vasputils 0.0.11 → 0.0.12

data/lib/vasputils/vaspdir.rb

@@ -6,98 +6,211 @@ require "pp"
 require "date"
 require "yaml"
 
-require "rubygems"
-gem "comana"
-require "comana/computationmanager.rb"
-require "comana/machineinfo.rb"
-
-require "vasputils.rb"
+#require "rubygems"
+#require "comana"
 
 # Class for VASP executable directory,
 # including input and output files.
 #
-class VaspUtils::VaspDir < ComputationManager
-  class InitializeError < Exception; end
-  class NoVaspBinaryError < Exception; end
-  class PrepareNextError < Exception; end
-  class ExecuteError < Exception; end
-
-  def initialize(dir)
-    super(dir)
-    @lockdir    = "lock_vaspdir"
-    %w(INCAR KPOINTS POSCAR POTCAR).each do |file|
-      infile = "#{@dir}/#{file}"
-      raise InitializeError, infile unless FileTest.exist? infile
+class VaspUtils::VaspDir < Comana::ComputationManager
+    MACHINEFILE = "machines"
+
+    class InitializeError < Exception; end
+    class NoVaspBinaryError < Exception; end
+    class PrepareNextError < Exception; end
+    class ExecuteError < Exception; end
+    class InvalidValueError < Exception; end
+    class AlreadyExistError < Exception; end
+
+    def initialize(dir)
+        super(dir)
+        @lockdir        = "lock_vaspdir"
+        %w(INCAR KPOINTS POSCAR POTCAR).each do |file|
+            infile = "#{@dir}/#{file}"
+            raise InitializeError, infile unless FileTest.exist? infile
+        end
+    end
+
+    # 配下の OUTCAR を Outcar インスタンスにして返す。
+    # 存在しなければ例外 Errno::ENOENT を返す。
+    def outcar
+        VaspUtils::Outcar.load_file("#{@dir}/OUTCAR")
     end
-  end
-
-  # 配下の OUTCAR を Outcar インスタンスにして返す。
-  # 存在しなければ例外 Errno::ENOENT を返す。
-  def outcar
-    VaspUtils::Outcar.load_file("#{@dir}/OUTCAR")
-  end
-
-  # 配下の POSCAR を Cell2 インスタンスにして返す。
-  # 存在しなければ例外 Errno::ENOENT を返す。
-  def poscar
-    VaspUtils::Poscar.load_file("#{@dir}/POSCAR")
-  end
-
-  # 配下の CONTCAR を Cell2 インスタンスにして返す。
-  # 存在しなければ例外 Errno::ENOENT を返す。
-  def contcar
-    VaspUtils::Poscar.load_file("#{@dir}/CONTCAR")
-  end
-
-  # 配下の KPOINTS を読み込んだ結果をハッシュにして返す。
-  #
-  # 存在しなければ例外 Errno::ENOENT を返す筈だが、
-  # vasp dir の判定を incar でやっているので置こる筈がない。
-  def incar
-    VaspUtils::Incar.load_file("#{@dir}/INCAR")
-  end
-
-  # 配下の KPOINTS を読み込んだ結果をハッシュにして返す。
-  def kpoints
-    VaspUtils::Kpoints.load_file("#{@dir}/KPOINTS")
-  end
-
-  # 正常に終了していれば true を返す。
-  # 実行する前や実行中、OUTCAR が完遂していなければ false。
-  #
-  # MEMO
-  # PI12345 ファイルは実行中のみ存在し、終了後 vasp (mpi？) に自動的に削除される。
-  def finished?
-    begin
-      return VaspUtils::Outcar.load_file("#{@dir}/OUTCAR")[:normal_ended]
-    rescue Errno::ENOENT
-      return false
+
+    # 配下の POSCAR を CrystalCell::Cell インスタンスにして返す。
+    # 存在しなければ例外 Errno::ENOENT を返す。
+    def poscar
+        VaspUtils::Poscar.load_file("#{@dir}/POSCAR")
+    end
+
+    # 配下の CONTCAR を CrystalCell::Cell インスタンスにして返す。
+    # 存在しなければ例外 Errno::ENOENT を返す。
+    def contcar
+        VaspUtils::Poscar.load_file("#{@dir}/CONTCAR")
     end
-  end
-
-  private
-
-  # vasp を投げる。
-  def calculate
