Changeset 3553

Timestamp:

Aug 3, 2018 10:51:26 PM (5 years ago)

Author:

toby

Message:

finish web tutorials for now

Files:

• Tutorials/2DCalibration/Calibration of an area detector in GSAS.htm (modified) (4 diffs)
• Tutorials/2DIntegration/Integration of area detector data in GSAS.htm (modified) (6 diffs)
• Tutorials/2DStrain/Strain fitting of 2D data in GSAS-II.htm (modified) (1 diff)
• Tutorials/2DTexture/Texture analysis of 2D data in GSAS-II.htm (modified) (1 diff)
• Tutorials/CWInstDemo/FindProfParamCW.htm (modified) (1 diff)
• Tutorials/DeterminingWavelength/DeterminingWavelength.html (modified) (1 diff)
• Tutorials/FitPeaks/Fit Peaks.htm (modified) (1 diff)
• Tutorials/MCsimanneal/MCSA in GSAS.htm (modified) (9 diffs)
• Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm (modified) (1 diff)
• Tutorials/SAfit/Fitting Small Angle Scattering Data.htm (modified) (1 diff)
• Tutorials/SAimages/Small Angle Image Processing.htm (modified) (1 diff)
• Tutorials/SAseqref/Sequential Refinement of Small Angle Scattering Data.htm (modified) (1 diff)
• Tutorials/SAsize/Small Angle Size Distribution.htm (modified) (4 diffs)
• Tutorials/SeqParametric/ParametricFitting.htm (modified) (4 diffs)
• Tutorials/SeqRefine/SequentialTutorial.htm (modified) (1 diff)
• Tutorials/StackingFaults-I/Stacking Faults-I.htm (modified) (7 diffs)
• Tutorials/TOF Calibration/Calibration of a TOF powder diffractometer.htm (modified) (12 diffs)
• Tutorials/TOF Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm (modified) (1 diff)
• Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm (modified) (2 diffs)
• trunk/GSASIIctrlGUI.py (modified) (1 diff)
• trunk/help/Tutorials.html (modified) (6 diffs)

Tutorials/2DCalibration/Calibration of an area detector in GSAS.htm

@@ -1144 +1144 @@
 color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/CalibrationofanareadetectorinG" target="_blank">
+https://anl.box.com/v/CalibrationofanareadetectorinG</A></B></P>
+
 <p class=MsoNormal>In this tutorial, data collected with a Perkin-Elmer area
 detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
@@ -1162 +1166 @@
 text-underline:none'>start GSAS-II</span></a></span></u>.</p>
 
-<h1>Step 1: read in the data file</h1>
+<h2>Step 1: read in the data file</h2>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
@@ -1244 +1248 @@
 v:shapes="Picture_x0020_16"><![endif]></span></p>
 
-<h1><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h1>
+<h2><span style='mso-spacerun:yes'> </span>Step 2: Edit image parameters</h2>
 
 <p class=MsoNormal>Note that, alas, very few image formats contain all of the
@@ -1273 +1277 @@
 minor-latin;mso-bidi-theme-font:minor-latin'>Color bar</span></b> selector. </p>
 
-<h1><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h1>
+<h2><span style='mso-spacerun:yes'> </span>Step 3: Calibrate</h2>
 
 <h3><span style='mso-spacerun:yes'> </span>First: </h3>

Tutorials/2DIntegration/Integration of area detector data in GSAS.htm

@@ -1309 +1309 @@
 <h1>Integration of area detector data in GSAS-II</h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/Integrationofareadetectordatai" target="_blank">
+https://anl.box.com/v/Integrationofareadetectordatai</A></B></P>
+
+
 <p class=MsoNormal>In this demo, data collected with a Perkin-Elmer area
 detector at APS 11-ID-C with a wavelength 0.10798 A, where the detector was
@@ -1336 +1341 @@
 <p class=MsoNormal>Assuming the previous step was calibration, the image plot
 will show the located rings and possibly all the picked points. These are no
-longer needed. The <b style='mso-bidi-font-weight:normal'><span
+longer needed.
+Go to the <B>Image Controls</B> window on the data tree.
+The <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calibration/Clear
@@ -1360 +1367 @@
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Show
-integration limits?</span></b> <span class=GramE>check</span> box. Note that
+integration limits?</span></b> <span class=GramE>check</span> box (if
+not already checked). Note that
 inner limit is shown as a green ellipse at 2deg and the outer is shown as a red
 ellipse at 5deg by default. These limits may also be dragged to the desired
@@ -1442 +1450 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5000</span></b>
-is a better choice than the default.</p>
+is a better choice than the default in that first box.</p>
 
