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Nov 7, 2018 11:49:11 AM (3 years ago)
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vondreele
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update tutorial

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  • Tutorials/Magnetic-IV/Magnetic-IV.htm

    r3701 r3726  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>vondreele</o:LastAuthor>
    25   <o:Revision>10</o:Revision>
    26   <o:TotalTime>452</o:TotalTime>
     25  <o:Revision>11</o:Revision>
     26  <o:TotalTime>463</o:TotalTime>
    2727  <o:Created>2018-10-01T13:36:00Z</o:Created>
    28   <o:LastSaved>2018-10-23T14:58:00Z</o:LastSaved>
     28  <o:LastSaved>2018-11-07T17:48:00Z</o:LastSaved>
    2929  <o:Pages>1</o:Pages>
    30   <o:Words>2037</o:Words>
    31   <o:Characters>11617</o:Characters>
     30  <o:Words>2041</o:Words>
     31  <o:Characters>11639</o:Characters>
    3232  <o:Lines>96</o:Lines>
    3333  <o:Paragraphs>27</o:Paragraphs>
    34   <o:CharactersWithSpaces>13627</o:CharactersWithSpaces>
     34  <o:CharactersWithSpaces>13653</o:CharactersWithSpaces>
    3535  <o:Version>16.00</o:Version>
    3636 </o:DocumentProperties>
     
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    12851285<p class=MsoNormal>In this tutorial, we will show how GSAS-II makes use of the
    12861286Bilbao crystallographic server (<a href="http://www.cryst.ehu.es/">www.cryst.ehu.es/</a>)
    1287 <i style='mso-bidi-font-style:normal'>Magnetic Symmetry and Applications</i>
    1288 routine k-SUBGROUPSMAG (<a
    1289 href="http://iopscience.iop.org/0953-8984/28/28/286001"><span style='font-size:
    1290 10.0pt;font-family:"Arial",sans-serif'>Perez-Mato, JM; <span class=SpellE>Gallego</span>,
    1291 SV; <span class=SpellE>Elcoro</span>, L; <span class=SpellE>Tasci</span>, E and
    1292 <span class=SpellE>Aroyo</span>, MI, <i>J. of Phys.: <span class=SpellE>Condens</span>
    1293 Matter</i> (2016), <b>28</b>:28601</span></a>) to determine a magnetic crystal
    1294 structure with a non-zero propagation vector. If you have not done so already,
    1295 you may wish to do the Simple Magnetic Structures tutorial first as it contains
    1296 some background information that will not be covered here. It is also helpful
    1297 to do parts I - III of the series of Magnetic Structures tutorials. To make
    1298 this work, your computer must have an internet connection for GSAS-II to access
    1299 this site. (We will supply the project file that results after k-SUBGROUPSMAG
    1300 is called in case you lack internet access).</p>
     1287<i style='mso-bidi-font-style:normal'>Magnetic Symmetry and Applications</i> routine
     1288k-SUBGROUPSMAG (<a href="http://iopscience.iop.org/0953-8984/28/28/286001"><span
     1289style='font-size:10.0pt;font-family:"Arial",sans-serif'>Perez-Mato, JM; <span
     1290class=SpellE>Gallego</span>, SV; <span class=SpellE>Elcoro</span>, L; <span
     1291class=SpellE>Tasci</span>, E and <span class=SpellE>Aroyo</span>, MI, <i>J. of
     1292Phys.: <span class=SpellE>Condens</span> Matter</i> (2016), <b>28</b>:28601</span></a>)
     1293to determine a magnetic crystal structure with a non-zero propagation vector.
     1294If you have not done so already, you may wish to do the Simple Magnetic
     1295Structures tutorial first as it contains some background information that will
     1296not be covered here. It is also helpful to do parts I - III of the series of
     1297Magnetic Structures tutorials. To make this work, your computer must have an
     1298internet connection for GSAS-II to access this site. (We will supply the
     1299project file that results after k-SUBGROUPSMAG is called in case you lack
     1300internet access).</p>
    13011301
    13021302<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    13241324 <v:imagedata src="Magnetic-IV_files/image001.png" o:title=""/>
    13251325</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=422
    1326 src="Magnetic-IV_files/image002.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1326src="Magnetic-IV_files/image043.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
    13271327
    13281328<p class=MsoNormal>In this tutorial we will be examining the perovskite (Pr<sub>0.5</sub>Sr<sub>0.5</sub><span
     
