Class: VaspUtils::VaspGeometryOptimizer

Inherits:
Comana::ComputationManager
  • Object
show all
Defined in:
lib/vasputils/vaspgeometryoptimizer.rb

Overview

The directory must has subdirs whose name is started by ‘geomopt’. This restriction of naming is necessary to distinguish from simple aggregation of vasp directories.

Defined Under Namespace

Classes: InitializeError, LatestDirStartedError, NoContcarError, NoIntegerEndedNameError, NoVaspDirError

Constant Summary collapse

PREFIX =

class InitializeError < Comana::ComputationManager::InitializeError; end

"geomopt"

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dir) ⇒ VaspGeometryOptimizer

Returns a new instance of VaspGeometryOptimizer.



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 20

def initialize(dir)
  super(dir)
  @lockdir        = "lock_vaspgeomopt"
  begin
    latest_dir # to check.
  rescue NoVaspDirError
    raise InitializeError
  end
end

Class Method Details

.next_name(name) ⇒ Object

Return incremented name. If the name of VaspDir ends with string of integer, return incremental value with the basename. If not ended with integer, this method assume “00”



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

def self.next_name(name)
  name =~ /^(.*#{PREFIX})(\d+)/
  return sprintf("%s%02d", $1, $2.to_i + 1)
end

Instance Method Details

#calculate ⇒ Object

注目した VaspDir が yet なら実行し、続ける。yet 以外なら例外。VaspDir になっているか。



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 43

def calculate
  $stdout.puts "Calculate #{latest_dir.dir}"
  $stdout.flush

  latest_dir.start
end

#finished? ⇒ Boolean

latest_dir から返って来る最新の VaspDir が finished? で真を返し、かつ Iteration が 1 であるか。Note: even when the geometry optimization does not include lattice shape,

calculate will continued till to converge to Iter 1 calculation.

Returns:

  • (Boolean) 


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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 54

def finished?
  return false unless latest_dir.finished?
  return false unless latest_dir.outcar[:ionic_steps] == 1
  return true
end

#latest_dir ⇒ Object

Find latest VaspDir. Return a last VaspDir which has the name by name sort and which can be made as a VaspDir instance. Note: in a series of geometry optimization,

the directory names should have a rule of naming
which can define a method <=>.
Usually, it is simple sort of String.

Raises:



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 67

def latest_dir
  Dir.glob("#{@dir}/#{PREFIX}*").sort.reverse.find do |dir|
    begin
      vd = VaspUtils::VaspDir.new(dir)
      return vd
    rescue VaspUtils::VaspDir::InitializeError
      next
    end
  end
  raise NoVaspDirError, @dir
end

#reset_initialize ⇒ Object

Keep ‘geomopt00/POSCAR,POTCAR,INCAR,POTCAR’, remove others.

Raises:



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 80

def reset_initialize
  poscars = Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort
  #poscar = nil
  path = nil

  # Find the first geometory optimization
  poscars.each do |poscar|
    begin
      VaspUtils::Poscar.load_file poscar
      path = File.dirname(poscar)
      break
    rescue VaspUtils::Poscar::ParseError
      next
    end
  end
  raise NoVaspDirError unless path

  ##geomopt*
  rm_list = Dir.glob "#{@dir}/#{PREFIX}*"
  rm_list.delete path
  ##input files
  rm_list << Dir.glob("#{path}/*")
  rm_list.flatten!
  ["KPOINTS", "INCAR", "POTCAR", "POSCAR"].each do |file|
    rm_list.delete "#{path}/#{file}"
  end
  files = Dir.glob("#{@dir}/*")
  files.delete( path)
  rm_list += files
  rm_list.each do |file|
    FileUtils.rm_rf file
  end
end

#reset_next(io = $stdout) ⇒ Object

Generate a new vaspdir as ‘geomopt00’. Other directories, including old ‘geomopt00’, are removed.



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

def reset_next(io = $stdout)
  begin
    latest_dir.contcar
    prepare_next
    clean_queue_files
  rescue Errno::ENOENT
    latest_dir.reset_initialize(io)
    clean_queue_files
  rescue VaspUtils::Poscar::ParseError
    latest_dir.reset_initialize(io)
    clean_queue_files
  end
end

#reset_reincarnate ⇒ Object

Generate a new vaspdir as ‘geomopt00’. Other directories, including old ‘geomopt00’, are removed.

Raises:



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 132

def reset_reincarnate
  #CONTCAR を最後から解釈していく。
  #全てだめだったら POSCAR を解釈する。
  #全部だめだったら例外を投げる。

  #CONTCAR を解釈できたディレクトリで INCAR, KPOINTS, POTCAR を取得。
  #geomopt01 という名前でディレクトリを作る。
  contcars = Dir.glob("#{@dir}/#{PREFIX}*/CONTCAR").sort.reverse
  contcars += Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort.reverse
  poscar = nil
  path = nil
  contcars.each do |contcar|
    begin
      VaspUtils::Poscar.load_file contcar
      poscar = contcar
      path = File.dirname(contcar)
      break
    rescue VaspUtils::Poscar::ParseError
      next
    end
  end
  raise NoVaspDirError unless poscar

  new_dir = "#{@dir}/new_#{PREFIX}00"
  Dir.mkdir new_dir
  FileUtils.mv("#{path}/KPOINTS", "#{new_dir}/KPOINTS")
  FileUtils.mv("#{path}/INCAR"    , "#{new_dir}/INCAR"    )
  FileUtils.mv("#{path}/POTCAR" , "#{new_dir}/POTCAR" )
  FileUtils.mv(poscar                     , "#{new_dir}/POSCAR")

  rm_list =    Dir.glob "#{@dir}/#{PREFIX}*"
  rm_list += Dir.glob "#{@dir}/lock*"
  rm_list += Dir.glob "#{@dir}/*.sh"
  rm_list += Dir.glob "#{@dir}/*.log"
  rm_list += Dir.glob "#{@dir}/*.o*"
  rm_list.each do |file|
    FileUtils.rm_rf file
  end

  FileUtils.mv new_dir, "#{@dir}/#{PREFIX}00"
end