lammps/tools/eff/h2.vmd

# module radii.vmd
# December, 2009 -(c)- Andres Jaramillo-Botero
# Script to load variable changing radii onto a pEFF lammpstrj file

# radii.vmd --
#    Script to read and change electron radii in vmd dynamics traj
#
 
# openFile --
#    Open the file and start looking for data
#
# Arguments:
#    filename    Name of the file to read
#
# Result:
#    infile      Handle to the opened file
#
# Side effects:
#    A file in question is opened. Lines containing a * or# as
#    the first non-blank character are considered comments. The
#    first line without this is considered to be a line with the
#    names of the columns.
#
proc openFile {filename} {
    set infile [open $filename "r"]
    return $infile
}

# readNames --
#    Read the names of the columns
#
# Arguments:
#    infile      Handle to the file
#
# Result:
#    names       List of names, the number indicates the number of
#                the snapshot frame
#
proc readNames {infile} {
  #
  # Skip the header - if any
  #
    set pos    0
    while { [gets $infile line] >= 0 } {
       if { [regexp {[ \t]*[*#]} $line] } {
          incr pos
       } else {
          break
       }
    }
    seek $infile 0 start
    while { $pos > 0 } {
       gets $infile line
       incr pos -1
    }

  #
  # Read the line with the column names
  #
    gets $infile line

  # Force the line to be interpreted as a list
    set nocols [llength $line]

    return $line
}

# readData --
#    Read the data per line
#
# Arguments:
#    infile      Handle to the file
#
# Result:
#    values      List of values, representing each column.
#                A list of length zero indicates the end of file
#
proc readData {infile} {
    while { [gets $infile values] == 0 } { ;# Just go on - skip empty lines }

    set nocols [llength $values]

    return $values
}

# readFile --
#    Read the file and store the data in a (global) array
#
# Arguments:
#    filename    Name of the file
#
# Result:
#    None
#
# Side effects:
#    Filled array, ready for display
#
proc readFile {filename} {
    global data_array

    set infile [openFile $filename]

    set data_array(names) [readNames $infile]
    set i 0
    foreach name $data_array(names) {
       set data_array($i) {}
       incr i
    }

    while 1 {
       set values [readData $infile]
       if { [llength $values] > 0 } {
          set i 0
          foreach value $values {
             lappend data_array($i) $value
             incr i
          }
       } else {
          break
       }
    }
}

# makeXYData --
#    Make a list useable by frame-electron
#
# Arguments:
#    xindex     Index of frame data
#    yindex     Index of electron data
#
# Result:
#    None
#
# Side effects:
#    A dataset for changing the electron radii, per trajectory frame
#
proc makeXYData {xindex yindex} {
    global data_array

    set xydata {}
    foreach x $data_array($xindex) y $data_array($yindex) {
        lappend xydata $x $y
    }
    return $xydata
}

proc returnXYPair {x y} {
   global data_array

   return [list $data_array($x) $data_array($y)]
}

# do_radii --
#    Changes the radii of electrons per trajectory frame
#
# Arguments:
#    xindex     Index of frame data
#    yindex     Index of electron data
#
# Result:
#    prints the frame:atomID:radius
#
proc do_radii {args} {
  global molid data_array

  #set n [molinfo $molid get numatoms]
  set f [molinfo $molid get frame]
 
  set fr [expr {$f+1}]

  foreach elec $data_array(0) r $data_array($fr) {
    set s [atomselect $molid "index [expr {$elec -1}]"]
    #set nr [expr {exp($r)}]
    set nr $r
    $s set radius $nr
    $s delete
    #puts stderr "$fr $elec $nr"
  }
}

# main --
#    Main control flow
#

# Check input arguments
#for {set i 0} {$i<[llength $argv]} {incr i}
#  puts " - $i: [lindex $argv $i]"

global data_array molid

# Set input files manually
set xyz h2.xyz
set data h2.out

# switch default rep to VDW.
mol default style VDW

# load nuclear and electron xyz trajectory 
#set xyz [lindex $::argv 0]

# load electron radii information for trajectory
#set datafile [lindex $::argv 1]

set molid [mol new $xyz waitfor all]
mol modstyle 0 [molinfo top] VDW 1.0 32.0

puts "Starting ..."
readFile $data
puts "Read datafile and created array of radii ..."

puts "Visualize trajectory" 
trace variable vmd_frame($molid) w do_radii
animate goto start
do_radii