vasputils 0.0.4 → 0.0.5

data/Gemfile

@@ -6,9 +6,9 @@ source "http://rubygems.org"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rdoc", "~> 3.12"
-  gem "bundler", "~> 1.1.3"
-  gem "jeweler", "~> 1.8.3"
+  gem "rdoc", ">= 3.12"
+  gem "bundler", ">= 1.1.3"
+  gem "jeweler", ">= 1.8.3"
   gem "simplecov", ">= 0"
   gem "crystalcell", ">= 0.0.0"
   gem "mageo", ">= 0.0.0"

data/VERSION

@@ -1 +1 @@
-0.0.4
+0.0.5

data/bin/qsubvasp

@@ -45,7 +45,7 @@ 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 "vaspgeomopt"
+  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"

data/bin/runvasp

@@ -1,8 +1,10 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
-
 require "rubygems"
+gem "comana"
+require "comana/computationmanager.rb"
+
 gem "vasputils"
 require "vasputils/vaspdir.rb"
 require "vasputils/vaspgeomopt.rb"
@@ -25,11 +27,11 @@ else
   calc_dir = VaspDir.new(dir)
 end
 
-#pp calc_dir
+#pp calc_dir.class.ancestors
 
 begin
   calc_dir.start
-rescue Comana::AlreadyStartedError
+rescue ComputationManager::AlreadyStartedError
   puts "Already started. Exit."
   exit
 end

data/lib/vasputils/vaspdir.rb

@@ -28,8 +28,10 @@ require "vasputils/kpoints.rb"
 # 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 VaspDir < Comana
+class VaspDir < ComputationManager
   class InitializeError < Exception; end
+  class NoVaspBinaryError < Exception; end
+  class PrepareNextError < 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)
@@ -37,6 +39,7 @@ class VaspDir < Comana
   ##- k 点探索モードは無理だろう。
   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
@@ -96,58 +99,29 @@ class VaspDir < Comana
   # 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
-    #File.open(lock_file, "w") do |lock_io|
-    #  lock_io.puts "HOST: #{ENV["HOST"]}"
-    #  lock_io.puts "START: #{Time.now.to_s}"
-    #  lock_io.flush
-
-    #  num_cores = 4 if /^Se\d\d/ =~ ENV["HOST"]
-    #  num_cores = 4 if /^Ge\d\d/ =~ ENV["HOST"]
-    #  num_cores = 4 if /^Ga\d\d/ =~ ENV["HOST"]
-    #  num_cores = 4 if /^At$/ =~ ENV["HOST"]
-    #  num_cores = 2 if /^yggdrasil$/ =~ ENV["HOST"]
-
-    #  # machines を生成
-    #  File.open("#{@dir}/machines", "w") do |io|
-    #    io.puts "localhost:#{num_cores}"
-    #  end
-    #end
-    #num_cores = 4
-
-    #settings = YAML.load_file("#{ENV["HOME"]}/.machineinfo")
-    #setting  = settings[ENV["HOST"]]
     begin
-      hi = MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo").get_host(ENV["HOST"])
-      vasp = hi["vasp"]
+      info =
+        MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo").get_info(ENV["HOST"])
+      vasp = info["vasp"]
     rescue
-      vasp = "vasp"
+      #vasp = "vasp"
+      raise NoVaspBinaryError, "No vasp path in #{ENV["HOME"]}/.machineinfo"
     end
     command = "cd #{@dir};"
     command += vasp
     command += "> stdout"
 
-    #if ENV["PBS_JOBID"]
-    #  command += "/usr/local/calc/mpiexec/bin/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
-    #else
-    #  /usr/local/calc/bin/vasp5212-mpich2"
-    ##  command = "cd #{@dir};" +
-    ##    "/usr/local/calc/mpich-1.2.7-ifc7/bin/mpirun " +
-    ##    "-np #{num_cores} " +
-    ##    "-machinefile machines " +
-    ##    "/usr/local/calc/vasp/vasp4631mpi" +
-    ##    "> stdout"
-    #end
-
     system command
   end
 
   def prepare_next
     #do_nothing
+    raise PrepareNextError, "VaspDir doesn't need next."
   end
 
 end
 
-#class VaspGeometryOptimization < Comana
+#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。

data/lib/vasputils/vaspgeomopt.rb

@@ -6,20 +6,21 @@ require "fileutils"
 
 require "rubygems"
 gem "comana"
-require "comana"
+require "comana/computationmanager.rb"
 
-require "vasputils/vaspdir"
+require "vasputils/vaspdir.rb"
 
 #
 #
 #
-class VaspGeomOpt < Comana
+class VaspGeomOpt < 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
 

data/memo.txt

@@ -1,3 +1,8 @@
+0.0.5
+  Modifiy error process in VaspDir.calculate.
+  Add runvasp.
+  Add qsubvasp.
+
 0.0.4 release
   Using Comana library.
   Add runvasp.

data/test/test_vaspdir.rb

@@ -5,7 +5,7 @@ $TEST = true
 
 require "rubygems"
 gem "comana"
-require "comana.rb"
+require "comana/computationmanager.rb"
 
 require "test/unit"
 require "vasputils/vaspdir.rb"
@@ -14,7 +14,7 @@ require "vasputils/vaspdir.rb"
 # assert_in_delta( cor, data, $tolerance )
 # assert_raise( RuntimeError ){}
 
-class VaspDir < Comana
+class VaspDir < ComputationManager
   attr_reader :mode
 
   def calculate
@@ -88,7 +88,7 @@ class TC_VaspDir < Test::Unit::TestCase
   end
 
   def test_calculate
-    lock_dir = "test/vaspdir/not-yet/comana_lock"
+    lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
     Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
     #pp @vd00;exit
     #@vd00.calculate
@@ -102,7 +102,7 @@ class TC_VaspDir < Test::Unit::TestCase
     assert(FileTest.exist? "test/vaspdir/not-yet/POSCAR")
     assert(FileTest.exist? "test/vaspdir/not-yet/POTCAR")
 
-    lock_dir = "test/vaspdir/not-yet/comana_lock"
+    lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
     Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
   end
 

data/test/test_vaspgeomopt.rb

@@ -3,10 +3,11 @@
 
 require "fileutils"
 require "test/unit"
+
 require "vasputils/vaspgeomopt.rb"
 
 
-class VaspGeomOpt < Comana
+class VaspGeomOpt < ComputationManager
   public :latest_dir, :prepare_next
 end
 

data/vasputils.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "vasputils"
-  s.version = "0.0.4"
+  s.version = "0.0.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-05-07"
+  s.date = "2012-05-08"
   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"]
@@ -207,9 +207,9 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.1.3"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_development_dependency(%q<rdoc>, [">= 3.12"])
+      s.add_development_dependency(%q<bundler>, [">= 1.1.3"])
+      s.add_development_dependency(%q<jeweler>, [">= 1.8.3"])
       s.add_development_dependency(%q<simplecov>, [">= 0"])
       s.add_development_dependency(%q<crystalcell>, [">= 0.0.0"])
       s.add_development_dependency(%q<mageo>, [">= 0.0.0"])
@@ -218,9 +218,9 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<comana>, [">= 0.0.5"])
       s.add_development_dependency(%q<builtinextension>, [">= 0.0.3"])
     else
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["~> 1.1.3"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+      s.add_dependency(%q<rdoc>, [">= 3.12"])
+      s.add_dependency(%q<bundler>, [">= 1.1.3"])
+      s.add_dependency(%q<jeweler>, [">= 1.8.3"])
       s.add_dependency(%q<simplecov>, [">= 0"])
       s.add_dependency(%q<crystalcell>, [">= 0.0.0"])
       s.add_dependency(%q<mageo>, [">= 0.0.0"])
@@ -230,9 +230,9 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<builtinextension>, [">= 0.0.3"])
     end
   else
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["~> 1.1.3"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
+    s.add_dependency(%q<rdoc>, [">= 3.12"])
+    s.add_dependency(%q<bundler>, [">= 1.1.3"])
+    s.add_dependency(%q<jeweler>, [">= 1.8.3"])
     s.add_dependency(%q<simplecov>, [">= 0"])
     s.add_dependency(%q<crystalcell>, [">= 0.0.0"])
     s.add_dependency(%q<mageo>, [">= 0.0.0"])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vasputils
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,44 +9,44 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-07 00:00:00.000000000 Z
+date: 2012-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &86738910 !ruby/object:Gem::Requirement
+  requirement: &82143140 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *86738910
+  version_requirements: *82143140
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &86737820 !ruby/object:Gem::Requirement
+  requirement: &82141240 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *86737820
+  version_requirements: *82141240
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &86753150 !ruby/object:Gem::Requirement
+  requirement: &82139430 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *86753150
+  version_requirements: *82139430
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &86752350 !ruby/object:Gem::Requirement
+  requirement: &82155010 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *86752350
+  version_requirements: *82155010
 - !ruby/object:Gem::Dependency
   name: crystalcell
-  requirement: &86751370 !ruby/object:Gem::Requirement
+  requirement: &82154520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *86751370
+  version_requirements: *82154520
 - !ruby/object:Gem::Dependency
   name: mageo
-  requirement: &86749640 !ruby/object:Gem::Requirement
+  requirement: &82153850 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *86749640
+  version_requirements: *82153850
 - !ruby/object:Gem::Dependency
   name: malge
-  requirement: &86748730 !ruby/object:Gem::Requirement
+  requirement: &82153190 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: 0.0.1
   type: :development
   prerelease: false
-  version_requirements: *86748730
+  version_requirements: *82153190
 - !ruby/object:Gem::Dependency
   name: maset
-  requirement: &86745950 !ruby/object:Gem::Requirement
+  requirement: &82152310 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *86745950
+  version_requirements: *82152310
 - !ruby/object:Gem::Dependency
   name: comana
-  requirement: &86584290 !ruby/object:Gem::Requirement
+  requirement: &82150690 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 0.0.5
   type: :development
   prerelease: false
-  version_requirements: *86584290
+  version_requirements: *82150690
 - !ruby/object:Gem::Dependency
   name: builtinextension
-  requirement: &86583340 !ruby/object:Gem::Requirement
+  requirement: &82149970 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
         version: 0.0.3
   type: :development
   prerelease: false
-  version_requirements: *86583340
+  version_requirements: *82149970
 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: -619006479
+      hash: -917063793
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: