Changeset 4045 for Tutorials


Ignore:
Timestamp:
Jun 27, 2019 5:32:56 PM (2 years ago)
Author:
toby
Message:

add autoread of G(r)

Location:
Tutorials
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CalibrationTutorial/CalibrationTutorial.html

    r3546 r4045  
    2929<p class="c3"><span class="c4 c9">Step 1: Finding Average Difference Between Set Distance and Calibrated Distance</span></p>
    3030<p class="c5"></p>
    31 <p class="c3"><span class="c1">Go to </span><span class="c2">Image Controls </span><span class="c1">for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, </span><span class="c1">and change </span><span class="c2">wavelength</span><span class="c1">&nbsp;to 0.241689 as determined in part 1. </span><span class="c2">Uncheck</span><span class="c1">&nbsp;</span><span class="c2">wavelength</span><span class="c1">, and </span><span class="c2">check</span><span class="c1">&nbsp;</span><span class="c2">Distance</span><span class="c0">. We are doing this because we now have a calibrated wavelength, and we want to calibrate the detector distances. The Image Controls should look like this:</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: 597.00px; height: 371.00px;"><img alt="" src="images/image9.png" style="width: 749.05px; height: 421.43px; margin-left: -86.03px; margin-top: -13.21px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the </span><span class="c2">Image Controls</span><span class="c1">&nbsp;tab for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, do </span><span class="c2">Calibrate/Recalibrate</span><span class="c1">. Keep doing this until </span><span class="c2">penetration</span><span class="c1">&nbsp;(under Calibration coefficients) is constant. Usually recalibrating </span><span class="c2">3</span><span class="c0">&nbsp;times will suffice. Our penetration value converged to 0.1139.</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: 612.00px; height: 381.00px;"><img alt="" src="images/image40.png" style="width: 769.15px; height: 432.26px; margin-left: -89.35px; margin-top: -12.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1">&nbsp;</span></p><p class="c3"><span class="c1">The parameters have been adjusted because of recalibration. We want to copy these new parameters to the rest of the images. Go to</span><span class="c2">&nbsp;Parms/Copy Selected</span><span class="c0">. A window will appear like the one 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: 437.50px; height: 297.56px;"><img alt="" src="images/image2.png" style="width: 919.19px; height: 517.05px; margin-left: -253.37px; margin-top: -94.28px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1">&nbsp;</span></p><p class="c3"><span class="c1">Scroll down and select </span><span class="c2">varyList (28)</span><span class="c1">&nbsp;and </span><span class="c2">wavelength (29)</span><span class="c0">. Take notice of what parameters are noted as true and false, such as &lsquo;dist&rsquo;: True, and &lsquo;wave&rsquo;: False&rsquo;, these are what will be refined.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 468.00px; height: 314.00px;"><img alt="" src="images/image6.png" style="width: 987.47px; height: 554.30px; margin-left: -272.61px; margin-top: -102.65px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c1">. A new screen will appear. Select </span><span class="c2">Set All</span><span class="c0">&nbsp;to select all images</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: 244.50px; height: 323.84px;"><img alt="" src="images/image38.png" style="width: 1010.38px; height: 568.34px; margin-left: -396.71px; margin-top: -105.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">&nbsp;and click </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Scroll to the bottom of the Data Tree and go to </span><span class="c2">Image Controls</span><span class="c1">&nbsp;for the last image, </span><span class="c2">IMG Si_free_dc1300_1-00000.tif</span><span class="c0">. All of the Image Control parameters set for the first image have been copied to the rest of the images.</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: 602.00px; height: 376.00px;"><img alt="" src="images/image23.png" style="width: 754.78px; height: 424.36px; margin-left: -87.46px; margin-top: -12.09px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Calibrate/Recalibrate All/Set All</span><span class="c1">. </span><span class="c1">This recalibration finds the offset of between the set distance and actual distance</span><span class="c1">. The amount of time that recalibrating takes is dependant on the number of pixels. So if there are a large number of pixels for that particular image, then recalibrating will take longer to complete. After the calibration, go to the table under the </span><span class="c2">Sequential image calibration results</span><span class="c0">&nbsp;tab in the GSAS data tree.</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: 646.50px; height: 404.18px;"><img alt="" src="images/image25.png" style="width: 810.07px; height: 456.16px; margin-left: -92.17px; margin-top: -13.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">From this table we see a column for the calibrated distance (dist) and set distance (setdist) that was recorded when the data was being collected. Although the values are similar, there are slight differences for each image. We will now set up an equation to find the differences between the dist and setdist values.</span></p><p class="c3"><span class="c1">In the GSAS-II Data Tree, go to </span><span class="c2">Sequential image calibration results/Pseudo Vars/Add formula. </span><span class="c0">A popup window will 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: 483.50px; height: 263.13px;"><img alt="" src="images/image42.png" style="width: 1026.20px; height: 577.24px; margin-left: -379.89px; margin-top: -174.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Type in the equation </span><span class="c2">a-b</span><span class="c1">&nbsp;next to </span><span class="c2">New PseudoVar=</span><span class="c2">&nbsp;</span><span class="c1">and press </span><span class="c2">Validate. </span><span class="c0">The popup window change and allow you to enter variable types.</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: 436.50px; height: 237.68px;"><img alt="" src="images/image1.png" style="width: 932.79px; height: 524.70px; margin-left: -346.81px; margin-top: -159.95px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Set the </span><span class="c2">a</span><span class="c1">&nbsp;variable as </span><span class="c2">global</span><span class="c0">&nbsp;and a drop down bar will 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: 453.50px; height: 209.06px;"><img alt="" src="images/image19.png" style="width: 959.27px; height: 539.56px; margin-left: -355.11px; margin-top: -198.30px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">dist Global dist</span><span class="c1">. Next, set the b variable as </span><span class="c2">global</span><span class="c0">&nbsp;as well and another drop down menu will 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: 459.50px; height: 207.16px;"><img alt="" src="images/image20.png" style="width: 971.96px; height: 546.73px; margin-left: -359.81px; margin-top: -199.38px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">setdist Global setdist</span><span class="c1">. Then press</span><span class="c2">&nbsp;OK</span><span class="c1">. A new column called </span><span class="c2">a-b</span><span class="c1">&nbsp;will now appear in the table under </span><span class="c4 c2">Sequential image calibration results. </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: 606.50px; height: 360.49px;"><img alt="" src="images/image29.png" style="width: 759.95px; height: 427.47px; margin-left: -96.21px; margin-top: -34.