 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
@@ -1456 +1464 @@
 when the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show
-integration limits?</span></b> <span class=GramE>check</span> box is checked. </p>
+integration limits?</span></b> <span class=GramE>check</span> box, if
+not already checked. </p>
 
 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Appl. Sample absorption</span></b> and <b
+mso-hansi-theme-font:minor-latin'>Apply Sample absorption</span></b> and <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>value</span></b>:
@@ -1470 +1479 @@
 <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Appl. det.
+mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Apply detector
 absorption</span></b> and <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;

Tutorials/2DStrain/Strain fitting of 2D data in GSAS-II.htm

@@ -1309 +1309 @@
 <h1>Strain fitting of 2D data in GSAS-II</h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/Strainfittingof2DdatainGSAS-II" target="_blank">
+https://anl.box.com/v/Strainfittingof2DdatainGSAS-II</A></B></P>
+
 <p class=MsoNormal>For this tutorial, data were collected with a MAR2300 area
 detector 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

@@ -1433 +1433 @@
 0in;line-height:115%'>Texture analysis of 2D data in GSAS-II</h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/Textureanalysisof2DdatainGSAS-" target="_blank">
+https://anl.box.com/v/Textureanalysisof2DdatainGSAS-</A></B></P>
+
 <h2 style='margin-top:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:
 0in;line-height:115%'>Introduction</h2>

Tutorials/CWInstDemo/FindProfParamCW.htm

@@ -713 +713 @@
 Parameters from a Standard<o:p></o:p></span></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/FindProfParamCW" target="_blank">
+https://anl.box.com/v/FindProfParamCW</A></B></P>
+
 <p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
 

Tutorials/DeterminingWavelength/DeterminingWavelength.html

@@ -27 +27 @@
 <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.
 </span></p><p class="c8"><span class="c4 c2">
-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.
+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. </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.
 If required, turn off refinement of Penetration with a value of 0.0 if that is the only way to keep
 the value from becoming negative. </span></p>

Tutorials/FitPeaks/Fit Peaks.htm

@@ -1457 +1457 @@
 <h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/FitPeaks" target="_blank">
+https://anl.box.com/v/FitPeaks</A></B></P>
+ 
 <p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
 cell that matches a set of diffraction peaks -- a process known as

