Changeset 2389 for Tutorials/FitPeaks


Ignore:
Timestamp:
Jul 28, 2016 2:17:46 PM (5 years ago)
Author:
vondreele
Message:
 
File:
1 edited

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  • Tutorials/FitPeaks/Fit Peaks.htm

    r1725 r2389  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>6</o:Revision>
    26   <o:TotalTime>948</o:TotalTime>
     25  <o:Revision>7</o:Revision>
     26  <o:TotalTime>1035</o:TotalTime>
    2727  <o:Created>2014-07-21T14:48:00Z</o:Created>
    28   <o:LastSaved>2015-03-17T15:22:00Z</o:LastSaved>
    29   <o:Pages>1</o:Pages>
    30   <o:Words>3024</o:Words>
    31   <o:Characters>17242</o:Characters>
     28  <o:LastSaved>2016-07-28T18:11:00Z</o:LastSaved>
     29  <o:Pages>27</o:Pages>
     30  <o:Words>3023</o:Words>
     31  <o:Characters>17232</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>143</o:Lines>
    3434  <o:Paragraphs>40</o:Paragraphs>
    35   <o:CharactersWithSpaces>20226</o:CharactersWithSpaces>
    36   <o:Version>15.00</o:Version>
     35  <o:CharactersWithSpaces>20215</o:CharactersWithSpaces>
     36  <o:Version>16.00</o:Version>
    3737 </o:DocumentProperties>
    3838 <o:OfficeDocumentSettings>
     
    4444<!--[if gte mso 9]><xml>
    4545 <w:WordDocument>
     46  <w:View>Print</w:View>
    4647  <w:SpellingState>Clean</w:SpellingState>
    4748  <w:GrammarState>Clean</w:GrammarState>
     
    663664        {font-family:"Cambria Math";
    664665        panose-1:2 4 5 3 5 4 6 3 2 4;
    665         mso-font-charset:0;
     666        mso-font-charset:1;
    666667        mso-generic-font-family:roman;
    667668        mso-font-pitch:variable;
    668         mso-font-signature:-536870145 1107305727 0 0 415 0;}
     669        mso-font-signature:0 0 0 0 0 0;}
    669670@font-face
    670671        {font-family:Calibri;
     
    11691170        mso-hansi-font-family:"Courier New";
    11701171        mso-bidi-font-family:"Courier New";}
     1172p.msonormal0, li.msonormal0, div.msonormal0
     1173        {mso-style-name:msonormal;
     1174        mso-style-noshow:yes;
     1175        mso-style-priority:99;
     1176        mso-style-unhide:no;
     1177        mso-margin-top-alt:auto;
     1178        margin-right:0in;
     1179        mso-margin-bottom-alt:auto;
     1180        margin-left:0in;
     1181        mso-pagination:widow-orphan;
     1182        font-size:12.0pt;
     1183        font-family:"Times New Roman",serif;
     1184        mso-fareast-font-family:"Times New Roman";
     1185        mso-fareast-theme-font:minor-fareast;}
    11711186span.TitleChar
    11721187        {mso-style-name:"Title Char";
     
    14601475the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14611476mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1462 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder data
    1463 file</span></b> menu item to read the data file into the current GSAS-II
     1477Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
     1478data file</span></b> menu item to read the data file into the current GSAS-II
    14641479project. This read option is set to read any of the powder data formats defined
    14651480for GSAS (angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other
     
    14911506minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
    14921507Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
    1493 downloaded the exercise files (recommended), then the </span><b
     1508downloaded the exercise files (recommended), then the </span><span
     1509class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1510"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
     1511Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
    14941512style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14951513mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
    1496 minor-latin;mso-hansi-theme-font:minor-latin'>Import/...</span></b><span
     1514minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
    14971515style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
    14981516entry will bring you to the location where the files have been downloaded. (It
     
    15171535mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    15181536Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1519 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1520 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1521 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1522 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1523 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1524 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1525 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    1526 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1527 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1528 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
    1529 proceed.</p>
     1537Dialog box asking <b style='mso-bidi-font-weight:normal'><span
     1538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1539mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1540minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
     1541normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1542minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1543mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
    15301544
    15311545<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    15751589src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
    15761590
    1577 <p class=MsoNormal><span class=GramE>and</span> the plot window will show the
    1578 powder pattern</p>
     1591<p class=MsoNormal>and the plot window will show the powder pattern</p>
    15791592
    15801593<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1581  id="_x0000_i1049" type="#_x0000_t75" style='width:525pt;height:450pt;
    1582  visibility:visible;mso-wrap-style:square'>
     1594 id="Picture_x0020_2" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
     1595 height:450pt;visibility:visible;mso-wrap-style:square'>
    15831596 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
    15841597</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1585 src="Fit%20Peaks_files/image002.png" v:shapes="_x0000_i1049"><![endif]></span></p>
     1598src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
    15861599
    15871600<h2>Step 2: Select Limits </h2>
     