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Double click on the new column: </span><span class="c2">a-b </span><span class="c0">so it is highlighted.</span></p><p class="c3"><span class="c1">Next, go to the graph called </span><span class="c2">sequential refinement</span><span class="c0">&nbsp;in the plot window. </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: 426.50px; height: 396.77px;"><img alt="" src="images/image18.png" style="width: 806.47px; height: 453.64px; margin-left: -226.17px; margin-top: -23.26px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">K</span><span class="c1">&nbsp;(at the bottom of the screen)</span><span class="c2">/Select x-axis/setdist. </span><span class="c0">Now the x axis is the set distance.</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: 471.50px; height: 439.97px;"><img alt="" src="images/image35.png" style="width: 894.27px; height: 503.03px; margin-left: -250.80px; margin-top: -25.80px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Next we want to calculate the average. In a perfect world, the graph should be constant at </span><span class="c2">0</span><span class="c1">&nbsp;with no error, but at very close and very far distances this is not possible. Select the </span><span class="c2">a-b</span><span class="c1">&nbsp;column once again. Go to </span><span class="c2">columns/rows/c</span><span class="c2">ompute average</span><span class="c2">. </span><span class="c0">Look at the terminal window.</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: 303.00px; height: 21.00px;"><img alt="" src="images/image26.png" style="width: 1264.48px; height: 719.55px; margin-left: -212.77px; margin-top: -569.50px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the terminal window, we can see the calculated </span><span class="c2">average</span><span class="c1">&nbsp;of -0.123759 and magnitude of +/- 0.287854 for </span><span class="c2">error</span><span class="c0">. The error in this case, is very high (around 0.3).</span></p><p class="c3"><span class="c1">Notice that the first and last few images are the least accurate because they are either too close or too far away from the detector to gather an accurate reading.</span></p><p class="c3"><span class="c1">Therefore, go to </span><span class="c2">Sequential image calibration results</span><span class="c1">&nbsp;and unclick image </span><span class="c2">use</span><span class="c0">&nbsp;for images 200-400 and 1050-1300. The table 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: 611.50px; height: 365.22px;"><img alt="" src="images/image36.png" style="width: 767.76px; height: 430.17px; margin-left: -98.43px; margin-top: -34.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To calculate the average again, select the </span><span class="c2">a-b</span><span class="c1">&nbsp;column again by double clicking on the column header then go to </span><span class="c2">Columns/Rows/Compute average</span><span class="c1">. The </span><span class="c2">terminal</span><span class="c0">&nbsp;window will show:</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: 333.00px; height: 25.00px;"><img alt="" src="images/image15.png" style="width: 1419.88px; height: 807.30px; margin-left: -236.54px; margin-top: -637.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">&nbsp;The magnitude of error of +/- 0.045307 is much smaller and more desirable. Therefore we feel more confident saying that the average distance between set distance and calibrated distance is -0.167927</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c4 c9">Step 2: Integrating the Calibrated Data</span></p><p class="c3"><span class="c1">This next step involves integration of the data. Go to </span><span class="c2">Image Controls</span><span class="c1">&nbsp;for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">&nbsp;and then go to the </span><span class="c2">GSAS-II plot window</span><span class="c0">. Select the tab with the powder data rings. Notice the beamstop and pin dial. In the final integration, we do not want to use these areas, so we will work on excluding these from the integration.</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: 519.00px; height: 483.00px;"><img alt="" src="images/image37.png" style="width: 519.00px; height: 483.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1">&nbsp;</span></p><p class="c3"><span class="c1">In the </span><span class="c2">GSAS-II data tree</span><span class="c1">, go to </span><span class="c2">Image Controls</span><span class="c1">&nbsp;for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">. We will be working in the </span><span class="c2">Integration coefficients </span><span class="c1">area. Click </span><span class="c2">Show integration limits?</span><span class="c0">. The plot should show the area that is to be integrated.</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: 467.50px; height: 434.82px;"><img alt="" src="images/image33.png" style="width: 886.69px; height: 498.76px; margin-left: -224.51px; margin-top: -17.05px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Zoom in </span><span class="c1">on the beamstop (bullseye of rings)</span><span class="c0">&nbsp;so we can make sure to exclude this from our final integration.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 436.50px; height: 404.66px;"><img alt="" src="images/image11.png" style="width: 827.89px; height: 465.69px; margin-left: -209.63px; margin-top: -17.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Change the</span><span class="c2">&nbsp;</span><span class="c2">inner 2-theta</span><span class="c1">&nbsp;to a smaller value of </span><span class="c2">0.8</span><span class="c0">&nbsp;to only exclude the small beamstop in the middle and not the surrounding data.</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: 466.50px; height: 435.40px;"><img alt="" src="images/image4.png" style="width: 882.11px; height: 496.19px; margin-left: -391.58px; margin-top: -29.69px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click the </span><span class="c2">home</span><span class="c1">&nbsp;button to see all the rings. Drag the mouse to the rights side of the image. As the mouse moves to the right, </span><span class="c2">2-theta</span><span class="c0">&nbsp;changes at the bottom of the screen. Note the outer 2-theta value when the mouse stops at the edge of the screen. </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: 600.00px; height: 560.00px;"><img alt="" src="images/image5.gif" style="width: 600.00px; height: 560.00px; 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="c1">Type this value (we used</span><span class="c1">&nbsp;</span><span class="c1">44.80</span><span class="c1">) into the </span><span class="c2">Outer 2-theta</span><span class="c1">&nbsp;box. Check the </span><span class="c2">Do full integration?</span><span class="c0">&nbsp;Box.</span></p><p class="c3"><span class="c0">The image controls screen should look like this:</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: 622.98px; height: 386.50px;"><img alt="" src="images/image27.png" style="width: 781.38px; height: 439.03px; margin-left: -108.31px; margin-top: -12.51px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits should look like:</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: 434.50px; height: 402.80px;"><img alt="" src="images/image3.png" style="width: 824.10px; height: 463.55px; margin-left: -217.91px; margin-top: -19.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see from the image, the inner and outer angles that we entered gave us a good integration area around the powder rings.</span></p><p class="c3"><span class="c1">At this point, we are going to cut out the beamstop, which yields poor intensity data. So, remove the </span><span class="c2">Do full integration?</span><span class="c0">&nbsp;Box.</span></p><p class="c3"><span class="c1">To exclude the beamstop we will adjust the start/end azimuth degrees. Make the </span><span class="c2">Start azimuth 5, </span><span class="c1">and </span><span class="c2">End azimuth </span><span class="c1">either</span><span class="c2">&nbsp;355 </span><span class="c1">or</span><span class="c2">&nbsp;-5.0</span><span class="c0">&nbsp;(it does not matter). The image controls window 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: 642.50px; height: 399.15px;"><img alt="" src="images/image12.png" style="width: 803.45px; height: 451.94px; margin-left: -109.44px; margin-top: -11.59px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits 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: 437.50px; height: 405.78px;"><img alt="" src="images/image14.png" style="width: 827.27px; height: 465.45px; margin-left: -218.75px; margin-top: -18.57px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the beamstop will now be excluded from our integration of the data.</span></p><p class="c3"><span class="c1">At this point it is a good idea to use </span><span class="c4 c2">Save project.</span></p>
     31<p class="c3"><span class="c1">Go to </span><span class="c2">Image Controls </span><span class="c1">for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, </span><span class="c1">and change </span><span class="c2">wavelength</span><span class="c1">&nbsp;to 0.241689 as determined in part 1. </span><span class="c2">Uncheck</span><span class="c1">&nbsp;</span><span class="c2">wavelength</span><span class="c1">, and </span><span class="c2">check</span><span class="c1">&nbsp;</span><span class="c2">Distance</span><span class="c0">. We are doing this because we now have a calibrated wavelength, and we want to calibrate the detector distances. The Image Controls should look like this:</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: 597.00px; height: 371.00px;"><img alt="" src="images/image9.png" style="width: 749.05px; height: 421.43px; margin-left: -86.03px; margin-top: -13.21px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the </span><span class="c2">Image Controls</span><span class="c1">&nbsp;tab for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, do </span><span class="c2">Calibrate/Recalibrate</span><span class="c1">. Keep doing this until </span><span class="c2">penetration</span><span class="c1">&nbsp;(under Calibration coefficients) is constant. Usually recalibrating </span><span class="c2">3</span><span class="c0">&nbsp;times will suffice. Our penetration value converged to 0.1139.</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: 612.00px; height: 381.00px;"><img alt="" src="images/image40.png" style="width: 769.15px; height: 432.26px; margin-left: -89.35px; margin-top: -12.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1">&nbsp;</span></p><p class="c3"><span class="c1">The parameters have been adjusted because of recalibration. We want to copy these new parameters to the rest of the images. Go to</span><span class="c2">&nbsp;Parms/Copy Selected</span><span class="c0">. A window will appear like the one 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: 437.50px; height: 297.56px;"><img alt="" src="images/image2.png" style="width: 919.19px; height: 517.05px; margin-left: -253.37px; margin-top: -94.28px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1">&nbsp;</span></p><p class="c3"><span class="c1">Scroll down and select </span><span class="c2">varyList (28)</span><span class="c1">&nbsp;and </span><span class="c2">wavelength (29)</span><span class="c0">. Take notice of what parameters are noted as true and false, such as &lsquo;dist&rsquo;: True, and &lsquo;wave&rsquo;: False&rsquo;, these are what will be refined.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 468.00px; height: 314.00px;"><img alt="" src="images/image6.png" style="width: 987.47px; height: 554.30px; margin-left: -272.61px; margin-top: -102.65px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c1">. A new screen will appear. Select </span><span class="c2">Set All</span><span class="c0">&nbsp;to select all images</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: 244.50px; height: 323.84px;"><img alt="" src="images/image38.png" style="width: 1010.38px; height: 568.34px; margin-left: -396.71px; margin-top: -105.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">&nbsp;and click </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Scroll to the bottom of the Data Tree and go to </span><span class="c2">Image Controls</span><span class="c1">&nbsp;for the last image, </span><span class="c2">IMG Si_free_dc1300_1-00000.tif</span><span class="c0">. All of the Image Control parameters set for the first image have been copied to the rest of the images.</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: 602.00px; height: 376.00px;"><img alt="" src="images/image23.png" style="width: 754.78px; height: 424.36px; margin-left: -87.46px; margin-top: -12.09px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Calibrate/Recalibrate All/Set All</span><span class="c1">. </span><span class="c1">This recalibration finds the offset of between the set distance and actual distance</span><span class="c1">. The amount of time that recalibrating takes is dependant on the number of pixels. So if there are a large number of pixels for that particular image, then recalibrating will take longer to complete. After the calibration, go to the table under the </span><span class="c2">Sequential image calibration results</span><span class="c0">&nbsp;tab in the GSAS data tree.</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: 646.50px; height: 404.18px;"><img alt="" src="images/image25.png" style="width: 810.07px; height: 456.16px; margin-left: -92.17px; margin-top: -13.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">From this table we see a column for the calibrated distance (dist) and set distance (setdist) that was recorded when the data was being collected. Although the values are similar, there are slight differences for each image. We will now set up an equation to find the differences between the dist and setdist values.</span></p><p class="c3"><span class="c1">In the GSAS-II Data Tree, go to </span><span class="c2">Sequential image calibration results/Pseudo Vars/Add formula. </span><span class="c0">A popup window will 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: 483.50px; height: 263.13px;"><img alt="" src="images/image42.png" style="width: 1026.20px; height: 577.24px; margin-left: -379.89px; margin-top: -174.