Changeset 2390 for Tutorials/SAsize


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Timestamp:
Jul 28, 2016 2:18:10 PM (5 years ago)
Author:
vondreele
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  • Tutorials/SAsize/Small Angle Size Distribution.htm

    r1739 r2390  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>13</o:Revision>
    28   <o:TotalTime>1916</o:TotalTime>
     27  <o:Revision>14</o:Revision>
     28  <o:TotalTime>1917</o:TotalTime>
    2929  <o:Created>2014-03-20T16:54:00Z</o:Created>
    30   <o:LastSaved>2015-03-18T17:22:00Z</o:LastSaved>
     30  <o:LastSaved>2016-07-28T18:49:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    3232  <o:Words>1272</o:Words>
    33   <o:Characters>7256</o:Characters>
     33  <o:Characters>7251</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>60</o:Lines>
    3636  <o:Paragraphs>17</o:Paragraphs>
    37   <o:CharactersWithSpaces>8511</o:CharactersWithSpaces>
    38   <o:Version>15.00</o:Version>
     37  <o:CharactersWithSpaces>8506</o:CharactersWithSpaces>
     38  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
    4040 <o:OfficeDocumentSettings>
     
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    12071218<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    12081219this tutorial you will determine the size distribution of particles in an
    1209 alumina polishing powder using data from a constant wavelength synchrotron
    1210 X-ray USAXS instrument. You will use both Maximum Entropy (<span class=SpellE>MaxEnt</span>)
     1220alumina polishing powder using data from a constant wavelength synchrotron X-ray
     1221USAXS instrument. You will use both Maximum Entropy (<span class=SpellE>MaxEnt</span>)
    12111222and Total Non-Negative Least Squares (TNNLS) methods assuming spherical
    12121223particles. The data were collected from <span style='mso-fareast-font-family:
     
    12281239the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12291240mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1230 Calibri;mso-bidi-theme-font:minor-latin'>Import/Small Angle Data/from q (A-1) step
    1231 X-ray QIE data file</span></b> menu item to read the data file into GSAS-II.
    1232 This read option is set to read three column small angle scattering data (SASD)
    1233 as Q in Å<sup>-1</sup>, intensity and estimated standard deviation in
    1234 intensity; there may be a header with metadata information in the front of this
    1235 file.<span style='mso-spacerun:yes'>  </span>Change the file directory to <b
     1241Calibri;mso-bidi-theme-font:minor-latin'>Import/Small Angle Data/from q (A-1)
     1242step X-ray QIE data file</span></b> menu item to read the data file into
     1243GSAS-II. This read option is set to read three column small angle scattering
     1244data (SASD) as Q in Å<sup>-1</sup>, intensity and estimated standard deviation
     1245in intensity; there may be a header with metadata information in the front of
     1246this file.<span style='mso-spacerun:yes'>  </span>Change the file directory to <span
     1247class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1248"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1249minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>SAsize</span></b></span><b
    12361250style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12371251mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1238 Calibri;mso-bidi-theme-font:minor-latin'>exercises/<span class=SpellE>SAsize</span></span></b><span
     1252Calibri;mso-bidi-theme-font:minor-latin'>/data</span></b><span
    12391253style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12401254mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     
    12561270mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    12571271Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1258 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1272Dialog box asking <b style='mso-bidi-font-weight:normal'><span
    12591273style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12601274mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1261 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1262 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1263 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1264 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    1265 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1266 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1267 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
    1268 proceed.</p>
     1275minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
     1276normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1277minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1278mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
    12691279
    12701280<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
     
    13301340
    13311341<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1332  id="_x0000_i1037" type="#_x0000_t75" style='width:225pt;height:195pt;
    1333  visibility:visible;mso-wrap-style:square'>
     1342 id="Picture_x0020_2" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
     1343 height:195pt;visibility:visible;mso-wrap-style:square'>
    13341344 <v:imagedata src="Small%20Angle%20Size%20Distribution_files/image002.png"
    13351345  o:title=""/>
    13361346</v:shape><![endif]--><![if !vml]><img width=300 height=260
    1337 src="Small%20Angle%20Size%20Distribution_files/image002.png" v:shapes="_x0000_i1037"><![endif]></span><span
     1347src="Small%20Angle%20Size%20Distribution_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span><span
    13381348style='mso-spacerun:yes'> </span></p>
    13391349
    13401350<h2>Step 3 Select the scattering substances for your sample</h2>
    13411351
    1342 <p class=MsoNormal><span style='mso-no-proof:yes'>Two scsttering substances need
    1343 to be defined for your sample to give the anticipated scattering contrast; in
    1344 this case one is alumina and the other is “vacuum” (really air). Parameters for
    1345 a number of substances are defined in the file </span><b style='mso-bidi-font-weight:
     1352<p class=MsoNormal><span style='mso-no-proof:yes'>Two scsttering substances
     1353need to be defined for your sample to give the anticipated scattering contrast;
     1354in this case one is alumina and the other is “vacuum” (really air). Parameters
     1355for a number of substances are defined in the file </span><b style='mso-bidi-font-weight:
    13461356normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    13471357minor-latin;mso-hansi-theme-font:minor-latin;mso-no-proof:yes'>Substances.py</span></b><span
     
    14271437minor-latin;mso-hansi-theme-font:minor-latin'>vacuum</span></b>). The window
    14281438will show at the bottom the computed contrast between alumina and vacuum
    1429 without and with consideration of resonant scattering effects; the latter is
    1430 used in subsequent calculations.</p>
     1439without and with consideration of resonant scattering effects; the latter is used
     1440in subsequent calculations.</p>
    14311441
    14321442<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14741484
    14751485<p class=MsoNormal>Many selections are made by default for this analysis;
    1476 however it is important that an appropriate value is selected for the
    1477 background. From the high Q end of the data plot</p>
     1486however it is important that an appropriate value is selected for the background.
     1487From the high Q end of the data plot</p>
    14781488
    14791489<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14921502style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14931503mso-hansi-theme-font:minor-latin'>0.12</span></b>; enter that into the
    1494 appropriate place in the data window. The plot will be redrawn showing a horizontal
    1495 red line for the background. All the other parameters seem reasonable for a 1<sup>st</sup>
    1496 attempt at a <span class=SpellE>MaxEnt</span> solution. Do <b style='mso-bidi-font-weight:
    1497 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1498 minor-latin;mso-hansi-theme-font:minor-latin'>Models/Fit</span></b>; the
    1499 console window will show that the calculation did not converge and the <b
    1500 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1501 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Size
    1502 Distribution</span></b> plot has a “choppy” appearance.</p>
     1504appropriate place in the data window. The plot will be redrawn showing a
     1505horizontal red line for the background. All the other parameters seem
     1506reasonable for a 1<sup>st</sup> attempt at a <span class=SpellE>MaxEnt</span>
     1507solution. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1508"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1509minor-latin'>Models/Fit</span></b>; the console window will show that the
     1510calculation did not converge and the <b style='mso-bidi-font-weight:normal'><span
     1511style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1512mso-hansi-theme-font:minor-latin'>Size Distribution</span></b> plot has a
     1513“choppy” appearance.</p>
    15031514
    15041515<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16191630style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16201631mso-hansi-theme-font:minor-latin'>2.0</span></b>; the IPG fit con<span
    1621 style='mso-no-proof:yes'>verges in &lt;20 cycles and gives a smoother size
    1622 distribution.<o:p></o:p></span></p>
     1632style='mso-no-proof:yes'>verges in &lt;20 cycles and gives a smoother size distribution.<o:p></o:p></span></p>
    16231633
    16241634<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16531663normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16541664minor-latin;mso-hansi-theme-font:minor-latin'>0-4</span></b>, that changes the
    1655 data weighting to <span class=SpellE><span class=GramE>Q<sup>p</sup></span></span>.
    1656 This can change the convergence of the IPG method and yield improved results if
    1657 one is unsuccessful with the default settings. I got a nice fit with a <b
    1658 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1659 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Q power
    1660 weight</span></b> of <b style='mso-bidi-font-weight:normal'><span
     1665data weighting to <span class=SpellE>Q<sup>p</sup></span>. This can change the
     1666convergence of the IPG method and yield improved results if one is unsuccessful
     1667with the default settings. I got a nice fit with a <b style='mso-bidi-font-weight:
     1668normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1669minor-latin;mso-hansi-theme-font:minor-latin'>Q power weight</span></b> of <b
     1670style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1671mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3</span></b>
     1672and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1673mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Error
     1674multiplier</span></b> of <b style='mso-bidi-font-weight:normal'><span
    16611675style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1662 mso-hansi-theme-font:minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:
    1663 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1664 minor-latin;mso-hansi-theme-font:minor-latin'>Error multiplier</span></b> of <b
    1665 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1666 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b>.</p>
    1667 
    1668 <p class=MsoNormal>You should save this GSAS-II project as it will be used in the
    1669 tutorial for fitting small angle scattering data; I used <span class=SpellE><b
    1670 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1671 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>alumina.gpx</span></b></span>.</p>
     1676mso-hansi-theme-font:minor-latin'>2.0</span></b>.</p>
     1677
     1678<p class=MsoNormal>You should save this GSAS-II project as it will be used in
     1679the tutorial for fitting small angle scattering data; I used <span
     1680class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1681"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1682minor-latin'>alumina.gpx</span></b></span>.</p>
    16721683
    16731684</div>
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