Dashboard improvements

vmd/cv_dashboard/VERSION

@@ -1 +1 @@
-2024-02-17
+2024-12-12

vmd/cv_dashboard/cv_dashboard.tcl

@@ -4,15 +4,17 @@
 # Usage (after installing):
 # package require cv_dashboard
 # cv_dashboard
+# or select the Extensions/Analysis menu item
 
 # Design principles:
 # - take advantage of colvars/VMD binding for maximum user interaction
 # - hide the colvars config text from user, instead expose colvar, names and values
 # - do not try to parse the colvars config (let the Colvars Module do it)
 #   to avoid coming up with an incompatible parser
 
-# This plugin only acts on the "top" molecule
-# which is most consistent for trajectory animation (determined by the frame number of mol)
+# Source file layout:
+# - this file contains utility functions and data structure, without GUI
+# - other files contain GUI elements
 
 # TODO Multiplot:
 # - properly calculate position of cursor in plot when not all the plot is visible (resized window)
@@ -130,8 +132,8 @@ Please upgrade to VMD 1.9.4 alpha or later."
   if { [vecdist $abc {1 1 1}] < 1e-10 } {
       set answer [tk_messageBox -icon warning -type okcancel -title "Warning: unlikely periodic box lengths"\
         -message "The periodic box lengths are (1, 1, 1), which can be the output of a\
- non-periodic simulation in NAMD. Overwrite with (0, 0, 0) to make Colvars detect as non-periodic?
- The command line is:
+ non-periodic simulation in NAMD. Overwrite with (0, 0, 0) to signal a non-periodic system?
+ This will run the following commands:
  package require pbctools
  pbc set {0 0 0} -all -molid $::cv_dashboard::mol"]
       if { $answer == "ok" } {
@@ -954,7 +956,8 @@ Read the standard output (terminal) for details."
 }
 
 
-#  Create a scripted colvar that returns values from a precomputed trajectory
+# Create a scripted colvar that returns values from a precomputed trajectory
+# (internal utility function for load_cv_traj, hence not in the main namespace)
 
 proc create_traj_colvar { molid cv } {
 
@@ -1010,3 +1013,20 @@ proc create_traj_colvar { molid cv } {
   "
   cv config $configString
 }
+
+# Save trajectory of currently defined colvars to a file in the colvars.traj format
+
+proc ::cv_dashboard::save_traj_file { fileName } {
+
+  puts "Writing colvars trajectory to file $fileName"
+  set o [open $fileName w]
+  puts -nonewline $o [cv printframelabels]
+
+  set nf [molinfo top get numframes]
+  for {set f 0} {$f< $nf} {incr f} {
+    cv frame $f
+    cv update
+    puts -nonewline $o [cv printframe]
+  }
+  close $o
+}

vmd/cv_dashboard/cv_dashboard_main.tcl

@@ -33,7 +33,7 @@ proc ::cv_dashboard::createWindow {} {
     -row $gridrow -column 0 -pady 2 -padx 2 -sticky nsew
   grid [ttk::button $w.save -text "Save" -command ::cv_dashboard::save -padding "2 0 2 0"] \
     -row $gridrow -column 1 -pady 2 -padx 2 -sticky nsew
-  grid [ttk::button $w.reset -text "Reset" -command ::cv_dashboard::reset -padding "2 0 2 0"] \
+  grid [ttk::button $w.reset -text "⚠ Reset ⚠" -command ::cv_dashboard::reset -padding "2 0 2 0"] \
     -row $gridrow -column 2 -pady 2 -padx 2 -sticky nsew
 
   # Table of colvars
@@ -100,7 +100,10 @@ proc ::cv_dashboard::createWindow {} {
   grid [ttk::button $main.del -text "Delete" -command ::cv_dashboard::del_cv -padding "2 0 2 0"] \
     -row $gridrow -column 2 -pady 2 -padx 2 -sticky nsew
   incr gridrow
-  grid [ttk::button $main.refresh -text "Refresh list \[F5\]" -command ::cv_dashboard::refresh_table -padding "2 0 2 0"] -row $gridrow -column 0 -columnspan 3 -pady 2 -padx 2 -sticky nsew
+  grid [ttk::button $main.refresh -text "Refresh list \[F5\]" -command ::cv_dashboard::refresh_table -padding "2 0 2 0"]  \
+    -row $gridrow -column 0 -columnspan 2 -pady 2 -padx 2 -sticky nsew
+  grid [ttk::button $main.save_traj -text "Save traj file" -command ::cv_dashboard::save_traj_dialog -padding "2 0 2 0"] \
+    -row $gridrow -column 2 -pady 2 -padx 2 -sticky nsew
 
