Changeset 1166

Timestamp:

08/17/2011 06:17:04 PM (19 months ago)

Author:

toby

Message:

bring sandbox changes over to main release

Location:

trunk

Files:

• Geo_Viewer.tcl (modified) (6 diffs)
• addcmds.tcl (modified) (6 diffs)
• disagledit.tcl (modified) (1 diff)
• distrest.tcl (modified) (17 diffs)
• doc/2.gif (modified) (previous)
• doc/2a.gif (deleted)
• doc/2a.jpg (added)
• doc/2g.gif (modified) (previous)
• doc/editreg.png (added)
• doc/excledt.html (modified) (1 diff)
• doc/expgui.html (modified) (16 diffs)
• doc/expgui0.html (modified) (1 diff)
• doc/expgui1.html (modified) (1 diff)
• doc/expgui2.html (modified) (3 diffs)
• doc/expgui3.html (modified) (2 diffs)
• doc/expgui4.html (modified) (1 diff)
• doc/expgui5.html (modified) (1 diff)
• doc/expgui6.html (modified) (4 diffs)
• doc/expgui6A.html (added)
• doc/expgui7.html (modified) (4 diffs)
• doc/expgui_intro.html (modified) (4 diffs)
• doc/expguic.html (modified) (14 diffs)
• doc/gsas2cif.html (modified) (2 diffs)
• doc/liveplot.html (modified) (16 diffs)
• doc/magreg.png (added)
• doc/rb001.jpg (added)
• doc/rb002.jpg (added)
• doc/rb003.jpg (added)
• doc/rb004.jpg (added)
• doc/rb005.jpg (added)
• doc/rb006.jpg (added)
• doc/rb007.png (added)
• doc/rb008.png (added)
• doc/rb009.png (added)
• doc/rb010.png (added)
• doc/rb011.jpg (added)
• doc/rb012.png (added)
• doc/rb013.png (added)
• doc/rb014.png (added)
• doc/rb015.png (added)
• doc/rb016.png (added)
• doc/revlog.html (modified) (2 diffs)
• doc/win_old_notes.html (modified) (4 diffs)
• doc/wishlist.html (modified) (1 diff)
• expgui (modified) (33 diffs)
• gnuplot.tcl (added)
• graceexport.tcl (modified) (1 diff)
• gsascmds.tcl (modified) (18 diffs)
• gsasmenu.tcl (modified) (6 diffs)
• instedit.tcl (modified) (5 diffs)
• liveplot (modified) (20 diffs)
• rb.tcl (added)
• rbimport_cartesian.tcl (added)
• rbimport_fixfrag.tcl (added)
• rbimport_zmatrix.tcl (added)
• readexp.tcl (modified) (14 diffs)
• rigid.tcl (added)
• single.tcl (deleted)
• widplt (modified) (8 diffs)

trunk/Geo_Viewer.tcl

@@ -47 +47 @@
      array set ::geo_bonds ""
      set ::geo_alist ""
+     set ::geo_filterval 5.00
 }
 
@@ -60 +61 @@
    set angle_total -1
 
+   set ::geo_phase_list {}
+   catch {unset ::geo_angles}
+   catch {unset ::geo_bonds}
    array set ::geo_bonds ""
    array set ::geo_angles ""
    array set ::geo_angle_keys ""
+
 
    while {[gets $fh line] >= 0} {
@@ -143 +148 @@
     Geo_Read $root.disagl
     donewait
+    if {[llength  $::geo_phase_list] == 0} {
+        MyMessageBox -parent . -title "DISAGL Problem" \
+            -message "No output found in DISAGL output. Is something wrong with DISAGL settings or this .EXP file?" \
+            -icon error
+        return
+    }
      set mcb .maincontrolbox
      catch {toplevel $mcb}
@@ -175 +186 @@
      eval tk_optionMenu $sc.phase ::geo_entryvar(phase) $::geo_phase_list
      label $sc.atom1 -text "Atom Type"
+     label $sc.filterlab -text "Dmax Filter"
+     entry $sc.filterval -textvariable ::geo_filterval
+          $sc.filterval config -width 6
      #button $sc.engage -text "Print Info" -command Geo_Fill_Display
      grid $sc.phlabel -row 0 -column 0
-     grid $sc.phase  -row 0 -column 1
-     grid $sc.atom1 -column 0 -row 1
+     grid $sc.phase   -row 0 -column 1
+     grid $sc.atom1   -row 1 -column 0
+     grid $sc.filterlab   -row 2 -column 0
+     grid $sc.filterval -row 2 -column 1
 
      label $as.atom -text "Choose Atom(s)"
@@ -270 +286 @@
      label $top.toplabel1 -text "Atom 2" -width 8
      label $top.toplabel2 -text "symm" -width 8
-     label $top.toplabel3 -text "Distance" -width 8
+     label $top.toplabel3 -text "Distance" -width 10
      label $top.toplabel4 -text "Angle"
 #     grid $top.toplabel0 -column 0 -row 0
@@ -293 +309 @@
              set symlist {}
              incr rownum
+             if {[string trim $::geo_filterval] == ""} {set ::geo_filterval 5.00}
              foreach j $slist {
-                 lappend keylist [lindex $j 10]
-                 lappend atmlist [lindex $j 6]
-                 lappend symlist [lindex $j 9]
-                 label $::geo_side.atom1${bondnum} -text [lindex $j 5] -width 8
-                 label $::geo_main.atom2${bondnum} -text [lindex $j 6] -width 8
-                 label $::geo_main.atom2symm${bondnum} -text [lindex $j 9] -width 8
-                 label $::geo_main.bonddist${bondnum} -text [lindex $j 7] -width 8
-
-                 grid $::geo_side.atom1${bondnum} -row $rownum -column 0
-                 grid $::geo_main.atom2${bondnum} -row $rownum -column 0
-                 grid $::geo_main.atom2symm${bondnum} -row $rownum -column 1
-                 grid $::geo_main.bonddist${bondnum} -row $rownum -column 2
-
-                 set key [lindex $j 10]
-                 set atom [lindex $j 1]
-                 set phase [lindex $j 0]
-
-
-                 foreach k $keylist {
-
-                 if {$key != $k} {
-                    if {[array name ::geo_angles "$phase,$key,$atom,$k"] != ""} {
-                    label $::geo_main.$counter -text [lindex $::geo_angles($phase,$key,$atom,$k) 7]
-                    grid $::geo_main.$counter -row $rownum -column $colnum -padx 5
-                    incr colnum
-                    incr counter
-                    } elseif {[array name ::geo_angles "$phase,$k,$atom,$key"] != ""} {
-                    label $::geo_main.$counter -text [lindex $::geo_angles($phase,$k,$atom,$key) 7]
-                    grid $::geo_main.$counter -row $rownum -column $colnum -padx 5
-
-                    incr colnum
-                    incr counter
+                 if {[lindex $j 7] <= $::geo_filterval} {
+                    lappend keylist [lindex $j 10]
+                    lappend atmlist [lindex $j 6]
+                    lappend symlist [lindex $j 9]
+                    label $::geo_side.atom1${bondnum} -text [lindex $j 5] -width 8
+                    label $::geo_main.atom2${bondnum} -text [lindex $j 6] -width 8
+                    label $::geo_main.atom2symm${bondnum} -text [lindex $j 9] -width 8
+                    set bonddist [lindex $j 7]
+                    set bondesd  [lindex $j 8]
+                    set bondentry [formatSU $bonddist $bondesd]
+                    label $::geo_main.bonddist${bondnum} -text $bondentry -width 10
+
+                    grid $::geo_side.atom1${bondnum} -row $rownum -column 0
+                    grid $::geo_main.atom2${bondnum} -row $rownum -column 0
+                    grid $::geo_main.atom2symm${bondnum} -row $rownum -column 1
+                    grid $::geo_main.bonddist${bondnum} -row $rownum -column 2
+
+                    set key [lindex $j 10]
+                    set atom [lindex $j 1]
+                    set phase [lindex $j 0]
+
+
+                    foreach k $keylist {
+
+                            if {$key != $k} {
+                            # search for atom 1 - central atom - atom 2 angle.
+                            if {[array name ::geo_angles "$phase,$key,$atom,$k"] != ""} {
+                               set ang  [lindex $::geo_angles($phase,$key,$atom,$k) 7]
+                               set angesd [lindex $::geo_angles($phase,$key,$atom,$k) 8]
+                               set angentry [formatSU $ang $angesd]
+                               label $::geo_main.$counter -text $angentry
+#                               label $::geo_main.$counter -text [lindex $::geo_angles($phase,$key,$atom,$k) 7]
+                               grid $::geo_main.$counter -row $rownum -column $colnum -padx 5
+                               incr colnum
+                               incr counter
+                               # search for atom 2 - central atom - atom 1 angle.
+                            } elseif {[array name ::geo_angles "$phase,$k,$atom,$key"] != ""} {
+                               set ang  [lindex $::geo_angles($phase,$k,$atom,$key) 7]
+                               set angesd [lindex $::geo_angles($phase,$k,$atom,$key) 8]
+                               set angentry [formatSU $ang $angesd]
+                               label $::geo_main.$counter -text $angentry
+#                              label $::geo_main.$counter -text [lindex $::geo_angles($phase,$k,$atom,$key) 7]
+                              grid $::geo_main.$counter -row $rownum -column $colnum -padx 5
+
+                              incr colnum
+                              incr counter
+                            }
+                            }
                     }
-
-                 }
-                 }
                  incr bondnum
-                incr rownum
+                 incr rownum
                  set colnum 3
-
+             }
              }
                   set colnum 3

trunk/addcmds.tcl

@@ -709 +709 @@
     # mode must be t-max or 2theta, at least for now
     if {$newhist(LimitMode) != 1} return
-    # is a instrument parameter file loaded? If not, try again later
-    if {[string trim $newhist(instfile)] == ""} return
     # get data bank number, test if valid
     set num $newhist(banknum)
     if {[catch {expr $num}]} {return}
     if {$newhist(insttype) == "TOF"} {
+        # is a instrument parameter file loaded? If not, try again later
+        if {[string trim $newhist(instfile)] == ""} return
         set newhist(2tLimit) [expr {$newhist(tmin$num) / 10.}]
         # at Ashfia's request, override the bank header # with the 
@@ -740 +740 @@
         set inp [
         tk_getOpenFile -parent $np -initialfile $newhist(instfile) -filetypes {
-            {"Inst files" .INS*} {"Inst files" .ins*} 
+            {"Inst files" .INS*} {"Inst files" .ins*}
             {"Inst files" .PRM}  {"Inst files" .prm} 
             {"All files" *}
@@ -937 +937 @@
     puts $fp "H"
     if {$tcl_platform(platform) == "windows"} {
-        puts $fp [file attributes $rawfile -shortname]
-        puts $fp [file attributes $instfile -shortname]
+        if {[string length $rawfile] > 50} {
+            puts $fp [file attributes $rawfile -shortname]
+        } else {
+            puts $fp $rawfile
+        }
+        if {[string length $instfile] > 50} {            
+            puts $fp [file attributes $instfile -shortname]
+        } else {
+            puts $fp $instfile
+        }
     } else {
         puts $fp $rawfile
@@ -1637 +1645 @@
         grid $top.scroll -sticky ns -column 4 -row 2
     } else {
-        grid forget $top.scroll 
+        grid forget $top.scroll
     }
     update
@@ -1949 +1957 @@
     }
 
+    # allow fixing of atom coordinates
+    if {[lindex $expmap(phasetype) [expr {$p - 1}]] != 4} {
+        grid [TitleFrame $w.10 -bd 6 -relief groove \
+                -text "Fix Atom$suffix Coordinates"] \
+                -row 9 -column 0 -columnspan 10 -sticky news
+        set fix [$w.10 getframe]
+        Fix_Initialize $numberList
+
+        label $fix.xlab -text "  x  " -width 8
+        label $fix.ylab -text "  y  " -width 8
+        label $fix.zlab -text "  z  " -width 8
+        grid $fix.xlab -row 2 -column 0
+        grid $fix.ylab -row 2 -column 1
+        grid $fix.zlab -row 2 -column 2
+
+
+        button $fix.x -text "$::fix_state_X" -width 8 \
+               -command "Fix_Atoms $phase [list $numberList] X $fix.x;
+               Fix_Write
+               DisplayAllAtoms $phase"
+
+        button $fix.y -text "$::fix_state_Y" -width 8 \
+                -command "Fix_Atoms $phase [list $numberList] Y $fix.y
+                Fix_Write
+                DisplayAllAtoms $phase"
+        button $fix.z -text "$::fix_state_Z" -width 8 \
+                -command "Fix_Atoms $phase [list $numberList] Z $fix.z
+                Fix_Write
+                DisplayAllAtoms $phase"
+        grid $fix.x -row 3 -column 0
+        grid $fix.y -row 3 -column 1
+        grid $fix.z -row 3 -column 2
+    }
+    #xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
     grid rowconfigure $w 11 -minsize 5
     grid [frame $w.b] -row 12 -column 0 -columnspan 10 -sticky ew
@@ -1966 +2009 @@
     if {[llength $expgui(selectedatomlist)] != 0} editRecord
 }
+
+#xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x
+
+proc Fix_Initialize {numberList} {
+     set phaselist $::expmap(phaselist)
+     catch {unset ::fix_param}
+     foreach i $phaselist {
+             set ::fix_list(X,$i) ""
+             set ::fix_list(Y,$i) ""
+             set ::fix_list(Z,$i) ""
+
+             set temp [atom_constraint_read $i]
+             foreach j $temp {
+                     set atomnum [string trim [string range $j 2 3]]
+                     set param [string trim [string range $j 4 6]]
+                     set ::fix_param($i,$atomnum,$param) 1
+                     if {$param == "X"} {lappend ::fix_list(X,$i) $atomnum}
+                     if {$param == "Y"} {lappend ::fix_list(Y,$i) $atomnum}
+                     if {$param == "Z"} {lappend ::fix_list(Z,$i) $atomnum}
+             }
+     }
+    set ::fix_state_X [Fix_State $i $numberList X]
+    set ::fix_state_Y [Fix_State $i $numberList Y]
+    set ::fix_state_Z [Fix_State $i $numberList Z]
+}
+
+proc Fix_State {phase numberList coord} {
+     set status_fixed "-1"
+     set status_unfixed "-1"
+     #puts "$coord before: $status_fixed $status_unfixed"
+     foreach i $numberList {
+         set temp [info exists ::fix_param($phase,$i,$coord)]
+         #puts "::fix_param($phase,$i,$coord) is variable present?: $temp"
+         if {$temp != 0} {set status_fixed 1}
+         if {$temp == 0} {set status_unfixed 1}
+     }
+     #puts "$coord after $status_fixed $status_unfixed"
+     if {$status_fixed == 1 && $status_unfixed != 1} {return "fixed"}
+     if {$status_fixed == 1 && $status_unfixed == 1} {return "mixed"}
+     if {$status_fixed != 1 && $status_unfixed == 1} {return "unfixed"}
+}
+
+proc Fix_Write {} {
+      incr ::expgui(changed)
+      #puts "Prepare to write [array names ::fix_Param]"
+      foreach j [array names ::fix_param] {
+             regexp {[0-9]+} $j  temp_phase
+             regexp {,[0-9]+} $j ans
+             set temp_atom [string range $ans 1 end]
+             regexp {[a-zA-Z]+} $j temp_param
+             if {$temp_param == "U"} {regexp {[a-zA-Z]+[0-9]+} $j temp_param}
+             set temp_entry [format "%1s %+2s%-4s" $temp_phase $temp_atom $temp_param]
+             lappend fix_list($temp_phase) $temp_entry
+     }
+     set phaselist $::expmap(phaselist)
+     foreach i $phaselist {
+             catch {atom_constraint_write $i $fix_list($i)}
+             catch  {RecordMacroEntry "catch {atom_constraint_write $i $fix_list($i)}" 0}
+             #puts $fix_list($i)
+     }
+}
+
+proc Fix_Atoms {phase numberList coord but} {
+#     puts "before  ::fix_state_$coord [set ::fix_state_$coord]"
+     #puts " before operationi: $::fix_list($coord,$phase)"
+     switch [set ::fix_state_$coord] {
+     "unfixed" {$but config -text "fixed"
+               set ::fix_state_$coord "fixed"
+               }
+     "fixed"   {$but config -text "unfixed"
+               set ::fix_state_$coord "unfixed"
+               }
+     "mixed"   {$but config -text "unfixed"
+               set ::fix_state_$coord "unfixed"
+               }
+     }
+     if {[set ::fix_state_$coord] == "fixed"} {
+        #puts "fixing atom number $numberList"
+        foreach i $numberList {
+                lappend ::fix_list($coord,$phase) $i
+                set ::fix_list($coord,$phase) [lsort -uniq -integer $::fix_list($coord,$phase)]
+                set ::fix_param($phase,$i,$coord) 1
+        }
+     }
+     if {[set ::fix_state_$coord] == "unfixed"} {
+        #puts "unfixing atoms $numberList"
+        foreach i $numberList {
+           set temp [lsearch $::fix_list($coord,$phase) $i]
+           if {$temp != -1} {
+              set ::fix_list($coord,$phase) [lreplace $::fix_list($coord,$phase) $temp $temp]
+              catch {unset ::fix_param($phase,$i,$coord)}
+           }
+        }
+     }
+     #puts "after operation: $::fix_list($coord,$phase)"
+}
+
 
