Class: Atom

Inherits:
Object show all
Defined in:
lib/lib/atom/atom.rb,
lib/lib/atom/lib/atom.rb,
lib/lib/atom/lib/elements.rb

Constant Summary collapse

Elements = 
{
  :O => {
    :z => 8,
    :m => 15.999,
    :fname => "Oxygen",
    :name => :O,
    :pp => []
  },
  :Ti => {
    :z => 22,
    :m => 47.867,
    :fname => "Titanium",
    :name => :Ti,
    :pp => []
  },
  :X => {
    :z => 1,
    :m => 1,
    :fname => "Unspecified",
    :name => :X,
    :pp => []
  }
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(params = {}) ⇒ Atom

Returns a new instance of Atom.



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# File 'lib/lib/atom/atom.rb', line 5

def initialize params = {}
  @type = Elements[params[:type]] || Elements[:X]
  @name = (params[:name]||@type.name).to_sym
  @pos = (params[:pos].to_v rescue nil)
  @crystal = params[:crystal]
  @fixed = params[:fixed]
end

Instance Attribute Details

#crystal ⇒ Object

Returns the value of attribute crystal.



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# File 'lib/lib/atom/atom.rb', line 4

def crystal
  @crystal
end

#fixed ⇒ Object

Returns the value of attribute fixed.



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# File 'lib/lib/atom/atom.rb', line 4

def fixed
  @fixed
end

#pos ⇒ Object

Returns the value of attribute pos.



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# File 'lib/lib/atom/atom.rb', line 4

def pos
  @pos
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/lib/atom/atom.rb', line 4

def type
  @type
end

Instance Method Details

#dist(other) ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 23

def dist other
  pos = other.is_a?(Atom) ? other.pos : other.to_v
  has_crystal? ? crystal.dist(self, other):(@pos - pos).magnitude
end

#dup ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 27

def dup
  Atom.new(to_hash)
end

#evaluate(str, b = nil) ⇒ Object 



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# File 'lib/lib/atom/atom.rb', line 30

def evaluate str, b=nil
  str = str.gsub(/={1,2}/,"==").gsub(/(\[[^\]]*\])/,'\1.to_v')
  eval(str) ? true : false
end

#has_crystal? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/lib/atom/lib/atom.rb', line 14

def has_crystal?() !(@crystal.nil?) end

#inspect ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 36

def inspect
  to_hash.to_s
end

#move(v, n = 1) ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 19

def move v, n = 1
  ret = self.dup
  ret.move! v,n
end

#move!(v, n = 1) ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 15

def move! v, n = 1
  @pos += v.to_v * n
  self
end

#name ⇒ Object 



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# File 'lib/lib/atom/atom.rb', line 16

def name() @name.to_s end

#name=(s) ⇒ Object 



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# File 'lib/lib/atom/atom.rb', line 17

def name=(s)
  @name = s.to_sym
end

#to_hash ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 30

def to_hash
  { :type => @type.name.to_sym, :name => @name, :pos => @pos, :fixed => @fixed, :crystal => @crystal }
end

#to_s(f = '%8.4f') ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 33

def to_s f = '%8.4f'
  ("%-6s" + "#{f} " * 3) % ([name] + pos.to_a) + (fixed.nil? ? "" : fixed.map{|v| v ? 0 : 1}.join(" "))
end

#x ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 2

def x() @pos[0] end

#x=(p) ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 5

def x=(p) 
  @pos = Vector[p,y,z] 
end

#y ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 3

def y() @pos[1] end

#y=(p) ⇒ Object 



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

def y=(p) 
  @pos = Vector[x,p,z] 
end

#z ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 4

def z() @pos[2] end

#z=(p) ⇒ Object 



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# File 'lib/lib/atom/lib/atom.rb', line 11

def z=(p) 
  @pos = Vector[x,y,p] 
end