UserAni 0.91 - VMD Easy User Defined Movie Animation System

AUTHOR: Norman Geist, Greifswald 2014 (

REQUIREMENTS: tested with VMD 1.9.2, 1.9.2a35, 1.9.2b1


  VMD offers the Extension->Visualization:Movie Maker where one can select "user defined procedure". To actually use this feature
  one would need to write a procedure to be called on trace of the variable "$::MovieMaker::userframe". As it requires a lot
  of scripting effort to write detailed and reusable animation procedures in that way, 
  especially if multiple things should happen in parallel, I developed this easy to use and to extend automatic animation system.
  With this system its possible to create animated movies without real experience in TCL programming, as long
  as one can stay with the animations already implemented. Creating new, own animation procedures is also quite 
  easy, as a smart skeleton can be used.

  General system keynotes :
    - The user plans to play across all frames loaded while performing different animations, a step is possible.
    - The user is supposed to write his animation story board to a file to be sourced to VMD console (or better TK Console).
    - The number of frames (top mol) and the trajectory step size set in the Movie Maker window
      control the movie duration. (Changes to the MovieMaker trj step or the top mol requires redefining the time sections,
      which mean re-source the animation script)
    - The user creates a timeline using time sections. The user then adds animations to this timeline.
      The animation system will care about when to call which animation procedure automatically, internally,
      after "Make Movie" has been clicked.
      Two types of animations are possible:
	1. Specially prepared "userani" procedures, useful whereever progressive threatment among frames is required,
	   they are used with "add_userani".
	2. Any TCL or VMD command. Use "VMD Main->File->Log TCL commands to console" to get commands for
	   things while doing them by hand. They are added with "add_eval".

  For now the most useful features of this system are: 

	- Animated Auto-Zoom
	- Animated Auto-Center
	- Material Transparency Fading
	- Material Property Fading
	- Rotations real and graphically
	- Graphical representation of the animation story board
	- Unlimited parallel actions

    #include the animation system (should be the 1st line)
    source userani.tcl

    #example for resets on start
    add_section kickoff -start first; 		#no end means 1 frame
    add_eval kickoff display resetview; 	#reset view on frame 0

    #some action
    add_section rotx -after kickoff -shiftend 10%;	#no end means 1 frame + 10%
    add_userani rotx AutoFocusAllVisible;		#Apply auto centering
    add_userani rotx AutoScaleAllVisible;		#Apply auto zoom
    add_userani rotx rotate x 360;			#rotate x by 360 degrees during section rotx

    add_section zoomout -after rotx -shiftend 10%;
    add_userani zoomout FadeZoomFromCurrent 0.5;	#fade out zoom to half the current start value

    add_section end -after zoomout -end last -noplay;	#until end not playing trj
    add_userani end rotate x 360;
    add_userani end rotate y -360;
    add_userani end rotate z 180;

    #output settings on source
    print_timeline 1.2

  Source to vmd after having a system loaded. Then in Movie Maker click "Make Movie" and see the magic happen.


  add_section secname [-start start] [-end end] [-step step] \
		      [-shiftstart shift] [-shiftend shift] [-shiftall shift] \
		      [-like sectionname] || [-after sectionname] [-noplay]
    special keywords: first,last, n% where n can be any decimal number
    defaults for ungiven values: start = 0; step = trjstep; end = start+step (same happens if a value equals "-1")
	  -start start		- Define the starting time of the section.
	  -end end		- Define the end time of the section.
	  -step step		- Define the step within the time section.
	  -like secname		- Copy start,step and end value from given secname.
	  -after secname	- Copy end value as own start from given secname.
	  -shiftstart shift	- Add a value of shift to the start value.
	  -shiftend shift	- Add a value of shift to the end value.
	  -shiftall shift	- Add a value of shift to both start and end.
	  -noplay		- Trajectory will not play (if section has an action)
  Used to create a timeline, departing the trajectory into time sections. This sections can overlap as you like,
  to perform parallel actions. Sections can easily be based on each other, making it easy to start one section,
  after another specific section has finished. Order of options is important. Its for example possible to
  use -like and change any value afterwards again f.i. by using one of the -shift* options.

  expr% expression - To make it easier calculating with "n%" values, a little wrapper function "expr%" is available, 
		     ignoring the "%" signs. Using the classical modulo operator of course isn't therefore possible with it.

  add_userani secname functionname args - Add a userani_* animation to the story. The functionname is prepended with "userani_".
  add_eval secname tclcommand		- Just add any TCL command to the story.
  print_story				- Output a list of animation actions added.
  print_sections			- Output a list of time sections defined.
  print_timeline scalefactor		- Output a graphical representation of the defined time sections. (very useful)