    13771377href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Magnetic-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Magnetic-IV/data/</a>.
    13781378In this case you will need to navigate to the download location manually.)<br>
    1379 For this tutorial the extension on the data file is the expected one, so it should
    1380 be immediately visible.</span></p>
     1379For this tutorial the extension on the data file is the expected one, so it
     1380should be immediately visible.</span></p>
    13811381
    13821382<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
     
    14271427 <v:imagedata src="Magnetic-IV_files/image003.png" o:title=""/>
    14281428</v:shape><![endif]--><![if !vml]><img border=0 width=431 height=383
    1429 src="Magnetic-IV_files/image004.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
     1429src="Magnetic-IV_files/image044.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
    14301430
    14311431<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
     
    15021502 <v:imagedata src="Magnetic-IV_files/image005.png" o:title=""/>
    15031503</v:shape><![endif]--><![if !vml]><img border=0 width=457 height=245
    1504 src="Magnetic-IV_files/image006.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1504src="Magnetic-IV_files/image045.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
    15051505
    15061506<h3>Step 3. Check powder pattern indexing</h3>
     
    15201520 <v:imagedata src="Magnetic-IV_files/image007.png" o:title=""/>
    15211521</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=167
    1522 src="Magnetic-IV_files/image008.gif" v:shapes="Picture_x0020_6"><![endif]></span><br>
     1522src="Magnetic-IV_files/image046.gif" v:shapes="Picture_x0020_6"><![endif]></span><br>
    15231523<span class=GramE>This</span> can use lattice parameters &amp; space groups to
    15241524generate expected reflection positions to check against the peaks in the powder
     
    15451545 <v:imagedata src="Magnetic-IV_files/image009.png" o:title=""/>
    15461546</v:shape><![endif]--><![if !vml]><img border=0 width=483 height=168
    1547 src="Magnetic-IV_files/image010.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1547src="Magnetic-IV_files/image047.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    15481548
    15491549<p class=MsoNormal><span class=GramE>showing</span> the lattice constants for
     
    15531553
    15541554<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1555  id="Picture_x0020_9" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:360.75pt;
    1556  height:320.25pt;visibility:visible;mso-wrap-style:square'>
     1555 id="_x0000_i1041" type="#_x0000_t75" style='width:360.75pt;height:320.25pt;
     1556 visibility:visible;mso-wrap-style:square'>
    15571557 <v:imagedata src="Magnetic-IV_files/image011.png" o:title=""/>
    15581558</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=427
    1559 src="Magnetic-IV_files/image012.gif" v:shapes="Picture_x0020_9"><![endif]></span></p>
     1559src="Magnetic-IV_files/image048.gif" v:shapes="_x0000_i1041"><![endif]></span></p>
    15601560
    15611561<p class=MsoNormal>I’ve zoomed into the 6-40 <span class=SpellE>deg</span>
     
