Changeset 2790 for Tutorials/SAsize


Ignore:
Timestamp:
Apr 19, 2017 10:17:54 AM (5 years ago)
Author:
vondreele
Message:

update SAsize tutorial

Location:
Tutorials/SAsize
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/SAsize/Small Angle Size Distribution.htm

    r2390 r2790  
    2424 <o:DocumentProperties>
    2525  <o:Author>Von Dreele</o:Author>
    26   <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>14</o:Revision>
    28   <o:TotalTime>1917</o:TotalTime>
     26  <o:LastAuthor>vondreele</o:LastAuthor>
     27  <o:Revision>16</o:Revision>
     28  <o:TotalTime>1960</o:TotalTime>
    2929  <o:Created>2014-03-20T16:54:00Z</o:Created>
    30   <o:LastSaved>2016-07-28T18:49:00Z</o:LastSaved>
     30  <o:LastSaved>2017-04-19T15:00:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>1272</o:Words>
    33   <o:Characters>7251</o:Characters>
     32  <o:Words>1274</o:Words>
     33  <o:Characters>7265</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>8506</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>8522</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
     
    4848<!--[if gte mso 9]><xml>
    4949 <w:WordDocument>
     50  <w:View>Print</w:View>
    5051  <w:SpellingState>Clean</w:SpellingState>
    5152  <w:GrammarState>Clean</w:GrammarState>
     
    660661 /* Font Definitions */
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    1181         mso-hansi-theme-font:minor-latin;}
     1178        mso-hansi-theme-font:minor-latin;
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    12181217<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    12191218this tutorial you will determine the size distribution of particles in an
    1220 alumina polishing powder using data from a constant wavelength synchrotron X-ray
    1221 USAXS instrument. You will use both Maximum Entropy (<span class=SpellE>MaxEnt</span>)
     1219alumina polishing powder using data from a constant wavelength synchrotron
     1220X-ray USAXS instrument. You will use both Maximum Entropy (<span class=SpellE>MaxEnt</span>)
    12221221and Total Non-Negative Least Squares (TNNLS) methods assuming spherical
    12231222particles. The data were collected from <span style='mso-fareast-font-family:
     
    12381237style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    12391238the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1240 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1241 Calibri;mso-bidi-theme-font:minor-latin'>Import/Small Angle Data/from q (A-1)
    1242 step X-ray QIE data file</span></b> menu item to read the data file into
    1243 GSAS-II. This read option is set to read three column small angle scattering
    1244 data (SASD) as Q in Å<sup>-1</sup>, intensity and estimated standard deviation
    1245 in intensity; there may be a header with metadata information in the front of
    1246 this file.<span style='mso-spacerun:yes'>  </span>Change the file directory to <span
     1239mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1240minor-latin'>Import/Small Angle Data/from q (A-1) step X-ray QIE data file</span></b>
     1241menu item to read the data file into GSAS-II. This read option is set to read
     1242three column small angle scattering data (SASD) as Q in Å<sup>-1</sup>,
     1243intensity and estimated standard deviation in intensity; there may be a header
     1244with metadata information in the front of this file.<span
     1245style='mso-spacerun:yes'>  </span>Change the file directory to <span
    12471246class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    12481247"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1249 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>SAsize</span></b></span><b
    1250 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1251 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1252 Calibri;mso-bidi-theme-font:minor-latin'>/data</span></b><span
    1253 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1254 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1248minor-latin;mso-bidi-theme-font:minor-latin'>SAsize</span></b></span><b
     1249style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1250mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1251minor-latin'>/data</span></b><span style='font-family:"Calibri",sans-serif;
     1252mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    12551253minor-latin'> to find the file</span>; you will have to select the ‘<b
    12561254style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     
    12621260style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    12631261the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1264 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1265 Calibri;mso-bidi-theme-font:minor-latin'>alumina data.dat</span></b><span
    1266 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1267 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1263minor-latin'>alumina data.dat</span></b><span style='font-family:"Calibri",sans-serif;
     1264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    12681265minor-latin'> data</span> file in the first dialog and press <b
    12691266style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1270 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1271 Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1272 Dialog box asking <b style='mso-bidi-font-weight:normal'><span
    1273 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1274 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1267mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1268minor-latin'>Open</span></b>. There will be a Dialog box asking <b
     1269style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1270mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    12751271minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
    12761272normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1277 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1278 mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
     1273minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
     1274button to proceed.</p>
    12791275
    12801276<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
    12811277style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1282 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1283 minor-latin'>GSAS-II data tree</span></b> window will have several entries and
    1284 the plot window will show the SASD pattern as a log-log plot of intensity vs. Q</p>
     1278mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
     1279tree</span></b> window will have several entries and the plot window will show
     1280the SASD pattern as a log-log plot of intensity vs. Q</p>
    12851281
    12861282<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    13041300 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    13051301 <o:lock v:ext="edit" aspectratio="t"/>
    1306 </v:shapetype><v:shape id="Picture_x0020_15" o:spid="_x0000_i1038" type="#_x0000_t75"
    1307  style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
     1302</v:shapetype><v:shape id="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
     1303 height:450pt;visibility:visible;mso-wrap-style:square'>
    13081304 <v:imagedata src="Small%20Angle%20Size%20Distribution_files/image001.png"
    13091305  o:title=""/>
    13101306</v:shape><![endif]--><![if !vml]><img width=700 height=600
    1311 src="Small%20Angle%20Size%20Distribution_files/image001.png" v:shapes="Picture_x0020_15"><![endif]></span></p>
     1307src="Small%20Angle%20Size%20Distribution_files/image001.png" v:shapes="_x0000_i1038"><![endif]></span></p>
    13121308
    13131309<h2>Step 2: Set Limits</h2>
     