    16741687
    16751688<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1676 auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1047"
    1677  type="#_x0000_t75" style='width:525pt;height:450pt;visibility:visible;
    1678  mso-wrap-style:square'>
     1689auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
     1690 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
     1691 visibility:visible;mso-wrap-style:square'>
    16791692 <v:imagedata src="Fit%20Peaks_files/image004.png" o:title=""/>
    16801693</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1681 src="Fit%20Peaks_files/image004.png" v:shapes="_x0000_i1047"><![endif]></span></p>
     1694src="Fit%20Peaks_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
    16821695
    16831696<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
    1684 auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
    1685 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1686 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1687 mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
    1688 increasing 2<span style='font-family:Symbol'>Q</span>.</p>
     1697auto'>and peaks are shown in the <b style='mso-bidi-font-weight:normal'><span
     1698style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1699mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1700minor-latin'>Peak List</span></b> window in order of increasing 2<span
     1701style='font-family:Symbol'>Q</span>.</p>
    16891702
    16901703<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
     
    16981711<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
    16991712will be 20 peaks in this example. You should examine both the list and the plot
    1700 to be sure the auto search did not pick a peak twice (quite rarely) or skip a
    1701 peak or shoulder. You can add a peak to the list by pressing the left mouse
    1702 button with the pointer on a data point at the peak top or shoulder; be sure
    1703 the zoom/shift buttons are off. You may drag a peak position as needed. A
    1704 position may be deleted with a right click with the mouse on the blue line. You
    1705 can also delete a peak by selecting the row in the table; it will be
    1706 highlighted in blue. Then press the <b style='mso-bidi-font-weight:normal'><span
    1707 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1708 mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be removed
    1709 from the table and the plot. The list will always show the peaks sorted by
    1710 position. When done you should have 20 unique peak positions.</p>
     1713to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
     1714shoulder. You can add a peak to the list by pressing the left mouse button with
     1715the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
     1716buttons are off. You may drag a peak position as needed. A position may be
     1717deleted with a right click with the mouse on the blue line. You can also delete
     1718a peak by selecting the row in the table; it will be highlighted in blue. Then
     1719press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1720mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
     1721key; it will be removed from the table and the plot. The list will always show
     1722the peaks sorted by position. When done you should have 20 unique peak
     1723positions.</p>
    17111724
    17121725<h2>Step 4: Refine Peak Positions</h2>
     
    17681781auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
    17691782style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    1770 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1771 class=GramE>single-click</span> on any value in the table to select it, for
    1772 example the first peak position. A black box appears around the value. </p>
     1783style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
     1784on any value in the table to select it, for example the first peak position. A
     1785black box appears around the value. </p>
    17731786
    17741787<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    17751788text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
    17761789style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    1777 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1778 class=GramE>single-click</span> on the <b style='mso-bidi-font-weight:normal'><span
    1779 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1780 mso-hansi-theme-font:minor-latin'>refine</span></b> label above the peak
    1781 position check-boxes. The entire column of checkboxes is highlighted in blue.
    1782 Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1783 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1784 Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
    1785 refinement flags (<b style='mso-bidi-font-weight:normal'><span
    1786 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1787 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1788 minor-latin'>n</span></b> would turn them off).</p>
     1790style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
     1791on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1792mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
     1793label above the peak position check-boxes. The entire column of checkboxes is
     1794highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
     1795style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1796mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1797minor-latin'>y</span></b> key to turn on all refinement flags (<b
     1798style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1799mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1800Calibri;mso-bidi-theme-font:minor-latin'>n</span></b> would turn them off).</p>
    17891801
    17901802<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
     
