vasputils 0.0.5 → 0.0.6

data/Gemfile

@@ -14,6 +14,6 @@ group :development do
   gem "mageo", ">= 0.0.0"
   gem "malge", ">= 0.0.1"
   gem "maset", ">= 0.0.0"
-  gem "comana", ">= 0.0.5"
+  gem "comana", ">= 0.0.6"
   gem "builtinextension", ">= 0.0.3"
 end

data/VERSION

@@ -1 +1 @@
-0.0.5
+0.0.6

data/bin/qsubvasp

@@ -1,66 +1,44 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
-
-SCRIPT_FILE = "pbs.sh"
-PBS_LOG = "pbs.log"
-
-
 require "optparse"
 require "yaml"
 require "pp"
 
+require "rubygems"
+gem "comana"
+require "comana/queuesubmitter.rb"
+require "comana/machineinfo.rb"
+
+require "vasputils/vaspdir.rb"
+require "vasputils/vaspgeomopt.rb"
+
 ## option analysis
 OPTS = {}
 op = OptionParser.new
-#op.on("-e", "--economy"  , "Prior efficiency."){OPTS[:e] = true}
-op.on("-s", "--speed"    , "Prior speed.")     {OPTS[:s] = true}
-
-op.on("-g", "--geom-opt" , "Geometry optimization.")     {OPTS[:g] = true}
-#op.on("-n", "--nebm"     , "Nudged Elastic Band method."){OPTS[:n] = true}
-#op.on("-c", "--cond-find", "Condition Finding.")         {OPTS[:c] = true}
-
+#op.on("-e"        , "--economy", "Prior efficiency."         ){OPTS[:e] = true}
+op.on("-s"        , "--speed"  , "Prior speed to efficiency."){OPTS[:s] = true}
+op.on("-n nodes"  , "--nodes"  , "Node series."              ){|v| OPTS[:n] = v}
+#op.on("-c command", "--command", "Command to calculate."     ){|v| OPTS[:c] = v}
+op.on("-d dir"    , "--dir"    , "Directory to calculate."   ){|v|
+  #OPTS[:d] = VaspDir.new(v)
+  OPTS[:d] = VaspGeomOpt.new(File.expand_path(v))
+}
 op.parse!(ARGV)
 
-cluster = ARGV[0]
-#cluster = ARGV
-#qsub で複数のクラスターを候補に入れることができるか？e.g., Ga, Ge
-#それによって、ここがかきかわる。
-
-#puts "Options -e and -s cannot be duplicated." if OPTS[:e] && OPTS[:s]
-#if [OPTS[:g], OPTS[:n], OPTS[:c]].select_all(true).size ==
-#  puts "Options -g, -n, and -c cannot be duplicated."
-#  exit
-#end
-
-yaml = YAML.load_file("#{ENV["HOME"]}/.machineinfo")
-pp yaml
+OPTS[:machineinfo] = MachineInfo.load_file
+OPTS[:c] = "runvasp -g"
 
-if File.exits?(SCRIPT_FILE)
-  puts "#{SCRIPT_FILE} already exist. Exit."
+qs = QueueSubmitter.new(OPTS)
+#pp qs; exit
+begin
+  qs.start
+  puts "Submitted. Exit."
+  exit
+rescue QueueSubmitter::AlreadyStartedError
+  puts "Already started. Exit."
+  exit
+rescue QueueSubmitter::PrepareNextError
+  puts "Must not happen."
   exit
 end
-
-File.open(SCRIPT_FILE, "w") do |io|
-  io.puts "#PBS -N task"
-  io.puts "#PBS -l nodes=4:ppn=1:Ga"
-  io.puts "cd $PBS_O_WORKDIR"
-  io.puts "runvasp"
-  #io.puts "#/usr/local/bin/mpiexec /usr/local/bin/vasp5212mpi-ifc11-fast"
-  #io.puts "#/home/ippei/local/mpi/mpiexec-0.84/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
-  #io.puts "#/usr/local/calc/mpiexec/bin/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
-  #io.puts "#~/tmp.rb #OK"
-
-  #io.puts condition
-  #io.puts rsync
-  #io.puts run
-  #io.puts rsync
-  #io.puts mv to trash？
-end
-
-# Record job_id in pbs. Overwrite if exists.
-job_id = `qsub #{SCRIPT_FILE}`
-File.open(PBS_LOG, "w") do |io|
-  io.puts job_id
-end
-