   # Plots
   incr gridrow
@@ -516,7 +519,7 @@ https://colvars.github.io
 In [vmdinfo versionmsg]
 Running Tcl/Tk [info patchlevel]
 
-Jérôme Hénin (jerome.henin@ibpc.fr), Giacomo Fiorin (giacomo.fiorin@nih.gov) and the Colvars developers.
+Jérôme Hénin (jerome.henin@cnrs.fr), Giacomo Fiorin (giacomo.fiorin@nih.gov) and the Colvars developers.
 
 #Please cite the following references for features currently in use:
 
@@ -1488,3 +1491,13 @@ proc ::cv_dashboard::createRotationMenu { row } {
 
   grid remove $menu.show_rotation $menu.hide_rotation
 }
+
+# Open file dialog to choose file name, then save colvars trajectory
+
+proc ::cv_dashboard::save_traj_dialog {} {
+  set file [tk_getSaveFile -title "Colvars trajectory file to be written" \
+      -filetypes {{"Colvars traj" .colvars.traj} {"All files" *}}]
+  if {[llength $file] > 0 } {
+    ::cv_dashboard::save_traj_file $file
+  }
+}

vmd/cv_dashboard/cv_dashboard_plots.tcl

@@ -85,6 +85,20 @@ proc ::cv_dashboard::plot { { type timeline } } {
     set plothandle [multiplot -title {Colvars trajectory   [click on markers, keyb arrows (+ Shift/Ctrl) to navigate]} \
     -xlabel $xname -ylabel $yname -nostats -marker circle -fill white -radius 4 -callback ::cv_dashboard::marker_clicked]
     $plothandle add $y($xname) $y($yname)
+
+    # Add custom Colvars menu item to Multiplot window
+    set plot_ns [$plothandle namespace]
+    set menubar "[set ${plot_ns}::w].menubar"
+    menubutton $menubar.colvars -text "Colvars" -underline 0 -menu $menubar.colvars.menu
+    menu $menubar.colvars.menu -tearoff 0
+    $menubar.colvars.menu add command -label "Swap axes" -command ::cv_dashboard::pairwise_swap_axes
+    $menubar.colvars.menu add command -label "Turn lines off" -command "::cv_dashboard::display_lines false"
+    $menubar.colvars.menu add command -label "Turn lines on" -command "::cv_dashboard::display_lines true"
+    # Add item to existing menu bar
+    set col [lindex [grid size $menubar] 0]
+    grid $menubar.colvars -row 0 -column $col -sticky nsw
+    grid columnconfigure $menubar $col -weight 2
+
   } elseif { $type == "histogram"} {
     set xname [lindex $name_list 0]
     # Save list of values for navigating
@@ -112,7 +126,6 @@ proc ::cv_dashboard::plot { { type timeline } } {
       -xlabel $xname -ylabel "N" -nostats -xmin $xmin -xmax $xmax \
       -ymin 0.0 -x $centers -y $frequencies -nolines -plot]
 
-    set ns [namespace qualifiers $plothandle]
     # force bars to start at zero
     set ymin 0.0
 
@@ -251,13 +264,13 @@ proc ::cv_dashboard::plot_bias_energy { } {
 # Callback for click inside plot window, at coords x y
 proc ::cv_dashboard::plot_clicked { x y } {
 
-  set ns [$::cv_dashboard::plothandle namespace]
-  set xplotmin [set ${ns}::xplotmin]
-  set xplotmax [set ${ns}::xplotmax]
-  set yplotmin [set ${ns}::yplotmin]
-  set yplotmax [set ${ns}::yplotmax]
-  set scalex [set ${ns}::scalex]
-  set xmin [set ${ns}::xmin]
+  set plot_ns [$::cv_dashboard::plothandle namespace]
+  set xplotmin [set ${plot_ns}::xplotmin]
+  set xplotmax [set ${plot_ns}::xplotmax]
+  set yplotmin [set ${plot_ns}::yplotmin]
+  set yplotmax [set ${plot_ns}::yplotmax]
+  set scalex [set ${plot_ns}::scalex]
+  set xmin [set ${plot_ns}::xmin]
 
   # note: ymax < ymin because of pixel coordinate convention
   if { [expr {($x < $xplotmin) || ($x > $xplotmax) || ($y > $yplotmin) || ($y < $yplotmax)}] } {
@@ -330,9 +343,9 @@ proc ::cv_dashboard::chg_frame { shift { order "traj" } } {
 proc ::cv_dashboard::zoom { factor } {
   variable ::cv_dashboard::plothandle
 
-  set ns [namespace qualifiers $plothandle]
-  set xmin [set ${ns}::xmin]
-  set xmax [set ${ns}::xmax]
+  set plot_ns [$plothandle namespace]
+  set xmin [set ${plot_ns}::xmin]
+  set xmax [set ${plot_ns}::xmax]
 
   set f $::cv_dashboard::current_frame
   # rescale current half-width
@@ -357,9 +370,9 @@ proc ::cv_dashboard::zoom { factor } {
 proc ::cv_dashboard::fit_vertically {} {
   variable ::cv_dashboard::plothandle
 
-  set ns [namespace qualifiers $plothandle]
-  set xmin [set ${ns}::xmin]
-  set xmax [set ${ns}::xmax]
+  set plot_ns [$plothandle namespace]
+  set xmin [set ${plot_ns}::xmin]
+  set xmax [set ${plot_ns}::xmax]
   set ydata [$plothandle ydata]
   set ymin [lindex [lindex $ydata 0] $xmin]
   set ymax $ymin
@@ -399,11 +412,11 @@ proc ::cv_dashboard::display_marker { f } {
       # we tinker a little with Multiplot's internals to get access to its Tk canvas
       # necessary because Multiplot does not expose an interface to draw & delete
       # objects without redrawing the whole plot - which takes too long for this
-      set ns [namespace qualifiers $plothandle]
+      set plot_ns [$plothandle namespace]
       if { $::cv_dashboard::plottype == "timeline" } {
 
-        set xmin [set ${ns}::xmin]
-        set xmax [set ${ns}::xmax]
+        set xmin [set ${plot_ns}::xmin]
+        set xmax [set ${plot_ns}::xmax]
         # Move plot boundaries if necessary
         if { $f < $xmin } {
           set xmax [expr { $xmax + $f - $xmin }]
@@ -416,49 +429,49 @@ proc ::cv_dashboard::display_marker { f } {
           $plothandle configure -xmin $xmin -xmax $xmax -plot
         }
 
-        set y1 [set ${ns}::yplotmin]
-        set y2 [set ${ns}::yplotmax]
-        set xplotmin [set ${ns}::xplotmin]
-        set scalex [set ${ns}::scalex]
+        set y1 [set ${plot_ns}::yplotmin]
+        set y2 [set ${plot_ns}::yplotmax]
+        set xplotmin [set ${plot_ns}::xplotmin]
+        set scalex [set ${plot_ns}::scalex]
         set x [expr $xplotmin+($scalex*($f-$xmin))]
 
-        set canv "[set ${ns}::w].f.cf"
+        set canv "[set ${plot_ns}::w].f.cf"
         $canv delete frame_marker
         $canv create line  $x $y1 $x $y2 -fill $timeline_color -tags frame_marker
       } elseif { $::cv_dashboard::plottype == "2cv" } {
         set x [lindex [ lindex [$plothandle xdata] 0] $f]
         set y [lindex [ lindex [$plothandle ydata] 0] $f]
 
-        set xmin [set ${ns}::xmin]
-        set ymin [set ${ns}::ymin]
+        set xmin [set ${plot_ns}::xmin]
+        set ymin [set ${plot_ns}::ymin]
 
         set radius 5
-        set xplotmin [set ${ns}::xplotmin]
-        set scalex [set ${ns}::scalex]
+        set xplotmin [set ${plot_ns}::xplotmin]
+        set scalex [set ${plot_ns}::scalex]
         set x1 [expr {$xplotmin+$scalex*($x-$xmin) - $radius}]
         set x2 [expr {$xplotmin+$scalex*($x-$xmin) + $radius}]
 
-        set yplotmin [set ${ns}::yplotmin]
-        set scaley [set ${ns}::scaley]
+        set yplotmin [set ${plot_ns}::yplotmin]
+        set scaley [set ${plot_ns}::scaley]
         set y1 [expr {$yplotmin+$scaley*($y-$ymin) - $radius}]
         set y2 [expr {$yplotmin+$scaley*($y-$ymin) + $radius}]
 
-        set canv "[set ${ns}::w].f.cf"
+        set canv "[set ${plot_ns}::w].f.cf"
         $canv delete frame_marker
         $canv create oval $x1 $y1 $x2 $y2 -outline white -fill $2cv_color -tags frame_marker
       } elseif { $::cv_dashboard::plottype == "histogram" } {
-        set xmin [set ${ns}::xmin]
-        set xmax [set ${ns}::xmax]
+        set xmin [set ${plot_ns}::xmin]
+        set xmax [set ${plot_ns}::xmax]
 
-        set y1 [set ${ns}::yplotmin]
-        set y2 [set ${ns}::yplotmax]
+        set y1 [set ${plot_ns}::yplotmin]
+        set y2 [set ${plot_ns}::yplotmax]
         set v [lindex $cv_dashboard::histogram_time_series $f]
 
-        set xplotmin [set ${ns}::xplotmin]
-        set scalex [set ${ns}::scalex]
+        set xplotmin [set ${plot_ns}::xplotmin]
+        set scalex [set ${plot_ns}::scalex]
         set x [expr $xplotmin+($scalex*($v-$xmin))]
 
-        set canv "[set ${ns}::w].f.cf"
+        set canv "[set ${plot_ns}::w].f.cf"
         $canv delete frame_marker
         $canv create line  $x $y1 $x $y2 -fill $histogram_color -tags frame_marker
       }
@@ -519,3 +532,31 @@ proc ::cv_dashboard::simplify x {
   set x [expr round($x / $factor) * $factor]
   return $x
 }
+
+
+proc ::cv_dashboard::pairwise_swap_axes {} {
+
+  variable ::cv_dashboard::plothandle
+  set plot_ns [$plothandle namespace]
+
+  set x [$plothandle xdata]
+  set y [$plothandle ydata]
+  set xlabel [set ${plot_ns}::xlabeltext]
+  set ylabel [set ${plot_ns}::ylabeltext]
+
+  $plothandle clear
+  $plothandle add $y $x -xlabel $ylabel -ylabel $xlabel -plot
+}
+
+
+proc ::cv_dashboard::display_lines { yesno } {
+
+  variable ::cv_dashboard::plothandle
+  if $yesno {
+    set param "-lines"
+  } else {
+    set param "-nolines"
+  }
+
+  $plothandle configure $param -plot
+}

vmd/cv_dashboard/templates/bias.colvars

@@ -101,18 +101,19 @@ harmonicWalls {
     outputEnergy   yes
     outputAccumulatedWork yes
 }
-#_harmonic walls with changing force constant
+#_harmonic wall with changing force constant: RFEP
+# (Restraint Free Energy Perturbation)
 harmonicWalls {
-    colvars        <names>
+    colvars         <names>
 
-    lowerWalls     0.1
-    upperWalls     0.2
-    forceConstant  10.0
+    upperWalls      10.0
+    forceConstant   200.0
 
-    targetForceconstant 0.0001
-    targetNumSteps 10
-    outputEnergy   yes
-    outputAccumulatedWork yes
+    decoupling      yes
+    lambdaExponent  4     # Nonlinear scaling of the force constant
+    targetNumSteps  10000
+    targetNumStages 40
+    outputEnergy    yes
 }
 #_histogram
 histogram {

vmd/scripts/calc_cv_mass.tcl

@@ -1,3 +1,8 @@
+# Compute the reduced mass of a collective variable
+# and write its trajectory to a file
+
+# M = (\nabla xi m^-1 \nabla_xi)^-1
+# where m is the diagonal matrix of Cartesian coordinate (ie atom) masses
 
 proc cv_mass_traj { cv filename } {