    15771577
    15781578<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1579  id="Picture_x0020_10" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:357.75pt;
    1580  height:317.25pt;visibility:visible;mso-wrap-style:square'>
     1579 id="_x0000_i1040" type="#_x0000_t75" style='width:357.75pt;height:317.25pt;
     1580 visibility:visible;mso-wrap-style:square'>
    15811581 <v:imagedata src="Magnetic-IV_files/image013.png" o:title=""/>
    15821582</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=423
    1583 src="Magnetic-IV_files/image014.gif" v:shapes="Picture_x0020_10"><![endif]></span></p>
     1583src="Magnetic-IV_files/image049.gif" v:shapes="_x0000_i1040"><![endif]></span></p>
    15841584
    15851585<p class=MsoListParagraph style='margin-left:0in;mso-add-space:auto'>Those line
    1586 up pretty well; note the lowest angle peak &amp; the one at about 21º2&#920;. Now
    1587 change <span class=SpellE>Bravais</span> lattice and Space group to <span
     1586up pretty well; note the lowest angle peak &amp; the one at about 21º2&#920;.
     1587Now change <span class=SpellE>Bravais</span> lattice and Space group to <span
    15881588class=SpellE>Bmmm</span>; a new plot will appear</p>
    15891589
     
    15931593 <v:imagedata src="Magnetic-IV_files/image015.png" o:title=""/>
    15941594</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=427
    1595 src="Magnetic-IV_files/image016.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
     1595src="Magnetic-IV_files/image050.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
    15961596
    15971597<p class=MsoNormal>The match is not quite as good; the 1<sup>st</sup> line just
    1598 misses the 1<sup>st</sup> peak top and the one at 21º2&#920; also misses the
    1599 peak top. Lastly, let’s try <span class=SpellE>Cmmm</span>; enter it for <span
     1598misses the 1<sup>st</sup> peak top and the one at 21º2&#920; also misses the peak
     1599top. Lastly, let’s try <span class=SpellE>Cmmm</span>; enter it for <span
    16001600class=SpellE>Bravais</span> lattice and space group. A new plot appears</p>
    16011601
    16021602<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1603  id="_x0000_i1038" type="#_x0000_t75" style='width:363pt;height:322.5pt;
    1604  visibility:visible;mso-wrap-style:square'>
     1603 id="Picture_x0020_9" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:363pt;
     1604 height:322.5pt;visibility:visible;mso-wrap-style:square'>
    16051605 <v:imagedata src="Magnetic-IV_files/image017.png" o:title=""/>
    16061606</v:shape><![endif]--><![if !vml]><img border=0 width=484 height=430
    1607 src="Magnetic-IV_files/image018.gif" v:shapes="_x0000_i1038"><![endif]></span></p>
    1608 
    1609 <p class=MsoNormal>This fit seems even worse, so the right description is lose the
    1610 B- and C-centering leaving just A-centering. However, we want the A-center to
    1611 be magnetic; the way to do this is to assign the propagation vector <span
     1607src="Magnetic-IV_files/image051.gif" v:shapes="Picture_x0020_9"><![endif]></span></p>
     1608
     1609<p class=MsoNormal>This fit seems even worse, so the right description is lose
     1610the B- and C-centering leaving just A-centering. However, we want the A-center
     1611to be magnetic; the way to do this is to assign the propagation vector <span
    16121612class=SpellE>k<sub>x</sub><span class=GramE>,k<sub>y</sub>,k<sub>z</sub></span></span>
    16131613= (1,0,0) when we run k-SUBGROUPSMAG on the parent space group (<span
     
    16241624
    16251625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1626  id="_x0000_i1037" type="#_x0000_t75" style='width:207.75pt;height:225.75pt;
    1627  visibility:visible;mso-wrap-style:square'>
     1626 id="Picture_x0020_10" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:207.75pt;
     1627 height:225.75pt;visibility:visible;mso-wrap-style:square'>
    16281628 <v:imagedata src="Magnetic-IV_files/image019.png" o:title=""/>
    16291629</v:shape><![endif]--><![if !vml]><img border=0 width=277 height=301
    1630 src="Magnetic-IV_files/image020.gif" v:shapes="_x0000_i1037"><![endif]></span></p>
     1630src="Magnetic-IV_files/image052.gif" v:shapes="Picture_x0020_10"><![endif]></span></p>
    16311631
    16321632<p class=MsoNormal>These are the controls for running the Bilbao routine. The
     