Tutorials/MCsimanneal/MCSA in GSAS.htm

@@ -1401 +1401 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
-minor-latin'>2-amino</span></b>’). You will need to vary at least <b
+minor-latin'>2-amino</span></b>’). You will need to refine at least <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
@@ -1432 +1432 @@
 both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
+mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>).
+Click on <B>Cell Index/Refine/Index Cell</B>. The correct unit
 cell should almost immediately appear with an M20 ~370 with a=7.748, b=7.650,
 c=12.736, Vol=755.01. NB: your solution may have a &amp; b switched. Do <b
@@ -1443 +1444 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub>
-2<sub>1</sub> 2<sub>1</sub></span></b>). You can then do <b style='mso-bidi-font-weight:
+2<sub>1</sub> 2<sub>1</sub></span></b>).
+Under the <B>General</B> tab, change the space group to <B>P 21 21 21</B>.
+You can then do <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
@@ -1508 +1511 @@
 to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
+minor-latin'>Pawley controls</span></b> under the <B>General</B> tab.
+Check the <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement?</span></b>
 box, enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
@@ -1784 +1788 @@
 C1-C3 defines the Z-axis (blue; default view direction) and the Y-axis is
 defined as Z-axis cross X-axis (green; down toward C5). You can change these
-via the pull downs (you can’t pick the same atom for two of these so pick them
+via the pull downs
+next to <B>Orientation reference non-H atoms A-B-C</B> 
+(you can’t pick the same atom for two of these so pick them
 appropriately; I chose C2, C3 &amp; C6). At each choice the structure will be
 transformed accordingly. My new model is</p>
@@ -1813 +1819 @@
 includes H-atoms; they are not really needed for MC/SA and will just make
 computation times a bit longer than necessary. They can be removed by selecting
-the Strip H-atoms box; for now leave them in. </p>
+the <B>Strip H-atoms box</B>; for now leave them in. </p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
@@ -2032 +2038 @@
 minor-latin'> current settings</span></b>; your choice becomes available immediately
 and is then set for all your future uses of GSAS-II. <span
-style='mso-spacerun:yes'> </span>Do <b style='mso-bidi-font-weight:normal'><span
+style='mso-spacerun:yes'> </span>Go to the <B>General</B> tab and
+select 
+<b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Multi
@@ -2056 +2064 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
-box. Using 10% of the ranges reduces the search volume in this case by ~6
+box under the <B>General</B> tab. Using 10% of the ranges reduces the search volume in this case by ~6
 orders of magnitude so that the true minimum is much easier to find. Now rerun <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
@@ -2166 +2174 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
-class=GramE>size</span></span></b> &amp; <span class=SpellE><b
+class=GramE>size</span></span></b> and both <span class=SpellE><b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>

Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm

@@ -810 +810 @@
 refinement in GSAS-II<o:p></o:p></span></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/MerohedraltwinrefinementinGSAS" target="_blank">
+https://anl.box.com/v/MerohedraltwinrefinementinGSAS</A></B></P>
+
 <h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
 

Tutorials/SAfit/Fitting Small Angle Scattering Data.htm

@@ -1222 +1222 @@
 Small Angle X-Ray Data – Alumina Powder</span><o:p></o:p></strong></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/FittingSmallAngleScatteringDat" target="_blank">
+https://anl.box.com/v/FittingSmallAngleScatteringDat</A></B></P>
+  
 <p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
 this tutorial you will fit small angle scattering data for an alumina polishing

Tutorials/SAimages/Small Angle Image Processing.htm

@@ -1172 +1172 @@
 <h1><strong>Small Angle X-Ray Data – Image Processing<o:p></o:p></strong></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/SmallAngleImageProcessing" target="_blank">
+https://anl.box.com/v/SmallAngleImageProcessing</A></B></P>
+
 <p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
 this tutorial you will reduce 2D SAXS data to create 1D absolute scaled data.

Tutorials/SAseqref/Sequential Refinement of Small Angle Scattering Data.htm

@@ -1222 +1222 @@
 Small Angle Scattering Data</span><o:p></o:p></strong></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/SequentialRefinementofSmallAng" target="_blank">
+https://anl.box.com/v/SequentialRefinementofSmallAng</A></B></P>
+
+  
 <p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
 this tutorial you will fit USAXS small angle scattering data for “<span

Tutorials/SAsize/Small Angle Size Distribution.htm

@@ -1222 +1222 @@
 Size Distribution in Alumina Powder</span><o:p></o:p></strong></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/SmallAngleSizeDistribution" target="_blank">
+https://anl.box.com/v/SmallAngleSizeDistribution</A></B></P>
+  
+
 <p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
 this tutorial you will determine the size distribution of particles in an
@@ -1353 +1358 @@
 <h2>Step 3 Select the scattering substances for your sample</h2>
 
-<p class=MsoNormal><span style='mso-no-proof:yes'>Two scsttering substances
+<p class=MsoNormal><span style='mso-no-proof:yes'>Two scattering substances
 need to be defined for your sample to give the anticipated scattering contrast;
 in this case one is alumina and the other is “vacuum” (really air). Parameters
@@ -1415 +1420 @@
 values will change accordingly. If your substance isn’t in the list, you can <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
+Substance/Add
 substance</span></b> to create a new one (you will be asked for a name and the
 set of elements in two successive popup windows). From this information the
@@ -1508 +1514 @@
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>0.12</span></b>; enter that into the
-appropriate place in the data window. The plot will be redrawn showing a
+appropriate place in the data window next to <B>Background</B>. The plot will be redrawn showing a
 horizontal red line for the background. All the other parameters seem
 reasonable for a 1<sup>st</sup> attempt at a <span class=SpellE>MaxEnt</span>

