Class: VaspUtils::Xdatcar

Inherits:
Object
  • Object
show all
Defined in:
lib/vasputils/xdatcar.rb

Overview

Class to manage XDATCAR format of VASP.

基本的に、読み込みだけを行う。

Defined Under Namespace

Classes: ElementMismatchError, ParseError

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash) ⇒ Xdatcar

Returns a new instance of Xdatcar.



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# File 'lib/vasputils/xdatcar.rb', line 16

def initialize(hash)
  hash.each do |key,val|
    @comment            = val if :comment            ==key
    @scale              = val if :scale              ==key
    @axes               = val if :axes               ==key
    @elements           = val if :elements           ==key
    @nums_elements      = val if :nums_elements      ==key
    #@selective_dynamics = val if :selective_dynamics ==key
    @direct             = val if :direct             ==key
    @steps_positions     = val if :steps_positions          ==key
  end
end

Instance Attribute Details

#axes ⇒ Object

Returns the value of attribute axes.



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# File 'lib/vasputils/xdatcar.rb', line 14

def axes
  @axes
end

#comment ⇒ Object (readonly)

Returns the value of attribute comment.



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# File 'lib/vasputils/xdatcar.rb', line 12

def comment
  @comment
end

#direct ⇒ Object (readonly)

Returns the value of attribute direct.



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# File 'lib/vasputils/xdatcar.rb', line 12

def direct
  @direct
end

#elements ⇒ Object (readonly)

Returns the value of attribute elements.



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# File 'lib/vasputils/xdatcar.rb', line 12

def elements
  @elements
end

#nums_elements ⇒ Object (readonly)

Returns the value of attribute nums_elements.



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# File 'lib/vasputils/xdatcar.rb', line 12

def nums_elements
  @nums_elements
end

#scale ⇒ Object (readonly)

Returns the value of attribute scale.



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# File 'lib/vasputils/xdatcar.rb', line 12

def scale
  @scale
end

#steps_positions ⇒ Object (readonly)

Returns the value of attribute steps_positions.



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# File 'lib/vasputils/xdatcar.rb', line 12

def steps_positions
  @steps_positions
end

Class Method Details

.load_file(file) ⇒ Object

file で与えられた名前のファイルを読み込んで self クラスインスタンスを返す。構文解析できなければ例外 Xdatcar::ParseError を投げる。



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# File 'lib/vasputils/xdatcar.rb', line 85

def self.load_file(file)
  io = File.open(file, "r")
  self.parse(io)
end

.parse(io) ⇒ Object

io を読み込んで Xdatcar クラスインスタンスを返す。構文解析できなければ例外 Xdatcar::ParseError を投げる。



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# File 'lib/vasputils/xdatcar.rb', line 31

def self.parse(io)
  # analyze XDATCAR.

  begin
    #line 1: comment (string)
    comment = io.readline.chomp

    #line 2: universal scaling factor (float)
    scale = io.readline.to_f
    raise "Xdatcar.load_file cannot use negative scaling factor.\n" if scale < 0

    #line 3-5: axes (3x3 Array of float)
    axes = []
    3.times do |i| #each axis of a, b, c.
      vec = io.readline.strip.split(/\s+/) #in x,y,z directions
      axes << vec.collect! { |j| j.to_f * scale } #multiply scaling factor
    end

    vals = io.readline.strip.split(/\s+/)
    elements = nil
    if vals[0].to_i == 0
      elements = vals
      vals = io.readline.strip.split(/\s+/)
    end
    nums_elements = vals.map{|i| i.to_i}

    io.readline # should be empty line
    steps_positions = []
    index = 0
    io.readlines.each do |line|
      steps_positions[index] ||= []
      if line =~ /^\s*$/
        index += 1
      else
        steps_positions[index] << line.strip.split(/\s+/).map {|coord| coord.to_f}
      end
    end
  rescue EOFError
    raise ParseError, "end of file reached"
  end

  options = {
    :comment            => comment           ,
    :scale              => scale             ,
    :axes               => axes              ,
    :elements           => elements          ,
    :nums_elements      => nums_elements     ,
    :steps_positions          => steps_positions         ,
  }
  self.new(options)
end