 # transform the coordinates

trunk/disagledit.tcl

@@ -1 +1 @@
 proc DA_Initialize {} {
-catch {unset ::da_ddrad}
-catch {unset ::da_darad}
-catch {unset ::da_drad}
-catch {unset ::da_arad}
-catch {unset ::da_acon}
-catch {unset ::da_dcon}
+    catch {unset ::da_ddrad}
+    catch {unset ::da_darad}
+    catch {unset ::da_drad}
+    catch {unset ::da_arad}
+    catch {unset ::da_acon}
+    catch {unset ::da_dcon}
     set ::da_quit 1
-set ::da_phase $::expmap(phaselist)
-foreach j $::da_phase {
+    set ::da_phase $::expmap(phaselist)
+    foreach j $::da_phase {
         set ::da_dcon($j) [phaseinfo $j DistCalc]
         set b [regexp -all {[0-9]} $::da_dcon($j)]
         if {$b > 0} {
-           set ::da_dval($j) $::da_dcon($j)]
-           } else {
-             set ::da_dval$j ""
+            set ::da_dval($j) $::da_dcon($j)]
+    } else {
+        set ::da_dval$j ""
+    }
+
+    set ::da_acon($j) [phaseinfo $j AngCalc]
+    set c [regexp -all {[0-9]} $::da_acon($j)]
+    if {$c > 0} {set ::da_aval$j $::da_acon($j)
+    } else {
+        set ::da_aval$j ""}
+
+}
+
+}
+
+proc DA_Read {} {
+
+    set ::da_list [AtmTypList]
+    set da_angrad [DefAtmTypInfo angrad]
+    set da_distrad [DefAtmTypInfo distrad]
+
+    #Build search arrays
+    #::da_darad array contains default angle search radii
+    #::da_ddrad array contains default distance search radii
+    #::da_arad array contains current angle search radii
+    #::da_drad array contains current distance search radii
+
+    foreach j $da_angrad {
+        set ::da_darad([lindex $j 0]) [lindex $j 1]
+    }
+    foreach k $da_distrad {
+        set ::da_ddrad([lindex $k 0]) [lindex $k 1]
+    }
+    foreach i $::da_list {
+        set ::da_drad($i) [AtmTypInfo distrad $i]
+        set ::da_arad($i) [AtmTypInfo angrad $i]
+    }
+}
+
+#**************** Build Disagl Control Panel ****************************
+
+proc DA_Control_Panel {"launchdisagl 0"} {
+    DA_Initialize
+    DA_Read
+    destroy .disaglcon
+    set dcb .disaglcon
+    catch {toplevel $dcb}
+    eval destroy [winfo children $dcb]
+
+    #construct phase control box in phasecon frame
+    set phasecon $dcb.phasecon
+    frame $phasecon -bd 2 -relief groove
+    grid $phasecon -column 0 -row 0
+
+    label $phasecon.lbl1 -text "Bond Search \n Method"
+    label $phasecon.lbl2 -text "Angle Search \n Method"
+    grid  $phasecon.lbl1 -column 1 -row 0
+    grid  $phasecon.lbl2 -column 2 -row 0
+
+
+    foreach i $::da_phase {
+        label  $phasecon.phase$i -text "Phase $i" -width 8
+        set tacon [regexp {[0-9]+.[0-9]+} $::da_acon($i)]
+        set tdcon [regexp {[0-9]+.[0-9]+} $::da_dcon($i)]
+        if {$tacon} {set alist {none radii $::da_acon($i)}
+        } else {set alist {none radii {fixed search range}}}
+        if {$tdcon} {set dlist {none radii $::da_dcon($i)}
+        } else {set dlist {none radii {fixed search range}}}
+
+        #            set list  {none radii {fixed search range}}
+        #if {[set ::da_dval$i] != ""} {lappend list [set ::da_dval$i]}
+        eval tk_optionMenu $phasecon.dist$i ::da_dcon($i) $dlist
+        $phasecon.dist$i config -width 10
+        eval tk_optionMenu $phasecon.ang$i  ::da_acon($i) $alist
+        $phasecon.ang$i config -width 10
+        grid   $phasecon.phase$i -row $i -column 0 -padx 10
+        grid   $phasecon.dist$i  -row $i -column 1 -padx 10
+        grid   $phasecon.ang$i   -row $i -column 2 -padx 10
+    }
+
+    trace var ::da_dcon w DA_Controls
+    trace var ::da_acon w DA_Controls
+
+
+    #save box
+    set dasave $dcb.dasave
+    frame $dasave -bd 2 -relief groove
+    grid $dasave -column 0 -row 2
+
+    if {$launchdisagl} {
+        wm title $dcb "DISAGL Control Panel"
+        grab release $dcb
+        checkbutton $dasave.option -text "DISAGL output in separate window" \
+            -variable ::expgui(disaglSeparateBox)
+        grid $dasave.option -row 0 -column 0
+        button $dasave.sexit -text "Save and run DISAGL" -command DA_Save -bg LightGreen
+        grid $dasave.sexit -row 1 -column 0
+    } else {
+        wm title $dcb "Distance Search Parameters"
+        grab release $dcb
+        button $dasave.sexit -text "Save and Exit" -command DA_Save -bg LightGreen
+        grid $dasave.sexit -row 0 -column 0
+    }
+    button $dasave.quit -text "Cancel" -command "destroy $dcb"
+    grid $dasave.quit -row 2 -column 0
+
+
+    #construct control box
+
+
+    set dacon $dcb.dacon
+    frame $dacon -bd 2 -relief groove
+    grid $dacon -column 1 -row 2
+
+    button $dacon.default -text "Restore to Default Radii" -command {
+        foreach i $::da_list {
+            set ::da_drad($i) $::da_ddrad([lindex [split $i {+-}] 0])
+            set ::da_arad($i) $::da_darad([lindex [split $i {+-}] 0])
+        }
+    }
+    grid $dacon.default -row 3 -column 0 -columnspan 3
+
+    label $dacon.dradcon -text "Increment All Bond Search Radii (0.10 A)"
+    label $dacon.aradcon -text "Increment All Angle Search Radii (0.10 A)"
+    button $dacon.dradup -text "\u2191" -command DA_Inc_Drad
+    button $dacon.draddn -text "\u2193" -command DA_Dec_Drad
+    button $dacon.aradup -text "\u2191" -command DA_Inc_Arad
+    button $dacon.araddn -text "\u2193" -command DA_Dec_Arad
+    grid $dacon.dradcon -column 0 -row 0 -pady 5
+    grid $dacon.dradup  -column 1 -row 0 -padx 5
+    grid $dacon.draddn  -column 2 -row 0 -padx 5
+    grid $dacon.aradcon -column 0 -row 1 -pady 5
+    grid $dacon.aradup  -column 1 -row 1 -padx 5
+    grid $dacon.araddn  -column 2 -row 1 -padx 5
+
+    #     button $dacon.radcon -text "Radii Editor" -command {DA_Radii_Box .disaglcon}
+    #     grid $dacon.radcon -row 1 -column 0
+
+    DA_Radii_Box .disaglcon
+    putontop  .disaglcon
+    tkwait window .disaglcon
+    afterputontop
+    return $::da_quit
+
+}
+
+proc DA_Controls {var phase junk } {
+    if {[set ${var}($phase)] == "none"} {
+        if {$var == "::da_acon"} {
+            set ::da_dcon($phase) "none"
+            #puts 1
+        } else {
+            set ::da_acon($phase) "none"
+            #puts 2
         }
-
-        set ::da_acon($j) [phaseinfo $j AngCalc]
-        set c [regexp -all {[0-9]} $::da_acon($j)]
-        if {$c > 0} {set ::da_aval$j $::da_acon($j)
+    }
+    if {[set ${var}($phase)] != "none" && ($::da_dcon($phase) == "none" || $::da_acon($phase) == "none")} {
+        if {$var == "::da_acon"} {
+            set ::da_dcon($phase) "radii"
         } else {
-          set ::da_aval$j ""}
-
-}
-
-}
-
-proc DA_Read {} {
-
-   set ::da_list [AtmTypList]
-   set da_angrad [DefAtmTypInfo angrad]
-   set da_distrad [DefAtmTypInfo distrad]
-
-   #Build search arrays
-   #::da_darad array contains default angle search radii
-   #::da_ddrad array contains default distance search radii
-   #::da_arad array contains current angle search radii
-   #::da_drad array contains current distance search radii
-
-   foreach j $da_angrad {
-       set ::da_darad([lindex $j 0]) [lindex $j 1]
-   }
-   foreach k $da_distrad {
-       set ::da_ddrad([lindex $k 0]) [lindex $k 1]
-   }
-   foreach i $::da_list {
-           set ::da_drad($i) [AtmTypInfo distrad $i]
-           set ::da_arad($i) [AtmTypInfo angrad $i]
-   }
-}
-
-#**************** Build Disagl Control Panel ****************************
-
-proc DA_Control_Panel {"launchdisagl 0"} {
-     DA_Initialize
-     DA_Read
-     destroy .disaglcon
-     set dcb .disaglcon
-     catch {toplevel $dcb}
-     eval destroy [winfo children $dcb]
-
-     #construct phase control box in phasecon frame
-     set phasecon $dcb.phasecon
-     frame $phasecon -bd 2 -relief groove
-     grid $phasecon -column 0 -row 0
-
-     label $phasecon.lbl1 -text "Bond Search \n Method"
-     label $phasecon.lbl2 -text "Angle Search \n Method"
-     grid  $phasecon.lbl1 -column 1 -row 0
-     grid  $phasecon.lbl2 -column 2 -row 0
-
-
-     foreach i $::da_phase {
-             label  $phasecon.phase$i -text "Phase $i" -width 8
-             set tacon [regexp {[0-9]+.[0-9]+} $::da_acon($i)]
-             set tdcon [regexp {[0-9]+.[0-9]+} $::da_dcon($i)]
-             if {$tacon} {set alist {none radii $::da_acon($i)}
-                } else {set alist {none radii {fixed search range}}}
-             if {$tdcon} {set dlist {none radii $::da_dcon($i)}
-                } else {set dlist {none radii {fixed search range}}}
-
-#            set list  {none radii {fixed search range}}
-             #if {[set ::da_dval$i] != ""} {lappend list [set ::da_dval$i]}
-             eval tk_optionMenu $phasecon.dist$i ::da_dcon($i) $dlist
-                  $phasecon.dist$i config -width 10
-             eval tk_optionMenu $phasecon.ang$i  ::da_acon($i) $alist
-                  $phasecon.ang$i config -width 10
-             grid   $phasecon.phase$i -row $i -column 0 -padx 10
-             grid   $phasecon.dist$i  -row $i -column 1 -padx 10
-             grid   $phasecon.ang$i   -row $i -column 2 -padx 10
-     }
-
-     trace var ::da_dcon w DA_Controls
-     trace var ::da_acon w DA_Controls
-
-
-     #save box
-     set dasave $dcb.dasave
-     frame $dasave -bd 2 -relief groove
-     grid $dasave -column 0 -row 2
-
-     if {$launchdisagl} {
-       wm title $dcb "DISAGL Control Panel"
-       grab release $dcb
-       checkbutton $dasave.option -text "DISAGL output in separate window" \
-                   -variable ::expgui(disaglSeparateBox)
-       grid $dasave.option -row 0 -column 0
-       button $dasave.sexit -text "Save and run DISAGL" -command DA_Save -bg LightGreen
-       grid $dasave.sexit -row 1 -column 0
-     } else {
-       wm title $dcb "Distance Search Parameters"
-       grab release $dcb
-       button $dasave.sexit -text "Save and Exit" -command DA_Save -bg LightGreen
-       grid $dasave.sexit -row 0 -column 0
-     }
-     button $dasave.quit -text "Cancel" -command "destroy $dcb"
-     grid $dasave.quit -row 2 -column 0
-
-
-     #construct control box
-
-
-     set dacon $dcb.dacon
-     frame $dacon -bd 2 -relief groove
-     grid $dacon -column 1 -row 2
-
-     button $dacon.default -text "Restore to Default Radii" -command {
-            foreach i $::da_list {
-                    set ::da_drad($i) $::da_ddrad([lindex [split $i {+-}] 0])
-                    set ::da_arad($i) $::da_darad([lindex [split $i {+-}] 0])
-            }
-     }
-     grid $dacon.default -row 3 -column 0 -columnspan 3
-
-     label $dacon.dradcon -text "Increment All Bond Search Radii (0.10 A)"
-     label $dacon.aradcon -text "Increment All Angle Search Radii (0.10 A)"
-     button $dacon.dradup -text "\u2191" -command DA_Inc_Drad
-     button $dacon.draddn -text "\u2193" -command DA_Dec_Drad
-     button $dacon.aradup -text "\u2191" -command DA_Inc_Arad
-     button $dacon.araddn -text "\u2193" -command DA_Dec_Arad
-     grid $dacon.dradcon -column 0 -row 0 -pady 5
-     grid $dacon.dradup  -column 1 -row 0 -padx 5
-     grid $dacon.draddn  -column 2 -row 0 -padx 5
-     grid $dacon.aradcon -column 0 -row 1 -pady 5
-     grid $dacon.aradup  -column 1 -row 1 -padx 5
-     grid $dacon.araddn  -column 2 -row 1 -padx 5
-
-#     button $dacon.radcon -text "Radii Editor" -command {DA_Radii_Box .disaglcon}
-#     grid $dacon.radcon -row 1 -column 0
-
-DA_Radii_Box .disaglcon
-             putontop  .disaglcon
-             tkwait window .disaglcon
-             afterputontop
-             return $::da_quit
-
-}
-
-proc DA_Controls {var phase junk } {
-     if {[set ${var}($phase)] == "none"} {
-        if {$var == "::da_acon"} {
-           set ::da_dcon($phase) "none"
-           puts 1
-        } else {
-           set ::da_acon($phase) "none"
-           puts 2
+            set ::da_acon($phase) "radii"
         }
-     }
-     if {[set ${var}($phase)] != "none" && ($::da_dcon($phase) == "none" || $::da_acon($phase) == "none")} {
-        if {$var == "::da_acon"} {
-           set ::da_dcon($phase) "radii"
-        } else {
-           set ::da_acon($phase) "radii"
-        }
-     }
-
-
-#     if {[set ${var}($phase)] == "fixed search range"} {}
-      if {[set ${var}($phase)] != "none" && [set ${var}($phase)] != "radii" } {
-           catch {destroy .disaglcon.top}
-           set dedit .disaglcon.top
-           toplevel $dedit
-           bind $dedit <Return> "destroy $dedit"
-#           frame $dedit -bd 2 -relief groove
-#           pack $dedit -side top
-           set temp [regexp {[0-9]+.[0-9]+} [set ${var}($phase)]]
-           if {$temp == 0} {set ${var}($phase) 0.00}
-           if {$var == "::da_acon"} {
-              label $dedit.lbl1    -text "set angle fixed search range \n for phase $phase in angstroms"
-#              set ::da_acon($phase) 0
-              entry  $dedit.entry1 -textvariable ::da_acon($phase) -takefocus 1 
-                     $dedit.entry1 selection range 0 end
-              grid $dedit.lbl1 -column 0 -row 0
-              grid $dedit.entry1 -column 0 -row 1
-              focus $dedit.entry1
-           }
-           if {$var == "::da_dcon"} {
- #             set ::da_dcon($phase) 0
-              label $dedit.lbl1    -text "set bond fixed search range \n for phase $phase in angstroms"
-              entry  $dedit.entry1 -textvariable ::da_dcon($phase) -takefocus 1
-                     $dedit.entry1 selection range 0 end
-              grid $dedit.lbl1 -column 0 -row 0
-              grid $dedit.entry1 -column 0 -row 1
-              focus $dedit.entry1
-           }
-           button $dedit.quit -text "Set" -command "destroy $dedit"
-           grid $dedit.quit -column 0 -row 2
-           putontop $dedit
-           tkwait window $dedit
-           afterputontop
-     }
-
-
-
-
-#     puts "phase = $phase"
-#     puts "var = $var"
-#     puts "new value = [set ${var}($phase)]"
+    }
+
+
+    #     if {[set ${var}($phase)] == "fixed search range"} {}
+    if {[set ${var}($phase)] != "none" && [set ${var}($phase)] != "radii" } {
+        catch {destroy .disaglcon.top}
+        set dedit .disaglcon.top
+        toplevel $dedit
+        bind $dedit <Return> "destroy $dedit"
+        #           frame $dedit -bd 2 -relief groove
+        #           pack $dedit -side top
+        set temp [regexp {[0-9]+.[0-9]+} [set ${var}($phase)]]
+        if {$temp == 0} {set ${var}($phase) 0.00}
+        if {$var == "::da_acon"} {
+            label $dedit.lbl1    -text "set angle fixed search range \n for phase $phase in angstroms"
+            #              set ::da_acon($phase) 0
+            entry  $dedit.entry1 -textvariable ::da_acon($phase) -takefocus 1 
+            $dedit.entry1 selection range 0 end
+            grid $dedit.lbl1 -column 0 -row 0
+            grid $dedit.entry1 -column 0 -row 1
+            focus $dedit.entry1
+        }
+        if {$var == "::da_dcon"} {
+            #             set ::da_dcon($phase) 0
+            label $dedit.lbl1    -text "set bond fixed search range \n for phase $phase in angstroms"
+            entry  $dedit.entry1 -textvariable ::da_dcon($phase) -takefocus 1
+            $dedit.entry1 selection range 0 end
+            grid $dedit.lbl1 -column 0 -row 0
+            grid $dedit.entry1 -column 0 -row 1
+            focus $dedit.entry1
+        }
+        button $dedit.quit -text "Set" -command "destroy $dedit"
+        grid $dedit.quit -column 0 -row 2
+        putontop $dedit
+        tkwait window $dedit
+        afterputontop
+    }
+
+
+
+
+    #     puts "phase = $phase"
+    #     puts "var = $var"
+    #     puts "new value = [set ${var}($phase)]"
 }
 
 proc DA_Radii_Box {dcb args} {
-     #construct radii control box
-     catch {destory $dcb.radcon}
-     catch {destory $dcb.discon}
-     set radcon $dcb.radcon
-     frame $radcon -bd 2 -relief groove
-     grid $radcon -column 1 -row 0 -rowspan 2
-
-     label $radcon.lbl1 -text "Atom/Ion"
-     label $radcon.lbl2 -text "Bond \n Search Radii"
-     label $radcon.lbl3 -text "Angle \n Search Radii"
-     grid $radcon.lbl1 -row 0 -column 0
-     grid $radcon.lbl2 -row 0 -column 1
-     grid $radcon.lbl3 -row 0 -column 2
-     set count 1
-     foreach j [array names ::da_drad] {
-             label $radcon.atom$j -text "$j" -width 5
-             entry $radcon.drad$j -textvariable ::da_drad($j) -width 6 -takefocus 1
-             entry $radcon.arad$j -textvariable ::da_arad($j) -width 6 -takefocus 1
-             grid  $radcon.atom$j -row $count -column 0
-             grid  $radcon.drad$j -row $count -column 1
-             grid  $radcon.arad$j -row $count -column 2
-             incr count
-     }
+    #construct radii control box
+    catch {destory $dcb.radcon}
+    catch {destory $dcb.discon}
+    set radcon $dcb.radcon
+    frame $radcon -bd 2 -relief groove
+    grid $radcon -column 1 -row 0 -rowspan 2
+
+    label $radcon.lbl1 -text "Atom/Ion"
+    label $radcon.lbl2 -text "Bond \n Search Radii"
+    label $radcon.lbl3 -text "Angle \n Search Radii"
+    grid $radcon.lbl1 -row 0 -column 0
+    grid $radcon.lbl2 -row 0 -column 1
+    grid $radcon.lbl3 -row 0 -column 2
+    set count 1
+    foreach j [array names ::da_drad] {
+        label $radcon.atom$j -text "$j" -width 5
+        entry $radcon.drad$j -textvariable ::da_drad($j) -width 6 -takefocus 1
+        entry $radcon.arad$j -textvariable ::da_arad($j) -width 6 -takefocus 1
+        grid  $radcon.atom$j -row $count -column 0
+        grid  $radcon.drad$j -row $count -column 1
+        grid  $radcon.arad$j -row $count -column 2
+        incr count
+    }
 }
 
 
 proc DA_Inc_Drad {args} {
-        foreach j [array names ::da_drad] {
-                set ::da_drad($j) [format %.1f [expr $::da_drad($j) + 0.1]]
-        }
+    foreach j [array names ::da_drad] {
+        set ::da_drad($j) [format %.1f [expr $::da_drad($j) + 0.1]]
+    }
 }
 
 proc DA_Dec_Drad {args} {
-        foreach j [array names ::da_drad] {
-                set ::da_drad($j) [format %.1f [expr $::da_drad($j) - 0.1]]
-        }
+    foreach j [array names ::da_drad] {
+        set ::da_drad($j) [format %.1f [expr $::da_drad($j) - 0.1]]
+    }
 }
 proc DA_Inc_Arad {args} {
-        foreach j [array names ::da_arad] {
-                set ::da_arad($j) [format %.1f [expr $::da_arad($j) + 0.1]]
-        }
+    foreach j [array names ::da_arad] {
+        set ::da_arad($j) [format %.1f [expr $::da_arad($j) + 0.1]]
+    }
 }
 proc DA_Dec_Arad {args} {
-        foreach j [array names ::da_drad] {
-                set ::da_arad($j) [format %.1f [expr $::da_arad($j) - 0.1]]
-        }
+    foreach j [array names ::da_drad] {
+        set ::da_arad($j) [format %.1f [expr $::da_arad($j) - 0.1]]
+    }
 }
 
 proc DA_Save {args} {
-     foreach i $::da_list {
-           if {$::da_drad($i) >= 0 && $::da_drad($i) <= 10000} {
-              AtmTypInfo distrad $i set $::da_drad($i)
-           }
-           puts 1
-           if {$::da_arad($i) >= 0 && $::da_arad($i) <= 10000} {
-              AtmTypInfo angrad $i set $::da_arad($i)
-           }
-
-     }
-     foreach j $::da_phase {
+    foreach i $::da_list {
+        if {$::da_drad($i) >= 0 && $::da_drad($i) <= 10000} {
+            AtmTypInfo distrad $i set $::da_drad($i)
+        }
+        puts 1
+        if {$::da_arad($i) >= 0 && $::da_arad($i) <= 10000} {
+            AtmTypInfo angrad $i set $::da_arad($i)
+        }
+
+    }
+    foreach j $::da_phase {
         phaseinfo $j DistCalc set $::da_dcon($j)
         phaseinfo $j AngCalc set $::da_acon($j)
-     }
-     # indicate a change to the .EXP file
-     incr ::expgui(changed)
-     set ::da_quit 0
-     destroy .disaglcon
-}
+    }
+    # indicate a change to the .EXP file
+    incr ::expgui(changed)
+    set ::da_quit 0
+    destroy .disaglcon
+}

trunk/distrest.tcl

@@ -37 +37 @@
 
 proc DisplayDistanceRestraints {args} {
+    #puts DisplayDistanceRestraints
     global expcons
     eval destroy [winfo children $expcons(distmaster)]
@@ -51 +52 @@
         -sticky nsew
     grid [frame $phasebox -bd 2 -relief groove] -column 0 -row 0 \
-         -sticky new -columnspan 2
+        -sticky new -columnspan 2
 
 
     grid [frame $editorbox -bd 2 -relief groove] -column 0 -row 2 \
-         -sticky sew -columnspan 2
+        -sticky sew -columnspan 2
 
 
@@ -64 +65 @@
     # Pick Phase to be Evaluated **********************************************
     label $phasebox.phlabel -text Phase
-#    set ::sr_phaselist $::expmap(phaselist)
+    #    set ::sr_phaselist $::expmap(phaselist)
 
     eval tk_optionMenu $phasebox.phase ::sr_entryvar(softphase) $::expmap(phaselist)
-#    eval tk_optionMenu $phasebox.phase ::sr_entryvar(softphase) $::sr_phaselist
-#   trace variable ::sr_entryvar(softphase) w DisplayDistanceRestraints
-#   bind $phasebox.phase <ButtonRelease> {DisplayDistanceRestraints}
+    #    eval tk_optionMenu $phasebox.phase ::sr_entryvar(softphase) $::sr_phaselist
+    #   trace variable ::sr_entryvar(softphase) w DisplayDistanceRestraints
+    #   bind $phasebox.phase <ButtonRelease> {DisplayDistanceRestraints}
 
     grid $phasebox.phlabel -column 0 -row 0
@@ -78 +79 @@
     grid [label $leftfr.lweight -text "Restraint Weight"] -column 0 -row 1 -sticky sw -pady 10
     grid [entry $leftfr.weight -width 8 -textvariable entryvar(distrestweight)] -column 1 -row 1 -sticky sw \
-         -padx 5 -pady 10
+        -padx 5 -pady 10
     set ::entrycmd(distrestweight) "SoftConst weight"
     set ::entrycmd(trace) 0
     set ::entryvar(distrestweight) [SoftConst weight]
+    RecordMacroEntry "set ::entryvar(distrestweight) [SoftConst weight]" 0
     set ::entrycmd(trace) 1
-
+    incr ::expgui(changed)
 
     #Run Disagl Commands *****************************************************
@@ -95 +97 @@
     grid [button $editorbox.edit -text "Activate Restraint \n Editor" -command SR_TEST] -column 0 -row 4 \
         -columnspan 2 -pady 5
-        $editorbox.edit config -bg LightGreen -bd 6
+    $editorbox.edit config -bg LightGreen -bd 6
 
     grid [button $editorbox.search -text "Edit Search Distance \n Parameters" -command DA_Control_Panel] -column 0 -row 3 \
         -columnspan 2
-        $editorbox.edit config -bd 4
+    $editorbox.edit config -bd 4
 
 
@@ -114 +116 @@
 
     label  $top.rlabel1 -text "Restraint" -width 9 -anchor center
-    label  $top.rlabel2 -text "esd"       -width 9 -anchor center
+    label  $top.rlabel2 -text "Tolerance" -width 9 -anchor center
 
     grid $top.alabel1 -column 1 -row 2 -padx 3
@@ -139 +141 @@
     SR_Show_RestraintsOnly $main $rightfr
     foreach item [trace vinfo ::sr_entryvar(softphase)] {
-    eval trace vdelete ::sr_entryvar(softphase) $item
+        eval trace vdelete ::sr_entryvar(softphase) $item
     }
 
@@ -148 +150 @@
     SR_Fill_Display  $main
     ResizeScrollTable $rightfr
+    #puts $rightfr
 }
 
@@ -336 +339 @@
 
     label  $sr_top.rlabel1 -text "Restraint"
-    label  $sr_top.rlabel2 -text "esd"
+    label  $sr_top.rlabel2 -text "Tolerance"
     grid $sr_top.rlabel1 -column 4 -row 2 -padx 20
     grid $sr_top.rlabel2 -column 5 -row 2 -padx 20
 
 
-    button $sr_top.rcon1   -text "Check All" -width 10 -command "
+    button $sr_top.rcon1   -text "Check\nAll" -width 4 -command "
         set ::sr_checkall 1;
         SR_Set_All_Check_Buttons;
@@ -348 +351 @@
     "
 
-    button $sr_top.rcon2   -text "Clear All" -width 10 -command "
+    button $sr_top.rcon2   -text "Clear\nAll" -width 4 -command "
         set ::sr_checkall 0;
         SR_Set_All_Check_Buttons;
@@ -396 +399 @@
                                 label $main.rdistance$i -text [lindex $rprint 8] -justify center -anchor center
                                 entry $main.restraint$i -width 8 -textvariable ::sr_restraintdist([lindex $rprint 13]) -takefocus 1
-                                      $main.restraint$i selection range 0 end
+                                $main.restraint$i selection range 0 end
                                 bind  $main.restraint$i <KeyRelease> {SR_Validate_Soft %W distance}
                                 entry $main.restesd$i -width 8 -textvariable ::sr_restraintesd([lindex $rprint 13]) -takefocus 1
-                                      $main.restesd$i selection range 0 end
+                                $main.restesd$i selection range 0 end
                                 bind  $main.restesd$i <KeyRelease> {SR_Validate_Soft %W esd}
                                 checkbutton $main.sr_crestraint$i -variable ::sr_crestraint([lindex $rprint 13])
@@ -458 +461 @@
         # valid value
         $win config -fg black
-        $::srcb3.rbutton3 config -bg LightGreen -text "Save Restraints to EXP File"
+        $::srcb3.rbutton3 config -bg LightGreen -text "Save Changes"
         set ::sr_error 0
     }
@@ -515 +518 @@
         set sr_write ""
         set new_list ""
-#       set len [llength $::sr_bond_list]
+        #       set len [llength $::sr_bond_list]
         set ::sr_key_list ""
         foreach temp $::sr_bond_list  {
-puts $temp
-#       for {set i 0} {$i <= [expr $len-1]} {incr i} {}
-#           set temp [lindex $::sr_bond_list $i]
-
-           catch {
-            if {[string trim $::sr_restraintdist([lindex $temp 13])] != ""} {
-                set softrest "[lindex $temp 0] [lindex $temp 1] \
+            #   for {set i 0} {$i <= [expr $len-1]} {incr i} {}
+            #       set temp [lindex $::sr_bond_list $i]
+
+            if {[catch {
+                if {[string trim $::sr_restraintdist([lindex $temp 13])] != ""} {
+                    set softrest "[lindex $temp 0] [lindex $temp 1] \
                                 [lindex $temp 2] [lindex $temp 3] [lindex $temp 4] \
                                 [lindex $temp 5] [lindex $temp 6] [lindex $temp 7]\
                                 $::sr_restraintdist([lindex $temp 13])\
                                 $::sr_restraintesd([lindex $temp 13])"
-                lappend sr_write $softrest
-puts $softrest
-                lappend new_list $temp
-            }
-            }
+                    lappend sr_write $softrest
+                    #lappend new_list $temp
+                }
+            } errmsg]} {puts "error: $errmsg"}
         }
-#
+        #
         #puts $sr_write
         # put the entire restraint list back into the .EXP file
+        #puts "SoftConst restraintlist set $sr_write"
         SoftConst restraintlist set $sr_write
-        set ::sr_bond_list $new_list
+        RecordMacroEntry "SoftConst restraintlist set $sr_write" 0
+        #set ::sr_bond_list $new_list
         # indicate a change to the .EXP file
         incr ::expgui(changed)
@@ -623 +626 @@
     label $srcb1.dmaxlabel    -text "Dmax"
     label $srcb2.restlabel    -text "Restraint Value" -width 16 -anchor w
-    label $srcb2.restlabelesd -text "esd"
+    label $srcb2.restlabelesd -text "Tolerance"
 
     eval tk_optionMenu $srcb1.atom1 ::sr_entryvar(softatom1) "[lsort [array names ::sr_lookuplist1${::sr_entryvar(softphase)}]] all"
@@ -630 +633 @@
 
     entry  $srcb1.sr_dminvalue -width 8 -textvariable ::sr_dminvalue        -takefocus 1
-           $srcb1.sr_dminvalue selection range 0 end
+    $srcb1.sr_dminvalue selection range 0 end
     entry  $srcb1.sr_dmaxvalue -width 8 -textvariable ::sr_dmaxvalue        -takefocus 1
-           $srcb1.sr_dmaxvalue selection range 0 end
+    $srcb1.sr_dmaxvalue selection range 0 end
     entry  $srcb2.sr_rvalue    -width 8 -textvariable ::sr_rvalue           -takefocus 1
-           $srcb2.sr_rvalue selection range 0 end
+    $srcb2.sr_rvalue selection range 0 end
     entry  $srcb2.sr_resd      -width 8 -textvariable ::sr_resd             -takefocus 1
-           $srcb2.sr_resd selection range 0 end
+    $srcb2.sr_resd selection range 0 end
 
     bind  $srcb1.sr_dminvalue <KeyRelease> {SR_Validate_Soft %W dmin}
@@ -644 +647 @@
 
     button $srcb1.recalc   -text "Filter" -bd 6 -command {SR_Display}
-    button $srcb2.rbutton1 -text "check update" -command {SR_Update_Restraints}
-    button $srcb2.rbutton2 -text "check delete" -command {SR_Delete_Restraints}
-    button $::srcb3.rbutton3 -text "Save Restraints to EXP File" -bd 6 -bg LightGreen -command {SR_Write_Restraints}
-    button $::srcb3.rbutton4 -text "Cancel" -command {destroy .mainrestraintbox
+    button $srcb2.rbutton1 -text "Set checked" -command {SR_Update_Restraints}
+    button $srcb2.rbutton2 -text "Delete checked" -command {SR_Delete_Restraints}
+    button $::srcb3.rbutton3 -text "Save changes" -bd 6 -bg LightGreen -command {SR_Write_Restraints}
+    button $::srcb3.rbutton4 -text "Cancel" -command {
+        destroy .mainrestraintbox
         afterputontop
         SR_Rest_Only
-        DisplayDistanceRestraints}
-    wm protocol .mainrestraintbox WM_DELETE_WINDOW {destroy .mainrestraintbox
+        DisplayDistanceRestraints
+    }
+    wm protocol .mainrestraintbox WM_DELETE_WINDOW {
+        destroy .mainrestraintbox
         afterputontop
         SR_Rest_Only
-        DisplayDistanceRestraints}
+        DisplayDistanceRestraints
+    }
 
     grid $srcb1.atomlabel1   -column 1 -row 0
@@ -725 +732 @@
     set ::sr_distance_button 1
     set ::sr_entryvar(choicenum) 0
-#    set ::sr_entryvar(softphase) "1"
-#    set ::sr_phaselist $::expmap(phaselist)
+    #    set ::sr_entryvar(softphase) "1"
+    #    set ::sr_phaselist $::expmap(phaselist)
     set ::sr_entryvar(softatom1) "all"
     set ::sr_entryvar(softatom2) "all"

trunk/doc/excledt.html

@@ -283 +283 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui.html

@@ -16 +16 @@
 EXPGUI<BR>
 A Graphical User Interface for 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
 GSAS</A>
 <HR noshade width="75%" size="2" align="center">
@@ -34 +34 @@
 <P><P>
 EXPGUI is a graphical interface for the 
-Los Alamos
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
-GSAS</A> package. 
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
+package, developed at Los Alamos and maintained now at Argonne. 
 EXPGUI does two things: 
 it can be used to directly modify the GSAS 
@@ -60 +59 @@
 <TH><A Href="expgui4.html">Scaling info</A></TH>
 <TH><A Href="expgui5.html">Profile terms</A></TH>
-<TH><A Href="expgui6.html">Constraints</A></TH>
+<TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
 </TR>
 <TR>
+<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
 <TH><A Href="expgui7.html">Preferred Orientation</A></TH>
 <TH><A Href="expguic.html">Menus</A></TH>
@@ -117 +117 @@
 A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)", 
 Los Alamos National Laboratory Report LAUR 86-748 (2000).
-<A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf">
+<A
+  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
 [link to PDF copy of manual]
 </A>
@@ -154 +155 @@
 are used. The File/Save operation is done automatically before any GSAS
 programs, such as GENLES or EXPEDT, are run.
+<P>
+<A name="badexp">
+The GSAS refinement program, GENLES, will sometimes "blow up", where the
+  program changes varied parameters to values very far from their
+  correct values. This occurs when parameters are highly correlated,
+  are refining to values that are not allowed, or some of the refined parameters have
+  very little impact on the quality of the fit. When this happens,
+  invalid values are written to the GSAS experiment file that contain
+  either asterisks (****) or the string "NAN" (not a number). Such
+  files cannot be used for additional GENLES runs.
+  <P>
+  When EXPGUI reads a .EXP file it scans it for evidence of a previous
+  failure of a GENLES refinement and warns if a problem is
+  noted. Please note that this scan is not perfect and occasionally
+  you may be warned in cases where the file is fine (if possible,
+  please send such .EXP file to Brian Toby so this scan can be improved.)
+  When such a "bad" .EXP file is located, one can "revert" to an
+  archived copy of a previous experiment file (with suffix .Oxx). This
+  can be done with the Revert menu item in the File menu. Note that
+clicking on a file in the file selection window causes it to be
+scanned and shows the status of that refinement. Also note that
+usually the last good archived file has settings that will produce the same bad
+refinement, so it is necessary to either revert further back, or to
+change the refinement options before running GENLES. 
 <P>
 
@@ -475 +500 @@
 
 The INSTEDIT utility is used to edit or create an instrument parameter file.
-At this time it can only be used to edit files for 
-constant-wavelength data. The utility can be started from the "Edit File"
-button in the 
+The utility can be started from the "Edit File" button in the 
 <A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the 
-the "instedit" option in the Powder menu. In the latter case, the user
-is given the chance to select an input file. If no file is selected,
-a new, empty, file is created. An example INSTEDIT window appears below.
+the "instedit" option in the Powder menu. Alternately, to create a new
+  instrument parameter file, choose Powder menu option "New InstParm
+  file". (It is also possible 
+  to create a new file using the standard instedit by selecting
+  "Cancel" when asked for an input file.)
+An example INSTEDIT window appears below.
 <P>
 <img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
@@ -593 +619 @@
 records can slow the GSAS programs 
 (this is less of a problem on faster computers). For these reasons, it may be 
-a good idea to prune the older history records from the file. If more than 100
-history records are found in an experiment file, EXPGUI suggests that the
-older history entries be deleted. Alternately the File/EraseHistory command
-can be used to invoke the this option.
+a good idea to prune the older history records from the file.
+The File/EraseHistory command can be used to invoke the this option.
 <P>
 On the dialog the number of history records to be retained is specified. 
@@ -681 +705 @@
 <A name=tcltk>
 <H2>
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
+<A Href="http://www.tcl.tk">
 Tcl/Tk</A></H2>
 The 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
+<A Href="http://www.tcl.tk">
 Tcl/Tk program</A> is a platform-independent scripting language that is
 used to implement most of EXPGUI. This software is available for free
-and must be loaded in order to use EXPGUI. See the 
-installation notes for 
-<A HREF="expgui_Win_readme.html">Windows</A>,
-and for
-<A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
+and must be loaded in order to use EXPGUI. A somewhat out of date
+version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
+more recent versions can be used, but note that the BLT package (see
+below) is needed for all features of EXPGUI.
 While learning Tcl/Tk is a great thing to do, it is not a requirement
 for using or installing EXPGUI.
-
-<A name=winexec>
-<H3>
-WINEXEC</H3>
-<UL>
-The WINEXEC package is needed under Windows-95 and its offspring 
-(-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation 
-notes</A> for more details.
-</UL>
 
 <A name=blt>
@@ -715 +729 @@
 If this is the case, a message, 
 "BLT Setup Error: could not access a Blt_ routine...", will be displayed.
-This is most common in UNIX and is discussed further in the 
-<A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see 
-<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
-http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
-</A> for more information on installation of BLT.
+Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
 </UL>
 
@@ -727 +737 @@
 <UL>
 The
-<A HREF="www.hume.com">Hume 
+<A HREF="http://www.hume.com">Hume 
 </A>
 Linear Algebra Tcl Package, 
-<A HREF="www.hume.com">
+<A HREF="http://www.hume.com/la/la.html">
 La</A>, 
 is used by the BKGEDIT
@@ -739 +749 @@
 should not happen, since the package is included with the EXPGUI files.
 So if get this error you probably have an incomplete installation.
-Note that the La package requires Tcl/Tk version 8.1 or higher, so that if 
-you are using an older version of Tcl/Tk, you will need to upgrade.
-See the installation instructions for
-<A HREF="expgui_Win_readme.html">Windows</A>,
-and for
-<A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
+</UL>
+
+<A name=winexec>
+<H3>
+WINEXEC</H3>
+<UL>
+The WINEXEC package was needed under Windows-95 and its offspring 
+(-98 and -ME). It was found in older versions of EXPGUI, but is no
+  longer included.
 </UL>
 
@@ -750 +763 @@
 Acknowledgments</H2>
 Praise to Larson and 
-Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
+Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
 for Tcl/Tk, 
-Przemek Klosowski</A>
+Przemek Klosowski
 for convincing me to learn Tcl/Tk 
-and Jonathan Wasserman for helping get this project started.
-Thanks also to 
+and Jonathan Wasserman for helping me get this project started.
+Thanks also to
+Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
+bond-distance restraints module and the (soon to come) rigid body editor;
 Pamela Whitfield of the NRC (Canada) for writing large 
 sections of the 
@@ -763 +778 @@
 code and to John Cowgill for the "Export to GRACE" code.
 <P>
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
 GSAS</A>
 is written by Allen C. Larson and Robert B. Von Dreele while at 
@@ -770 +785 @@
 <A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
 EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
-<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> 
-with help from Jonathan Wasserman.
+<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
 
 <P><hr><blockquote>
@@ -786 +800 @@
 software.
 
-<P>The author of EXPGUI is a U.S. Government employee which means that
+<P>EXPGUI was written by a U.S. Government employee, which means that
 EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write 
 new sections and make them available to the rest of the world. 
@@ -793 +807 @@
 expressed or implied, or assumes any liability or responsibility 
 for the use of this information or the software described
-here. Brand names cited herein are used for
-identification purposes and do not constitute an endorsement by NIST.
+here.
 </blockquote>
 

trunk/doc/expgui0.html

@@ -44 +44 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
-</blockquote>
+/blockquote>
 </body>
 </html>

trunk/doc/expgui1.html

@@ -186 +186 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui2.html

@@ -80 +80 @@
 <P>
 <a name="xform"></a>
-<h4>A.2.2 Transform Coordinates</h4> 
-<DL><DL>
-<img SRC="2a.gif" align=RIGHT alt="EXPGUI Screen snapshot">
-If one or more atoms have been selected
-<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
-to make changes to those atoms by pressing the "Xform atom(s)" button. 
-This raises the window shown to the right.
-Note that no changes are actually made, until the 
-"Transform Coordinates", "Set Occupancies",... buttons are pressed.
-<P>
-This window can be used 
-to transform the coordinates coordinates of the selected atoms, 
-globally set occupancy or Uiso (Uequiv) 
-values for the selected atoms, or erase the selected atoms. by pressing the 
-It is also possible to transform the selected atoms
-from isotropic to anisotropic, or the reverse. 
-<P>
-<IMG SRC="new.gif" alt="New!">
-The "Xform Origin 1 to Origin 2" button is only available for those 
+<h4>A.2.2 Modify Atom</h4> 
+<DL><DL>
+<img SRC="2a.jpg" align=RIGHT alt="EXPGUI Screen snapshot">
+The "Modify Atom" button ("Modify Atoms" when multiple atoms are
+  selected) provides access to additional options that can
+  transform or modify the selected atom(s) from the phase panel  
+<A href="expgui.html#mouseactions">(see Mouse Actions</A> for
+  information on selecting atoms); this opens the menu window shown to
+  the right.
+Note that changes are made to the coordinates when the buttons on this
+  window (such as 
+"Transform Coordinates", "Set Occupancies",...) are pressed.
+<P><B>Modify Coordinates:</B>
+  This is used 
+to transform the coordinates coordinates of the selected atoms using a
+set of  transformation relationships.
+  
+<P><B>Reset Multiplicities:</B>
+ When atom positions are edited in EXPGUI, they may be moved off from
+  or onto special positions in the cell, changing the site
+  multiplicity -- but this will not be reflected in the phase
+  display. When atoms are subsequently refined, GENLES will update the
+  multiplcities. Pressing the  "Reset Multiplicities" button cases
+  this to be done right away (I think this may not work if there are no
+  histograms present). 
+
+<P><B>Xform Origin 1 to Origin 2:</B> This button is only available for those 
 orthorhombic, tetragonal and cubic space groups that are listed in the
 International Tables with two origin settings. (These space groups have 
@@ -106 +114 @@
 of symmetry. GSAS only uses the origin 2 settings.)
 If coordinates have been entered in the origin 1 setting, they may be 
-transformed to the origin 2 setting using this button.
+transformed to the origin 2 setting using this button. It is important
+  to select all atoms in the asymmetric unit before using this button.
+
+  <P><B>Modify Occupancies:</B>
+ This allows the occupancy to be set for one or more atoms. It is
+  most convenient for when many atoms will have their occupancy
+  changed at one time.
+
+<P><B>Modify Displacement Parameters:</B>
+  This allows one to set Uiso (or Uequiv) values for the selected
+  atoms (<B>Set U</B>). To change the flag that determines if the
+  selected atom(s) are represented as Isotropic or Anisotropic, press
+  the <B>Set Isotropic</B> or <B>Set Anisotropic</B> buttons.
+
+<P><B>Erase Atoms:</B>
+  The "Erase Atoms" removes the selected atoms from the phase. I
+  usually set the occupancy to 0. instead. 
+  
+<P><B>Fix Atom Coordinates:</B>
+When an atom is refined in GSAS, only the coordinates that are not
+defined by site symmetry are refined. However, in some space groups,
+it is necessary to not refine additional coordinates. The most common
+example are polar space groups (P1, P2, P2<sub>1</sub>, C2,  P4, P4<sub>1</sub>, P
+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
+P6<sub>3</sub> - from
+<a href="http://www.ruppweb.org/Xray/comp/space_instr.htm"> Bernard Rupp's
+web site, http://www.ruppweb.org/Xray/comp/space_instr.htm</A>) where
+one or more coordinates of the origin are not defined by symmetry. In
+these space groups an appropriate number of coordinates must be fixed
+to define the origin. As an example, in P1, one x, one y and one z
+coordinate must not be refined; in space group P2<sub>1</sub>, the
+2<sub>1</sub> screw axis defines the origin at (0,0,z) so one z
+coordinate cannot be varied.
+
+Occasionally, while symmetry may allow
+atom coordinates to be varied, a crystallographer may choose to
+simplify or constrain the representation to fix the atom in a
+particular location and not refine with all allowed degrees of freedom.
+
+<IMG SRC="new.gif" alt="New!">
+ The "Fix Atom Coordinates" buttons allows a flag to be set (or
+cleared) for an atom
+to prevent refinement of selected coordinates, even when the X
+refinement flag is set. Note the addition of an "F" for the x and z
+coordinates of the first atom as shown in the phase panel, above. This
+indicates that x & z have been fixed. When the atom position is
+varied, only y will be optimized. 
 
 <br clear=all>
@@ -248 +302 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui3.html

@@ -31 +31 @@
 <HR noshade width="75%" size="2" align="center">
 </h1></center>
-<h3>A.3 Histogram panel</h3> 
-<DL><DL>
-The histogram panel is used to edit background
-and diffractometer constants for a histogram, as well as 
+<h3>A.3 Powder panel</h3> 
+<DL><DL>
+The Powder (was histogram) panel is used to edit background
+and diffractometer constants for powder histogram(s), as well as 
 set damping and refinement flags for these parameters.
 <P>
@@ -288 +288 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui4.html

@@ -60 +60 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui5.html

@@ -118 +118 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui6.html

@@ -22 +22 @@
 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
-</TH><TH><A Href="expgui7.html">Next page</A>
+</TH><TH><A Href="expgui6A.html">Next page</A>
 </TH><TH><A Href="expgui5.html">Previous page</A>
 </TH></TR></TABLE><BR CLEAR=ALL>
@@ -32 +32 @@
 </h1></center>
 
-<h3>A.6 Constraints panel</h3>
+<h3>A.6 Re/Constraints panel</h3>
 <DL><DL>
 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 
 applied to each parameter in the group.
-The constraints panel is used to set these "hard constraints."
+The Re/Constraints panel is used to set these "hard constraints" or in
+  the case of bond distances, "restraints".
 At this time the only constraints that can be set in EXPGUI are on atomic
-and profile profile (others can be set in EXPEDT).
+and profile profile (others can be set in EXPEDT). EXPEDT offers many
+  other types of restraints as well.
 <P>
 Note that these constraints are only applied to shifts, but not to the
@@ -212 +214 @@
 usually make sense and EXPGUI does not allow it.
 </DL></DL>
+<a name="DistanceRestraints"></a>
+<H4>Distance Restraints</H4>
+<DL><DL>
+  When the distance restraints tab is first selected, the active
+  distance restraints for the selected phase are shown. The <B>Atom 1</B> and
+  <B>Atom 2</B> buttons can be used to sort this list.
+  <P>
+  The <B>Restraint Weight</B> parameter is very important. As this
+  determines how strongly the distance restraints will be used in the
+  refinement relative to the diffraction data. This value is sometimes
+  set as high as 500,000 in the initial stages of a fit, but should be
+  lowered as much as is possible in the final stages of the fit, as
+  needed to obtain chemically plausible interatomic distances. For
+  some refinements, a value of 0.0 is possible for the Restraint
+  Weight in the final stages. This removes any restraint effect.
+
+  To see how restraints are affecting the refinement, one can look at
+  the ratio of the "Sum(w*d**2)" (shown in the .LST file) for the
+  diffraction histograms vs. the restraint histogram.
+<P>
+  The <B>Active Restraints Editor</B> can be used to select distances
+  to be restrained or edit the restraints. If there are too many
+  distances shown, the options at the top of the window can be used to
+  select a distance range, or specific atoms to include. Likewise,
+  only restrained or unrestrained distances can be selected. The
+  changes are applied when the <B>Filter</B> button is pressed.
+<P>
+  The bottom section of the window shows individual interatomic
+  distances. A <B>Restraint</B> and <B>Tolerance</B> value is needed to restrain
+  that distance. The quantity minimized is
+<blockquote>
+<blockquote>
+ "Restraint Weight" * SUM{  [ (Distance - Restraint) / Tolerance ]**2 } 
+</blockquote>
+</blockquote>
+thus the "Tolerance" provides individual weighting for each
+  restraint.
+<P>
+  To set a large number of restraints at the same time, select the
+  check button next to the distance(s), or use the <B>Check
+  All</B>. Then use the section above to enter a global
+  <B>Restraint</B> and <B>Tolerance</B> value. These values are set
+  when the <B>Set Checked</B> button is used.  The <B>Delete
+  Checked</B> button removes restraints from all selected distances.
+<P>
+The entered restraint information will be used onlt when the <B>Save
+  Changes</B> button is pressed. The <B>Cancel</B> button will reverse
+  any changes made while the window is open. Closing the window has
+  the same effect as "Cancel."
+  <P>
+  Note that the interatomic distances that are shown are determined by
+  the parameters to program DISAGL. These are controlled with the
+  <B>Edit Search Distance Parameters</B> button. 
+
+</DL></DL>
 <hr>
 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
-</TH><TH><A Href="expgui7.html">Next page</A>
+</TH><TH><A Href="expgui6A.html">Next page</A>
 </TH><TH><A Href="expgui5.html">Previous page</A>
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui7.html

@@ -23 +23 @@
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
 </TH><TH><A Href="expguic.html">Next page (Menus)</A>
-</TH><TH><A Href="expgui6.html">Previous page</A>
+</TH><TH><A Href="expgui6A.html">Previous page</A>
 </TH></TR></TABLE><BR CLEAR=ALL>
 
 <center><h1>
 <HR noshade width="75%" size="2" align="center">
-EXPGUI, part 7
+EXPGUI, part 8
 <HR noshade width="75%" size="2" align="center">
 </h1></center>
 
-<h3>A.7 Preferential Orientation Panel</h3></a>
+<h3>A.8 Preferential Orientation Panel</h3></a>
 <DL><DL>
 The Preferential Orientation Panel is used to control parameters related
@@ -43 +43 @@
 </DL></DL>
 <a name="MD"></a>
-<h4>A.7.a March-Dollase</H4>
+<h4>A.8.a March-Dollase</H4>
 <DL><DL>
 In this model one or more axes are designated
@@ -67 +67 @@
 </DL></DL>
 <a name="ODF"></a>
-<H4>A.7.b Spherical harmonic</H4>
+<H4>A.8.b Spherical harmonic</H4>
 <DL><DL>
 The spherical harmonic formulation, also referred to as an "orientation
@@ -98 +98 @@
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
 </TH><TH><A Href="expguic.html">Next page (Menus)</A>
-</TH><TH><A Href="expgui6.html">Previous page</A>
+</TH><TH><A Href="expgui6A.html">Previous page</A>
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/expgui_intro.html

@@ -70 +70 @@
 Customization notes</A>
 <LI>
-<A HREF="tutorial3/index.html">
+<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
 A well-annotated CW neutron tutorial (Alumina).</A>
 <B><I>A very good place to start!</I></B>
 <LI>
-<A HREF="tutorial1/index.html">
+<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">
 A TOF Tutorial Example (Nickel)</A>
 <LI>
-<A HREF="tutorial2/index.html">
+<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">
 A CW Neutron Tutorial Example (Garnet)</A>
 </UL>
@@ -164 +164 @@
 <p><br><B>Who is to blame for EXPGUI?</B>
 <blockquote>The initial version of the GUI part of EXPGUI was created by
-Jonathan Wasserman (thanks Jon!) <a href="http://www.ncnr.nist.gov/staff/toby/">Brian
+Jonathan Wasserman (thanks Jon!) Brian
 Toby</a> is irresponsible for the rest.</blockquote>
 
@@ -170 +170 @@
 <blockquote>Gee, you want to add some features... Great! You have all the
 EXPGUI sources and
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">Tcl/Tk</A>
-is free. Oh, you want me to do it. Well, please 
+Tcl/Tk is free. Oh, you want me to do it. Well, please 
 ask and I will try. In particular, I am looking for good ideas on 
 how to design GUI's for different aspects of experiment editing, 
@@ -177 +176 @@
 
 <p><br><B>Mailing List</B>
-<blockquote>If you would like to get news about EXPGUI, please send 
-<a href="mailto:brian.toby@anl.gov?subject=EXPGUI Mailing List">Brian.Toby@ANL.GOV</a> e-mail. The mailing list is not active at present, but 
-I hope to use it again to provide 
+<blockquote>If you would like to get news about EXPGUI, please 
+<a href="http://www.aps.anl.gov/mailman/listinfo/expgui">see this
+link</a>.
+The mailing list is used only to provide 
 information about updates and bug fixes. 
 </blockquote>

trunk/doc/expguic.html

@@ -49 +49 @@
         experiment file from scratch.
 <DT>expnam<DD>
-Equivalent to Open, included since this is the command used in other 
-GSAS shells to select GSAS experiments.
+Equivalent to Open (included for historical reasons.)
+
 <DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
 <DT>Save As<DD>Saves modifications to the current experiment file to disk
@@ -60 +60 @@
   offers the program user the option to update these files. The update
   will fail if the user does not have permission to change the EXPGUI
-  or GSAS files. In this case, a system administrator may be needed. 
+  or GSAS files. In this case, a system administrator may be needed.
+  <DT>revert<DD>Used to load an <a href="#archive">archived</A>
+    (backup) version of the current .EXP file. 
 <DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
-<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
+<DT>convert<DD>Convert a standard ASCII file to the direct access
+  format used by GSAS (and for UNIX, the reverse) -- this is not
+  likely to be needed, as GSAS now does most conversions automatically.
 <DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
 </DL>
@@ -99 +103 @@
 revised .EXP file, which means that you reject the last set of changes.
 This is useful if 
-GENLES blows up or you have done something wrong. The advantage 
-of turning "autoload EXP" on is
+GENLES blows up or you have done something wrong. The reason to  
+turning "autoload EXP" on is
 that there is one less thing to do when running GSAS programs.
 Note that it is still possible to reverse changes, if 
-<a href="#archive">archive files</A>, but this may require more effort.
-
+<a href="#archive">archive files</A>, but this may require more
+  effort. See the File/revert menu entry.
 <a name="execprompt"></a>
 <DT>Prompt after GSAS run<DD>
@@ -121 +125 @@
 screen cluttered with EXPGUI when it can't be used, 
 but this is an option so that the mode can be turned off by those people
-who find this behavior annoying.
+who find this behavior annoying. It appears this option causes
+  problems on Windows 7. 
 