data/bin/runvasp

@@ -5,7 +5,7 @@ require "rubygems"
 gem "comana"
 require "comana/computationmanager.rb"
 
-gem "vasputils"
+#gem "vasputils"
 require "vasputils/vaspdir.rb"
 require "vasputils/vaspgeomopt.rb"
 
@@ -15,10 +15,8 @@ require "optparse"
 OPTIONS = {}
 op = OptionParser.new
 op.on("-g"    , "--geom-opt", "Geometry optimization"){OPTIONS[:g] = true}
-#op.on("-b val", "--bak=val", "descriptionB"){|v| OPTIONS[:bak] = v}
 op.parse!(ARGV)
 
-
 dir = ARGV[0] || "."
 
 if OPTIONS[:g]

data/lib/vasputils/vaspdir.rb

@@ -16,27 +16,15 @@ require "vasputils/outcar.rb"
 require "vasputils/poscar.rb"
 require "vasputils/kpoints.rb"
 
-# vasp 実行ディレクトリ(入力・出力ファイルを含む)を扱うクラス
-#
-# MEMO
-# interrupted? みたいなメソッドは作れない。
-# 実行が開始したあと、その計算の状態が中断されているのか、
-# 単に実行中でファイルが書き込まれている途中なのか、
-# プログラムを実行しているプロセス自身以外は、外部からは判別がつかない。
-#
-# ルール
-# try00 形式の postfix がついていることを前提とする。
-# 00 の部分には CONTCAR を POSCAR にする手続きで連続して行う計算の番号を示す。
+# Class for VASP executable directory,
+# including input and output files.
 #
 class VaspDir < ComputationManager
   class InitializeError < Exception; end
   class NoVaspBinaryError < Exception; end
   class PrepareNextError < Exception; end
+  class ExecuteError < Exception; end
 
-  #INCAR 解析とかして、モードを調べる。
-  #- 格子定数の構造最適化モード(ISIF = 3)
-  #- 格子定数を固定した構造最適化モード(ISIF = 2)
-  ##- k 点探索モードは無理だろう。
   def initialize(dir)
     super(dir)
     @lockdir    = "lock_vaspdir"
@@ -87,17 +75,6 @@ class VaspDir < ComputationManager
   private
 
   # vasp を投げる。
-  # 計算実行時に lock を生成する。
-  # もし既に lock が存在していれば、例外 VaspDirLockedError を
-  # 投げる。
-  # lock は作られっぱなしで、プログラムからは削除されない。
-  # 通常、一度計算したらもう二度と計算しないし。
-  #
-  # MEMO
-  # mpirun で投げる場合は
-  # machinefile を生成しないとどのホストで計算するか、安定しない。
-  # そのうち mpiexec from torque に対応するが、
-  # まずは mpirun で動くように作る。
   def calculate
     begin
       info =
@@ -111,7 +88,8 @@ class VaspDir < ComputationManager
     command += vasp
     command += "> stdout"
 
