Changeset 1718 for Tutorials/MCsimanneal


Ignore:
Timestamp:
Mar 16, 2015 4:18:34 PM (7 years ago)
Author:
vondreele
Message:

updating images in tutorials

Location:
Tutorials/MCsimanneal
Files:
8 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/MCsimanneal/MCSA in GSAS.htm

    r1705 r1718  
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    2323  <o:Author>vondreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>15</o:Revision>
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    3232  <o:Company>Argonne National Laboratory</o:Company>
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     114  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     115   UnhideWhenUsed="true" Name="toc 3"/>
     116  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     117   UnhideWhenUsed="true" Name="toc 4"/>
     118  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     119   UnhideWhenUsed="true" Name="toc 5"/>
     120  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     121   UnhideWhenUsed="true" Name="toc 6"/>
     122  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     123   UnhideWhenUsed="true" Name="toc 7"/>
     124  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     125   UnhideWhenUsed="true" Name="toc 8"/>
     126  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     127   UnhideWhenUsed="true" Name="toc 9"/>
     128  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     129   Name="Normal Indent"/>
     130  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     131   Name="footnote text"/>
     132  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     133   Name="annotation text"/>
     134  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     135   Name="header"/>
     136  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     137   Name="footer"/>
     138  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     139   Name="index heading"/>
     140  <w:LsdException Locked="false" Priority="35" SemiHidden="true"
     141   UnhideWhenUsed="true" QFormat="true" Name="caption"/>
     142  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     143   Name="table of figures"/>
     144  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     145   Name="envelope address"/>
     146  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     147   Name="envelope return"/>
     148  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     149   Name="footnote reference"/>
     150  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     151   Name="annotation reference"/>
     152  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     153   Name="line number"/>
     154  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     155   Name="page number"/>
     156  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     157   Name="endnote reference"/>
     158  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     159   Name="endnote text"/>
     160  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     161   Name="table of authorities"/>
     162  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     163   Name="macro"/>
     164  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     165   Name="toa heading"/>
     166  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     167   Name="List"/>
     168  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     169   Name="List Bullet"/>
     170  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     171   Name="List Number"/>
     172  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     173   Name="List 2"/>
     174  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     175   Name="List 3"/>
     176  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     177   Name="List 4"/>
     178  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     179   Name="List 5"/>
     180  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     181   Name="List Bullet 2"/>
     182  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     183   Name="List Bullet 3"/>
     184  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     185   Name="List Bullet 4"/>
     186  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     187   Name="List Bullet 5"/>
     188  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     189   Name="List Number 2"/>
     190  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     191   Name="List Number 3"/>
     192  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     193   Name="List Number 4"/>
     194  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     195   Name="List Number 5"/>
     196  <w:LsdException Locked="false" Priority="10" QFormat="true" Name="Title"/>
     197  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     198   Name="Closing"/>
     199  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     200   Name="Signature"/>
     201  <w:LsdException Locked="false" Priority="1" SemiHidden="true"
     202   UnhideWhenUsed="true" Name="Default Paragraph Font"/>
     203  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     204   Name="Body Text"/>
     205  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     206   Name="Body Text Indent"/>
     207  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     208   Name="List Continue"/>
     209  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     210   Name="List Continue 2"/>
     211  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     212   Name="List Continue 3"/>
     213  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     214   Name="List Continue 4"/>
     215  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     216   Name="List Continue 5"/>
     217  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     218   Name="Message Header"/>
     219  <w:LsdException Locked="false" Priority="11" QFormat="true" Name="Subtitle"/>
     220  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     221   Name="Salutation"/>
     222  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     223   Name="Date"/>
     224  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     225   Name="Body Text First Indent"/>
     226  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     227   Name="Body Text First Indent 2"/>
     228  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     229   Name="Note Heading"/>
     230  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     231   Name="Body Text 2"/>
     232  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     233   Name="Body Text 3"/>
     234  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     235   Name="Body Text Indent 2"/>
     236  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     237   Name="Body Text Indent 3"/>
     238  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     239   Name="Block Text"/>
     240  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     241   Name="Hyperlink"/>
     242  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     243   Name="FollowedHyperlink"/>
     244  <w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/>
     245  <w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/>
     246  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     247   Name="Document Map"/>
     248  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     249   Name="Plain Text"/>
     250  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     251   Name="E-mail Signature"/>
     252  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     253   Name="HTML Top of Form"/>
     254  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     255   Name="HTML Bottom of Form"/>
     256  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     257   Name="Normal (Web)"/>
     258  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     259   Name="HTML Acronym"/>
     260  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     261   Name="HTML Address"/>
     262  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     263   Name="HTML Cite"/>
     264  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     265   Name="HTML Code"/>
     266  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     267   Name="HTML Definition"/>
     268  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     269   Name="HTML Keyboard"/>
     270  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     271   Name="HTML Preformatted"/>
     272  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     273   Name="HTML Sample"/>
     274  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     275   Name="HTML Typewriter"/>
     276  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     277   Name="HTML Variable"/>
     278  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     279   Name="Normal Table"/>
     280  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     281   Name="annotation subject"/>
     282  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     283   Name="No List"/>
     284  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     285   Name="Outline List 1"/>
     286  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     287   Name="Outline List 2"/>
     288  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     289   Name="Outline List 3"/>
     290  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     291   Name="Table Simple 1"/>
     292  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     293   Name="Table Simple 2"/>
     294  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     295   Name="Table Simple 3"/>
     296  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     297   Name="Table Classic 1"/>
     298  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     299   Name="Table Classic 2"/>
     300  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     301   Name="Table Classic 3"/>
     302  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     303   Name="Table Classic 4"/>
     304  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     305   Name="Table Colorful 1"/>
     306  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     307   Name="Table Colorful 2"/>
     308  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     309   Name="Table Colorful 3"/>
     310  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     311   Name="Table Columns 1"/>
     312  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     313   Name="Table Columns 2"/>
     314  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     315   Name="Table Columns 3"/>
     316  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     317   Name="Table Columns 4"/>
     318  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     319   Name="Table Columns 5"/>
     320  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     321   Name="Table Grid 1"/>
     322  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     323   Name="Table Grid 2"/>
     324  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     325   Name="Table Grid 3"/>
     326  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     327   Name="Table Grid 4"/>
     328  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     329   Name="Table Grid 5"/>
     330  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     331   Name="Table Grid 6"/>
     332  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     333   Name="Table Grid 7"/>
     334  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     335   Name="Table Grid 8"/>
     336  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     337   Name="Table List 1"/>
     338  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     339   Name="Table List 2"/>
     340  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     341   Name="Table List 3"/>
     342  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     343   Name="Table List 4"/>
     344  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     345   Name="Table List 5"/>
     346  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     347   Name="Table List 6"/>
     348  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     349   Name="Table List 7"/>
     350  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     351   Name="Table List 8"/>
     352  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     353   Name="Table 3D effects 1"/>
     354  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     355   Name="Table 3D effects 2"/>
     356  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     357   Name="Table 3D effects 3"/>
     358  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     359   Name="Table Contemporary"/>
     360  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     361   Name="Table Elegant"/>
     362  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     363   Name="Table Professional"/>
     364  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     365   Name="Table Subtle 1"/>
     366  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     367   Name="Table Subtle 2"/>
     368  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     369   Name="Table Web 1"/>
     370  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     371   Name="Table Web 2"/>
     372  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     373   Name="Table Web 3"/>
     374  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     375   Name="Balloon Text"/>
     376  <w:LsdException Locked="false" Priority="59" Name="Table Grid"/>
     377  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
     378   Name="Table Theme"/>
     379  <w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/>
     380  <w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/>
     381  <w:LsdException Locked="false" Priority="60" Name="Light Shading"/>
     382  <w:LsdException Locked="false" Priority="61" Name="Light List"/>
     383  <w:LsdException Locked="false" Priority="62" Name="Light Grid"/>
     384  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/>
     385  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/>
     386  <w:LsdException Locked="false" Priority="65" Name="Medium List 1"/>
     387  <w:LsdException Locked="false" Priority="66" Name="Medium List 2"/>
     388  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/>
     389  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/>
     390  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/>
     391  <w:LsdException Locked="false" Priority="70" Name="Dark List"/>
     392  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/>
