Class: Cell

Inherits:
Array show all
Defined in:
lib/cell/cell.rb,
lib/cell/lib/redef.rb,
lib/cell/lib/write.rb,
lib/cell/lib/private.rb,
lib/cell/lib/boundary.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from Array

#numbers!, #numerify!

Constructor Details

#initialize(params = {}) ⇒ Cell

Returns a new instance of Cell.



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# File 'lib/cell/cell.rb', line 9

def initialize params = {}
  add_to_atoms params[:atoms] unless params[:atoms].nil?
  params[:units].lowercase! if params[:units].is_a? String
  @units = params[:units] || :crystal
  @celldm = (@units == :crystal ? [1,1,1] : params[:celldm].dup) rescue @celldm = []
  @realcelldm = (@units == :bohr ? params[:celldm].map{|v| v*0.52918} : params[:celldm]) rescue @realcelldm = []
  @min = []
  @max = []
end

Instance Attribute Details

#celldm ⇒ Object

Returns the value of attribute celldm.



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# File 'lib/cell/cell.rb', line 8

def celldm
  @celldm
end

#max ⇒ Object (readonly)

Returns the value of attribute max.



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# File 'lib/cell/cell.rb', line 8

def max
  @max
end

#min ⇒ Object (readonly)

Returns the value of attribute min.



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# File 'lib/cell/cell.rb', line 8

def min
  @min
end

#units ⇒ Object

Returns the value of attribute units.



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# File 'lib/cell/cell.rb', line 8

def units
  @units
end

Instance Method Details

#+(arg) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 64

def + arg 
    if arg.is_a?(Cell)
      update_mins_maxes arg.min
      update_mins_maxes arg.max
      self.old_plus(arg)
    else false
    end
end

#<<(arg) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 24

def << arg
  if arg.is_a?(Atom)
    cell_bindings arg
    update_mins_maxes arg.coor
    self.old_p(arg.dup)
  else false
  end
end

#dist(x, y) ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 2

def dist x, y
  $stderr.puts "Distance in crystal units is usually not meaningful!" if @units == :crystal
  arr = wrap(0)
  return arr[x].dist arr[y]
end

#dup ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 72

def dup
  if @units ==  :bohr 
    arr = Cell.new(:units => @units, :celldm => @celldm)
  else
    arr = Cell.new(:units => @units, :celldm => @realcelldm)
  end
  self.each do |atom|
    arr << atom.dup
  end
  return arr 
end

#insert(arg, index) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 52

def insert arg, index
  if arg.is_a?(Atom)
    cell_bindings arg, index
    update_mins_maxes arg.coor
    self.each do |atom|
      atom.uid+=1 if atom uid >= index
    end
    self.old_insert(arg.dup, index)
  else false
  end
end

#move(*args) ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 28

def move *args
  arr = self.dup
  return arr.move! *args
end

#move!(*args) ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 19

def move! *args
  args.flatten!
  args*=3 if args.length == 1
  self.each do |atom|
    atom.move! args
  end
  for i in 0..2;@max[i]+=args[i];@min[i]+=args[i];end
  return self
end

#old_insert ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 51

alias :old_insert :insert

#old_p ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 23

alias :old_p :<<

#old_plus ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 63

alias :old_plus :+

#old_push ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 42

alias :old_push :push

#old_sort! ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 2

alias :old_sort! :sort!

#old_unshift ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 32

alias :old_unshift :unshift

#push(arg) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 43

def push arg
  if arg.is_a?(Atom)
    cell_bindings arg
    update_mins_maxes arg.coor
    self.old_push(arg.dup)
  else false
  end
end

#reset_order ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 36

def reset_order
  arr = self.dup
  return arr.reset_order!
end

#reset_order! ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 32

def reset_order!
  self.old_sort!{|x,y| x.uid <=> y.uid}
  return self
end

#sort(*args) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 19

def sort *args
  arr = self.dup
  return arr.sort!(*args)
end

#sort!(fields, tol = 0.5) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 3

def sort! fields, tol = 0.5
  tol = [tol, tol, tol] unless tol.is_a? Array
  self.old_sort! do |a, b|
    g = fields.to_s.split(//)
    t = a.name <=> b.name
    x = a.x.approx_sort(b.x, tol[0])
    y = a.y.approx_sort(b.y, tol[1])
    z = a.z.approx_sort(b.z, tol[2])
    result = 0
    while result == 0 and g.length > 0
      result = eval(g.shift)
    end
    result
  end 
  return self
end

#to_pdb ⇒ Object 



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# File 'lib/cell/lib/write.rb', line 9

def to_pdb
  arr = (@units == :angstrom ? self : self.dup)
  arr.units = :angstrom
  output = "CRYST1%9.3f%9.3f%9.3f  90.00  90.00  90.00 P             1\n" % arr.celldm
  i = 0
  arr.each do |atom|
    i += 1
    output += "ATOM  %5d %-4s     X   1    %8.3f%8.3f%8.3f  1.00  1.00          %-2s\n" % ([i, atom.name] + atom.coor + [atom.name])
  end
  return output
end

#to_s ⇒ Object 



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# File 'lib/cell/lib/write.rb', line 2

def to_s
  output = ""
  self.each do |atom|
    output += "%s\n" % atom.to_s
  end
  return output
end

#to_xyz ⇒ Object 



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# File 'lib/cell/lib/write.rb', line 20

def to_xyz
  arr = (@units == :angstrom ? self : self.dup)
  arr.units = :angstrom
  output = "%d\n" % arr.length
  output += "Cell Dimensions %10.6f %10.6f %10.6f\n" % arr.celldm
  arr.each do |atom|
    output += "%-2s  %10.6f %10.6f %10.6f\n" % ([atom.name] + atom.coor)
  end
  return output
end

#unshift(arg) ⇒ Object 



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# File 'lib/cell/lib/redef.rb', line 33

def unshift arg
  if arg.is_a?(Atom)
    cell_bindings arg, 0
    self.each{|atom| atom.uid+=1}
    update_mins_maxes arg.coor
    self.old_unshift(arg.dup)
  else false
  end
end

#wrap(tol = 0.5) ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 15

def wrap tol = 0.5
  arr = self.dup
  return arr.wrap!(tol)
end

#wrap!(tol = 0.5) ⇒ Object 



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# File 'lib/cell/lib/boundary.rb', line 7

def wrap! tol = 0.5
  self.each do |atom|
    (0..2).each {|i| atom.coor[i] -= @celldm[i] while atom.coor[i] - @celldm[i] > tol}
    (0..2).each {|i| atom.coor[i] += @celldm[i] while atom.coor[i] < -tol}
  end
  scan_mins_maxes
  return self
end