Changeset 3553


Ignore:
Timestamp:
Aug 3, 2018 10:51:26 PM (3 years ago)
Author:
toby
Message:

finish web tutorials for now

Files:
21 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/2DCalibration/Calibration of an area detector in GSAS.htm

    r2972 r3553  
    11441144color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
    11451145
     1146<P><B>A video version of this tutorial is available at
     1147<A href="https://anl.box.com/v/CalibrationofanareadetectorinG" target="_blank">
     1148https://anl.box.com/v/CalibrationofanareadetectorinG</A></B></P>
     1149
    11461150<p class=MsoNormal>In this tutorial, data collected with a Perkin-Elmer area
    11471151detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
     
    11621166text-underline:none'>start GSAS-II</span></a></span></u>.</p>
    11631167
    1164 <h1>Step 1: read in the data file</h1>
     1168<h2>Step 1: read in the data file</h2>
    11651169
    11661170<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
     
    12441248v:shapes="Picture_x0020_16"><![endif]></span></p>
    12451249
    1246 <h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
     1250<h2><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h2>
    12471251
    12481252<p class=MsoNormal>Note that, alas, very few image formats contain all of the
     
    12731277minor-latin;mso-bidi-theme-font:minor-latin'>Color bar</span></b> selector. </p>
    12741278
    1275 <h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
     1279<h2><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h2>
    12761280
    12771281<h3><span style='mso-spacerun:yes'> </span>First: </h3>
  • Tutorials/2DIntegration/Integration of area detector data in GSAS.htm

    r2973 r3553  
    13091309<h1>Integration of area detector data in GSAS-II</h1>
    13101310
     1311<P><B>A video version of this tutorial is available at
     1312<A href="https://anl.box.com/v/Integrationofareadetectordatai" target="_blank">
     1313https://anl.box.com/v/Integrationofareadetectordatai</A></B></P>
     1314
     1315
    13111316<p class=MsoNormal>In this demo, data collected with a Perkin-Elmer area
    13121317detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
     
    13361341<p class=MsoNormal>Assuming the previous step was calibration, the image plot
    13371342will show the located rings and possibly all the picked points. These are no
    1338 longer needed. The <b style='mso-bidi-font-weight:normal'><span
     1343longer needed.
     1344Go to the <B>Image Controls</B> window on the data tree.
     1345The <b style='mso-bidi-font-weight:normal'><span
    13391346style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13401347mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibration/Clear
     
    13601367style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13611368mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Show
    1362 integration limits?</span></b> <span class=GramE>check</span> box. Note that
     1369integration limits?</span></b> <span class=GramE>check</span> box (if
     1370not already checked). Note that
    13631371inner limit is shown as a green ellipse at 2deg and the outer is shown as a red
    13641372ellipse at 5deg by default. These limits may also be dragged to the desired
     
    14421450style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14431451mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5000</span></b>
    1444 is a better choice than the default.</p>
     1452is a better choice than the default in that first box.</p>
    14451453
    14461454<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
     
    14561464when the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14571465mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show
    1458 integration limits?</span></b> <span class=GramE>check</span> box is checked. </p>
     1466integration limits?</span></b> <span class=GramE>check</span> box, if
     1467not already checked. </p>
    14591468
    14601469<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    14611470style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1462 mso-hansi-theme-font:minor-latin'>Appl. Sample absorption</span></b> and <b
     1471mso-hansi-theme-font:minor-latin'>Apply Sample absorption</span></b> and <b
    14631472style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14641473mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>value</span></b>:
     
    14701479<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
    14711480style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1472 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Appl. det.
     1481mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Apply detector
    14731482absorption</span></b> and <b style='mso-bidi-font-weight:normal'><span
    14741483style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
  • Tutorials/2DStrain/Strain fitting of 2D data in GSAS-II.htm

    r3040 r3553  
    13091309<h1>Strain fitting of 2D data in GSAS-II</h1>
    13101310
     1311<P><B>A video version of this tutorial is available at
     1312<A href="https://anl.box.com/v/Strainfittingof2DdatainGSAS-II" target="_blank">
     1313https://anl.box.com/v/Strainfittingof2DdatainGSAS-II</A></B></P>
     1314
    13111315<p class=MsoNormal>For this tutorial, data were collected with a MAR2300 area
    13121316detector at APS 1-ID-C with a wavelength 0.12398 Å (100<span style='font-family:
  • Tutorials/2DTexture/Texture analysis of 2D data in GSAS-II.htm

    r3055 r3553  
    143314330in;line-height:115%'>Texture analysis of 2D data in GSAS-II</h1>
    14341434
     1435<P><B>A video version of this tutorial is available at
     1436<A href="https://anl.box.com/v/Textureanalysisof2DdatainGSAS-" target="_blank">
     1437https://anl.box.com/v/Textureanalysisof2DdatainGSAS-</A></B></P>
     1438
    14351439<h2 style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:
    143614400in;line-height:115%'>Introduction</h2>
  • Tutorials/CWInstDemo/FindProfParamCW.htm

    r3354 r3553  
    713713Parameters from a Standard<o:p></o:p></span></h1>
    714714
     715<P><B>A video version of this tutorial is available at
     716<A href="https://anl.box.com/v/FindProfParamCW" target="_blank">
     717https://anl.box.com/v/FindProfParamCW</A></B></P>
     718
    715719<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
    716720
  • Tutorials/DeterminingWavelength/DeterminingWavelength.html