 <a name="AutostartGRWND"></a>
@@ -225 +230 @@
 <DT>rawplot<DD>Plot powder data
 <DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
-<DT>tofnorm<DD>Normalize a TOF spectrum
 <DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
 <DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
@@ -233 +237 @@
 to set the upper and lower limits for a histogram, as well as
 edit excluded regions.
+<DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run
+  GENLES on a set of very similar data files.
+<DT>mustrplot<DD>Plot microstrain results
+<DT><a HREF="expgui.html#INSTEDIT">instedit</A><DD>Invokes the <a HREF="expgui.html#INSTEDIT">instedit</A>
+  to edit an instrument parameter file.
+<DT>New InstParm file<DD>Creates a new instrument parameter file using
+  <a HREF="expgui.html#INSTEDIT">instedit</A>.
+
+
 </DL>
 <img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
@@ -238 +251 @@
 
 <a name="4"></a>
-<h3>C.4 Single Crystal Menu</h3>
+<h3>C.4 Xtal (Single Crystal) Menu</h3>
 <BLOCKQUOTE>
 This menu contains links to GSAS programs used for 
@@ -268 +281 @@
 <DT>fourier<DD>Generate Fourier map
 <DT>forsrh<DD>Search Fourier map for peaks
+<DT>gsas2map<DD>Exports a Fourier map in formats used by other
+  programs (for example Fox and DRAWxtl).
 <DT><a HREF="liveplot.html#liveplot">liveplot</a>
 <DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
@@ -274 +289 @@
 <DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
 <DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
+<DT><a HREF="expgui.html#ABSPLT">absplt</A>
+<DD>The <a HREF="expgui.html#ABSPLT">absplt</A> program displays the
+  absorption/reflectivity correction curve for values used in a histogram.
+<DT>mustrplot<DD>Plot microstrain results
+<DT>seqplot<DD>Plot results from seqgsas
 </DL>
 <img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
@@ -287 +307 @@
 <DT>bijcalc<DD>Thermal parameter analysis
 <DT>disagl<DD>Distance/angle calculations
+<DT>disaglviewer<DD>Display results from distance/angle calculations
+  in a graphical browser.
 <DT>reflist<DD>List reflection data
 <DT>geometry<DD>Molecular geometry calculations
@@ -297 +319 @@
 <DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
 chains, for use in restraints.
+<DT>seqplot<DD>Plot results from seqgsas
 </DL>
 <img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
@@ -307 +330 @@
 <DL>
 <DT>cllchg<DD>Transform unit cell
-<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
+<DT>composition<DD>Computes the chemical composition of a unit cell
+accounting for site multiplicies and occupancies
 <DT>rducll<DD>Unit cell reduction
 <DT>spcgroup<DD>Space group symbol interpreter
+<DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run
+  GENLES on a set of very similar data files.
+<DT>seqplot<DD>Plot results from seqgsas
 <DT>unimol<DD>Unique molecule assembler
 </DL>
@@ -315 +342 @@
 </BLOCKQUOTE>
 
-<a name="8"></a>
-<h3>C.8 Import/Export Menu</h3>
-<BLOCKQUOTE>
-This menu contains utilities for importing information into GSAS and
-exporting.
-<DL>
-<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
-file is used in MSI software such as Cerius and InsightII.
-<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
-<DT>hklsort<DD>Prepare HKL tables
-<DT>pubtable<DD>Prepare atom parameter tables
-<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
-<DT>cad4rd<DD>Prepare CAD4 single crystal data
-<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
-<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
-<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
-<DT>sxtldata<DD>Prepare generic single crystal data
-<DT>gsas2pdb<DD>
-Import (using GSAS2PDB & EXPEDT) and export coordinates (for 
-macromolecular phases) to/from Protein Data Base files
-<DT>ref2asc<DD>
-Exports a GSAS reflection file to ASCII for use in non-GSAS programs
-<DT>ref2bin<DD>
-Imports an ASCII reflection file to the GSAS binary format
-</DL>
-<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
-</BLOCKQUOTE>
-
 <a name="9"></a>
-<h3>C.9 Macro Menu
+<h3>C.8 Macro Menu
 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
 </h3>
@@ -402 +401 @@
 </DL>
 </BLOCKQUOTE>
+
+<a name="8"></a>
+<h3>C.9 Import/Export Menu</h3>
+<BLOCKQUOTE>
+This menu contains utilities for importing information into GSAS and
+exporting it to other programs.
+<DL>
+<DT>Coord Export<DD>This provides a series of routines that are used
+to write coordinates and possibly other information to files:<P>
+<DL>
+<DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file
+that documents the current refinement. The CIF contains the
+coordinates for all phases as well as the observed and computed
+diffraction patterns. The templates used by GSAS2CIF can be customized
+to provide a detailed description of the experimental measurements and
+results for use in documenting analysis for publication or
+deposition. 
+<DT>coords-only CIF<DD>For export of intermediate results to another
+program, CIF can be a useful exchange format. This routine provides a
+CIF with the current coordinates from one phase and not much else.
+<DT>export to DRAWxtl<DD>This writes a .STR file used in the DRAWxtl
+program and optionally launches DRAWxtl. 
+<DT>export to SHELX<DD>This writes coordinates for a selected phase in
+the .INS format used by SHELX and several other programs.
+<DT>export to PLATON<DD>This writes coordinates for a selected phase in
+the .SPF format used by PLATON
+<DT>export test format<DD>This demonstrates how a coordinate export
+routine can be added to EXPGUI. See the <A
+HREF="expgui_cfg.html#export">documentation on this</A> for further
+information. 
+<DT>export to FOX<DD>This prepares a XML file with coordinates for use
+in the FOX program
+<DT>MSI .xtl<DD>Prepare a .XTL format file of atomic positions. This
+file is used in older Accelrys software such as Cerius and
+Insight-II. It may no longer be of value.
+</DL>
+
+<DT>CIF Export<DD>This provides a series of routines that are used
+to prepare CIF files:<P>
+<DL>
+<DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file
+that documents the current refinement. The CIF contains the
+coordinates for all phases as well as the observed and computed
+diffraction patterns. The templates used by GSAS2CIF can be customized
+to provide a detailed description of the experimental measurements and
+results for use in documenting analysis for publication or
+deposition.
+<DT>FillTemplate<DD>Used to edit the CIF template files used in GSAS2CIF
+<DT>CIFselect<DD>Used to select interatomic distances and angles to be
+included in the CIF created by GSAS2CIF.
+</DL>
+
+<DT>hklsort<DD>Prepare HKL tables
+<DT>pubtable<DD>Prepare atom parameter tables
+<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
+<DT>cad4rd<DD>Prepare CAD4 single crystal data
+<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
+<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
+<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
+<DT>sxtldata<DD>Prepare generic single crystal data
+<DT>gsas2pdb<DD>
+Import (using GSAS2PDB & EXPEDT) and export coordinates (for 
+macromolecular phases) to/from Protein Data Base files
+<DT>ref2asc<DD>
+Exports a GSAS reflection file to ASCII for use in non-GSAS programs
+<DT>ref2bin<DD>
+Imports an ASCII reflection file to the GSAS binary format
+<DT>gsas2map<DD>Exports a Fourier map in formats used by other
+  programs (for example Fox and DRAWxtl).
+</DL>
+<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
+</BLOCKQUOTE>
+
 <hr>
 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>

trunk/doc/gsas2cif.html

@@ -33 +33 @@
 <BR>
 to export
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
-GSAS</A>
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
 results
 <HR noshade width="75%" size="2" align="center">
@@ -575 +574 @@
 </BLOCKQUOTE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?></font>
-$Revision$ $Date$
 </font>
 </BLOCKQUOTE>

trunk/doc/liveplot.html

@@ -40 +40 @@
 <P>
 Both LIVEPLOT and BKGEDIT get the current diffraction information 
-by running the GSAS TCLDUMP program, if installed, or
-the GSAS HSTDUMP otherwise. The TCLDUMP program has been optimized for use 
-with LIVEPLOT and allows LIVEPLOT to offer a number of extra 
-options that are not available when HSTDUMP is used. Since TCLDUMP has been 
-included in GSAS since April of 2000, the following documentation assumes 
-that TCLDUMP is installed.
+by running the GSAS TCLDUMP program. (In GSAS/EXPGUI before 2001, the
+GSAS HSTDUMP program was used, which was less powerful. This code has
+not been removed, but will not be used if TCLDUMP is present.)
 
 <a name="liveplot"></a>
@@ -54 +51 @@
 Some of the features available in LIVEPLOT are:
 <UL>
-<LI>The plot is updated automatically after each refinement run
+<LI><IMG SRC="new.gif" alt="New!"> 
+Regions of the plot can be magnified to show more detail, for example
+  in regions at high Q. 
+<LI><IMG SRC="new.gif" alt="New!"> 
+Plots can be <a href="#export">exported to obtain publication-quality
+graphics </a> -- <B><I>now on all platforms</I></B>.
+<LI><IMG SRC="new.gif" alt="New!"> Intensity can be displayed as I/sigma(I)
+ <LI>The plot is updated automatically after each refinement run
 <LI>The plot can be "zoomed-in", by clicking on the corners of the 
 area to be magnified and "zoomed-out" using the 
@@ -61 +65 @@
 The units used for plotting histograms can be selected. Choices are: 
 native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>)
-<LI>
-The background (fixed plus fitted) can be plotted or can be subtracted. 
+ <LI>
+  The background (fixed plus fitted) can be plotted or can be subtracted. 
 <LI>
 Reflection tickmarks can be displayed in a variety of formats 
@@ -73 +77 @@
 <LI>
 The cumulative chi<sup>2</sup> function or 
-<IMG SRC="new.gif" alt="New!"> (obs-calc)/sigma can be plotted.
+ (obs-calc)/sigma can be plotted.
 <LI>
 The cursor position can be displayed
-<LI>
-Plots can be <a href="#export">exported to obtain publication-quality
-graphics.</a>
 </UL>
 
@@ -285 +286 @@
 <P>
 <a name="zoomshift"></a>
-<IMG SRC="new.gif" alt="New!">
 To shift the zoom region around, 
 the right and left arrow keys can be used to shift the 
@@ -363 +363 @@
 <br clear=all>
 <P>
+<a name="magnification"></a>
+<B>Plot Magnification</B>
+Sections of the plot can be magnified through use of options in the
+Magnification menu or by using control-1 through control-9. 
+<img SRC="magreg.png" align=RIGHT alt="LIVEPLOT Screen snapshot">
+<UL>
+<LI>The Magnification/Add region menu item requests a location in the
+  pattern (2Theta/TOF/KeV/d-space/Q) and a multiplier. Data where the
+  scan variable (2Theta...) is of that value or higher, up to the
+  next region or end of the pattern are multiplied by that factor. The
+  factor, must be >0.
+<LI>Magnification/Edit regions brings up a menu (see below) where the previously
+ defined regions can be changed. The region boundaries can be moved
+  and the multiplier values can be changed. If a multiplier is set to
+  zero (or negative) that region is removed.
+<LI>Magnification/Clear deletes all previously defined regions
+<LI>Pressing control plus a positive digit (1,2,3,...9) also adds a
+  magnification region. The digit determines the magnification
+  multiplier. Data where the
+  scan variable (2Theta...) from the mouse position up to the
+  next region or end of the pattern are multiplied by that factor.
+<img SRC="editreg.png" align=RIGHT alt="LIVEPLOT menu">
+</UL>
+ <br clear=all>
+<P>
 <a name="export"></a>
 <B>Export plot options</B>
 <UL><LI>
-The plot can be exported to 
+<IMG SRC="new.gif" alt="New!"> 
+The LIVEPLOT program can export plots to to a <I>high quality</I> PDF
+  file for presentations or publications using <A
+  HREF="http://www.gnuplot.info/">gnuplot</A>.
+  The PDF will match what is is shown on fairly
+  closely with respect to colors, <A href="#plotfont">font sizes</a>
+  and <a href="#zoom">zoom</a>. The new <A href="#magnification">plot magnification</a> to show detail in
+  the fit and for publication increase the 
+  <A href="#plotfont">plot font</a> so that the figure size can be
+  reduced to the standard Rietveld postage stamp, required by so many
+  Journals -- allowing the text to be discerned, even if the problems in the
+  fit cannot.
+  <P>Starting August
+  2011, windows and Mac versions of gnuplot are included with the GSAS
+  binaries; gnuplot is easily
+  installed on Linux with standard tools such as yum (Redhat),
+  apt-get (ubuntu) or zypper (openSuse). 
+
+<P><LI>  The plot can be exported to 
 <A HREF="http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
-that produces publication-quality graphics. Many UNIX users know 
-this program under a previous name, xmgr.
-The export is implemented 
-by producing an ASCII file with instructions that 
-creates a plot with similar formatting to what appears on the 
-screen in LIVEPLOT/BKGEDIT. However, the output quality from 
-Grace is much higher quality. Further, Grace
-can be used to enhanced and annotate the plot further.
-<LI>
+that produces publication-quality graphics that appear very similar to
+  what is seen in LIVEPLOT/BKGEDIT. Further, Grace
+  can be used to enhance the plot, for example by editing captions,
+  figure display options and even annotate the plot.
+  Grace runs well on Linux and Mac computers; Many UNIX users know 
+  this program under a previous name, xmgr.
+  For Windows,
+  installation of <A HREF="http://cygwin.com/">Cygwin</A> is required.
+  <P><LI>
 For use in many other graphics programs, LIVEPLOT will produce a 
 "comma separated variable" data file with the data displayed on the screen. 
@@ -382 +425 @@
 set line styles and scaling, etc., but this does provide an option for 
 generating high-quality graphics for presentations and publications.
-<LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
+<P><LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
 but the quality is rather low (this is a limitation of the BLT graphics
 package).
+  <P><LI>LIVEPLOT/BKGFIT can also be used to prepare input for FOX (Free
+  Objects for Xtallography). 
+  
 </UL>
 
@@ -408 +454 @@
 <DT><a href="#zoomshift">arrow keys</A>
 <DD>Moves zoom region around in plot
+<DT><a href="#mag">Control+1, 2,...</a>
+<DD>Defines a <a href="#magnification">magnification region</A> at the
+  cursor location.
 </DL>
 
@@ -438 +487 @@
 <DT>Export Plot
 <DD>This offers options for exporting the plot in multiple formats.
-I am hoping to add more export formats eventually.
-<DL><DL>
+<DL><DL>
+<DT>to PDF
+ <IMG SRC="new.gif" alt="New!"> 
+<DD>Creates a <I>high quality</I> PDF file that may be useful for
+  presentations or publications. Note that you may wish to use
+  <A href="#magnification">plot magnification</a> to show detail in
+  the fit and for publication increase the 
+  <A href="#plotfont">plot font</a> so that the figure size can be
+  reduced.
+
 <DT>to PostScript
 <DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT 
@@ -446 +503 @@
 On Windows, a program such ghostview may be needed to translate the 
 PostScript to a format that can be viewed or printed.
-<A name="grace">
+
+  <A name="grace">
 <DT>to Grace
 <IMG SRC="note.gif" alt="Note!">
@@ -454 +512 @@
 After the plot is exported, it can be further 
 enhanced and annotated in grace.
+
+<DT>to .csv file
+  <DD>Creates a "comma separated variable" file. This contains all the
+  diffraction data shown in the plot. It can be used to produce a plot
+  in some other graphics program. 
+  <DT>Fox XML
+  <DD>The Fox program provides structure solution capabilities. This
+  option can be used to write data in the XML format that Fox uses. 
 </DL></DL>
 <DT>Quit
@@ -505 +571 @@
 <DT>Y units
 <DD>The intensity values can be normalized by the incident spectrum
-(for energy dispersive methods).
+(for energy dispersive methods) or
+  <IMG SRC="new.gif" alt="New!"> can be displayed as a ratio with the
+  experimental uncertainty [I<sub>obs</sub>/sigma(I<sub>obs</sub>),
+  I<sub>calc</sub>/sigma(I<sub>obs</sub>) and their difference].
 </DL></DL>
 <br clear=all>
@@ -535 +604 @@
 <DT>Set screen font
 <DD>This option is used to control the font used for menus, graphics and 
-other aspects of windows. 
+other aspects of windows. This value can be saved as a default value. 
+<A name="plotfont">
+  <DT>Set plot font
+<DD>This option is used to change the font used in the plot
+  window. This has a similar effect to changing the screen font, but
+  can be changed over a wider range and only affects the
+  graph. Changing the font size either way will change the font used
+  in the exported .PDF.
 <DT>Raise on update
 <DD>This causes the plot to be placed on top of other windows, if partially
@@ -650 +726 @@
 <P>
 <hr><H2>Interfacing External Programs</H2>
-<IMG SRC="new.gif" alt="New!">
 <B>Combining LIVEPLOT with CMPR & LOGIC</B>
 If you have the 
-<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">
-CMPR/LOGIC</A>
-programs installed on your computer, you can use superimpose on the 
+<A HREF="https://subversion.xor.aps.anl.gov/trac/CMPR">CMPR</A>
+program installed on your computer, you can use superimpose on the 
 GSAS results the peaks for an arbitrary unit cell.
-If you have an old version of the 
-<A HREF="http://www.icdd.com/products/overview.htm">
-ICDD-JCPDS PDF-2 powder diffraction database</a>, 
-(when distributed as an AIDS*83 format flat file)
-you can also superimpose entries from this database on the 
-GSAS results displayed in LIVEPLOT. 
-<P>
-When the CMPR/LOGIC program is installed in the same location
+<P>
+When the CMPR program is installed in the same location
 as the GSAS package (<i>e.g.</i> 
 <font face="courier">/home/gsas</font> & 
@@ -692 +760 @@
 software is located. The
 "Display a cell" option produces a window similar to the
-<A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">
+<A href="https://subversion.xor.aps.anl.gov/CMPR/trunk/doc/cmprdoc.html#editcell">
 Edit Cell feature in CMPR</A>
 where allowed reflection positions are displayed for a set of unit cell 
 parameters and optionally a space group or extinction conditions.
-The "Plot ICDD Entry" provides a window similar to the 
-<A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">
-LOGIC interface in CMPR</A>
-where ICDD searches may be conducted. From the resulting list of matches,
-selected entries may be displayed.
 <P>
 Note that these routines display peak positions in units of 2Theta, Q or
@@ -718 +781 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>
-$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/revlog.html

@@ -32 +32 @@
     </h1></center>
     <P>
-    This page describes all revisions logged for changes to the EXPGUI source
+    This page has been superceeded by the Trac registry, see
+    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline">
+    https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline</A>.
+    <HR><HR>
+    Below is information on older revisions logged for changes to the EXPGUI source
     files, sorted by date. 
-    See the <A HREF="wishlist.html">EXPGUI Wish List</A> for a more 
-    descriptive listing.
-
+    See the
+    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report">
+    View Tickets</A> section of the Trac site for active and closed
+    projects. There is some older information on the 
+    <A HREF="wishlist.html">EXPGUI Wish List</A>.
+    
 <h2>since 1-Jun-2009</h2><DL><DL>
 </DL></DL>
@@ -1633 +1640 @@
     </TH><TH><A Href="wishlist.html">Past and Planned<BR>Updates</A>  
     </TH></TR></TABLE>
-    <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>
-    <font size=-1><? lastmod(); ?> </font>
-    <br>
-    </blockquote>
+   </blockquote>
 
 Created Fri Jul 03 20:35:34 CDT 2009

trunk/doc/win_old_notes.html

@@ -43 +43 @@
 Nonetheless, please report problems, including improvements on 
 these instructions to
-<A HREF="mailto:brian.toby@nist.gov">Brian Toby</A>.
+<A HREF="mailto:brian.toby@anl.gov">Brian Toby</A>.
 Otherwise, Windows-specific issues are unlikely to be addressed or repaired.
 </EM>
@@ -57 +57 @@
 <P>
 <LI>Get 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
-GSAS</A> from one of the following sites:
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
+from one of the following sites:
 <DL><P>
 <DT>UK<DD>
@@ -296 +296 @@
 <A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
 <P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
-<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
+<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> 
 with help from Jonathan Wasserman.
 
@@ -325 +325 @@
 </TH></TR></TABLE>
 
-<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
-<font size=-1><? lastmod(); ?> </font>
-<br>
-$Revision$ $Date$
 </blockquote>
 </body>

trunk/doc/wishlist.html

@@ -31 +31 @@
 <HR noshade width="75%" size="2" align="center">
 </h1></center>
+<I><blockquote><blockquote>
+Information on desired (and completed) development tasks for EXPGUI
+are now captured as "Tickets" in the
+    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/">
+EXPGUI Trac system</A>. In particular, see the
+    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline">
+    timeline of changes</A> and the 
+   <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report">
+    reports on Tickets</A>. Any other information on this page is no
+longer being updated -- though there are still some good ideas for
+development here.
+</blockquote></blockquote></I>
+<P>
+<hr><hr>
+
+
 <P>
 This page describes recent features added to EXPGUI or that are being 

trunk/expgui

@@ -327 +327 @@
             file copy -force $expgui(expfile) $expnam.EXP
             set expgui(expfile) $expnam.EXP
+            wm title . "EXPGUI interface to GSAS: [file tail $expgui(expfile)]"
+            set expgui(titleunchanged) 1
         } else {
             MyMessageBox -parent . -title "File not found" \
@@ -334 +336 @@
         }
     } else {
-        SetEXPfile $expgui(expfile)
+        set expgui(expfile) [SetEXPfile $expgui(expfile)]
     }
 }
@@ -349 +351 @@
     # I am not sure it is still needed.
     update
-    SetEXPfile [getExpFileName ""]
+    set expgui(expfile) [SetEXPfile [getExpFileName ""]]
     set expgui(resize) 1
 }
@@ -361 +363 @@
 proc loadexp {expfile} {
     global expgui expmap entryvar entrycmd tcl_platform
-    set prevexp $expgui(expfile)
-    # is this a compressed archive file? 
-    if {[string match {*.O[0-9A-F][0-9A-F]} $expfile]} {
-        set expnam [file rootname $expfile]
-        set ans [MyMessageBox -parent . -title "Load Archived File" \
-                -message "Loading archived version of $expnam. Do you want to continue using the same experiment name or work with the archived version under a new name?" \
-                -icon question -type "{Use New Name} {Continue with current}" \
-                -default {Use New Name} \
-                -helplink "expguierr.html LoadArchived"
-        ]
-        # archive the current .EXP file
-        if {$ans != "use new name" && [file exists $expfile]} {
-            # get the last archived version
-            set lastf [lindex [lsort [glob -nocomplain $expnam.{O\[0-9A-F\]\[0-9A-F\]}]] end]
-            if {$lastf == ""} {
-                set num 01
-            } else {
-                regexp {.*\.O([0-9A-F][0-9A-F])$} $lastf a num
-                scan $num %x num
-                if {$num >= 255} {
-                    set num FF
-                } else {
-                    set num [string toupper [format %.2x [incr num]]]
-                }
-            }
-            catch {
-                set newfile $expnam.O$num
-                file rename -force $expnam.EXP $newfile
-                set fp [open $expnam.LST a+]
-                puts $fp "\n----------------------------------------------"
-                puts $fp "     Regressing to archive file [file tail $expfile]"
-                puts $fp "     but first archiving [file tail $expnam.EXP] as [file tail $newfile]"
-                puts $fp "----------------------------------------------\n"
-                close $fp
-            }
-            file copy -force $expfile $expnam.EXP
-            set expfile $expnam.EXP
-        }
-        if {$ans == "use new name"} {
-            set newexpfile [getExpFileName new]
-            if {$newexpfile == ""} return 
-            file copy -force $expfile $newexpfile
-            catch {cd [string trim [file dirname $expgui(expfile)]]}
-            set expfile [file tail $newexpfile]
-            set expgui(needpowpref) 2
-            set expgui(needpowpref_why) "\tA new .EXP file was created\n" 
-            SetEXPfile $newexpfile
-        } else {
-            SetEXPfile $expfile
-        }
-        if {$expgui(expfile) == ""} {
-            set expgui(expfile) $prevexp
-            return
-        }
-    }
-
+    set expfile [SetEXPfile $expfile]
+    if {$expfile == ""} {
+        return
+    }
     # change the icon and assign an app to this .EXP file
     if {$tcl_platform(os) == "Darwin" && $expgui(MacAssignApp)} {
         MacSetResourceFork $expfile
     }
-
-    SetEXPfile $expfile
-    if {$expgui(expfile) == ""} {
-        set expgui(expfile) $prevexp
-        return
-    }
     # read in the .EXP file
     set fmt [expload $expfile]
+    set expgui(expfile) $expfile
     # if the file was not in the correct format, force a rewrite before use
     if {$fmt < 0} {
@@ -453 +398 @@
     set expgui(last_History) [string range [string trim [lindex [exphistory last] 1]] 0 50 ]
     # set the window/icon title
-    wm title . "EXPGUI interface to GSAS: $expfile"
+    wm title . "EXPGUI interface to GSAS: [file tail $expgui(expfile)]"
     set expgui(titleunchanged) 1
     wm iconname . [file tail $expfile]
@@ -462 +407 @@
     # start checking for external changes
     afterawhile
+    # check if the file seems corrupt
+    set warnings [ScanEXPforError]
+    if {$warnings != ""} {
+        ExplainEXPerror . $warnings $expfile
+    }
 }
 
@@ -547 +497 @@
     global expgui
     global tcl_platform
-    set prevexp $expgui(expfile) 
-    set newexpfile [getExpFileName new]
-    if {$newexpfile == ""} return 
-    SetEXPfile $newexpfile 1
-    if {$expgui(expfile) == ""} {
-        set expgui(expfile) $prevexp
-        return
-    }
+    set newexpfile [SetEXPfile [getExpFileName new] 1]
+    if {$newexpfile == ""} return
     expwrite $newexpfile
+    set expgui(expfile) $newexpfile
     # change the icon and assign an app to this .EXP file
     if {$tcl_platform(os) == "Darwin" && $expgui(MacAssignApp)} {
@@ -574 +519 @@
 
 # called to read a different .EXP file
-proc readnewexp {} {
+proc readnewexp {"mode 0"} {
     global expgui expmap
     if $expgui(changed) {
@@ -586 +531 @@
         }
     }
-    set prevexp $expgui(expfile) 
-    set newexpfile [getExpFileName old]
-    if {$newexpfile == ""} return 
-    SetEXPfile $newexpfile
-    if {$expgui(expfile) == ""} {
-        set expgui(expfile) $prevexp
-        return
-    }
-
-    # switch to the 1st page
-    RaisePage lsFrame
+    if {$mode == 0} {
+        set newexpfile [getExpFileName old]
+    } else {
+        set newexpfile [RevertExpFile]
+    }
+    if {$newexpfile == ""} return
+
     set expgui(globalmode) 0
-    loadexp $expgui(expfile)
+    loadexp $newexpfile
+
+    # switch to the appropriate 1st page
+    #StageTabUse
+    SetStartPanel
 
     # reset the phase selection
@@ -609 +554 @@
         set expgui(curhist) {}
     }
-    if {[CountHistory] > 100} {
-        DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
-    }
+#    if {[CountHistory] > 100} {
+#       DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
+#    }
 }
 
@@ -1058 +1003 @@
 
     set crsPhase {}
-    $expgui(atomxform) config -text "Xform Atoms" -state disabled
+    $expgui(atomxform) config -text "Modify Atoms" -state disabled
     foreach n $expmap(phaselist) type $expmap(phasetype) {
         if {$n == $num} {
@@ -1099 +1044 @@
         DisplayRefFlags 0 0
         $expgui(atomlistbox) delete 0 end
+        $expgui(AddAtomBut)  config -state disabled
         return
     }
 
     # don't reload the last displayed phase
-    if {$expgui(curPhase) == $crsPhase} return
+    if {$expgui(curPhase) == $crsPhase} {
+       DisplayAllAtoms $crsPhase
+       return
+    }
 
     ##########################################################
@@ -1127 +1076 @@
     DisplayRefFlags 0 0
     $expgui(EditingAtoms) config -text ""
+    $expgui(AddAtomBut)  config -state normal
 
