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| 2 | <head> |
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| 3 | <title>EXPGUI Alumina Tutorial, part #2</title> |
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| 11 | <BODY BGCOLOR="#FFFFFF" |
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| 13 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
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| 14 | |
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| 15 | <? |
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| 16 | include("/var/www/include/navigation.inc"); |
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| 17 | include("/var/www/include/utility.inc"); |
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| 18 | ?> |
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| 19 | <blockquote> |
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| 20 | |
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| 21 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 22 | <TR><TH><A Href="index.html">Intro</A> |
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| 23 | </TH><TH><A Href="alumina3.html">Next page</A> |
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| 24 | </TH><TH><A Href="alumina1.html">Previous page</A> |
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| 25 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 26 | |
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| 27 | |
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| 28 | <CENTER> |
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| 29 | <H1><HR noshade width="75%" size="2" align="center"> |
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| 30 | GSAS/EXPGUI Alumina tutorial (part 2)<BR> |
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| 31 | Adding a phase |
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| 32 | <HR noshade width="75%" size="2" align="center"> |
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| 33 | </H1> |
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| 34 | </CENTER> |
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| 35 | <I>When a GSAS experiment file is first created, a fair amount of information |
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| 36 | must be supplied before the refinement of parameters can be started. At a |
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| 37 | minimum, a crystallographic phase must be defined, a set of diffraction |
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| 38 | data must be loaded and a starting values for experimental parameters |
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| 39 | must be defined. Fortunately, this can be a fairly simple operation |
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| 40 | with GSAS and EXPGUI. |
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| 41 | </I> |
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| 42 | <P> |
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| 43 | This page shows how a crystallographic phase is |
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| 44 | specified in EXPGUI. For a mixture, this step would be repeated for |
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| 45 | each crystallographic phase. If an impurity is identified in a later |
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| 46 | stage of the refinement, this step can be run at that point to define |
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| 47 | this additional crystallographic phase. GSAS allows up to nine crystallographic |
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| 48 | phases to be included in a model. |
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| 49 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 50 | |
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| 51 | To enter information about a crystallographic phase, modify |
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| 52 | crystallographic parameters, or select crystallographic parameters |
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| 53 | to be optimized the "Phase" panel must be selected by clicking on the |
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| 54 | "Phase" tab in the upper left of the EXPGUI window. The window then appears |
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| 55 | as shown just below this text. |
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| 56 | <P><img alt="tutorial screen dump" src="2a.gif" align=RIGHT> |
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| 57 | <BR clear=all><P> |
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| 58 | <blockquote><I> |
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| 59 | |
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| 60 | It should be noted that the Phase panel will have a slightly different |
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| 61 | appearance after one or more phases have been entered, |
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| 62 | (<a href="#withphase">see below</a>). |
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| 63 | </I></blockquote> |
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| 64 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 65 | |
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| 66 | The next step is to press the "Add Phase" button in the upper left. |
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| 67 | The "Add New Phase" window, shown immediately below, is then generated. |
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| 68 | <P><img alt="tutorial screen dump" src="2b.gif" align=RIGHT> |
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| 69 | <BR clear=all> |
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| 70 | <img alt="tutorial screen dump" src="2c.gif" align=RIGHT> |
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| 71 | Information about the phase can be added directly into the boxes, |
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| 72 | or phase information can be read from a file. For this exercise, |
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| 73 | we will read unit cell parameters, the space group and atom parameters |
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| 74 | from a CIF file. This means that we need to select the "Crystallographic |
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| 75 | Information File (CIF)" |
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| 76 | format from |
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| 77 | the options by pressing the file format button |
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| 78 | in the lower right-hand corner. |
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| 79 | <BR clear=all> |
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| 80 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 81 | |
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| 82 | When the "Import Phase from" button is pressed, an "open file" |
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| 83 | window is created (this window has a slightly different appearance, |
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| 84 | but the same function in Windows). On this window, the file to be read is |
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| 85 | selected, and then the "Read" button is pressed. |
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| 86 | <P><img alt="tutorial screen dump" src="2d.gif" align=RIGHT> |
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| 87 | <BR clear=all> |
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| 88 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 89 | |
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| 90 | The CIF is then read and the unit cell information is included |
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| 91 | in the appropriate entry boxes, as shown below. |
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| 92 | If this input is acceptable, press "Continue". |
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| 93 | <P><img alt="tutorial screen dump" src="2e.gif" align=RIGHT> |
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| 94 | <BR clear=all> |
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| 95 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 96 | |
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| 97 | One of the places where errors occur in the preparation of GSAS input |
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| 98 | is in the entering of space group symbols. For this reason, after the |
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| 99 | "Continue" button is pressed, a window such as the one below, is |
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| 100 | created to help you confirm that the correct space group has been entered. |
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| 101 | <P><img alt="tutorial screen dump" src="2f.gif" align=RIGHT> |
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| 102 | <BR clear=all> |
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| 103 | <blockquote><I> |
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| 104 | <P>It is recommended that you read through this information to check that |
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| 105 | this is correct. As an example of a possible error, if one entered the |
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| 106 | corundum example in the rhombohedral setting, |
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| 107 | rather than the hexagonal setting, |
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| 108 | then the space group should be entered as "R -3 c R" (where the final R |
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| 109 | indicates the rhombohedral setting). The listing of lattice centering vectors |
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| 110 | is only appropriate for the hexagonal (centered) cell. |
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| 111 | </I></blockquote> |
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| 112 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 113 | |
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| 114 | Since the symmetry information is correct in this example, press the "Continue" |
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| 115 | button on the "check symmetry" window. At this point, since atom |
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| 116 | coordinates were read from the CIF file, the "add new atoms" window is |
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| 117 | opened and the atom coordinates are entered into the appropriate boxes, |
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| 118 | as seen below. Press the "Add Atoms" button at the lower left to continue. |
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| 119 | <P><img alt="tutorial screen dump" src="2g.gif" align=RIGHT> |
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| 120 | <BR clear=all> |
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| 121 | <blockquote><I> |
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| 122 | Note that if atoms were not being read in from a file, |
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| 123 | it would now be necessary |
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| 124 | to press the "Add New Atoms" button to input atoms to the phase. |
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| 125 | In this case, there would be no atoms entered into the window. |
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| 126 | </I></blockquote> |
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| 127 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 128 | After pressing the "Add Atoms" button, the two atoms are added to the |
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| 129 | experiment and the phase panel appears, as below. |
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| 130 | <a name="withphase"> |
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| 131 | <P><img alt="tutorial screen dump" src="2h.gif" align=RIGHT> |
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| 132 | </a> |
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| 133 | <BR clear=all> |
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| 134 | <HR> |
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| 135 | Previous: <A HREF="alumina1.html"> |
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| 136 | Creating an Experiment File</A> |
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| 137 | <BR> |
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| 138 | Next step: <A HREF="alumina3.html"> |
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| 139 | Add data file to the Experiment</A> |
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| 140 | |
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| 141 | <HR> |
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| 142 | </blockquote> |
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| 143 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 144 | <font size=-1><? lastmod(); ?> |
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| 145 | <BR>$Revision: 682 $ $Date: 2009-12-04 23:10:15 +0000 (Fri, 04 Dec 2009) $</font> |
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| 146 | </body> |
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| 147 | </html> |
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