Changeset 1173

Timestamp:

Sep 27, 2011 11:35:12 AM (9 years ago)

Author:

toby

Message:

fix RB where atoms are missing in sequence; turn of X flag when atoms are added to a RB; put 'r' on RB atoms in listbox; doc 'r'

Location:

branches/sandbox

Files:

• doc/expgui6A.html (modified) (1 diff)
• expgui (modified) (1 diff)
• readexp.tcl (modified) (2 diffs)
• rigid.tcl (modified) (8 diffs)

branches/sandbox/doc/expgui6A.html

@@ -355 +355 @@
  These flags were set automatically when
 the rigid body position parameter were set to be refined. If these flags are
-turned off, it is likely that GENLES will crash. 
-
+turned off, it is likely that GENLES will crash. Note that atoms in a
+  rigid body are now tagged with the letter "r" in the atom listings.
   </DL></DL>
 <hr>

branches/sandbox/expgui

@@ -1333 +1333 @@
 }
 
-# format a coordinate from a non-mm phase as 10 chars; mark fixed coordinates differently
+# format a coordinate from a non-mm phase as 10 chars; mark fixed 
+# and Rigid body 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 {
+    # is this fixed?
+    set param [string toupper $var]
+    if {[array name ::fix_param "$phase,$atom,$param"] != ""} {
+        return [format "%9.5fF" [atominfo $phase $atom $var]]
+    }
+    # is this atom in a rigid body?
+    if {[lsearch $::expmap(rbatoms_$phase) $atom] != -1} {
+        return [format "%9.5fr" [atominfo $phase $atom $var]]
+    }
     return [format "%10.6f" [atominfo $phase $atom $var]]
-  }
 }
 

branches/sandbox/readexp.tcl

@@ -191 +191 @@
     # load the constrained parameters
     atom_constraint_load
+    # construct tables of mapped atoms in rigid bodies
+    foreach phase $::expmap(phaselist) {
+        set expmap(rbatoms_$phase) {}
+        foreach bodnum [RigidBodyList] {
+            set natoms [llength [lindex [lindex [lindex [ReadRigidBody $bodnum] 1] 0] 3]]
+            foreach mapnum [RigidBodyMappingList $phase $bodnum] {
+                set atomnum [lindex [ReadRigidBodyMapping $phase $bodnum $mapnum] 0]
+                set st [lsearch $::expmap(atomlist_$phase) $atomnum]
+                set en [expr {$st+$natoms-1}]
+                set atoms [lrange $::expmap(atomlist_$phase) $st $en]
+                set expmap(rbatoms_$phase) [concat $expmap(rbatoms_$phase) $atoms]
+            }
+        }
+    }
     set expgui(mapstat) 1
 }
@@ -4191 +4205 @@
     makeexprec "${key} LSTF"
     setexp "${key} LSTF" [format "%5d" 0] 1 5
+    # turn off the X refinement flags for the new body
+    set st [lsearch $::expmap(atomlist_$phase) $firstatom]
+    set natoms [llength [lindex [lindex [lindex [ReadRigidBody $bodytyp] 1] 0] 3]]
+    set en [expr {$st+$natoms-1}]
+    set atomlist [lrange $::expmap(atomlist_$phase) $st $en]
+    atominfo $phase $atomlist xref set 0
+    # redo the mapping to capture the newly mapped atoms
+    mapexp
     return $rbnum
 }