    r3544 r3553  
    2727<p class="c3"><span class="c4 c2">Since the single-image calibration looks good, it is time to copy these parameters onto the rest of the images.</span></p><p class="c3"><span class="c2">Next select </span><span class="c0">Parms/Copy Selected</span><span class="c4 c2">. A text box like this will pop up:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 446.50px; height: 299.36px;"><img alt="" src="images/image7.png" style="width: 936.47px; height: 523.88px; margin-left: -321.16px; margin-top: -99.15px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Click </span><span class="c0">Set All</span><span class="c2">&nbsp;on the bottom then go back and unselect both </span><span class="c0">distance (10)</span><span class="c2">&nbsp;and</span><span class="c0">&nbsp;setdist</span><span class="c2">&nbsp;</span><span class="c0">(25)</span><span class="c2">, as below, then press</span><span class="c0">&nbsp;OK</span><span class="c4 c2">. We want to copy all parameters except for the distances because they differ for each image. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 465.50px; height: 414.40px;"><img alt="" src="images/image16.png" style="width: 902.09px; height: 506.81px; margin-left: -284.79px; margin-top: -30.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Another dialog box will appear for selection of the images to copy these parameters to, hit </span><span class="c0">Set All</span><span class="c2">&nbsp;and press </span><span class="c4 c0">OK</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 246.75px; height: 321.50px;"><img alt="" src="images/image23.png" style="width: 1015.29px; height: 565.44px; margin-left: -466.62px; margin-top: -106.06px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Next select </span><span class="c0">C</span><span class="c0">alibration/Recalibrate all </span><span class="c2">to recalibrate all images with the new parameters.
    2828</span></p><p class="c8"><span class="c4 c2">
    29 Do </span><span class="c0">File/Save project as...</span><span class="c2">&nbsp;and name it </span><span class="c0">Wavelength_Determination</span><span class="c4 c2">. This will create a copy of the project to use for calibration.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">The next step is to check to make sure the Min calib d-spacing setting value ensures that only full rings are used in each calibration. The </span><span class="c2">Min calib d-spacing restrict the set of reflections to be used in the MC/SA run</span><span class="c2">. To do this, start at the </span><span class="c0">Image Controls</span><span class="c2">&nbsp;for the first image and then go in increasing order through the images until you find one where the outer rings are cut off. For us, the first image with rings cut off is </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c4 c2">, as below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 582.00px; height: 543.00px;"><img alt="" src="images/image21.png" style="width: 1104.29px; height: 620.82px; margin-left: -279.84px; margin-top: -21.22px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c4 c2">Start with your cursor in the center of the rings and then pan your mouse over to the right edge. Watch the Min calib d-spacing decrease as you continue to move the mouse to the right.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 488.00px;"><img alt="" src="images/image18.gif" style="width: 624.00px; height: 488.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Look at the dsp value at the bottom of the plot window. Look at the value when the cursor is on the edge. That will be the new Min calib d-spacing. The default value of 0.50 is allowing the outer rings to be cut off.</span><span class="c2">&nbsp;</span><span class="c2">&nbsp;We then looked at what the dsp value was when the cursor was on the edge of the image. Here it is 0.529, so we went to image controls &nbsp;for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">&nbsp;</span><span class="c2">a</span><span class="c2">nd changed </span><span class="c0">Min calib d-spacing</span><span class="c4 c2">&nbsp;to 0.53.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 637.00px; height: 394.00px;"><img alt="" src="images/image5.png" style="width: 799.07px; height: 449.01px; margin-left: -109.57px; margin-top: -14.07px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and the image should now have all the rings intact. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 561.00px; height: 527.00px;"><img alt="" src="images/image14.png" style="width: 1070.53px; height: 602.04px; margin-left: -271.06px; margin-top: -20.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">After you fix the first image where the Min calib d-spacing is off you can fix the rest of the images that also have this problem. To fix this, select image controls for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">. </span><span class="c2">Then select </span><span class="c0">Parms/XFer Angles </span><span class="c4 c2">and a window will pop up.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 252.50px; height: 441.38px;"><img alt="" src="images/image20.png" style="width: 1240.63px; height: 697.85px; margin-left: -536.81px; margin-top: -107.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Select </span><span class="c0">Set All </span><span class="c2">but then </span><span class="c0">unselect</span><span class="c2">&nbsp;all the earlier images that did not have a Min calib d-spacing problem. For us, this was </span><span class="c0">images 200-350</span><span class="c2">. Then </span><span class="c0">select</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled calib d-min </span><span class="c2">option on the bottom of the window and </span><span class="c0">unselect</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled 2-theta max </span><span class="c4 c2">option. This takes min calibrated d-spacing from the image selected and determines the accurate d-spacing for all other images. The text box should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 262.00px; height: 454.00px;"><img alt="" src="images/image22.png" style="width: 1277.25px; height: 717.60px; margin-left: -552.66px; margin-top: -108.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select</span><span class="c0">&nbsp;OK</span><span class="c4 c2">&nbsp;and the rest of the Min calib d-spacing will be adjusted for the rest of the images.</span></p><p class="c3"><span class="c2">Now it&rsquo;s time to recalibrate all of the images with the new Min calib d-spacing values. Go to any image controls window and select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">and select </span><span class="c4 c0">Set All. </span></p><p class="c3"><span class="c4 c2">This will take a bit of time as each image is being recalibrated. </span></p><p class="c3"><span class="c2">After the recalibration, all the images should only have full intact rings. Once the process is complete go to the bottom of the data tree and select </span><span class="c0">Sequential image calibration results </span><span class="c4 c2">and a table should appear. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 605.50px; height: 376.16px;"><img alt="" src="images/image17.png" style="width: 757.18px; height: 425.91px; margin-left: -103.14px; margin-top: -12.13px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">In </span><span class="c0">Sequential Image Calibration results</span><span class="c2">, a table should appear with a column labeled dep containing detector penetration depths (</span><span class="c0">dep</span><span class="c2">). As we look over the table we need to make sure that the detector penetration depths have roughly the same values except for the first few rows (these will be off due to the close distances). As we look at our data we notice that the last few values are inconsistent with the rest. To investigate we select the </span><span class="c0">IMG Si_free_dc1250_1</span><span class="c0">-00000.tif</span><span class="c0">/ Image Controls</span><span class="c2">&nbsp;and view the second to last image.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 537.50px; height: 503.19px;"><img alt="" src="images/image15.png" style="width: 1019.45px; height: 573.44px; margin-left: -258.13px; margin-top: -17.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c4 c2">We can see from the image that there is a fake (or fragmented) fourth ring that should not actually be there (the last &ldquo;1300&rdquo; image does not have this issue of the fake fourth ring). In order to fix this we will pan the mouse over to the space in between the last full ring and the fake ring as shown below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 577.33px;"><img alt="" src="images/image26.gif" style="width: 624.00px; height: 577.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We found a value of the dsp to be 1.592 and changed the Min calib d-spacing to that value under </span><span class="c0">Image controls </span><span class="c4 c2">for the &ldquo;1250&rdquo; image. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 620.00px; height: 383.00px;"><img alt="" src="images/image2.png" style="width: 776.56px; height: 436.77px; margin-left: -106.78px; margin-top: -12.44px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We then selected </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and our image now excludes the fake fourth ring.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 497.50px; height: 464.33px;"><img alt="" src="images/image3.png" style="width: 940.73px; height: 529.16px; margin-left: -236.69px; margin-top: -16.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Continue to go through the i</span><span class="c2">mages in decreasing distance from</span><span class="c2">&nbsp;the detector and check to see whether there is a phantom ring and adjust the Min calib d-spacing accordingly. However once you get to an image where there is another full ring outside of the phantom ring, there is no need to adjust the Min calib d-spacing. We adjusted the Min calib d-spacing value to </span><span class="c0">1.59</span><span class="c2">&nbsp;for images </span><span class="c0">IMG Si_free_dc1200_1</span><span class="c0">-00000.tif</span><span class="c0">&nbsp;</span><span class="c2">and </span><span class="c0">IMG Si_free_dc1150_1</span><span class="c0">-00000.tif</span><span class="c4 c2">. The &ldquo;1100&rdquo; image had a fifth full ring that we did not want to exclude.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">After completing this process select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again. Continue calibrating until the dep values</span><span class="c2">&nbsp;</span><span class="c2">converge. After a few recalibrations, the table under </span><span class="c0">Sequential image calibration results</span><span class="c2 c4">&nbsp;shows our dep values converge the detector distances are further from the sample.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 636.00px; height: 395.00px;"><img alt="" src="images/image25.png" style="width: 796.57px; height: 447.24px; margin-left: -109.51px; margin-top: -12.74px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Our new values have improved quite a bit. If the any </span><span class="c2">&nbsp;detector penetration depth (dep) </span><span class="c2">values are negative then go to </span><span class="c0">Image Controls </span><span class="c2">for the images with negative dep values. You will see that the penetration values for those images are also negative. As this should not be possible, change the value of </span><span class="c0">Penetration </span><span class="c2">to </span><span class="c0">zero</span><span class="c2">&nbsp;and then did </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again and the penetration values should become positive.
     29Do </span><span class="c0">File/Save project as...</span><span class="c2">&nbsp;and name it </span><span class="c0">Wavelength_Determination</span><span class="c4 c2">. This will create a copy of the project to use for calibration.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">The next step is to check to make sure the Min calib d-spacing setting value ensures that only full rings are used in each calibration. The </span><span class="c2">Min calib d-spacing restrict the set of reflections to be used. </span><span class="c2">To do this, start at the </span><span class="c0">Image Controls</span><span class="c2">&nbsp;for the first image and then go in increasing order through the images until you find one where the outer rings are cut off. For us, the first image with rings cut off is </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c4 c2">, as below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 582.00px; height: 543.00px;"><img alt="" src="images/image21.png" style="width: 1104.29px; height: 620.82px; margin-left: -279.84px; margin-top: -21.22px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c4 c2">Start with your cursor in the center of the rings and then pan your mouse over to the right edge. Watch the Min calib d-spacing decrease as you continue to move the mouse to the right.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 488.00px;"><img alt="" src="images/image18.gif" style="width: 624.00px; height: 488.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Look at the dsp value at the bottom of the plot window. Look at the value when the cursor is on the edge. That will be the new Min calib d-spacing. The default value of 0.50 is allowing the outer rings to be cut off.</span><span class="c2">&nbsp;</span><span class="c2">&nbsp;We then looked at what the dsp value was when the cursor was on the edge of the image. Here it is 0.529, so we went to image controls &nbsp;for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">&nbsp;</span><span class="c2">a</span><span class="c2">nd changed </span><span class="c0">Min calib d-spacing</span><span class="c4 c2">&nbsp;to 0.53.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 637.00px; height: 394.00px;"><img alt="" src="images/image5.png" style="width: 799.07px; height: 449.01px; margin-left: -109.57px; margin-top: -14.07px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and the image should now have all the rings intact. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 561.00px; height: 527.00px;"><img alt="" src="images/image14.png" style="width: 1070.53px; height: 602.04px; margin-left: -271.06px; margin-top: -20.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">After you fix the first image where the Min calib d-spacing is off you can fix the rest of the images that also have this problem. To fix this, select image controls for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">. </span><span class="c2">Then select </span><span class="c0">Parms/XFer Angles </span><span class="c4 c2">and a window will pop up.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 252.50px; height: 441.38px;"><img alt="" src="images/image20.png" style="width: 1240.63px; height: 697.85px; margin-left: -536.81px; margin-top: -107.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Select </span><span class="c0">Set All </span><span class="c2">but then </span><span class="c0">unselect</span><span class="c2">&nbsp;all the earlier images that did not have a Min calib d-spacing problem. For us, this was </span><span class="c0">images 200-350</span><span class="c2">. Then </span><span class="c0">select</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled calib d-min </span><span class="c2">option on the bottom of the window and </span><span class="c0">unselect</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled 2-theta max </span><span class="c4 c2">option. This takes min calibrated d-spacing from the image selected and determines the accurate d-spacing for all other images. The text box should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 262.00px; height: 454.00px;"><img alt="" src="images/image22.png" style="width: 1277.25px; height: 717.60px; margin-left: -552.66px; margin-top: -108.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select</span><span class="c0">&nbsp;OK</span><span class="c4 c2">&nbsp;and the rest of the Min calib d-spacing will be adjusted for the rest of the images.</span></p><p class="c3"><span class="c2">Now it&rsquo;s time to recalibrate all of the images with the new Min calib d-spacing values. Go to any image controls window and select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">and select </span><span class="c4 c0">Set All. </span></p><p class="c3"><span class="c4 c2">This will take a bit of time as each image is being recalibrated. </span></p><p class="c3"><span class="c2">After the recalibration, all the images should only have full intact rings. Once the process is complete go to the bottom of the data tree and select </span><span class="c0">Sequential image calibration results </span><span class="c4 c2">and a table should appear. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 605.50px; height: 376.16px;"><img alt="" src="images/image17.png" style="width: 757.18px; height: 425.91px; margin-left: -103.14px; margin-top: -12.13px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">In </span><span class="c0">Sequential Image Calibration results</span><span class="c2">, a table should appear with a column labeled dep containing detector penetration depths (</span><span class="c0">dep</span><span class="c2">). As we look over the table we need to make sure that the detector penetration depths have roughly the same values except for the first few rows (these will be off due to the close distances). As we look at our data we notice that the last few values are inconsistent with the rest. To investigate we select the </span><span class="c0">IMG Si_free_dc1250_1</span><span class="c0">-00000.tif</span><span class="c0">/ Image Controls</span><span class="c2">&nbsp;and view the second to last image.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 537.50px; height: 503.19px;"><img alt="" src="images/image15.png" style="width: 1019.45px; height: 573.44px; margin-left: -258.13px; margin-top: -17.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c4 c2">We can see from the image that there is a fake (or fragmented) fourth ring that should not actually be there (the last &ldquo;1300&rdquo; image does not have this issue of the fake fourth ring). In order to fix this we will pan the mouse over to the space in between the last full ring and the fake ring as shown below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 577.33px;"><img alt="" src="images/image26.gif" style="width: 624.00px; height: 577.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We found a value of the dsp to be 1.592 and changed the Min calib d-spacing to that value under </span><span class="c0">Image controls </span><span class="c4 c2">for the &ldquo;1250&rdquo; image. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 620.00px; height: 383.00px;"><img alt="" src="images/image2.png" style="width: 776.56px; height: 436.77px; margin-left: -106.78px; margin-top: -12.44px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We then selected </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and our image now excludes the fake fourth ring.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 497.50px; height: 464.33px;"><img alt="" src="images/image3.png" style="width: 940.73px; height: 529.16px; margin-left: -236.69px; margin-top: -16.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Continue to go through the i</span><span class="c2">mages in decreasing distance from</span><span class="c2">&nbsp;the detector and check to see whether there is a phantom ring and adjust the Min calib d-spacing accordingly. However once you get to an image where there is another full ring outside of the phantom ring, there is no need to adjust the Min calib d-spacing. We adjusted the Min calib d-spacing value to </span><span class="c0">1.59</span><span class="c2">&nbsp;for images </span><span class="c0">IMG Si_free_dc1200_1</span><span class="c0">-00000.tif</span><span class="c0">&nbsp;</span><span class="c2">and </span><span class="c0">IMG Si_free_dc1150_1</span><span class="c0">-00000.tif</span><span class="c4 c2">. The &ldquo;1100&rdquo; image had a fifth full ring that we did not want to exclude.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">After completing this process select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again. Continue calibrating until the dep values</span><span class="c2">&nbsp;</span><span class="c2">converge. After a few recalibrations, the table under </span><span class="c0">Sequential image calibration results</span><span class="c2 c4">&nbsp;shows our dep values converge the detector distances are further from the sample.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 636.00px; height: 395.00px;"><img alt="" src="images/image25.png" style="width: 796.57px; height: 447.24px; margin-left: -109.51px; margin-top: -12.74px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Our new values have improved quite a bit. If the any </span><span class="c2">&nbsp;detector penetration depth (dep) </span><span class="c2">values are negative then go to </span><span class="c0">Image Controls </span><span class="c2">for the images with negative dep values. You will see that the penetration values for those images are also negative. As this should not be possible, change the value of </span><span class="c0">Penetration </span><span class="c2">to </span><span class="c0">zero</span><span class="c2">&nbsp;and then did </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again and the penetration values should become positive.
    3030If required, turn off refinement of Penetration with a value of 0.0 if that is the only way to keep
    3131the value from becoming negative. </span></p>
  • Tutorials/FitPeaks/Fit Peaks.htm

    r2983 r3553  
    14571457<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
    14581458
     1459<P><B>A video version of this tutorial is available at
     1460<A href="https://anl.box.com/v/FitPeaks" target="_blank">
     1461https://anl.box.com/v/FitPeaks</A></B></P>
     1462 
    14591463<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
    14601464cell that matches a set of diffraction peaks -- a process known as
  • Tutorials/MCsimanneal/MCSA in GSAS.htm

    r3078 r3553  
    14011401style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14021402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1403 minor-latin'>2-amino</span></b>’). You will need to vary at least <b
     1403minor-latin'>2-amino</span></b>’). You will need to refine at least <b
    14041404style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14051405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     
    14321432both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
    14331433style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1434 mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
     1434mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>).
     1435Click on <B>Cell Index/Refine/Index Cell</B>. The correct unit
    14351436cell should almost immediately appear with an M20 ~370 with a=7.748, b=7.650,
    14361437c=12.736, Vol=755.01. NB: your solution may have a &amp; b switched. Do <b
     
    14431444style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14441445mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub>
    1445 2<sub>1</sub> 2<sub>1</sub></span></b>). You can then do <b style='mso-bidi-font-weight:
     14462<sub>1</sub> 2<sub>1</sub></span></b>).
     1447Under the <B>General</B> tab, change the space group to <B>P 21 21 21</B>.
     1448You can then do <b style='mso-bidi-font-weight:
    14461449normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    14471450minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
     
    15081511to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    15091512"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1510 minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
    1511 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1512 minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
     1513minor-latin'>Pawley controls</span></b> under the <B>General</B> tab.
     1514Check the <b style='mso-bidi-font-weight:
     1515normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1516minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement?</span></b>
    15131517box, enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
    15141518style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     
    17841788C1-C3 defines the Z-axis (blue; default view direction) and the Y-axis is
    17851789defined as Z-axis cross X-axis (green; down toward C5). You can change these
    1786 via the pull downs (you can’t pick the same atom for two of these so pick them
     1790via the pull downs
     1791next to <B>Orientation reference non-H atoms A-B-C</B>
     1792(you can’t pick the same atom for two of these so pick them
    17871793appropriately; I chose C2, C3 &amp; C6). At each choice the structure will be
    17881794transformed accordingly. My new model is</p>
     