-    system command
+    end_status = system command
+    raise ExecuteError, "end_status is #{end_status.inspect}" unless end_status
   end
 
   def prepare_next
@@ -120,70 +98,3 @@ class VaspDir < ComputationManager
   end
 
 end
-
-#class VaspGeometryOptimization < ComputationManager
-#  # 次の計算ディレクトリを作成し、
-#  # その VaspDir クラスで self を置き換える。
-#  # 計算が正常終了していなければ、例外 VaspDirNotEndedError を生じる。
-#  # 次の計算ディレクトリが既に存在していれば例外 Errno::EEXIST が投げられる。
-#  def next
-#    raise NotEndedError unless normal_ended?
-#    raise ConvergedError unless to_be_continued?
-#    #postfix = /try(\d+)$/
-#    POSTFIX =~ @dir
-#    try_num = $1.to_i
-#    next_dir = @dir.sub(POSTFIX, sprintf("try%02d", try_num + 1))
-#    Dir.mkdir next_dir
-#    FileUtils.cp( "#{@dir}/INCAR"  , "#{next_dir}/INCAR")
-#    FileUtils.cp( "#{@dir}/KPOINTS", "#{next_dir}/KPOINTS")
-#    FileUtils.cp( "#{@dir}/POTCAR" , "#{next_dir}/POTCAR")
-#    FileUtils.cp( "#{@dir}/CONTCAR", "#{next_dir}/POSCAR")
-#    initialize(next_dir)
-#  end
-#
-#  # Return number of electronic steps.
-#  def internal_steps
-#    return outcar[:electronic_steps] if outcar
-#    return 0
-#  end
-#
-#  # Return number of ionic steps.
-#  def external_steps
-#    return outcar[:ionic_steps] if outcar
-#    return 0
-#  end
-#
-#  # Return elapsed time.
-#  def elapsed_time
-#    return outcar[:elapsed_time] if outcar
-#    return 0.0
-#  end
-#
-#  # normal_ended? が false なら false。
-#  # normal_ended? が true のうち、
-#  # 結果を使って次に計算すべきなら true を、そうでなければ false を返す。
-#  #
-#  # 計算すべき、の条件はモードによって異なる。
-#  #   NSW = 0 もしくは NSW = 1 のとき、必ず false。
-#  #   - :single_point     モードならば、常に false。
-#  #   - :geom_opt_lattice モードならば、ionic step が 2 以上なら true。
-#  #   - :geom_opt_atoms   モードならば、ionic step が NSW と同じなら true。
-#  #
-#  def to_be_continued?
-#    begin
-#      outcar = Outcar.load_file("#{@dir}/OUTCAR")
-#    rescue Errno::ENOENT
-#      return false
-#    end
-#    ionic_steps = outcar[:ionic_steps]
-#    return false unless outcar[:normal_ended]
-#    return false if @incar["NSW"].to_i <= 1
-#    if @mode == :geom_opt_lattice
-#      return ionic_steps != 1
-#    elsif @mode == :geom_opt_atoms
-#      return ionic_steps == @incar["NSW"].to_i
-#    else
-#      return false
-#    end
-#  end
-#

data/lib/vasputils/vaspgeomopt.rb

@@ -57,7 +57,7 @@ class VaspGeomOpt < ComputationManager
     #  end
     #end
     #puts "Geometry optimization fihished. Exit."
-    sleep 1 # for interrupt
+    #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、
@@ -108,7 +108,7 @@ class VaspGeomOpt < ComputationManager
         next
       end
     end
-    raise NoVaspDirError
+    raise NoVaspDirError, @dir
   end
 
 end

data/memo.txt

@@ -1,12 +1,18 @@
-0.0.5
+#
+
+0.0.6 release [2012-05-10]
+  bin/qsubvasp is added.
+  lib/vaspdir is modified to raise ExecuteError when vasp failed.
+
+0.0.5 release
   Modifiy error process in VaspDir.calculate.
   Add runvasp.
   Add qsubvasp.
 
 0.0.4 release
-  Using Comana library.
-  Add runvasp.
-  Modify VaspDir.
-  Add VaspGeomOpt.
+  Modified to use Comana.
+  bin/runvasp is added.
+  VaspDir is modified.
+  VaspGeomOpt is added.
 