  Current userani_* list:

  FadeTransparency material startvalue endvalue	- Fade the Opacity value of a given material from startvalue to endvalue.
  FadeMaterialProperty material property startvalue endvalue - Fade the Property value of a given material from startvalue to endvalue.
  FadeZoom startvalue endvalue			- Fade the scale (zoom) from startvalue to endvalue.
  FadeZoomFromCurrent factor			- Fade the scale (zoom) from the current value by a factor.
  FadeOutTranslate *				- Fade the global graphical translation offset to zero.
  rotate x|y|z degrees				- Animated rotatation around a axis (x|y|z) for a specific angle degrees.
						  (as this rotations are global, simultanous rotations around different
						  axes by f.i. 360 will not recover the correct starting orientation,
						  as the axes around which are rotated do also change)
  rotatemol molid x|y|z degrees			- Animated (real) rotation around a axis (x|y|z) for a specific angle degrees.
  movemol molid x|y|z degrees			- Animated (real) translation by {x y z}.
  AutoFocusAllVisible *				- Automatically translate the view graphically so that the COM of all
					  	  visible (displayed molecules and representation) is in the middle
					  	  of the graphics window.
  AutoFocusMolidsVisible {molid molid} *	- Automatically translate the view graphically so that the COM of all
						  visible in selected molids is in the middle
						  of the graphics window.
  AutoFocusMolRepVisible molid repid *		- Automatically translate the view graphically so that the COM of all
						  visible in selected molid and repid is in the middle
						  of the graphics window.
  AutoScaleAllVisible [scalefactor] *		- Automatically apply a zoom factor so that all visible 
						  (displayed molecules and representation) is inside the viewport.
  AutoScaleMolidsVisible {molid molid} [scalefactor] *	- Automatically apply a zoom factor so that all visible 
							  in selected molids is inside the viewport.
  AutoScaleMolRepVisible molid repid [scalefactor] *	- Automatically apply a zoom factor so that all visible in selected molid
							  and repid is inside the viewport.
  raster_replicas shiftX shiftY			- Animate rastering of REMD replicas from aligned bunch.

  ( * This functions knowingly don't scale among the whole time range given, building
    a compromise between "smooth animation" and "keeping" the focus/zoom suitable while playing the trj )

  Current other list:

  raster_replicas shiftX shiftY	- Non animated rastering of REMD replicas from aligned bunch.
  dummy				- Dummy function. Can be used for -noplay sections which must have
				  an action in order to take effect.
  TransparencyStalker		- A nice helper function that will automatically disables
				  representations that are fully transparent and re-enables
				  them if they get visible again. This is useful to save time
				  while not passing thing to the renderer that aren't visible at all.


  Can I start sectionB 10% after sectionA?
    add_section sectionB -after sectionA -shiftstart 10%

  Can I start sectionB 10 frames before sectionA?
    add_section sectionB -like sectionA -shiftstart -10

  Can I visualize the arrangement and order of my time sections?

  How can I influence the width of print_timeline?
    print_timeline 0.7
    print_timeline 2.2

  Can I use TCL scripting to generate complex animations? (see exampleREMD.*)
    #fly and zoom from replica to replica among the raster
    set start 15%
    set each 4%
    set each2 2%
    for {set i 0} {$i < $num_replicas} {incr i} {
      if {$i == 0} {
	add_section focus${i} -start $start -end [expr% $start+$each]
	add_section autoscale${i} -like focus${i} -end [expr% $start+$each2]
	add_section zoomout${i} -like autoscale${i} -shiftall $each2
      } else {
	add_section focus${i} -like focus[expr $i-1] -shiftall $each
	add_section autoscale${i} -like autoscale[expr $i-1] -shiftall $each
	add_section zoomout${i} -like zoomout[expr $i-1] -shiftall $each 
      if {$i < [expr $num_replicas -1]} {
	add_userani zoomout${i} FadeZoomFromCurrent 0.5
      add_userani focus${i} AutoFocusMolidsVisible $i
      add_userani autoscale${i} AutoScaleMolidsVisible $i

  How can I invert $prog so it's running from 1 to 0?
    set prog [expr abs($prog-1)]

  How will trajectory step size in Movie Maker come together with section step?
    Both get multiplied to result in the overall section step.

  If a section ends at frame X and another starts at frame X, will they interfere?
    No. Sections are treated as: start >= now < end.