     DisplayAllAtoms $crsPhase
@@ -1308 +1258 @@
             } else {
                 append refflag " [mmatominfo $phase $atom ${type}damp] "
-            }   
+            }
         }
         set line [format \
@@ -1323 +1273 @@
                 [mmatominfo $phase $atom z] \
                 [mmatominfo $phase $atom frac] \
-                [mmatominfo $phase $atom Uiso] 
+                [mmatominfo $phase $atom Uiso]
         ]
     } elseif {[atominfo $phase $atom temptype] == "A"} {
@@ -1337 +1287 @@
         set maxline A
         # aniso
-        set line [format "%3d %-6s %-6s %8s %10.6f%10.6f%10.6f%4d%9.4f" \
+        set fmt "%3d %-6s %-6s %8s %s%s%s%4d%9.4f"
+        set line [format $fmt \
                 $atom \
                 [atominfo $phase $atom label] \
                 [atominfo $phase $atom type] \
                 $refflag \
-                [atominfo $phase $atom x] \
-                [atominfo $phase $atom y] \
-                [atominfo $phase $atom z] \
+                [ShowFixAtom $phase $atom x] \
+                [ShowFixAtom $phase $atom y] \
+                [ShowFixAtom $phase $atom z] \
                 [atominfo $phase $atom mult] \
-                [atominfo $phase $atom frac] 
+                [atominfo $phase $atom frac]
         ]
         append line [format "  %9.5f%9.5f%9.5f%9.5f%9.5f%9.5f" \
@@ -1354 +1305 @@
                 [atominfo $phase $atom U12] \
                 [atominfo $phase $atom U23] \
-                [atominfo $phase $atom U13] 
+                [atominfo $phase $atom U13]
         ]
     } else {
@@ -1362 +1313 @@
             } else {
                 append refflag " [atominfo $phase $atom ${type}damp] "
-            }   
-        }
-        set line [format \
-                "%3d %-6s %-6s %8s %10.6f%10.6f%10.6f%4d%9.4f  %9.5f" \
+            }
+        }
+        #set fmt "%3d %-6s %-6s %8s %10.6f%10.6f%10.6f%4d%9.4f  %9.5f"
+        set fmt "%3d %-6s %-6s %8s %s%s%s%4d%9.4f  %9.5f"
+        set line [format $fmt \
                 $atom \
                 [atominfo $phase $atom label] \
                 [atominfo $phase $atom type] \
                 $refflag \
-                [atominfo $phase $atom x] \
-                [atominfo $phase $atom y] \
-                [atominfo $phase $atom z] \
+                [ShowFixAtom $phase $atom x] \
+                [ShowFixAtom $phase $atom y] \
+                [ShowFixAtom $phase $atom z] \
                 [atominfo $phase $atom mult] \
                 [atominfo $phase $atom frac] \
-                [atominfo $phase $atom Uiso] 
+                [atominfo $phase $atom Uiso]
         ]
     }
     return $line
+}
+
+# format a coordinate from a non-mm phase as 10 chars; mark fixed coordinates differently
+proc ShowFixAtom {phase atom var} {
+  # is this fixed?
+  set param [string toupper $var]
+  if {[array name ::fix_param "$phase,$atom,$param"] != ""} {
+    return [format "%9.5fF" [atominfo $phase $atom $var]]
+  } else {
+    return [format "%10.6f" [atominfo $phase $atom $var]]
+  }
 }
 
@@ -1442 +1405 @@
     DisplayRefFlags $atomnum $p
     $expgui(EditingAtoms) config -text "Editing atom #$atomnum -- [atominfo $p $atomnum label]"
-    $expgui(atomxform) config -text "Xform Atom" -state normal
+    $expgui(atomxform) config -text "Modify Atom" -state normal
 }
 
@@ -1467 +1430 @@
     # this needs to track by phase
     DisplayRefFlags $numberList $p
-    $expgui(atomxform) config -text "Xform Atoms" -state normal
+    $expgui(atomxform) config -text "Modify Atoms" -state normal
 }
 
@@ -1849 +1812 @@
         set expgui(backtermlbl) ""
         set expgui(backtypelbl) ""
+        set expgui(abstypelbl) "" 
         foreach var {bref bdamp absref absdamp} {
             set entrycmd($var) ""
@@ -1865 +1829 @@
         set expgui(backtermlbl) ""
         set expgui(backtypelbl) ""
-        set expgui(abstypelbl) ""
+        set expgui(abstypelbl) "" 
         foreach var {bref bdamp absref absdamp} {
             set entrycmd($var) "histinfo [list $histlist] $var"
@@ -3349 +3313 @@
             {SelectOnePhase $expgui(curPhase)} \
             0  expgui2.html ""}
-    {histFrame    Histogram \
+    {histFrame    Powder \
             MakeHistPane \
             DisplayHistogram \
@@ -3365 +3329 @@
             DisplayConstraintsPane \
             0  expgui6.html ""}
+    {rbFrame   "Rigid Body" \
+            "source  [file join $expgui(scriptdir) rigid.tcl]; MakeRBPane" \
+            DisplayRB \
+            1  expguiRB.html ""}
     {orientFrame  "MD Pref Orient" \
             MakeOrientPane \
@@ -3374 +3342 @@
             0  expgui7.html ODF}
 }
+
+# future expansion: single crystal panel goes here -- if present
+catch {
+   source  [file join $expgui(scriptdir) single.tcl]
+   set expgui(notebookpagelist) [linsert $expgui(notebookpagelist) 3 \
+       {singFrame   Single \
+       "MakeSinglePane" \
+       DisplaySingle \
+       1  expguiSing.html ""}]
+} err
+
 
 pack [NoteBook .n -bd 2] -expand yes -fill both
@@ -3396 +3375 @@
     }
 }
+
+set expgui(startpanel) 2
 # procedure to disable tabs when phases or histograms are not defined
 proc StageTabUse {args} {
     global expgui
+    set expgui(startpanel) 2
     # reset everything
     foreach item [lrange $::expgui(notebookpagelist) 0 end] {
@@ -3423 +3405 @@
             .n itemconfigure $frm -state disabled
         }
+        set expgui(startpanel) 0
         return
     }
@@ -3441 +3424 @@
             .n itemconfigure $frm -state disabled
         }
+        set expgui(startpanel) 0
         return
     }
@@ -3450 +3434 @@
             .n itemconfigure $frm -state disabled
         }
+        set expgui(startpanel) 1
         return
     }
@@ -3463 +3448 @@
     .n see $nextpage
     .n raise $nextpage
+}
+
+proc SetStartPanel {} {
+    global expgui
+    if {$expgui(startpanel) == 0} {
+        RaisePage phaseFrame
+    } elseif {$expgui(startpanel) == 1} {
+        RaisePage histFrame
+    } else {
+        RaisePage lsFrame
+    }
 }
 
@@ -4307 +4303 @@
     $expgui(fm).option.menu  add checkbutton -label "Prompt after GSAS run" \
             -variable expgui(execprompt)
-    $expgui(fm).option.menu  add checkbutton -label "Iconify during GSAS" \
+    if {$tcl_platform(platform) == "windows" && \
+            $tcl_platform(osVersion) == 6.1} {
+        set expgui(autoiconify) 0
+        $expgui(fm).option.menu  add checkbutton -label "Iconify during GSAS" \
+            -variable expgui(autoiconify) -state disabled
+    } else {
+        $expgui(fm).option.menu  add checkbutton -label "Iconify during GSAS" \
             -variable expgui(autoiconify)
+    }
     if {$tcl_platform(platform) == "windows" && \
             $tcl_platform(os) == "Windows 95"} {
@@ -4453 +4456 @@
     }
 }
+$expgui(fm).powder.menu add command -label "New InstParm file" -command {EditInstFile (new)}
 
 # Macro menu
@@ -4555 +4559 @@
 LocateWindow "." $xpos $ypos $poscntr
 update
-RaisePage lsFrame
-if {[CountHistory] > 200} {
-    DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
-}
+SetStartPanel
+#if {[CountHistory] > 200} {
+#    DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
+#}

trunk/graceexport.tcl

@@ -241 +241 @@
                 set center 10
             } elseif {[string range $just 0 0] == "e"} {
-                # is this correct?
+                # is this correct? 
+                set center 1
+            } else {
                 set center 0
-            } else {
-                set center 1
             }
             set color_data 1

trunk/gsascmds.tcl

@@ -464 +464 @@
     afterputontop
     return $makenew(result)
+}
+
+# format numbers & errors in crystallographic notation
+proc formatSU {num err} {
+    # errors less or equal to t are expressed as 2 digits
+    set T 19
+    set lnT [expr { log10($T) }]  
+    # error is zero
+    if {$err == 0} {
+        # is this an integer?
+        if {int($num) == $num} {
+            return [format %d [expr int($num)]]
+        }
+        # allow six sig figs with a zero error (except for 0.0)
+        set dec [expr int(5.999999-log10( abs($num) ))]
+        if {$dec < -2 || $dec > 9} {
+            return [format %.5E $num]
+        } elseif {$dec <= 0} {
+            return [format %d [expr int($num)]]
+        } else {
+            return [format %.${dec}f $num]
+        }
+    } else {
+        #set sigfigs [expr log10( abs(10) / abs(.012/$T) ) + 1]
+        # should the number be expressed in scientific notation?
+        if {$err > $T || abs($num) < 0.0001} {
+            # get the exponent
+            set exp [lindex [split [format %E $num] E] end]
+            # strip leading zeros
+            regsub {([-\+])0+} $exp {\1} exp
+            # number of decimals in exponetial notation
+            set dec [expr int($lnT - log10( abs($err) ) + $exp)]
+            # should the error be displayed?
+            if {$err < 0} {
+                return [format "%.${dec}E" $num]
+            } else {
+                # scale the error into a decimal number
+                set serr [expr int(0.5 + $err * pow(10,$dec-$exp))]
+                return [format "%.${dec}E(%d)" $num $serr]
+            }
+        } else {
+            # number of digits
+            set dec [expr int($lnT - log10( abs($err) ))]
+            # should the error be displayed?
+            if {$err < 0} {
+                return [format "%.${dec}f" $num]
+            } else {
+                set serr [expr int(0.5 + $err * pow(10,$dec))]
+                return [format "%.${dec}f(%d)" $num $serr]
+            }
+        }
+    }
 }
 
@@ -974 +1026 @@
             }
         }
-        # so sorry, have to use Internet Explorer
+        # so sorry, have to use Safari, even if not default
         set url [file nativename $url]; # replace ~/ if present
         if {[file pathtype $url] == "relative"} {
             set url [file join [pwd] $url]
         }
-        exec osascript -e "tell application \"Internet Explorer\"\rGetURL \"file://$url\"\rend tell"
+        exec osascript -e "tell application \"Safari\" to open location \"file://$url\""
     } elseif {$tcl_platform(platform) == "unix"} {
         set browserlist {}
@@ -1959 +2011 @@
 proc SetEXPfile {expfile "newOK 0"} {
     global expgui tcl_platform
-    set expgui(expfile) {}
     if {[string trim $expfile] == ""} return
 
@@ -2015 +2066 @@
     # force exp files to be upper case, set to force save if name changes
     set origexp $expname
-    if {$expname != [string toupper $expfile]} {
-        set expname [string toupper [file tail $expfile]]
-        if {$tcl_platform(platform) != "windows"} {set expgui(changed) 1}
-    }
-    if {[file extension $expname] != ".EXP"} {
+    if {$expname != [file tail $expfile] && $tcl_platform(platform) != "windows"} {
+        set expgui(changed) 1
+    }
+    #puts $expgui(expfile)
+    if {[string match {.O[0-9A-F][0-9A-F]} [file extension $expname]]} {
+        set expname [ArchiveChoice $expname]
+        set dirname ""
+        if {$expname == ""} return
+    } elseif {[file extension $expname] != ".EXP"} {
         append expname ".EXP"
     }
-    if {$dirname == "."} {
+    if {$dirname == "." || $dirname == ""} {
         set newexpfile $expname
     } else {
@@ -2081 +2136 @@
         if {[string tolower $ans] == "create"} {
             # you've been warned this .EXP does not exist!
-            # create an "empty" exp file
-            createexp $newexpfile \
-                [getstring "title for experiment $expname" 60 0]
-            if {! [file exists [file join $dirname $expname]]} {
-                update
-                MyMessageBox -parent . -title "File Creation Error" \
-                    -message "Experiment file name \"$expname\" was not created -- This is unexpected, please try a different name" \
-                    -icon warning -type Continue -default continue
-                set expgui(resize) 1
-                return
-            }
+            if [CreateMTexpfile $newexpfile] return
         } else {
             return
         }
     }
-    set expgui(expfile) $newexpfile
-    catch {cd [string trim [file dirname $expgui(expfile)]]}
+    catch {cd [string trim [file dirname $newexpfile]]}
+    return $newexpfile
+}
+
+proc ArchiveChoice {expfile} {
+    set expnam [file rootname $expfile]
+    set ans [MyMessageBox -parent . -title "Load Archived File" \
+        -message "Loading archived version of $expnam. Do you want to continue using the same experiment name or work with the archived version under a new name?" \
+        -icon question -type "{Use New Name} {Continue with current}" \
+        -default {Use New Name} \
+        -helplink "expguierr.html LoadArchived"
+    ]
+    # archive the current .EXP file
+    if {$ans != "use new name" && [file exists $expfile]} {
+        # get the last archived version
+        set lastf [lindex [lsort [glob -nocomplain $expnam.{O\[0-9A-F\]\[0-9A-F\]}]] end]
+        if {$lastf == ""} {
+            set num 01
+        } else {
+            regexp {.*\.O([0-9A-F][0-9A-F])$} $lastf a num
+            scan $num %x num
+            if {$num >= 255} {
+                set num FF
+            } else {
+                set num [string toupper [format %.2x [incr num]]]
+            }
+        }
+        catch {
+            set newfile $expnam.O$num
+            file rename -force $expnam.EXP $newfile
+            set fp [open $expnam.LST a+]
+            puts $fp "\n----------------------------------------------"
+            puts $fp "     Regressing to archive file [file tail $expfile]"
+            puts $fp "     but first archiving [file tail $expnam.EXP] as [file tail $newfile]"
+            puts $fp "----------------------------------------------\n"
+            close $fp
+        }
+        file copy -force $expfile $expnam.EXP
+        set expfile $expnam.EXP
+    }
+    if {$ans == "use new name"} {
+        set newexpfile [getExpFileName new]
+        if {$newexpfile == ""} {
+            set expgui(FileMenuEXPNAM) ""
+            return 
+        }
+        file copy -force $expfile $newexpfile
+        set expgui(needpowpref) 2
+        set expgui(needpowpref_why) "\tA new .EXP file was created\n" 
+        return $newexpfile
+    } else {
+        return $expfile
+    }
+}
+
+# create an "empty" exp file
+proc CreateMTexpfile {newexpfile} {
+    set expname [file tail $newexpfile]
+    createexp $newexpfile \
+        [getstring "title for experiment $expname" 60 0]
+    if {! [file exists $newexpfile]} {
+        update
+        MyMessageBox -parent . -title "File Creation Error" \
+            -message "Experiment file name \"$expname\" was not created -- This is unexpected, please try a different name" \
+            -icon warning -type Continue -default continue
+        set ::expgui(resize) 1
+        return 1
+    }
+    return 0
 }
 
@@ -2129 +2241 @@
                 -side top -fill both -expand yes -pady 5
     } elseif {$mode != "new"} {
-        # for initial read, don't access archived files
+        # for initial read, don't offer access to archived files
         pack [frame $expgui(FileInfoBox) -bd 4 -relief groove \
                 -class SmallFont] \
@@ -2158 +2270 @@
     afterputontop
     if {$expgui(FileMenuEXPNAM) == ""} return
-    # is there a space in the EXP name?
-#    if {[string first " " [file tail $expgui(FileMenuEXPNAM)]] != -1} {
-#       update
-#       MyMessageBox -parent . -title "File Name Error" \
-#           -message "File name \"$expgui(FileMenuEXPNAM)\" is invalid -- EXPGUI can#not process experiment files with spaces in the name" \
-#           -icon warning -type Continue -default continue
-#               -helplink "expguierr.html OpenErr"
-#       return
-#    }
-#    if {[string first " " $expgui(FileMenuDir)] != -1} {
-#       set warn 1
-#       catch {set warn $expgui(warnonexpdirspace)}
-#       if $warn {
-#           update
-#           MyMessageBox -parent . -title "Good luck..." \
-#               -message "You are using a directory with a space in the name ($expgui(FileMenuDir)) -- You may encounter bugs in EXPGUI. Please e-mail them to Brian.Toby@ANL.gov so they can be fixed." \
-#               -icon warning -type Continue -default continue
-#           #           -helplink "expguierr.html OpenErr"
-#           set expgui(warnonexpdirspace) 0
-#       }
-#    }
+    #puts "end getexp $expgui(expfile)"
     return [file join $expgui(FileMenuDir) $expgui(FileMenuEXPNAM)]
 }
 
 # validation routine
+# called from getExpFileName, either from Read button or from SelectExpFil (see expfilebox)
 proc valid_exp_file {frm mode} {
     global expgui tcl_platform
@@ -2208 +2301 @@
         return
     }
-    # append a .EXP if not present
-    if {[file extension $expgui(FileMenuEXPNAM)] == ""} {
+    set ext [string toupper [file extension $expgui(FileMenuEXPNAM)]]
+    if {$ext == ""} {
+        # append a .EXP if not present
         append expgui(FileMenuEXPNAM) ".EXP"
-    }
-    # is there a space in the name?
-#    if {[string first " " $expgui(FileMenuEXPNAM)] != -1} {
-#       MyMessageBox -parent . -title "File Name Error" \
-#               -message "File name $expgui(FileMenuEXPNAM) is invalid -- EXPGUI cannot process experiment files with spaces in the name" \
-#               -icon warning -type Continue -default continue
-#               -helplink "expguierr.html OpenErr"
-#       return
-#    }
-    # check for archive files
-    if {[string match {*.O[0-9A-F][0-9A-F]} $expgui(FileMenuEXPNAM)] && \
+    } elseif {[string match {*.O[0-9A-F][0-9A-F]} $ext] && \
             $mode == "old" && [file exists $expgui(FileMenuEXPNAM)]} {
+        # check for archive files
         destroy .file
         return
-    } elseif {[string toupper [file extension $expgui(FileMenuEXPNAM)]] != ".EXP"} {
+    } elseif {$ext != ".EXP"} {
         # check for files that end in something other than .EXP .exp or .Exp...
         MyMessageBox -parent . -title "File Open Error" \
@@ -2258 +2343 @@
                 -helplink "expguierr.html OpenErr"
         ]
-        if {[string tolower $ans] == "create"} {destroy .file}
+        if {[string tolower $ans] == "create"} {
+            if [CreateMTexpfile $file] return
+            destroy .file
+        }
         return
     }
@@ -2417 +2505 @@
             - [winfo height $box.top] - [winfo height $box.scroll]-25]
 }
-
+proc RevertExpFile {} {
+    global expgui tcl_platform
+    set frm .file
+    catch {destroy $frm}
+    toplevel $frm
+    wm title $frm "Experiment file"
+    bind $frm <Key-F1> "MakeWWWHelp expguierr.html open"
+    pack [frame [set frmA $frm.1] -bd 2 -relief groove] -padx 3 -pady 3 -side left
+    pack [frame [set frmC $frm.3] ] -padx 3 -pady 3 -side left \
+            -fill y -expand yes
+    pack [button $frmC.help -text Help -bg yellow \
+            -command "MakeWWWHelp expguierr.html open"] \
+            -side top -anchor e
+    set expgui(filesort) 0
+    set expgui(includearchived) 1
+    set expgui(FileInfoBox) $frmC.info
+    pack [label $frmC.ar -text "(Showing Archived Files Only)"] -side top -pady 10
+    pack [frame $expgui(FileInfoBox) -bd 4 -relief groove \
+              -class SmallFont] \
+        -side top -fill both -expand yes -pady 5
+
+    pack [button $frmC.b -text Read \
+            -command "valid_exp_file $frmA old"] -side bottom
+    pack [button $frmC.q -text Cancel \
+            -command "set expgui(FileMenuEXPNAM) {}; destroy $frm"] -side bottom
+    bind $frm <Return> "$frmC.b invoke"
+
+    pack [label $frmA.0 -text "Select an archived experiment file to read"] \
+                -side top -anchor center
+    set bx $frmA 
+    pack [frame $bx.top] -side top 
+    #pack [label $bx.top.a -text "Directory" ] -side left 
+    set expgui(FileDirButtonMenu) [tk_optionMenu $bx.top.d expgui(FileMenuDir) [pwd] ]
+    #pack $bx.top.d -side left
+    #set expgui(FileMenuDir) [pwd]
+    # the icon below is from tk8.0/tkfbox.tcl
+    pack [frame $bx.a -width 200 -height 75] -side top -expand yes -fill both
+    listbox $bx.a.files -relief raised -bd 2 \
+            -yscrollcommand "sync2boxesY $bx.a.files $bx.a.dates $bx.a.scroll" \
+            -height 15 -width 0 -exportselection 0 
+    listbox $bx.a.dates -relief raised -bd 2 \
+            -yscrollcommand "sync2boxesY $bx.a.dates $bx.a.files $bx.a.scroll" \
+            -height 15 -width 0 -takefocus 0 -exportselection 0 
+    scrollbar $bx.a.scroll -command "move2boxesY \" $bx.a.files $bx.a.dates \" "
+    ChooseExpFil $bx 1
+    if {[llength [$bx.a.files get 0 end]] == 0} {
+        destroy $frm
+        MyMessageBox -parent . -title "No Archives" \
+            -message "Sorry no archived versions of $::expgui(expfile) are present" \
+                    -icon warning -type ok -default ok
+        return
+    }
+    bind $bx.a.files <ButtonRelease-1> "ReleaseExpFil $bx"
+    bind $bx.a.dates <ButtonRelease-1> "ReleaseExpFil $bx"
+    bind $bx.a.files <Double-1> "SelectExpFil $bx old"
+    bind $bx.a.dates <Double-1> "SelectExpFil $bx old"
+    pack $bx.a.scroll -side left -fill y 
+    pack $bx.a.files $bx.a.dates -side left -fill both -expand yes
+    pack [entry $bx.c -textvariable expgui(FileMenuEXPNAM)] -side top
+    # force the window to stay on top
+    putontop $frm
+    focus $frmC.b
+    tkwait window $frm
+    afterputontop
+    if {$expgui(FileMenuEXPNAM) == ""} return
+    return [file join $expgui(FileMenuDir) $expgui(FileMenuEXPNAM)]
+}
 
