Changeset 729


Ignore:
Timestamp:
Aug 22, 2012 4:18:59 PM (10 years ago)
Author:
vondreele
Message:

minor fixes to mapPeaks plotting
begin to add charge flipping tutorial

Location:
trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIphsGUI.py

    r727 r729  
    39333933            Ind = MapPeaks.GetSelectedRows()
    39343934            for ind in Ind:
    3935                 x,y,z = mapPeaks[ind][1:]
     3935                x,y,z,d = mapPeaks[ind][1:]
    39363936                AtomAdd(x,y,z,'C')
    39373937   
  • trunk/GSASIIplot.py

    r728 r729  
    23802380        if G2frame.dataDisplay.GetPageText(getSelection()) == 'Map peaks':
    23812381            for i,peak in enumerate(mapPeaks):
    2382                 x,y,z,d = peak[1:]
     2382                x,y,z = peak[1:4]
    23832383                X,Y,Z = gluProject(x,y,z,Model,Proj,View)
    23842384                XY = [int(X),int(View[3]-Y)]
  • trunk/help/Fit Peaks.htm

    r724 r729  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>18</o:Revision>
    26   <o:TotalTime>293</o:TotalTime>
     25  <o:Revision>19</o:Revision>
     26  <o:TotalTime>303</o:TotalTime>
    2727  <o:Created>2012-05-05T16:28:00Z</o:Created>
    28   <o:LastSaved>2012-08-21T14:48:00Z</o:LastSaved>
     28  <o:LastSaved>2012-08-22T19:19:00Z</o:LastSaved>
    2929  <o:Pages>9</o:Pages>
    30   <o:Words>1902</o:Words>
    31   <o:Characters>10843</o:Characters>
     30  <o:Words>1909</o:Words>
     31  <o:Characters>10887</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>90</o:Lines>
    3434  <o:Paragraphs>25</o:Paragraphs>
    35   <o:CharactersWithSpaces>12720</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>12771</o:CharactersWithSpaces>
    3636  <o:Version>14.00</o:Version>
    3737 </o:DocumentProperties>
     
    599599        mso-font-kerning:14.0pt;}
    600600a:link, span.MsoHyperlink
    601         {mso-style-noshow:yes;
    602         mso-style-priority:99;
     601        {mso-style-priority:99;
    603602        color:blue;
    604603        text-decoration:underline;
     
    14151414style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    14161415style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
    1417 add refinement of the peak positions. This can be done by clicking on all the refinement
    1418 flags for the individual peaks or it is possible to set them all at the same
    1419 time using this recipe: </p>
     1416add refinement of the peak positions. This can be done by clicking on all the
     1417refinement flags for the individual peaks or it is possible to set them all at
     1418the same time using this recipe: </p>
    14201419
    14211420<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    15551554style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    15561555mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
    1557 List</span></b> data item. This brings up a window for indexing and cell
    1558 refinement options</p>
     1556List</span></b> data item. This brings up a window for indexing and cell refinement
     1557options</p>
    15591558
    15601559<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15711570style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    15721571mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1573 minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
    1574 console shows a running list of possible cells as they are found; the sorted by
    1575 M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
     1572minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the console
     1573shows a running list of possible cells as they are found; the sorted by M20
     1574list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
    15761575normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    15771576minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
     
    17331732<p class=MsoNormal>Pick all peaks you can see between the limits (including the
    17341733small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
    1735 7.81deg. I found 28 peaks (there were a few very weak ones I skipped – they might
    1736 be from a second phase? We’ll see later).</p>
     17347.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
     1735might be from a second phase? We’ll see later).</p>
    17371736
    17381737<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_s1026"
     