    18871899style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18881900mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1889 Calibri;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b> to copy
    1890 the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
     1901Calibri;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b> to
     1902copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
    18911903style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18921904mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     
    19611973style='mso-spacerun:yes'> </span></p>
    19621974
    1963 <p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
    1964 a=2.93932 Å generates not enough lines to match all the peaks</p>
     1975<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
     1976enough lines to match all the peaks</p>
    19651977
    19661978<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19821994two-theta zero: click on the <b style='mso-bidi-font-weight:normal'><span
    19831995style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1984 mso-hansi-theme-font:minor-latin'>Refine?</span></b> <span class=GramE>checkbox</span>
    1985 next to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1986 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1987 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Zero
    1988 offset</span></b> value and then the <b style='mso-bidi-font-weight:normal'><span
    1989 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1990 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1991 minor-latin'>Cell Index/Refine/Refine Cell</span></b> menu option. The M20
    1992 improves to ~3600 and <span class=GramE>the a</span> cell parameter value
    1993 shifts from 4.15683 to 4.15691 when zero is refined. (NB: The certificate value
    1994 for NIST SRM 660a is 4.15692 Å). Press the <b style='mso-bidi-font-weight:normal'><span
    1995 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1996 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1997 minor-latin'>Show <span class=SpellE>hkl</span> positions </span></b>button to
    1998 update the plot including the refined <b style='mso-bidi-font-weight:normal'><span
    1999 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2000 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2001 minor-latin'>Zero offset</span></b> (in this case hardly anything
    2002 happens!).<span style='mso-spacerun:yes'>  </span></p>
     1996mso-hansi-theme-font:minor-latin'>Refine?</span></b> checkbox next to the <b
     1997style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1998mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1999Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then
     2000the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2001mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2002Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
     2003menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
     2004parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
     2005certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
     2006style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2007mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2008Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
     2009positions </span></b>button to update the plot including the refined <b
     2010style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2012Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
     2013hardly anything happens!).<span style='mso-spacerun:yes'>  </span></p>
    20032014
    20042015<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    20162027mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    20172028Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window with
    2018 an improved <span class=GramE>M20(</span>~3600) and a new value for <b
    2019 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2020 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2021 Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown. NB:
    2022 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2023 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
    2024 class=SpellE>hkl</span> positions</span></b> button has an additional use; you
    2025 can enter the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2026 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2027 mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight:
    2028 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2029 minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>, <b
    2030 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2031 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
    2032 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2029an improved M20(~3600) and a new value for <b style='mso-bidi-font-weight:normal'><span
     2030style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2031mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2032minor-latin'>Zero offset</span></b> is shown. NB: the <b style='mso-bidi-font-weight:
     2033normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2034minor-latin;mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
     2035positions</span></b> button has an additional use; you can enter the <span
     2036class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2037"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2038minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight:normal'><span
     2039style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2040mso-hansi-theme-font:minor-latin'> lattice</span></b>, <b style='mso-bidi-font-weight:
     2041normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2042minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b> &amp; <b
     2043style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20332044mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
    20342045for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
     
    20632074mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    20642075minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
    2065 the current project saved; if <span class=GramE><b style='mso-bidi-font-weight:
    2066 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2067 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    2068 mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the peak
    2069 fitting/indexing &amp; cell refinement results will be saved to the <b
    2070 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2071 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2072 Calibri;mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
    2073 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2074 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2075 Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
    2076 remain as it was when created at Step 4 above.</p>
     2076the current project saved; if <b style='mso-bidi-font-weight:normal'><span
     2077style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2078mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2079minor-latin'>Yes</span></b> then all the peak fitting/indexing &amp; cell
     2080refinement results will be saved to the <b style='mso-bidi-font-weight:normal'><span
     2081style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2082mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2083minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
     2084style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2085mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2086minor-latin'>No</span></b> then the file will remain as it was when created at
     2087Step 4 above.</p>
    20772088
    20782089<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
     
    20812092
    20822093<p class=MsoNormal>In this exercise we will fit peaks and index them for the
    2083 new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
    2084 (aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
    2085 data were also collected on 11BM-B at APS. The unit cell is monoclinic so it is
    2086 a more substantial test of the indexing capability of GSAS-II. The required
    2087 data files should have been downloaded when you downloaded this tutorial.
    2088 Otherwise you will need to get them manually from <span style='mso-fareast-font-family:
    2089 Calibri;mso-fareast-theme-font:minor-latin'><a
     2094new mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
     2095href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
     2096also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
     2097substantial test of the indexing capability of GSAS-II. The required data files
     2098should have been downloaded when you downloaded this tutorial. Otherwise you
     2099will need to get them manually from <span style='mso-fareast-font-family:Calibri;
     2100mso-fareast-theme-font:minor-latin'><a
    20902101href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
    20912102Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
     
