Class: PoscarCommand

Inherits:
Thor
  • Object
show all
Defined in:
bin/poscar

Overview

Command template

Instance Method Summary collapse

Instance Method Details

#distance(*args) ⇒ Object 



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# File 'bin/poscar', line 26

def distance(* args)
  if args.size > 3
    puts "USAGE: poscar distance poscar_file [id1] [id2]"
    puts "Note: id count from 1"
    exit
  end

  poscar = VaspUtils::Poscar.load_file(args.shift)
  id = args.shift
  atom1s = [id.to_i]
  atom1s = 1..poscar.positions.size if id == nil

  id = args.shift
  atom2s = [id.to_i]
  atom2s = 1..poscar.positions.size if id == nil

  printf("atom1, atom2, %8s, %8s\n", "distance", "periodic_distance")
  atom1s.each do |atom1|
    atom2s.each do |atom2|
      index1 = atom1 - 1
      index2 = atom2 - 1

      cell = poscar.to_cell
      positions = cell.positions
      d =  cell.distance(positions[index1], positions[index2]) #not periodic

      pcell = cell.to_pcell
      pd = pcell.nearest_distance(positions[index1], positions[index2]) #not periodic
      printf("%5i, %5i, %8.5f, %8.5f\n", atom1, atom2 , d, pd)
    end
  end
end

#lattice_constants(*args) ⇒ Object 



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# File 'bin/poscar', line 12

def lattice_constants(* args)
  puts "      a,       b,       c,  alpha,   beta,  gamma,   volume, file"
  args.each do |file|
    axes = VaspUtils::Poscar.load_file(file).axes
    latticeconstants = CrystalCell::LatticeAxes.axes_to_lc(axes)
    printf("%7.4f, %7.4f, %7.4f, %6.2f, %6.2f, %6.2f, ",
      *(latticeconstants))
    printf("%8.3f, ", CrystalCell::Cell.new(axes).calc_volume) # show volume
    puts file
  end
end

#povray(*args) ⇒ Object

‘-b conditions’,



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# File 'bin/poscar', line 113

def povray(* args)
  poscar = args[0] || 'POSCAR'
  tolerance = options[:tolerance].to_f || 0.0

  cell = VaspUtils::Poscar.load_file(poscar).to_cell(CrystalCell::Povray::Cell)
  puts cell.atoms_to_povs(tolerance).join
  puts cell.lattice_to_povs.join
  if options[:bonds]
    elem0, elem1, min, max = (options[:bonds].split(','))
    puts cell.bonds_to_povs(elem0, elem1, min.to_f, max.to_f).join
  end
end

#snapgeomopt ⇒ Object 



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# File 'bin/poscar', line 130

def snapgeomopt
  if options[:xdatcar]
    xdatcar = VaspUtils::Xdatcar.load_file("./XDATCAR")
    positions_list = xdatcar.steps_positions
    elements = xdatcar.elements
    nums_elements = xdatcar.nums_elements
    bases = Array.new( positions_list.size).fill(xdatcar.axes)
  else
    xml = VaspUtils::VasprunXml.load_file("./vasprun.xml")
    bases =  xml.bases
    positions_list = xml.positions_list
    elements = xml.elements
    nums_elements = xml.nums_elements
  end

  num_iteration = positions_list.size
  width = num_iteration.to_s.size

  bases.size.times do |i|
    prefix = sprintf("%0#{width}d", i +1)
    File.open(prefix + ".vasp", "w") do |io|

      poscar = VaspUtils::Poscar.new(
        hash = {
          :comment            => "Generated by poscar_snapgeomopt, #{prefix}/#{num_iteration}",
          :scale              => 1.0,
          :axes               => bases[i],
          :elements           => elements,
          :nums_elements      => nums_elements,
          :selective_dynamics => false,
          :direct             => 'direct',
          :positions          => positions_list[i],
        }
      )
      poscar.dump(io)
    end
  end
end

#substitute(*args) ⇒ Object 



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# File 'bin/poscar', line 63

def substitute(* args)
  usage = "Usage: #{File.basename("#{__FILE__}")} POSCAR old_elem new_elem"

  poscar, elem1, elem2 = * args
  old_poscar = VaspUtils::Poscar.load_file(poscar)

  unless elem1 && elem2
    num = old_poscar.elements.size
    width = 7
    printf("%7s" * num, * old_poscar.elements)
    puts
    printf("%7d" * num, * old_poscar.nums_elements)
    puts
    exit
  end

  new_poscar = old_poscar.substitute(elem1, elem2)

  sum_old_radius = 0.0
  old_poscar.elements.size.times do |i|
    radius = CrystalCell::Element.atomic_radius( old_poscar.elements[i])
    sum_old_radius+= radius * old_poscar.nums_elements[i]
  end
  sum_new_radius = 0.0
  new_poscar.elements.size.times do |i|
    radius = CrystalCell::Element.atomic_radius( new_poscar.elements[i])
    sum_new_radius+= radius * new_poscar.nums_elements[i]
  end

  new_poscar.axes = old_poscar.axes.map{|axis| axis.map{|v| v * sum_new_radius/sum_old_radius}}
  new_poscar.dump($stdout)
end

#vaspdir ⇒ Object 



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# File 'bin/poscar', line 171

def vaspdir
  system "potcar generate --poscar > POTCAR"
  system "incar generate base singlepoint spin2 metal_geomopt --enmax130 > INCAR"
  system "kpoints generate --length=#{options[:wavelength]} > KPOINTS"
end

#vaspgeomopt ⇒ Object 



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# File 'bin/poscar', line 179

def vaspgeomopt
  poscar = VaspUtils::Poscar.load_file('POSCAR')
  es = poscar.elements
  ns = poscar.nums_elements
  dirname = ''
  poscar.elements.size.times do |i|
    dirname += es[i]
    dirname += ns[i].to_s
  end
  FileUtils.mkdir_p dirname
  subdir = dirname + '/geomopt00'
  FileUtils.mkdir_p subdir

  FileUtils.cp("POSCAR", subdir)
  system "potcar generate --poscar > #{subdir}/POTCAR"
  system "incar generate base full_relax spin2 metal_geomopt --enmax130=#{subdir}/POTCAR > #{subdir}/INCAR"
  system "kpoints generate --length=#{options[:wavelength]} > #{subdir}/KPOINTS"
end