-    begin
-      info =
-        MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo").get_info(ENV["HOST"])
-      vasp = info["vasp"]
-    rescue
-      #vasp = "vasp"
-      raise NoVaspBinaryError, "No vasp path in #{ENV["HOME"]}/.machineinfo"
+
+    # 配下の KPOINTS を読み込んだ結果をハッシュにして返す。
+    #
+    # 存在しなければ例外 Errno::ENOENT を返す筈だが、
+    # vasp dir の判定を incar でやっているので生じる筈がない。
+    def incar
+        VaspUtils::Incar.load_file("#{@dir}/INCAR")
+    end
+
+    # 配下の KPOINTS を読み込んだ結果をハッシュにして返す。
+    def kpoints
+        VaspUtils::Kpoints.load_file("#{@dir}/KPOINTS")
+    end
+
+    # 正常に終了していれば true を返す。
+    # 実行する前や実行中、OUTCAR が完遂していなければ false。
+    #
+    # MEMO
+    # PI12345 ファイルは実行中のみ存在し、終了後 vasp (mpi？) に自動的に削除される。
+    def finished?
+        begin
+            return VaspUtils::Outcar.load_file("#{@dir}/OUTCAR")[:normal_ended]
+        rescue Errno::ENOENT
+            return false
+        end
+    end
+
+    def reset_init(io = $stdout)
+        #fullpath = File.expand_path @dir
+        keep_files   = ["INCAR", "KPOINTS", "POSCAR", "POTCAR"]
+        remove_files = []
+        Dir.entries( @dir ).sort.each do |file|
+            next if file == "."
+            next if file == ".."
+            remove_files << file unless keep_files.include? file
+        end
+
+        if remove_files.size == 0
+            io.puts "    No remove files."
+            return
+        else
+            #pp @dir; exit
+            #puts "  Remove files:"
+            #remove_files.each { |file| puts "      #{file}" }
+
+            #puts "  Keep files:"
+            #keep_files.each { |file| puts "        #{file}" }
+
+            remove_files.each do |file|
+                io.puts "    Removing: #{file}"
+                FileUtils.rm_rf "#{@dir}/#{file}"
+            end
+        end
+    end
+
+    # 'tgt_name' is a String.
+    # 'conditions' is a Hash.
+    #   E.g., {:encut => 500.0, :ka => 2, :kb => 4}
+    def mutate(tgt_name, condition)
+        raise AlreadyExistError, "Already exist: #{tgt_name}" if File.exist? tgt_name
+
+        Dir.mkdir tgt_name
+
+        ##POSCAR
+        FileUtils.cp("#{@dir}/POSCAR", "#{tgt_name}/POSCAR")
+
+        ##POTCAR
+        FileUtils.cp("#{@dir}/POTCAR", "#{tgt_name}/POTCAR")
+
+        ##INCAR
+        new_incar = incar
+        new_incar["ENCUT"] = condition[:encut] if condition[:encut]
+        File.open("#{tgt_name}/INCAR", "w") do |io|
+            VaspUtils::Incar.dump(new_incar, io)
+        end
+
+        ##KPOINTS
+        new_kpoints = kpoints
+        new_kpoints[:mesh][0] = condition[:ka] if condition[:ka]
+        new_kpoints[:mesh][1] = condition[:kb] if condition[:kb]
+        new_kpoints[:mesh][2] = condition[:kc] if condition[:kc]
+        if condition[:kab]
+            new_kpoints[:mesh][0] = condition[:kab]
+            new_kpoints[:mesh][1] = condition[:kab]
+        end
+        if condition[:kbc]
+            new_kpoints[:mesh][1] = condition[:kbc]
+            new_kpoints[:mesh][2] = condition[:kbc]
+        end
+        if condition[:kca]