     393  <w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
     394  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
     395  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
     396  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
     397  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
     398  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
     399  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
     400  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
     401  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
     402  <w:LsdException Locked="false" Priority="34" QFormat="true"
     403   Name="List Paragraph"/>
     404  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
     405  <w:LsdException Locked="false" Priority="30" QFormat="true"
     406   Name="Intense Quote"/>
     407  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
     408  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
     409  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
     410  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
     411  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
     412  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
     413  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
     414  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
     415  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
     416  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
     417  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
     418  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
     419  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
     420  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
     421  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
     422  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
     423  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
     424  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
     425  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
     426  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
     427  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
     428  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
     429  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
     430  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
     431  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
     432  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
     433  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
     434  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
     435  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
     436  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
     437  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
     438  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
     439  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
     440  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
     441  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
     442  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
     443  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
     444  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
     445  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
     446  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
     447  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
     448  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
     449  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
     450  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
     451  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
     452  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
     453  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
     454  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
     455  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
     456  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
     457  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
     458  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
     459  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
     460  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
     461  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
     462  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
     463  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
     464  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
     465  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
     466  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
     467  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
     468  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
     469  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
     470  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
     471  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
     472  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
     473  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
     474  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
     475  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
     476  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
     477  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
     478  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
     479  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
     480  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
     481  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
     482  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
     483  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
     484  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
     485  <w:LsdException Locked="false" Priority="19" QFormat="true"
     486   Name="Subtle Emphasis"/>
     487  <w:LsdException Locked="false" Priority="21" QFormat="true"
     488   Name="Intense Emphasis"/>
     489  <w:LsdException Locked="false" Priority="31" QFormat="true"
     490   Name="Subtle Reference"/>
     491  <w:LsdException Locked="false" Priority="32" QFormat="true"
     492   Name="Intense Reference"/>
     493  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
     494  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
     495   UnhideWhenUsed="true" Name="Bibliography"/>
     496  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
     497   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
     498  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
     499  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
     500  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
     501  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
     502  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
     503  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
     504  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
     505  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
     506  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
     507  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
     508  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
     509  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
     510  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
     511  <w:LsdException Locked="false" Priority="46"
     512   Name="Grid Table 1 Light Accent 1"/>
     513  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
     514  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
     515  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
     516  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
     517  <w:LsdException Locked="false" Priority="51"
     518   Name="Grid Table 6 Colorful Accent 1"/>
     519  <w:LsdException Locked="false" Priority="52"
     520   Name="Grid Table 7 Colorful Accent 1"/>
     521  <w:LsdException Locked="false" Priority="46"
     522   Name="Grid Table 1 Light Accent 2"/>
     523  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
     524  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
     525  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
     526  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
     527  <w:LsdException Locked="false" Priority="51"
     528   Name="Grid Table 6 Colorful Accent 2"/>
     529  <w:LsdException Locked="false" Priority="52"
     530   Name="Grid Table 7 Colorful Accent 2"/>
     531  <w:LsdException Locked="false" Priority="46"
     532   Name="Grid Table 1 Light Accent 3"/>
     533  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
     534  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
     535  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
     536  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
     537  <w:LsdException Locked="false" Priority="51"
     538   Name="Grid Table 6 Colorful Accent 3"/>
     539  <w:LsdException Locked="false" Priority="52"
     540   Name="Grid Table 7 Colorful Accent 3"/>
     541  <w:LsdException Locked="false" Priority="46"
     542   Name="Grid Table 1 Light Accent 4"/>
     543  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
     544  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
     545  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
     546  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
     547  <w:LsdException Locked="false" Priority="51"
     548   Name="Grid Table 6 Colorful Accent 4"/>
     549  <w:LsdException Locked="false" Priority="52"
     550   Name="Grid Table 7 Colorful Accent 4"/>
     551  <w:LsdException Locked="false" Priority="46"
     552   Name="Grid Table 1 Light Accent 5"/>
     553  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
     554  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
     555  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
     556  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
     557  <w:LsdException Locked="false" Priority="51"
     558   Name="Grid Table 6 Colorful Accent 5"/>
     559  <w:LsdException Locked="false" Priority="52"
     560   Name="Grid Table 7 Colorful Accent 5"/>
     561  <w:LsdException Locked="false" Priority="46"
     562   Name="Grid Table 1 Light Accent 6"/>
     563  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
     564  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
     565  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
     566  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
     567  <w:LsdException Locked="false" Priority="51"
     568   Name="Grid Table 6 Colorful Accent 6"/>
     569  <w:LsdException Locked="false" Priority="52"
     570   Name="Grid Table 7 Colorful Accent 6"/>
     571  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
     572  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
     573  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
     574  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
     575  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
     576  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
     577  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
     578  <w:LsdException Locked="false" Priority="46"
     579   Name="List Table 1 Light Accent 1"/>
     580  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
     581  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
     582  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
     583  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
     584  <w:LsdException Locked="false" Priority="51"
     585   Name="List Table 6 Colorful Accent 1"/>
     586  <w:LsdException Locked="false" Priority="52"
     587   Name="List Table 7 Colorful Accent 1"/>
     588  <w:LsdException Locked="false" Priority="46"
     589   Name="List Table 1 Light Accent 2"/>
     590  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
     591  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
     592  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
     593  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
     594  <w:LsdException Locked="false" Priority="51"
     595   Name="List Table 6 Colorful Accent 2"/>
     596  <w:LsdException Locked="false" Priority="52"
     597   Name="List Table 7 Colorful Accent 2"/>
     598  <w:LsdException Locked="false" Priority="46"
     599   Name="List Table 1 Light Accent 3"/>
     600  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
     601  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
     602  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
     603  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
     604  <w:LsdException Locked="false" Priority="51"
     605   Name="List Table 6 Colorful Accent 3"/>
     606  <w:LsdException Locked="false" Priority="52"
     607   Name="List Table 7 Colorful Accent 3"/>
     608  <w:LsdException Locked="false" Priority="46"
     609   Name="List Table 1 Light Accent 4"/>
     610  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
     611  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
     612  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
     613  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
     614  <w:LsdException Locked="false" Priority="51"
     615   Name="List Table 6 Colorful Accent 4"/>
     616  <w:LsdException Locked="false" Priority="52"
     617   Name="List Table 7 Colorful Accent 4"/>
     618  <w:LsdException Locked="false" Priority="46"
     619   Name="List Table 1 Light Accent 5"/>
     620  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
     621  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
     622  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
     623  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
     624  <w:LsdException Locked="false" Priority="51"
     625   Name="List Table 6 Colorful Accent 5"/>
     626  <w:LsdException Locked="false" Priority="52"
     627   Name="List Table 7 Colorful Accent 5"/>
     628  <w:LsdException Locked="false" Priority="46"
     629   Name="List Table 1 Light Accent 6"/>
     630  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
     631  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
     632  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
     633  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
     634  <w:LsdException Locked="false" Priority="51"
     635   Name="List Table 6 Colorful Accent 6"/>
     636  <w:LsdException Locked="false" Priority="52"
     637   Name="List Table 7 Colorful Accent 6"/>
    336638 </w:LatentStyles>
    337639</xml><![endif]-->
     
