Class: VaspUtils::Poscar

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

Overview

Class to manage POSCAR format of VASP.

parse と dump のどちらかだけでなく、両方を統括して扱うクラス。

Defined Under Namespace

Classes: ElementMismatchError, ParseError

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash) ⇒ Poscar

Returns a new instance of Poscar.



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# File 'lib/vasputils/poscar.rb', line 19

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
    @positions          = val if :positions          ==key
  end
end

Instance Attribute Details

#axes ⇒ Object

Returns the value of attribute axes.



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# File 'lib/vasputils/poscar.rb', line 17

def axes
  @axes
end

#comment ⇒ Object (readonly)

Returns the value of attribute comment.



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# File 'lib/vasputils/poscar.rb', line 15

def comment
  @comment
end

#direct ⇒ Object (readonly)

Returns the value of attribute direct.



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# File 'lib/vasputils/poscar.rb', line 15

def direct
  @direct
end

#elements ⇒ Object (readonly)

Returns the value of attribute elements.



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# File 'lib/vasputils/poscar.rb', line 15

def elements
  @elements
end

#nums_elements ⇒ Object (readonly)

Returns the value of attribute nums_elements.



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# File 'lib/vasputils/poscar.rb', line 15

def nums_elements
  @nums_elements
end

#positions ⇒ Object (readonly)

Returns the value of attribute positions.



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# File 'lib/vasputils/poscar.rb', line 15

def positions
  @positions
end

#scale ⇒ Object (readonly)

Returns the value of attribute scale.



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# File 'lib/vasputils/poscar.rb', line 15

def scale
  @scale
end

#selective_dynamics ⇒ Object (readonly)

Returns the value of attribute selective_dynamics.



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# File 'lib/vasputils/poscar.rb', line 15

def selective_dynamics
  @selective_dynamics
end

Class Method Details

.interpolate(poscar0, poscar1, ratio, periodic = false) ⇒ Object

selective_dynamics は常に on にする。各要素の真偽値は 2つの POSCAR の論理積。指定がなければ true と見做す。ratio は poscar1 の比率。0だと poscar0 に、1だとposcar1 となる。Return Poscar class instance



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# File 'lib/vasputils/poscar.rb', line 232

def self.interpolate(poscar0, poscar1, ratio, periodic = false)
  poscar0.interpolate(poscar1, ratio, periodic)
end

.load_cell(cell) ⇒ Object

CrystalCell::Cell クラスインスタンスからPoscar クラスインスタンスを生成



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# File 'lib/vasputils/poscar.rb', line 120

def self.load_cell(cell)
  elements = cell.elements.sort.uniq

  atoms = cell.atoms.sort_by{|atom| atom.element}

  nums_elements = {}
  atoms.each do |atom|
    nums_elements[atom.element] ||= 0
    nums_elements[atom.element] += 1
  end
  nums_elements = elements.map{|elem| nums_elements[elem]}

  positions = []
  movable_flags = []
  selective_dynamics = false
  atoms.each do |atom|
    positions << atom.position
    movable_flags << atom.movable_flags
    selective_dynamics = true if movable_flags
  end

  selective_dynamics = movable_flags if movable_flags

  options = {
    :comment            => cell.comment           ,
    :scale              => 1.0               ,
    :axes               => cell.axes.to_a,
    :elements           => elements          ,
    :nums_elements      => nums_elements     ,
    :selective_dynamics => selective_dynamics,
    :direct             => true,
    :positions          => positions             ,
  }
  self.new(options)
end

.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 Poscar::ParseError を投げる。



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# File 'lib/vasputils/poscar.rb', line 113

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

.parse(io) ⇒ Object

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



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# File 'lib/vasputils/poscar.rb', line 34

def self.parse(io)
  # analyze POSCAR.

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

    #line 2: universal scaling factor (float)
    scale = io.readline.to_f
    raise "Poscar.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

    # Element symbol (vasp 5). Nothing in vasp 4.

    #elements = io.readline.strip.split(/\s+/).map{|i| i.to_i}
    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}

    # 'Selective dynamics' or not (bool)
    line = io.readline
    selective_dynamics = false
    if line =~ /^\s*s/i
      selective_dynamics = []
      line = io.readline      # when this situation, reading one more line is nessesarry
    end

    if (line =~ /^\s*d/i) # allow only 'Direct' now
      direct = true
    else
      raise "Not 'direct' indication."
    end

    positions = []
    nums_elements.size.times do |elem_index|
      nums_elements[elem_index].times do |index|
        items = io.readline.strip.split(/\s+/)
        positions << items[0..2].map {|coord| coord.to_f}

        if selective_dynamics
          mov_flags = []
          if items.size >= 6 then
            items[3..5].each do |i|
              (i =~ /^t/i) ? mov_flags << true : mov_flags << false
            end
            selective_dynamics << mov_flags
          end
        end
      end
    end
  rescue EOFError
    raise ParseError, "end of file reached"
  end