+            new_kpoints[:mesh][2] = condition[:kca]
+            new_kpoints[:mesh][0] = condition[:kca]
+        end
+        if condition[:kabc]
+            new_kpoints[:mesh][0] = condition[:kabc]
+            new_kpoints[:mesh][1] = condition[:kabc]
+            new_kpoints[:mesh][2] = condition[:kabc]
+        end
+        File.open("#{tgt_name}/KPOINTS", "w") do |io|
+            VaspUtils::Kpoints.dump(new_kpoints, io)
+        end
+    end
+
+    private
+
+    # vasp を投げる。
+    def calculate
+        #HOSTNAME is for GridEngine
+        hostname = (ENV["HOST"] || ENV["HOSTNAME"]).sub(/\..*$/, "") #ignore domain name
+
+        begin
+            clustersettings = Comana::ClusterSetting.load_file("#{ENV["HOME"]}/.clustersetting")
+            info = clustersettings.settings_host(hostname)
+        rescue
+            puts "No vasp path in #{ENV["HOME"]}/.clustersetting"
+            pp info
+            raise NoVaspBinaryError
+        end
+
+        if ENV["SGE_EXECD_PIDFILE"] #grid engine 経由のとき
+            nslots = ENV["NSLOTS"]
+            lines = open(ENV["PE_HOSTFILE"], "r").readlines.collect do |line|
+                line =~ /^(\S+)\s+(\S+)/
+                "#{$1} cpu=#{$2}"
+            end
+            generate_machinefile(lines)
+        else
+            nslots = 1
+            lines = ["localhost cpu=1"]
+            generate_machinefile(lines)
+        end
+
+        raise InvalidValueError,
+            "`clustersettings' is #{clustersettings.inspect}." unless clustersettings
+        raise InvalidValueError, "`info' is #{info.inspect}." unless info
+        raise InvalidValueError, "`info['mpi']' is #{info['mpi']}" unless info['mpi']
+        raise InvalidValueError, "`info['vasp']' is #{info['vasp']}" unless info['vasp']
+        raise InvalidValueError, "`MACHINEFILE' is #{MACHINEFILE}" unless MACHINEFILE
+        raise InvalidValueError, "`nslots' is #{nslots}" unless nslots
+        raise InvalidValueError, "`nslots' is #{nslots}" unless nslots
+
+        #pp "#{info["mpi"]} -machinefile #{MACHINEFILE} -np #{nslots} #{info["vasp"]}"
+        command = "cd #{@dir};"
+        command += "#{info["mpi"]} -machinefile #{MACHINEFILE} -np #{nslots} #{info["vasp"]}"
+        command += "> stdout"
+
+        io = File.open("#{@dir}/runvasp.log", "w")
+        io.puts command
+        io.close
+
+        end_status = system command
+        raise ExecuteError, "end_status is #{end_status.inspect}" unless end_status
+    end
+
+    def prepare_next
+        #do_nothing
+        raise PrepareNextError, "VaspDir doesn't need next."
+    end
+
+    def generate_machinefile(lines)
+        io = File.open("#{@dir}/#{MACHINEFILE}", "w")
+        io.puts lines
+        io.close
     end
-    command = "cd #{@dir};"
-    command += vasp
-    command += "> stdout"
-
-    end_status = system command
-    raise ExecuteError, "end_status is #{end_status.inspect}" unless end_status
-  end
-
-  def prepare_next
-    #do_nothing
-    raise PrepareNextError, "VaspDir doesn't need next."
-  end
 
