Changeset 4659 for trunk/help/gsasII.html

Timestamp:

Nov 21, 2020 2:15:49 PM (13 months ago)

Author:

toby

Message:

extensive Origin 1->2 updates; merge SetupGeneral? into a single routine in G2Elem; read sym ops from CIF; fix sites sym/mult after cood xform

File:

• trunk/help/gsasII.html (modified) (5 diffs)

trunk/help/gsasII.html

@@ -5823 +5823 @@
 "Times New Roman"'>This gives overall parameters describing the phase such as
 the name, space group, the unit cell parameters and overall parameters for the
-atom present in the phase. It also has the controls for computing Fourier maps
-for this phase.<span class=MsoHyperlink><span style='color:windowtext;
+atom present in the phase. It also has the controls for Pawley
+intensity extraction and for computing Fourier maps
+for this phase. It can also be used to compute new structures based on
+the unit cell and atom poistions. 
+<span class=MsoHyperlink><span style='color:windowtext;
 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
 
@@ -5838 +5841 @@
 </span></span></span></span><![endif]><span style='mso-fareast-font-family:
 "Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> –
-The compute menu shows computations that are possible for this phase.<span
-class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
-text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Fourier maps</span></b><span
-style='mso-fareast-font-family:"Times New Roman"'> – compute Fourier maps
-according to the controls set at bottom of General page.<span
-class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
-text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
+The compute menu shows computations that are possible for this phase.
+
+<DL class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space: 
+  auto;mso-list:l2 level2 lfo27'>
+<DT><B>Fourier maps</B></DT>
+  <DD>compute Fourier maps
+  according to the controls set at bottom of General page.</DD>
+<DT><B>Search maps</B></DT>
+<DD>search the computed Fourier
 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
 procedure; they will be printed on the console and will be shown in the ‘<a
-href="Map_peaks">Map peaks</a><span
-style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be
+href="Map_peaks">Map peaks</a>’ page. This page will immediately be
 shown and the peaks will be shown on the structure drawing for this phase as
-white 3-D crosses.<span class=MsoHyperlink><span style='color:windowtext;
-text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Charge flipping </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
+  white 3-D crosses.</DD>
+<DT><B>Charge flipping </B></DT>
+<DD>This performs a charge
 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
 using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
@@ -5890 +5869 @@
 properly place symmetry operators (NB: depends on the quality of the resulting
 phases), searched for peaks and the display shifts to <b style='mso-bidi-font-weight:
-normal'>Map peaks</b> to show them.<span class=MsoHyperlink><span
-style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
-
-<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
-auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
-class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
-color:windowtext;text-decoration:none;text-underline:none'><span
-style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
-style='mso-fareast-font-family:"Times New Roman"'>Clear map </span></b><span
-style='mso-fareast-font-family:"Times New Roman"'>– This clears any
-Fourier/charge flip map from memory; the Fourier map controls are also cleared.<span
+  normal'>Map peaks</b> to show them.</DD>
+<DT><B>Clear map </B></DT>
+<DD>This clears any
+Fourier/charge flip map from memory; the Fourier map controls are also
+  cleared.</DD>
+<DT><B>Transform</B></DT>
+<DD>This allows for a change in axes, symmetry or unit cell. It is
+  also used to create a magnetic phase from a chemical (nuclear)
+  phase. One important transformation that can be done here is for
+  Origin 1 settings to Origin 2 (<a href="#Origin1">described below</a>)
+
+  
+</DD>
+</DL>
+
+<span
 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
 text-underline:none'><o:p></o:p></span></span></span></p>
@@ -6281 +6264 @@
 algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p>
 
+<h5 style='margin-left:0.5in'><a name=Origin1></a>Origin 1 ->
+Origin 2 Transformations</h5>
+
+<p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+An important transformation may be needed in certain cases when space
+groups that two alternate origin settings
+(<A
+href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed here</a>).
+These are centrosymmetric space groups where the highest symmetry
+point in the structure does not contain a center of symmetry. Origin 1
+places the origin at the highest symmetry setting while Origin 2
+places the origin at a center of symmetry (creating a -x,-y,-z
+symmetry operator, which means that reflection phases can only be 0 or π.)
+GSAS-II requires use of the Origin 2 settings because computations are much
+faster and simpler without complex structure factors.
+Alas, the literature contains a number of structures reported in
+Origin 1, where the origin choice may not be clearly communicated. (The
+CIF standard does not require that origin choice be indicated.)
+When a structure is imported that uses any of the space groups where
+an origin choice is possible, a message is shown in GSAS-II notifying
+the user that they must confirm that the origin choice is correct. 
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+<B>Example:</B>
+An
+example of what can go wrong is illustrated with the structure of
+anatase. The space group is <I>I</I> 4<sub>1</sub>/<I>a m d</I>. In
+Origin 1 the coordinates are:
+<TABLE border=2; style='margin-left:2.0in'>
+  <TR>
+    <th colspan=4>Origin 1</th>
+  </TR>
+  <TR>
+    <th>atom</th>
+    <th colspan=3>coordinates</th>
+  </TR>
+  <TR>
+    <TD>Ti</TD>
+    <TD>0</TD>
+    <TD>0</TD>
+    <TD>0</TD>
+  </TR>
+  <TR>
+    <TD>O</TD>
+    <TD>0</TD>
+    <TD>0</TD>
+    <TD>0.208</TD>
+  </TR>
+</TABLE>
+
+and in Origin 2 the coordinates are: 
+<TABLE border=2; style='margin-left:2.0in'>
+  <TR>
+    <th colspan=4>Origin 2</th>
+  </TR>
+  <TR>
+    <th>atom</th>
+    <th colspan=3>coordinates</th>
+  </TR>
+  <TR>
+    <TD>Ti</TD>
+    <TD>0</TD>
+    <TD>1/4</TD>
+    <TD>-1/8</TD>
+  </TR>
+  <TR>
+    <TD>O</TD>
+    <TD>0</TD>
+    <TD>1/4</TD>
+    <TD>0.083</TD>
+  </TR>
+</TABLE>
+where the origin is shifted by (0,0.25,-0.125).
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+<img src="gsasII_files/wrong.png" align="right">
+Since GSAS-II always the symmetry operators for Origin 2,
+if structure is input incorrectly with the coordinates set for Origin
+1, there are several fairly obvious signs of problems: (1) the
+site symmetries and multiplicities are wrong, often giving an incorrect
+chemical formula, (2) the interatomic distances are incorrect, and (3)
+a plot of the structure is improbable. 
+In this case incorrect multiplicities gives
+rise to a density of 7.9 g/cc, double the correct value.
+Impossible interatomic distances of 1.88&Aring for Ti-Ti, and
+1.39&Aring; for Ti-O are seen. The unit
+cell contents with the wrong space group operators is shown to the
+right. 
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
+With coordinates that match the space
+group operations, the correct Ti-O distances are 1.92&Aring; and
+1.97&Aring; and the shortest Ti-Ti distance is 3.0&Aring;. 
+(Note that interatomic distances can be computed in GSAS-II using the Phase Atoms
+tab and the Compute/"Show Distances & Angles" menu item.) 
+
+</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span 
+style='mso-fareast-font-family:"Times New Roman"'>
+<img src="gsasII_files/xform.png" align="right">
+<B>Transform Origin:</B>
+To transform a space group setting from Origin setting 1 to 2, use the
+Transform option in the Compute menu and then select the last option in the "Common
+transformations" pulldown menu, which will be setting 1->2 for space
+groups where both origins are available, as shown to the right. The
+transformation matrix will be set to the identity and the "V" vector
+will have the required origin shift loaded. Press OK. The changes can
+be seen by selecting the Atoms tab. 
+
+</span></p>
+<BR CLEAR="right" />
 <h4 style='margin-left:0.25in'><a name=Data></a><u>Data</u></h4>
 
@@ -7353 +7443 @@
 <hr size=2 width="100%" align=center>
 
-<!-- hhmts start -->Last modified: Fri Oct 23 15:56:02 CDT 2020 <!-- hhmts end -->
+<!-- hhmts start -->Last modified: Sat Nov 21 12:25:40 CST 2020 <!-- hhmts end -->
 
 </div>