  Why one can use n% values for frames?
    Making animation scripts reusable for different simulations and easier to edit/adapt.

  I choosed a section as -noplay but it is still playing.
    Check if the section has an action, actually. (use f.i. add_eval secname dummy for fake action) 
    Check if there are playing sections in the same time range.

  How can I realize a slow playing of my trajectory while keeping animations smooth?
    Simply define a noplay and a playing section for the same time range. Now select a step for
    the playing section. Example:
      add_section smoothrot -start first -end last -noplay
      add_section slowplay -like slow -step 10%
      add_userani smoothrot rotate y 360
      add_eval slowplay dummy()
    This will cause a smooth rotation with jumping frame changes.

  Can I let several parts of my system slowly appear and disappear?
    Just create representations with different materials and use "FadeTransparency".
    For appearings, you need to hide the representation before, of course, usually from a kickoff section.
    (f.i. add_eval kickoff material change opacity Glossy 0.)
  I have periodically shown representations and Auto*AllVisible* doesn seem to care?
    Sorry, this has't been implemented, yet. If enough people complain I might do it.

  How can I influence the zoom which is applied by the AutoScale* functions?
    Usually the automatically applied zoom is quite nice. But you can control the zoom
    by using the optional parameter zoomfactor. A value of 0.5 f.i. will cause
    half of the default zoom to be used, so you are twice as far away.



To write your own animation procedures, you just need to understand the
principle of the smart skeleton below. A value of $prog (0 > prog <= 1) and $part (1/sectionframes)
is automatically passed to such functions as arguments. This values indicate either the progress of
the time section or a constant step. Both can be used to scale any parameter to do f.i. fading or
animated rotating for exact degrees across multiple steps, without
any need to care about frames and frame ranges etc. Whenever the threatment of previous calls
to a userani_* function persists (like global rotation, translation, scale, or noplay modifications
via atomselect) use $part, otherwise $prog is of choice.
It might be necessary to have both variants implemented decided by $play (see userani_rotatemol,
userani_raster_replicas) as time sections can be set -noplay, means the coordinate frame
won't change. You will find your additional arguments in $funcargs.

  proc userani_skeleton { args } {
    set id [lindex $args 0]
    set prog [lindex $args 1]
    set part [lindex $args 2]
    set play [lindex $args 3]
    set funcargs [lindex $args 4]
    set me [lindex [info level [info level]] 0]
    if {[llength $funcargs] != 2} {error "$me:improper number of arguments:should be whatever!"}


Example for $prog use:
  # args: material startvalue endvalue
  proc userani_FadeTransparency { args } {
    set id [lindex $args 0]
    set prog [lindex $args 1]
    set part [lindex $args 2]
    set play [lindex $args 3]
    set funcargs [lindex $args 4]
    set me [lindex [info level [info level]] 0]
    if {[llength $funcargs] != 3} {error "$me:improper number of arguments:should be material startval endval!"}
    set val [expr [lindex $funcargs 1] + ($prog * ([lindex $funcargs 2] - [lindex $funcargs 1]))]
    set mat [lindex $funcargs 0]
    eval "material change opacity $mat $val"

Example for $part use:
  #args: axis degrees
  proc userani_rotate { args } {
    set id [lindex $args 0]
    set prog [lindex $args 1]
    set part [lindex $args 2]
    set play [lindex $args 3]
    set funcargs [lindex $args 4]
    set me [lindex [info level [info level]] 0]
    if {[llength $funcargs] != 2} {error "$me:improper number of arguments:should be \[x|y|z\] degrees!"}

    set val [expr $part * [lindex $funcargs 1] ]
    eval "rotate [lindex $funcargs 0] by $val"

Example for both used, decided by $play:
  #args: molid axis degrees
  proc userani_rotatemol { args } {
    set id [lindex $args 0]
    set prog [lindex $args 1]
    set part [lindex $args 2]
    set play [lindex $args 3]
    set funcargs [lindex $args 4]
    set me [lindex [info level [info level]] 0]
    if {[llength $funcargs] != 3} {error "$me:improper number of arguments:should be molid \[x|y|z\] degrees!"}

    set molid [lindex $funcargs 0]
    set axis [lindex $funcargs 1]
    set degrees [lindex $funcargs 2]
    set sel [atomselect $molid "all"]

    if {[$sel num] > 0} {
      set val [expr $play == 1 ? $prog * $degrees : $part * $degrees ]
      set center [measure center $sel]
      set tran [trans center $center axis $axis $val ]
      $sel move $tran
      $sel delete
    } else {error "$me: ups, selection was empty, does molid exist!?"}