    13401336
    13411337<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1342  id="Picture_x0020_2" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
    1343  height:195pt;visibility:visible;mso-wrap-style:square'>
     1338 id="Picture_x0020_15" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
     1339 height:96.75pt;visibility:visible;mso-wrap-style:square'>
    13441340 <v:imagedata src="Small%20Angle%20Size%20Distribution_files/image002.png"
    13451341  o:title=""/>
    1346 </v:shape><![endif]--><![if !vml]><img width=300 height=260
    1347 src="Small%20Angle%20Size%20Distribution_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span><span
     1342</v:shape><![endif]--><![if !vml]><img width=300 height=129
     1343src="Small%20Angle%20Size%20Distribution_files/image002.png" v:shapes="Picture_x0020_15"><![endif]></span><span
    13481344style='mso-spacerun:yes'> </span></p>
    13491345
     
    13681364under <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13691365mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SASD alumina
    1370 data.dat</span></b> from the GSAS-II tree. Then do <b style='mso-bidi-font-weight:
    1371 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1372 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Load</span></b> <b
    1373 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1366data.dat</span></b> from the GSAS-II tree. Then do <span class=GramE><b
     1367style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1368mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit</span></b></span><b
     1369style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1370mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> substance/Load</span></b>
     1371<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13741372mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>substance</span></b>
    13751373from the menu; a popup window will appear with possible selections</p>
     
    13931391
    13941392<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1395  id="Picture_x0020_16" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:259.5pt;
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     1394 height:246pt;visibility:visible;mso-wrap-style:square'>
    13971395 <v:imagedata src="Small%20Angle%20Size%20Distribution_files/image004.png"
    13981396  o:title=""/>
    1399 </v:shape><![endif]--><![if !vml]><img width=346 height=260
     1397</v:shape><![endif]--><![if !vml]><img width=374 height=328
    14001398src="Small%20Angle%20Size%20Distribution_files/image004.png" v:shapes="Picture_x0020_16"><![endif]></span><span
    14011399style='mso-spacerun:yes'> </span></p>
     
    14031401<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    14041402
    1405 <p class=MsoNormal>If desired you can load/add as many substances as you desire
    1406 into this list; you can also delete any of them (except vacuum). The
    1407 composition, volume occupied by the atoms in the composition and the density
    1408 are given for each substance. These can each be edited; the other values will
    1409 change accordingly. If your substance isn’t in the list, you can <b
     1403<p class=MsoNormal>If desired you can load/add as many substances as you want into
     1404this list; you can also delete any of them (except vacuum &amp; unit scatter).
     1405The composition, volume occupied by the atoms in the composition and the
     1406density are given for each substance. These can each be edited; the other
     1407values will change accordingly. If your substance isn’t in the list, you can <b
    14101408style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14111409mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
     
    14161414style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14171415mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    1418 Parameters</span></b> GSAS-II tree item if needed). The resonant scattering
    1419 value is used for contrast calculations.</p>
     1416Parameters</span></b> GSAS-II tree item if needed). The real density value is
     1417used for contrast calculations.</p>
    14201418
    14211419<h2>Step 4: Set Sample parameters </h2>
     
    14371435minor-latin;mso-hansi-theme-font:minor-latin'>vacuum</span></b>). The window
    14381436will show at the bottom the computed contrast between alumina and vacuum
    1439 without and with consideration of resonant scattering effects; the latter is used
    1440 in subsequent calculations.</p>
     1437without and with consideration of resonant scattering effects; the latter is
     1438used in subsequent calculations.</p>
    14411439
    14421440<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14841482
    14851483<p class=MsoNormal>Many selections are made by default for this analysis;
    1486 however it is important that an appropriate value is selected for the background.
    1487 From the high Q end of the data plot</p>
     1484however it is important that an appropriate value is selected for the
     1485background. From the high Q end of the data plot</p>
    14881486
    14891487<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15031501mso-hansi-theme-font:minor-latin'>0.12</span></b>; enter that into the
    15041502appropriate place in the data window. The plot will be redrawn showing a
    1505 horizontal red line for the background. All the other parameters seem
    1506 reasonable for a 1<sup>st</sup> attempt at a <span class=SpellE>MaxEnt</span>
    1507 solution. 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:
    1509 minor-latin'>Models/Fit</span></b>; the console window will show that the
    1510 calculation did not converge and the <b style='mso-bidi-font-weight:normal'><span
    1511 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1512 mso-hansi-theme-font:minor-latin'>Size Distribution</span></b> plot has a
    1513 “choppy” appearance.</p>
     1503horizontal red line for the background. All the other parameters seem reasonable
     1504for a 1<sup>st</sup> attempt at a <span class=SpellE>MaxEnt</span> solution. Do
     1505<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1506mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Models/Fit</span></b>;
     1507the console window will show that the calculation did not converge and the <b
     1508style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1509mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Size
     1510Distribution</span></b> plot has a “choppy” appearance.</p>
    15141511
    15151512<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16301627style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16311628mso-hansi-theme-font:minor-latin'>2.0</span></b>; the IPG fit con<span
    1632 style='mso-no-proof:yes'>verges in &lt;20 cycles and gives a smoother size distribution.<o:p></o:p></span></p>
     1629style='mso-no-proof:yes'>verges in &lt;20 cycles and gives a smoother size
     1630distribution.<o:p></o:p></span></p>
    16331631
    16341632<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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