Changeset 1150 for branches/sandbox
- Timestamp:
- Jul 6, 2011 3:35:40 PM (12 years ago)
- Location:
- branches/sandbox
- Files:
-
- 1 added
- 1 deleted
- 19 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/sandbox/addcmds.tcl
r1141 r1150 2032 2032 #puts "$coord before: $status_fixed $status_unfixed" 2033 2033 foreach i $numberList { 2034 2035 2036 2037 2034 set temp [info exists ::fix_param($phase,$i,$coord)] 2035 #puts "::fix_param($phase,$i,$coord) is variable present?: $temp" 2036 if {$temp != 0} {set status_fixed 1} 2037 if {$temp == 0} {set status_unfixed 1} 2038 2038 } 2039 2039 #puts "$coord after $status_fixed $status_unfixed" -
branches/sandbox/doc/excledt.html
r971 r1150 283 283 </TH></TR></TABLE> 284 284 285 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>286 <font size=-1><? lastmod(); ?> </font>287 <br>$Revision$ $Date$288 285 </blockquote> 289 286 </body> -
branches/sandbox/doc/expgui.html
r1115 r1150 59 59 <TH><A Href="expgui4.html">Scaling info</A></TH> 60 60 <TH><A Href="expgui5.html">Profile terms</A></TH> 61 <TH><A Href="expgui6.html">Constraints </A></TH>61 <TH><A Href="expgui6.html">Constraints & Restraints</A></TH> 62 62 </TR> 63 63 <TR> 64 <TH><A Href="expgui6A.html">Rigid Bodies</A></TH> 64 65 <TH><A Href="expgui7.html">Preferred Orientation</A></TH> 65 66 <TH><A Href="expguic.html">Menus</A></TH> -
branches/sandbox/doc/expgui0.html
r971 r1150 44 44 </TH></TR></TABLE> 45 45 46 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> 47 <font size=-1><? lastmod(); ?> </font> 48 <br>$Revision$ $Date$ 49 </blockquote> 46 /blockquote> 50 47 </body> 51 48 </html> -
branches/sandbox/doc/expgui1.html
r971 r1150 186 186 </TH></TR></TABLE> 187 187 188 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>189 <font size=-1><? lastmod(); ?> </font>190 <br>$Revision$ $Date$191 188 </blockquote> 192 189 </body> -
branches/sandbox/doc/expgui2.html
r971 r1150 80 80 <P> 81 81 <a name="xform"></a> 82 <h4>A.2.2 Transform Coordinates</h4> 83 <DL><DL> 84 <img SRC="2a.gif" align=RIGHT alt="EXPGUI Screen snapshot"> 85 If one or more atoms have been selected 86 <A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible 87 to make changes to those atoms by pressing the "Xform atom(s)" button. 88 This raises the window shown to the right. 89 Note that no changes are actually made, until the 90 "Transform Coordinates", "Set Occupancies",... buttons are pressed. 91 <P> 92 This window can be used 93 to transform the coordinates coordinates of the selected atoms, 94 globally set occupancy or Uiso (Uequiv) 95 values for the selected atoms, or erase the selected atoms. by pressing the 96 It is also possible to transform the selected atoms 97 from isotropic to anisotropic, or the reverse. 98 <P> 99 <IMG SRC="new.gif" alt="New!"> 100 The "Xform Origin 1 to Origin 2" button is only available for those 82 <h4>A.2.2 Modify Atom</h4> 83 <DL><DL> 84 <img SRC="2a.jpg" align=RIGHT alt="EXPGUI Screen snapshot"> 85 The "Modify Atom" button ("Modify Atoms" when multiple atoms are 86 selected) provides access to additional options that can 87 transform or modify the selected atom(s) from the phase panel 88 <A href="expgui.html#mouseactions">(see Mouse Actions</A> for 89 information on selecting atoms); this opens the menu window shown to 90 the right. 91 Note that changes are made to the coordinates when the buttons on this 92 window (such as 93 "Transform Coordinates", "Set Occupancies",...) are pressed. 94 <P><B>Modify Coordinates:</B> 95 This is used 96 to transform the coordinates coordinates of the selected atoms using a 97 set of transformation relationships. 98 99 <P><B>Reset Multiplicities:</B> 100 When atom positions are edited in EXPGUI, they may be moved off from 101 or onto special positions in the cell, changing the site 102 multiplicity -- but this will not be reflected in the phase 103 display. When atoms are subsequently refined, GENLES will update the 104 multiplcities. Pressing the "Reset Multiplicities" button cases 105 this to be done right away (I think this may not work if there are no 106 histograms present). 107 108 <P><B>Xform Origin 1 to Origin 2:</B> This button is only available for those 101 109 orthorhombic, tetragonal and cubic space groups that are listed in the 102 110 International Tables with two origin settings. (These space groups have … … 106 114 of symmetry. GSAS only uses the origin 2 settings.) 107 115 If coordinates have been entered in the origin 1 setting, they may be 108 transformed to the origin 2 setting using this button. 116 transformed to the origin 2 setting using this button. It is important 117 to select all atoms in the asymmetric unit before using this button. 118 119 <P><B>Modify Occupancies:</B> 120 This allows the occupancy to be set for one or more atoms. It is 121 most convenient for when many atoms will have their occupancy 122 changed at one time. 123 124 <P><B>Modify Displacement Parameters:</B> 125 This allows one to set Uiso (or Uequiv) values for the selected 126 atoms (<B>Set U</B>). To change the flag that determines if the 127 selected atom(s) are represented as Isotropic or Anisotropic, press 128 the <B>Set Isotropic</B> or <B>Set Anisotropic</B> buttons. 129 130 <P><B>Erase Atoms:</B> 131 The "Erase Atoms" removes the selected atoms from the phase. I 132 usually set the occupancy to 0. instead. 133 134 <P><B>Fix Atom Coordinates:</B> 135 When an atom is refined in GSAS, only the coordinates that are not 136 defined by site symmetry are refined. However, in some space groups, 137 it is necessary to not refine additional coordinates. The most common 138 example are polar space groups (P1, P2, P2<sub>1</sub>, C2, P4, P4<sub>1</sub>, P 139 4<sub>2</sub>, P4<sub>3</sub>, I4, I4<sub>1</sub>, P3, P3<sub>1</sub>, P3<sub>2</sub>, R3, P6, P6<sub>1</sub>, P6<sub>5</sub>, P6<sub>2</sub>, P6<sub>4</sub> and 140 P6<sub>3</sub> - from 141 <a href="http://www.ruppweb.org/Xray/comp/space_instr.htm"> Bernard Rupp's 142 web site, http://www.ruppweb.org/Xray/comp/space_instr.htm</A>) where 143 one or more coordinates of the origin are not defined by symmetry. In 144 these space groups an appropriate number of coordinates must be fixed 145 to define the origin. As an example, in P1, one x, one y and one z 146 coordinate must not be refined; in space group P2<sub>1</sub>, the 147 2<sub>1</sub> screw axis defines the origin at (0,0,z) so one z 148 coordinate cannot be varied. 149 150 Occasionally, while symmetry may allow 151 atom coordinates to be varied, a crystallographer may choose to 152 simplify or constrain the representation to fix the atom in a 153 particular location and not refine with all allowed degrees of freedom. 154 155 <IMG SRC="new.gif" alt="New!"> 156 The "Fix Atom Coordinates" buttons allows a flag to be set (or 157 cleared) for an atom 158 to prevent refinement of selected coordinates, even when the X 159 refinement flag is set. Note the addition of an "F" for the x and z 160 coordinates of the first atom as shown in the phase panel, above. This 161 indicates that x & z have been fixed. When the atom position is 162 varied, only y will be optimized. 109 163 110 164 <br clear=all> … … 248 302 </TH></TR></TABLE> 249 303 250 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>251 <font size=-1><? lastmod(); ?> </font>252 <br>$Revision$ $Date$253 304 </blockquote> 254 305 </body> -
branches/sandbox/doc/expgui3.html
r971 r1150 31 31 <HR noshade width="75%" size="2" align="center"> 32 32 </h1></center> 33 <h3>A.3 Histogrampanel</h3>34 <DL><DL> 35 The histogrampanel is used to edit background36 and diffractometer constants for a histogram, as well as33 <h3>A.3 Powder panel</h3> 34 <DL><DL> 35 The Powder (was histogram) panel is used to edit background 36 and diffractometer constants for powder histogram(s), as well as 37 37 set damping and refinement flags for these parameters. 38 38 <P> … … 288 288 </TH></TR></TABLE> 289 289 290 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>291 <font size=-1><? lastmod(); ?> </font>292 <br>$Revision$ $Date$293 290 </blockquote> 294 291 </body> -
branches/sandbox/doc/expgui4.html