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

Instance Method Details

#==(other) ⇒ Object 



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# File 'lib/vasputils/poscar.rb', line 278

def ==(other)
  result = true
  result = false unless @comment             == other.comment            
  result = false unless @scale               == other.scale              
  result = false unless @axes                == other.axes               
  result = false unless @elements            == other.elements           
  result = false unless @nums_elements       == other.nums_elements      
  result = false unless @selective_dynamics  == other.selective_dynamics 
  result = false unless @direct              == other.direct             
  result = false unless @positions           == other.positions          
  result
end

#dump(io, version = 5) ⇒ Object

POSCAR 形式で書き出す。cell は CrystalCell::Cell クラスインスタンスと同等のメソッドを持つもの。elements は書き出す元素の順番。

elems が cell の持つ元素リストとマッチしなければ
例外 Poscar::ElementMismatchError を投げる。
nil ならば、原子の element でソートした順に出力する。

io は書き出すファイルハンドル。‘version’ indicates a poscar style for vasp 4 or 5. def dump(io, elements = nil, version = 5)



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# File 'lib/vasputils/poscar.rb', line 166

def dump(io, version = 5)
  elements = @elements unless elements
  elem_indices = elements.map {|elem| @elements.find_index(elem)}
  unless (Mapping::map?(@elements.uniq, elements){ |i, j| i == j })
      raise ElementMismatchError,
      "elements [#{elements.join(",")}] mismatches to cell.elements [#{cell.elements.join(",")}."
  end

  io.puts @comment
  io.puts "1.0" #scale
  3.times do |i|
    io.printf("  % 18.15f    % 18.15f    % 18.15f\n", @axes[i][0], @axes[i][1], @axes[i][2]
    )
  end

  ## Element symbols for vasp 5.
  if version >= 5
    io.puts elem_indices.map{|i| @elements[i]}.join(' ')
  end

  ## Atom numbers.
  io.puts elem_indices.map{|i| @nums_elements[i]}.join(' ')

  ## Selective dynamics
  io.puts "Selective dynamics" if @selective_dynamics
  io.puts "Direct"

  @positions.size.times do |i|
    io.puts sprint_position(i)
  end
end

#interpolate(other, ratio, periodic = false) ⇒ Object

selective_dynamics は常に on にする。other は Poscar クラスインスタンス

Raises:

  • (PoscarMismatchError) 


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# File 'lib/vasputils/poscar.rb', line 238

def interpolate(other, ratio, periodic = false)
  #self.class.interpolate(self, poscar, ratio, periodic = false)
  axes0 = self.axes
  axes1 = other.axes
  new_axes = []
  3.times do |i|
    new_axes << interpolate_coords(axes0[i], axes1[i], ratio)
  end

  raise PoscarMismatchError unless self.elements == other.elements
  raise PoscarMismatchError unless self.nums_elements == other.nums_elements

  new_positions = []
  self.positions.size.times do |i|
    ##positions
    coord0 = self.positions[i]
    coord1 = other.positions[i]
    coord1 = periodic_nearest(coord0, coord1) if periodic
    new_positions << interpolate_coords(
      coord0, coord1, ratio)
  end

  hash = {
    :comment => "Generated by interpolation of #{ratio}",
    :scale   => 1.0,
    :axes    => new_axes,
    :elements           => self.elements,
    :nums_elements      => self.nums_elements,
    :selective_dynamics => merge_selective_dynamics(
      self.selective_dynamics,
      other.selective_dynamics
    ),
    :direct             => true,
    :positions          => new_positions
  }

  VaspUtils::Poscar.new(hash)
end

#substitute(elem1, elem2) ⇒ Object 



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# File 'lib/vasputils/poscar.rb', line 291

def substitute(elem1, elem2)
  result = Marshal.load(Marshal.dump(self))
  result.substitute!(elem1, elem2)
  result
end

#substitute!(elem1, elem2) ⇒ Object 



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# File 'lib/vasputils/poscar.rb', line 297

def substitute!(elem1, elem2)
  @elements.map! do |elem|
    if elem == elem1 
      elem2
    else
      elem
    end
  end
  unite_elements
end

#to_cell(klass = CrystalCell::Cell) ⇒ Object

Generate CrystalCell::Cell class. If klass is argued, try to generate the class.



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# File 'lib/vasputils/poscar.rb', line 200

def to_cell(klass = CrystalCell::Cell)
  axes = CrystalCell::LatticeAxes.new( @axes)

  atoms = []
  total_id = 0
  @nums_elements.each_with_index do |num, elem_id|
    num.times do |atom_id|
      element = elem_id
      element = @elements[elem_id] if @elements

      movable_flags = nil
      if @selective_dynamics
        movable_flags = @selective_dynamics[total_id]
      end
      atoms << CrystalCell::Atom.new(
        element, 
        @positions[total_id],
        movable_flags
      )
      total_id += 1
    end
  end

  klass.new(axes, atoms)
end