    18061805mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    18071806minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
    1808 and suitable results will be slow in coming so be patient. Watch the console window;
    1809 the right answer will have an obviously large M20 (~630) and a volume of ~594Å<sup>3</sup>
    1810 (10<sup>th</sup> column of console display). Once this is seen (it may take
    1811 more than one try to get this) you can stop the indexing search by pressing <b
    1812 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1813 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1814 minor-latin'>Cancel</span></b> on the progress bar window. It may take more
    1815 than one press to fully stop it. My result was </p>
     1807and suitable results will be slow in coming so be patient. Watch the console
     1808window; the right answer will have an obviously large M20 (~630) and a volume
     1809of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
     1810seen (it may take more than one try to get this) you can stop the indexing
     1811search by pressing <b style='mso-bidi-font-weight:normal'><span
     1812style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1813mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
     1814on the progress bar window. It may take more than one press to fully stop it.
     1815My result was </p>
    18161816
    18171817<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18781878style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18791879mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1880 minor-latin'>Charge Flipping</span></b> exercise. The features of the <b
    1881 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1882 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1883 minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
     1880minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
     1881exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
     1882style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1883mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data</span></b>
     1884window will be presented in other exercises.</p>
    18841885
    18851886</div>
  • trunk/help/gsasII.html

    r624 r729  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>94</o:Revision>
    28   <o:TotalTime>2877</o:TotalTime>
     27  <o:Revision>95</o:Revision>
     28  <o:TotalTime>2878</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2012-05-18T18:22:00Z</o:LastSaved>
     30  <o:LastSaved>2012-08-22T19:17:00Z</o:LastSaved>
    3131  <o:Pages>8</o:Pages>
    32   <o:Words>7200</o:Words>
    33   <o:Characters>41042</o:Characters>
     32  <o:Words>7206</o:Words>
     33  <o:Characters>41077</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>342</o:Lines>
    3636  <o:Paragraphs>96</o:Paragraphs>
    37   <o:CharactersWithSpaces>48146</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>48187</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    605605        mso-font-kerning:14.0pt;}
    606606a:link, span.MsoHyperlink
    607         {mso-style-noshow:yes;
    608         mso-style-priority:99;
     607        {mso-style-priority:99;
    609608        color:blue;
    610609        text-decoration:underline;
     
    19641963 <o:lock v:ext="edit" aspectratio="t"/>
    19651964</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75"
    1966  alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
     1965 alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
    19671966 style='position:absolute;margin-left:44.8pt;margin-top:0;width:96pt;height:96pt;
    19681967 z-index:251657728;visibility:visible;mso-wrap-style:square;
     
    19771976</v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
    19781977align=right
    1979 alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
     1978alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
    19801979v:shapes="Picture_x0020_2"><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Help
    19811980for GSAS-II<o:p></o:p></span></h1>
     
    20222021<p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement<o:p></o:p></strong></p>
    20232022
    2024 <p class=MsoNormal><strong>Charge flipping structure solution (future)<o:p></o:p></strong></p>
     2023<p class=MsoNormal><strong><a href="Charge%20Flipping%20in%20GSAS.htm"><span
     2024style='font-weight:normal'>Charge flipping structure solution</span></a>
     2025(future)<o:p></o:p></strong></p>
    20252026
    20262027<div class=MsoNormal align=center style='text-align:center'><span
     
    21592160style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    21602161style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2161 style='mso-bidi-font-weight:normal'>Add phase</b> &#8211; This begins the
    2162 creation of a new phase in the data tree (under Phases). You are first prompted
    2163 in a dialog box for a name to be assigned to the new phase. Then the <b
     2162style='mso-bidi-font-weight:normal'>Add phase</b> &#8211; This begins the creation
     2163of a new phase in the data tree (under Phases). You are first prompted in a
     2164dialog box for a name to be assigned to the new phase. Then the <b
    21642165style='mso-bidi-font-weight:normal'><a href="#General">General</a></b> tab is
    21652166opened for this phase; you should first select the phase type, enter the space
     
    25672568style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    25682569style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    2569 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the
    2570 parameter types you wish to constrain. Each will have the same possibilities in
    2571 the &#8216;Edit menu.<o:p></o:p></span></p>
     2570style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the parameter
     2571types you wish to constrain. Each will have the same possibilities in the
     2572&#8216;Edit menu.<o:p></o:p></span></p>
    25722573
    25732574<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l17 level1 lfo3'><![if !supportLists]><span
     
