Changeset 1470
- Timestamp:
- Aug 19, 2014 2:31:12 PM (9 years ago)
- Location:
- trunk
- Files:
-
- 6 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/GSASIIimgGUI.py
r1419 r1470 290 290 keys = ['type','wavelength','calibrant','distance','center', 291 291 'tilt','rotation','azmthOff','fullIntegrate','LRazimuth', 292 'IOtth','out Azimuths','invert_x','invert_y','DetDepth',292 'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth', 293 293 'calibskip','pixLimit','cutoff','calibdmin','chisq', 294 294 'binType','SampleShape','PolaVal','SampleAbs','dark image','background image'] … … 303 303 def OnLoadControls(event): 304 304 cntlList = ['wavelength','distance','tilt','invert_x','invert_y','type', 305 'fullIntegrate','out Azimuths','LRazimuth','IOtth','azmthOff','DetDepth',305 'fullIntegrate','outChannels','outAzimuths','LRazimuth','IOtth','azmthOff','DetDepth', 306 306 'calibskip','pixLimit','cutoff','calibdmin','chisq', 307 307 'PolaVal','SampleAbs','dark image','background image'] -
trunk/GSASIIphsGUI.py
r1453 r1470 4517 4517 # UpdateMCSA executable code starts here 4518 4518 MCSA.DestroyChildren() 4519 if not data['Drawing']: #if new drawing - no drawing data! 4520 SetupDrawingData() 4519 4521 general = data['General'] 4520 4522 Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) -
trunk/GSASIIplot.py
r1466 r1470 3827 3827 atomData = data['Atoms'] 3828 3828 mapPeaks = [] 3829 drawingData = data['Drawing'] 3829 drawingData = data['Drawing'] 3830 if not drawingData: 3831 return #nothing setup, nothing to draw 3830 3832 if 'Map Peaks' in data: 3831 3833 mapPeaks = np.array(data['Map Peaks']) -
trunk/help/Charge Flipping in GSAS.htm
r1435 r1470 23 23 <o:Author>vondreele</o:Author> 24 24 <o:LastAuthor>Von Dreele</o:LastAuthor> 25 <o:Revision> 4</o:Revision>26 <o:TotalTime>1 4</o:TotalTime>25 <o:Revision>5</o:Revision> 26 <o:TotalTime>15</o:TotalTime> 27 27 <o:Created>2014-07-21T14:56:00Z</o:Created> 28 <o:LastSaved>2014-0 7-23T17:41:00Z</o:LastSaved>28 <o:LastSaved>2014-08-19T14:01:00Z</o:LastSaved> 29 29 <o:Pages>10</o:Pages> 30 <o:Words>223 9</o:Words>31 <o:Characters>127 63</o:Characters>30 <o:Words>2235</o:Words> 31 <o:Characters>12746</o:Characters> 32 32 <o:Company>Argonne National Laboratory</o:Company> 33 33 <o:Lines>106</o:Lines> 34 34 <o:Paragraphs>29</o:Paragraphs> 35 <o:CharactersWithSpaces>149 73</o:CharactersWithSpaces>35 <o:CharactersWithSpaces>14952</o:CharactersWithSpaces> 36 36 <o:Version>14.00</o:Version> 37 37 </o:DocumentProperties> … … 1233 1233 <div class=WordSection1> 1234 1234 1235 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in 1236 GSAS-II - <span class=SpellE>jadarite</span><o:p></o:p></span></h1> 1235 <h1><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA in GSAS-II<o:p></o:p></span></h1> 1237 1236 1238 1237 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1> … … 1240 1239 <p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure 1241 1240 of <span class=SpellE>jadarite</span> (aka kryptonite) from powder 1242 diffraction data via charge flipping. This structure was originally solved by 1243 PamWhitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>1241 diffraction data via charge flipping. This structure was originally solved by Pam 1242 Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p> 1244 1243 1245 1244 <p class=MsoNormal>If you have not done so already, <a … … 1345 1344 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image001.png" o:title=""/> 1346 1345 </v:shape><![endif]--><![if !vml]><img border=0 width=723 height=475 1347 src="Charge%20Flipping%20in%20GSAS_files/image0 02.gif" v:shapes="_x0000_i1047"><![endif]></span></p>1346 src="Charge%20Flipping%20in%20GSAS_files/image047.gif" v:shapes="_x0000_i1047"><![endif]></span></p> 1348 1347 1349 1348 <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span … … 1356 1355 1357 1356 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1358 id=" Picture_x0020_5" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:259.5pt;1359 height:252pt;visibility:visible;mso-wrap-style:square'>1357 id="_x0000_i1046" type="#_x0000_t75" style='width:259.5pt;height:252pt; 1358 visibility:visible;mso-wrap-style:square'> 1360 1359 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image003.png" o:title=""/> 1361 1360 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336 1362 src="Charge%20Flipping%20in%20GSAS_files/image0 04.