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Type in the equation </span><span class="c2">a-b</span><span class="c1">&nbsp;next to </span><span class="c2">New PseudoVar=</span><span class="c2">&nbsp;</span><span class="c1">and press </span><span class="c2">Validate. </span><span class="c0">The popup window change and allow you to enter variable types.</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: 436.50px; height: 237.68px;"><img alt="" src="images/image1.png" style="width: 932.79px; height: 524.70px; margin-left: -346.81px; margin-top: -159.95px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Set the </span><span class="c2">a</span><span class="c1">&nbsp;variable as </span><span class="c2">global</span><span class="c0">&nbsp;and a drop down bar will 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: 453.50px; height: 209.06px;"><img alt="" src="images/image19.png" style="width: 959.27px; height: 539.56px; margin-left: -355.11px; margin-top: -198.30px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">dist Global dist</span><span class="c1">. Next, set the b variable as </span><span class="c2">global</span><span class="c0">&nbsp;as well and another drop down menu will 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: 459.50px; height: 207.16px;"><img alt="" src="images/image20.png" style="width: 971.96px; height: 546.73px; margin-left: -359.81px; margin-top: -199.38px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">setdist Global setdist</span><span class="c1">. Then press</span><span class="c2">&nbsp;OK</span><span class="c1">. A new column called </span><span class="c2">a-b</span><span class="c1">&nbsp;will now appear in the table under </span><span class="c4 c2">Sequential image calibration results. </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: 606.50px; height: 360.49px;"><img alt="" src="images/image29.png" style="width: 759.95px; height: 427.47px; margin-left: -96.21px; margin-top: -34.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Double click on the new column: </span><span class="c2">a-b </span><span class="c0">so it is highlighted.</span></p><p class="c3"><span class="c1">Next, go to the graph called </span><span class="c2">sequential refinement</span><span class="c0">&nbsp;in the plot window. </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: 426.50px; height: 396.77px;"><img alt="" src="images/image18.png" style="width: 806.47px; height: 453.64px; margin-left: -226.17px; margin-top: -23.26px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">K</span><span class="c1">&nbsp;(at the bottom of the screen)</span><span class="c2">/Select x-axis/setdist. </span><span class="c0">Now the x axis is the set distance.</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: 471.50px; height: 439.97px;"><img alt="" src="images/image35.png" style="width: 894.27px; height: 503.03px; margin-left: -250.80px; margin-top: -25.80px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Next we want to calculate the average. In a perfect world, the graph should be constant at </span><span class="c2">0</span><span class="c1">&nbsp;with no error, but at very close and very far distances this is not possible. Select the </span><span class="c2">a-b</span><span class="c1">&nbsp;column once again. Go to </span><span class="c2">columns/rows/c</span><span class="c2">ompute average</span><span class="c2">. </span><span class="c0">Look at the terminal window.</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: 303.00px; height: 21.00px;"><img alt="" src="images/image26.png" style="width: 1264.48px; height: 719.55px; margin-left: -212.77px; margin-top: -569.50px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the terminal window, we can see the calculated </span><span class="c2">average</span><span class="c1">&nbsp;of -0.123759 and magnitude of +/- 0.287854 for </span><span class="c2">error</span><span class="c0">. The error in this case, is very high (around 0.3).</span></p><p class="c3"><span class="c1">Notice that the first and last few images are the least accurate because they are either too close or too far away from the detector to gather an accurate reading.</span></p><p class="c3"><span class="c1">Therefore, go to </span><span class="c2">Sequential image calibration results</span><span class="c1">&nbsp;and unclick image </span><span class="c2">use</span><span class="c0">&nbsp;for images 200-400 and 1050-1300. The table 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: 611.50px; height: 365.22px;"><img alt="" src="images/image36.png" style="width: 767.76px; height: 430.17px; margin-left: -98.43px; margin-top: -34.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To calculate the average again, select the </span><span class="c2">a-b</span><span class="c1">&nbsp;column again by double clicking on the column header then go to </span><span class="c2">Columns/Rows/Compute average</span><span class="c1">. The </span><span class="c2">terminal</span><span class="c0">&nbsp;window will show:</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: 333.00px; height: 25.00px;"><img alt="" src="images/image15.png" style="width: 1419.88px; height: 807.30px; margin-left: -236.54px; margin-top: -637.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">&nbsp;The magnitude of error of +/- 0.045307 is much smaller and more desirable. Therefore we feel more confident saying that the average distance between set distance and calibrated distance is -0.167927</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c4 c9">Step 2: Integrating the Calibrated Data</span></p><p class="c3"><span class="c1">This next step involves integration of the data. Go to </span><span class="c2">Image Controls</span><span class="c1">&nbsp;for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">&nbsp;and then go to the </span><span class="c2">GSAS-II plot window</span><span class="c0">. Select the tab with the powder data rings. Notice shadowed regions from the beamstop and pin diode. In the final integration, we do not want to use these areas, so we will work on excluding these from the integration.</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: 519.00px; height: 483.00px;"><img alt="" src="images/image37.png" style="width: 519.00px; height: 483.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1">&nbsp;</span></p><p class="c3"><span class="c1">In the </span><span class="c2">GSAS-II data tree</span><span class="c1">, go to </span><span class="c2">Image Controls</span><span class="c1">&nbsp;for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">. We will be working in the </span><span class="c2">Integration coefficients </span><span class="c1">area. Click </span><span class="c2">Show integration limits?</span><span class="c0">. The plot should show the area that is to be integrated.</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: 467.50px; height: 434.82px;"><img alt="" src="images/image33.png" style="width: 886.69px; height: 498.76px; margin-left: -224.51px; margin-top: -17.05px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Zoom in </span><span class="c1">on the beamstop (bullseye of rings)</span><span class="c0">&nbsp;so we can make sure to exclude this from our final integration.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 436.50px; height: 404.66px;"><img alt="" src="images/image11.png" style="width: 827.89px; height: 465.69px; margin-left: -209.63px; margin-top: -17.