Class: VaspUtils::VasprunXml

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

Defined Under Namespace

Classes: IllegalArgumentError

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data) ⇒ VasprunXml

Returns a new instance of VasprunXml.



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# File 'lib/vasputils/vasprunxml.rb', line 13

def initialize(data)
  @data = data
end

Instance Attribute Details

#data ⇒ Object (readonly)

Returns the value of attribute data.



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# File 'lib/vasputils/vasprunxml.rb', line 8

def data
  @data
end

Class Method Details

.load_file(path) ⇒ Object 



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

def self.load_file(path)
  data = Nokogiri::XML(open(path))
  self.new(data)
end

Instance Method Details

#bases ⇒ Object 



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

def bases
  results = @data.xpath("/modeling/calculation").map do |c|
    c.xpath("./structure/crystal/varray[@name='basis']/v").map do |axis|
      axis.text.strip.split.map {|i| i.to_f}
    end
  end
  results
end

#calculation_basis ⇒ Object 



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

def calculation_basis
  results = []
  @data.xpath('/modeling/calculation/structure/crystal/varray[@name="basis"]').each do |i|
    results << i.xpath('v').children.map{|j| j.to_s.strip.split.map{|k| k.to_f}}
  end
  results
end

#calculation_cells ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 128

def calculation_cells
  #calculation_basis #格子定数リスト
  #pp calculation_basis
  #pp elements
  #pp positions_list[0].size

  basis = calculation_basis
  elems = elements
  poss_list = positions_list
  
  results = []
  poss_list.size.times do |i_step|
    basis[i_step]

    atoms = []
    elems.size.times do |atom_id|
      #pp atom_id
      atoms << CrystalCell::Atom.new(elems[atom_id], poss_list[i_step][atom_id])
    end

    results << CrystalCell::Cell.new(basis[i_step], atoms)
  end
  results
end

#calculation_energies ⇒ Object

energies of each ionic step



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# File 'lib/vasputils/vasprunxml.rb', line 116

def calculation_energies
  @data.xpath("/modeling/calculation/energy/i[@name='e_fr_energy']").children.to_a.map{|i| i.to_s.to_f}
end

#elements ⇒ Object

元素リストuniq していないものを返す。



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# File 'lib/vasputils/vasprunxml.rb', line 56

def elements
  results = []
  @data.xpath('/modeling/atominfo/array[@name="atoms"]/set/rc').each do |i|
    results << i.children[0].children.to_s.strip
  end
  results
end

#fermi_energy ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 102

def fermi_energy
  @data.xpath("/modeling/calculation/dos/i[@name='efermi']").children.to_s.to_f
end

#num_atoms ⇒ Object Also known as: num_ions 



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# File 'lib/vasputils/vasprunxml.rb', line 106

def num_atoms
  @data.xpath("/modeling/atominfo/atoms").children.to_s.to_i
end

#num_spins ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 111

def num_spins
  @data.xpath("/modeling/parameters/separator[@name='electronic']/separator[@name='electronic spin']/i[@name='ISPIN']").children.to_s.to_i
end

#nums_elements ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 48

def nums_elements
  @data.xpath("/modeling/atominfo/array[@name='atomtypes']/set/rc").map do |elem|
    elem.xpath('./c').children[0].text.to_i
  end
end

#partial_dos(ion, spin) ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 87

def partial_dos(ion, spin)
  if (spin < 1) || (num_ions < ion)
    raise IllegalArgumentError, "'ion' is indicated as #{ion}"
  end

  if (spin < 1) || (num_spins < spin)
    raise IllegalArgumentError, "'spin' is indicated as #{spin}"
  end

  result = @data.xpath("/modeling/calculation/dos/partial/array/set/set[@comment='ion #{ion}']/set[@comment='spin #{spin}']/r").children.map do |elem|
    elem.to_s.strip.split.map{|i| i.to_f}
  end
  result
end

#partial_dos_labels ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 83

def partial_dos_labels
  @data.xpath("/modeling/calculation/dos/partial/array/field").map{|i| i.children.to_s.strip}
end

#positions_list ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 40

def positions_list
  @data.xpath("/modeling/calculation").map do |c|
    c.xpath("./structure/varray[@name='positions']/v").map do |pos|
      pos.text.strip.split.map {|i| i.to_f}
    end
  end
end

#stress ⇒ Object

Return stress tensor of last ionic step



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# File 'lib/vasputils/vasprunxml.rb', line 23

def stress
  items = @data.xpath("/modeling/calculation/varray[@name='stress']/v").children
  items = items.map do |line|
    line.to_s.strip.split(/ +/).map {|item| item.to_f}
  end
  items[-3..-1]
end

#total_dos(spin) ⇒ Object

Return an array of [energy, total, integrated] for spin. ‘spin’ is indicated by number started from 1 (should be 1 or 2). If the ‘spin’ does not exist, raise IllegalArgumentError



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# File 'lib/vasputils/vasprunxml.rb', line 68

def total_dos(spin)
  if (spin < 1) || (num_spins < spin)
    raise IllegalArgumentError, "'spin' is indicated as #{spin}"
  end

  result = @data.xpath("/modeling/calculation/dos/total/array/set/set[@comment='spin #{spin}']/r").children.map do |elem|
    elem.to_s.strip.split.map{|i| i.to_f}
  end
  result
end

#total_dos_labels ⇒ Object 



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# File 'lib/vasputils/vasprunxml.rb', line 79

def total_dos_labels
  @data.xpath("/modeling/calculation/dos/total/array/field").map{|i| i.children.to_s}
end