    18131819includes H-atoms; they are not really needed for MC/SA and will just make
    18141820computation times a bit longer than necessary. They can be removed by selecting
    1815 the Strip H-atoms box; for now leave them in. </p>
     1821the <B>Strip H-atoms box</B>; for now leave them in. </p>
    18161822
    18171823<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    20322038minor-latin'> current settings</span></b>; your choice becomes available immediately
    20332039and is then set for all your future uses of GSAS-II. <span
    2034 style='mso-spacerun:yes'> </span>Do <b style='mso-bidi-font-weight:normal'><span
     2040style='mso-spacerun:yes'> </span>Go to the <B>General</B> tab and
     2041select
     2042<b style='mso-bidi-font-weight:normal'><span
    20352043style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20362044mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Multi
     
    20562064style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20572065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
    2058 box. Using 10% of the ranges reduces the search volume in this case by ~6
     2066box under the <B>General</B> tab. Using 10% of the ranges reduces the search volume in this case by ~6
    20592067orders of magnitude so that the true minimum is much easier to find. Now rerun <b
    20602068style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     
    21662174style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21672175mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
    2168 class=GramE>size</span></span></b> &amp; <span class=SpellE><b
     2176class=GramE>size</span></span></b> and both <span class=SpellE><b
    21692177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21702178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm

    r3059 r3553  
    810810refinement in GSAS-II<o:p></o:p></span></h1>
    811811
     812<P><B>A video version of this tutorial is available at
     813<A href="https://anl.box.com/v/MerohedraltwinrefinementinGSAS" target="_blank">
     814https://anl.box.com/v/MerohedraltwinrefinementinGSAS</A></B></P>
     815
    812816<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
    813817
  • Tutorials/SAfit/Fitting Small Angle Scattering Data.htm

    r3032 r3553  
    12221222Small Angle X-Ray Data – Alumina Powder</span><o:p></o:p></strong></h1>
    12231223
     1224<P><B>A video version of this tutorial is available at
     1225<A href="https://anl.box.com/v/FittingSmallAngleScatteringDat" target="_blank">
     1226https://anl.box.com/v/FittingSmallAngleScatteringDat</A></B></P>
     1227 
    12241228<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    12251229this tutorial you will fit small angle scattering data for an alumina polishing
  • Tutorials/SAimages/Small Angle Image Processing.htm

    r2799 r3553  
    11721172<h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
    11731173
     1174<P><B>A video version of this tutorial is available at
     1175<A href="https://anl.box.com/v/SmallAngleImageProcessing" target="_blank">
     1176https://anl.box.com/v/SmallAngleImageProcessing</A></B></P>
     1177
    11741178<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    11751179this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.
  • Tutorials/SAseqref/Sequential Refinement of Small Angle Scattering Data.htm

    r3552 r3553  
    12221222Small Angle Scattering Data</span><o:p></o:p></strong></h1>
    12231223
     1224<P><B>A video version of this tutorial is available at
     1225<A href="https://anl.box.com/v/SequentialRefinementofSmallAng" target="_blank">
     1226https://anl.box.com/v/SequentialRefinementofSmallAng</A></B></P>
     1227
     1228 
    12241229<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    12251230this tutorial you will fit USAXS small angle scattering data for “<span
  • Tutorials/SAsize/Small Angle Size Distribution.htm

    r3031 r3553  
    12221222Size Distribution in Alumina Powder</span><o:p></o:p></strong></h1>
    12231223
     1224<P><B>A video version of this tutorial is available at
     1225<A href="https://anl.box.com/v/SmallAngleSizeDistribution" target="_blank">
     1226https://anl.box.com/v/SmallAngleSizeDistribution</A></B></P>
     1227 
     1228
    12241229<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    12251230this tutorial you will determine the size distribution of particles in an
     
    13531358<h2>Step 3 Select the scattering substances for your sample</h2>
    13541359
    1355 <p class=MsoNormal><span style='mso-no-proof:yes'>Two scsttering substances
     1360<p class=MsoNormal><span style='mso-no-proof:yes'>Two scattering substances
    13561361need to be defined for your sample to give the anticipated scattering contrast;
    13571362in this case one is alumina and the other is “vacuum” (really air). Parameters
     
    14151420values will change accordingly. If your substance isn’t in the list, you can <b
    14161421style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1417 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
     1422mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
     1423Substance/Add
    14181424substance</span></b> to create a new one (you will be asked for a name and the
    14191425set of elements in two successive popup windows). From this information the
     
    15081514style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15091515mso-hansi-theme-font:minor-latin'>0.12</span></b>; enter that into the
    1510 appropriate place in the data window. The plot will be redrawn showing a
     1516appropriate place in the data window next to <B>Background</B>. The plot will be redrawn showing a
    15111517horizontal red line for the background. All the other parameters seem
    15121518reasonable for a 1<sup>st</sup> attempt at a <span class=SpellE>MaxEnt</span>
  • Tutorials/SeqParametric/ParametricFitting.htm

    r3094 r3553  
    12671267
    12681268<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1269 
     1270<P><B>A video version of this tutorial is available at
     1271<A href="https://anl.box.com/v/ParametricFitting" target="_blank">
     1272https://anl.box.com/v/ParametricFitting</A></B></P>
    12691273
    12701274<p class=MsoNormal>Once a sequential fit has been performed, any function of
     
    21472151style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
    21482152style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2149 </span></span></span><![endif]>Then enter the equation as </p>
     2153</span></span></span><![endif]>Then enter the equation
     2154(you can copy and paste the equation above into the text box) as:
     2155</p>
    21502156
    21512157<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     
    21662172style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    21672173</span></span></span><![endif]>Assign the free and fixed variables, as shown
    2168 below. Note that the exponent (<b style='mso-bidi-font-weight:normal'><span
     2174below.
     2175Note: if no option under Phase for ‘Temperature’, then select variable
     2176type <B>Global</B> and select <B>Global Temperature</B>.
     2177Note that the exponent (<b style='mso-bidi-font-weight:normal'><span
    21692178style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    21702179mso-hansi-theme-font:major-latin'>k</span></b>) and scaling factor (<b
     
    21762185should be set to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    21772186"Calibri",sans-serif;mso-ascii-theme-font:major-latin;mso-hansi-theme-font:
    2178 major-latin;mso-bidi-theme-font:major-latin'>120</span></b><span class=GramE>.<b
    2179 style='mso-bidi-font-weight:normal'>.</b></span><b style='mso-bidi-font-weight:
    2180 normal'> </b></p>
     2187major-latin;mso-bidi-theme-font:major-latin'>120</span></b><span class=GramE>.</span><b style='mso-bidi-font-weight:
     2188normal'> </b>
     2189</p>
    21812190
    21822191<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
  • Tutorials/SeqRefine/SequentialTutorial.htm

    r3451 r3553  
    13871387CuCr<sub>2</sub>O<sub>4</sub> from 7K to 300K<o:p></o:p></span></h1>
    13881388
    1389 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1390 
     1389<P><B>A video version of this tutorial is available at
     1390<A href="https://anl.box.com/v/SequentialTutorial" target="_blank">
     1391https://anl.box.com/v/SequentialTutorial</A></B></P>
     1392 
    13911393<p class=MsoNormal>Sequential refinement is a way to fit a series of datasets
    13921394with a set of closely related models that evolve over the course of the
  • Tutorials/StackingFaults-I/Stacking Faults-I.htm

    r3081 r3553  
    11311131Simulations – I<o:p></o:p></span></h1>
    11321132
     1133<P><B>A video version of this tutorial is available at
     1134<A href="https://anl.box.com/v/StackingFaults-I" target="_blank">
     1135https://anl.box.com/v/StackingFaults-I</A></B></P>
     1136
    11331137<p class=MsoNormal>In this exercise you will use GSAS-II to simulate the
    11341138diffraction patterns from faulted diamond. Diamond most commonly has the
     
    13841388<p class=MsoNormal>You can explore the result of various stacking sequences in
    13851389the next block of commands; enter <b><span style='font-family:"Calibri",sans-serif'>1
    1386 1 1 1 2 2 2</span></b> into the box and press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
     13901 1 1 2 2 2</span></b> into the box (remember to include spaces in between each number) and press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
    13871391A plot showing the result of a single twin fault will be shown.</p>
    13881392
     
    15081512for the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale
    15091513factor</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
    1510 type</span></b> to <b><span style='font-family:"Calibri",sans-serif'>Bragg-Brentano</span></b>.
     1514type</span></b> to <b><span
     1515style='font-family:"Calibri",sans-serif'>Bragg-Brentano</span></b> (if
     1516not already set to that).
    15111517Finally, find your phase (<b><span style='font-family:"Calibri",sans-serif'>random
    15121518faults</span></b>) and select it and then the <b><span style='font-family:"Calibri",sans-serif'>Layers</span></b>
     
    15251531the powder pattern will be displayed with the result. On the plot press the ‘<b><span
    15261532style='font-family:"Calibri",sans-serif'>+</span></b>’ key to suppress the ‘+’
    1527 marks. The plot should look like: I’ve expanded the scale to show the
    1528 interesting stuff around each peak.</p>
     1533marks. The plot should look like: </p>
    15291534
    15301535<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15341539</v:shape><![endif]--><![if !vml]><img width=624 height=535
    15351540src="Stacking%20Faults-I_files/image042.gif" v:shapes="Picture_x0020_51"><![endif]></span></p>
    1536 
     1541(I’ve expanded the scale to show the
     1542interesting stuff around each peak.)
     1543<p></p>
    15371544<p class=MsoNormal>The blue line is a simulated observed pattern with imposed
    15381545Poisson noise, the red line is the calculated background and the green curve is
     
    15721579as layer 2 to layer 2 at each step in the simulation. We can force this by
    15731580selecting <b><span style='font-family:"Calibri",sans-serif'>Symmetric
    1574 probabilities?</span></b> <span class=GramE>on</span> the Layers page. Do this
     1581probabilities?</span></b> <span class=GramE>on</span> the Layers tab. Do this
    15751582and repeat the sequential simulation as above. Now the matrices are symmetric
    15761583as one could expect. When the simulation is finished, select the <b><span
     
    18371844"Calibri",sans-serif'>Edit range</span></b> from the data window. Don’t change
    18381845anything, just press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
    1839 this will clear the previous simulation. Then return to the clustered phase
     1846this will clear the previous simulation. Then return to the random
     1847faults phase
    18401848Layers tab. Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Simulate
    18411849pattern</span></b> and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>
  • Tutorials/TOF Calibration/Calibration of a TOF powder diffractometer.htm

    r3064 r3553  
    11531153color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
    11541154
     1155<P><B>A video version of this tutorial is available at
     1156<A href="https://anl.box.com/v/CalibrationofaTOFpowderdiffrac" target="_blank">
     1157https://anl.box.com/v/CalibrationofaTOFpowderdiffrac</A></B></P>
     1158
    11551159<p class=MsoNormal>In this tutorial, data collected on the SNS instrument
    11561160POWGEN, are used. The calibration process will use the fitted positions of all
     
    11791183text-underline:none'>start GSAS-II</span></a></span></u>.</p>
    11801184
    1181 <h1>Part I. Determine the diffractometer constants</h1>
    1182 
    1183 <h2>Step 1: Read in the data file</h2>
     1185<h2>Part I. Determine the diffractometer constants</h2>
     1186
     1187<h3>Step 1: Read in the data file</h3>
    11841188
    11851189<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
     
    12651269style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
    12661270
    1267 <h2><span style='mso-spacerun:yes'> </span>Step 2: Select peaks</h2>
     1271<h3><span style='mso-spacerun:yes'> </span>Step 2: Select peaks</h3>
    12681272
    12691273<p class=MsoNormal>Under the <b style='mso-bidi-font-weight:normal'><span
     