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Change the</span><span class="c2">&nbsp;</span><span class="c2">inner 2-theta</span><span class="c1">&nbsp;to a smaller value of </span><span class="c2">0.8</span><span class="c0">&nbsp;to only exclude the small beamstop in the middle and not the surrounding data.</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: 466.50px; height: 435.40px;"><img alt="" src="images/image4.png" style="width: 882.11px; height: 496.19px; margin-left: -391.58px; margin-top: -29.69px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click the </span><span class="c2">home</span><span class="c1">&nbsp;button to see all the rings. Drag the mouse to the rights side of the image. As the mouse moves to the right, </span><span class="c2">2-theta</span><span class="c0">&nbsp;changes at the bottom of the screen. Note the outer 2-theta value when the mouse stops at the edge of the screen. </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: 600.00px; height: 560.00px;"><img alt="" src="images/image5.gif" style="width: 600.00px; height: 560.00px; 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="c1">Type this value (we used</span><span class="c1">&nbsp;</span><span class="c1">44.80</span><span class="c1">) into the </span><span class="c2">Outer 2-theta</span><span class="c1">&nbsp;box. Check the </span><span class="c2">Do full integration?</span><span class="c0">&nbsp;Box.</span></p><p class="c3"><span class="c0">The image controls screen should look like this:</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: 622.98px; height: 386.50px;"><img alt="" src="images/image27.png" style="width: 781.38px; height: 439.03px; margin-left: -108.31px; margin-top: -12.51px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits should look like:</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: 434.50px; height: 402.80px;"><img alt="" src="images/image3.png" style="width: 824.10px; height: 463.55px; margin-left: -217.91px; margin-top: -19.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see from the image, the inner and outer angles that we entered gave us a good integration area around the powder rings.</span></p><p class="c3"><span class="c1">At this point, we are going to cut out the beamstop, which yields poor intensity data. So, remove the </span><span class="c2">Do full integration?</span><span class="c0">&nbsp;Box.</span></p><p class="c3"><span class="c1">To exclude the beamstop we will adjust the start/end azimuth degrees. Make the </span><span class="c2">Start azimuth 5, </span><span class="c1">and </span><span class="c2">End azimuth </span><span class="c1">either</span><span class="c2">&nbsp;355 </span><span class="c1">or</span><span class="c2">&nbsp;-5.0</span><span class="c0">&nbsp;(it does not matter). The image controls window 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: 642.50px; height: 399.15px;"><img alt="" src="images/image12.png" style="width: 803.45px; height: 451.94px; margin-left: -109.44px; margin-top: -11.59px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits 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: 437.50px; height: 405.78px;"><img alt="" src="images/image14.png" style="width: 827.27px; height: 465.45px; margin-left: -218.75px; margin-top: -18.57px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the beamstop will now be excluded from our integration of the data.</span></p><p class="c3"><span class="c1">At this point it is a good idea to use </span><span class="c4 c2">Save project.</span></p>
    3232<p class="c5"></p>
    33 <p class="c3"><span class="c1">The value for </span><span class="c2">No. 2-theta </span><span class="c1">depends on the number of pixels in the detector. A 1:1 ratio of pixels to No. 2-theta is optimal. </span><span class="c2">2250 </span><span class="c1">for our </span><span class="c2">No. 2-theta </span><span class="c1">value works with our detector size and pixels so we will leave it as is. However, know that that value should be determined by the detector size and number of pixels. </span><span class="c2">Azimuth bins</span><span class="c1">&nbsp;finds powder patterns every so many degrees. We have it set at </span><span class="c2">1</span><span class="c0">. </span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Parms/Copy Selected </span><span class="c1">and select </span><span class="c2">fullintegrate = false (12), IOtth (15), LRazimuth (16), </span><span class="c1">and</span><span class="c4 c2">&nbsp;outAzimuths (18), . </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: 591.50px; height: 382.88px;"><img alt="" src="images/image10.png" style="width: 765.76px; height: 430.74px; margin-left: -92.04px; margin-top: -6.14px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c0">. </span></p><p class="c3"><span class="c1">A new window appears. Click </span><span class="c2">Set All</span><span class="c0">&nbsp;</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: 234.50px; height: 310.60px;"><img alt="" src="images/image17.png" style="width: 969.06px; height: 545.10px; margin-left: -402.22px; margin-top: -99.39px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then select </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Now go to the </span><span class="c2">Image Controls</span><span class="c1">&nbsp;of the last image, </span><span class="c2">Si_free_dc1300_1-00000.tif.</span><span class="c1">&nbsp;Check </span><span class="c2">Show integration limits?</span><span class="c1">&nbsp;and change the </span><span class="c2">auto scaler</span><span class="c1">&nbsp;to </span><span class="c2">95%.</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: 328.00px; height: 306.00px;"><img alt="" src="images/image16.png" style="width: 624.00px; height: 351.00px; margin-left: -166.00px; margin-top: -14.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the 2-theta max angle is off for this image. </span></p><p class="c3"><span class="c1">To fix this, go to the first image, </span><span class="c2">Si_free_dc200_1-00000.tif, </span><span class="c1">then </span><span class="c2">Image Controls,</span><span class="c1">&nbsp;and finally</span><span class="c2">&nbsp;Parms/Xfer angles. </span><span class="c1">Select </span><span class="c2">Xfer scaled 2-theta max</span><span class="c1">&nbsp;and </span><span class="c4 c2">Set All. </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: 220.50px; height: 385.44px;"><img alt="" src="images/image22.png" style="width: 1083.40px; height: 609.41px; margin-left: -470.52px; margin-top: -92.02px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click</span><span class="c2">&nbsp;OK. </span><span class="c0">This fixes the maximum angle on all of the images based off the scale we set to the first image. The minimum angle does not change. Here are the correct integration limits for the &ldquo;1300&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: 459.50px; height: 428.77px;"><img alt="" src="images/image31.png" style="width: 871.51px; height: 490.23px; margin-left: -230.45px; margin-top: -19.55px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c2">Save project</span><span class="c0">&nbsp;once again.</span></p><p class="c3"><span class="c1">We have changed the parameters so that GSAS-II does not integrate the beamstop. We will now use a mask to exclude the pin dial. Go back to the first image once again, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">, but this time go to the</span><span class="c2">&nbsp;Masks </span><span class="c1">section under the data tree</span><span class="c2">. </span><span class="c0">Zoom in on the pin dial in the GSAS-II plots window.