Changeset 1009 for trunk/help/Fit Peaks.htm

Timestamp:

Jul 24, 2013 4:39:06 PM (10 years ago)

Author:

vondreele

Message:

auto peak search for TOF - no duplicates either
small amendment to peak fit tutorial

File:

• trunk/help/Fit Peaks.htm (modified) (14 diffs)

trunk/help/Fit Peaks.htm

@@ -23 +23 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>30</o:Revision>
-  <o:TotalTime>770</o:TotalTime>
+  <o:Revision>31</o:Revision>
+  <o:TotalTime>773</o:TotalTime>
   <o:Created>2012-05-05T16:28:00Z</o:Created>
-  <o:LastSaved>2013-04-30T18:16:00Z</o:LastSaved>
+  <o:LastSaved>2013-07-24T21:07:00Z</o:LastSaved>
   <o:Pages>11</o:Pages>
-  <o:Words>2633</o:Words>
-  <o:Characters>15011</o:Characters>
+  <o:Words>2707</o:Words>
+  <o:Characters>15435</o:Characters>
   <o:Company>Argonne National Laboratory</o:Company>
-  <o:Lines>125</o:Lines>
-  <o:Paragraphs>35</o:Paragraphs>
-  <o:CharactersWithSpaces>17609</o:CharactersWithSpaces>
+  <o:Lines>128</o:Lines>
+  <o:Paragraphs>36</o:Paragraphs>
+  <o:CharactersWithSpaces>18106</o:CharactersWithSpaces>
   <o:Version>14.00</o:Version>
  </o:DocumentProperties>
@@ -1143 +1143 @@
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS file</span></b>
-menu item to read the data file into the current GSAS-II project. This read option
-is set to read any of the powder data formats defined for GSAS (angles in <span
-class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
-the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+menu item to read the data file into the current GSAS-II project. This read
+option is set to read any of the powder data formats defined for GSAS (angles
+in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items
+will read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
@@ -1298 +1298 @@
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
-point it is wise to zoom in on the data that will be used for indexing. </p>
+mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this point
+it is wise to zoom in on the data that will be used for indexing. </p>
 
 <p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
@@ -1367 +1367 @@
 
 <p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
-will be 22-23 peaks in this example. You should examine both the list and the
-plot to be sure the auto search did not pick a peak twice (there may be three
-of these!) or skip a peak or shoulder. You can add a peak to the list by
-pressing the left mouse button with the pointer on a data point at the peak top
-or shoulder; be sure the zoom/shift buttons are off. You may drag a peak
-position as needed. A position may be deleted with a right click with the mouse
-on the blue line. You can also delete a peak by selecting the row in the table;
-it will be highlighted in blue. Then press the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be
-removed from the table and the plot. The list will always show the peaks sorted
-by position. When done you should have 20 unique peak positions.</p>
+will be 20+ peaks in this example. You should examine both the list and the
+plot to be sure the auto search did not pick a peak twice (quite rarely) or
+skip a peak or shoulder. You can add a peak to the list by pressing the left
+mouse button with the pointer on a data point at the peak top or shoulder; be
+sure the zoom/shift buttons are off. You may drag a peak position as needed. A
+position may be deleted with a right click with the mouse on the blue line. You
+can also delete a peak by selecting the row in the table; it will be
+highlighted in blue. Then press the <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be removed
+from the table and the plot. The list will always show the peaks sorted by
+position. When done you should have 20 unique peak positions.</p>
 
 <h2>Step 4: Refine Peak Positions</h2>
@@ -1535 +1535 @@
 src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
 
-<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
-the right of the peak top. This is a consequence of the peak asymmetry arising
-from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
-is ~6% as shown on the console window. Again the <b style='mso-bidi-font-weight:
+<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to the
+right of the peak top. This is a consequence of the peak asymmetry arising from
+axial divergence in the diffractometer. The <span class=SpellE>Rwp</span> is
+~6% as shown on the console window. Again the <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
@@ -1644 +1644 @@
 
 <p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
-indexes all peaks with almost a perfect fit to the peak positions (compare
-dashed red lines to solid blue ones). Import the cell information using the <b
+indexes all peaks with almost a perfect fit to the peak positions (compare dashed
+red lines to solid blue ones). Import the cell information using the <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
@@ -1703 +1703 @@
 can be used in future analysis (e.g. Rietveld or Pawley refinement).</p>
 