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     644        {font-family:"Cambria Math";
    343645        panose-1:2 4 5 3 5 4 6 3 2 4;
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     646        mso-font-charset:1;
    345647        mso-generic-font-family:roman;
     648        mso-font-format:other;
    346649        mso-font-pitch:variable;
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    348651@font-face
    349652        {font-family:Calibri;
     
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     659        {font-family:Cambria;
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     662        mso-generic-font-family:roman;
     663        mso-font-pitch:variable;
     664        mso-font-signature:-536870145 1073743103 0 0 415 0;}
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    370680        font-size:12.0pt;
    371         font-family:"Times New Roman","serif";
     681        font-family:"Times New Roman",serif;
    372682        mso-fareast-font-family:"Times New Roman";
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    384694        mso-outline-level:1;
    385695        font-size:24.0pt;
    386         font-family:"Times New Roman","serif";
     696        font-family:"Times New Roman",serif;
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    401711        font-size:18.0pt;
    402         font-family:"Times New Roman","serif";
     712        font-family:"Times New Roman",serif;
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    417727        font-size:13.5pt;
    418         font-family:"Times New Roman","serif";
     728        font-family:"Times New Roman",serif;
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    435745        font-size:13.0pt;
    436         font-family:"Cambria","serif";
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    454764        font-size:12.0pt;
    455         font-family:"Times New Roman","serif";
     765        font-family:"Times New Roman",serif;
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    472         font-family:"Cambria","serif";
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    497807        font-size:8.0pt;
    498         font-family:"Tahoma","sans-serif";
     808        font-family:"Tahoma",sans-serif;
    499809        mso-fareast-font-family:"Times New Roman";
    500810        mso-fareast-theme-font:minor-fareast;}
     
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    509819        font-size:12.0pt;
    510         font-family:"Times New Roman","serif";
     820        font-family:"Times New Roman",serif;
    511821        mso-fareast-font-family:"Times New Roman";
    512822        mso-fareast-theme-font:minor-fareast;}
     
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    532842        font-size:8.0pt;
    533         font-family:"Tahoma","sans-serif";
     843        font-family:"Tahoma",sans-serif;
    534844        mso-fareast-font-family:"Times New Roman";
    535845        mso-fareast-theme-font:minor-fareast;}
     
    548858        mso-pagination:widow-orphan;
    549859        font-size:12.0pt;
    550         font-family:"Times New Roman","serif";
     860        font-family:"Times New Roman",serif;
    551861        mso-fareast-font-family:"Times New Roman";
    552862        mso-fareast-theme-font:minor-fareast;}
     
    563873        mso-pagination:widow-orphan;
    564874        font-size:12.0pt;
    565         font-family:"Times New Roman","serif";
     875        font-family:"Times New Roman",serif;
    566876        mso-fareast-font-family:"Times New Roman";
    567877        mso-fareast-theme-font:minor-fareast;}
     
    582892        mso-style-locked:yes;
    583893        mso-style-link:"Heading 1";
    584         font-family:"Times New Roman","serif";
     894        font-family:"Times New Roman",serif;
    585895        mso-ascii-font-family:"Times New Roman";
    586896        mso-hansi-font-family:"Times New Roman";
     
    594904        mso-style-locked:yes;
    595905        mso-style-link:"Heading 2";
    596         font-family:"Times New Roman","serif";
     906        font-family:"Times New Roman",serif;
    597907        mso-ascii-font-family:"Times New Roman";
    598908        mso-hansi-font-family:"Times New Roman";
     
    606916        mso-style-locked:yes;
    607917        mso-style-link:"Heading 3";
    608         font-family:"Times New Roman","serif";
     918        font-family:"Times New Roman",serif;
    609919        mso-ascii-font-family:"Times New Roman";
    610920        mso-hansi-font-family:"Times New Roman";
     
    618928        mso-style-locked:yes;
    619929        mso-style-link:"Heading 4";
    620         font-family:"Cambria","serif";
     930        font-family:"Cambria",serif;
    621931        mso-ascii-font-family:Cambria;
    622932        mso-hansi-font-family:Cambria;
     
    631941        mso-style-locked:yes;
    632942        mso-style-link:"Heading 5";
    633         font-family:"Times New Roman","serif";
     943        font-family:"Times New Roman",serif;
    634944        mso-ascii-font-family:"Times New Roman";
    635945        mso-hansi-font-family:"Times New Roman";
     
    654964        mso-style-locked:yes;
    655965        mso-style-link:Title;
    656         font-family:"Cambria","serif";
     966        font-family:"Cambria",serif;
    657967        mso-ascii-font-family:Cambria;
    658968        mso-hansi-font-family:Cambria;
     
    666976        mso-style-locked:yes;
    667977        mso-style-link:"Document Map";
    668         font-family:"Tahoma","sans-serif";
     978        font-family:"Tahoma",sans-serif;
    669979        mso-ascii-font-family:Tahoma;
    670980        mso-hansi-font-family:Tahoma;
     
    677987        mso-style-locked:yes;
    678988        mso-style-link:"Balloon Text";
    679         font-family:"Tahoma","sans-serif";
     989        font-family:"Tahoma",sans-serif;
    680990        mso-ascii-font-family:Tahoma;
    681991        mso-hansi-font-family:Tahoma;
     
    6901000        mso-pagination:widow-orphan;
    6911001        font-size:26.0pt;
    692         font-family:"Cambria","serif";
     1002        font-family:"Cambria",serif;
    6931003        mso-fareast-font-family:"Times New Roman";
    6941004        mso-fareast-theme-font:minor-fareast;
     
    7051015        mso-pagination:widow-orphan;
    7061016        font-size:26.0pt;
    707         font-family:"Cambria","serif";
     1017        font-family:"Cambria",serif;
    7081018        mso-fareast-font-family:"Times New Roman";
    7091019        mso-fareast-theme-font:minor-fareast;
     
    7221032        mso-pagination:widow-orphan;
    7231033        font-size:26.0pt;
    724         font-family:"Cambria","serif";
     1034        font-family:"Cambria",serif;
    7251035        mso-fareast-font-family:"Times New Roman";
    7261036        mso-fareast-theme-font:minor-fareast;
     
    7401050        mso-pagination:widow-orphan;
    7411051        font-size:12.0pt;
    742         font-family:"Times New Roman","serif";
     1052        font-family:"Times New Roman",serif;
    7431053        mso-fareast-font-family:"Times New Roman";
    7441054        mso-fareast-theme-font:minor-fareast;}
     
    7551065        mso-pagination:widow-orphan;
    7561066        font-size:12.0pt;
    757         font-family:"Times New Roman","serif";
     1067        font-family:"Times New Roman",serif;
    7581068        mso-fareast-font-family:"Times New Roman";
    7591069        mso-fareast-theme-font:minor-fareast;}
     
    7701080        mso-pagination:widow-orphan;
    7711081        font-size:12.0pt;
    772         font-family:"Times New Roman","serif";
     1082        font-family:"Times New Roman",serif;
    7731083        mso-fareast-font-family:"Times New Roman";
    7741084        mso-fareast-theme-font:minor-fareast;}
     
    7841094        mso-pagination:widow-orphan;
    7851095        font-size:10.0pt;
    786         font-family:"Calibri","sans-serif";
     1096        font-family:"Calibri",sans-serif;
    7871097        mso-fareast-font-family:"Times New Roman";
    7881098        mso-fareast-theme-font:minor-fareast;
    7891099        mso-bidi-font-family:Calibri;}
    790 span.SpellE
    791         {mso-style-name:"";
    792         mso-spl-e:yes;}
    793 span.GramE
    794         {mso-style-name:"";
    795         mso-gram-e:yes;}
    7961100.MsoChpDefault
    7971101        {mso-style-type:export-only;
     