 end

data/lib/vasputils/vaspgeometryoptimizer.rb

@@ -5,112 +5,245 @@ require "pp"
 require "fileutils"
 
 require "rubygems"
-gem "comana"
-require "comana/computationmanager.rb"
+#gem "comana"
+#require "comana/computationmanager.rb"
+#require "comana/computationmanager.rb"
 
-require "vasputils.rb"
+#require "vasputils.rb"
 #require "vasputils/vaspdir.rb"
 
 #
+#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.
 #
-#
-class VaspUtils::VaspGeometryOptimizer < ComputationManager
-  class NoVaspDirError < Exception; end
-  class LatestDirStartedError < Exception; end
-  class NoIntegerEndedNameError < Exception; end
-
-  def initialize(dir)
-    super(dir)
-    @lockdir    = "lock_vaspgeomopt"
-    latest_dir # to check.
-  end
-
-  # 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"
-  def self.next_name(name)
-    basename = name.sub(/(\d*)$/, "")
-    new_num = $1.to_i + 1
-    return basename + sprintf("%02d", new_num)
-  end
-
-  # 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。
-  def calculate
-    #pp latest_dir.dir
-    $stdout.puts "Calculate #{latest_dir.dir}"
-    $stdout.flush
-
-    #pp latest_dir
-
-    latest_dir.start
-    #dir = latest_dir
-    #while (! finished?)
-    #  raise LatestDirStartedError if dir.state == :started
-    #  dir.start
-    #  if dir.finished?
-    #    break
-    #  else
-    #    #dir = prepare_next
-    #    puts "Geometry optimization fihished. Exit."
-    #  end
-    #end
-    #puts "Geometry optimization fihished. Exit."
-    #sleep 1 # for interrupt
-  end
-
-  # 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.
-  def finished?
-    return false unless latest_dir.finished?
-    return false unless latest_dir.outcar[:ionic_steps] == 1
-    return true
-  end
-
-  # 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.
-  def latest_dir
-    Dir.glob("#{@dir}/*").sort.reverse.find do |dir|
-      begin
-        vd = VaspUtils::VaspDir.new(dir)
-        return vd
-      rescue VaspUtils::VaspDir::InitializeError
-        next
-      end
+class VaspUtils::VaspGeometryOptimizer < Comana::ComputationManager
+    class NoVaspDirError < Exception; end
+    class LatestDirStartedError < Exception; end
+    class NoIntegerEndedNameError < Exception; end
+    class NoContcarError < Exception; end
+    class InitializeError < Exception; end
+
+    PREFIX = "geomopt"
+
+    def initialize(dir)
+        super(dir)
+        @lockdir        = "lock_vaspgeomopt"
+        begin
+            latest_dir # to check.
+        rescue NoVaspDirError
+            raise InitializeError
+        end
+    end
+
+    # 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"
+    def self.next_name(name)
+        basename = name.sub(/(\d*)$/, "")
+        new_num = $1.to_i + 1
+        return basename + sprintf("%02d", new_num)
+    end
+
+    # 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。
+    def calculate
+        $stdout.puts "Calculate #{latest_dir.dir}"
+        $stdout.flush
+
+        latest_dir.start
+        #dir = latest_dir
+        #while (! finished?)
+        #    raise LatestDirStartedError if dir.state == :started
+        #    dir.start
+        #    if dir.finished?
+        #        break
+        #    else
+        #        #dir = prepare_next
+        #        puts "Geometry optimization fihished. Exit."
+        #    end
+        #end
+        #puts "Geometry optimization fihished. Exit."
+        #sleep 1 # for interrupt
+    end
+
+    # 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.
+    def finished?
+        return false unless latest_dir.finished?
+        return false unless latest_dir.outcar[:ionic_steps] == 1
+        return true
+    end
+
+    # 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.
+    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
+
+    #Keep 'geomopt00/{POSCAR,POTCAR,INCAR,POTCAR}', remove others.
+    def reset_init
+        poscars = Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort
+        poscar = nil
+        path = nil
+        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
+        ##queeue