 # support routine for SetHistUseFlags
@@ -2542 +2696 @@
     return
 }
+
+proc ScanEXPforError {"ns {}"} {
+    # record types to ignore
+    set ignorelist {DESCR HSTRY PNAM HNAM "REFN STATS"}
+    set warn {}
+    set badkeylist {}
+    # scan file for warnings
+    foreach key [array names ${ns}::exparray] {
+        if {[string first "***" [set ${ns}::exparray($key)]] != -1 || 
+            [string first "#IN" [set ${ns}::exparray($key)]] != -1 ||
+            [string first "nan" [set ${ns}::exparray($key)]] != -1 ||
+            [string first "NAN" [set ${ns}::exparray($key)]] != -1 
+        } {
+            #puts [set ${ns}::exparray($key)]
+            set OK 0
+            foreach i $ignorelist {
+                if {[string first $i $key] != -1} {
+                    set OK 1
+                    break
+                }
+            }
+            # ignore atom name section of Atom records
+            if {(! $OK) && [string match  "CRS*AT*A" $key]} {
+                foreach str [list [string range [set ${ns}::exparray($key)] 0 49] 
+                             [string range [set ${ns}::exparray($key)] 58 end]] {
+                    if {[string first "***" $str] || 
+                        [string first "#INF" $str] || 
+                        [string first "nan" $str] || 
+                        [string first "NAN" $str]} {
+                        append warn "  Record \"$key\": [set ${ns}::exparray($key)]\n"
+                        lappend badkeylist $key
+                        break
+                    }
+                }
+                continue
+            }
+            if {! $OK} {
+                append warn "  Record \"$key\": [set ${ns}::exparray($key)]\n"
+                lappend badkeylist $key
+            }
+        }
+    }
+    if {$warn == ""} return
+    set hint ""
+    set unknown ""
+    foreach key $badkeylist {
+        if {[string match  "CRS*AT*" $key]} {
+            if {[string first "atomic parameter" $hint] == -1} {
+                append hint "\t* An atomic parameter (coordinate, occupancy or U) appears out of range\n"
+            }
+        } elseif {[string match  "CRS*ABC*" $key] || 
+                  [string match  "CRS*ANGLES*" $key] || 
+                  [string match  "CRS*CELVOL*" $key]} {
+            if {[string first "cell parameter" $hint] == -1} {
+                append hint "\t* A unit cell parameter appears out of range\n"
+            }
+        } elseif {[string match  "CRS*ODF*" $key]} {
+            if {[string first "spherical harmonic" $hint] == -1} {
+                append hint "\t* A spherical harmonic (ODF) parameter appears out of range\n"
+            }
+        } elseif {[string match  "HST*ICONS" $key]} {
+            if {[string first "diffractometer constant" $hint] == -1} {
+                append hint "\t* A diffractometer constant (wave, DIFC,...) appears out of range\n"
+            }
+        } elseif {[string match  "HST*TRNGE" $key]} {
+            if {[string first "histogram data range" $hint] == -1} {
+                append hint "\t* A histogram data range value appears out of range\n"
+            }
+        } elseif {[string match "*GNLS  RUN*" $key] || 
+                  [string match "*GNLS SHFTS" $key] ||
+                  [string match "HST*RPOWD" $key] ||
+                  [string match " REFN RPOWD " $key] ||
+                  [string match " REFN GDNFT " $key]
+              } {
+            if {[string first "refinement statistics" $hint] == -1} {
+                append hint "\t* The refinement statistics imply the last refinement diverged\n"
+            }
+        } else {
+            lappend unknown $key
+        }
+    }
+    if {$unknown != ""} {
+        append hint "\t* The following less common problem record(s) appear out of range:\n\t\t"
+        foreach key $unknown {
+            append hint "\"" [string trim $key] "\" "
+        }
+    }
+    return "Likely error(s) noted:\n$hint\nDetails of problem(s):\n$warn"
+}
+
+proc ExplainEXPerror {parent message file} {
+    if {$parent == "."} {
+        set w .experr
+    } else {
+        set w $parent.experr
+    }
+    catch {destroy $w}
+    toplevel $w -class Dialog
+    wm title $w "Corrupt .EXP file"
+    wm iconname $w Dialog
+    wm protocol $w WM_DELETE_WINDOW { }
+    # Make the message box transient if the parent is viewable.
+    if {[winfo viewable [winfo toplevel $parent]] } {
+        wm transient $w $parent
+    } 
+    frame $w.bot
+    pack $w.bot -side bottom -fill both
+    frame $w.top
+    pack $w.top -side top -fill both -expand 1
+    frame $w.msg
+    pack $w.msg -in $w.top -side right -expand 1 -fill both -padx 3m -pady 3m
+    set txt {Likely errors were noted when reading this file}
+    append txt " ([file tail $file]). "
+    append txt "These problems probably\narose from the last refinement, "
+    append txt "based on settings applied in the previous saved file.\n"
+    append txt "It is probably not possible to continue with this file.\n"
+    append txt "You likely need to revert at least two archived versions back."
+    grid [label $w.msg.s -text $txt -justify left] -row 0 -column 0 -sticky nws
+    grid [button $w.msg.1 -text Help -bg yellow \
+              -command "MakeWWWHelp expgui.html badexp"] -row 0 -column 1 -columnspan 2 -sticky ne
+    bind $w <Key-F1> "MakeWWWHelp expgui.html badexp"
+    set filelist [lsort -dictionary -decreasing \
+                      [glob -nocomplain \
+                           [file root $file.O* ]]]
+    grid [text  $w.msg.t -font {Times 12} \
+              -height 10 -width 90 -relief flat -wrap word \
+              -yscrollcommand "$w.msg.rscr set" \
+             ] -row 1 -column 0  -columnspan 2 -sticky news
+    grid [scrollbar $w.msg.rscr  -command "$w.msg.t yview" \
+             ] -row 1 -column 2 -sticky ns
+    # give extra space to the text box
+    grid columnconfigure $w.msg 0 -weight 1
+    grid rowconfigure $w.msg 1 -weight 1
+    $w.msg.t insert end $message
+    button $w.ok -command [list destroy $w] -text OK -default active
+    pack $w.ok -in $w.bot -side left -expand 1 -padx 3m -pady 2m
+    putontop $w
+    tkwait window $w
+    afterputontop
+}
+
 proc UpdateInfoBox {} {
     global expgui
@@ -2548 +2843 @@
     set file [file join [set expgui(FileMenuDir)] $expgui(FileMenuEXPNAM)]
     if [file isdirectory $file] return
-    if [file exists $file] {
+    if [file exists $file] {    
         pack [label $expgui(FileInfoBox).1 -text $expgui(FileMenuEXPNAM)] \
                 -side top
         catch {
+            # load the EXP file into a namespace & scan for errors
+            expload $file scan
+            set warnings [ScanEXPforError scan]
+            if {$warnings != ""} {
+                pack [frame $expgui(FileInfoBox).1a -bg yellow -padx 4 -pady 4] -side top
+                pack [label $expgui(FileInfoBox).1a.err -justify left \
+                          -text "WARNING: Likely corrupt" -bg yellow] \
+                    -side left -anchor w -fill both
+                pack [button $expgui(FileInfoBox).1a.show \
+                          -text "More..." -padx 0 \
+                          -command "ExplainEXPerror $expgui(FileInfoBox) [list $warnings] $file"\
+                         ] -side right -anchor w
+            }
             set fp [open $file r]
             global testline
@@ -2562 +2870 @@
                     -text "last GENLES run:\n  $last\n  total cycles: $cycles"] \
                 -side top -anchor w
+            set chi2 ?
+            set vars ?
             regexp {REFN GDNFT.*= *([0-9]*\.[0-9]*) +for *([0-9]+) variables} \
                     $testline a chi2 vars
@@ -2600 +2910 @@
                     -text $lbl] \
                     -side top -anchor w     
-        }
+        } err
     }
 }
@@ -2634 +2944 @@
 # fill the files & dates & Directory selection box with current directory,
 # also called when box is created to fill it
-proc ChooseExpFil {frm} {
+proc ChooseExpFil {frm "archiveonly 0"} {
     global expgui
     set files $frm.a.files
@@ -2641 +2951 @@
     $files delete 0 end
     $dates delete 0 end
-    $files insert end {<Parent>}
-    $dates insert end {(Directory)}
-    set filelist [glob -nocomplain \
-            [file join [set expgui(FileMenuDir)] *] ]
-    foreach file [lsort -dictionary $filelist] {
-        if {[file isdirectory $file]} {
-            $files insert end [file tail $file]
-            $dates insert end {(Directory)}
-        }
+    if {$archiveonly == 0} {
+        $files insert end {<Parent>}
+        $dates insert end {(Directory)}
+        set filelist [glob -nocomplain \
+                          [file join [set expgui(FileMenuDir)] *] ]
+        foreach file [lsort -dictionary $filelist] {
+            if {[file isdirectory $file]} {
+                $files insert end [file tail $file]
+                $dates insert end {(Directory)}
+            }
+        }
+    } else {    
+        set filelist [glob -nocomplain \
+                          [file root $expgui(expfile)].O* ]
     }
     set pairlist {}
     foreach file [lsort -dictionary $filelist] {
         if {![file isdirectory $file]  && \
-                [string toupper [file extension $file]] == ".EXP"} {
+                [string toupper [file extension $file]] == ".EXP" \
+                && $archiveonly == 0} {
             set modified [file mtime $file]
             lappend pairlist [list $file $modified]
@@ -2704 +3020 @@
         if {$expgui(expfile) == [file join $expgui(FileMenuDir) $file]} {
             $files selection set $i
+            set expgui(FileMenuEXPNAM) $file
+            UpdateInfoBox
         }
     }
@@ -3398 +3716 @@
     global expgui
     if {$expgui(MacroChanged)} {
+
         set ans [MyMessageBox -parent $txt -title "Save macro file?" \
                      -message "Macro file has been changed, do you want to save it?" \

trunk/gsasmenu.tcl

@@ -9 +9 @@
 array set expgui_menulist {
     file {
+        revert
         EraseHistory
         convert
@@ -25 +26 @@
         bkgedit
         excledt
-        instedit
         seqgsas
         mustrplot
+        instedit
     }
     xtal {
@@ -57 +58 @@
         cllchg
         composition
-        fprime
         hklgen
         rducll
@@ -158 +158 @@
     }
 
+    revert {{readnewexp archive} {
+        Select an old version of the current GSAS file}
+    }
+
     {archive EXP} {- {
         Toggles archiving of .EXP files. When on, files are 
@@ -304 +308 @@
     fitspec     {{runGSASprog $cmd} {
         Fit a TOF vanadium scattering spectrum}
-    }
-
-    fprime      {{runGSASprog $cmd} {
-        Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths}
     }
 
@@ -363 +363 @@
     instedit    {{EditInstFile} {
         Edit an instrument parameter file}
+    }
+    {New InstParm file} {- {
+        Create a new instrument parameter file}
     }
 

trunk/instedit.tcl

@@ -78 +78 @@
     # loop over banks
     set msg {}
-    for {set i 1} {$i <= $instdat(lastbank)} {incr i} {
-        instbankinfo rad $i set $instdat(rad$i) 
-        instbankinfo head $i set $instdat(head$i) 
-        if {[string trim $instdat(name$i)] == ""} {
-            append msg "\n  The instrument name may not be blank"
-        }
-        instbankinfo name $i set $instdat(name$i)
-        set l {}
-        foreach var {difc difa zero pola ipola kratio} {
-            lappend l $instdat(${var}$i)
-        }
-        if {[instbankinfo icons $i set $l] != 1} {
-            append msg "\n  There is an error in values for:\n    the wavelength, zero or polarization"
-        }
-        # loop over the profile terms
-
-        for {set j 1} {$j <= $instparms(proftypes${i})} {incr j} {
-            set l {}
-            for {set k 1} {$k <= $instparms(profterms${i}_$j)} {incr k} {
-                lappend l $instdat(prof${i}_${j}_$k)
-            }
-            if {[instprofinfo $i $j set [list \
-                    $instdat(proftype${i}_$j) $instdat(profcut${i}_$j) $l]\
-                    ] != 1} {
-                append msg "\n  There is an error in the values for profile set $j."
-            }
-        }
-        if {$msg != ""} {
-            MyMessageBox -parent . -title "No save" \
+    if {[catch {
+        for {set i 1} {$i <= $instdat(lastbank)} {incr i} {
+            instbankinfo rad $i set $instdat(rad$i) 
+            instbankinfo head $i set $instdat(head$i) 
+            if {[string trim $instdat(name$i)] == ""} {
+                append msg "\n  The instrument name may not be blank"
+            }
+            instbankinfo name $i set $instdat(name$i)
+            set l {}
+            foreach var {difc difa zero pola ipola kratio} {
+                lappend l $instdat(${var}$i)
+            }
+            if {[instbankinfo icons $i set $l] != 1} {
+                append msg "\n  There is an error in values for:\n    the wavelength, zero or polarization"
+            }
+            # loop over the profile terms
+            
+            for {set j 1} {$j <= $instparms(proftypes${i})} {incr j} {
+                set l {}
+                for {set k 1} {$k <= $instparms(profterms${i}_$j)} {incr k} {
+                    lappend l $instdat(prof${i}_${j}_$k)
+                }
+                if {[instprofinfo $i $j set [list \
+                                                 $instdat(proftype${i}_$j) $instdat(profcut${i}_$j) $l]\
+                        ] != 1} {
+                    append msg "\n  There is an error in the values for profile set $j."
+                }
+            }
+            if {$msg != ""} {
+                MyMessageBox -parent . -title "No save" \
                     -message "Error in input for bank $i:$msg" -icon warning \
                     -type Sorry -default sorry
-            return
-        }
+                return
+            }
+        }
+    } errmsg]} {
+        if {$errmsg == ""} return
+        MyMessageBox -parent . -title "No save" \
+            -message "Error in input (did you define data type, profile type, etc?):\n$errmsg" -icon warning \
+            -type Sorry -default sorry
+        return
     }
     if {$filename == ""} {
@@ -150 +158 @@
 proc instShowBank {box} {
     global instdat instparms
+    set instparms(profileframe) {}
+
     set topfr $box.a
     if {$instparms(bank) == 0} return
@@ -159 +169 @@
     }
     if {$instparms(banklabel) == ""} {
-        puts starting
         return
     }
@@ -562 +571 @@
 proc AddInstProfile {box b} {
     global instparms instdat
-    set frame $instparms(profileframe)
     incr instparms(proftypes${b})
     instShowBank $box
@@ -759 +767 @@
                 -parent $instparms(top) -defaultextension .ins \
                 -filetypes {{"Instrument parameters file" ".ins .inst .prm"} {All *.*}}]
+    } elseif {$filename == "(new)"} {
+        set instparms(filename) ""
     } else {
         set instparms(filename) $filename

trunk/liveplot

@@ -14 +14 @@
 # process command line arguments
 set exitstat 0
-set expnam [lindex $argv 0]
+set expnam [file root [lindex $argv 0]]
 if {$expnam == ""} {catch {puts "error -- no experiment name"}; set exitstat 1}
 if $exitstat {
@@ -20 +20 @@
     exit
 }
-
+# work in .EXP directory (in case files will be exported).
+catch {
+    cd [file dirname $expnam]
+}
 # get name of script
 set expgui(script) [info script]
@@ -42 +45 @@
     set graph(legend) [lindex $argv 2]
 }
+set plot_title "(None)"
 
 set graph(backsub) 0
@@ -79 +83 @@
 set expgui(fadetime) 10
 set expgui(hklbox) 1
-set expgui(autotick) 0
+set expgui(autotick) 1
 set expgui(phaselabel) 0
 set expgui(pixelregion) 5
@@ -174 +178 @@
 source [file join $expgui(scriptdir) readexp.tcl]
 source [file join $expgui(scriptdir) opts.tcl]
+#----------------------------------------------------------------
+# use EXPGUI directory for packages
+lappend auto_path $expgui(scriptdir)
 
 if {$program == "bkgedit"}  {
@@ -357 +364 @@
         catch {$vec variable $vec}
     }
-    set maxdiff  [set diffvec(max)]
-    set cmin [set calcvec(min)]
-    set omin [set obsvec(min)]
-    set cmax [set calcvec(max)]
-    set omax [set obsvec(max)]
-    set expgui(min) [expr {$omin < $cmin ? $omin : $cmin}]
-    set expgui(max) [expr {$omax > $cmax ? $omax : $cmax}]
-    set ymin1 [expr {$cmin - 1.1*$maxdiff}]
-    set ymin2 [expr {$omin - 1.1*$maxdiff}]
-    if {$ymin1 < $ymin2} {
-        diffvec set [diffvec + $ymin1]
-    } {
-        diffvec set [diffvec + $ymin2]
-    }
+    ApplyMag
     plotdata
 }
@@ -441 +435 @@
         wifdvec set $sumlist
         wifdvec set [wifdvec / [wifdvec length]]
-    }
-    if {$graph(OmCoS)} {
+    } elseif {$graph(OmCoS)} {
         wifdvec set $WGT
         wifdvec expr sqrt(wifdvec)
         wifdvec set [wifdvec * diffvec]
+    } else {
+        wifdvec length 0
     }
     if $graph(backsub) {
@@ -451 +446 @@
         calcvec set [calcvec - bckvec]
     }
-    global obsvec calcvec diffvec 
-    set maxdiff  [set diffvec(max)]
-    set cmin [set calcvec(min)]
-    set omin [set obsvec(min)]
-    set cmax [set calcvec(max)]
-    set omax [set obsvec(max)]
-    set expgui(min) [expr {$omin < $cmin ? $omin : $cmin}]
-    set expgui(max) [expr {$omax > $cmax ? $omax : $cmax}]
-    set ymin1 [expr {$cmin - 1.1*$maxdiff}]
-    set ymin2 [expr {$omin - 1.1*$maxdiff}]
-    if {$ymin1 < $ymin2} {
-        diffvec set [diffvec + $ymin1]
-    } {
-        diffvec set [diffvec + $ymin2]
-    }
-    
+    ApplyMag
+    plotdata
+}
+
+proc SetTitle {} {
+    set bx .title
+    toplevel $bx
+    wm title $bx "Edit plot title"
+    wm iconname $bx "Edit plot title"
+    grid [label $bx.txt -text "Enter plot title below"] -row 1 -column 1
+    grid [entry $bx.title -width 70] -row 2 -column 1
+    grid [frame $bx.a] -row 3 -column 1
+    grid [button $bx.a.save -text "Save" \
+              -command "set plot_title \"\[$bx.title get\]\"; destroy $bx" \
+             ] -row 1 -column 1
+    grid [button $bx.a.quit -text "Quit" \
+              -command "destroy $bx" \
+             ] -row 1 -column 2
+    putontop $bx
+    tkwait window $bx
+    afterputontop
     plotdata
 }
@@ -572 +572 @@
     global expnam hst peakinfo xunits yunits cycle reflns modtime
     global lasthst graph expgui box
+    global obsvec calcvec diffvec 
+
+    if {$graph(yunits) == 2} {
+        set yunits {Intensity/sigma(I)}
+        wifdvec set $::weightlist
+        wifdvec expr sqrt(wifdvec)
+        obsvec set [obsvec * wifdvec]
+        calcvec set [calcvec * wifdvec]
+        bckvec set {}
+        diffvec set [obsvec - calcvec]
+        wifdvec set {}
+        $box element config 1 -label {} -line 0 -hide 1
+    } else {
+        $box element config 1 -label bckgr -line 1 -hide 0
+    }
+
+    set cmin [set calcvec(min)]
+    set omin [set obsvec(min)]
+    set cmax [set calcvec(max)]
+    set omax [set obsvec(max)]
+    set expgui(min) [expr {$omin < $cmin ? $omin : $cmin}]
+    set expgui(max) [expr {$omax > $cmax ? $omax : $cmax}]
 
     foreach p $::expmap(phaselist) {
@@ -592 +614 @@
         return
     }
-    $box config -title "$expnam cycle $cycle Hist $hst"
+    if {$::plot_title == "(None)"} {
+        $box config -title "$expnam cycle $cycle Hist $hst"
+    } else {
+        $box config -title $::plot_title
+    }
     $box xaxis config -title $xunits
     $box yaxis config -title $yunits
@@ -622 +648 @@
     calcvec notify now
     bckvec notify now
-    diffvec notify now
     wifdvec notify now
     # now deal with peaks
-    for {set i 1} {$i < 10} {incr i} {
-        if {$expgui(autotick)} {
-            set div [expr {( $expgui(max) - $expgui(min) )/40.}]
-            set ymin [expr {$expgui(min) - ($i+1) * $div}]
-            set ymax [expr {$expgui(min) - $i * $div}]
-        } else {
-            set ymin $peakinfo(min$i)
-            set ymax $peakinfo(max$i)
-        }
-        set j 0
-        if [set peakinfo(flag$i)] {
-            foreach X $reflns($i) {
-                incr j
-                catch {
-                    $box marker create line -name peaks${i}_$j 
-                }
-                $box marker config peaks${i}_$j  -under 1 \
-                        -coords "$X $ymin $X $ymax" 
-                catch {
-                    $box marker config peaks${i}_$j \
-                            $graph(MarkerColorOpt) [list $peakinfo(color$i)]
-                    if {$peakinfo(dashes$i) && ! $expgui(autotick)} {
-                        $box marker config peaks${i}_$j -dashes "5 5"
-                    }
-                }
+    #for {set i 1} {$i < 10} {incr i} 
+    set k 0
+    set cmin $expgui(min)
+    foreach i $::expmap(phaselist) {
+        if {[set peakinfo(flag$i)]} {
+            incr k
+            if {$expgui(autotick)} {
+                set div [expr {( $expgui(max) - $expgui(min) )/40.}]
+                set ymin [expr {$expgui(min) - ($k+1) * $div}]
+                set ymax [expr {$expgui(min) - $k * $div}]
+                if {$cmin > $ymin} {set cmin $ymin}
+            } else {
+                set ymin $peakinfo(min$i)
+                set ymax $peakinfo(max$i)
+            }
+            set j 0
+            foreach X $reflns($i) {
+                incr j
+                catch {
+                    $box marker create line -name peaks${i}_$j 
+                }
+                $box marker config peaks${i}_$j  -under 1 \
+                    -coords "$X $ymin $X $ymax" 
+                catch {
+                    $box marker config peaks${i}_$j \
+                        $graph(MarkerColorOpt) [list $peakinfo(color$i)]
+                    if {$peakinfo(dashes$i) && ! $expgui(autotick)} {
+                        $box marker config peaks${i}_$j -dashes "5 5"
+                    }
+                }
             }
             catch {$box element create phase$i}
             catch {
                 $box element config phase$i -color $peakinfo(color$i) \
-                        -label $graph(label$i)
+                    -label $graph(label$i)
             }
         } else {
@@ -661 +691 @@
         }
     }
+    # offset the difference pattern
+    set maxdiff  [set diffvec(max)]
+    if {$expgui(autotick)} {
+        diffvec set [diffvec + [expr {$cmin - $maxdiff}]]
+    } else {
+        diffvec set [diffvec + [expr {$cmin - 1.1*$maxdiff}]]
+    }
+    diffvec notify now
+
     # force an update of the plot as BLT may not
     $box config -title [$box cget -title]
@@ -1122 +1161 @@
         eval $box y2axis config $graph(ElementHideOption) 
         $box element config 0 -label ""
+        # clear the vector
+        wifdvec set {}
+        wifdvec notify now
     }
 }
@@ -2046 +2088 @@
 setlegend $box $graph(legend)
 
+set ps2pdfcmd {}
+set gnuplotpath {}
+# find gnuplot
+if {$::tcl_platform(platform) == "windows"} {
+    set gnuplotpath [file join $::expgui(gsasexe) "gnuplot/gnuplot.exe"]
+    if {![file exists $gnuplotpath]} {
+        set gnuplotpath [auto_execok gnuplot.exe]
+    }
+} else {
+    set ::env(PATH) "${::expgui(gsasexe)}:${::env(PATH)}"
+    auto_reset
+    set gnuplotpath [auto_execok gnuplot]
+}
+# find postscript conversion routine
+if {$::tcl_platform(platform) == "windows"} {
+    set gspath [file join $::expgui(gsasexe) "gs/bin/gswin32c.exe"]
+    if {![file exists $gspath]} {
+        set gspath [auto_execok gswin32c.exe]
+    }
+    if {[file exists $gspath]} {
+        set ps2pdfcmd "$gspath -q -P- -dSAFER -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=\$pdfoutname -c save pop -f \$psoutname"
+    }
+} else {
+    # look for ghostscript
+    set gspath [auto_execok gs]
+    if {[file exists $gspath]} {
+        set ps2pdfcmd "$gspath -q -P- -dSAFER -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=\$pdfoutname -c save pop -f \$psoutname"
+    } else {
+        set gspath [auto_execok pstopdf]; # this is on Mac only
+        if {[file exists $gspath]} {
+            set ps2pdfcmd "$gspath \$psoutname -o \$pdfoutname"
+        }
+    }
+}
+set gnuplotexport {}
+catch {
+    source [file join $expgui(scriptdir) gnuplot.tcl]
+}
+
+#======================================================================
+# make menus
 frame .a -bd 3 -relief groove
 pack [menubutton .a.file -text File -underline 0 -menu .a.file.menu] -side left
@@ -2054 +2137 @@
 .a.file.menu add command -label "Update Plot" \
         -command {set cycle [getcycle];readdata .g}
+.a.file.menu add command -label "Set Plot Title" \
+        -command SetTitle
 .a.file.menu add cascade -label "Export plot" -menu .a.file.menu.export
 menu .a.file.menu.export
@@ -2062 +2147 @@
     .a.file.menu.export add command -label "to Grace" -command exportgrace
 }
+if {$gnuplotpath == {}} {
+    .a.file.menu.export add cascade -label "gnuplot program not found"
+} elseif {$gnuplotexport == ""} {
+    .a.file.menu.export add cascade -label "file gnuplot.tcl not found"
+} elseif {$ps2pdfcmd == ""} {
+    .a.file.menu.export add cascade -label "gs or pstopdf program not found"
+} else {
+    .a.file.menu.export add command -label "to PDF" -command ExportPDF
+}
+
 .a.file.menu add command -label Quit -command "destroy ."
 .a.file.menu.export add command -label "as .csv file" \
@@ -2089 +2184 @@
 .a.options.menu.tick add separator
 