 0.0.3 release

data/vasputils.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "vasputils"
-  s.version = "0.0.5"
+  s.version = "0.0.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-05-08"
+  s.date = "2012-05-10"
   s.description = "This gem provides parsers for some of input and output files for VASP.\n    This will provide support command for computations."
   s.email = "ippei94da@gmail.com"
   s.executables = ["addVolumeToten.rb", "latticeconstants", "lsvasp", "lsvaspdir", "lsvaspseries", "qsubvasp", "runvasp", "symposcar"]
@@ -215,7 +215,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<mageo>, [">= 0.0.0"])
       s.add_development_dependency(%q<malge>, [">= 0.0.1"])
       s.add_development_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_development_dependency(%q<comana>, [">= 0.0.5"])
+      s.add_development_dependency(%q<comana>, [">= 0.0.6"])
       s.add_development_dependency(%q<builtinextension>, [">= 0.0.3"])
     else
       s.add_dependency(%q<rdoc>, [">= 3.12"])
@@ -226,7 +226,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<mageo>, [">= 0.0.0"])
       s.add_dependency(%q<malge>, [">= 0.0.1"])
       s.add_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_dependency(%q<comana>, [">= 0.0.5"])
+      s.add_dependency(%q<comana>, [">= 0.0.6"])
       s.add_dependency(%q<builtinextension>, [">= 0.0.3"])
     end
   else
@@ -238,7 +238,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<mageo>, [">= 0.0.0"])
     s.add_dependency(%q<malge>, [">= 0.0.1"])
     s.add_dependency(%q<maset>, [">= 0.0.0"])
-    s.add_dependency(%q<comana>, [">= 0.0.5"])
+    s.add_dependency(%q<comana>, [">= 0.0.6"])
     s.add_dependency(%q<builtinextension>, [">= 0.0.3"])
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vasputils
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-08 00:00:00.000000000 Z
+date: 2012-05-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &82143140 !ruby/object:Gem::Requirement
+  requirement: &79249910 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *82143140
+  version_requirements: *79249910
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &82141240 !ruby/object:Gem::Requirement
+  requirement: &79246810 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *82141240
+  version_requirements: *79246810
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &82139430 !ruby/object:Gem::Requirement
+  requirement: &79590980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *82139430
+  version_requirements: *79590980
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &82155010 !ruby/object:Gem::Requirement
+  requirement: &79586380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *82155010
+  version_requirements: *79586380
 - !ruby/object:Gem::Dependency
   name: crystalcell
-  requirement: &82154520 !ruby/object:Gem::Requirement
+  requirement: &79583830 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *82154520
+  version_requirements: *79583830
 - !ruby/object:Gem::Dependency
   name: mageo
-  requirement: &82153850 !ruby/object:Gem::Requirement
+  requirement: &79580340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *82153850
+  version_requirements: *79580340
 - !ruby/object:Gem::Dependency
   name: malge
-  requirement: &82153190 !ruby/object:Gem::Requirement
+  requirement: &79577480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: 0.0.1
   type: :development
   prerelease: false
-  version_requirements: *82153190
+  version_requirements: *79577480
 - !ruby/object:Gem::Dependency
   name: maset
-  requirement: &82152310 !ruby/object:Gem::Requirement
+  requirement: &79577090 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,21 +98,21 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *82152310
+  version_requirements: *79577090
 - !ruby/object:Gem::Dependency
   name: comana
-  requirement: &82150690 !ruby/object:Gem::Requirement
+  requirement: &79576480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.5
+        version: 0.0.6
   type: :development
   prerelease: false
-  version_requirements: *82150690
+  version_requirements: *79576480
 - !ruby/object:Gem::Dependency
   name: builtinextension
-  requirement: &82149970 !ruby/object:Gem::Requirement
+  requirement: &79566760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
         version: 0.0.3
   type: :development
   prerelease: false
-  version_requirements: *82149970
+  version_requirements: *79566760
 description: ! "This gem provides parsers for some of input and output files for VASP.\n
   \   This will provide support command for computations."
 email: ippei94da@gmail.com
@@ -331,7 +331,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -917063793
+      hash: -103563277
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: