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

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

1 edited


  • trunk/help/gsasII.html

    r4621 r4659  
    58235823"Times New Roman"'>This gives overall parameters describing the phase such as
    58245824the name, space group, the unit cell parameters and overall parameters for the
    5825 atom present in the phase. It also has the controls for computing Fourier maps
    5826 for this phase.<span class=MsoHyperlink><span style='color:windowtext;
     5825atom present in the phase. It also has the controls for Pawley
     5826intensity extraction and for computing Fourier maps
     5827for this phase. It can also be used to compute new structures based on
     5828the unit cell and atom poistions.
     5829<span class=MsoHyperlink><span style='color:windowtext;
    58385841</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    58395842"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Compute’</b> –
    5840 The compute menu shows computations that are possible for this phase.<span
    5841 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5842 text-underline:none'><o:p></o:p></span></span></span></p>
    5844 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5845 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5846 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5847 color:windowtext;text-decoration:none;text-underline:none'><span
    5848 style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5849 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5850 style='mso-fareast-font-family:"Times New Roman"'>Fourier maps</span></b><span
    5851 style='mso-fareast-font-family:"Times New Roman"'> – compute Fourier maps
    5852 according to the controls set at bottom of General page.<span
    5853 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    5854 text-underline:none'><o:p></o:p></span></span></span></p>
    5856 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5857 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5858 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5859 color:windowtext;text-decoration:none;text-underline:none'><span
    5860 style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5861 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5862 style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
    5863 style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
     5843The compute menu shows computations that are possible for this phase.
     5845<DL class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     5846  auto;mso-list:l2 level2 lfo27'>
     5847<DT><B>Fourier maps</B></DT>
     5848  <DD>compute Fourier maps
     5849  according to the controls set at bottom of General page.</DD>
     5850<DT><B>Search maps</B></DT>
     5851<DD>search the computed Fourier
    58645852map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
    58655853procedure; they will be printed on the console and will be shown in the ‘<a
    5866 href="Map_peaks">Map peaks</a><span
    5867 style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be
     5854href="Map_peaks">Map peaks</a>’ page. This page will immediately be
    58685855shown and the peaks will be shown on the structure drawing for this phase as
    5869 white 3-D crosses.<span class=MsoHyperlink><span style='color:windowtext;
    5870 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5872 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5873 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5874 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5875 color:windowtext;text-decoration:none;text-underline:none'><span
    5876 style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5877 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5878 style='mso-fareast-font-family:"Times New Roman"'>Charge flipping </span></b><span
    5879 style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
     5856  white 3-D crosses.</DD>
     5857<DT><B>Charge flipping </B></DT>
     5858<DD>This performs a charge
    58805859flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    58815860using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
    58905869properly place symmetry operators (NB: depends on the quality of the resulting
    58915870phases), searched for peaks and the display shifts to <b style='mso-bidi-font-weight:
    5892 normal'>Map peaks</b> to show them.<span class=MsoHyperlink><span
    5893 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    5895 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
    5896 auto;text-indent:-.25in;mso-list:l2 level2 lfo27'><![if !supportLists]><span
    5897 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    5898 color:windowtext;text-decoration:none;text-underline:none'><span
    5899 style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5900 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    5901 style='mso-fareast-font-family:"Times New Roman"'>Clear map </span></b><span
    5902 style='mso-fareast-font-family:"Times New Roman"'>– This clears any
    5903 Fourier/charge flip map from memory; the Fourier map controls are also cleared.<span
     5871  normal'>Map peaks</b> to show them.</DD>
     5872<DT><B>Clear map </B></DT>
     5873<DD>This clears any
     5874Fourier/charge flip map from memory; the Fourier map controls are also
     5875  cleared.</DD>
     5877<DD>This allows for a change in axes, symmetry or unit cell. It is
