args=(rings,wave,phi),full_output=True)
     828    vals = list(result[0])
     829    chi = np.sqrt(np.sum(strainCalc(result[0],rings,wave,phi)**2))
     830    sig = list(chi*np.sqrt(np.diag(result[1])))
     831    ValSig = zip(names,fmt,vals,sig)
     832    StrainPrint(ValSig)
     833#    return np.array([[vals[0],vals[3],vals[4]],[vals[3],vals[1],vals[5]],[vals[4],vals[5],vals[2]]])
     834    return np.array([[vals[0],0,0],[0,vals[1],0],[0,0,0]])
     835   
     836       
  • trunk/GSASIIphsGUI.py

    r709 r710  
    717717        def DenSizer():
    718718           
     719            mass = G2mth.getMass(generalData)
    719720            density,mattCoeff = G2mth.getDensity(generalData)
    720721            denSizer = wx.BoxSizer(wx.HORIZONTAL)
  • trunk/GSASIIplot.py

    r706 r710  
    29032903#                G2frame.G2plotNB.status.SetStatusText('test point %.4f,%.4f,%.4f'%(x,y,z),1)           
    29042904            RenderUnitVectors(x,y,z)
    2905         Backbone = []
     2905        Backbones = {}
    29062906        BackboneColor = []
    29072907        time0 = time.time()
     
    29782978            elif atom[cs] == 'backbone':
    29792979                if atom[ct-1].split()[0] in ['C','N']:
    2980                     Backbone.append(list(np.inner(Amat,np.array([x,y,z]))))
     2980                    if atom[2] not in Backbones:
     2981                        Backbones[atom[2]] = []
     2982                    Backbones[atom[2]].append(list(np.inner(Amat,np.array([x,y,z]))))
    29812983                    BackboneColor.append(list(color))
    29822984                   
     
    30023004                else:
    30033005                    RenderMapPeak(x,y,z,Wt)
    3004         if Backbone:
    3005             RenderBackbone(Backbone,BackboneColor,bondR)
     3006        if Backbones:
     3007            for chain in Backbones:
     3008                Backbone = Backbones[chain]
     3009                RenderBackbone(Backbone,BackboneColor,bondR)
    30063010#        print time.time()-time0
    30073011        Page.canvas.SwapBuffers()
  • trunk/help/Neutron CW Powder Data.htm

    r624 r710  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>11</o:Revision>
    26   <o:TotalTime>637</o:TotalTime>
     25  <o:Revision>12</o:Revision>
     26  <o:TotalTime>670</o:TotalTime>
    2727  <o:Created>2012-05-06T20:38:00Z</o:Created>
    28   <o:LastSaved>2012-05-18T18:07:00Z</o:LastSaved>
     28  <o:LastSaved>2012-08-15T15:04:00Z</o:LastSaved>
    2929  <o:Pages>8</o:Pages>
    30   <o:Words>1693</o:Words>
    31   <o:Characters>9651</o:Characters>
     30  <o:Words>1783</o:Words>
     31  <o:Characters>10169</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>80</o:Lines>
    34   <o:Paragraphs>22</o:Paragraphs>
    35   <o:CharactersWithSpaces>11322</o:CharactersWithSpaces>
     33  <o:Lines>84</o:Lines>
     34  <o:Paragraphs>23</o:Paragraphs>
     35  <o:CharactersWithSpaces>11929</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    983983
    984984<p class=MsoNormal>In this training exercise you will refine the structure of
    985 yttrium iron/aluminum garnet using constant wavelength neutron data. The structure
    986 is cubic with four different atomic sites two of which are occupied by both
    987 iron and aluminum. The data was taken on the D1a powder diffractometer at the
    988 ILL, Grenoble, France using 1.909Å wavelength neutrons.</p>
     985yttrium iron/aluminum garnet using constant wavelength neutron data. The
     986structure is cubic with four different atomic sites two of which are occupied
     987by both iron and aluminum. The data was taken on the D1a powder diffractometer
     988at the ILL, Grenoble, France using 1.909Å wavelength neutrons.</p>
    989989
    990990<p class=MsoNormal>If you have not done so already, <a
     
    999999mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    10001000minor-latin'>Import/Powder Data/from GSAS file</span></b> menu item to read the
    1001 data file into GSAS-II. This read option is set to read any of the powder data
    1002 formats (except neutron TOF time map files) defined for GSAS (angles in <span
     1001data file into GSAS-II. This read option is set to read any of the powder data formats
     1002(except neutron TOF time map files) defined for GSAS (angles in <span
    10031003class=SpellE>centidegrees</span>). Other submenu items will read the <span
    10041004class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     
    11501150to exit. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
    11511151"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1152 minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b> tab display will
    1153 change (principally changes in lattice parameter display).</p>
     1152minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b> tab display
     1153will change (principally changes in lattice parameter display).</p>
    11541154
    11551155<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
     