+pack [menubutton .a.mag -text Magnification -underline 0 -menu .a.mag.menu] \
+        -side left
+menu .a.mag.menu
+set maglist {}
+set mag0 1.0
+# display magnification routines
+proc ShowMag {} {
+    global blt_version tcl_platform peakinfo expgui
+    set bx .opt
+    catch {destroy $bx}
+    toplevel $bx
+    putontop $bx
+    wm iconname $bx "Mag Regs"
+    wm title $bx "Plot Magnification Regions"
+    pack [label $bx.0 -text "Magnification Regions:"] -side top
+    if {[llength $::maglist] == 0} {
+        set lbl "None"
+    } else {
+        set lbl ""
+        set xm $::xvec(min)
+        set ym $::mag0
+        set ::maglist [lsort -real -index 0 $::maglist]
+        foreach pair $::maglist {
+            foreach {xh ymh} $pair {}
+            append lbl "\tfrom $xm to $xh: times $ym\n"
+            set xm $xh
+            set ym $ymh
+        }
+        set xh $::xvec(max)
+        append lbl "\tfrom $xm to $xh: times $ym"
+    }
+    pack [label $bx.1 -text $lbl -justify left] -side top
+    pack [button $bx.2 -text "Close" -command "destroy $bx"] -side top
+    tkwait window $bx
+    afterputontop
+}
+
+# edit magnification regions
+proc EditMag {} {
+    set ::multrow 1
+    set bx .opt
+    catch {destroy $bx}
+    toplevel $bx
+    putontop $bx
+    wm iconname $bx "Mag Regs"
+    wm title $bx "Edit Magnification Regions"
+    pack [label $bx.0 -text "Vertical Magnification Regions:"] -side top
+    if {[llength $::maglist] == 0} {
+        set lbl "None"
+        pack [label $bx.1 -text $lbl -justify left] -side top
+        pack [button $bx.2 -text "Close" -command "destroy $bx"] -side top
+        tkwait window $bx
+        afterputontop
+        return
+    } else {
+        pack [frame $bx.1] -side top
+        set ::maglist [lsort -real -index 0 $::maglist]
+        set row 0
+        foreach pair $::maglist {
+            foreach {xh ymh} $pair {}
+            set row1 [expr {$row + 1}]
+            set ::xmag($row1) $xh
+            set ::mag($row1) $ymh
+            if {$row == 0} {
+                grid [label $bx.1.a$row -text "From "] -column 1 -row $row
+                grid [label $bx.1.b$row -text $::xvec(min)] -column 2 -row $row
+                grid [label $bx.1.c$row -text " to "] -column 3 -row $row
+                grid [entry $bx.1.d$row -textvariable xmag(1) -width 6] -column 4 -row $row
+                grid [label $bx.1.e$row -text " times "] -column 5 -row $row
+                grid [entry $bx.1.f$row -textvariable mag0 -width 4] -column 6 -row $row
+            } else {
+                grid [label $bx.1.a$row -text "From "] -column 1 -row $row
+                grid [entry $bx.1.b$row -textvariable xmag($row) -width 6] -column 2 -row $row
+                grid [label $bx.1.c$row -text " to "] -column 3 -row $row
+                grid [entry $bx.1.d$row -textvariable xmag($row1) -width 6] -column 4 -row $row
+                grid [label $bx.1.e$row -text " times "] -column 5 -row $row
+                grid [entry $bx.1.f$row -textvariable mag($row) -width 4] -column 6 -row $row
+            }
+            incr row
+        }
+        grid [label $bx.1.a$row -text "From "] -column 1 -row $row
+        grid [entry $bx.1.b$row -textvariable xmag($row) -width 6] -column 2 -row $row
+        grid [label $bx.1.c$row -text " to "] -column 3 -row $row
+        grid [label $bx.1.d$row -text $::xvec(max)] -column 4 -row $row
+        grid [label $bx.1.e$row -text " times "] -column 5 -row $row
+        grid [entry $bx.1.f$row -textvariable mag($row) -width 4] -column 6 -row $row
+        set ::multrow $row
+    }
+    pack [label $bx.l -text "\nSet the multiplier to zero to delete a region"] -side top
+    pack [frame $bx.2] -side top
+    pack [button $bx.2.a -text "Edit" -command "destroy $bx"] -side left
+    pack [button $bx.2.b -text "Cancel" -command "set multrow 0; destroy $bx"] -side left
+    tkwait window $bx
+    afterputontop
+    if {$::multrow == 0} return
+    set newmaglist {}
+    set xp $::xvec(min)
+    for {set i 1} {$i <= $::multrow} {incr i} {
+        if {$::mag($i) > 0} {
+            lappend newmaglist [list $::xmag($i) $::mag($i)]
+        }
+        set xp $::xmag($i)
+    }
+    set ::maglist $newmaglist
+    readdata .g
+}
+
+# show a menu to add a magnification region
+proc AddMag {} {
+    set bx .opt
+    catch {destroy $bx}
+    toplevel $bx
+    putontop $bx
+    wm iconname $bx "Add Regs"
+    wm title $bx "Add Plot Magnification Region"
+    pack [frame $bx.0] -side top
+    pack [label $bx.0.a -text "Magnify from "] -side left
+    pack [entry $bx.0.b -textvariable xmin -width 6] -side left
+    pack [label $bx.0.c -text " to next region. Multiply by "] -side left
+    pack [entry $bx.0.d -textvariable mult -width 4] -side left
+    pack [frame $bx.2] -side top
+    pack [button $bx.2.a -text "Add" -command "destroy $bx"] -side left
+    pack [button $bx.2.b -text "Cancel" -command "set mult {}; destroy $bx"] -side left
+    if {[catch {expr $::mult}]} {set ::mult 1.0}
+    if {$::mult <= 0} {set ::mult 1.0}
+    tkwait window $bx
+    afterputontop
+    catch {
+        if {$::xmin < $::xvec(min)} {set ::xmin $::xvec(min)} 
+        if {$::xmin > $::xvec(max)} {set ::xmin $::xvec(max)} 
+        if {$::mult > 0} {
+            lappend ::maglist [list $::xmin $::mult]
+            readdata .g
+        } else {
+            MyMessageBox -parent . -title "Invalid" \
+                -message "Invalid input, try again" \
+                -icon error -type Continue -default continue
+        }
+    }
+}
+proc AddCursorMag {p m} {
+    set x [.g xaxis invtransform $p]
+    if {$x < $::xvec(min) || $x > $::xvec(max) } {
+        bell
+        return
+    }
+    lappend ::maglist [list $x $m]
+    readdata .g
+}
+
+# scale the data with magnification regions
+proc ApplyMag {} {
+    foreach mrk [.g marker names mag*] {
+        .g marker delete $mrk
+    }
+    if {[llength $::maglist] == 0} return
+    global xvec
+    vector create ymult([xvec length])
+    set xl $xvec(min)
+    set ym $::mag0
+    set i 0
+    set ::maglist [lsort -real -index 0 $::maglist]
+    foreach pair $::maglist {
+        foreach {xh ymh} $pair {}
+        set xr [xvec search $xl $xh]
+        #puts "$xl $xh [lindex $xr 0]:[lindex $xr end] $ym"
+        if {[lindex $xr 0] != [lindex $xr end]} {
+            set ymult([lindex $xr 0]:[lindex $xr end]) $ym
+            if {$xl != $xvec(min)} {
+                .g marker create line -coords "$xl -Inf $xl Inf" -name mag[incr i]
+            }
+            .g marker create text -coords "$xl Inf" -name mag[incr i] -text "x$ym" -anchor w
+        }
+        set xl $xh
+        set ym $ymh
+    }
+    set xh $xvec(max)
+    set xr [xvec search $xl $xh]
+    set ymult([lindex $xr 0]:[lindex $xr end]) $ym
+    #puts "$xl $xh [lindex $xr 0]:[lindex $xr end] $ym"
+    .g marker create line -coords "$xl -Inf $xl Inf" -name mag[incr i]
+    .g marker create text -coords "$xl Inf" -name mag[incr i] -text "x$ym" -anchor w
+    foreach vec {obsvec calcvec bckvec diffvec} {
+        global $vec
+        $vec expr {$vec * ymult}
+    }
+}
+
+# create a PDF using GNUPLOT & GhostScript
+proc ExportPDF {} {
+    set msg {}
+    if {$::gnuplotpath == {}} {
+        append msg "\n\tThe gnuplot program was not found"
+    } 
+    if {$::gnuplotexport == ""} {
+        append msg "\n\tfile gnuplot.tcl not found in $::expgui(scriptdir)"
+    } 
+    if {$::ps2pdfcmd == ""} {
+        append msg "\n\tNo PDF conversion routine (ghostscript or pstopdf on Mac was found"
+    }
+    if {$msg != ""} {
+        MyMessageBox -parent . -title "Gnuplot/GS Error" \
+                -message $msg \
+                -icon error -type OK -default OK
+        return 0
+    }
+
+    set pdfoutname [tk_getSaveFile -title "Select output file" -parent . \
+                        -defaultextension ".pdf" \
+                        -initialdir [pwd] \
+                        -initialfile "[file rootname $::expnam].pdf"]
+    if { $pdfoutname == "" } { return }
+    cd [file dirname $pdfoutname]
+    set pdfoutname [regsub -all " " [file tail $pdfoutname] "_"]
+    set rootname [file root $pdfoutname]
+    set csvoutname "$rootname.csv"
+    set gplotname "$rootname.gplot"
+    set psoutname "$rootname.ps"
+    foreach filename [list $pdfoutname $csvoutname $gplotname $psoutname] {
+        catch {file -force delete $filename}
+    }
+    waitmsg "running gnuplot, Please wait"
+    Graph2Gnuplot .g $gplotname $psoutname $csvoutname
+    if {![file exists $gplotname]} {
+        set msg "\n  Output file for gnuplot not created! ($gplotname)"
+    }
+    if {![file exists $csvoutname]} {
+        append msg "\n   Output file for gnuplot not created! ($csvoutname)"
+    }
+    if {$msg == ""} {
+        if {[catch { exec $::gnuplotpath $gplotname } err]} {
+            if {[string first "Warning" $err] == -1} {
+                append msg "Error in running gnuplot: $err"
+            }
+        }
+        if {![file exists $psoutname]} {
+            append msg "\n   Output file from gnuplot not created! ($psoutname)"
+        }
+    }
+    if {$msg == ""} {
+        if {[catch { eval exec [subst $::ps2pdfcmd]} err]} {
+            append msg "Error in PDF conversion: $err"
+        }
+        if {![file exists $pdfoutname]} {
+            append msg "\n   PDF file not created! ($pdfoutname)"
+        }
+    }
+    donewaitmsg
+    if {$msg == ""} {
+        # clean up
+        foreach filename [list $csvoutname $gplotname $psoutname] {
+            catch {file -force delete $filename}
+        }
+        MyMessageBox -parent . -title "PDF created" \
+            -message "Success: PDF file created ($pdfoutname)" \
+            -type OK -default OK
+        return 1
+    } else {
+        # something failed
+        MyMessageBox -parent . -title "Gnuplot/GS Error" \
+                -message "Error: $msg" \
+                -icon error -type OK -default OK
+        return 0
+    }
+}
+
+# resize graph font only
+proc ResizeGraphFont {graph font} {
+    foreach w {legend xaxis yaxis xaxis yaxis \
+                   x2axis y2axis x2axis y2axis} \
+        o {-font -tickfont -tickfont -titlefont -titlefont \
+               -tickfont -tickfont -titlefont -titlefont} {
+                   catch {
+                       $graph $w configure $o $font
+                   }
+               }
+    catch {
+        set curfont [$graph cget -font]
+        if {[string tolower [lindex $curfont 0]] == "symbol"} {
+            $graph configure -font "Symbol [lrange $font 1 end]"
+        } else {
+            $graph configure -font $font
+        }
+    }
+}
+
 if {$program == "liveplot"} {
+    .a.mag.menu add command -label "Add region" -command "AddMag"
+    .a.mag.menu add command -label "Edit Regions" -command "EditMag"
+    .a.mag.menu add separator
+    .a.mag.menu add command -label "Clear" \
+        -command "set maglist {}; readdata .g"
     .a.options.menu add command -label "Obs symbol" -command getsymopts
+    foreach i {1 2 3 4 5 6 7 8 9} {
+        bind . <Control-Key-$i> "AddCursorMag %x $i"
+    }
 } else {
     .a.options.menu add cascade -label "Symbol Type" -menu .a.options.menu.sym
@@ -2131 +2520 @@
             -variable graph(yunits) -value 1 \
             -command {set cycle [getcycle];readdata .g}
+    .a.options.menu.yunits add radiobutton -label "I/Sigma(I)" \
+            -variable graph(yunits) -value 2 \
+            -command {set cycle [getcycle];readdata .g}
     .a.options.menu add command -label "HKL labeling" -command setlblopts
     .a.options.menu add checkbutton -label "Subtract background" \
@@ -2155 +2547 @@
 }
 if {$program == "liveplot"} {
+    .a.options.menu add cascade -menu  .a.options.menu.gfont \
+        -label "Graph font"
+    menu .a.options.menu.gfont
+    foreach f {12 14 16 18 20 22 24 26 28 32 36 40} {
+        .a.options.menu.gfont add radiobutton \
+            -command "ResizeGraphFont .g \[list Helvetica -$f\]" \
+            -label $f -font "Helvetica -$f"
+    }
     .a.options.menu add checkbutton -label "Raise on update" \
             -variable graph(autoraise)
@@ -2314 +2714 @@
 expload $expnam.EXP
 mapexp
-
+if {$expgui(autotick)} {
+    foreach i $::expmap(phaselist) {
+        set peakinfo(flag$i) 1
+    }
+}
+        
 # fill the histogram menu
 if {[llength $expmap(powderlist)] > 15} {

trunk/readexp.tcl

@@ -9 +9 @@
 # returns 1 if the file is 80 char/line + cr/lf
 # returns 2 if the file is sequential but not fixed-record length
-proc expload {expfile} {
-    global exparray tcl_platform
-    # $expfile is the path to the data file. 
-
+proc expload {expfile "ns {}"} {
+    # expfile is the path to the data file. 
+    # ns is the namespace to place the output array (default is global)
+    if {$ns != ""} {
+        namespace eval $ns {}
+    }
     if [catch {set fil [open "$expfile" r]}] {
         tk_dialog .expFileErrorMsg "File Open Error" \
@@ -27 +29 @@
     }
     catch {
-        unset exparray
+        unset ${ns}::exparray
     }
     if {$len > 160} {
@@ -39 +41 @@
             incr i2 80
             set key [string range $nline 0 11]
-            set exparray($key) [string range $nline 12 end]
+            set ${ns}::exparray($key) [string range $nline 12 end]
         }
     } else {
@@ -45 +47 @@
         while {$len > 0} {
             set key [string range $line 0 11]
-            set exparray($key) [string range $line 12 79]
+            set ${ns}::exparray($key) [string range $line 12 79]
             if {$len != 81 || [string range $line end end] != "\r"} {set fmt 2}
             set len [gets $fil line]
@@ -187 +189 @@
         }
     }
+    # load the constrained parameters
+    atom_constraint_load
     set expgui(mapstat) 1
 }
@@ -294 +298 @@
             set digits 1
         }
+        if {$digits <= 0} {set digits 1}
         if {$digits + $sign >= $length} {
             # the number is much too big -- use exponential notation
@@ -307 +312 @@
             set decimal [expr {$length - $digits - $sign - 1}]
             set tmp [format "%#.${decimal}f" $value]
-        } elseif {abs($value) < pow(10,2-$decimal) && $length > 6} {
+        } elseif {abs($value) < pow(10,2-$decimal) && $length > 6 && $value != 0} {
             # for small values, switch to exponential notation (2-$decimal -> three sig figs.)
             set decimal [expr {$length - 6 - $sign}]
@@ -1388 +1393 @@
 #     absdamp -- damping for absorption refinement (*)
 #     absref -- refinement damping for absorption refinement (*)
-#     proftbl -- returns number of profile table termns
+#     proftbl -- returns number of profile table terms
+#     anomff -- returns a list of elements, f' and f"
 #   parameters transferred from the instrument parameter file:
 #     ITYP    -- returns the contents of the ITYP record
@@ -1977 +1983 @@
                 return $val
             }
+            anomff-get {
+                set l {}
+                foreach i {1 2 3 4 5 6 7 8 9} {
+                    if {![existsexp "${key}FFANS$i"]} continue
+                    set line [readexp "${key}FFANS$i"]
+                    set elem [string trim [string range $line 2 9]]
+                    set fp [string trim [string range $line 10 19]]
+                    set fpp [string trim [string range $line 20 29]]
+                    lappend l [list $elem $fp $fpp]
+                }
+                return $l
+            }
+            anomff-set {
+                # match up input against elements in list. 
+                # change elements included, return any elements that are 
+                # not found.
+                set errorlist {}
+                foreach triplet $value {
+                    foreach {e fp fpp} $triplet {}                
+                    foreach i {1 2 3 4 5 6 7 8 9} {
+                        if {![existsexp "${key}FFANS$i"]} continue
+                        # note that the element name is not used or validated
+                        set elem [string trim [string range \
+                                                   [readexp "${key}FFANS$i"] 2 9]]
+                        if {[string match -nocase $e $elem]} { 
+                            if ![validreal fp 10 3] {return 0}
+                            setexp "${key}FFANS$i" $fp 11 10
+                            if ![validreal fpp 10 3] {return 0}
+                            setexp "${key}FFANS$i" $fpp 21 10
+                            set e {}
+                            break
+                        }
+                    }
+                    if {$e != ""} {
+                        # oops, no match
+                        lappend errorlist $e
+                    }
+                }
+                if {$errorlist != ""} {return [list 0 $errorlist]}
+            }
             default {
                 set msg "Unsupported histinfo access: parm=$parm action=$action"
@@ -2173 +2219 @@
     return 1
 }
+
+#  read fixed constraints
+
+proc atom_constraint_read {phase} {
+    set fix_list ""
+    foreach k {1 2 3 4 5 6 7 8 9} {
+        set key [format "LEQV HOLD%1d%2d" $phase $k]
+        set line [readexp $key]
+        foreach j {2 10 18 26 34 42 50 58} {
+            set fix_param [string range $line $j [expr $j+7]]
+            if {[string trim $fix_param] == ""} {return $fix_list}
+            lappend fix_list $fix_param
+        }
+    }
+}
+
+# load all atom constraints into global array fix_param
+proc atom_constraint_load { } {
+    catch {unset ::fix_param}
+    foreach i $::expmap(phaselist) {
+        set temp [atom_constraint_read $i]
+        foreach j $temp {
+            set atomnum [string trim [string range $j 2 3]]
+            set param [string trim [string range $j 4 6]]
+            set ::fix_param($i,$atomnum,$param) 1    
+        }
+    }
+}
+
+proc atom_constraint_write {phase fix_list} {
+    foreach key [array names ::exparray "LEQV HOLD$phase*"] {
+        delexp $key
+    }
+    set k 0
+    set j 1
+    set line ""
+    foreach fix $fix_list {
+        incr k
+        append line $fix
+        if {$k == 8} {
+            set key [format "LEQV HOLD%1d%2d" $phase $j]
+            makeexprec $key
+            setexp $key $line 3 [expr ($k * 8) + 2]
+            set k 0
+            incr j
+            set line ""
+        }
+    }
+    if {$line != ""} {
+        set key [format "LEQV HOLD%1d%2d" $phase $j]
+        makeexprec $key
+        setexp $key $line 3 [expr ($k * 8) + 2]
+    }   
+}
+
 
 #  get a logical constraint
@@ -3099 +3200 @@
         }
     }
-    if {$HST == ""} {return "1"}
     if {$HST <=9} {
         set key "HST  $HST"
@@ -3119 +3219 @@
             makeexprec $key
         }
-        setexp $key "RSN" [expr 3 + 5*(($HST-1) % 12)] 5
+        setexp $key "RSN " [expr 3 + 5*(($HST-1) % 12)] 5
         # create other HST  xx recs
         if {$HST <=9} {
@@ -3130 +3230 @@
         makeexprec "$key FACTR"
         makeexprec "$key NBNDS"
+        mapexp
+    } elseif {$HST == ""} {
+        if $::expgui(debug) {puts "no restraints"}
+        return "1"
     }
 