r971 r1150 60 60 </TH></TR></TABLE> 61 61 62 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>63 <font size=-1><? lastmod(); ?> </font>64 <br>$Revision$ $Date$65 62 </blockquote> 66 63 </body> -
branches/sandbox/doc/expgui5.html
r971 r1150 118 118 </TH></TR></TABLE> 119 119 120 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>121 <font size=-1><? lastmod(); ?> </font>122 <br>$Revision$ $Date$123 120 </blockquote> 124 121 </body> -
branches/sandbox/doc/expgui6.html
r971 r1150 22 22 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> 23 23 <TR><TH><A Href="expgui.html">EXPGUI top</A> 24 </TH><TH><A Href="expgui 7.html">Next page</A>24 </TH><TH><A Href="expgui6A.html">Next page</A> 25 25 </TH><TH><A Href="expgui5.html">Previous page</A> 26 26 </TH></TR></TABLE><BR CLEAR=ALL> … … 32 32 </h1></center> 33 33 34 <h3>A.6 Constraints panel</h3>34 <h3>A.6 Re/Constraints panel</h3> 35 35 <DL><DL> 36 36 GSAS offers two types of restraints that can be included in a model. … … 41 41 by grouping parameters so that a single shift (possibly scaled) is 42 42 applied to each parameter in the group. 43 The constraints panel is used to set these "hard constraints." 43 The Re/Constraints panel is used to set these "hard constraints" or in 44 the case of bond distances, "restraints". 44 45 At this time the only constraints that can be set in EXPGUI are on atomic 45 and profile profile (others can be set in EXPEDT). 46 and profile profile (others can be set in EXPEDT). EXPEDT offers many 47 other types of restraints as well. 46 48 <P> 47 49 Note that these constraints are only applied to shifts, but not to the … … 212 214 usually make sense and EXPGUI does not allow it. 213 215 </DL></DL> 216 <a name="DistanceRestraints"></a> 217 <H4>Distance Restraints</H4> 218 <DL><DL> 219 When the distance restraints tab is first selected, the active 220 distance restraints for the selected phase are shown. The <B>Atom 1</B> and 221 <B>Atom 2</B> buttons can be used to sort this list. 222 <P> 223 The <B>Restraint Weight</B> parameter is very important. As this 224 determines how strongly the distance restraints will be used in the 225 refinement relative to the diffraction data. This value is sometimes 226 set as high as 500,000 in the initial stages of a fit, but should be 227 lowered as much as is possible in the final stages of the fit, as 228 needed to obtain chemically plausible interatomic distances. For 229 some refinements, a value of 0.0 is possible for the Restraint 230 Weight in the final stages. This removes any restraint effect. 231 232 To see how restraints are affecting the refinement, one can look at 233 the ratio of the "Sum(w*d**2)" (shown in the .LST file) for the 234 diffraction histograms vs. the restraint histogram. 235 <P> 236 The <B>Active Restraints Editor</B> can be used to select distances 237 to be restrained or edit the restraints. If there are too many 238 distances shown, the options at the top of the window can be used to 239 select a distance range, or specific atoms to include. Likewise, 240 only restrained or unrestrained distances can be selected. The 241 changes are applied when the <B>Filter</B> button is pressed. 242 <P> 243 The bottom section of the window shows individual interatomic 244 distances. A <B>Restraint</B> and <B>Tolerance</B> value is needed to restrain 245 that distance. The quantity minimized is 246 <blockquote> 247 <blockquote> 248 "Restraint Weight" * SUM{ [ (Distance - Restraint) / Tolerance ]**2 } 249 </blockquote> 250 </blockquote> 251 thus the "Tolerance" provides individual weighting for each 252 restraint. 253 <P> 254 To set a large number of restraints at the same time, select the 255 check button next to the distance(s), or use the <B>Check 256 All</B>. Then use the section above to enter a global 257 <B>Restraint</B> and <B>Tolerance</B> value. These values are set 258 when the <B>Set Checked</B> button is used. The <B>Delete 259 Checked</B> button removes restraints from all selected distances. 