    11941194
    11951195<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1196  id="Picture_x0020_5" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:342.75pt;
    1197  height:342pt;visibility:visible;mso-wrap-style:square'>
     1196 id="_x0000_i1041" type="#_x0000_t75" style='width:350.25pt;height:342pt;
     1197 visibility:visible;mso-wrap-style:square'>
    11981198 <v:imagedata src="Neutron%20CW%20Powder%20Data_files/image004.png" o:title=""/>
    1199 </v:shape><![endif]--><![if !vml]><img border=0 width=457 height=456
    1200 src="Neutron%20CW%20Powder%20Data_files/image004.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1199</v:shape><![endif]--><![if !vml]><img border=0 width=467 height=456
     1200src="Neutron%20CW%20Powder%20Data_files/image004.png" v:shapes="_x0000_i1041"><![endif]></span></p>
    12011201
    12021202<p class=MsoListParagraphCxSpLast>I’ve pulled down the bottom of the window to
     
    12041204and data set dependent. These include phase fraction, crystallite size, <span
    12051205class=SpellE>mustrain</span> &amp; preferred orientation. None of these are
    1206 needed for this refinement so you can unclick the Show check box.</p>
     1206needed for this refinement so you can unclick the <b style='mso-bidi-font-weight:
     1207normal'>Show</b> check box.</p>
    12071208
    12081209<h2><span class=GramE>Step 3.</span> Insert the atoms</h2>
     
    14501451
    14511452<p class=MsoNormal>Each element has a small pull down selection for the
    1452 possible valences (usually choose the “zero” one). Select “Y”, the Table will
    1453 vanish and the Name and Type for that atom will change. Then enter the values
    1454 for x, y and z; you can use Tab to move to the next one. Do this for each atom
    1455 in the Atom table. You can leave both <span class=SpellE>frac</span> and <span
    1456 class=SpellE>Uiso</span> at the default values. Your result should look like</p>
     1453possible valences (usually choose the “zero” one). Select “<b style='mso-bidi-font-weight:
     1454normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1455minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Y</span></b>”,
     1456the Table will vanish and the <b style='mso-bidi-font-weight:normal'><span
     1457style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1458mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Name</span></b>
     1459and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1460mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1461minor-latin'>Type</span></b> for that atom will change. Then enter the values
     1462for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1463mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1464minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:normal'><span
     1465style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1466mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
     1467and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1468mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1469minor-latin'>z</span></b>; you can use Tab to move to the next one. You may use
     1470fractions for the atom coordinates (e.g. 1/4, 3/8). Do this for each atom in
     1471the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1472mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1473minor-latin'>Atoms</span></b> table. You can leave both <span class=SpellE><b
     1474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1475mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1476minor-latin'>frac</span></b></span> and <span class=SpellE><b style='mso-bidi-font-weight:
     1477normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1478minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
     1479at the default values. Your result should look like</p>
    14571480
    14581481<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_s1026"
     
    14701493src="Neutron%20CW%20Powder%20Data_files/image007.png" align=left hspace=12
    14711494v:shapes="Picture_x0020_9"><![endif]><br clear=all>
    1472 You can now do your first Rietveld refinement on this problem. To do this, do
    1473 Calculate/Refine in the GSAS-II data tree menu; a file dialog will ask you for
    1474 a name for this project; you can change the directory if you wish. We assume
    1475 the name “YAG”; the current project will be saved as <span class=SpellE>YAG.gpx</span>
    1476 and the first backup file (YAG.bak0.gpx) will also be created and then the
    1477 Rietveld refinement will be performed. By default, only the histogram scale
    1478 factor (found under Sample Parameters for PWDR <span class=SpellE>garnet.raw</span>:
    1479 BANK1 in the GSAS-II data tree) and 3 background coefficients are refined. The
    1480 resulting powder pattern</p>
     1495You can now do your first Rietveld refinement on this problem. To do this, do <b
     1496style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1498minor-latin'>Calculate/Refine</span></b> in the <b style='mso-bidi-font-weight:
     1499normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1500minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
     1501data tree</span></b> menu; a file dialog will ask you for a name for this
     1502project; you can change the directory if you wish. We assume the name “<b
     1503style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1504mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1505minor-latin'>YAG</span></b>”; the current project will be saved as <span
     1506class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1507"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1508minor-latin;mso-bidi-theme-font:minor-latin'>YAG.gpx</span></b></span> and the
     1509first backup file (<b style='mso-bidi-font-weight:normal'><span
     1510style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1511mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>YAG.bak0.gpx</span></b>)
     1512will also be created and then the Rietveld refinement will be performed. By
     1513default, only the histogram scale factor (found under <b style='mso-bidi-font-weight:
     1514normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1515minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample
     1516Parameters</span></b> for <b style='mso-bidi-font-weight:normal'><span
     1517style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1518mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>PWDR <span
     1519class=SpellE>garnet.raw</span>: BANK1</span></b> in the <b style='mso-bidi-font-weight:
     1520normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1521minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
     1522data tree</span></b>) and 3 background coefficients are refined. The resulting
     1523powder pattern</p>
    14811524
    14821525<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14881531
    14891532<p class=MsoNormal><span class=GramE>shows</span> a pretty poor fit (<span
    1490 class=SpellE>Rwp</span> ~33%) and details can be found on the console window.
     1533class=SpellE>Rwp</span> ~33%) and details can be found in the <span
     1534class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1535"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1536minor-latin;mso-bidi-theme-font:minor-latin'>YAG.lst</span></b></span> file.
    14911537What appears to be in error includes some structural features (I’d first
    14921538suspect site fractions for the Fe/Al sites) and something about the peak
     
    16281674<p class=MsoListParagraphCxSpMiddle>This process set the
    16291675equivalences/constraints for the two Fe/Al sites in the garnet so that
    1630 refinement of <span class=SpellE>frac</span> and <span class=SpellE>Uiso</span>
     1676refinement of <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1677style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1678mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
     1679and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1680style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1681mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
    16311682will succeed. GSAS-II constraints will correct the site fractions and <span
    16321683class=SpellE>Uiso</span> values so that they conform to the constraints as
     
    16681719style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    16691720mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
    1670 for the Fe/Al sites. There are many ways to do <span class=GramE>this,</span> we
    1671 will show you one method now. Select row <b style='mso-bidi-font-weight:normal'><span
    1672 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1673 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1</span></b>
     1721for the Fe/Al sites. There are many ways to do <span class=GramE>this,</span>
     1722we will show you one method now. Select row <b style='mso-bidi-font-weight:
     1723normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1724minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1</span></b>
    16741725for <span class=GramE>Fe(</span>2) and then holding the Ctrl key down select
    16751726rows <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    16951746minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>F
    16961747– site fraction</span></b>. You could select all <span class=GramE>three,</span>
    1697 GSAS-II would refine <span class=SpellE>frac</span> &amp; <span class=SpellE>Uiso</span>
     1748GSAS-II would refine <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1749style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1750mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>frac</span></b></span>
     1751&amp; <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1752style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1753mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Uiso</span></b></span>
    16981754but not the coordinates as they are fixed as special positions in this case.
    16991755The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    17131769
    17141770<p class=MsoNormal>You are now ready for your second Rietveld refinement;
    1715 select Calculate/Refine from the GSAS-II data tree window. There is now a much
    1716 better fit with <span class=SpellE>Rwp</span> ~12% and a powder pattern that
    1717 looks like</p>
     1771select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1772mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1773minor-latin'>Calculate/Refine</span></b> from the GSAS-II data tree window.
     1774There is now a much better fit with <span class=SpellE>Rwp</span> ~12% and a
     1775powder pattern that looks like</p>
    17181776
    17191777<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17641822
    17651823<p class=MsoNormal><span class=GramE>when</span> done. Now you can do your
    1766 third Rietveld refinement; select Calculate/Refine. The resulting fit is</p>
     1824third Rietveld refinement; select <b style='mso-bidi-font-weight:normal'><span
     1825style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1826mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>.
     1827The resulting fit is</p>
    17671828
    17681829<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17781839
    17791840<p class=MsoNormal>The latter are determined by the U, V &amp; W parameters
    1780 found in the PWDR <span class=SpellE>garnet.raw</span>: BANK1/Instrument
    1781 Parameters window. Go there and select their Refine? <span class=GramE>flags</span>.
    1782 Next go to Sample Parameters.</p>
     1841found in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1842"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1843minor-latin;mso-bidi-theme-font:minor-latin'>PWDR <span class=SpellE>garnet.raw</span>:
     1844BANK1/Instrument Parameters</span></b> window. Go there and select their
     1845Refine? <span class=GramE>flags</span>. Next go to Sample Parameters.</p>
    17831846
    17841847<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17901853
    17911854<p class=MsoNormal>Notice that the Histogram scale factor is already being
    1792 refined. Now you will want to refine both Sample X displacement and Sample Y
    1793 displacement. The values will be in <span style='font-family:Symbol'>m</span>m
    1794 if the Goniometer radius is correct; enter 700 for that value. Now you can do
    1795 another Rietveld refinement; the fit</p>
     1855refined. Now you will want to refine both <b style='mso-bidi-font-weight:normal'><span
     1856style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1857mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample X
     1858displacement</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1859style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1860mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Sample Y
     1861displacement</span></b>. The values will be in <span style='font-family:Symbol'>m</span>m
     1862if the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1863mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1864minor-latin'>Goniometer radius</span></b> is correct; enter 650 for that value.
     1865Now you can do another Rietveld refinement; the fit</p>
    17961866
    17971867<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18031873
    18041874<p class=MsoNormal><span class=GramE>is</span> nearly perfect! <span
    1805 class=SpellE>Rwp</span> = 4.78%. You can look at the console output for all the
    1806 parameters and their respective <span class=SpellE>esds</span>. I’ve passed
    1807 some of my results in below for you to compare.</p>
     1875class=SpellE>Rwp</span> = 4.87%. You can look at the <span class=SpellE><b
     1876style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1877mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1878minor-latin'>YAG.lst</span></b></span> output file for all the parameters and
     1879their respective <span class=SpellE>esds</span>. I’ve pasted some of my results
     1880in below for you to compare.</p>
    18081881
    18091882<p class=MsoNormal><span style='font-family:"Courier New"'>Number of function
    1810 calls: <span class=GramE>7<span style='mso-spacerun:yes'>  </span>Number</span>
     1883calls: <span class=GramE>9<span style='mso-spacerun:yes'>  </span>Number</span>
    18111884of observations:<span style='mso-spacerun:yes'>  </span>2677<span
    18121885style='mso-spacerun:yes'>  </span>Number of parameters:<span
    18131886style='mso-spacerun:yes'>  </span>20<o:p></o:p></span></p>
    18141887
    1815 <p class=MsoNormal><span style='font-family:"Courier New"'>Refinement time
    1816 =<span style='mso-spacerun:yes'>    </span>2.704s,<span
    1817 style='mso-spacerun:yes'>    </span>0.676s/cycle, for 4 cycles<o:p></o:p></span></p>
    1818 
    1819 <p class=MsoNormal><span class=SpellE><span class=GramE><span style='font-family:
    1820 "Courier New"'>wRp</span></span></span><span style='font-family:"Courier New"'>
    1821 =<span style='mso-spacerun:yes'>    </span>4.78%, chi**2 =<span
    1822 style='mso-spacerun:yes'>      </span>8544.01, reduced chi**2 =<span
    1823 style='mso-spacerun:yes'>   </span>3.22<o:p></o:p></span></p>
     1888<p class=MsoNormal><span style='font-family:"Courier New"'><span
     1889style='mso-spacerun:yes'> </span>Refinement time =<span
     1890style='mso-spacerun:yes'>    </span>2.802s,<span style='mso-spacerun:yes'>   
     1891</span>0.934s/cycle, for 3 cycles<o:p></o:p></span></p>
     1892
     1893<p class=MsoNormal><span style='font-family:"Courier New"'><span
     1894style='mso-spacerun:yes'> </span><span class=SpellE><span class=GramE>wR</span></span>
     1895=<span style='mso-spacerun:yes'>    </span>4.87%, chi**2 =<span
     1896style='mso-spacerun:yes'>      </span>8893.61, reduced chi**2 =<span
     1897style='mso-spacerun:yes'>   </span>3.35<o:p></o:p></span></p>
    18241898
    18251899<p class=MsoNormal><span style='font-family:"Courier New"'>
    18261900<o:p></o:p></span></p>
    18271901
    1828 <p class=MsoNormal><span style='font-family:"Courier New"'>Atoms:<o:p></o:p></span></p>
     1902<p class=MsoNormal><span style='font-family:"Courier New"'>Atoms:<span
     1903style='mso-spacerun:yes'>                                               </span><o:p></o:p></span></p>
    18291904
    18301905<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    18331908</span>y<span style='mso-spacerun:yes'>         </span>z<span
    18341909style='mso-spacerun:yes'>      </span><span class=SpellE>frac</span><span
    1835 style='mso-spacerun:yes'>  </span><span style='mso-spacerun:yes'> </span><span
    1836 class=SpellE>Uiso</span><o:p></o:p></span></p>
     1910style='mso-spacerun:yes'>   </span><span class=SpellE>Uiso</span><span
     1911style='mso-spacerun:yes'>   </span><o:p></o:p></span></p>
    18371912
    18381913<p class=MsoNormal><span style='font-family:"Courier New"'>------------------------------------------------------<o:p></o:p></span></p>
     
    18401915<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18411916style='mso-spacerun:yes'>   </span><span class=GramE>Y(</span>1)<span
    1842 style='mso-spacerun:yes'>      </span>Y:<o:p></o:p></span></p>
     1917style='mso-spacerun:yes'>      </span>Y:<span
     1918style='mso-spacerun:yes'>                                       </span><o:p></o:p></span></p>
    18431919
    18441920<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18451921style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    1846 style='mso-spacerun:yes'>   </span>0.12500<span style='mso-spacerun:yes'>  
    1847 </span>0.00000<span style='mso-spacerun:yes'>   </span>0.25000<span
    1848 style='mso-spacerun:yes'>   </span>1.000 0.00532<o:p></o:p></span></p>
     1922style='mso-spacerun:yes'>   </span>0.12500 <span
     1923style='mso-spacerun:yes'>  </span>0.00000<span style='mso-spacerun:yes'>  
     1924</span>0.25000<span style='mso-spacerun:yes'>   </span>1.000 0.00453<o:p></o:p></span></p>
    18491925
    18501926<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18511927style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    18521928style='mso-spacerun:yes'>   </span>:<span
    1853 style='mso-spacerun:yes'>                                       </span>0.00032<o:p></o:p></span></p>
     1929style='mso-spacerun:yes'>                                       </span>0.00033<o:p></o:p></span></p>
    18541930
    18551931<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18561932style='mso-spacerun:yes'>  </span><span class=GramE>Fe(</span>2)<span
    1857 style='mso-spacerun:yes'>     </span>Fe:<o:p></o:p></span></p>
     1933style='mso-spacerun:yes'>     </span>Fe:<span
     1934style='mso-spacerun:yes'>                                       </span><o:p></o:p></span></p>
    18581935
    18591936<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    18611938style='mso-spacerun:yes'>   </span>0.00000<span style='mso-spacerun:yes'>  
    18621939</span>0.00000<span style='mso-spacerun:yes'>   </span>0.00000<span
    1863 style='mso-spacerun:yes'>   </span>0.574 0.00421<o:p></o:p></span></p>
     1940style='mso-spacerun:yes'>   </span>0.575 0.00347<o:p></o:p></span></p>
    18641941
    18651942<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18661943style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    18671944style='mso-spacerun:yes'>   </span>:<span
    1868 style='mso-spacerun:yes'>                                 </span>0.008 0.00055<o:p></o:p></span></p>
     1945style='mso-spacerun:yes'>                                 </span>0.008 0.00056<o:p></o:p></span></p>
    18691946
    18701947<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18711948style='mso-spacerun:yes'>  </span><span class=GramE>Al(</span>3)<span
    1872 style='mso-spacerun:yes'>     </span>Al:<o:p></o:p></span></p>
     1949style='mso-spacerun:yes'>     </span>Al:<span
     1950style='mso-spacerun:yes'>                                       </span><o:p></o:p></span></p>
    18731951
    18741952<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    18761954style='mso-spacerun:yes'>   </span>0.00000<span style='mso-spacerun:yes'>  
    18771955</span>0.00000<span style='mso-spacerun:yes'>   </span>0.00000<span
    1878 style='mso-spacerun:yes'>   </span>0.426 0.00421<o:p></o:p></span></p>
     1956style='mso-spacerun:yes'>   </span>0.425 0.00347<o:p></o:p></span></p>
    18791957
    18801958<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18811959style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    18821960style='mso-spacerun:yes'>   </span>:<span
    1883 style='mso-spacerun:yes'>                                 </span>0.008 0.00055<o:p></o:p></span></p>
     1961style='mso-spacerun:yes'>                                 </span>0.008 0.00056<o:p></o:p></span></p>
    18841962
    18851963<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18861964style='mso-spacerun:yes'>  </span><span class=GramE>Al(</span>4)<span
    1887 style='mso-spacerun:yes'>     </span>Al:<o:p></o:p></span></p>
     1965style='mso-spacerun:yes'>     </span>Al:<span
     1966style='mso-spacerun:yes'>                                       </span><o:p></o:p></span></p>
    18881967
    18891968<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    18911970style='mso-spacerun:yes'>   </span>0.37500<span style='mso-spacerun:yes'>  
    18921971</span>0.00000<span style='mso-spacerun:yes'>   </span>0.25000<span
    1893 style='mso-spacerun:yes'>   </span>0.702 0.00072<o:p></o:p></span></p>
     1972style='mso-spacerun:yes'>   </span>0.702-0.00021<o:p></o:p></span></p>
    18941973
    18951974<p class=MsoNormal><span style='font-family:"Courier New"'><span
    18961975style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    18971976style='mso-spacerun:yes'>   </span>:<span
    1898 style='mso-spacerun:yes'>                                 </span>0.007 0.00068<o:p></o:p></span></p>
     1977style='mso-spacerun:yes'>                                 </span>0.007 0.00069<o:p></o:p></span></p>
    18991978
    19001979<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19011980style='mso-spacerun:yes'>  </span><span class=GramE>Fe(</span>5)<span
    1902 style='mso-spacerun:yes'>     </span>Fe:<o:p></o:p></span></p>
     1981style='mso-spacerun:yes'>     </span>Fe:<span
     1982style='mso-spacerun:yes'>                                       </span><o:p></o:p></span></p>
    19031983
