Changeset 4659 for trunk/help/gsasII.html
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- Nov 21, 2020 2:15:49 PM (2 years ago)
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trunk/help/gsasII.html
r4621 r4659 5823 5823 "Times New Roman"'>This gives overall parameters describing the phase such as 5824 5824 the 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; 5825 atom present in the phase. It also has the controls for Pawley 5826 intensity extraction and for computing Fourier maps 5827 for this phase. It can also be used to compute new structures based on 5828 the unit cell and atom poistions. 5829 <span class=MsoHyperlink><span style='color:windowtext; 5827 5830 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 5828 5831 … … 5838 5841 </span></span></span></span><![endif]><span style='mso-fareast-font-family: 5839 5842 "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> 5843 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"'> 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> 5855 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"'> 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 5843 The compute menu shows computations that are possible for this phase. 5844 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 5864 5852 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this 5865 5853 procedure; 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 5854 href="Map_peaks">Map peaks</a>’ page. This page will immediately be 5868 5855 shown 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> 5871 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"'> 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 5880 5859 flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution 5881 5860 using the method of Oszlanyi & Suto (Acta Cryst. A60, 134-141, 2004). You … … 5890 5869 properly place symmetry operators (NB: depends on the quality of the resulting 5891 5870 phases), 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> 5894 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"'> 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 5874 Fourier/charge flip map from memory; the Fourier map controls are also 5875 cleared.</DD> 5876 <DT><B>Transform</B></DT> 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>) 5881 5882 5883 </DD> 5884 </DL> 5885 5886 <span 5904 5887 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 5905 5888 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> 6282 6265 6266 <h5 style='margin-left:0.5in'><a name=Origin1></a>Origin 1 -> 6267 Origin 2 Transformations</h5> 6268 6269 <p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'> 6270 An important transformation may be needed in certain cases when space 6271 groups that two alternate origin settings 6272 (<A 6273 href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#GSASIIspc.spg2origins">listed here</a>). 6274 These are centrosymmetric space groups where the highest symmetry 6275 point in the structure does not contain a center of symmetry. Origin 1 6276 places the origin at the highest symmetry setting while Origin 2 6277 places the origin at a center of symmetry (creating a -x,-y,-z 6278 symmetry operator, which means that reflection phases can only be 0 or π.) 6279 GSAS-II requires use of the Origin 2 settings because computations are much 6280 faster and simpler without complex structure factors. 6281 Alas, the literature contains a number of structures reported in 6282 Origin 1, where the origin choice may not be clearly communicated. (The 6283 CIF standard does not require that origin choice be indicated.) 6284 When a structure is imported that uses any of the space groups where 6285 an origin choice is possible, a message is shown in GSAS-II notifying 6286 the 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"'> 6288 <B>Example:</B> 6289 An 6290 example of what can go wrong is illustrated with the structure of 6291 anatase. The space group is <I>I</I> 4<sub>1</sub>/<I>a m d</I>. In 6292 Origin 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> 6313 </TABLE> 6314 6315 and 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> 6336 </TABLE> 6337 where 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"> 6340 Since GSAS-II always the symmetry operators for Origin 2, 6341 if structure is input incorrectly with the coordinates set for Origin 6342 1, there are several fairly obvious signs of problems: (1) the 6343 site symmetries and multiplicities are wrong, often giving an incorrect 6344 chemical formula, (2) the interatomic distances are incorrect, and (3) 6345 a plot of the structure is improbable. 6346 In this case incorrect multiplicities gives 6347 rise to a density of 7.9 g/cc, double the correct value. 6348 Impossible interatomic distances of 1.88Å for Ti-Ti, and 6349 1.39Å for Ti-O are seen. The unit 6350 cell contents with the wrong space group operators is shown to the 6351 right. 6352 </p><p></p><p class=MsoNormal style='margin-left:1.0in'><span style='mso-fareast-font-family:"Times New Roman"'> 6353 With coordinates that match the space 6354 group operations, the correct Ti-O distances are 1.92Å and 6355 1.97Å and the shortest Ti-Ti distance is 3.0Å. 6356 (Note that interatomic distances can be computed in GSAS-II using the Phase Atoms 6357 tab and the Compute/"Show Distances & Angles" menu item.) 6358 6359 </p><p></p><p class=MsoNormal style='margin-left:1.0in'><span 6360 style='mso-fareast-font-family:"Times New Roman"'> 6361 <img src="gsasII_files/xform.png" align="right"> 6362 <B>Transform Origin:</B> 6363 To transform a space group setting from Origin setting 1 to 2, use the 6364 Transform option in the Compute menu and then select the last option in the "Common 6365 transformations" pulldown menu, which will be setting 1->2 for space 6366 groups where both origins are available, as shown to the right. The 6367 transformation matrix will be set to the identity and the "V" vector 6368 will have the required origin shift loaded. Press OK. The changes can 6369 be seen by selecting the Atoms tab. 6370 6371 </span></p> 6372 <BR CLEAR="right" /> 6283 6373 <h4 style='margin-left:0.25in'><a name=Data></a><u>Data</u></h4> 6284 6374 … … 7353 7443 <hr size=2 width="100%" align=center> 7354 7444 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 --> 7356 7446 7357 7447 </div>
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