    26712672<h3>Histograms</h3>
    26722673
    2673 <p class=MsoNormal>These are shown in the data tree with a prefix of &#8216;PWDR&#8217;,
    2674 &#8217;HKLF&#8217;, &#8216;IMG&#8217;, &#8216;PDF&#8217; or &#8216;XXXX&#8217;
    2675 (future &#8211; restraints??) and usually a file name. These constitute the
    2676 data sets (&#8216;Histograms&#8217;) to be used by GSAS-II for analysis.
    2677 Selection of these items does not produce any information in the data window
    2678 but does display the data in the Plots Window. They are described below.</p>
     2674<p class=MsoNormal>These are shown in the data tree with a prefix of
     2675&#8216;PWDR&#8217;, &#8217;HKLF&#8217;, &#8216;IMG&#8217;, &#8216;PDF&#8217; or
     2676&#8216;XXXX&#8217; (future &#8211; restraints??) and usually a file name. These
     2677constitute the data sets (&#8216;Histograms&#8217;) to be used by GSAS-II for
     2678analysis. Selection of these items does not produce any information in the data
     2679window but does display the data in the Plots Window. They are described below.</p>
    26792680
    26802681<h3><a name="PWD_Analysis"></a>Powder Histograms - PWDR</h3>
     
    27182719whatever comment lines (preceded by &#8220;#&#8221;) found when the powder data
    27192720file was read by GSAS-II. If you are lucky, there will be useful information
    2720 here (e.g. sample name, date collected, wavelength used, etc.). If not, this
    2721 window will be blank. The text is read-only in that anything you try to enter
    2722 here is not saved.</span></p>
     2721here (e.g. sample name, date collected, wavelength used, etc.). If not, this window
     2722will be blank. The text is read-only in that anything you try to enter here is
     2723not saved.</span></p>
    27232724
    27242725<span style='mso-bookmark:Comments'></span>
     
    27412742class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the
    27422743&#8216;changed&#8217; row as needed. Use the mouse to select the value to be
    2743 changed (the background on the box will be blue or have a black border or a
    2744 vertical bar will appear in the value), then enter the new value and press
    2745 Enter or click the mouse elsewhere in the Background window. This will set the
    2746 new value.<o:p></o:p></span></p>
     2744changed (the background on the box will be blue or have a black border or a vertical
     2745bar will appear in the value), then enter the new value and press Enter or
     2746click the mouse elsewhere in the Background window. This will set the new
     2747value.<o:p></o:p></span></p>
    27472748
    27482749<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo6'><![if !supportLists]><span
     
    27832784for the background:<o:p></o:p></span></p>
    27842785
    2785 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1). A
    2786 continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
     2786<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1).
     2787A continuous empirical function (&#8216;<span class=SpellE>chebyschev</span>&#8217;,
    27872788&#8216;cosine&#8217;, &#8216;<span class=SpellE><span class=GramE>lin</span></span>
    27882789interpolate&#8217;, &#8216;inv interpolate&#8217; &amp; &#8216;log
     
    29993000flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>-
    30003001&#8211; this copies the instrument parameter refinement flags shown to other
    3001 selected powder patterns. If used, a dialog box (Copy refinement flags) will appear
    3002 showing the list of available powder patterns, you can copy the instrument
    3003 parameter refinement flags to any or all of them; select &#8216;All&#8217; to
    3004 copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
    3005 &#8216;Cancel&#8217; to cancel the operation. The copy will only work for
    3006 instrument parameters that are commensurate with the one that is shown, e.g.
    3007 single radiation patterns will not be updated from K</span><sub><span
     3002selected powder patterns. If used, a dialog box (Copy refinement flags) will
     3003appear showing the list of available powder patterns, you can copy the
     3004instrument parameter refinement flags to any or all of them; select
     3005&#8216;All&#8217; to copy them to all patterns. Then select &#8216;OK&#8217; to
     3006do the copy; &#8216;Cancel&#8217; to cancel the operation. The copy will only
     3007work for instrument parameters that are commensurate with the one that is
     3008shown, e.g. single radiation patterns will not be updated from K</span><sub><span
    30083009style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    30093010style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span
     
    30403041style='mso-fareast-font-family:"Times New Roman"'>You can choose to refine any
    30413042profile coefficients. <b style='mso-bidi-font-weight:normal'>NB</b>: In certain
    3042 circumstances some choices are ignored e.g. Zero is not refined during peak fitting.
    3043 Also some choices may lead to unstable refinement, e.g. <span class=GramE>Lam</span>
    3044 refinement and lattice parameter refinement. Examine the &#8216;</span><a
    3045 href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
     3043circumstances some choices are ignored e.g. Zero is not refined during peak
     3044fitting. Also some choices may lead to unstable refinement, e.g. <span
     3045class=GramE>Lam</span> refinement and lattice parameter refinement. Examine the
     3046&#8216;</span><a href="#Covariance"><span style='mso-fareast-font-family:"Times New Roman"'>Covariance&#8217;</span></a><span
    30463047style='mso-fareast-font-family:"Times New Roman"'> display for highly
    30473048correlated parameters.<o:p></o:p></span></p>
     
    30553056fixed. All values can be changed in this window.<o:p></o:p></span></p>
    30563057
    3057 <h5><a name="Peak_List"></a><a name="Powder_Peaks"><span style='mso-bookmark:
    3058 Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>What can I
    3059 do here?</span></span></a><span style='mso-bookmark:Powder_Peaks'><span
    3060 style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman";
     3058<h5><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
     3059Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>What can
     3060I do here?</span></span></a><span style='mso-bookmark:Peak_List'><span
     3061style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    30613062color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'><o:p></o:p></span></span></span></h5>
    30623063
    30633064<h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo11'><span
    3064 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
     3065style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
    30653066style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30663067normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>1.<span
     
    30683069style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30693070normal;mso-bidi-font-weight:bold'>Menu &#8216;</span></span></span><span
    3070 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3071style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30713072style='mso-fareast-font-family:"Times New Roman";color:windowtext'>File&#8217;</span></span></span><span
    3072 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3073style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30733074style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30743075normal;mso-bidi-font-weight:bold'> &#8211; <o:p></o:p></span></span></span></h5>
     
    30763077<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    30773078text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
    3078 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
     3079style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
    30793080style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    30803081style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    30813082style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b></span></span><span
    3082 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3083style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30833084style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
    30843085sample parameters shown to other selected powder patterns. If used, a dialog
     
    30903091<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    30913092text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
    3092 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
     3093style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
    30933094style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    30943095style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    30953096style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
    3096 flags</span></b></span></span><span style='mso-bookmark:Powder_Peaks'><span
    3097 style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>
     3097flags</span></b></span></span><span style='mso-bookmark:Peak_List'><span
     3098style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>
    30983099- &#8211; this copies the sample parameter refinement flags shown to other
    30993100selected powder patterns. If used, a dialog box (Copy refinement flags) will
     
    31033104&#8216;Cancel&#8217; to cancel the operation. <o:p></o:p></span></span></span></p>
    31043105
    3105 <h4><span style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3106<h4><span style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    31063107style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></span><span
    31073108style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
     
    31363137class=SpellE><span style='mso-fareast-font-family:"Times New Roman";color:windowtext'>UnDo</span></span></span><span
    31373138style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    3138 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> &#8211; resets peak
    3139 parameters, background and instrument parameter values varied in the last peak
    3140 fitting refinement back to their original values. Use this to recover from a
    3141 failed refinement. Note:<span style='mso-spacerun:yes'>&nbsp; </span>there is
     3139color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> &#8211; resets
     3140peak parameters, background and instrument parameter values varied in the last
     3141peak fitting refinement back to their original values. Use this to recover from
     3142a failed refinement. Note:<span style='mso-spacerun:yes'>&nbsp; </span>there is
    31423143only a single level of recovery available.<o:p></o:p></span></span></h5>
    31433144
     