-<p class=MsoNormal>To continue with the second part of this exercise, select
-the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/Close
-project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
-it saved; if <span class=GramE><b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>Yes</span></b></span> then all the peak fitting/indexing &amp;
-cell refinement results will be saved to the <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
-mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
+<p class=MsoNormal>To continue with the second part of this exercise, select the
+menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>File/Close project</span></b> in the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree </span></b>window.
+You will be asked if you want it saved; if <span class=GramE><b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
+peak fitting/indexing &amp; cell refinement results will be saved to the <b
+style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
+Calibri;mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
@@ -1739 +1738 @@
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
-minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
-corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
+minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a corresponding
+<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
@@ -1770 +1769 @@
 small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin'>Auto search</span></b> to start and then fill in by hand:
-Add peaks by left-clicking on a data point near the top of the
-peak. Peak positions can be moved by dragging the peak line and peaks
-can be deleted by right-clicking on them. This only works when the
-zoom and reposition modes (below) are not selected. Also note
-some peaks have shoulders most notably at 5.07, 6.04, 7.81deg. I found 28 peaks
-(there was one very weak shoulder at ~7.3 deg. I skipped – it might be from a
-second phase? We’ll see later).</p>
+minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
+peaks by left-clicking on a data point near the top of the peak. Peak positions
+can be moved by dragging the peak line and peaks can be deleted by
+right-clicking on them. This only works when the zoom and reposition modes
+(below) are not selected. Also note some peaks have shoulders most notably at
+5.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
+deg. I skipped – it might be from a second phase? We’ll see later).</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1034" type="#_x0000_t75" style='width:525pt;height:450pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_19" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image020.png" v:shapes="_x0000_i1034"><![endif]></span><br
+src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_19"><![endif]></span><br
 clear=all style='mso-special-character:line-break'>
 </p>
@@ -1790 +1788 @@
 <h2><span class=GramE>Step 4.</span> Refine peaks</h2>
 
-<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
-above, refine the peaks and the profile shape parameters in <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
-will be asked for a project file name at the first refinement (I used ‘<span
+<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example above,
+refine the peaks and the profile shape parameters in <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
+mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You will be
+asked for a project file name at the first refinement (I used ‘<span
 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
@@ -1864 +1862 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1033" type="#_x0000_t75" style='width:525pt;height:450pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_20" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
+ height:450pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
-src="Fit%20Peaks_files/image021.png" v:shapes="_x0000_i1033"><![endif]><!--[if gte vml 1]><v:shape
+src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]><!--[if gte vml 1]><v:shape
  id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;
  height:376.5pt;visibility:visible;mso-wrap-style:square'>
@@ -1909 +1907 @@
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;height:303.75pt;
- visibility:visible;mso-wrap-style:square'>
+ id="Picture_x0020_22" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;
+ height:303.75pt;visibility:visible;mso-wrap-style:square'>
  <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
 </v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
-src="Fit%20Peaks_files/image023.png" v:shapes="_x0000_i1031"><![endif]></span><span
+src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
@@ -1929 +1927 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
-Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project
-file as it is needed for the <b style='mso-bidi-font-weight:normal'><span
+Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project file
+as it is needed for the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
@@ -1992 +1990 @@
 small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin'>Auto search</span></b> to start and then fill in by hand:
-Add peaks by left-clicking on a data point near the top of the
-peak. Peak positions can be moved by dragging the peak line and peaks
-can be deleted by right-clicking on them. This only works when the
-zoom and reposition modes (below) are not selected. Also note the
-shoulder at ~6.3 <span class=SpellE>deg</span> that should be added to the
-list. I skipped a couple of very weak peaks; the total list has 28 peaks.</p>
+minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
+peaks by left-clicking on a data point near the top of the peak. Peak positions
+can be moved by dragging the peak line and peaks can be deleted by
+right-clicking on them. This only works when the zoom and reposition modes
+(below) are not selected. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
+that should be added to the list. I skipped a couple of very weak peaks; the
+total list has 28 peaks.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape