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Timestamp:
Aug 19, 2012 1:17:28 PM (8 years ago)
Author:
toby
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update main docs

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  • trunk/doc/expgui6A.html

    r1184 r1218  
    2323<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    2424</TH><TH><A Href="expgui7.html">Next page</A>
    25 </TH><TH><A Href="expgui6.html">Previous page</A>
     25</TH><TH><A Href="expgui6R.html">Previous page</A>
    2626</TH></TR></TABLE><BR CLEAR=ALL>
    2727
    2828<center><h1>
    2929<HR noshade width="75%" size="2" align="center">
    30 EXPGUI, part 7
     30EXPGUI, part 8
    3131<HR noshade width="75%" size="2" align="center">
    3232</h1></center>
    3333
    34 <h3>A.7 Rigid Body Introduction</h3>
     34<h3>A.8 Rigid Body Introduction</h3>
    3535<DL><DL>
    3636GSAS Rigid bodies are another way to constrain relative atomic
     
    108108</OL> 
    109109</DL></DL>
    110 <H3>A.7.a Main Rigid Body Panel</H3>
     110<H3>A.8.a Main Rigid Body Panel</H3>
    111111<DL><DL>
    112112The main panel for rigid bodies presents a interface where bodies can
     
    156156  </UL>
    157157 
    158  <H4>A.7.a1 Manual rigid body definition</H4>
     158 <H4>A.8.a1 Manual rigid body definition</H4>
    159159<DL>
    160160  The manual definition window allows input of coordinates and
     
    167167  <BR><img src="rb002.jpg" alt="Manual RB creation window">
    168168</DL>
    169  <H4>A.7.a2 Cartesian coordinates from ASCII text file</H4>
     169 <H4>A.8.a2 Cartesian coordinates from ASCII text file</H4>
    170170<DL>
    171171Cartesian coordinates
     
    184184</DL>
    185185
    186   <H4>A.7.a3 Cartesian coordinates from a Z-matrix</H4>
     186  <H4>A.8.a3 Cartesian coordinates from a Z-matrix</H4>
    187187<DL>
    188188Cartesian coordinates
     
    195195 <BR><img src="rb004.jpg" alt="Z-matrix RB input window">
    196196</DL>
    197   <H4>A.7.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
    198 <DL>
    199   Cartesian coordinates
    200 can also be determined from atoms in the EXP file.
    201   In order to generate Cartesian
    202 coordinates, the number of sites in the rigid body framework must be specified
    203 as well as the starting atom (remember rigid bodies are mapped consecutively).
     197<A name="fromEXP">
     198<H4>A.8.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
     199</A>
     200<DL>
     201  A rigid body can also be created directly by computing Cartesian coordinates
     202for atoms in the current EXP file.
     203  In order to do this, the number of atom sites in the rigid body framework must be specified
     204as well as the starting atom number (remember rigid bodies are mapped
     205  consecutively) using the window shown below.
    204206  Once the number of atoms in the body is
    205207set, the "Choose Start Atom" button is pressed. This creates buttons for
    206 all possible choices for the first atom to define the body. Once the starting
    207 atom is selected by pressing one of these button(s), the atoms to be used to
    208 define the rigid body framework have been determined. The user must than select
     208all possible choices for the first atom to define the body. The starting
     209atom is selected by pressing one of these button(s) and this defines
     210  the atoms to be used in the rigid body framework. The user must then
     211  select
    209212which atoms will be used to define the origin (the origin will be at the
    210 centroid of the atoms chosen) and must define the axes that will be used to
    211 generate the x-axis and the xy plane.
    212 The Cartesian coordinates can then be generated.
    213 Either the defined body can be determined and mapped (with the "Save and Map
    214 Rigid Body" button), or the Cartesian coordinates can exported to an
     213centroid of the atoms chosen) as well as define the axes that will be used to
     214generate the x-axis and the xy plane for the Cartesian coordinate system.
     215The Cartesian coordinates for the body that are generated can be exported to an
    215216ASCII text file (with the "Export Cartesian Coordinates"
    216 button).
    217   <BR><img src="rb005.jpg" alt="Fraction Coords RB input window">
     217button) for later use. More commonly, the "Save and Map
     218Rigid Body" button is used; this creates a new rigid body type and
     219  maps that body (<A href="#MapBody">see A.8.b2</A>) to the selected atoms in the phase.
     220 <BR><img src="rb005.jpg" alt="Fraction Coords RB input window">
    218221</DL>
    219222
    220223</DL></DL>
    221 <H3>A.7.b Rigid Body Panel</H3>
     224<H3>A.8.b Rigid Body Panel</H3>
    222225<DL><DL>
    223226 As each rigid body is
     
    232235  <BR><img src="rb006.jpg" alt="RB edit panel">
    233236
    234   <H4>A.7.b1 Plot Rigid Body</H4>
     237  <H4>A.8.b1 Plot Rigid Body</H4>
    235238<DL>
    236239  <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A>
     
    238241EXPGUI can invoke, if installed. It
    239242allows for the viewing of the rigid body to ensure it is correct before mapping
    240 and matches the ordering of the atoms in the EXP file. The plot below
    241   was obtained from the "Plot Rigid Body" button.
     243and matches the ordering of the atoms in the EXP file. Note that plots
     244  to not display atom types, since there is no type information
     245  associated with position in a rigid body. Atom types are determined
     246  by the atoms when the body is mapped. A sample plot
     247  obtained from the "Plot Rigid Body" button is shown below.
    242248  <BR><img src="rb007.png" alt="DRAWxtl screen">
    243249</DL>
    244 
    245  <H4>A.7.b2 Map Rigid Body</H4>
    246 <DL>
     250<A name="MapBody">
     251 <H4>A.8.b2 Map Rigid Body</H4>
     252</A><DL>
    247253The rigid body must be mapped to the
    248254crystal structure to define the constraint. This is done by pressing
    249255  the "Map Rigid Body" button, which raises the window below.
    250256  <BR><img src="rb008.png" alt="Map RB"><BR>
     257Note that when a rigid body is created from atoms already in the .EXP
     258  file (<A href="#fromEXP">see A.8.a4</A>), the "Save and Map" command
     259  performs this step automatically.
     260  <P>
    251261  In order to map the rigid body the user
    252262will need to specify the phase and the sequence number of the first atom in the
     
    281291<BR Clear="all">
    282292  </DL>
    283  <H4>A.7.b3 Edit Rigid Body</H4>
     293 <H4>A.8.b3 Edit Rigid Body</H4>
    284294  <DL>
    285295
     
    303313
    304314</DL></DL>
    305 <H3>A.7.c Setting Rigid Body Refinement Flags</H3>
     315<H3>A.8.c Setting Rigid Body Refinement Flags</H3>
    306316<DL><DL>
    307317 The "Refinement Flags" button opens a window that allows the
     
    345355 These flags were set automatically when
    346356the rigid body position parameter were set to be refined. If these flags are
    347 turned off, it is likely that GENLES will crash.
    348 
     357turned off, it is likely that GENLES will crash. Note that atoms in a
     358  rigid body are now tagged with the letter "r" in the atom listings.
    349359  </DL></DL>
    350360<hr>
     
    352362<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    353363</TH><TH><A Href="expgui7.html">Next page</A>
    354 </TH><TH><A Href="expgui6.html">Previous page</A>
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    356366
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