    8001104        mso-ansi-font-size:10.0pt;
    8011105        mso-bidi-font-size:10.0pt;
    802         font-family:"Calibri","sans-serif";
     1106        font-family:"Calibri",sans-serif;
    8031107        mso-ascii-font-family:Calibri;
    8041108        mso-hansi-font-family:Calibri;
     
    9351239        mso-pagination:widow-orphan;
    9361240        font-size:10.0pt;
    937         font-family:"Calibri","sans-serif";}
     1241        font-family:"Calibri",sans-serif;}
    9381242</style>
    9391243<![endif]--><!--[if gte mso 9]><xml>
     
    9551259<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
    9561260structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
    957 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
    958 were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
    959 and were originally collected on NSLS beam line X3b1. The MC/SA technique is
    960 needed in these cases because as you will see the data does not extend very far
    961 in 2&#920; so one cannot use charge flipping to solve them. The steps for each
    962 begin with peak selection and fitting, then indexing to identify the lattice
    963 parameters. A Pawley refinement is used to obtain a set of structure factors
    964 needed for the MC/SA runs. We will use previously developed models for the two
    965 molecules; I used the freeware program Avogadro (<a
    966 href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
     1261diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
     1262kindly provided by Peter Stephens (SUNY StonyBrook) and were originally
     1263collected on NSLS beam line X3b1. The MC/SA technique is needed in these cases
     1264because as you will see the data does not extend very far in 2&#920; so one
     1265cannot use charge flipping to solve them. The steps for each begin with peak
     1266selection and fitting, then indexing to identify the lattice parameters. A
     1267Pawley refinement is used to obtain a set of structure factors needed for the
     1268MC/SA runs. We will use previously developed models for the two molecules; I
     1269used the freeware program Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
    9671270to create them.</p>
    9681271
    9691272<p class=MsoNormal>If you have not done so already, <a
    970 href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
    971 
    972 <h2><span class=GramE>Step 1.</span> Import powder data for 3-aminoquinoline</h2>
     1273href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a>.</p>
     1274
     1275<h2>Step 1. Import powder data for 3-aminoquinoline</h2>
    9731276
    9741277<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
    9751278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    9761279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    977 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1280the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    9781281mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    9791282Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
    9801283data file</span></b> menu item to read the data file into the current GSAS-II
    9811284project. Change the file directory to <b style='mso-bidi-font-weight:normal'><span
    982 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1285style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    9831286mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    984 minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri","sans-serif";
     1287minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri",sans-serif;
    9851288mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    9861289Calibri;mso-bidi-theme-font:minor-latin'> to find the file; you may need to
     
    9911294style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    9921295style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    993 the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    994 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1296the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1298Calibri;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b><span
     1299style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    9951300mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    996 minor-latin'>Quinoli.gda</span></b></span><span style='font-family:"Calibri","sans-serif";
    997 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    998 Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
    999 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1301minor-latin'> data</span> file in the first dialog and press <b
     1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10001303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    10011304Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1002 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1003 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1305Dialog box asking <b style='mso-bidi-font-weight:normal'><span
     1306style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10041307mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1005 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1006 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1007 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1008 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    1009 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1010 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1011 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
    1012 proceed.</p>
     1308minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
     1309normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1310minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1311mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
    10131312
    10141313<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
    10151314style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    10161315style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    1017 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1316the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10181317mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1019 Calibri;mso-bidi-theme-font:minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b>
    1020 instrument parameter file in the second dialog and press <b style='mso-bidi-font-weight:
    1021 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1318Calibri;mso-bidi-theme-font:minor-latin'>BNL-I.instprm</span></b> instrument
     1319parameter file in the second dialog and press <b style='mso-bidi-font-weight:
     1320normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    10221321minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    10231322mso-bidi-theme-font:minor-latin'>Open</span></b>. You’ll have to change the
    10241323file type to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1025 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1026 minor-latin'>*.<span class=SpellE>instprm</span></span></b> (GSAS-II instrument
    1027 parameter file). The powder pattern will immediately appear.</p>
     1324"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1325minor-latin'>*.instprm</span></b> (GSAS-II instrument parameter file). The
     1326powder pattern will immediately appear.</p>
    10281327
    10291328<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    10511350 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
    10521351</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1053 src="MCSA%20in%20GSAS_files/image031.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
     1352src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
    10541353
    10551354<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    105913581Å or better. </p>
    10601359
    1061 <h2><span class=GramE>Step 2.</span> Peak picking &amp; fitting</h2>
     1360<h2>Step 2. Peak picking &amp; fitting</h2>
    10621361
    10631362<p class=MsoNormal>Next you need to select limits so that ~20 peaks are
    10641363selected for indexing; go to <b style='mso-bidi-font-weight:normal'><span
    1065 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1364style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10661365mso-hansi-theme-font:minor-latin'>Limits</span></b> and choose <b
    1067 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1366style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10681367mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>°
    106913682&#920;. Next go to <b style='mso-bidi-font-weight:normal'><span
    1070 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1369style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    10711370mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks
    10721371you can see between the limits. This is most easily done by hand as the <b
    1073 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1372style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10741373mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b>
    10751374routine gives a lot of spurious peaks for this rather noisy and weak data; I
    10761375picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
    1077 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1078 minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span
    1079 class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at
    1080 least <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1081 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1082 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1083 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    1084 in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1376normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1377minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ PeakFit </span></b>to
     1378fit them. You will need to vary at least <b style='mso-bidi-font-weight:normal'><span
     1379style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1380mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
     1381normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1382minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> in <b
     1383style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    10851384mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    1086 Parameters</span></b> along with <span class=SpellE><b style='mso-bidi-font-weight:
    1087 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1088 minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span> &amp; <span
    1089 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1090 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1091 minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span
    1092 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1093 mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit
    1094 suitable for indexing.</p>
    1095 
    1096 <h2><span class=GramE>Step 3.</span> Indexing</h2>
     1385Parameters</span></b> along with <b style='mso-bidi-font-weight:normal'><span
     1386style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1387mso-hansi-theme-font:minor-latin'>pos</span></b> &amp; <b style='mso-bidi-font-weight:
     1388normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1389minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> in the <b
     1390style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1391mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
     1392to get a reasonable fit suitable for indexing.</p>
     1393
     1394<h2>Step 3. Indexing</h2>
    10971395
    10981396<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
    1099 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1397style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11001398mso-hansi-theme-font:minor-latin'>Index Peak List</span></b> and do <b
    1101 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1399style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11021400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
    11031401to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight:
    1104 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1402normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    11051403minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
    1106 indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
    1107 small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
    1108 both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
    1109 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1110 mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
    1111 cell should almost immediately appear with an M20 ~330 with a=7.748, b=7.651,
    1112 c=12.736, <span class=SpellE>Vol</span>=755.01. Do <b style='mso-bidi-font-weight:
    1113 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1114 minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>;
    1115 you can then try various space groups. Press the <b style='mso-bidi-font-weight:
    1116 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1117 minor-latin;mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to
    1118 see the lines with extinctions (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
    1119 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1404indexing. The most likely Bravais lattice for these small organic molecules is
     1405either Orthorhombic-P or Monoclinic-P; you can try both and see what comes out
     1406(Hint: it’s <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1407"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1408minor-latin'>Orthorhombic-P</span></b>). The correct unit cell should almost
     1409immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736,
     1410Vol=755.01. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1411"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1412minor-latin'>Cell Index/Refine/Copy Cell</span></b>; you can then try various
     1413space groups. Press the <b style='mso-bidi-font-weight:normal'><span
     1414style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1415mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to see the
     1416lines with extinctions (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
     1417style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11201418mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub> 2<sub>1</sub> 2<sub>1</sub></span></b>).
    11211419You can then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1122 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1420"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    11231421minor-latin'>Cell Index/Refine/Refine Cell</span></b> to improve the lattice
    11241422parameters with M20 ~380. Finally do <b style='mso-bidi-font-weight:normal'><span
    1125 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1423style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11261424mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b>
    11271425to create the phase; I named it <b style='mso-bidi-font-weight:normal'><span
    1128 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1426style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11291427mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
    11301428
    1131 <h2><span class=GramE>Step 4.</span> Setup for Pawley refinement</h2>
     1429<h2>Step 4. Setup for Pawley refinement</h2>
    11321430
    11331431<p class=MsoNormal>There are a number of steps that must be done in preparation
     