+        rm_list += Dir.glob "#{@dir}/lock*"
+        rm_list += Dir.glob "#{@dir}/*.sh"
+        rm_list += Dir.glob "#{@dir}/*.log"
+        rm_list += Dir.glob "#{@dir}/*.o*"
+        ##remove
+        rm_list.each do |file|
+            FileUtils.rm_rf file
+        end
+    end
+
+    #Generate a new vaspdir as 'geomopt00'.
+    #Other directories, including old 'geomopt00', are removed.
+    def reset_next(io = $stdout)
+        begin
+            latest_dir.contcar
+            prepare_next
+            clean_queue_files
+        rescue Errno::ENOENT
+            latest_dir.reset_init(io)
+            clean_queue_files
+        rescue VaspUtils::Poscar::ParseError
+            latest_dir.reset_init(io)
+            clean_queue_files
+        end
+    end
+
+    #Generate a new vaspdir as 'geomopt00'.
+    #Other directories, including old 'geomopt00', are removed.
+    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
+
+    private
+
+    # Generate next directory from latest_dir.
+    # Need proper CONTCAR. If not, raise NoContcarError.
+    def prepare_next
+        raise NoContcarError unless File.exist? "#{latest_dir.dir}/CONTCAR"
+
+        new_dir = self.class.next_name(latest_dir.dir)
+        Dir.mkdir new_dir
+
+        #FileUtils.cp("#{latest_dir.dir}/CHG"           , "#{new_dir}/CHG"       )
+        #FileUtils.cp("#{latest_dir.dir}/CHGCAR"    , "#{new_dir}/CHGCAR"    )
+        #FileUtils.cp("#{latest_dir.dir}/DOSCAR"    , "#{new_dir}/DOSCAR"    )
+        #FileUtils.cp("#{latest_dir.dir}/EIGENVAL", "#{new_dir}/EIGENVAL")
+        #FileUtils.cp("#{latest_dir.dir}/INCAR"     , "#{new_dir}/INCAR"     )
+        #FileUtils.cp("#{latest_dir.dir}/KPOINTS" , "#{new_dir}/KPOINTS" )
+        #FileUtils.cp("#{latest_dir.dir}/OSZICAR" , "#{new_dir}/OSZICAR" )
+        #FileUtils.cp("#{latest_dir.dir}/PCDAT"     , "#{new_dir}/PCDAT"     )
+        #FileUtils.cp("#{latest_dir.dir}/POTCAR"    , "#{new_dir}/POTCAR"    )
+        #FileUtils.cp("#{latest_dir.dir}/WAVECAR" , "#{new_dir}/WAVECAR" )
+        #FileUtils.cp("#{latest_dir.dir}/XDATCAR" , "#{new_dir}/XDATCAR" )
+
+        possible_files = ["CHG", "CHGCAR", "DOSCAR", "EIGENVAL", 
+            "OSZICAR", "PCDAT", "WAVECAR", "XDATCAR"]
+        possible_files.each do |file|
+            if File.exist? "#{latest_dir.dir}/#{file}"
+                FileUtils.cp("#{latest_dir.dir}/#{file}", "#{new_dir}/#{file}")
+            end
+        end
+
+        necessary_files = ["INCAR", "KPOINTS", "POTCAR"]
+        necessary_files.each do |file|
+            FileUtils.cp("#{latest_dir.dir}/#{file}", "#{new_dir}/#{file}")
+        end
+
+        FileUtils.cp("#{latest_dir.dir}/CONTCAR" , "#{new_dir}/POSCAR"  ) # change name
+        # without POSCAR, OUTCAR, vasprun.xml
+        VaspUtils::VaspDir.new(new_dir)
+    end
+
+    def clean_queue_files
+        rm_list = []
+        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
     end
-    raise NoVaspDirError, @dir
-  end
-
-  private
-
-  # Generate next directory of latest_dir.
-  def prepare_next
-    new_dir = self.class.next_name(latest_dir.dir)
-    Dir.mkdir new_dir
-    FileUtils.cp("#{latest_dir.dir}/CHG"     , "#{new_dir}/CHG"     )
-    FileUtils.cp("#{latest_dir.dir}/CHGCAR"  , "#{new_dir}/CHGCAR"  )
-    FileUtils.cp("#{latest_dir.dir}/DOSCAR"  , "#{new_dir}/DOSCAR"  )
-    FileUtils.cp("#{latest_dir.dir}/EIGENVAL", "#{new_dir}/EIGENVAL")
-    FileUtils.cp("#{latest_dir.dir}/INCAR"   , "#{new_dir}/INCAR"   )
-    FileUtils.cp("#{latest_dir.dir}/KPOINTS" , "#{new_dir}/KPOINTS" )
-    FileUtils.cp("#{latest_dir.dir}/OSZICAR" , "#{new_dir}/OSZICAR" )
-    FileUtils.cp("#{latest_dir.dir}/PCDAT"   , "#{new_dir}/PCDAT"   )
-    FileUtils.cp("#{latest_dir.dir}/POTCAR"  , "#{new_dir}/POTCAR"  )
-    FileUtils.cp("#{latest_dir.dir}/WAVECAR" , "#{new_dir}/WAVECAR" )
-    FileUtils.cp("#{latest_dir.dir}/XDATCAR" , "#{new_dir}/XDATCAR" )
-    FileUtils.cp("#{latest_dir.dir}/CONTCAR" , "#{new_dir}/POSCAR"  ) # change name
-    # without POSCAR, OUTCAR, vasprun.xml
-    VaspUtils::VaspDir.new(new_dir)
-  end
 
 end