@@ -3449 +3553 @@
     }
 }
+#============================================================================
+# rigid body EXP editing routines (to move into readexp.tcl)
+# RigidBodyList -- returns a list of the defined rigid body types
+# SetRigidBodyVar -- set variables and damping for rigid body type multipliers
+# ReadRigidBody  -- # of times a body is mapped, scaling factors, var #s & coordinates
+# RigidBodyMappingList - return a list instances where a RB is mapped in phase
+# RigidBodyEnableTLS -- Enable or Disable TLS use for a rigid body mapping
+# RigidBodySetTLS  -- change the TLS values for a rigid body mapping
+# RigidBodySetDamp -- change the damping values for a rigid body mapping
+# RigidBodyVary    -- set refinement variable numbers for a rigid body mapping
+# RigidBodyTLSVary -- set TLS refinement variable nums for a rigid body mapping
+# AddRigidBody -- defines a new rigid body type
+# DeleteRigidBody -- remove a rigid body definition
+# ReplaceRigidBody -- replaces a previous rigid body type
+# ReadRigidBodyMapping  -- get parameters for a rigid body mapping
+# MapRigidBody -- map a rigid body type into a phase
+# EditRigidBodyMapping -- change the parameters in a rigid body mapping
+# UnMapRigidBody --remove a rigid body constraint by removing a RB "instance"
+#----- note that these older routines should not be used ------
+# RigidBodyCount -- returns the number of defined rigid bodies (body types)
+#    use RigidBodyList instead
+# RigidBodyMappingCount -- # of times a rigid body is mapped in phase
+#    use RigidBodyMappingList instead
+#============================================================================
+# returns the number of defined rigid bodies 
+proc RigidBodyCount {} {
+    set n [string trim [readexp "RGBD  NRBDS"]]
+    if {$n == ""} {
+        set n 0
+    }
+    return $n
+}
+
+# returns a list of the defined rigid body types 
+proc RigidBodyList {} {
+    set n [string trim [readexp "RGBD  NRBDS"]]
+    if {$n == ""} {
+        set n 0
+    }
+    set rblist {}
+    foreach rbnum {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15} {
+        set value $rbnum
+        validint value 2
+        set key "RGBD${value}"
+        if {[existsexp "$key NATR "]} {
+            lappend rblist $rbnum
+        }
+        if {[llength $rblist] == $n} break
+    }
+    return $rblist
+}
+
+# ReadRigidBody provides all information associated with a rigid body type
+#  rbnum is the rigid body type number
+# it returns two items: 
+#   the number of times the rigid body is mapped
+#   a list containing an element for each scaling factor in rigid body #rbnum.
+# in each element there are four items: 
+#    a multiplier value for the rigid body coordinates
+#    a damping value (0-9) for the refinement of the multiplier
+#    a variable number if the multiplier will be refined
+#    a list of cartesian coordinates coordinates 
+# each cartesian coordinate contains 4 items: x,y,z and a label
+#  note that the label is present only when the RB is created in EXPGUI and is
+#  not used in GSAS.
+proc ReadRigidBody {rbnum} {
+    if {[lsearch [RigidBodyList] $rbnum] == -1} {
+        return ""
+    }
+    set value $rbnum
+    validint value 2
+    set key "RGBD${value}"
+    set n [string trim [string range [readexp "$key NATR"] 0 4]]
+    set used [string trim [string range [readexp "$key NBDS"] 0 4]]
+    set nmult [string trim [string range [readexp "$key NSMP"] 0 4]]
+    set out {}
+    for {set i 1} {$i <= $nmult} {incr i} {
+        set line [readexp "${key}${i}PARM"]
+        set mult [string trim [string range $line 0 9]]
+        set var [string trim [string range $line 10 14]]
+        set damp [string trim [string range $line 15 19]]
+        set coordlist {}
+        for {set j 1} {$j <= $n} {incr j} {
+            set value $j
+            validint value 3
+            set line [readexp "${key}${i}SC$value"]
+            set x [string trim [string range $line 0 9]]
+            set y [string trim [string range $line 10 19]]
+            set z [string trim [string range $line 20 29]]
+            set lbl [string trim [string range $line 30 39]]
+            lappend coordlist [list $x $y $z $lbl]
+        }
+        lappend out [list $mult $damp $var $coordlist]
+    }
+    return [list $used $out]
+}
+
+# SetRigidBodyVar
+#   rbnum is the rigid body type number
+#   varnumlist is a list of variable numbers
+#      note that if this list is shorter than the number of actual multipliers
+#      for the body, the unspecified variable will not be changed
+#   damplist   is a list of damping values (0-9)
+#      note that if the damplist is shorter than the number of actual multipliers
+#      the unspecified values are not changed
+#  SetRigidBodVar 2 {1 2 3} {}
+#       will vary the (first 3) translations in body #3 and will not change the
+#       damping values
+#  SetRigidBodVar 3 {} {0 0 0}
+#       will not change variable settings but will change the (first 3) damping values
+#  SetRigidBodVar 4 {11 11} {8 8}
+#      changes both variable numbers and damping at the same time
+# Nothing is returned
+proc SetRigidBodyVar {rbnum varnumlist damplist} {
+    if {[lsearch [RigidBodyList] $rbnum] == -1} {
+        return ""
+    }
+    set value $rbnum
+    validint value 2
+    set key "RGBD${value}"
+    set nmult [string trim [string range [readexp "$key NSMP"] 0 4]]
+    for {set i 1} {$i <= $nmult} {incr i} {
+        set j $i
+        incr j -1
+        set var [lindex $varnumlist $j]
+        if {$var != ""} {
+            validint var 5
+            setexp "${key}${i}PARM" $var 11 15
+        }
+        set damp [lindex $damplist $j]
+        if {$damp != ""} {
+            if {$damp > 9} {set damp 9}
+            if {$damp < 0} {set damp 0}
+            validint damp 5
+        }
+        setexp "${key}${i}PARM" $damp 16 20
+    }
+}
+
+
+# return the number of times rigid body $bodytyp is mapped in phase $phase
+proc RigidBodyMappingCount {phase bodytyp} {
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1]"
+    if {! [existsexp "$key  NBDS"]} {return 0}
+    set n [string trim [readexp "$key  NBDS"]]
+    if {$n == ""} {
+        set n 0
+    }
+    return $n
+}
+# return a list of the instances where rigid body $bodytyp is mapped in phase $phase
+proc RigidBodyMappingList {phase bodytyp} {
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1]"
+    if {! [existsexp "$key  NBDS"]} {return {}}
+    set n [string trim [readexp "$key  NBDS"]]
+    if {$n == ""} {
+        set n 0
+    }
+    set rblist {}
+    foreach rbnum {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15} {
+        set value $rbnum
+        validint value 2
+        set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $rbnum 1]"
+        if {[existsexp "$key  NDA"]} {
+            lappend rblist $rbnum
+        }
+        if {[llength $rblist] == $n} break
+    }
+    return $rblist
+}
+
+
+
+# reads rigid body mapping parameters for phase ($phase), body type # ($bodytyp) and instance # ($num)
+# returns a list of items (most lists) as follows:
+#   1) sequence # of first atom in body
+#   2) origin of body in fractional coordinates (3 elements)
+#   3) Euler angles as 6 pairs of numbers (see below)
+#   4) variable numbers for the 9 position variables (origin followed by rotations)
+#   5) damping vals for the 9 position variables (origin followed by rotations)
+#   6) the TLS values, in order below (empty list if TLS is not in use)
+#   7) the variable numbers for each TLS values, in order below (or empty)
+#   8) three damping values for the T, L and S terms.
+# returns an empty list if no such body exists.
+#
+# Euler angles are a list of axes and angles to rotate: 
+#   { {axis1 angle1} {axis2 angle2} ...} 
+# where axis1,... can be 1, 2 or 3 corresponding to the cartesian X, Y or Z axes
+#
+# The 20 TLS terms are ordered:
+#    T11, T22, T33, T12, T13, T23
+#    L11, L22, L33, L12, L13, L23
+#    S12, S13, S21, S23, S31, S32, SAA, SBB
+#
+proc ReadRigidBodyMapping {phase bodytyp num} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $num] == -1} {
+        return ""
+    }
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $num 1]"
+    set first [string trim [string range [readexp "$key  NDA"] 0 4]]
+    set line [readexp "$key BDFL"]
+    set varlist {}
+    set damplist {}
+    foreach i {0 1 2 3 4 5 6 7 8} {
+        lappend varlist [string trim [string range $line [expr {5*$i}] [expr {4 + 5*$i}] ]]
+        lappend damplist [string trim [string range $line [expr {45 + $i}] [expr {45 + $i}] ]]
+    }
+    set TLSdamplist {}
+    foreach i {54 55 56} {
+        lappend TLSdamplist [string trim [string range $line $i $i ]]
+    }
+    set line [readexp "${key} BDLC"]
+    set x [string trim [string range $line 0 9]]
+    set y [string trim [string range $line 10 19]]
+    set z [string trim [string range $line 20 29]]
+    set origin [list $x $y $z]
+    set line [readexp "${key} BDOR"]
+    set rotations {}
+    foreach i {0 10 20 30 40 50} {
+        set angle [string trim [string range $line $i [expr {$i+7}]]]
+        set axis [string trim [string range $line [expr {$i+8}] [expr {$i+9}]]]
+        lappend rotations [list $angle $axis]
+    }
+    set TLS [string trim [string range [readexp "${key} LSTF"] 0 4]]
+    set tlsvars {}
+    set tlsvals {}
+    if {$TLS != 0} {
+        set line [readexp "${key}TLSF1"]
+        for {set j 0} {$j < 20} {incr j} {
+            set var [string trim [string range $line [expr {3*$j}] [expr {3*$j+2}]]]
+            if {$var == ""} {set var 0}
+            lappend tlsvars $var
+        }
+        for {set j 0} {$j < 20} {incr j} {
+            set i 0
+            if {$j == 0} {
+                set i 1
+            } elseif {$j == 8} {
+                set i 2
+            } elseif {$j == 16} {
+                set i 3
+            }
+            if {$i != 0} {
+                set line [readexp "${key}TLSP$i"]
+                set i 0
+                set j1 0
+                set j2 7
+            } else {
+                incr j1 8
+                incr j2 8
+            }
+            set val [string trim [string range $line $j1 $j2]]
+            if {$val == ""} {set val 0}
+            lappend tlsvals $val
+        }
+    }
+    return [list $first $origin $rotations $varlist $damplist $tlsvals $tlsvars $TLSdamplist]
+}
+
+# Control TLS representation for phase, body # and instance number of a Rigid body mapping 
+#   for mapping with phase ($phase), body type # ($bodytyp) and instance # ($num)
+# Enable TLS use if TLS is non-zero (true). Disable if zero
+proc RigidBodyEnableTLS {phase bodytyp num TLS} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $num] == -1} {
+        return ""
+    }
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $num 1]"
+    if {$TLS} {
+        setexp "${key} LSTF" [format "%5d" 1] 1 5
+        if {![existsexp "${key}TLSF1"]} {makeexprec "${key}TLSF1"}
+        if {![existsexp "${key}TLSP1"]} {
+            makeexprec "${key}TLSP1"
+            set str {}
+            foreach v {.01 .01 .01 0 0 0 0 0} d {4 4 4 4 4 4 2 2} {
+                validreal v 8 $d
+                append str $v
+            }
+            setexp "${key}TLSP1" $str 1 64
+        }
+        if {![existsexp "${key}TLSP2"]} {
+            makeexprec "${key}TLSP2"
+            set str {}
+            set v 0
+            foreach d {2 2 2 2 4 4 4 4} {
+                validreal v 8 $d
+                append str $v
+            }
+            setexp "${key}TLSP2" $str 1 64
+        }
+        if {![existsexp "${key}TLSP3"]} {
+            makeexprec "${key}TLSP3"
+            set str {}
+            set v 0
+            foreach d {4 4 4 4} {
+                validreal v 8 $d
+                append str $v
+            }
+            setexp "${key}TLSP3" $str 1 64
+        }
+    } else {
+        setexp "${key} LSTF" [format "%5d" 0] 1 5
+    }
+    return 1
+}
+
+# Control the TLS values for Rigid body mapping for mapping with
+#    phase ($phase), body type # ($bodytyp) and instance # ($num)
+# set the 20 TLS values to the values in TLSvals
+# There must be exactly 20 TLS terms, which are ordered:
+#    T11, T22, T33, T12, T13, T23
+#    L11, L22, L33, L12, L13, L23
+#    S12, S13, S21, S23, S31, S32, SAA, SBB
+proc RigidBodySetTLS {phase bodytyp num TLSvals} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $num] == -1} {
+        return ""
+    }
+    if {[llength $TLSvals] != 20} {return ""}
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $num 1]"
+    set TLS [string trim [string range [readexp "${key} LSTF"] 0 4]]
+    if {$TLS == 0} {return ""}
+    if {![existsexp "${key}TLSF1"]} {makeexprec "${key}TLSF1"}
+    foreach n {1 2 3} {
+        if {![existsexp "${key}TLSP$n"]} {makeexprec "${key}TLSP$n"}
+    }
+    set str {}
+    set n 1
+    set i 0
+    foreach v $TLSvals d {4 4 4 4 4 4 2 2 2 2 2 2 4 4 4 4 4 4 4 4} {
+        incr i
+        validreal v 8 $d
+        append str $v
+        if {$i == 8} {
+            set i 0
+            setexp "${key}TLSP$n" $str 1 64
+            incr n
+            set str {}
+        }
+    }
+    setexp "${key}TLSP$n" $str 1 64
+    return 1
+}
+
+# set damping values for a Rigid body mapping
+#   for mapping with phase ($phase), body type # ($bodytyp) and instance # ($num)
+# there must be 9 damping values in RBdamp for the 9 position variables (origin followed by rotations)
+# Use of TLSdamp is optional, but to be used, TLS representation must be enabled and there must be
+# three damping terms (for all T terms; for all L terms and for all S terms)
+proc RigidBodySetDamp {phase bodytyp num RBdamp "TLSdamp {}"} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $num] == -1} {
+        return ""
+    }
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $num 1]"
+    if {[llength $RBdamp] != 9} {return ""}
+    set str {}
+    foreach v $RBdamp {
+        if {[validint v 1] != 1} {set v " "}
+        append str $v
+    }
+    setexp "$key BDFL" $str 46 9
+    set TLS [string trim [string range [readexp "${key} LSTF"] 0 4]]
+    if {$TLS != 0 &&  [llength $TLSdamp] == 3} {
+        set str {}
+        foreach v $TLSdamp {
+        if {[validint v 1] != 1} {set v " "}
+            append str $v
+        }
+        setexp "$key BDFL" $str 55 3
+    }
+    return 1
+}
+
+# set refinement variable numbers for a Rigid body mapping
+#   for mapping with phase ($phase), body type # ($bodytyp) and instance # ($num)
+# there must be 9 variable values in RBvar for the 9 position variables (origin followed by rotations)
+# note that the variable values should be unique integers 
+proc RigidBodyVary {phase bodytyp num RBvar} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $num] == -1} {
+        return ""
+    }
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $num 1]"
+    if {[llength $RBvar] != 9} {return ""}
+    set str {}
+    foreach v $RBvar {
+        if {[validint v 5] != 1} {set v " "}
+        append str $v
+    }
+    setexp "$key BDFL" $str 1 45    
+}
+
+# set TLS refinement variable numbers for a Rigid body mapping
+#   for mapping with phase ($phase), body type # ($bodytyp) and instance # ($num)
+# there must be 20 variable values in TLSvar for the 20 parameters:
+#    T11, T22, T33, T12, T13, T23
+#    L11, L22, L33, L12, L13, L23
+#    S12, S13, S21, S23, S31, S32, SAA, SBB
+# note that the variable values should be unique integers 
+proc RigidBodyTLSVary {phase bodytyp num TLSvar} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $num] == -1} {
+        return ""
+    }
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $num 1]"
+    if {[llength $TLSvar] != 20} {return ""}
+    set TLS [string trim [string range [readexp "${key} LSTF"] 0 4]]
+    if {$TLS == 0} {return ""}
+    set str {}
+    foreach v $TLSvar {
+        if {[validint v 3] != 1} {set v " "}
+        append str $v
+    }
+    setexp "${key}TLSF1" $str 1 60
+
+# AddRigidBody: add a new rigid body definition into the .EXP file
+# arguments are:
+#   multlist: defines a list of multipliers for each set of coordinates. In the
+#             simplest case this will be {1}
+#   coordlist: a nested list of coordinates such as { { {0 0 0} {.1 .1 .1} {.2 .2 .2} } }
+# note that when the length of multlist > 1 then coordlist must have the same length.
+# for input where
+#     multlist = {s1 s2} and
+#     coordlist = { { {0 0 0} {1 1 0} {.0 .0 .0} ...}
+#                     {0 0 0} {1 1 0} {2 1 2} ...}
+#                 }
+# the cartesian coordinates are defined from the input as
+#    atom 1 = s1 * (0,0,0) + s2*(0,0,0) [ = (0,0,0)]
+#    atom 2 = s1 * (1,1,0) + s2*(1,1,0) [ = (s1+s2) * (1,1,0)]
+#    atom 3 = s1 * (0,0,0) + s2*(2,1,2) [ = s2 * (2,1,2)]
+#    ...
+# Returns the number of the rigid body that has been created
+proc AddRigidBody {multlist coordlist} {
+    # find the first unused body #
+    foreach rbnum {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16} {
+        set value $rbnum
+        validint value 2
+        set key "RGBD${value}"
+        if {! [existsexp "$key NATR "]} {break}
+    }
+    # did we go too far?
+    if {$rbnum == 16} {return ""}
+    # increment the RB counter
+    set n [string trim [readexp "RGBD  NRBDS"]]
+    if {$n == ""} {
+        makeexprec "RGBD  NRBDS"
+        set n 0
+    }
+    incr n
+    validint n 5
+    setexp "RGBD  NRBDS" $n 1 5
+    SetRigidBody $rbnum $multlist $coordlist
+    return $rbnum
+}
+
+# DeleteRigidBody: remove a rigid body definition from the .EXP file
+# The body may not be mapped. I am not sure if GSAS allows more than 9 bodies,
+# but if it does, the simplifed approach used here will fail, so this
+# is not allowed.
+# Input:
+#   Rigid body number
+# Returns:
+#   1 on success
+#   -1 if the body number is 11 or greater
+#   -2 if the body is mapped
+#   -3 if the body is not defined
+proc DeleteRigidBody {rbnum} {
+    # can't delete bodies with numbers higher than 10, since the key prefix
+    # (RGBD11... will overlap with rigid body instance records, which would be
+    # deleted below
+    if {$rbnum > 10} {
+        return -1
+    }
+    set value $rbnum
+    validint value 2
+    set key "RGBD${value}"
+    if {![existsexp "$key NATR "]} {
+        return -2
+    }
+    # make sure the body is not mapped
+    if {[string trim [string range [readexp "$key NBDS"] 0 4]] != 0} {
+        return -3
+    }
+    # delete the records starting with "RGBD x" or "RGBD10"
+    foreach key [array names ::exparray "${key}*"] {
+        #puts $key
+        delexp $key
+    }
+    # decrement the RB counter
+    set n [string trim [readexp "RGBD  NRBDS"]]
+    if {$n == ""} {
+        set n 0
+    }
+    incr n -1
+    validint n 5
+    if {$n > 0} {
+        setexp "RGBD  NRBDS" $n 1 5
+    } else {
+        delexp "RGBD  NRBDS"
+    }
+    return 1
+}
+
+# ReplaceRigidBody: replace all the information for rigid body #rbnum
+# Works the sames as AddRigidBody (see above) except that the rigid body is replaced rather
+# than added.
+# Note that count of the # of times the body is used is preserved
+proc ReplaceRigidBody {rbnum multlist coordlist {varlist ""} {damplist ""}} {
+    set value $rbnum
+    validint value 2
+    set key "RGBD${value}"
+    set line [readexp "$key NBDS"]
+    foreach key [array names ::exparray "${key}*"] {
+        #puts $key
+        delexp $key
+    }
+    SetRigidBody $rbnum $multlist $coordlist $varlist $damplist
+    setexp "$key NBDS" $line 1 68
+}
+
+# Edit the parameters for rigid body #rbnum
+# (normally called from ReplaceRigidBody or AddRigidBody)
+proc SetRigidBody {rbnum multlist coordlist {varlist ""} {damplist ""}} {
+    set value $rbnum
+    validint value 2
+    set key "RGBD${value}"
+    # number of atoms
+    set value [llength [lindex $coordlist 0]]
+    validint value 5
+    makeexprec "$key NATR"
+    setexp "$key NATR" $value 1 5
+    # number of times used
+    set value 0
+    validint value 5
+    makeexprec "$key NBDS"
+    setexp "$key NBDS" $value 1 5
+    # number of coordinate matrices
+    set value [llength $multlist]
+    validint value 5
+    makeexprec "$key NSMP"
+    setexp "$key NSMP" $value 1 5
+    set i 0
+    foreach mult $multlist coords $coordlist {
+        set var [lindex $varlist $i]
+        if {$var == ""} {set var 0}
+        set damp [lindex $damplist $i]
+        if {$damp == ""} {set damp 0}
+        incr i
+        makeexprec "${key}${i}PARM"
+        setexp "${key}${i}PARM" [format "%10.5f%5d%5d" $mult $var $damp] 1 20
+        set j 0
+        foreach item $coords {
+            #puts $item
+            incr j
+            set value $j
+            validint value 3
+            makeexprec "${key}${i}SC$value"
+            if {[llength $item] == 4} {
+                setexp "${key}${i}SC$value" [eval format "%10.6f%10.6f%10.6f%10s" $item] 1 40
+            } elseif {[llength $item] == 3} {
+                setexp "${key}${i}SC$value" [eval format "%10.6f%10.6f%10.6f" $item] 1 30
+            } else {
+                return -code 3 "Invalid number of coordinates"
+            }
+        }
+    }
+}
+
+# convert a decimal to the GSAS hex encoding with a field $digits long.
+proc ToHex {num digits} {
+    return [string toupper [format "%${digits}x" $num]]
+}
+
+# convert a GSAS hex encoding to a decimal integer
+proc FromHex {hex} {
+    return [scan $hex "%x"]
+}
+
+# MapRigidBody: define an "instance" of a rigid body: meaning that the coordinates 
+# (and optionally U values) for a set of atoms will be generated from the rigid body
+# arguments:
+#   phase: phase number (1-9)
+#   bodytyp: number of rigid body (1-15) as returned from AddRigidBody
+#   firstatom: sequence number of the first atom in phase (note that atoms may 
+#              not be numbered sequentially)
+#   position: list of three fractional coordinates for the origin of the rigid body coordinates
+#   angles: list of 3 angles to rotate the rigid body coordinates around x, y, z of the 
+#           cartesian system before the body is translated to position. 
+# returns the instance # (number of times body $bodytyp has been used in phase $phase)
+proc MapRigidBody {phase bodytyp firstatom position angles} {
+    # find the first unused body # for this phase & type
+    foreach rbnum {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16} {
+        set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $rbnum 1]"
+        if {! [existsexp "$key  NDA"]} {break}
+    }
+    # did we go too far?
+    if {$rbnum == 16} {return ""}
+    # increment number of mapped bodies of this type overall
+    set value $bodytyp
+    validint value 2
+    set key "RGBD${value}"
+    set used [string trim [string range [readexp "$key NBDS"] 0 4]]
+    incr used
+    set value $used
+    validint value 5
+    setexp "$key NBDS" $value 1 5
+    # increment number of mapped bodies of this type in this phase
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1]"
+    if {[existsexp "$key  NBDS"]} {
+        set used [string trim [string range [readexp "$key  NBDS"] 0 4]]
+    } else {
+        makeexprec "$key  NBDS"
+        set used 0
+    }
+    incr used
+    set value $used
+    validint value 5
+    setexp "$key  NBDS" $value 1 5
+    # now write the mapping parameters
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $rbnum 1]"
+    set value $firstatom
+    validint value 5
+    makeexprec "$key  NDA"
+    setexp "$key  NDA" $value 1 5
+    set l1 {}
+    set l2 {}
+    for {set i 0} {$i < 9} {incr i} {
+        append l1 [format %5d 0]
+        append l2 [format %1d 0]
+    }
+    makeexprec "$key BDFL"
+    setexp "$key BDFL" $l1$l2 1 54
+    makeexprec "${key} BDLC"
+    setexp "${key} BDLC" [eval format "%10.6f%10.6f%10.6f" $position] 1 30
+    makeexprec "${key} BDOR"
+    set l1 {}
+    foreach val "$angles 0 0 0" dir "1 2 3 1 1 1" {
+        append l1 [format "%8.2f%2d" $val $dir]
+    }
+    setexp "${key} BDOR" $l1 1 60
+    makeexprec "${key} LSTF"
+    setexp "${key} LSTF" [format "%5d" 0] 1 5
+    return $rbnum
+}
+
+# EditRigidBodyMapping: edit parameters that define an "instance" of a rigid body (see MapRigidBody)
+# arguments:
+#   phase: phase number (1-9)
+#   bodytyp: number of rigid body (1-15) as returned from AddRigidBody
+#   bodynum: instance number, as returned by MapRigidBody
+#   position: list of three fractional coordinates for the origin of the rigid body coordinates
+#   angles: list of 3 angles to rotate the rigid body coordinates around x, y, z of the 
+#           cartesian system before the body is translated to position. 
+# 
+proc EditRigidBodyMapping {phase bodytyp bodynum position angles} {
+    # number of bodies of this type in this phase
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $bodynum 1]"
+    setexp "${key} BDLC" [eval format "%10.6f%10.6f%10.6f" $position] 1 30
+    set l1 {}
+    foreach val "$angles 0 0 0" dir "1 2 3 1 1 1" {
+        append l1 [format "%8.2f%2d" $val $dir]
+    }
+    setexp "${key} BDOR" $l1 1 60
+}
+
+# UnMapRigidBody: remove a rigid body constraint by removing a RB "instance"
+# (undoes MapRigidBody)
+# arguments:
+#   phase: phase number (1-9)
+#   bodytyp: number of rigid body (1-15) as returned from AddRigidBody
+#   bodynum: instance number, as returned by MapRigidBody
+proc UnMapRigidBody {phase bodytyp mapnum} {
+    if {[lsearch [RigidBodyMappingList $phase $bodytyp] $mapnum] == -1} {
+        return ""
+    }
+    # decrement number of mapped bodies of this type overall
+    set value $bodytyp
+    validint value 2
+    set key "RGBD${value}"
+    set used [string trim [string range [readexp "$key NBDS"] 0 4]]
+    incr used -1
+    set value $used
+    validint value 5
+    setexp "$key NBDS" $value 1 5
+    # decrement number of mapped bodies of this type in this phase
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1]"
+    if {[existsexp "$key  NBDS"]} {
+        set used [string trim [string range [readexp "$key  NBDS"] 0 4]]
+    } else {
+        set used 0
+    }
+    incr used -1
+    set value $used
+    validint value 5
+    if {$used > 0} {
+        setexp "$key  NBDS" $value 1 5
+    } else {
+        delexp "$key  NBDS"
+    }
+    # now delete the mapping parameter records
+    set key "RGBD[ToHex $phase 1][ToHex $bodytyp 1][ToHex $mapnum 1]"
+    foreach key [array names ::exparray "${key}*"] {
+        delexp $key
+    }
+    return $used
+}
+

trunk/widplt

@@ -11 +11 @@
 package require Tk
 bind all <Control-KeyPress-c> {destroy .}
+
 set expnam [lindex $argv 0]
 if {$expnam != ""} {
@@ -442 +443 @@
     global UVWP XY wave lblarr WidSetList WidDisplay ttrange 
     global ABS absSetList AbsDisplay
+    if {$program == "absplt"} {
+        $top yaxis config -title {Abs. Corr.} 
+    } else {
+        $top yaxis config -title {FWHM} 
+    }
     if {$graph(plotunits) == "d"} {
         $top xaxis configure -title "d (A)"
+    } elseif {$graph(plotunits) == "deltad"} {
+        $top xaxis configure -title "d (A)"
+        $top yaxis configure -title "delta-d/d"
     } elseif {$graph(plotunits) == "q"} {
         $top xaxis configure -title "Q (A-1)"
@@ -450 +459 @@
     } else {
         $top xaxis configure -title "2Theta @ $graph(equivwave)"
-    }
-    if {$program == "absplt"} {
-        $top yaxis config -title {Abs. Corr.} 
-    } else {
-        $top yaxis config -title {FWHM} 
     }
     $top yaxis configure -min 0 
@@ -492 +496 @@
                 if {$graph(plotunits) == "d"} {
                     set ttlist [tod $ttlist $item]
+                } elseif {$graph(plotunits) == "deltad"} {
+                    set ttlist [tod $ttlist $item]
                 } elseif {$graph(plotunits) == "q"} {
                     set ttlist [toQ $ttlist $item]
@@ -530 +536 @@
                                         [eval LFWHM $tt $XY($item)]]
                                 lappend lfwhmlist $lfwhm
+                            }
+                        } elseif {$graph(plotunits) == "deltad"} {
+                            set d [tt2d $wave($item) $tt ]
+                            lappend ttlist $d
+                            set gfwhm [deltad $wave($item) $tt \
+                                    [eval FWHM $tt $UVWP($item)]]
+                            lappend fwhmlist [expr {$gfwhm/$d}]
+                            if $lflag {
+                                set lfwhm [deltad $wave($item) $tt \
+                                        [eval LFWHM $tt $XY($item)]]
+                                lappend lfwhmlist [expr {$lfwhm/$d}]
                             }
                         } elseif {$graph(plotunits) == "q"} {
@@ -982 +999 @@
 }
 
+proc BLTmanualZoom {} {
+    global graph box
+    catch {toplevel .zoom}
+    eval destroy [grid slaves .zoom]
+    raise .zoom
+    wm title .zoom {Manual Scaling}
+    grid [label .zoom.l1 -text minimum] -row 1 -column 2 
+    grid [label .zoom.l2 -text maximum] -row 1 -column 3 
+    grid [label .zoom.l3 -text x] -row 2 -column 1 
+    grid [label .zoom.l4 -text y] -row 3 -column 1 
+    grid [entry .zoom.xmin -textvariable graph(xmin) -width 10] -row 2 -column 2 
+    grid [entry .zoom.xmax -textvariable graph(xmax) -width 10] -row 2 -column 3 
+    grid [entry .zoom.ymin -textvariable graph(ymin) -width 10] -row 3 -column 2 
+    grid [entry .zoom.ymax -textvariable graph(ymax) -width 10] -row 3 -column 3 
+    grid [frame .zoom.b] -row 4 -column 1 -columnspan 3
+    grid [button .zoom.b.1 -text "Set Scaling" \
+             -command "SetManualZoom set"]  -row 4 -column 1 -columnspan 2
+    grid [button .zoom.b.2 -text Reset \
+            -command "SetManualZoom clear"] -row 4 -column 3
+    grid [button .zoom.b.3 -text Close -command "destroy .zoom"] -row 4 -column 4 
+    grid rowconfigure .zoom 1 -weight 1 -pad 5
+    grid rowconfigure .zoom 2 -weight 1 -pad 5
+    grid rowconfigure .zoom 3 -weight 1 -pad 5
+    grid rowconfigure .zoom 4 -weight 0 -pad 5
+    grid columnconfigure .zoom 1 -weight 1 -pad 20
+    grid columnconfigure .zoom 1 -weight 1 
+    grid columnconfigure .zoom 3 -weight 1 -pad 10
+    foreach item {min min max max} \
+            format {3   2   3   2} \
+            axis   {x   y   x   y} {
+        set val [$box ${axis}axis cget -${item}]
+        set graph(${axis}${item}) {(auto)}
+        catch {set graph(${axis}${item}) [format %.${format}f $val]}
+    }
+    bind .zoom <Return> "SetManualZoom set"
+}
+
+proc SetManualZoom {mode} {
+    global graph box
+    if {$mode == "clear"} {
+        foreach item {xmin ymin xmax ymax} {
+            set graph($item) {(auto)}
+        }
+    }
+    foreach item {xmin ymin xmax ymax} {
+        if {[catch {expr $graph($item)}]} {
+            set $item ""
+        } else {
+            set $item $graph($item)
+        }
+    }
+    # reset the zoomstack
+    catch {Blt_ZoomStack $box}
+    catch {$box xaxis config -min $xmin -max $xmax}
+    catch {$box yaxis config -min $ymin -max $ymax}
+    #global program
+    #if {$program == "bkgedit"} {bkgEditMode ""}
+}
+
 #-------------------------------------------------------------------------
 # export current plot to Grace
@@ -1242 +1318 @@
         -variable graph(plotunits) \
         -command "plotdata $box"
+.a.options.menu add radiobutton -label "delta-d/d" -value deltad \
+        -variable graph(plotunits) \
+        -command "plotdata $box"
 .a.options.menu add checkbutton -label "Include legend" \
         -variable graph(legend) \
@@ -1274 +1353 @@
 #----------------------------------------------------------------
 
-    trace variable newmenu(opt) w setoptmsg
+trace variable newmenu(opt) w setoptmsg
+
+bind . <Key-z> {BLTmanualZoom}
+bind . <Key-Z> {BLTmanualZoom}
 
 proc setoptmsg {args} {