    21002111<h2>Step 1. Read in the data. </h2>
    21012112
    2102 <p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
    2103 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2104 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2105 minor-latin'>\exercises\<span class=SpellE>FitPeaks</span>\11bmb_6231.fxye</span></b>;
    2106 it has a corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2113<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
     2114normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2115minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2116mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b style='mso-bidi-font-weight:
     2117normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2118minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2119mso-bidi-theme-font:minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a
     2120corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    21072121style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21082122mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     
    22422256indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
    22432257style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2244 mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
    2245 new indexing runs. The best solution is the one with the smaller volume and
    2246 &#946; &gt; 90 deg. The plot shows every peak indexed including a weak peak not
     2258mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try new
     2259indexing runs. The best solution is the one with the smaller volume and &#946;
     2260&gt; 90 deg. The plot shows every peak indexed including a weak peak not
    22472261selected for the peak fitting, although the weak peak at 2<span
    22482262style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
     
    22902304src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
    22912305
    2292 <p class=MsoNormal>This concludes this exercise; <span class=GramE><b
    2293 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2294 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2295 Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project
    2296 file as it is needed for the <b style='mso-bidi-font-weight:normal'><span
    2297 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2298 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2299 minor-latin'>Charge Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
     2306<p class=MsoNormal>This concludes this exercise; <b style='mso-bidi-font-weight:
     2307normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2308minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2309mso-bidi-theme-font:minor-latin'>Save</span></b> the project file as it is
     2310needed for the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2311"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2312minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Charge
     2313Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
    23002314style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23012315mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of
     
    23242338mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
    23252339minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
    2326 font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span
     2340font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11</span>bmb_8716.fxye</span></b><span
    23272341style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
    23282342the corresponding .<span class=SpellE>prm</span> files.</span></p>
     
    23302344<h2>Step 1. Read in the data. </h2>
    23312345
    2332 <p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
    2333 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2334 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2335 minor-latin'>\exercises\<span class=SpellE>FitPeaks</span>\11bmb_8716.fxye</span></b>;
    2336 it has a corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2346<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
     2347normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2348minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2349mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b style='mso-bidi-font-weight:
     2350normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2351minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2352mso-bidi-theme-font:minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a
     2353corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    23372354style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    23382355mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     
    23562373
    23572374<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
    2358 lower part of the pattern; I’ve also chosen to plot the square root of the intensity
    2359 (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2360 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>S</span></b>’
    2361 key) as this shows weak peaks better.</p>
     2375lower part of the pattern; I’ve also chosen to plot the square root of the
     2376intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
     2377"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2378minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
    23622379
    23632380<h2>Step 2 Set limits</h2>
     
    23802397can be moved by dragging the peak line and peaks can be deleted by
    23812398right-clicking on them. This only works when the zoom and reposition modes
    2382 (below) are not selected. An easy to shift the view is to use the ‘&lt;’ and ‘&gt;’
    2383 buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span> that
    2384 should be added to the list. I skipped a couple of very weak peaks; the total
    2385 list has &gt;28 peaks.</p>
     2399(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
     2400‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
     2401that should be added to the list. I skipped a couple of very weak peaks; the
     2402total list has &gt;28 peaks.</p>
    23862403
    23872404<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    24832500new indexing runs. The best solution is the one with the smaller volume and
    24842501&#946; &gt; 90 deg. The plot shows every peak indexed including the weak peaks
    2485 not selected for the peak fitting. Copy the best cell and try to refine it
    2486 along with the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2487 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2488 minor-latin'>Zero offset</span></b>. I obtained an improved M20 ~1300 and
    2489 slightly different lattice parameters. Try different space groups, pressing the
    2490 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2491 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
    2492 class=SpellE>hkl</span> positions</span></b> each time to see which lines
    2493 vanish. The correct space group is P2<sub>1</sub>. Armed with this information you
    2494 can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2495 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2496 Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
    2497 indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
    2498 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2499 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2500 minor-latin'>sucrose</span></b>) and select <b style='mso-bidi-font-weight:
    2501 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2502 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> from
    2503 the GSAS-II data tree.</p>
     2502not selected for the peak fitting. Copy the best cell and try to refine it along
     2503with the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2504mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
     2505I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
     2506different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
     2507style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2508mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
     2509each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
     2510Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
     2511style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2512mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     2513minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
     2514style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2515mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2516Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>) and select <b
     2517style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2518mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
     2519from the GSAS-II data tree.</p>
    25042520
    25052521<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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