</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: 458.00px; height: 424.00px;"><img alt="" src="images/image21.png" style="width: 868.67px; height: 488.65px; margin-left: -229.70px; margin-top: -20.88px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Operations/Create new/Polygon mask</span><span class="c0">. Go to the plot window. Pan the mouse around the pin dial to create a quadrilateral surrounding the light area (pin dial). Click on the plot for each corner of the mask. Lines will be drawn in to connect the corners. Create the mask so that it borders the pin dial.</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: 581.33px;"><img alt="" src="images/image24.gif" style="width: 624.00px; height: 581.33px; 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="c1">We have successfully masked the pin dial so it will not be included in our integration.</span></p><p class="c3"><span class="c2 c4">File/Save project.</span></p><p class="c3"><span class="c1">Unzoom on the 2D powder image (can be done by clicking the </span><span class="c2">home</span><span class="c0">&nbsp;button). </span></p><p class="c3"><span class="c1">We will now check to make sure there is no pin dial in any of the other images. Go to the 2nd image, </span><span class="c2">Si_free_dc250_1-00000.tif/Image Controls. </span><span class="c1">Change the </span><span class="c2">Autoscale</span><span class="c1">&nbsp;to </span><span class="c4 c2">95%. </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: 420.50px; height: 389.73px;"><img alt="" src="images/image28.png" style="width: 799.98px; height: 449.99px; margin-left: -210.25px; margin-top: -8.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">As we can see, the pin dial did not show up in this image or any of the following. Therefore, we do not need to do any more masking.</span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Integration/Integrate all.</span><span class="c1">&nbsp;In the pop-up window, select </span><span class="c4 c2">Set All.</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: 187.50px; height: 286.26px;"><img alt="" src="images/image34.png" style="width: 893.13px; height: 502.39px; margin-left: -385.02px; margin-top: -91.60px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">The data tree now shows PWDR files for each image.</span><span class="c2">&nbsp;</span><span class="c0">The new graphs show the powder patterns from each of the integrations and should look something like this:</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 459.50px; height: 382.29px;"><img alt="" src="images/image39.png" style="width: 777.04px; height: 437.09px; margin-left: -154.41px; margin-top: -6.23px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">In order to show continuous lines on the graph, press the + key on your keyboard.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 632.33px; height: 524.21px;"><img alt="" src="images/image13.png" style="width: 1069.31px; height: 599.35px; margin-left: -212.49px; margin-top: -8.54px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To overlap all the cells onto one graph, click on the </span><span class="c2">K/toggle multidata plot</span><span class="c1">&nbsp;or click </span><span class="c2">m</span><span class="c0">&nbsp;on your keyboard.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 472.00px; height: 390.00px;"><img alt="" src="images/image8.png" style="width: 796.02px; height: 446.73px; margin-left: -156.91px; margin-top: -6.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">To get a better view of the overlap of data, we zoomed in on the second peak from the left.</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: 386.24px;"><img alt="" src="images/image30.png" style="width: 785.06px; height: 441.60px; margin-left: -154.75px; margin-top: -6.29px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">s</span><span class="c0">&nbsp;to show a choice of color schemes. </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: 174.50px; height: 239.51px;"><img alt="" src="images/image41.png" style="width: 1067.53px; height: 600.49px; margin-left: -485.86px; margin-top: -160.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">We prefer </span><span class="c2">spectral</span><span class="c1">&nbsp;(lowercase option). Choose the desired scheme then press</span><span class="c2">&nbsp;OK</span><span class="c0">.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 536.50px; height: 444.36px;"><img alt="" src="images/image7.png" style="width: 904.80px; height: 508.05px; margin-left: -178.35px; margin-top: -7.24px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">We can tell this is a very accurate calibration because all of the peaks from each image line up very well.</span></p><p class="c3"><span class="c4 c2">File/Save project.</span></p><p class="c3"><span class="c0">We will now save this calibration data into a folder on your computer so it can be used at anytime as a calibrant for measuring an unknown substance. </span></p><p class="c3"><span class="c1">Make a </span><span class="c2">new folder</span><span class="c1">&nbsp;on your computer (wherever you want to store these calibration files) and call it </span><span class="c2">Image Controls</span><span class="c0">.</span></p><p class="c3"><span class="c1">In any image, go to </span><span class="c2">Image Controls</span><span class="c1">, then go to </span><span class="c2">Parms/Save Multiple Controls </span><span class="c1">and a popup window will appear. Click </span><span class="c2">Set All</span><span class="c0">.</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: 190.50px; height: 299.14px;"><img alt="" src="images/image32.png" style="width: 928.69px; height: 522.39px; margin-left: -403.32px; margin-top: -93.76px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then press </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">Click on the newly made folder (</span><span class="c2">Image Controls</span><span class="c1">) where you want to store these files and click </span><span class="c2">Select Folder</span><span class="c0">.</span></p><p class="c3"><span class="c0">This folder will now contain all the image controls and parameters to be used for future measurements.</span></p>
     33<p class="c3"><span class="c1">The value for </span><span class="c2">No. 2-theta </span><span class="c1">depends on the number of pixels in the detector. A 1:1 ratio of pixels to No. 2-theta is optimal. </span><span class="c2">2250 </span><span class="c1">for our </span><span class="c2">No. 2-theta </span><span class="c1">value works with our detector size and pixels so we will leave it as is. However, know that that value should be determined by the detector size and number of pixels. </span><span class="c2">Azimuth bins</span><span class="c1">&nbsp;finds powder patterns every so many degrees. We have it set at </span><span class="c2">1</span><span class="c0">. </span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Parms/Copy Selected </span><span class="c1">and select </span><span class="c2">fullintegrate = false (12), IOtth (15), LRazimuth (16), </span><span class="c1">and</span><span class="c4 c2">&nbsp;outAzimuths (18), . </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: 591.50px; height: 382.88px;"><img alt="" src="images/image10.png" style="width: 765.76px; height: 430.74px; margin-left: -92.04px; margin-top: -6.14px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c0">. </span></p><p class="c3"><span class="c1">A new window appears. Click </span><span class="c2">Set All</span><span class="c0">&nbsp;</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: 234.50px; height: 310.60px;"><img alt="" src="images/image17.png" style="width: 969.06px; height: 545.10px; margin-left: -402.22px; margin-top: -99.39px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then select </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Now go to the </span><span class="c2">Image Controls</span><span class="c1">&nbsp;of the last image, </span><span class="c2">Si_free_dc1300_1-00000.tif.</span><span class="c1">&nbsp;Check </span><span class="c2">Show integration limits?</span><span class="c1">&nbsp;and change the </span><span class="c2">auto scaler</span><span class="c1">&nbsp;to </span><span class="c2">95%.</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: 328.00px; height: 306.00px;"><img alt="" src="images/image16.png" style="width: 624.00px; height: 351.00px; margin-left: -166.00px; margin-top: -14.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the 2-theta max angle is off for this image. </span></p><p class="c3"><span class="c1">To fix this, go to the first image, </span><span class="c2">Si_free_dc200_1-00000.tif, </span><span class="c1">then </span><span class="c2">Image Controls,</span><span class="c1">&nbsp;and finally</span><span class="c2">&nbsp;Parms/Xfer angles. </span><span class="c1">Select </span><span class="c2">Xfer scaled 2-theta max</span><span class="c1">&nbsp;and </span><span class="c4 c2">Set All. </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: 220.50px; height: 385.44px;"><img alt="" src="images/image22.png" style="width: 1083.40px; height: 609.41px; margin-left: -470.52px; margin-top: -92.02px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click</span><span class="c2">&nbsp;OK. </span><span class="c0">This fixes the maximum angle on all of the images based off the scale we set to the first image. The minimum angle does not change. Here are the correct integration limits for the &ldquo;1300&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: 459.50px; height: 428.77px;"><img alt="" src="images/image31.png" style="width: 871.51px; height: 490.23px; margin-left: -230.45px; margin-top: -19.55px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c2">Save project</span><span class="c0">&nbsp;once again.</span></p><p class="c3"><span class="c1">We have changed the parameters so that GSAS-II does not integrate the beamstop. We will now use a mask to exclude the pin diode. Go back to the first image once again, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">, but this time go to the</span><span class="c2">&nbsp;Masks </span><span class="c1">section under the data tree</span><span class="c2">. </span><span class="c0">Zoom in on the pin diode in the GSAS-II plots window.</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: 458.00px; height: 424.00px;"><img alt="" src="images/image21.png" style="width: 868.67px; height: 488.65px; margin-left: -229.70px; margin-top: -20.88px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Operations/Create new/Polygon mask</span><span class="c0">. Go to the plot window. Pan the mouse around the pin diode to create a quadrilateral surrounding the light area (pin diode). Click on the plot for each corner of the mask. Lines will be drawn in to connect the corners. Create the mask so that it borders the pin diode.</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: 581.33px;"><img alt="" src="images/image24.gif" style="width: 624.00px; height: 581.33px; 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="c1">We have successfully masked the pin diode so it will not be included in our integration.</span></p><p class="c3"><span class="c2 c4">File/Save project.</span></p><p class="c3"><span class="c1">Unzoom on the 2D powder image (can be done by clicking the </span><span class="c2">home</span><span class="c0">&nbsp;button). </span></p><p class="c3"><span class="c1">We will now check to make sure there is no pin diode in any of the other images. Go to the 2nd image, </span><span class="c2">Si_free_dc250_1-00000.tif/Image Controls. </span><span class="c1">Change the </span><span class="c2">Autoscale</span><span class="c1">&nbsp;to </span><span class="c4 c2">95%. </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: 420.50px; height: 389.73px;"><img alt="" src="images/image28.png" style="width: 799.98px; height: 449.99px; margin-left: -210.25px; margin-top: -8.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">As we can see, the pin diode did not show up in this image or any of the following. Therefore, we do not need to do any more masking.</span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Integration/Integrate all.</span><span class="c1">&nbsp;In the pop-up window, select </span><span class="c4 c2">Set All.</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: 187.50px; height: 286.26px;"><img alt="" src="images/image34.png" style="width: 893.13px; height: 502.39px; margin-left: -385.02px; margin-top: -91.60px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">The data tree now shows PWDR files for each image.</span><span class="c2">&nbsp;</span><span class="c0">The new graphs show the powder patterns from each of the integrations and should look something like this:</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 459.50px; height: 382.29px;"><img alt="" src="images/image39.png" style="width: 777.04px; height: 437.09px; margin-left: -154.41px; margin-top: -6.23px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">In order to show continuous lines on the graph, press the + key on your keyboard.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 632.33px; height: 524.21px;"><img alt="" src="images/image13.png" style="width: 1069.31px; height: 599.35px; margin-left: -212.49px; margin-top: -8.54px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To overlap all the cells onto one graph, click on the </span><span class="c2">K/toggle multidata plot</span><span class="c1">&nbsp;or click </span><span class="c2">m</span><span class="c0">&nbsp;on your keyboard.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 472.00px; height: 390.00px;"><img alt="" src="images/image8.png" style="width: 796.02px; height: 446.73px; margin-left: -156.91px; margin-top: -6.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">To get a better view of the overlap of data, we zoomed in on the second peak from the left.</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: 386.24px;"><img alt="" src="images/image30.png" style="width: 785.06px; height: 441.60px; margin-left: -154.75px; margin-top: -6.29px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">s</span><span class="c0">&nbsp;to show a choice of color schemes. </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: 174.50px; height: 239.51px;"><img alt="" src="images/image41.png" style="width: 1067.53px; height: 600.49px; margin-left: -485.86px; margin-top: -160.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">We prefer </span><span class="c2">spectral</span><span class="c1">&nbsp;(lowercase option). Choose the desired scheme then press</span><span class="c2">&nbsp;OK</span><span class="c0">.</span></p><p class="c3"><span class="c1">&nbsp;</span><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: 536.50px; height: 444.36px;"><img alt="" src="images/image7.png" style="width: 904.80px; height: 508.05px; margin-left: -178.35px; margin-top: -7.24px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">We can tell this is a very accurate calibration because all of the peaks from each image line up very well.</span></p><p class="c3"><span class="c4 c2">File/Save project.</span></p><p class="c3"><span class="c0">We will now save this calibration data into a folder on your computer so it can be used at anytime as a calibrant for measuring an unknown substance. </span></p><p class="c3"><span class="c1">Make a </span><span class="c2">new folder</span><span class="c1">&nbsp;on your computer (wherever you want to store these calibration files) and call it </span><span class="c2">Image Controls</span><span class="c0">.</span></p><p class="c3"><span class="c1">In any image, go to </span><span class="c2">Image Controls</span><span class="c1">, then go to </span><span class="c2">Parms/Save Multiple Controls </span><span class="c1">and a popup window will appear. Click </span><span class="c2">Set All</span><span class="c0">.</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: 190.50px; height: 299.14px;"><img alt="" src="images/image32.png" style="width: 928.69px; height: 522.39px; margin-left: -403.32px; margin-top: -93.76px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then press </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">Click on the newly made folder (</span><span class="c2">Image Controls</span><span class="c1">) where you want to store these files and click </span><span class="c2">Select Folder</span><span class="c0">.</span></p><p class="c3"><span class="c0">This folder will now contain all the image controls and parameters to be used for future measurements.</span></p>
    3434
    3535<p class="c5"></p>
  • Tutorials/SeqRefine/SequentialTutorial.htm

    r3918 r4045  
    22182218<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    22192219
    2220 <p class=MsoListParagraphCxSpMiddle>Note that the files must be read in in the
    2221 sequence they will be processed. This is not an issue here, but for some
    2222 sequential refinements, one may need to use multiple Import operations to read
    2223 the files in the desired order or rename files so they are listed in the
    2224 correct order in the file browser. </p>
     2220<p class=MsoListParagraphCxSpMiddle>Note that the files will be
     2221processed in the order they appear in the tree (or the reverse of that
     2222order, as set in Controls). It will be most convenient if the files
     2223are imported in a logical sequence, which could require multiple
     2224Import operations to read the files in the desired order or to
     2225rename files prior to reading so they are listed in the
     2226correct order in the file browser. If files are not read in the
     2227intended order, it will be necessary to
     2228manually change the positions of the tree items (by dragging them with
     2229the right mouse button pressed).
     2230This is not an issue in this example, since the files are listing in a
     2231zip file in the order they need to be read, but may be of concern
     2232for other cases.
     2233</p>
    22252234
    22262235<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
  • Tutorials/StartingGSASII/Starting GSAS.htm

    r3552 r4045  
    12011201<p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'><span
    12021202style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1203 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>python</span></b></span><b
     1203mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin' translate="no">Python</span></b></span><b
    12041204style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12051205mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     
    12101210mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></b></p>
    12111211
    1212 <p class=MsoNormal>This will work if the default python is as described in the
     1212<p class=MsoNormal>This will work if the default <span translate="no">Python</span> is as described in the
    12131213GSAS-II Wiki pages you found when downloading GSAS-II, otherwise you may have
    1214 to enter the correct path for that version of python.</p>
     1214to enter the correct path for that version of <span translate="no">Python</span>.</p>
    12151215
    12161216<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12301230<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12311231
    1232 <p class=MsoNormal>When GSAS-II starts, you should see three windows, two of which are almost empty.
    1233 The topmost one is a vertically split window; we will refer to this as the <b
    1234 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1235 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1236 minor-latin'>Data Window</span></b>. The left side will contain a tree-like
     1232When GSAS-II starts, you should see three windows, two of which are almost empty.
     1233The topmost one is a vertically split window; we will refer to this as
     1234the <b><span translate="no">Data</span> <span translate="no">Window</span></b>. The left side will contain a tree-like
    12371235outline of your GSAS-II project as you add data, phases, etc. The right side
    12381236will contain a display of data depending on your tree item selection; you can
     
    12411239style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12421240mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1243 minor-latin'>GSASII Plots</span></b>; this will contain tabbed graphical
     1241minor-latin' translate="no">GSASII Plots</span></b>; this will contain tabbed graphical
    12441242displays, when appropriate, corresponding to the selected tree item. This may
    12451243be a crystal structure, powder pattern plot, etc. The tabs allow you to view
     
    12571255of the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12581256mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1259 minor-latin'>Data Window</span></b>; on a Mac this menu will appear in the
     1257minor-latin' translate="no">Data Window</span></b>; on a Mac this menu will appear in the
    12601258system menu bar location (usually at the screen top).
    12611259The items in the menu bar are separated by a vertical
     
    12651263<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12661264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1267 minor-latin'>Data Window</span></b>. On my Windows machine the screen looked
     1265minor-latin' translate="no">Data Window</span></b>. On my Windows machine the screen looked
    12681266like:</p>
    12691267
     
    13011299(Exception: image files are not stored in the project; to save space only the
    13021300file name is saved.) The console window displays a banner and some information
    1303 about the version of python and the packages used by GSAS-II. This console
     1301about the version of <span translate="no">Python</span> and the packages used by GSAS-II. This console
    13041302window will display important information as data processing by GSAS-II
    13051303proceeds. You may wish to cut-and-paste parts of this window to another place
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