    19041984<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    19061986style='mso-spacerun:yes'>   </span>0.37500<span style='mso-spacerun:yes'>  
    19071987</span>0.00000<span style='mso-spacerun:yes'>   </span>0.25000<span
    1908 style='mso-spacerun:yes'>   </span>0.298 0.00072<o:p></o:p></span></p>
     1988style='mso-spacerun:yes'>   </span>0.298-0.00021<o:p></o:p></span></p>
    19091989
    19101990<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19111991style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    19121992style='mso-spacerun:yes'>   </span>:<span
    1913 style='mso-spacerun:yes'>                                 </span>0.007 0.00068<o:p></o:p></span></p>
     1993style='mso-spacerun:yes'>                            </span><span
     1994style='mso-spacerun:yes'>     </span>0.007 0.00069<o:p></o:p></span></p>
    19141995
    19151996<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19161997style='mso-spacerun:yes'>   </span><span class=GramE>O(</span>6)<span
    1917 style='mso-spacerun:yes'>      </span>O:<o:p></o:p></span></p>
     1998style='mso-spacerun:yes'>      </span>O:<span
     1999style='mso-spacerun:yes'>                                       </span><o:p></o:p></span></p>
    19182000
    19192001<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19202002style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    1921 style='mso-spacerun:yes'>  </span>-0.02938<span style='mso-spacerun:yes'>  
    1922 </span>0.05390<span style='mso-spacerun:yes'>   </span>0.15065<span
    1923 style='mso-spacerun:yes'>   </span>1.000 0.00595<o:p></o:p></span></p>
     2003style='mso-spacerun:yes'>  </span>-0.02940<span style='mso-spacerun:yes'>  
     2004</span>0.05391<span style='mso-spacerun:yes'>   </span>0.15061<span
     2005style='mso-spacerun:yes'>   </span>1.000 0.00496<o:p></o:p></span></p>
    19242006
    19252007<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19262008style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    1927 style='mso-spacerun:yes'>  </span><span style='mso-spacerun:yes'> </span>:<span
    1928 style='mso-spacerun:yes'>   </span>0.00005<span style='mso-spacerun:yes'>  
    1929 </span>0.00006<span style='mso-spacerun:yes'>   </span>0.00006<span
    1930 style='mso-spacerun:yes'>         </span>0.00024<o:p></o:p></span></p>
     2009style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>  
     2010</span>0.00005<span style='mso-spacerun:yes'>   </span>0.00006<span
     2011style='mso-spacerun:yes'>   </span>0.00006<span
     2012style='mso-spacerun:yes'>         </span>0.00025<o:p></o:p></span></p>
    19312013
    19322014<p class=MsoNormal><span style='font-family:"Courier New"'>
    19332015<o:p></o:p></span></p>
    19342016
    1935 <p class=MsoNormal><span style='font-family:"Courier New"'>Sample Parameters:<o:p></o:p></span></p>
     2017<p class=MsoNormal><span style='font-family:"Courier New"'>Sample
     2018Parameters:<span
     2019style='mso-spacerun:yes'>                                                     
     2020</span><span style='mso-spacerun:yes'>        </span><o:p></o:p></span></p>
    19362021
    19372022<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    19402025style='mso-spacerun:yes'>    </span>Absorption<span
    19412026style='mso-spacerun:yes'>     </span><span class=SpellE>DisplaceX</span><span
    1942 style='mso-spacerun:yes'>     </span><span class=SpellE>DisplaceY</span><o:p></o:p></span></p>
     2027style='mso-spacerun:yes'>     </span><span class=SpellE>DisplaceY</span><span
     2028style='mso-spacerun:yes'>                 </span><o:p></o:p></span></p>
    19432029
    19442030<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19452031style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    1946 style='mso-spacerun:yes'>      </span>609.0600<span
     2032style='mso-spacerun:yes'>      </span>609.7746<span
    19472033style='mso-spacerun:yes'>        </span>0.0000<span
    1948 style='mso-spacerun:yes'>      </span>459.5009<span
    1949 style='mso-spacerun:yes'>    </span>-4053.6717<o:p></o:p></span></p>
     2034style='mso-spacerun:yes'>     </span>1759.4498<span