branches/sandbox/rigid.tcl

@@ -507 +507 @@
                       set col 11
                       set atomnum $::rb_map_beginning($phase,$bodnum,$mapnum)
-                      for {set coordnum 1} {$coordnum <=$::rb_coord_num($bodnum,1)} {incr coordnum} {
-                          set atom [atominfo $phase $atomnum label]
-                          grid [label $main.rb_site$phase$mapnum$coordnum -text "$atom"] -row $row -column $col -padx 5
-                          incr atomnum
-                          incr col
-                      }
+                 # get a list of the atoms in the RB
+                 set st [lsearch $::expmap(atomlist_$phase) $atomnum]
+                 set en [expr {$st+$::rb_coord_num($bodnum,1)-1}]
+                 set atoms [lrange $::expmap(atomlist_$phase) $st $en]
+                 foreach a $atoms {
+                     set lbl [atominfo $phase $a label]
+                     grid [label $main.rb_site$phase$mapnum$a -text $lbl] -row $row -column $col -padx 5
+                     incr col
+                 }
              }
      incr row
@@ -798 +801 @@
 #   puts "position = $origin"
 #   puts "Euler = $euler"
-   MapRigidBody $::rb_phase $::body_type $::rb_firstatom $origin $euler
-   RecordMacroEntry "MapRigidBody $::rb_phase $::body_type $::rb_firstatom $origin $euler" 0
+    MapRigidBody $::rb_phase $::body_type $::rb_firstatom $origin $euler
+    RecordMacroEntry "MapRigidBody $::rb_phase $::body_type $::rb_firstatom $origin $euler" 0
    incr ::rb_map($::body_type)
-   incr ::expgui(changed)
    set curpage [$::rb_notebook raise]
    $::rb_notebook raise [$::rb_notebook page end]
@@ -881 +883 @@
     grid [label $main.ph -text "Phase"] -row 1 -column 2 -padx 5
     set matrixnum $::rb_matrix_num($bodnum)
+    grid [label $main.rb_sitelbl -text "Site number"] -row 0 -column 3 -columnspan 5 -sticky w
     for {set coordnum 1} {$coordnum <= $::rb_coord_num($bodnum,$matrixnum)} {incr coordnum} {
-        label $main.rb_site$coordnum -text "Site $coordnum"
+        label $main.rb_site$coordnum -text "$coordnum"
         grid $main.rb_site$coordnum -row 1 -column [expr 2 + $coordnum]
     }
@@ -889 +892 @@
         incr row
         foreach coordnum [RigidBodyMappingList $phase $bodnum] {
-                set row [expr $row + $coordnum]
-                RB_Load_Mapdata $phase $bodnum $coordnum
-                checkbutton $main.unmap$phase$coordnum -variable ::rb_unmap($phase,$bodnum,$coordnum)
-                grid $main.unmap$phase$coordnum -row $row -column 0
-                grid [label $main.rb_map$phase$coordnum -text "$coordnum"] -row $row -column 1
-                grid [label $main.rb_cb$phase$coordnum -text $phase] -row $row -column 2
-                      set atomnum $::rb_map_beginning($phase,$bodnum,$coordnum)
-                      set col 3
-                      for {set j 1} {$j <=$::rb_coord_num($bodnum,$matrixnum)} {incr j} {
-                          set atom [atominfo $phase $atomnum label]
-                          grid [label $main.rb_site$phase$coordnum$j -text "$atom"] -row $row -column $col
-                          incr atomnum
-                          incr col
-                      }
-             }
-     incr row
-     }
-     ResizeScrollTable $um
+            set row [expr $row + $coordnum]
+            RB_Load_Mapdata $phase $bodnum $coordnum
+            checkbutton $main.unmap$phase$coordnum -variable ::rb_unmap($phase,$bodnum,$coordnum)
+            grid $main.unmap$phase$coordnum -row $row -column 0
+            grid [label $main.rb_map$phase$coordnum -text "$coordnum"] -row $row -column 1
+            grid [label $main.rb_cb$phase$coordnum -text $phase] -row $row -column 2
+            set atomnum $::rb_map_beginning($phase,$bodnum,$coordnum)
+            # get a list of the atoms in the RB
+            set st [lsearch $::expmap(atomlist_$phase) $atomnum]
+            set en [expr {$st+$::rb_coord_num($bodnum,0)-1}]
+            set atoms [lrange $::expmap(atomlist_$phase) $st $en]
+            set col 3
+            foreach a $atoms {
+                set lbl [atominfo $phase $a label]
+                grid [label $main.rb_site$phase$coordnum$col -text $lbl -padx 3] -row $row -column $col
+                incr col
+            }
+        }
+        incr row
+    }
+    ResizeScrollTable $um
 
      grid [frame $um.update -bd 2 -relief groove] -row 0 -column 1 -pady 10
@@ -1046 +1052 @@
 
 }
-
-
 
 proc RB_Edit_Matrix_Abort {bodnum location} {
@@ -1646 +1650 @@
         set ::rb_coord_num($bodnum,1) $::gcon_atoms
 
-        MapRigidBody $::rb_phase $bodnum $::gcon_start [lindex $temp1 0] [lindex $temp1 1]
-        RecordMacroEntry "MapRigidBody $::rb_phase $bodnum $::gcon_start [lindex $temp1 0] [lindex $temp1 1]" 0
+     MapRigidBody $::rb_phase $bodnum $::gcon_start [lindex $temp1 0] [lindex $temp1 1]
+     RecordMacroEntry "MapRigidBody $::rb_phase $bodnum $::gcon_start [lindex $temp1 0] [lindex $temp1 1]" 0
      incr ::expgui(changed)
      RecordMacroEntry "incr expgui(changed)" 0
@@ -1785 +1789 @@
 #                         puts "first atom = $atomnum"
 #                         set atomlist "atoms in rigid body #$bodnum:    "
-                         set atomlist "atoms in rigid body:    "
-                         for {set j 1} {$j <=$::rb_coord_num($bodnum,1)} {incr j} {
-                             set atom [atominfo $phasenum $atomnum label]
-                             lappend atomlist $atom
-#                            grid [label $main.rb_site$phasenum$mapnum$j -text "$atom"] -row [expr $row +1] -column $col -padx 5
-                             incr atomnum
-#                             incr col
+                         set atomlist {}
+                         # get a list of the atoms in the RB
+                         set st [lsearch $::expmap(atomlist_$phase) $atomnum]
+                         set en [expr {$st+$::rb_coord_num($bodnum,1)-1}]
+                         set atoms [lrange $::expmap(atomlist_$phase) $st $en]
+                         foreach a $atoms {
+                             if {$atomlist != ""} {append atomlist ", "}
+                             set lbl [atominfo $phase $a label]
+                             append atomlist $lbl
                         }
-                        grid [label $main.rb_site$phasenum$bodnum$mapnum -text "$atomlist"] -row [expr $row + 1] -column 4 -padx 5 -columnspan 999 -sticky w
+                        grid [label $main.rb_site$phasenum$bodnum$mapnum \
+                                  -text "atoms in rigid body:    $atomlist"] \
+                             -row [expr $row + 1] -column 4 -padx 5 -columnspan 999 -sticky w
                         incr row 2
                      }
@@ -1923 +1931 @@
 #procedure for enabling refinement flags
 proc RB_Ref_FlagEnable {phasenum bodnum mapnum var val args} {
-          set atomlist ""
-          set atomnum $::rb_map_beginning($phasenum,$bodnum,$mapnum)
-          for {set j 1} {$j <=$::rb_coord_num($bodnum,1)} {incr j} {
-               lappend atomlist $atomnum
-               incr atomnum
-          }
-          atominfo $phasenum $atomlist $var set $val
-
+    set atomnum $::rb_map_beginning($phasenum,$bodnum,$mapnum)
+    # get a list of the atoms in the RB
+    set st [lsearch $::expmap(atomlist_$phase) $atomnum]
+    set en [expr {$st+$::rb_coord_num($bodnum,1)-1}]
+    set atomlist [lrange $::expmap(atomlist_$phase) $st $en]
+    atominfo $phasenum $atomlist $var set $val
  }