    11391437style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    11401438style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    1141 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1439<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11421440mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
    11431441in the GSAS-II data tree for the PWDR data set and expand the plot so that the
     
    11531451style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    11541452style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    1155 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1453<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11561454mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    11571455Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
    1158 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1456style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11591457mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
    1160 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1458style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11611459mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
    11621460profile</span></b> to recover the default values. The peak fitting done earlier
     
    11711469style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    11721470style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    1173 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1174 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>
    1175 and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
    1176 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1177 mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
     1471<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1472mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
     1473Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
     1474normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1475minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
    11781476
    11791477<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    11801478style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    11811479style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
    1182 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1480to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    11831481mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b>
    11841482to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1185 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1483"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    11861484minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
    1187 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1485normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    11881486minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
    11891487box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight:
    1190 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1191 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
    1192 box.</p>
     1488normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1489minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> box.</p>
    11931490
    11941491<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
    1195 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1492style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    11961493mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
    11971494
     
    12011498 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
    12021499</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
    1203 src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1500src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
    12041501
    12051502<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12061503
    12071504<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    1208 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1505style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12091506mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
    12101507for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
    1211 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1508style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12121509mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
    12131510dialog box will appear</p>
     
    12181515 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
    12191516</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
    1220 src="MCSA%20in%20GSAS_files/image033.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1517src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
    12211518
    12221519<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12241521<p class=MsoNormal>Select either choice; the desired data set will be added to
    12251522this phase for analysis. The data tab now shows the new data set; check the <b
    1226 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1523style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12271524mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    12281525button to see the full information</p>
     
    12331530 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
    12341531</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
    1235 src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1532src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    12361533
    12371534<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    12381535
    12391536<p class=MsoNormal>This is the location for all the phase dependent parameters
    1240 for this histogram. Notice that it includes phase fraction, size &amp; <span
    1241 class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
    1242 and extinction corrections. The <span class=SpellE>Babinet</span> correction is
    1243 intended for protein work where a significant region of the structure is
    1244 disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
    1245 surfaces and preferred orientation correction curves.</p>
     1537for this histogram. Notice that it includes phase fraction, size &amp; mustrain
     1538as well as preferred orientation, elastic strain and extinction corrections.
     1539The Babinet correction is intended for protein work where a significant region
     1540of the structure is disordered solvent. There are buttons for plotting size and
     1541mustrain surfaces and preferred orientation correction curves.</p>
    12461542
    12471543<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    1248 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1544style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12491545mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
    1250 empty except for column headings. <span class=GramE>Do</span> <b
    1251 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1252 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
    1253 create</span></b>; this makes the reflection set over the range covered by
    1254 setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1255 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
    1256 class=SpellE>dmin</span></span></b>. The table should list reflections 0-91.
    1257 Select and check the <b style='mso-bidi-font-weight:normal'><span
    1258 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1259 mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same
    1260 technique you used for the peak list. </p>
     1546empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
     1547style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1548mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
     1549makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
     1550normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1551minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
     1552should list reflections 0-91. Select and check the <b style='mso-bidi-font-weight:
     1553normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1554minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column using
     1555the same technique you used for the peak list. </p>
    12611556
    12621557<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    12651560 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
    12661561</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
    1267 src="MCSA%20in%20GSAS_files/image035.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1562src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
    12681563
    12691564<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    12721567you didn’t skip a step as it might not work correctly if you did.</p>
    12731568
    1274 <h2><span class=GramE>Step 5.</span> Pawley refinement</h2>
     1569<h2>Step 5. Pawley refinement</h2>
    12751570
    12761571<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
    1277 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1572normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    12781573minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
    12791574the main GSAS-II data tree window. Before it begins a backup of the project
    12801575file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
    1281 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1576style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12821577mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
    12831578used to recover from a bad refinement. A progress dialog box will appear
    1284 showing the residual as the refinement proceeds. My refinement completed with <span
    1285 class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load
    1286 the result. Press <b style='mso-bidi-font-weight:normal'><span
    1287 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1288 mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
    1289 PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
     1579showing the residual as the refinement proceeds. My refinement completed with
     1580Rwp ~12.9%; a dialog box appears asking if you wish to load the result. Press <b
     1581style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1582mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     1583To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
     1584the width and height).</p>
    12901585
    12911586<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    12941589 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
    12951590</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1296 src="MCSA%20in%20GSAS_files/image036.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
     1591src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
    12971592
    12981593<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    13021597background model. One easy way to fit that broad hump is to add a peak to the
    13031598background. Go to <b style='mso-bidi-font-weight:normal'><span
    1304 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1599style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13051600mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b
    1306 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1601style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13071602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b>
    1308 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1603to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13091604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
    1310 then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1311 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1312 mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <b style='mso-bidi-font-weight:
    1313 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1314 minor-latin;mso-hansi-theme-font:minor-latin'>19</span></b>, <span
    1315 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1316 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1317 minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span
    1318 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1319 mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight:
    1320 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1321 minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
    1322 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1605then change <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1606"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1607minor-latin'>pos</span></b> to <b style='mso-bidi-font-weight:normal'><span
     1608style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1609mso-hansi-theme-font:minor-latin'>19</span></b>, <b style='mso-bidi-font-weight:
     1610normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1611minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> to <b
     1612style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1613mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
     1614and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
     1616to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13231617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>;
    13241618for the peak only refine <b style='mso-bidi-font-weight:normal'><span
    1325 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1619style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13261620mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
    1327 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1328 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
    1329 class=SpellE>coeff</span>.</span></b> <span class=GramE>to</span> <b
    1330 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1621style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1622mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
     1623to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13311624mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>;
    13321625the window shows</p>
     
    13371630 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
    13381631</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
    1339 src="MCSA%20in%20GSAS_files/image037.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1632src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    13401633
    13411634<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    13421635
    13431636<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    1344 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1345 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
    1346 class=SpellE>Rwp</span> fell to ~8.5%. In <b style='mso-bidi-font-weight:normal'><span
    1347 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1348 mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
    1349 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1350 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1351 minor-latin'>pos</span></b></span> &amp; <b style='mso-bidi-font-weight:normal'><span
    1352 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1353 mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b
    1354 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1355 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    1356 Parameters</span></b> select <b style='mso-bidi-font-weight:normal'><span
    1357 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1358 mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
    1359 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1360 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then
    1361 do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1362 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1363 mso-hansi-theme-font:minor-latin'>Calculate</span></b></span><b
    1364 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1365 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> /Refine</span></b>
    1366 again. I got Rwp~7.5% at convergence and the fit looked like</p>
     1637style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1638mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my Rwp fell to
     1639~8.5%. In <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>
     1641select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1642mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>
     1643&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
     1645for refinement and in <b style='mso-bidi-font-weight:normal'><span
     1646style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1647mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> select <b
     1648style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1649mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     1650&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1651mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
     1652for refinement; then do <b style='mso-bidi-font-weight:normal'><span
     1653style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1654mso-hansi-theme-font:minor-latin'>Calculate /Refine</span></b> again. I got
     1655Rwp~7.5% at convergence and the fit looked like</p>
    13671656
    13681657<p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
     