Tutorials/SeqParametric/ParametricFitting.htm

@@ -1267 +1267 @@
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
+  
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/ParametricFitting" target="_blank">
+https://anl.box.com/v/ParametricFitting</A></B></P>
 
 <p class=MsoNormal>Once a sequential fit has been performed, any function of
@@ -2147 +2151 @@
 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
 style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span><![endif]>Then enter the equation as </p>
+</span></span></span><![endif]>Then enter the equation
+(you can copy and paste the equation above into the text box) as: 
+</p>
 
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
@@ -2166 +2172 @@
 style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span></span><![endif]>Assign the free and fixed variables, as shown
-below. Note that the exponent (<b style='mso-bidi-font-weight:normal'><span
+below.
+Note: if no option under Phase for ‘Temperature’, then select variable
+type <B>Global</B> and select <B>Global Temperature</B>.
+Note that the exponent (<b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
 mso-hansi-theme-font:major-latin'>k</span></b>) and scaling factor (<b
@@ -2176 +2185 @@
 should be set to <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri",sans-serif;mso-ascii-theme-font:major-latin;mso-hansi-theme-font:
-major-latin;mso-bidi-theme-font:major-latin'>120</span></b><span class=GramE>.<b
-style='mso-bidi-font-weight:normal'>.</b></span><b style='mso-bidi-font-weight:
-normal'> </b></p>
+major-latin;mso-bidi-theme-font:major-latin'>120</span></b><span class=GramE>.</span><b style='mso-bidi-font-weight:
+normal'> </b>
+</p>
 
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>

Tutorials/SeqRefine/SequentialTutorial.htm

@@ -1387 +1387 @@
 CuCr<sub>2</sub>O<sub>4</sub> from 7K to 300K<o:p></o:p></span></h1>
 
-<p class=MsoNormal><o:p>&nbsp;</o:p></p>
-
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/SequentialTutorial" target="_blank">
+https://anl.box.com/v/SequentialTutorial</A></B></P>
+  
 <p class=MsoNormal>Sequential refinement is a way to fit a series of datasets
 with a set of closely related models that evolve over the course of the

Tutorials/StackingFaults-I/Stacking Faults-I.htm

@@ -1131 +1131 @@
 Simulations – I<o:p></o:p></span></h1>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/StackingFaults-I" target="_blank">
+https://anl.box.com/v/StackingFaults-I</A></B></P>
+
 <p class=MsoNormal>In this exercise you will use GSAS-II to simulate the
 diffraction patterns from faulted diamond. Diamond most commonly has the
@@ -1384 +1388 @@
 <p class=MsoNormal>You can explore the result of various stacking sequences in
 the next block of commands; enter <b><span style='font-family:"Calibri",sans-serif'>1
-1 1 1 2 2 2</span></b> into the box and press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
+1 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>.
 A plot showing the result of a single twin fault will be shown.</p>
 
@@ -1508 +1512 @@
 for the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale
 factor</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
-type</span></b> to <b><span style='font-family:"Calibri",sans-serif'>Bragg-Brentano</span></b>.
+type</span></b> to <b><span
+style='font-family:"Calibri",sans-serif'>Bragg-Brentano</span></b> (if
+not already set to that).
 Finally, find your phase (<b><span style='font-family:"Calibri",sans-serif'>random
 faults</span></b>) and select it and then the <b><span style='font-family:"Calibri",sans-serif'>Layers</span></b>
@@ -1525 +1531 @@
 the powder pattern will be displayed with the result. On the plot press the ‘<b><span
 style='font-family:"Calibri",sans-serif'>+</span></b>’ key to suppress the ‘+’
-marks. The plot should look like: I’ve expanded the scale to show the
-interesting stuff around each peak.</p>
+marks. The plot should look like: </p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1534 +1539 @@
 </v:shape><![endif]--><![if !vml]><img width=624 height=535
 src="Stacking%20Faults-I_files/image042.gif" v:shapes="Picture_x0020_51"><![endif]></span></p>
-
+(I’ve expanded the scale to show the
+interesting stuff around each peak.)
+<p></p>
 <p class=MsoNormal>The blue line is a simulated observed pattern with imposed
 Poisson noise, the red line is the calculated background and the green curve is
@@ -1572 +1579 @@
 as layer 2 to layer 2 at each step in the simulation. We can force this by
 selecting <b><span style='font-family:"Calibri",sans-serif'>Symmetric
-probabilities?</span></b> <span class=GramE>on</span> the Layers page. Do this
+probabilities?</span></b> <span class=GramE>on</span> the Layers tab. Do this
 and repeat the sequential simulation as above. Now the matrices are symmetric
 as one could expect. When the simulation is finished, select the <b><span
@@ -1837 +1844 @@
 "Calibri",sans-serif'>Edit range</span></b> from the data window. Don’t change
 anything, just press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
-this will clear the previous simulation. Then return to the clustered phase
+this will clear the previous simulation. Then return to the random
+faults phase
 Layers tab. Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Simulate
 pattern</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

@@ -1153 +1153 @@
 color:#365F91;mso-themecolor:accent1;mso-themeshade:191'><o:p></o:p></span></b></p>
 
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/CalibrationofaTOFpowderdiffrac" target="_blank">
+https://anl.box.com/v/CalibrationofaTOFpowderdiffrac</A></B></P>
+
 <p class=MsoNormal>In this tutorial, data collected on the SNS instrument
 POWGEN, are used. The calibration process will use the fitted positions of all
@@ -1179 +1183 @@
 text-underline:none'>start GSAS-II</span></a></span></u>.</p>
 
-<h1>Part I. Determine the diffractometer constants</h1>
-
-<h2>Step 1: Read in the data file</h2>
+<h2>Part I. Determine the diffractometer constants</h2>
+
+<h3>Step 1: Read in the data file</h3>
 
 <p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the <b
@@ -1265 +1269 @@
 style='mso-spacerun:yes'> </span><b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
 
-<h2><span style='mso-spacerun:yes'> </span>Step 2: Select peaks</h2>
+<h3><span style='mso-spacerun:yes'> </span>Step 2: Select peaks</h3>
 
 <p class=MsoNormal>Under the <b style='mso-bidi-font-weight:normal'><span
@@ -1305 +1309 @@
 turned off.</p>
 
-<h2>Step 3: Fit peaks</h2>
+<h3>Step 3: Fit peaks</h3>
 
 <p class=MsoNormal>To do the initial fit to the peaks, select the <b
@@ -1365 +1369 @@
 v:shapes="Picture_x0020_40"><![endif]></span></p>
 
-<h2>Step 4: Setup for calibration</h2>
+<h3>Step 4: Setup for calibration</h3>
 
 <p class=MsoNormal>Now that we have a reasonably well fit set of peak
@@ -1445 +1449 @@
 <p class=MsoNormal>The calibration set up is now complete.</p>
 
-<h2>Step 5: Calibration of diffractometer constants</h2>
+<h3>Step 5: Calibration of diffractometer constants</h3>
 
 <p class=MsoNormal>As we now have a set of reflection positions each properly
@@ -1602 +1606 @@
 in the second part of the tutorial.</p>
 
-<h1>Part II. Determine the instrument profile coefficients</h1>
+<h2>Part II. Determine the instrument profile coefficients</h2>
 
 <p class=MsoNormal>To best establish the profile coefficients one must have the
@@ -1610 +1614 @@
 automatic procedure used above.</p>
 
-<h2>Step 1. Change background</h2>
+<h3>Step 1. Change background</h3>
 
 <p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
@@ -1655 +1659 @@
 v:shapes="Picture_x0020_51"><![endif]></span></p>
 
-<h2>Step 2. Add more peaks to be fitted</h2>
+<h3>Step 2. Add more peaks to be fitted</h3>
 
 <p class=MsoNormal>Now zoom in on the right hand end of the pattern and select
@@ -1715 +1719 @@
 project</span></b> from the main GSAS-II data tree window.</p>
 
-<h2>Step 3. Refine profile coefficients</h2>
+<h3>Step 3. Refine profile coefficients</h3>
 
 <p class=MsoNormal>In this step you will be selecting some profile coefficients
@@ -2125 +2129 @@
 curve to be about zero.</p>
 
-<h2>Step 4. Check diffractometer constants </h2>
+<h3>Step 4. Check diffractometer constants </h3>
 
 <p class=MsoNormal>Since these calibration fits for profile coefficients varied
@@ -2179 +2183 @@
 the main GSAS-II data tree menu).</p>
 
-<h2>Step 5. Make instrument parameter file</h2>
+<h3>Step 5. Make instrument parameter file</h3>
 
 <p class=MsoNormal>We now have a fully calibrated instrument with

Tutorials/TOF Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm

@@ -1194 +1194 @@
 <h1>TOF Sequential Single Peak Fits and loading curve</h1>
 
-<p class=MsoNormal>A common analysis of diffraction data obtained from a
+<P><B>A video version of this tutorial is available at 
+<A href="https://anl.box.com/v/TOFSequentialSinglePeakFit" target="_blank">
+https://anl.box.com/v/TOFSequentialSinglePeakFit</A></B></P>
+
+ <p class=MsoNormal>A common analysis of diffraction data obtained from a
 polycrystalline sample subjected to a changing uniaxial load is to follow the behavior
 of fitted single peaks. The data sets considered here were obtained on the

Tutorials/TOF Single Crystal Refinement/TOF single crystal refinement in GSAS.htm

@@ -1298 +1298 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Enter
 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R -3 c</span></b>
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R
+-3 c</span></b> for the space group
 (don’t forget the spaces between axial fields) &amp; press <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
@@ -1421 +1422 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Structure
-Factor/from Neutron TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
+Factor/from Neutron ISIS SXD TOF HKL F<sup>2 </sup>file</span></b>; a file dialog box
 will appear. Change the directory to the location of this exercise (<b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;

trunk/GSASIIctrlGUI.py

@@ -5019 +5019 @@
      '''This explores the results of the sequential refinement obtained in the previous tutorial; includes 
      plotting of variables and fitting the changes with simple equations.'''],
-     ['TOF Sequential Single Peak Fit','TOF Sequential Single Peak Fit.htm','     Sequential fitting of single peaks and strain analysis of reult',
+     ['TOF Sequential Single Peak Fit','TOF Sequential Single Peak Fit.htm','Sequential fitting of single peaks and strain analysis of result',
       '''This shows the fitting of single peaks in a sequence of TOF powder patterns from a sample under load; includes
       fitting of the result to get Hookes Law coefficients for elastic deformations.'''],

trunk/help/Tutorials.html

@@ -49 +49 @@
 </UL><h4>Parametric sequential fitting</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/SequentialTutorial.htm">Sequential refinement of multiple datasets</A>
+ [link: <A href="https://anl.box.com/v/SequentialTutorial">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/data">Exercise files</A>].
 <blockquote><I>This shows the fitting of a structural model to multiple data sets collected as a function of temperature (7-300K). 
      This tutorial is the prerequisite for the next one.</I></blockquote>
 <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>
+ [link: <A href="https://anl.box.com/v/ParametricFitting">video</A>]
  [No exercise files].
 <blockquote><I>This explores the results of the sequential refinement obtained in the previous tutorial; includes 
      plotting of variables and fitting the changes with simple equations.</I></blockquote>
 </UL>
-<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>
+<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>
+ [link: <A href="https://anl.box.com/v/TOFSequentialSinglePeakFit">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Sequential Single Peak Fit/data">Exercise files</A>].
 <blockquote><I>This shows the fitting of single peaks in a sequence of TOF powder patterns from a sample under load; includes
       fitting of the result to get Hookes Law coefficients for elastic deformations.</I></blockquote>
-</UL>
 </UL><h4>Structure solution</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/Fit Peaks.htm">Fitting individual peaks & autoindexing</A>
+ [link: <A href="https://anl.box.com/v/FitPeaks">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data">Exercise files</A>].
 <blockquote><I>This covers two examples of selecting individual powder diffraction peaks, fitting them and then 
@@ -88 +91 @@
 </UL><h4>Stacking Fault Modeling</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/StackingFaults-I/Stacking Faults-I.htm">Stacking fault simulations for diamond</A>
+ [link: <A href="https://anl.box.com/v/StackingFaults-I">video</A>]
  [No exercise files].
 <blockquote><I>This shows how to simulate the diffraction patterns from faulted diamond.</I></blockquote>
@@ -98 +102 @@
 </UL><h4>Powder diffractometer calibration</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWInstDemo/FindProfParamCW.htm">Determining Starting Profile Parameters from a Standard</A>
+ [link: <A href="https://anl.box.com/v/FindProfParamCW">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWInstDemo/data">Exercise files</A>].
 <blockquote><I>This shows how to determine profile parameters by fitting individual peaks
         with data collected on a standard using a lab diffractometer.</I></blockquote>
 <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>
+ [link: <A href="https://anl.box.com/v/CalibrationofaTOFpowderdiffrac">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Calibration/data">Exercise files</A>].
 <blockquote><I>This uses the fitted positions of all visible peaks in a pattern of NIST SRM 660b La11B6 
@@ -111 +117 @@
 </UL><h4>2D Image Processing</H4><UL>
 <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>
+ [link: <A href="https://anl.box.com/v/CalibrationofanareadetectorinG">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DCalibration/data">Exercise files</A>].
 <blockquote><I>A demonstration of calibrating a Perkin-Elmer area detector,  where the detector was intentionally tilted at 45 degrees.
      This exercise is the prerequisite for the next one.</I></blockquote>
 <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>
+ [link: <A href="https://anl.box.com/v/Integrationofareadetectordatai">video</A>]
  [No exercise files].
 <blockquote><I>Integration of the image from a Perkin-Elmer area detector, where the detector was intentionally tilted at 45 degrees.</I></blockquote>
 </UL>
 <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>
+ [link: <A href="https://anl.box.com/v/Strainfittingof2DdatainGSAS-II">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DStrain/data">Exercise files</A>].
 <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) 
      directly froom a sequence of 2D imges from a loaded sample.</I></blockquote>
 <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>
+ [link: <A href="https://anl.box.com/v/Textureanalysisof2DdatainGSAS-">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/2DTexture/data">Exercise files</A>].
 <blockquote><I>This shows 3 different methods for determining texture via spherical harmonics from 2D x-ray diffraction images. </I></blockquote>
@@ -141 +151 @@
 </UL><h4>Small-Angle Scattering</H4><UL>
 <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>
+ [link: <A href="https://anl.box.com/v/SmallAngleSizeDistribution">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAsize/data">Exercise files</A>].
 <blockquote><I>This shows how to determine the size distribution of particles using data from a constant 
      wavelength synchrotron X-ray USAXS instrument. This is the prerequisite for the next tutorial</I></blockquote>
 <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>
+ [link: <A href="https://anl.box.com/v/FittingSmallAngleScatteringDat">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAfit/data">Exercise files</A>].
 <blockquote><I>This shows how to fit small angle scattering data using data from a constant wavelength synchrotron X-ray USAXS instrument. </I></blockquote>
 </UL>
 <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>
+ [link: <A href="https://anl.box.com/v/SmallAngleImageProcessing">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAimages/data">Exercise files</A>].
 <blockquote><I>This shows how to  reduce 2D SAXS data to create 1D absolute scaled data. </I></blockquote>
 <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>
+ [link: <A href="https://anl.box.com/v/SequentialRefinementofSmallAng">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SAseqref/data">Exercise files</A>].
 <blockquote><I>This shows how to fit USAXS small angle scattering data for a suite of samples to demonstrate the 
@@ -158 +172 @@
 </UL><h4>Other</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm">Merohedral twin refinements</A>
+ [link: <A href="https://anl.box.com/v/MerohedraltwinrefinementinGSAS">video</A>]
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/MerohedralTwins/data">Exercise files</A>].
 <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>