vaspdir.rb in vasputils-0.1.1

- old
+ new
@@ -11,206 +11,223 @@
 
 # Class for VASP executable directory,
 # including input and output files.
 #
 class VaspUtils::VaspDir < Comana::ComputationManager
-    MACHINEFILE = "machines"
+  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
+  #class InitializeError < Comana::ComputationManager::InitializeError; end
+  class InitializeError < StandardError; end
+  class NoVaspBinaryError < StandardError; end
+  class PrepareNextError < StandardError; end
+  class ExecuteError < StandardError; end
+  class InvalidValueError < StandardError; end
+  class AlreadyExistError < StandardError; 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
+  def initialize(dir)
+    super(dir)
+    @lockdir        = "lock_execute"
+    %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
+  # 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 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 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
+  # 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
 
-    # 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 INCAR を表現する Incar クラスインスタンスを返す。
+  # 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
+  # 配下の KPOINTS を表現する Kpoints クラスインスタンスを返す。
+  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
+  # 配下の vasprun.xml を表現する VasprunXml クラスインスタンスを返す。
+  def vasprun_xml
+    VaspUtils::VasprunXml.load_file("#{@dir}/vasprun.xml")
+  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}" }
+  # 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
 
-            #puts "  Keep files:"
-            #keep_files.each { |file| puts "        #{file}" }
+  # VASP の出力ファイルを削除する。
+  #入力のみに使うもの、残す
+  #   INCAR KPOINTS POSCAR POTCAR
+  #主に出力。消す。
+  #   CHG CHGCAR CONTCAR DOSCAR EIGENVAL EIGENVALUE ELFCAR
+  #   EXHCAR IBZKPT LOCPOT OSZICAR OUTCAR PCDAT PRJCAR PROCAR
+  #   PROOUT STOPCAR TMPCAR WAVECAR XDATCAR vasprun.xml
+  #
+  #付随する出力ファイル。残す。
+  #   machines stderr stdout
+  def reset_clean(io = $stdout)
+    remove_files = %w(
+      CHG CHGCAR CONTCAR DOSCAR EIGENVAL EIGENVALUE
+      ELFCAR EXHCAR IBZKPT LOCPOT OSZICAR OUTCAR PCDAT
+      PRJCAR PROCAR
+      PROOUT STOPCAR TMPCAR WAVECAR XDATCAR vasprun.xml
+    )
+    remove_files.each do |file|
+      io.puts "    Removing: #{file}"
+      FileUtils.rm_rf "#{@dir}/#{file}"
+    end
+  end
 
-            remove_files.each do |file|
-                io.puts "    Removing: #{file}"
-                FileUtils.rm_rf "#{@dir}/#{file}"
-            end
-        end
+  # Delete all except for four files, INCAR, KPOINTS, POSCAR, POTCAR.
+  def reset_initialize(io = $stdout)
+    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
 
-    # '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
+    if remove_files.size == 0
+      io.puts "    No remove files."
+      return
+    else
+      remove_files.each do |file|
+        io.puts "    Removing: #{file}"
+        FileUtils.rm_rf "#{@dir}/#{file}"
+      end
+    end
+  end
 
-        Dir.mkdir tgt_name
+  # '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
 
-        ##POSCAR
-        FileUtils.cp("#{@dir}/POSCAR", "#{tgt_name}/POSCAR")
+    Dir.mkdir tgt_name
 
-        ##POTCAR
-        FileUtils.cp("#{@dir}/POTCAR", "#{tgt_name}/POTCAR")
+    ##POSCAR
+    FileUtils.cp("#{@dir}/POSCAR", "#{tgt_name}/POSCAR")
 
-        ##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
+    ##POTCAR
+    FileUtils.cp("#{@dir}/POTCAR", "#{tgt_name}/POTCAR")
 
-        ##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
+    ##INCAR
+    new_incar = incar
+    new_incar["ENCUT"] = condition[:encut] if condition[:encut]
+    File.open("#{tgt_name}/INCAR", "w") do |io|
+      new_incar.dump(io)
     end
 
-    private
+    ##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|
+      new_kpoints.dump(io)
+    end
+  end
 
-    # vasp を投げる。
-    def calculate
-        #HOSTNAME is for GridEngine
-        hostname = (ENV["HOST"] || ENV["HOSTNAME"]).sub(/\..*$/, "") #ignore domain name
+  private
 
-        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
+  # vasp を投げる。
+  def calculate
+    #HOSTNAME is for GridEngine
+    hostname = (ENV["HOST"] || ENV["HOSTNAME"]).sub(/\..*$/, "") #ignore domain name
 
-        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
+    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
 
-        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
+    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
 
-        #pp "#{info["mpi"]} -machinefile #{MACHINEFILE} -np #{nslots} #{info["vasp"]}"
-        command = "cd #{@dir};"
-        command += "#{info["mpi"]} -machinefile #{MACHINEFILE} -np #{nslots} #{info["vasp"]}"
-        command += "> stdout"
+    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
 
-        io = File.open("#{@dir}/runvasp.log", "w")
-        io.puts command
-        io.close
+    command = "cd #{@dir};"
+    command += "#{info["mpi"]} -machinefile #{MACHINEFILE} -np #{nslots} #{info["vasp"]}"
+    command += "| tee stdout"
 
-        end_status = system command
-        raise ExecuteError, "end_status is #{end_status.inspect}" unless end_status
-    end
+    io = File.open("#{@dir}/executevasp.log", "w")
+    io.puts command
+    io.close
 
-    def prepare_next
-        #do_nothing
-        raise PrepareNextError, "VaspDir doesn't need next."
-    end
+    end_status = system command
+    raise ExecuteError, "end_status is #{end_status.inspect}" unless end_status
+  end
 
-    def generate_machinefile(lines)
-        io = File.open("#{@dir}/#{MACHINEFILE}", "w")
-        io.puts lines
-        io.close
-    end
+  def prepare_next
+    raise PrepareNextError, "VaspDir doesn't need next."
+  end
 
+  def generate_machinefile(lines)
+    io = File.open("#{@dir}/#{MACHINEFILE}", "w")
+    io.puts lines
+    io.close
+  end
 end