    13711660 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
    13721661</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1373 src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1662src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    13741663
    13751664<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    13781667Annealing.</p>
    13791668
    1380 <h2><span class=GramE>Step 6.</span> Setup for Monte Carlo/Simulated Annealing</h2>
    1381 
    1382 <p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic rings
    1383 with one N-substituted position and an amino side group</p>
     1669<h2>Step 6. Setup for Monte Carlo/Simulated Annealing</h2>
     1670
     1671<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
     1672rings with one N-substituted position and an amino side group</p>
    13841673
    13851674<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    13891678  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
    13901679</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
    1391 src="MCSA%20in%20GSAS_files/image039.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
     1680src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
    13921681
    13931682<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
     
    13951684freedom. Thus we need to determine essentially six parameters. To do this in
    13961685GSAS-II we need to put a model of this molecule in as a rigid body. One must
    1397 create the model outside of GSAS-<span class=GramE>II,</span> it has no
    1398 facilities for model building. I used the Avogadro (<a
    1399 href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
     1686create the model outside of GSAS-II, it has no facilities for model building. I
     1687used the Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
    14001688package for this and created a simple xyz Cartesian coordinate file for it (if
    14011689you have Avogadro or something equivalent you can try this for yourself). To
    14021690start go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1403 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1691"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    14041692minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will
    14051693see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span
    1406 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1694style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14071695mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
    1408 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1696style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14091697mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Import
    14101698XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span
    1411 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1412 mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <span
    1413 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1414 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1415 minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight:
    1416 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1417 minor-latin;mso-hansi-theme-font:minor-latin'>Rigid <span class=GramE>bodies</span></span></b>
     1699style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1700mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <b
     1701style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1702mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b>.
     1703The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1704mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b>
    14181705window will show</p>
    14191706
     
    14231710 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
    14241711</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
    1425 src="MCSA%20in%20GSAS_files/image040.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
     1712src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
    14261713
    14271714<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    14281715
    1429 <p class=MsoNormal><span class=GramE>If you select the <b style='mso-bidi-font-weight:
    1430 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1431 minor-latin;mso-hansi-theme-font:minor-latin'>Plot?</span></b></span> <span
    1432 class=GramE>box</span> a drawing will appear</p>
     1716<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
     1717style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1718mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p>
    14331719
    14341720<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14381724  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
    14391725</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
    1440 src="MCSA%20in%20GSAS_files/image041.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1726src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
    14411727
    14421728<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14541740  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
    14551741</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
    1456 src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     1742src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    14571743
    14581744<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14611747needed for MC/SA and will just make computation times a bit longer than
    14621748necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
    1463 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1464 mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something meaningful,
    1465 I used <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1466 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
     1749style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1750mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
     1751meaningful, I used <b style='mso-bidi-font-weight:normal'><span
     1752style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1753mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
    14671754
    14681755<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
    1469 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1756style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14701757mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select
    1471 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1758the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14721759mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b>
    14731760tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1474 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1761"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    14751762minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b
    1476 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1763style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14771764mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>)
    14781765from the popup selection box. The MC/SA window shows</p>
     
    14831770 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
    14841771</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
    1485 src="MCSA%20in%20GSAS_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
     1772src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
    14861773
    14871774<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    14921779 id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
    14931780 height:232.5pt;visibility:visible;mso-wrap-style:square'>
    1494  <v:imagedata src="MCSA%20in%20GSAS_files/image044.png" o:title="" croptop="17592f"
     1781 <v:imagedata src="MCSA%20in%20GSAS_files/image027.png" o:title="" croptop="17592f"
    14951782  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
    14961783</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
    1497 src="MCSA%20in%20GSAS_files/image045.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1784src="MCSA%20in%20GSAS_files/image028.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    14981785
    14991786<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15011788<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
    15021789whose centers fall within the unit cell; the reference one is that in the lower
    1503 left corner with C1 at the origin. You can enter values in the <span
    1504 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1505 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1506 minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
    1507 the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
    1508 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1509 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
    1510 or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1511 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1512 mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
     1790left corner with C1 at the origin. You can enter values in the <b
     1791style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1792mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>x,y,z</span></b>
     1793boxes and see how the structure changes. Similarly, you can enter an angle in <b
     1794style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1795mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b>
     1796or a vector in the <b style='mso-bidi-font-weight:normal'><span
     1797style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1798mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok</span></b><span
    15131799style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
    15141800molecule. Each of these parameters has a defined range for the MC/SA
     
    15191805with the default. We want to optimize the position and orientation of this
    15201806molecule; check the <b style='mso-bidi-font-weight:normal'><span
    1521 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1807style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15221808mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
    1523 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1809normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    15241810minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
    1525 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1811style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15261812mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
    15271813boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1528 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1529 minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight:
    1530 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1531 minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
    1532 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1533 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1534 minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
    1535 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1536 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
    1537 <span class=SpellE><span class=GramE>pulldown</span></span>. The MC/SA window
    1538 should look like</p>
     1814"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1815minor-latin'>AV</span></b> from the <b style='mso-bidi-font-weight:normal'><span
     1816style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1817mso-hansi-theme-font:minor-latin'>Oa</span></b>, <b style='mso-bidi-font-weight:
     1818normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1819minor-latin;mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok Vary?</span></b>
     1820pulldown. The MC/SA window should look like</p>
    15391821
    15401822<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15431825 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
    15441826</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
    1545 src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
     1827src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
    15461828style='mso-spacerun:yes'> </span></p>
    15471829
     
    15501832<p class=MsoNormal>This completes the set up for MC/SA processing. </p>
    15511833
    1552 <h2><span class=GramE>Step 7.</span> Monte Carlo/Simulated Annealing</h2>
     1834<h2>Step 7. Monte Carlo/Simulated Annealing</h2>
    15531835
    15541836<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
    1555 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1837style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15561838mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls
    15571839are at the bottom of the window. To begin the setup of these controls, select a
    15581840source of the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1559 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1841"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    15601842minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice
    15611843is to use either the Pawley reflections or the Reflection List for the PWDR
    15621844data set. If you choose <b style='mso-bidi-font-weight:normal'><span
    1563 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1845style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15641846mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
    1565 structure factors will be Pawley model values, <span class=SpellE><span
    1566 class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>)
    1567 in Pawley table, and the covariance matrix developed from the refinement will
    1568 be used for peak overlap effects in the MC/SA calculations. Alternatively, if
    1569 you choose <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1570 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1571 minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then
    1572 the structure factors will be those, <span class=SpellE>Fosq</span> in
     1847structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and
     1848the covariance matrix developed from the refinement will be used for peak
     1849overlap effects in the MC/SA calculations. Alternatively, if you choose <b
     1850style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1851mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
     1852Quinoli.gda Bank 1 </span></b>then the structure factors will be those, Fosq in
    15731853Reflection table, extracted during the Pawley refinement and the peak FWHMs
    15741854will be used for peak overlap effects in the MC/SA calculations. Notice that
    1575 the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span
    1576 class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span
    1577 class=SpellE>Fcsq</span> Reflection List values. Here I chose <b
    1578 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1579 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley
    1580 reflections</span></b> for the <b style='mso-bidi-font-weight:normal'><span
    1581 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1582 mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it give slightly
    1583 better performance in MC/SA.</p>
     1855the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values.
     1856Here I chose <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1857"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1858minor-latin'>Pawley reflections</span></b> for the <b style='mso-bidi-font-weight:
     1859normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1860minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
     1861give slightly better performance in MC/SA.</p>
    15841862
    15851863<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
    1586 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1864style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15871865mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>).
    15881866Smaller values gives minima in the MC/SA minimization surface that are more
     
    15911869should have 5-8 reflections for each MC/SA parameter; in this case 35-50
    15921870reflections are needed. If you examine the reflection list (either <b
    1593 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1871style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15941872mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b>
    1595 or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1873or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    15961874mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
    15971875List</span></b>) you’ll see that a <b style='mso-bidi-font-weight:normal'><span
    1598 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1876style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15991877mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight:
    1600 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1878normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16011879minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give
    16021880sufficient reflections.</p>
    16031881
    16041882<p class=MsoNormal>Lastly, you need to set the run controls. I used <b
    1605 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1883style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16061884mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b>
    1607 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1885for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16081886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
    16091887this is the number of random tries at each “temperature” in the annealing
    16101888schedule. When done the <b style='mso-bidi-font-weight:normal'><span
    1611 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1889style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16121890mso-hansi-theme-font:minor-latin'>General</span></b> window should look like</p>
    16131891
     
    16151893 id="Picture_x0020_16" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
    16161894 height:375pt;visibility:visible;mso-wrap-style:square'>
    1617  <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
     1895 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
    16181896</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
    1619 src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1897src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
    16201898
    16211899<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16221900
    16231901<p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b
    1624 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1902style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16251903mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>
    1626 from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1904from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16271905mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    16281906window menu. A progress bar will appear that shows the MC/SA residual (an
     
    16301908as indicating which MC/SA run is being done. When it finishes, control is
    16311909shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1632 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1910"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    16331911minor-latin'>MC/SA</span></b> window which gives a list of the solutions it
    16341912found at the bottom of the window (scroll down to see them).</p>
     
    16371915 id="Picture_x0020_19" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:560.25pt;
    16381916 height:273.75pt;visibility:visible;mso-wrap-style:square'>
    1639  <v:imagedata src="MCSA%20in%20GSAS_files/image048.png" o:title=""/>
     1917 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
    16401918</v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
    1641 src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1919src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
    16421920
    16431921<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16491927 id="Picture_x0020_20" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:279.75pt;
    16501928 height:243.75pt;visibility:visible;mso-wrap-style:square'>
    1651  <v:imagedata src="MCSA%20in%20GSAS_files/image050.png" o:title="" croptop="11773f"
     1929 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="11773f"
    16521930  cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
    16531931</v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
    1654 src="MCSA%20in%20GSAS_files/image060.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1932src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    16551933
    16561934<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16611939molecules clashing), then you should just rerun MC/SA perhaps using more runs
    16621940or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
    1663 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1941style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16641942mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
    16651943want to retain; the others will be cleared before the next MC/SA run starts.
    1666 When you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
    1667 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1668 minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the
    1669 parameters will be copied to the appropriate boxes in the upper part of the
    1670 MC/SA window and the structure is drawn again. Next we want to refine this
    1671 solution so go back to the <b style='mso-bidi-font-weight:normal'><span
    1672 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1673 mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
     1944When you think you have a good one, <b style='mso-bidi-font-weight:normal'><span
     1945style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1946mso-hansi-theme-font:minor-latin'>Select</span></b> it; the parameters will be
     1947copied to the appropriate boxes in the upper part of the MC/SA window and the
     1948structure is drawn again. Next we want to refine this solution so go back to
     1949the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1950mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     1951tab.</p>
    16741952
    16751953<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
    16761954and rerunning the MC/SA calculations. This is done by checking the <b
    1677 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1955style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16781956mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
    16791957box. Using 10% of the ranges reduces the search volume in this case by ~6
    16801958orders of magnitude so that the true minimum is much easier to find. Now rerun <b
    1681 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1959style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16821960mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
    16831961be sure to select the best one before starting. The residual should drop to a
     
    16881966 id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt;
    16891967 height:285pt;visibility:visible;mso-wrap-style:square'>
    1690  <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
     1968 <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
    16911969</v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
    1692 src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
     1970src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
    16931971
    16941972<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    16951973
    1696 <p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>0.4%</span>!)
    1697 and the structure</p>
     1974<p class=MsoNormal>This is clearly a good result (R ~ 0.4%!) and the structure</p>
    16981975
    16991976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    17001977 id="Picture_x0020_23" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:288.75pt;
    17011978 height:248.25pt;visibility:visible;mso-wrap-style:square'>
    1702  <v:imagedata src="MCSA%20in%20GSAS_files/image054.png" o:title="" croptop="11555f"
     1979 <v:imagedata src="MCSA%20in%20GSAS_files/image039.png" o:title="" croptop="11555f"
    17031980  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
    17041981</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
    1705 src="MCSA%20in%20GSAS_files/image062.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
     1982src="MCSA%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
    17061983
    17071984<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17081985
    1709 <p class=MsoNormal><span class=GramE>is</span> identical to the published one</p>
     1986<p class=MsoNormal>is identical to the published one</p>
    17101987
    17111988<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    17121989 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt;
    17131990 height:225.75pt;visibility:visible;mso-wrap-style:square'>
    1714  <v:imagedata src="MCSA%20in%20GSAS_files/image056.png" o:title="" croptop="14378f"
     1991 <v:imagedata src="MCSA%20in%20GSAS_files/image041.png" o:title="" croptop="14378f"
    17151992  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
    17161993</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
    1717 src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    1718 
    1719 <p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
     1994src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
     1995
     1996<p class=MsoNormal>as drawn by the Mercury program </p>
    17201997
    17211998<p class=MsoNormal>(<a
    17221999href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>).
    17232000To save this solution to the <b style='mso-bidi-font-weight:normal'><span
    1724 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2001style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    17252002mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
    1726 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2003normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    17272004minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
    17282005the drawing will show the new atom positions</p>
     
    17312008 id="Picture_x0020_25" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:4in;
    17322009 height:243.75pt;visibility:visible;mso-wrap-style:square'>
    1733  <v:imagedata src="MCSA%20in%20GSAS_files/image064.png" o:title="" croptop="12581f"
     2010 <v:imagedata src="MCSA%20in%20GSAS_files/image043.png" o:title="" croptop="12581f"
    17342011  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
    17352012</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
    1736 src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
     2013src="MCSA%20in%20GSAS_files/image044.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
    17372014
    17382015<p class=MsoNormal>And they will be listed in the Atoms table.</p>
     
    17412018 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
    17422019 height:225pt;visibility:visible;mso-wrap-style:square'>
    1743  <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
     2020 <v:imagedata src="MCSA%20in%20GSAS_files/image045.png" o:title=""/>
    17442021</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    1745 src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    1746 
    1747 <p class=MsoNormal>It is now ready for <span class=SpellE>Rietveld</span>
    1748 refinement; this needs to use the rigid body as the data will not support
    1749 independent atom position refinement.</p>
    1750 
    1751 <h2><span class=GramE>Step 8.</span> Initial <span class=SpellE>Rietveld</span>
    1752 refinement</h2>
     2022src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     2023
     2024<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
     2025the rigid body as the data will not support independent atom position
     2026refinement.</p>
     2027
     2028<h2>Step 8. Initial Rietveld refinement</h2>
    17532029
    17542030<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
    1755 be ready for the first <span class=SpellE>Rietveld</span> refinement: 1) On the
    1756 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1757 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1758 tab uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1759 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1760 minor-latin'>Do Pawley refinement?</span></b> box, 2) check the <b
    1761 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1762 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
    1763 scale factor</span></b> box in <b style='mso-bidi-font-weight:normal'><span
    1764 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1765 mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and 3) zero both
    1766 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1767 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1768 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1769 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    1770 and uncheck their refine boxes in <b style='mso-bidi-font-weight:normal'><span
    1771 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1772 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>. Then do <b
    1773 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1774 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1775 from the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
    1776 was ~9%. Next check the <b style='mso-bidi-font-weight:normal'><span
    1777 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1778 mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
    1779 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1780 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1781 window and in the <b style='mso-bidi-font-weight:normal'><span
    1782 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1783 mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
    1784 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1785 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
    1786 model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
    1787 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1788 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
    1789 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1790 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
    1791 class=GramE>size</span></span></b> &amp; <span class=SpellE><b
    1792 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1793 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
     2031be ready for the first Rietveld refinement: 1) On the <b style='mso-bidi-font-weight:
     2032normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2033minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab uncheck
     2034the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2035mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley
     2036refinement?</span></b> box, 2) check the <b style='mso-bidi-font-weight:normal'><span
     2037style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2038mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> box in <b
     2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
     2041Parameters</span></b> and 3) zero both <b style='mso-bidi-font-weight:normal'><span
     2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2043mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
     2044normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2045minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> and uncheck their
     2046refine boxes in <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2047"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2048minor-latin'>Instrument Parameters</span></b>. Then do <b style='mso-bidi-font-weight:
     2049normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2050minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
     2051the main GSAS-II data tree window; my R<sub>wp</sub> was ~9%. Next check the <b
     2052style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2053mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
     2054cell</span></b> in the <b style='mso-bidi-font-weight:normal'><span
     2055style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2056mso-hansi-theme-font:minor-latin'>General</span></b> window and in the <b
     2057style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2058mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
     2059window, using the <b style='mso-bidi-font-weight:normal'><span
     2060style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2061mso-hansi-theme-font:minor-latin'>uniaxial</span></b> model for mustrain, check
     2062both <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2063mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst. size</span></b>
     2064&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b>
    17942066boxes and do another <b style='mso-bidi-font-weight:normal'><span
    1795 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1796 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an <span
    1797 class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not refined atom
    1798 positions or thermal parameters; to do this we need to describe the structure
    1799 as a rigid body.</p>
    1800 
    1801 <h2><span class=GramE>Step 9.</span> Rigid body model</h2>
     2067style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2068mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an R<sub>wp</sub>
     2069~8.5% for this. We’ve not refined atom positions or thermal parameters; to do
     2070this we need to describe the structure as a rigid body.</p>
     2071
     2072<h2>Step 9. Rigid body model</h2>
    18022073
    18032074<p class=MsoNormal>The rigid body itself has already been defined; it was used
    18042075for the MC/SA structure solution. Now we have to place it in the unit cell
    18052076matching the atom positions obtained from the MC/SA runs. First go to the <b
    1806 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2077style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18072078mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
    18082079tab and change the <b style='mso-bidi-font-weight:normal'><span
    1809 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2080style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18102081mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight:
    1811 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2082normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18122083minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp; sticks</span></b> and
    1813 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2084the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18142085mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
    1815 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2086to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18162087mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>.
    18172088Double click on the column headings and select the item from the popup control.
    18182089Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1819 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2090"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    18202091minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
    1821 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2092style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18222093mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
    18232094atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
    1824 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2095normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18252096minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
    1826 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2097style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18272098mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
    18282099body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
    1829 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2100normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18302101minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
    18312102show</p>
     
    18342105 id="Picture_x0020_27" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:337.5pt;
    18352106 height:218.25pt;visibility:visible;mso-wrap-style:square'>
    1836  <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
     2107 <v:imagedata src="MCSA%20in%20GSAS_files/image047.png" o:title=""/>
    18372108</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
    1838 src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     2109src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    18392110
    18402111<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    18422113<p class=MsoNormal>You will orient the rigid body against the atoms by matching
    18432114up the 3 reference atoms in the rigid body (C1, C2 &amp; C5) to the
    1844 corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do <span
    1845 class=GramE>these in order</span>; the drawing will show the shift of molecular
    1846 origin and then its reorientation as the three atoms are selected. Press <span
    1847 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1848 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1849 minor-latin'>Ready</span></b></span> when done; the structure will be drawn
    1850 with yellow bonds indicating that it is now a rigid body and not independent
    1851 atoms. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1852 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1853 minor-latin'>RB Models</span></b> window shows the new rigid body</p>
     2115corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
     2116order; the drawing will show the shift of molecular origin and then its
     2117reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
     2118normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2119minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b> when done; the
     2120structure will be drawn with yellow bonds indicating that it is now a rigid
     2121body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
     2122style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2123mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new
     2124rigid body</p>
    18542125
    18552126<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    18562127 id="Picture_x0020_29" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:474.75pt;
    18572128 height:210pt;visibility:visible;mso-wrap-style:square'>
    1858  <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
     2129 <v:imagedata src="MCSA%20in%20GSAS_files/image049.png" o:title=""/>
    18592130</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
    1860 src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
     2131src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    18612132
    18622133<p class=MsoNormal>To refine the rigid body parameters check the <b
    1863 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2134style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18642135mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
    1865 <span class=GramE>box</span>, select <b style='mso-bidi-font-weight:normal'><span
    1866 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1867 mso-hansi-theme-font:minor-latin'>AV</span></b> from the pull down, choose <span
    1868 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1869 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1870 minor-latin'>Uiso</span></b></span> from the thermal parameter model and check
    1871 its <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1872 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
    1873 <span class=GramE>box</span>. Then do <b style='mso-bidi-font-weight:normal'><span
    1874 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1875 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
    1876 of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
    1877 the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1878 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1879 mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
    1880 new parameters</p>
     2136box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2137"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2138minor-latin'>AV</span></b> from the pull down, choose <b style='mso-bidi-font-weight:
     2139normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2140minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b> from the thermal
     2141parameter model and check its <b style='mso-bidi-font-weight:normal'><span
     2142style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2143mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b
     2144style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
     2146after a couple of refinement runs I got an R<sub>wp</sub> ~7.9% and the <b
     2147style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2148mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RBModels</span></b>
     2149window shows the new parameters</p>
    18812150
    18822151<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    18832152 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:474.75pt;
    18842153 height:225.75pt;visibility:visible;mso-wrap-style:square'>
    1885  <v:imagedata src="MCSA%20in%20GSAS_files/image073.png" o:title=""/>
     2154 <v:imagedata src="MCSA%20in%20GSAS_files/image051.png" o:title=""/>
    18862155</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
    1887 src="MCSA%20in%20GSAS_files/image075.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    1888 
    1889 <p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
     2156src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
     2157
     2158<p class=MsoNormal>and the profile shows the fit</p>
    18902159
    18912160<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    18922161 id="Picture_x0020_31" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
    18932162 height:450pt;visibility:visible;mso-wrap-style:square'>
    1894  <v:imagedata src="MCSA%20in%20GSAS_files/image074.png" o:title=""/>
     2163 <v:imagedata src="MCSA%20in%20GSAS_files/image053.png" o:title=""/>
    18952164</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1896 src="MCSA%20in%20GSAS_files/image081.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
     2165src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    18972166
    18982167<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
    18992168Next is a more complex case involving some internal degrees of freedom in the
    1900 molecule of a-d-<span class=GramE>lactose.</span></p>
     2169molecule of a-d-lactose.</p>
    19012170
    19022171</div>
  • Tutorials/MCsimanneal/MCSA in GSAS_files/filelist.xml

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  • Tutorials/MCsimanneal/MCSA in GSAS_files/props061.xml

    r1705 r1718  
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