260 <P> 261 The entered restraint information will be used onlt when the <B>Save 262 Changes</B> button is pressed. The <B>Cancel</B> button will reverse 263 any changes made while the window is open. Closing the window has 264 the same effect as "Cancel." 265 <P> 266 Note that the interatomic distances that are shown are determined by 267 the parameters to program DISAGL. These are controlled with the 268 <B>Edit Search Distance Parameters</B> button. 269 270 </DL></DL> 214 271 <hr> 215 272 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> 216 273 <TR><TH><A Href="expgui.html">EXPGUI top</A> 217 </TH><TH><A Href="expgui 7.html">Next page</A>274 </TH><TH><A Href="expgui6A.html">Next page</A> 218 275 </TH><TH><A Href="expgui5.html">Previous page</A> 219 276 </TH></TR></TABLE> 220 277 221 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>222 <font size=-1><? lastmod(); ?> </font>223 <br>$Revision$ $Date$224 278 </blockquote> 225 279 </body> -
branches/sandbox/doc/expgui7.html
r971 r1150 23 23 <TR><TH><A Href="expgui.html">EXPGUI top</A> 24 24 </TH><TH><A Href="expguic.html">Next page (Menus)</A> 25 </TH><TH><A Href="expgui6 .html">Previous page</A>25 </TH><TH><A Href="expgui6A.html">Previous page</A> 26 26 </TH></TR></TABLE><BR CLEAR=ALL> 27 27 … … 98 98 <TR><TH><A Href="expgui.html">EXPGUI top</A> 99 99 </TH><TH><A Href="expguic.html">Next page (Menus)</A> 100 </TH><TH><A Href="expgui6 .html">Previous page</A>100 </TH><TH><A Href="expgui6A.html">Previous page</A> 101 101 </TH></TR></TABLE> 102 102 103 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>104 <font size=-1><? lastmod(); ?> </font>105 <br>$Revision$ $Date$106 103 </blockquote> 107 104 </body> -
branches/sandbox/doc/gsas2cif.html
r971 r1150 33 33 <BR> 34 34 to export 35 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> 36 GSAS</A> 35 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A> 37 36 results 38 37 <HR noshade width="75%" size="2" align="center"> … … 575 574 </BLOCKQUOTE> 576 575 577 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>578 <font size=-1><? lastmod(); ?></font>579 $Revision$ $Date$580 576 </font> 581 577 </BLOCKQUOTE> -
branches/sandbox/doc/liveplot.html
r1144 r1150 682 682 <B>Combining LIVEPLOT with CMPR & LOGIC</B> 683 683 If you have the 684 <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr"> 685 CMPR/LOGIC</A> 686 programs installed on your computer, you can use superimpose on the 684 <A HREF="https://subversion.xor.aps.anl.gov/trac/CMPR">CMPR</A> 685 program installed on your computer, you can use superimpose on the 687 686 GSAS results the peaks for an arbitrary unit cell. 688 If you have an old version of the 689 <A HREF="http://www.icdd.com/products/overview.htm"> 690 ICDD-JCPDS PDF-2 powder diffraction database</a>, 691 (when distributed as an AIDS*83 format flat file) 692 you can also superimpose entries from this database on the 693 GSAS results displayed in LIVEPLOT. 694 <P> 695 When the CMPR/LOGIC program is installed in the same location 687 <P> 688 When the CMPR program is installed in the same location 696 689 as the GSAS package (<i>e.g.</i> 697 690 <font face="courier">/home/gsas</font> & … … 721 714 software is located. The 722 715 "Display a cell" option produces a window similar to the 723 <A href="http ://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">716 <A href="https://subversion.xor.aps.anl.gov/CMPR/trunk/doc/cmprdoc.html#editcell"> 724 717 Edit Cell feature in CMPR</A> 725 718 where allowed reflection positions are displayed for a set of unit cell 726 719 parameters and optionally a space group or extinction conditions. 727 The "Plot ICDD Entry" provides a window similar to the728 <A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">729 LOGIC interface in CMPR</A>730 where ICDD searches may be conducted. From the resulting list of matches,731 selected entries may be displayed.732 720 <P> 733 721 Note that these routines display peak positions in units of 2Theta, Q or … … 747 735 </TH></TR></TABLE> 748 736 749 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>750 <font size=-1><? lastmod(); ?> </font>751 <br>752 $Revision$ $Date$753 737 </blockquote> 754 738 </body> -