    13051309turned off.</p>
    13061310
    1307 <h2>Step 3: Fit peaks</h2>
     1311<h3>Step 3: Fit peaks</h3>
    13081312
    13091313<p class=MsoNormal>To do the initial fit to the peaks, select the <b
     
    13651369v:shapes="Picture_x0020_40"><![endif]></span></p>
    13661370
    1367 <h2>Step 4: Setup for calibration</h2>
     1371<h3>Step 4: Setup for calibration</h3>
    13681372
    13691373<p class=MsoNormal>Now that we have a reasonably well fit set of peak
     
    14451449<p class=MsoNormal>The calibration set up is now complete.</p>
    14461450
    1447 <h2>Step 5: Calibration of diffractometer constants</h2>
     1451<h3>Step 5: Calibration of diffractometer constants</h3>
    14481452
    14491453<p class=MsoNormal>As we now have a set of reflection positions each properly
     
    16021606in the second part of the tutorial.</p>
    16031607
    1604 <h1>Part II. Determine the instrument profile coefficients</h1>
     1608<h2>Part II. Determine the instrument profile coefficients</h2>
    16051609
    16061610<p class=MsoNormal>To best establish the profile coefficients one must have the
     
    16101614automatic procedure used above.</p>
    16111615
    1612 <h2>Step 1. Change background</h2>
     1616<h3>Step 1. Change background</h3>
    16131617
    16141618<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
     
    16551659v:shapes="Picture_x0020_51"><![endif]></span></p>
    16561660
    1657 <h2>Step 2. Add more peaks to be fitted</h2>
     1661<h3>Step 2. Add more peaks to be fitted</h3>
    16581662
    16591663<p class=MsoNormal>Now zoom in on the right hand end of the pattern and select
     
    17151719project</span></b> from the main GSAS-II data tree window.</p>
    17161720
    1717 <h2>Step 3. Refine profile coefficients</h2>
     1721<h3>Step 3. Refine profile coefficients</h3>
    17181722
    17191723<p class=MsoNormal>In this step you will be selecting some profile coefficients
     
    21252129curve to be about zero.</p>
    21262130
    2127 <h2>Step 4. Check diffractometer constants </h2>
     2131<h3>Step 4. Check diffractometer constants </h3>
    21282132
    21292133<p class=MsoNormal>Since these calibration fits for profile coefficients varied
     
    21792183the main GSAS-II data tree menu).</p>
    21802184
    2181 <h2>Step 5. Make instrument parameter file</h2>
     2185<h3>Step 5. Make instrument parameter file</h3>
    21822186
    21832187<p class=MsoNormal>We now have a fully calibrated instrument with
  • Tutorials/TOF Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm

    r3547 r3553  
    11941194<h1>TOF Sequential Single Peak Fits and loading curve</h1>
    11951195
    1196 <p class=MsoNormal>A common analysis of diffraction data obtained from a
     1196<P><B>A video version of this tutorial is available at
     1197<A href="https://anl.box.com/v/TOFSequentialSinglePeakFit" target="_blank">
     1198https://anl.box.com/v/TOFSequentialSinglePeakFit</A></B></P>
     1199
     1200 <p class=MsoNormal>A common analysis of diffraction data obtained from a
    11971201polycrystalline sample subjected to a changing uniaxial load is to follow the behavior
    11981202of fitted single peaks. The data sets considered here were obtained on the
  • Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm

    r3073 r3553  
    12981298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
    12991299<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1300 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
     1300mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R
     1301-3 c</span></b> for the space group
    13011302(don’t forget the spaces between axial fields) &amp; press <b style='mso-bidi-font-weight:
    13021303normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     
    14211422style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14221423mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
    1423 Factor/from Neutron TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
     1424Factor/from Neutron ISIS SXD TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
    14241425will appear. Change the directory to the location of this exercise (<b
    14251426style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
  • trunk/GSASIIctrlGUI.py

    r3551 r3553  
    50195019     '''This explores the results of the sequential refinement obtained in the previous tutorial; includes
    50205020     plotting of variables and fitting the changes with simple equations.'''],
    5021      ['TOF Sequential Single Peak Fit','TOF Sequential Single Peak Fit.htm','     Sequential fitting of single peaks and strain analysis of reult',
     5021     ['TOF Sequential Single Peak Fit','TOF Sequential Single Peak Fit.htm','Sequential fitting of single peaks and strain analysis of result',
    50225022      '''This shows the fitting of single peaks in a sequence of TOF powder patterns from a sample under load; includes
    50235023      fitting of the result to get Hookes Law coefficients for elastic deformations.'''],
  • trunk/help/Tutorials.html

    r3552 r3553  
    4949</UL><h4>Parametric sequential fitting</H4><UL>
    5050<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/SequentialTutorial.htm">Sequential refinement of multiple datasets</A>
     51 [link: <A href="https://anl.box.com/v/SequentialTutorial">video</A>]
    5152 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/data">Exercise files</A>].
    5253<blockquote><I>This shows the fitting of a structural model to multiple data sets collected as a function of temperature (7-300K).
    5354     This tutorial is the prerequisite for the next one.</I></blockquote>
    5455<UL><LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqParametric/ParametricFitting.htm">Parametric Fitting and Pseudo Variables for Sequential Fits</A> <A href="#prereq">*</A>
     56 [link: <A href="https://anl.box.com/v/ParametricFitting">video</A>]
    5557 [No exercise files].
    5658<blockquote><I>This explores the results of the sequential refinement obtained in the previous tutorial; includes
    5759     plotting of variables and fitting the changes with simple equations.</I></blockquote>
    5860</UL>
    59 <UL><LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm">Sequential fitting of single peaks and strain analysis of reult</A> <A href="#prereq">*</A>
     61<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm">Sequential fitting of single peaks and strain analysis of result</A>
     62 [link: <A href="https://anl.box.com/v/TOFSequentialSinglePeakFit">video</A>]
    6063 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Sequential Single Peak Fit/data">Exercise files</A>].
    6164<blockquote><I>This shows the fitting of single peaks in a sequence of TOF powder patterns from a sample under load; includes
    6265      fitting of the result to get Hookes Law coefficients for elastic deformations.</I></blockquote>
    63 </UL>
    6466</UL><h4>Structure solution</H4><UL>
    6567<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/Fit Peaks.htm">Fitting individual peaks & autoindexing</A>
     68 [link: <A href="https://anl.box.com/v/FitPeaks">video</A>]
    6669 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data">Exercise files</A>].
    6770<blockquote><I>This covers two examples of selecting individual powder diffraction peaks, fitting them and then
     
    8891</UL><h4>Stacking Fault Modeling</H4><UL>
    8992<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/StackingFaults-I/Stacking Faults-I.htm">Stacking fault simulations for diamond</A>
     93 [link: <A href="https://anl.box.com/v/StackingFaults-I">video</A>]
    9094 [No exercise files].
    9195<blockquote><I>This shows how to simulate the diffraction patterns from faulted diamond.</I></blockquote>
     
    98102</UL><h4>Powder diffractometer calibration</H4><UL>
    99103<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWInstDemo/FindProfParamCW.htm">Determining Starting Profile Parameters from a Standard</A>
     104 [link: <A href="https://anl.box.com/v/FindProfParamCW">video</A>]
    100105 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWInstDemo/data">Exercise files</A>].
    101106<blockquote><I>This shows how to determine profile parameters by fitting individual peaks
    102107        with data collected on a standard using a lab diffractometer.</I></blockquote>
    103108<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Calibration/Calibration of a TOF powder diffractometer.htm">Calibration of a Neutron TOF diffractometer</A>
     109 [link: <A href="https://anl.box.com/v/CalibrationofaTOFpowderdiffrac">video</A>]
    104110 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Calibration/data">Exercise files</A>].
    105111<blockquote><I>This uses the fitted positions of all visible peaks in a pattern of NIST SRM 660b La11B6
     
    111117</UL><h4>2D Image Processing</H4><UL>
    112118<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DCalibration/Calibration of an area detector in GSAS.htm">Calibration of an area detector</A>
     119 [link: <A href="https://anl.box.com/v/CalibrationofanareadetectorinG">video</A>]
    113120 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DCalibration/data">Exercise files</A>].
    114121<blockquote><I>A demonstration of calibrating a Perkin-Elmer area detector,  where the detector was intentionally tilted at 45 degrees.
    115122     This exercise is the prerequisite for the next one.</I></blockquote>
    116123<UL><LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DIntegration/Integration of area detector data in GSAS.htm">Integration of area detector data</A> <A href="#prereq">*</A>
     124 [link: <A href="https://anl.box.com/v/Integrationofareadetectordatai">video</A>]
    117125 [No exercise files].
    118126<blockquote><I>Integration of the image from a Perkin-Elmer area detector, where the detector was intentionally tilted at 45 degrees.</I></blockquote>
    119127</UL>
    120128<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DStrain/Strain fitting of 2D data in GSAS-II.htm">Strain fitting of 2D data</A>
     129 [link: <A href="https://anl.box.com/v/Strainfittingof2DdatainGSAS-II">video</A>]
    121130 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DStrain/data">Exercise files</A>].
    122131<blockquote><I>This show how to determine 3 strain tensor values using the method of He & Smith (Adv. in X-ray Anal. 41, 501, 1997)
    123132     directly froom a sequence of 2D imges from a loaded sample.</I></blockquote>
    124133<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DTexture/Texture analysis of 2D data in GSAS-II.htm">Texture analysis of 2D data</A>
     134 [link: <A href="https://anl.box.com/v/Textureanalysisof2DdatainGSAS-">video</A>]
    125135 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DTexture/data">Exercise files</A>].
    126136<blockquote><I>This shows 3 different methods for determining texture via spherical harmonics from 2D x-ray diffraction images. </I></blockquote>
     
    141151</UL><h4>Small-Angle Scattering</H4><UL>
    142152<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAsize/Small Angle Size Distribution.htm">Small angle x-ray data size distribution (alumina powder)</A>
     153 [link: <A href="https://anl.box.com/v/SmallAngleSizeDistribution">video</A>]
    143154 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAsize/data">Exercise files</A>].
    144155<blockquote><I>This shows how to determine the size distribution of particles using data from a constant
    145156     wavelength synchrotron X-ray USAXS instrument. This is the prerequisite for the next tutorial</I></blockquote>
    146157<UL><LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAfit/Fitting Small Angle Scattering Data.htm">Fitting small angle x-ray data (alumina powder)</A> <A href="#prereq">*</A>
     158 [link: <A href="https://anl.box.com/v/FittingSmallAngleScatteringDat">video</A>]
    147159 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAfit/data">Exercise files</A>].
    148160<blockquote><I>This shows how to fit small angle scattering data using data from a constant wavelength synchrotron X-ray USAXS instrument. </I></blockquote>
    149161</UL>
    150162<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAimages/Small Angle Image Processing.htm">Image Processing of small angle x-ray data</A>
     163 [link: <A href="https://anl.box.com/v/SmallAngleImageProcessing">video</A>]
    151164 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAimages/data">Exercise files</A>].
    152165<blockquote><I>This shows how to  reduce 2D SAXS data to create 1D absolute scaled data. </I></blockquote>
    153166<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAseqref/Sequential Refinement of Small Angle Scattering Data.htm">Sequential refinement with small angle scattering data</A>
     167 [link: <A href="https://anl.box.com/v/SequentialRefinementofSmallAng">video</A>]
    154168 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAseqref/data">Exercise files</A>].
    155169<blockquote><I>This shows how to fit USAXS small angle scattering data for a suite of samples to demonstrate the
     
    158172</UL><h4>Other</H4><UL>
    159173<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm">Merohedral twin refinements</A>
     174 [link: <A href="https://anl.box.com/v/MerohedraltwinrefinementinGSAS">video</A>]
    160175 [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/MerohedralTwins/data">Exercise files</A>].
    161176<blockquote><I>This shows how to use GSAS-II to refine the structure of a few single crystal structures where there is merohedral twinning. </I></blockquote>
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