Changeset 720


Ignore:
Timestamp:
Aug 17, 2012 4:55:11 PM (10 years ago)
Author:
vondreele
Message:

fix to map peak plotting

Location:
trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIplot.py

    r713 r720  
    27812781
    27822782    def RenderMapPeak(x,y,z,color):
    2783         vecs = np.array([[[-.01,0,0],[.01,0,0]],[[0,-.01,0],[0,.01,0]],[[0,0,-.01],[0,0,.01]]])
     2783        vecs = np.array([[[-.1/cell[0],0,0],[.1/cell[0],0,0]],
     2784            [[0,-.1/cell[1],0],[0,.1/cell[1],0]],
     2785            [[0,0,-.1/cell[2]],[0,0,.1/cell[2]]]])
    27842786        xyz = np.array([x,y,z])
    27852787        glEnable(GL_COLOR_MATERIAL)
  • trunk/help/Laboratory X.htm

    r718 r720  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>16</o:Revision>
    26   <o:TotalTime>1446</o:TotalTime>
     25  <o:Revision>18</o:Revision>
     26  <o:TotalTime>1510</o:TotalTime>
    2727  <o:Created>2012-05-08T16:04:00Z</o:Created>
    28   <o:LastSaved>2012-08-16T17:41:00Z</o:LastSaved>
     28  <o:LastSaved>2012-08-16T19:34:00Z</o:LastSaved>
    2929  <o:Pages>9</o:Pages>
    30   <o:Words>3132</o:Words>
    31   <o:Characters>17855</o:Characters>
     30  <o:Words>3133</o:Words>
     31  <o:Characters>17863</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>148</o:Lines>
    3434  <o:Paragraphs>41</o:Paragraphs>
    35   <o:CharactersWithSpaces>20946</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>20955</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    980980<p class=MsoNormal>In this tutorial you will refine the structure of <span
    981981class=SpellE>fluoroapatite</span>, <span class=GramE>Ca<sub>5</sub>F(</span>PO<sub>4</sub>)<sub>3</sub>,
    982 using constant wavelength laboratory X-ray powder diffraction data. At the completion
    983 of the refinement you will then prepare a drawing of the <span class=SpellE>fluoroapatite</span>
    984 structure. The structure is hexagonal with four different kinds of atoms spread
    985 over seven different sites. The data was taken on a conventional Bragg-Brentano
    986 powder diffractometer using <span class=SpellE>CuK</span><sub><span
    987 style='font-family:Symbol'>a</span></sub> radiation.</p>
     982using constant wavelength laboratory X-ray powder diffraction data. At the
     983completion of the refinement you will then prepare a drawing of the <span
     984class=SpellE>fluoroapatite</span> structure. The structure is hexagonal with
     985four different kinds of atoms spread over seven different sites. The data was
     986taken on a conventional Bragg-Brentano powder diffractometer using <span
     987class=SpellE>CuK</span><sub><span style='font-family:Symbol'>a</span></sub>
     988radiation.</p>
    988989
    989990<p class=MsoNormal>If you have not done so already, <a
     
    13381339class=SpellE>pulldown</span> menu. Select <b style='mso-bidi-font-weight:normal'><span
    13391340style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1340 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>from GSAS
    1341 .EXP file. </span></b>The file selection dialog will still be set to the
    1342 directory the data was found; click on <b style='mso-bidi-font-weight:normal'><span
     1341mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>from GSAS .EXP
     1342file. </span></b>The file selection dialog will still be set to the directory
     1343the data was found; click on <b style='mso-bidi-font-weight:normal'><span
    13431344style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    13441345mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FAP.EXP</span></b>
     
    13741375src="Laboratory%20X_files/image002.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
    13751376
    1376 <p class=MsoNormal>You can see that the number of each kind of atom gives 2
    1377 formula units per cell. To add the powder data to this phase click on the Data
    1378 tab and then select <b style='mso-bidi-font-weight:normal'><span
    1379 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1380 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Edit/Add
    1381 powder histograms</span></b> from the menu. A <b style='mso-bidi-font-weight:
    1382 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1383 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Use
    1384 data</span></b> window will appear with only one choice <b style='mso-bidi-font-weight:
    1385 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1386 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>PWDR
    1387 FAP.XRA: BANK 1</span></b>. Select it and press <b style='mso-bidi-font-weight:
    1388 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1389 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
     1377<p class=MsoNormal>You can see that the number of each kind of atom gives 2 formula
     1378units per cell. To add the powder data to this phase click on the Data tab and
     1379then select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1380"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1381minor-latin;mso-bidi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>
     1382from the menu. A <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1383"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1384minor-latin;mso-bidi-theme-font:minor-latin'>Use data</span></b> window will
     1385appear with only one choice <b style='mso-bidi-font-weight:normal'><span
     1386style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1387mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>PWDR FAP.XRA:
     1388BANK 1</span></b>. Select it and press <b style='mso-bidi-font-weight:normal'><span
     1389style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1390mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
    13901391The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    13911392mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     
    14021403src="Laboratory%20X_files/image003.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
    14031404
    1404 <p class=MsoNormal>We will return to this window later when we consider the effect
    1405 of crystallite size and mustrain broadening.</p>
     1405<p class=MsoNormal>We will return to this window later when we consider the
     1406effect of crystallite size and mustrain broadening.</p>
    14061407
    14071408<h2>Step 4: Adjust background parameterization</h2>
     
    17261727src="Laboratory%20X_files/image015.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
    17271728
    1728 <p class=MsoNormal>The refinement is now essentially complete. The console
    1729 displays the result of the last cycle of refinement with values and <span
    1730 class=SpellE>esds</span> for all the parameters</p>
     1729<p class=MsoNormal>The refinement is now essentially complete. The file <span
     1730class=SpellE>fap.lst</span> has the result of the last cycle of refinement with
     1731values and <span class=SpellE>esds</span> for all the parameters</p>
    17311732
    17321733<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>Refinement
     
    21562157Atoms</span></b> menu. A color selection dialog box will appear (NB: this
    21572158dialog is operating system dependent – we will assume you are using a Windows7
    2158 machine). The dialog box looks like</p>
     2159machine). The dialog box looks like (I pressed <b style='mso-bidi-font-weight:
     2160normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2161minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Define
     2162Custom Colors</span></b>)</p>
    21592163
    21602164<p class=MsoNormal style='margin-left:.25in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21662170
    21672171<p class=MsoNormal style='margin-left:.25in'>The steps for changing a color is
    2168 to a) choose your color by either finding it in <b style='mso-bidi-font-weight:
     2172to either a) choose your color by finding it in <b style='mso-bidi-font-weight:
    21692173normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    21702174minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Basic
    2171 colors</span></b> or by moving the cross around on the spectrum display b)
    2172 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2173 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2174 minor-latin'>Add to Custom Colors</span></b>; that puts it in the <b
    2175 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2176 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2177 minor-latin'>Custom colors</span></b> table c) Select that custom color and
    2178 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2179 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    2180 minor-latin'>OK</span></b>. The drawing will now show that color for the atoms
    2181 (you may have to select the plot for that to happen) and the color will appear
    2182 in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2175colors</span></b> and then press <b style='mso-bidi-font-weight:normal'><span
     2176style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2177mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
     2178or b) press <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2179"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2180minor-latin;mso-bidi-theme-font:minor-latin'>Define Custom Colors</span></b>, move
     2181the cross around on the spectrum display, set the vertical slider for the
     2182luminosity (<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2183style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2184mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>ColorSolid</span></b></span>
     2185will show the result), and then press <b style='mso-bidi-font-weight:normal'><span
     2186style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2187mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
     2188The drawing will now show that color for the atoms and the color will appear in
     2189the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    21832190mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    21842191minor-latin'>Draw Atoms</span></b> table. If you don’t like your colors select <b
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