branches/sandbox/doc/revlog.html
r971 r1150 32 32 </h1></center> 33 33 <P> 34 This page describes all revisions logged for changes to the EXPGUI source 34 This page has been superceeded by the Trac registry, see 35 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline"> 36 https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline</A>. 37 <HR><HR> 38 Below is information on older revisions logged for changes to the EXPGUI source 35 39 files, sorted by date. 36 See the <A HREF="wishlist.html">EXPGUI Wish List</A> for a more 37 descriptive listing. 38 40 See the 41 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report"> 42 View Tickets</A> section of the Trac site for active and closed 43 projects. There is some older information on the 44 <A HREF="wishlist.html">EXPGUI Wish List</A>. 45 39 46 <h2>since 1-Jun-2009</h2><DL><DL> 40 47 </DL></DL> … … 1633 1640 </TH><TH><A Href="wishlist.html">Past and Planned<BR>Updates</A> 1634 1641 </TH></TR></TABLE> 1635 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> 1636 <font size=-1><? lastmod(); ?> </font> 1637 <br> 1638 </blockquote> 1642 </blockquote> 1639 1643 1640 1644 Created Fri Jul 03 20:35:34 CDT 2009 -
branches/sandbox/doc/win_old_notes.html
r971 r1150 43 43 Nonetheless, please report problems, including improvements on 44 44 these instructions to 45 <A HREF="mailto:brian.toby@ nist.gov">Brian Toby</A>.45 <A HREF="mailto:brian.toby@anl.gov">Brian Toby</A>. 46 46 Otherwise, Windows-specific issues are unlikely to be addressed or repaired. 47 47 </EM> … … 57 57 <P> 58 58 <LI>Get 59 <A Href="http ://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">60 GSAS</A>from one of the following sites:59 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A> 60 from one of the following sites: 61 61 <DL><P> 62 62 <DT>UK<DD> … … 296 296 <A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A> 297 297 <P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research, 298 <A HREF="MAILTO:Brian.Toby@ NIST.GOV">Brian.Toby@NIST.GOV</A>298 <A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> 299 299 with help from Jonathan Wasserman. 300 300 … … 325 325 </TH></TR></TABLE> 326 326 327 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>328 <font size=-1><? lastmod(); ?> </font>329 <br>330 $Revision$ $Date$331 327 </blockquote> 332 328 </body> -
branches/sandbox/doc/wishlist.html
r971 r1150 31 31 <HR noshade width="75%" size="2" align="center"> 32 32 </h1></center> 33 <I><blockquote><blockquote> 34 Information on desired (and completed) development tasks for EXPGUI 35 are now captured as "Tickets" in the 36 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/"> 37 EXPGUI Trac system</A>. In particular, see the 38 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline"> 39 timeline of changes</A> and the 40 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report"> 41 reports on Tickets</A>. Any other information on this page is no 42 longer being updated -- though there are still some good ideas for 43 development here. 44 </blockquote></blockquote></I> 45 <P> 46 <hr><hr> 47 48 33 49 <P> 34 50 This page describes recent features added to EXPGUI or that are being -
branches/sandbox/expgui
r1131 r1150 3307 3307 DisplayHistogram \ 3308 3308 1 expgui3.html ""} 3309 {singFrame Single \3310 "source [file join $expgui(scriptdir) single.tcl]; MakeSinglePane" \3311 DisplaySingle \3312 1 expguiSing.html ""}3313 3309 {fracFrame Scaling \ 3314 3310 MakeScalingPane \ … … 3336 3332 0 expgui7.html ODF} 3337 3333 } 3334 3335 # future expansion: single crystal panel goes here -- if present 3336 catch { 3337 source [file join $expgui(scriptdir) single.tcl] 3338 set expgui(notebookpagelist) [linsert $expgui(notebookpagelist) 3 \ 3339 {singFrame Single \ 3340 "MakeSinglePane" \ 3341 DisplaySingle \ 3342 1 expguiSing.html ""}] 3343 } err 3344 3338 3345 3339 3346 pack [NoteBook .n -bd 2] -expand yes -fill both
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