    31593160&amp; SH/L). To determine how to proceed, examine in detail the powder pattern
    31603161difference curve displayed in the GSASII Plots window. If individual peaks show
    3161 peak widths that are widely different, their individual sigma and gamma
    3162 parameters may be refined. If the refinement results in negative peak
    3163 coefficients, these will be highlighted in red. If this happens, you should </span></span><span
     3162peak widths that are widely different, their individual sigma and gamma parameters
     3163may be refined. If the refinement results in negative peak coefficients, these
     3164will be highlighted in red. If this happens, you should </span></span><span
    31643165style='mso-bookmark:Index_Peaks'><span class=SpellE><span style='mso-fareast-font-family:
    31653166"Times New Roman";color:windowtext'>UnDo</span></span></span><span
     
    31993200style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Clear peaks </span></span><span
    32003201style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    3201 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>&#8211; this
    3202 removes all the peaks from the Peak List.<o:p></o:p></span></span></h5>
     3202color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'>&#8211; this removes
     3203all the peaks from the Peak List.<o:p></o:p></span></span></h5>
    32033204
    32043205<h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo12'><span
     
    32133214vertical line will be plotted on that position. Be sure that the Zoom/Pan
    32143215buttons are not selected on the Plot window. We recommend that you begin
    3215 picking peaks from the right side of the pattern; that way the tool tip
    3216 won&#8217;t be in your way as you select peaks.<o:p></o:p></span></span></h5>
     3216picking peaks from the right side of the pattern; that way the tool tip won&#8217;t
     3217be in your way as you select peaks.<o:p></o:p></span></span></h5>
    32173218
    32183219<h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l9 level1 lfo12'><span
     
    32803281style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
    32813282style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
    3282 style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
    3283 positions &amp; intensities from the </span><a href="#Peak_List"><span
    3284 style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></a><span
    3285 style='mso-fareast-font-family:"Times New Roman"'> to make them available for the
    3286 indexing routine. The d-<span class=SpellE>obs</span> is obtained from
    3287 Bragg&#8217;s Law after applying the Zero correction shown on the </span><a
    3288 href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
    3289 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'>
    3290 table to the position shown here.<o:p></o:p></span></p>
     3283style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak positions
     3284&amp; intensities from the </span><a href="#Peak_List"><span style='mso-fareast-font-family:
     3285"Times New Roman"'>Peak List</span></a><span style='mso-fareast-font-family:
     3286"Times New Roman"'> to make them available for the indexing routine. The d-<span
     3287class=SpellE>obs</span> is obtained from Bragg&#8217;s Law after applying the
     3288Zero correction shown on the </span><a href="#Instrument_Parameters"><span
     3289style='mso-fareast-font-family:"Times New Roman"'>Instrument Parameters</span></a><span
     3290style='mso-fareast-font-family:"Times New Roman"'> table to the position shown
     3291here.<o:p></o:p></span></p>
    32913292
    32923293<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l21 level1 lfo13'><![if !supportLists]><span
     
    35503551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    35513552style='mso-fareast-font-family:"Times New Roman"'>If there are entries in the
    3552 Atoms page then the Elements table is shown next on the General page; you may
    3553 select the isotope (only relevant for neutron diffraction experiments). The
    3554 density is computed depending on this choice, the unit cell volume and the atom
     3553Atoms page then the Elements table is shown next on the General page; you may select
     3554the isotope (only relevant for neutron diffraction experiments). The density is
     3555computed depending on this choice, the unit cell volume and the atom
    35553556fractions/site multiplicities in the entries on the Atoms page.<u><o:p></o:p></u></span></p>
    35563557
     
    36383639you to select a rendering option for all the atoms. For Color a color choice
    36393640dialog is displayed that covers the entire color spectrum. Choose a color by
    3640 any of the means available, press the &#8220;Add to Custom Colors&#8221;, select
    3641 that color in the Custom colors display and then press OK. <b style='mso-bidi-font-weight:
    3642 normal'>NB</b>: selecting Color will make all atoms have the same color and for
    3643 Style &#8220;blank&#8221; means the atoms aren&#8217;t rendered and thus the
    3644 plot will not show any atoms or bonds!</p>
     3641any of the means available, press the &#8220;Add to Custom Colors&#8221;,
     3642select that color in the Custom colors display and then press OK. <b
     3643style='mso-bidi-font-weight:normal'>NB</b>: selecting Color will make all atoms
     3644have the same color and for Style &#8220;blank&#8221; means the atoms
     3645aren&#8217;t rendered and thus the plot will not show any atoms or bonds!</p>
    36453646
    36463647<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
     
    36623663style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    36633664style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    3664 style='mso-bidi-font-weight:normal'>Atom label</b> &#8211; select the item to be
    3665 shown as a label for each atom in selection. The choices are: none, type, name
    3666 or number.</p>
     3665style='mso-bidi-font-weight:normal'>Atom label</b> &#8211; select the item to
     3666be shown as a label for each atom in selection. The choices are: none, type,
     3667name or number.</p>
    36673668
    36683669<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    37333734</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete
    37343735atoms</b> &#8211; clear the entire draw atom table; it is then refilled from
    3735 the Atoms table. You should do this operation after any changes in the Atoms
    3736 table, e.g. by a structure refinement.</p>
     3736the Atoms table. You should do this operation after any changes in the Atoms table,
     3737e.g. by a structure refinement.</p>
    37373738
    37383739<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l10 level1 lfo15'><![if !supportLists]><span
     
    37533754computed for the atoms in their selection order. The torsion angle is a right
    37543755hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An
    3755 estimated standard deviation is given for the calculated value if a current variance-covariance
    3756 matrix is available. The result is shown on the console window; it may be cut
    3757 &amp; pasted to another application (e.g. Microsoft Word).</p>
     3756estimated standard deviation is given for the calculated value if a current
     3757variance-covariance matrix is available. The result is shown on the console
     3758window; it may be cut &amp; pasted to another application (e.g. Microsoft
     3759Word).</p>
    37583760
    37593761<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
     
    38433845<span style='mso-bookmark:Map_peaks'></span>
    38443846
    3845 <p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks
    3846 found within the unit cell from the last Fourier map search sorted in order of
     3847<p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks found
     3848within the unit cell from the last Fourier map search sorted in order of
    38473849decreasing peak magnitude. The crystal structure plot shows each peak position
    38483850as a white 3-D cross.</p>
     
    39113913mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
    39123914src=graphbar.jpg
    3913 alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
     3915alt="Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
    39143916style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    39153917
     
    39643966powder patterns that are part of your project are shown on this page. They can
    39653967be displayed as a stack of powder patterns, just a single pattern or as a
    3966 contour image of the peak intensities. What can be done here will depend on
    3967 which is displayed and on which item in the GSAS-II data tree you have
    3968 selected.<o:p></o:p></span></p>
     3968contour image of the peak intensities. What can be done here will depend on which
     3969is displayed and on which item in the GSAS-II data tree you have selected.<o:p></o:p></span></p>
    39693970
    39703971<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    39943995class=GramE><b style='mso-bidi-font-weight:normal'>l</b></span><b
    39953996style='mso-bidi-font-weight:normal'>: offset left</b> &#8211; for a waterfall
    3996 plot of multiple powder profiles, increase the offset to the left. Does not
    3997 apply if only one pattern.</p>
     3997plot of multiple powder profiles, increase the offset to the left. Does not apply
     3998if only one pattern.</p>
    39983999
    39994000<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    42464247contribution that were set when the powder pattern was first read in to
    42474248GSAS-II. If individual peak fitting has been performed, the values of
    4248 &#8216;sig&#8217; &amp; &#8216;gam&#8217; for the peaks are plotted as
    4249 &#8216;+&#8217;; these are computed from the fitted values of U, V, W, X and Y
    4250 as well as any sig or gam individually refined.<o:p></o:p></span></p>
     4249&#8216;sig&#8217; &amp; &#8216;gam&#8217; for the peaks are plotted as &#8216;+&#8217;;
     4250these are computed from the fitted values of U, V, W, X and Y as well as any
     4251sig or gam individually refined.<o:p></o:p></span></p>
    42514252
    42524253<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture </span></h4>
  • trunk/help/gsasII_files/props011.xml

    r624 r729  
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