     2035style='mso-spacerun:yes'>    </span>-2244.2982<span
     2036style='mso-spacerun:yes'>                 </span><o:p></o:p></span></p>
    19502037
    19512038<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19522039style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    19532040style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>       
    1954 </span>3.1816<span style='mso-spacerun:yes'>                    
    1955 </span>52.8438<span style='mso-spacerun:yes'>      </span>116.3967<o:p></o:p></span></p>
    1956 
    1957 <p class=MsoNormal><span style='font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    1958 
    1959 <p class=MsoNormal><span style='font-family:"Courier New"'><span
    1960 style='mso-spacerun:yes'> </span>Instrument Parameters:<o:p></o:p></span></p>
     2041</span>3.2463<span style='mso-spacerun:yes'>                    
     2042</span>50.3991<span style='mso-spacerun:yes'>      </span>110.1830<span
     2043style='mso-spacerun:yes'>                 </span><o:p></o:p></span></p>
     2044
     2045<p class=MsoNormal><span style='font-family:"Courier New"'><span
     2046style='mso-spacerun:yes'> </span><span
     2047style='mso-spacerun:yes'>                                                                               
     2048</span><o:p></o:p></span></p>
     2049
     2050<p class=MsoNormal><span style='font-family:"Courier New"'><span
     2051style='mso-spacerun:yes'> </span>Instrument Parameters:<span
     2052style='mso-spacerun:yes'>                                                         
     2053</span><o:p></o:p></span></p>
    19612054
    19622055<p class=MsoNormal><span style='font-family:"Courier New"'><span
     
    19672060style='mso-spacerun:yes'>           </span>U<span
    19682061style='mso-spacerun:yes'>           </span>V<span
    1969 style='mso-spacerun:yes'>           </span>W<o:p></o:p></span></p>
     2062style='mso-spacerun:yes'>           </span>W <o:p></o:p></span></p>
    19702063
    19712064<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19722065style='mso-spacerun:yes'> </span><span class=GramE>value :</span><span
    1973 style='mso-spacerun:yes'>    </span>1.909000<span style='mso-spacerun:yes'>  
    1974 </span>-0.199110<span style='mso-spacerun:yes'>    </span>0.000000<span
    1975 style='mso-spacerun:yes'>  </span>283.626148 -677.650574<span
    1976 style='mso-spacerun:yes'>  </span>606.542065<o:p></o:p></span></p>
     2066style='mso-spacerun:yes'>   </span><span
     2067style='mso-spacerun:yes'> </span>1.909000<span style='mso-spacerun:yes'>  
     2068</span>-0.084918<span style='mso-spacerun:yes'>    </span>0.000000<span
     2069style='mso-spacerun:yes'>  </span>266.108676 -655.916341<span
     2070style='mso-spacerun:yes'>  </span>585.853296 <o:p></o:p></span></p>
    19772071
    19782072<p class=MsoNormal><span style='font-family:"Courier New"'><span
    19792073style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    19802074style='mso-spacerun:yes'>   </span>:<span
    1981 style='mso-spacerun:yes'>                </span>0.005497<span
    1982 style='mso-spacerun:yes'>                </span>3.956233<span
    1983 style='mso-spacerun:yes'>    </span>9.461548<span style='mso-spacerun:yes'>   
    1984 </span>5.438615<o:p></o:p></span></p>
    1985 
    1986 <p class=MsoNormal>A useful display to examine is given by selecting Covariance
    1987 in the GSAS-II data tree</p>
     2075style='mso-spacerun:yes'>                </span>0.005611<span
     2076style='mso-spacerun:yes'>                </span>3.981181<span
     2077style='mso-spacerun:yes'>    </span>9.537597<span style='mso-spacerun:yes'>   
     2078</span>5.489050 <o:p></o:p></span></p>
     2079
     2080<p class=MsoNormal>A useful display to examine is given by selecting <b
     2081style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2082mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2083minor-latin'>Covariance</span></b> in the GSAS-II data tree</p>
    19882084
    19892085<p class=MsoNormal><span style='font-family:"Courier New";mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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