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>1361 src="Charge%20Flipping%20in%20GSAS_files/image048.gif" v:shapes="_x0000_i1046"><![endif]></span></p> 1363 1362 1364 1363 <p class=MsoNormal>Select either choice; the desired data set will be added to … … 1373 1372 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image005.png" o:title=""/> 1374 1373 </v:shape><![endif]--><![if !vml]><img border=0 width=479 height=535 1375 src="Charge%20Flipping%20in%20GSAS_files/image0 06.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>1374 src="Charge%20Flipping%20in%20GSAS_files/image049.gif" v:shapes="Picture_x0020_25"><![endif]></span></p> 1376 1375 1377 1376 <p class=MsoNormal>Ive stretched the window slightly to see the entire … … 1407 1406 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image007.png" o:title=""/> 1408 1407 </v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300 1409 src="Charge%20Flipping%20in%20GSAS_files/image0 08.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>1408 src="Charge%20Flipping%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_4"><![endif]></span></p> 1410 1409 1411 1410 <p class=MsoNormal>This completes the Pawley refinement setup; be careful that … … 1424 1423 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1425 1424 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1426 To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted the1427 width and height).</p>1425 To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted 1426 the width and height).</p> 1428 1427 1429 1428 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1430 id=" _x0000_i1043" type="#_x0000_t75" style='width:525pt;height:450pt;1431 visibility:visible;mso-wrap-style:square'>1429 id="Picture_x0020_5" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt; 1430 height:450pt;visibility:visible;mso-wrap-style:square'> 1432 1431 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/> 1433 1432 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1434 src="Charge%20Flipping%20in%20GSAS_files/image0 10.gif" v:shapes="_x0000_i1043"><![endif]></span></p>1433 src="Charge%20Flipping%20in%20GSAS_files/image051.gif" v:shapes="Picture_x0020_5"><![endif]></span></p> 1435 1434 1436 1435 <p class=MsoNormal>It is evident from examining the plot that improvement can … … 1470 1469 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image011.png" o:title=""/> 1471 1470 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1472 src="Charge%20Flipping%20in%20GSAS_files/image0 12.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>1471 src="Charge%20Flipping%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_8"><![endif]></span></p> 1473 1472 1474 1473 <p class=MsoNormal>This may be good enough to try charge flipping.</p> … … 1552 1551 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/> 1553 1552 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300 1554 src="Charge%20Flipping%20in%20GSAS_files/image0 14.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>1553 src="Charge%20Flipping%20in%20GSAS_files/image053.gif" v:shapes="Picture_x0020_7"><![endif]></span></p> 1555 1554 1556 1555 <p class=MsoNormal><o:p> </o:p></p> … … 1562 1561 croptop="2431f" cropbottom="25578f" cropleft="38673f" cropright="11746f"/> 1563 1562 </v:shape><![endif]--><![if !vml]><img border=0 width=451 height=386 1564 src="Charge%20Flipping%20in%20GSAS_files/image0 16.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>1563 src="Charge%20Flipping%20in%20GSAS_files/image054.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p> 1565 1564 1566 1565 <p class=MsoNormal>The result looks very promising! Charge flipping operates … … 1615 1614 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1616 1615 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b></span> 1617 column heading. This will sort the peaks in increasing distance from the origin.</p> 1616 column heading. This will sort the peaks in increasing distance from the 1617 origin.</p> 1618 1618 1619 1619 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1638 1638 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image017.png" o:title=""/> 1639 1639 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=506 1640 src="Charge%20Flipping%20in%20GSAS_files/image0 18.gif" v:shapes="Picture_x0020_9"><![endif]></span></p>1640 src="Charge%20Flipping%20in%20GSAS_files/image055.gif" v:shapes="Picture_x0020_9"><![endif]></span></p> 1641 1641 1642 1642 <p class=MsoNormal>These are now ready to turn into atoms. Do <b 1643 1643 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1644 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks/Move1645 peaks </span></b>. The drawing will show white balls for each of the selected1646 positions and the <b style='mso-bidi-font-weight:normal'><span1644 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map 1645 peaks/Move peaks</span></b>. The drawing will show white balls for each of the 1646 selected positions and the <b style='mso-bidi-font-weight:normal'><span 1647 1647 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1648 1648 mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 13 new H … … 1656 1656 croptop="3527f" cropbottom="24386f" cropleft="38043f" cropright="12462f"/> 1657 1657 </v:shape><![endif]--><![if !vml]><img border=0 width=451 height=389 1658 src="Charge%20Flipping%20in%20GSAS_files/image0 20.jpg" v:shapes="Picture_x0020_10"><![endif]></span></p>1658 src="Charge%20Flipping%20in%20GSAS_files/image056.jpg" v:shapes="Picture_x0020_10"><![endif]></span></p> 1659 1659 1660 1660 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1663 1663 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image021.png" o:title=""/> 1664 1664 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=390 1665 src="Charge%20Flipping%20in%20GSAS_files/image0 22.gif" v:shapes="Picture_x0020_11"><![endif]></span></p>1665 src="Charge%20Flipping%20in%20GSAS_files/image057.gif" v:shapes="Picture_x0020_11"><![endif]></span></p> 1666 1666 1667 1667 <p class=MsoNormal>The atom names indicate the peak magnitude to aid 1668 1668 identification (M100 for the largest in the <b style='mso-bidi-font-weight: 1669 1669 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1670 minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which may1671 not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span1670 minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which 1671 may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span 1672 1672 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1673 1673 mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort … … 1685 1685 the operating system; use <b style='mso-bidi-font-weight:normal'><span 1686 1686 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1687 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. My1688 list is now </p>1687 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. 1688 My list is now </p> 1689 1689 1690 1690 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1693 1693 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image023.png" o:title=""/> 1694 1694 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=394 1695 src="Charge%20Flipping%20in%20GSAS_files/image0 24.gif" v:shapes="Picture_x0020_12"><![endif]></span></p>1695 src="Charge%20Flipping%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_12"><![endif]></span></p> 1696 1696 1697 1697 <p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span … … 1740 1740 croptop="2450f" cropbottom="26950f" cropleft="39199f" cropright="11167f"/> 1741 1741 </v:shape><![endif]--><![if !vml]><img border=0 width=702 height=576 1742 src="Charge%20Flipping%20in%20GSAS_files/image0 26.jpg" v:shapes="Picture_x0020_13"><![endif]></span></p>1742 src="Charge%20Flipping%20in%20GSAS_files/image059.jpg" v:shapes="Picture_x0020_13"><![endif]></span></p> 1743 1743 1744 1744 <p class=MsoNormal>The original charge flipping solution is still visible and … … 1750 1750 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image027.png" o:title=""/> 1751 1751 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=387 1752 src="Charge%20Flipping%20in%20GSAS_files/image0 28.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>1752 src="Charge%20Flipping%20in%20GSAS_files/image060.gif" v:shapes="Picture_x0020_18"><![endif]></span></p> 1753 1753 1754 1754 <p class=MsoNormal>Interestingly the atoms identified exactly matched with the … … 1779 1779 croptop="2054f" cropbottom="23166f" cropleft="37518f" cropright="9679f"/> 1780 1780 </v:shape><![endif]--><![if !vml]><img border=0 width=701 height=531 1781 src="Charge%20Flipping%20in%20GSAS_files/image0 30.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>1781 src="Charge%20Flipping%20in%20GSAS_files/image061.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p> 1782 1782 1783 1783 <p class=MsoNormal>Save the project file; the next step is to complete the … … 1849 1849 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image031.png" o:title=""/> 1850 1850 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1851 src="Charge%20Flipping%20in%20GSAS_files/image0 32.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>1851 src="Charge%20Flipping%20in%20GSAS_files/image062.gif" v:shapes="Picture_x0020_16"><![endif]></span></p> 1852 1852 1853 1853 <p class=MsoNormal>Ive shifted & zoomed in to make the differences more … … 1874 1874 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image033.png" o:title=""/> 1875 1875 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300 1876 src="Charge%20Flipping%20in%20GSAS_files/image0 34.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>1876 src="Charge%20Flipping%20in%20GSAS_files/image063.gif" v:shapes="Picture_x0020_17"><![endif]></span></p> 1877 1877 1878 1878 <p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span … … 1961 1961 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image035.png" o:title=""/> 1962 1962 </v:shape><![endif]--><![if !vml]><img border=0 width=366 height=450 1963 src="Charge%20Flipping%20in%20GSAS_files/image0 36.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>1963 src="Charge%20Flipping%20in%20GSAS_files/image064.gif" v:shapes="Picture_x0020_19"><![endif]></span></p> 1964 1964 1965 1965 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1969 1969 croptop="5231f" cropbottom="8930f" cropleft="11448f" cropright="20374f"/> 1970 1970 </v:shape><![endif]--><![if !vml]><img border=0 width=466 height=399 1971 src="Charge%20Flipping%20in%20GSAS_files/image0 38.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>1971 src="Charge%20Flipping%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p> 1972 1972 1973 1973 <p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots … … 2012 2012 cropbottom="13787f" cropleft="10923f" cropright="20900f"/> 2013 2013 </v:shape><![endif]--><![if !vml]><img border=0 width=467 height=403 2014 src="Charge%20Flipping%20in%20GSAS_files/image0 40.jpg" v:shapes="Picture_x0020_21"><![endif]></span></p>2014 src="Charge%20Flipping%20in%20GSAS_files/image066.jpg" v:shapes="Picture_x0020_21"><![endif]></span></p> 2015 2015 2016 2016 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 2041 2041 croptop="374f" cropbottom="13600f" cropleft="10817f" cropright="20795f"/> 2042 2042 </v:shape><![endif]--><![if !vml]><img border=0 width=464 height=396 2043 src="Charge%20Flipping%20in%20GSAS_files/image0 42.jpg" v:shapes="Picture_x0020_22"><![endif]></span></p>2043 src="Charge%20Flipping%20in%20GSAS_files/image067.jpg" v:shapes="Picture_x0020_22"><![endif]></span></p> 2044 2044 2045 2045 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 2048 2048 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image043.png" o:title=""/> 2049 2049 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300 2050 src="Charge%20Flipping%20in%20GSAS_files/image0 44.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>2050 src="Charge%20Flipping%20in%20GSAS_files/image068.gif" v:shapes="Picture_x0020_23"><![endif]></span></p> 2051 2051 2052 2052 <p class=MsoNormal>Change the <b style='mso-bidi-font-weight:normal'><span … … 2087 2087 cropbottom="13413f" cropleft="10818f" cropright="21005f"/> 2088 2088 </v:shape><![endif]--><![if !vml]><img border=0 width=464 height=403 2089 src="Charge%20Flipping%20in%20GSAS_files/image0 46.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>2089 src="Charge%20Flipping%20in%20GSAS_files/image069.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p> 2090 2090 2091 2091 <p class=MsoNormal>I moved the cross to a very interesting feature of the map … … 2099 2099 mso-hansi-theme-font:minor-latin'>Type</span></b> to <b style='mso-bidi-font-weight: 2100 2100 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2101 minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b> (I know it is H already2102 but this step changes the name from <b style='mso-bidi-font-weight:normal'><span 2103 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2104 m so-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the Calculate/Refine2105 without varying any of the H-atom parameters; my final <span class=SpellE>Rwp</span> 2106 = 10.69% (you dont get much improvement for adding an H-atom to an oxide 2107 structure).</p>2101 minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b> (I know it is H 2102 already but this step changes the name from <b style='mso-bidi-font-weight: 2103 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 2104 minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the 2105 Calculate/Refine without varying any of the H-atom parameters; my final <span 2106 class=SpellE>Rwp</span> = 10.69% (you dont get much improvement for adding an 2107 H-atom to an oxide structure).</p> 2108 2108 2109 2109 </div> -
trunk/help/Charge Flipping in GSAS_files/filelist.xml
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trunk/help/Charge Flipping in GSAS_files/props053.xml
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