     5878  also used to create a magnetic phase from a chemical (nuclear)
     5879  phase. One important transformation that can be done here is for
     5880  Origin 1 settings to Origin 2 (<a href="#Origin1">described below</a>)
    59045887class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    62816264algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p>
     6266<h5 style='margin-left:0.5in'><a name=Origin1></a>Origin 1 ->
     6267Origin 2 Transformations</h5>
     6269<p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6270An important transformation may be needed in certain cases when space
     6271groups that two alternate origin settings
     6273href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed here</a>).
     6274These are centrosymmetric space groups where the highest symmetry
     6275point in the structure does not contain a center of symmetry. Origin 1
     6276places the origin at the highest symmetry setting while Origin 2
     6277places the origin at a center of symmetry (creating a -x,-y,-z
     6278symmetry operator, which means that reflection phases can only be 0 or π.)
     6279GSAS-II requires use of the Origin 2 settings because computations are much
     6280faster and simpler without complex structure factors.
     6281Alas, the literature contains a number of structures reported in
     6282Origin 1, where the origin choice may not be clearly communicated. (The
     6283CIF standard does not require that origin choice be indicated.)
     6284When a structure is imported that uses any of the space groups where
     6285an origin choice is possible, a message is shown in GSAS-II notifying
     6286the user that they must confirm that the origin choice is correct.
     6287</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6290example of what can go wrong is illustrated with the structure of
     6291anatase. The space group is <I>I</I> 4<sub>1</sub>/<I>a m d</I>. In
     6292Origin 1 the coordinates are:
     6293<TABLE border=2; style='margin-left:2.0in'>
     6294  <TR>
     6295    <th colspan=4>Origin 1</th>
     6296  </TR>
     6297  <TR>
     6298    <th>atom</th>
     6299    <th colspan=3>coordinates</th>
     6300  </TR>
     6301  <TR>
     6302    <TD>Ti</TD>
     6303    <TD>0</TD>
     6304    <TD>0</TD>
     6305    <TD>0</TD>
     6306  </TR>
     6307  <TR>
     6308    <TD>O</TD>
     6309    <TD>0</TD>
     6310    <TD>0</TD>
     6311    <TD>0.208</TD>
     6312  </TR>
     6315and in Origin 2 the coordinates are:
     6316<TABLE border=2; style='margin-left:2.0in'>
     6317  <TR>
     6318    <th colspan=4>Origin 2</th>
     6319  </TR>
     6320  <TR>
     6321    <th>atom</th>
     6322    <th colspan=3>coordinates</th>
     6323  </TR>
     6324  <TR>
     6325    <TD>Ti</TD>
     6326    <TD>0</TD>
     6327    <TD>1/4</TD>
     6328    <TD>-1/8</TD>
     6329  </TR>
     6330  <TR>
     6331    <TD>O</TD>
     6332    <TD>0</TD>
     6333    <TD>1/4</TD>
     6334    <TD>0.083</TD>
     6335  </TR>
     6337where the origin is shifted by (0,0.25,-0.125).
     6338</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6339<img src="gsasII_files/wrong.png" align="right">
     6340Since GSAS-II always the symmetry operators for Origin 2,
     6341if structure is input incorrectly with the coordinates set for Origin
     63421, there are several fairly obvious signs of problems: (1) the
     6343site symmetries and multiplicities are wrong, often giving an incorrect
     6344chemical formula, (2) the interatomic distances are incorrect, and (3)
     6345a plot of the structure is improbable.
     6346In this case incorrect multiplicities gives
     6347rise to a density of 7.9 g/cc, double the correct value.
     6348Impossible interatomic distances of 1.88&Aring for Ti-Ti, and
     63491.39&Aring; for Ti-O are seen. The unit
     6350cell contents with the wrong space group operators is shown to the
     6352</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'>
     6353With coordinates that match the space
     6354group operations, the correct Ti-O distances are 1.92&Aring; and
     63551.97&Aring; and the shortest Ti-Ti distance is 3.0&Aring;.
     6356(Note that interatomic distances can be computed in GSAS-II using the Phase Atoms
     6357tab and the Compute/"Show Distances & Angles" menu item.)
     6359</p><p></p><p class=MsoNormal style='margin-left:1.0in'><span
     6360style='mso-fareast-font-family:"Times New Roman"'>
     6361<img src="gsasII_files/xform.png" align="right">
     6362<B>Transform Origin:</B>
     6363To transform a space group setting from Origin setting 1 to 2, use the
     6364Transform option in the Compute menu and then select the last option in the "Common
     6365transformations" pulldown menu, which will be setting 1->2 for space
     6366groups where both origins are available, as shown to the right. The
     6367transformation matrix will be set to the identity and the "V" vector
     6368will have the required origin shift loaded. Press OK. The changes can
     6369be seen by selecting the Atoms tab.
     6372<BR CLEAR="right" />
    62836373<h4 style='margin-left:0.25in'><a name=Data></a><u>Data</u></h4>
    73537443<hr size=2 width="100%" align=center>
    7355 <!-- hhmts start -->Last modified: Fri Oct 23 15:56:02 CDT 2020 <!-- hhmts end -->
     7445<!-- hhmts start -->Last modified: Sat Nov 21 12:25:40 CST 2020 <!-- hhmts end -->
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