    16561656 <v:imagedata src="Magnetic-IV_files/image021.png" o:title=""/>
    16571657</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=165
    1658 src="Magnetic-IV_files/image022.gif" v:shapes="Picture_x0020_11"><![endif]></span></p>
     1658src="Magnetic-IV_files/image053.gif" v:shapes="Picture_x0020_11"><![endif]></span></p>
    16591659
    16601660<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
     
    16871687
    16881688<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1689  id="Picture_x0020_12" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:358.5pt;
    1690  height:240.75pt;visibility:visible;mso-wrap-style:square'>
    1691  <v:imagedata src="Magnetic-IV_files/image023.png" o:title=""/>
    1692 </v:shape><![endif]--><![if !vml]><img border=0 width=478 height=321
    1693 src="Magnetic-IV_files/image024.gif" v:shapes="Picture_x0020_12"><![endif]></span></p>
     1689 id="_x0000_i1035" type="#_x0000_t75" style='width:5in;height:292.5pt;
     1690 visibility:visible;mso-wrap-style:square'>
     1691 <v:imagedata src="Magnetic-IV_files/image054.png" o:title=""/>
     1692</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=390
     1693src="Magnetic-IV_files/image055.gif" v:shapes="_x0000_i1035"><![endif]></span></p>
    16941694
    16951695<p class=MsoNormal>The <span class=SpellE>Uniq</span> column gives the number
     
    16991699mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    17001700minor-latin'>preserve axes</span></b> option on the k-SUBGROUPSMAG is set by
    1701 default to transform the standard setting result from k-SUBGROUPSMAG for orthorhombic
    1702 to one that closely is aligned, if possible, to the parent cell axes. So this
    1703 list contains non-standard settings of orthorhombic space groups (e.g. the
    1704 chemical version of #3 P<sub>C</sub> <span class=SpellE>bmn</span> is a
    1705 non-standard version of P <span class=SpellE>mna</span>, #53 in International
     1701default to transform the standard setting result from k-SUBGROUPSMAG for
     1702orthorhombic to one that closely is aligned, if possible, to the parent cell
     1703axes. So this list contains non-standard settings of orthorhombic space groups
     1704(e.g. the chemical version of #3 P<sub>C</sub> <span class=SpellE>bmn</span> is
     1705a non-standard version of P <span class=SpellE>mna</span>, #53 in International
    17061706Tables for Crystallography Vol A.). If desired, clearing the flag and rerunning
    17071707k-SUBGROUPSMAG will produce magnetic space groups in standard settings; we will
     
    17141714on the 4 marked Keep out of the 1<sup>st</sup> 8 solutions. Only #7 &amp; #8
    17151715will index the low angle peaks correctly. We’ll go with these. The solutions
    1716 further down are ones in which more than one symmetry generator was removed; if
    1717 need be we can go back and look at those. NB: running k-SUBGROUPSMAG with the
    1718 “Landau transition” checked will give just these 1<sup>st</sup> 8 solutions.
    1719 This might be appropriate because the magnetic transition for (Pr<sub>.5</sub>Sr<sub>.5</sub><span
    1720 class=GramE>)MnO<sub>3</sub></span><sub> </sub>is a continuous 2<sup>nd</sup>
    1721 order transition. However, by doing this one might not see the correct result!</p>
     1716further down are ones in which more than one symmetry generator was removed (<span
     1717class=SpellE>nSup</span> &gt; 1); if need be we can go back and look at those.
     1718NB: running k-SUBGROUPSMAG with the “Landau transition” checked will give just
     1719these 1<sup>st</sup> 8 solutions. This might be appropriate because the
     1720magnetic transition for (Pr<sub>.5</sub>Sr<sub>.5</sub><span class=GramE>)MnO<sub>3</sub></span><sub>
     1721</sub>is a continuous 2<sup>nd</sup> order transition. However, by doing this in
     1722other cases one might not see the correct result!</p>
    17221723
    17231724<h3>Step 5. Select 1<sup>st</sup> magnetic structure</h3>
     
    17341735 <v:imagedata src="Magnetic-IV_files/image025.png" o:title=""/>
    17351736</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=267
    1736 src="Magnetic-IV_files/image026.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1737src="Magnetic-IV_files/image056.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
    17371738
    17381739<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
     
    17461747 <v:imagedata src="Magnetic-IV_files/image027.png" o:title=""/>
    17471748</v:shape><![endif]--><![if !vml]><img border=0 width=369 height=297
    1748 src="Magnetic-IV_files/image028.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>
     1749src="Magnetic-IV_files/image057.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>
    17491750
    17501751<p class=MsoNormal>This shows all magnetic phases that were marked <span
     
    17611762 <v:imagedata src="Magnetic-IV_files/image029.png" o:title=""/>
    17621763</v:shape><![endif]--><![if !vml]><img border=0 width=369 height=123
    1763 src="Magnetic-IV_files/image030.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>
     1764src="Magnetic-IV_files/image058.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>
    17641765
    17651766<p class=MsoNormal>This one <span class=SpellE>Mn</span> atom has an allowed
     
    17811782 <v:imagedata src="Magnetic-IV_files/image031.png" o:title=""/>
    17821783</v:shape><![endif]--><![if !vml]><img border=0 width=472 height=263
    1783 src="Magnetic-IV_files/image032.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1784src="Magnetic-IV_files/image059.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
    17841785
    17851786<p class=MsoNormal>Select Atoms, enter <b style='mso-bidi-font-weight:normal'><span
     
    18001801 <v:imagedata src="Magnetic-IV_files/image033.png" o:title=""/>
    18011802</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=426
    1802 src="Magnetic-IV_files/image034.gif" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1803src="Magnetic-IV_files/image060.gif" v:shapes="Picture_x0020_20"><![endif]></span></p>
    18031804
    18041805<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
     
    18541855 <v:imagedata src="Magnetic-IV_files/image035.png" o:title=""/>
    18551856</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=422
    1856 src="Magnetic-IV_files/image036.gif" v:shapes="Picture_x0020_21"><![endif]></span></p>
     1857src="Magnetic-IV_files/image061.gif" v:shapes="Picture_x0020_21"><![endif]></span></p>
    18571858
    18581859<p class=MsoNormal>I show the plot with <span class=SpellE><span class=GramE>sqrt</span></span><span
     
    18821883 <v:imagedata src="Magnetic-IV_files/image037.png" o:title=""/>
    18831884</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=268
    1884 src="Magnetic-IV_files/image038.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
     1885src="Magnetic-IV_files/image062.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
    18851886
    18861887<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
     
    18941895 <v:imagedata src="Magnetic-IV_files/image027.png" o:title=""/>
    18951896</v:shape><![endif]--><![if !vml]><img border=0 width=369 height=297
    1896 src="Magnetic-IV_files/image028.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
     1897src="Magnetic-IV_files/image057.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
    18971898
    18981899<p class=MsoNormal>We already tried the 1<sup>st</sup> one; now select the 2<sup>nd</sup>
     
    19061907 <v:imagedata src="Magnetic-IV_files/image039.png" o:title=""/>
    19071908</v:shape><![endif]--><![if !vml]><img border=0 width=375 height=123
    1908 src="Magnetic-IV_files/image040.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
     1909src="Magnetic-IV_files/image063.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
    19091910
    19101911<p class=MsoNormal>In this case, the <span class=SpellE>Mn</span> atom has
     
    19251926 <v:imagedata src="Magnetic-IV_files/image041.png" o:title=""/>
    19261927</v:shape><![endif]--><![if !vml]><img border=0 width=474 height=279
    1927 src="Magnetic-IV_files/image042.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1928src="Magnetic-IV_files/image064.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
    19281929
    19291930<p class=MsoNormal>Select the Atoms tab &amp; set <span class=SpellE>Mx</span>
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