vasputils 0.0.7 → 0.0.8

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", ">= 0.0.8"
+  gem "comana", ">= 0.0.9"
   gem "builtinextension", ">= 0.0.3"
 end

data/VERSION

@@ -1 +1 @@
-0.0.7
+0.0.8

data/bin/lsvasp

@@ -5,34 +5,34 @@
 
 #require "vasputils/calcseries.rb"
 require "vasputils/vaspgeomopt.rb"
-require "optparse"
-
-# option analysis
-OPTIONS = Hash.new
-op = OptionParser.new
-op.on("-c", "--cutoff"          , "Show cutoff energy.    "){ OPTIONS[:cutoff ] = true }
-op.on("-e", "--electronic-steps", "Show electronic-steps." ){ OPTIONS[:e_steps] = true }
-op.on("-i", "--ionic-steps"     , "Show ionic-steps."      ){ OPTIONS[:i_steps] = true }
-op.on("-k", "--k-mesh"          , "Show k-mesh."           ){ OPTIONS[:k_mesh] = true }
-op.on("-K", "--irr-kpoints"     , "Show irreducible k-points."){ OPTIONS[:irr_k    ] = true }
-op.on("-l", "--lattice-const"   , "Show lattice constants."){ OPTIONS[:lattice] = true }
-op.on("-t", "--elapsed-time"    , "Show elapsed-time."     ){ OPTIONS[:time   ] = true }
-op.on("-T", "--time-estesp"     , "Show time per elec. steps."){ OPTIONS[:time_e] = true }
-op.on("-E", "--toten"           , "Show toten."            ){ OPTIONS[:toten  ] = true }
-op.on("-a", "--all"             , "Show all information."  ){
-  # -a で出力される順序はここで決まる。
-  OPTIONS[:cutoff    ] = true
-  OPTIONS[:irr_k     ] = true
-  OPTIONS[:k_mesh    ] = true
-  OPTIONS[:i_steps   ] = true
-  OPTIONS[:e_steps   ] = true
-  OPTIONS[:time      ] = true
-  OPTIONS[:time_e    ] = true
-  OPTIONS[:lattice   ] = true
-  OPTIONS[:toten     ] = true
-}
-
-op.parse!(ARGV)
+#require "optparse"
+#
+## option analysis
+#OPTIONS = Hash.new
+#op = OptionParser.new
+#op.on("-c", "--cutoff"          , "Show cutoff energy.    "){ OPTIONS[:cutoff ] = true }
+#op.on("-e", "--electronic-steps", "Show electronic-steps." ){ OPTIONS[:e_steps] = true }
+#op.on("-i", "--ionic-steps"     , "Show ionic-steps."      ){ OPTIONS[:i_steps] = true }
+#op.on("-k", "--k-mesh"          , "Show k-mesh."           ){ OPTIONS[:k_mesh] = true }
+#op.on("-K", "--irr-kpoints"     , "Show irreducible k-points."){ OPTIONS[:irr_k    ] = true }
+#op.on("-l", "--lattice-const"   , "Show lattice constants."){ OPTIONS[:lattice] = true }
+#op.on("-t", "--elapsed-time"    , "Show elapsed-time."     ){ OPTIONS[:time   ] = true }
+#op.on("-T", "--time-estesp"     , "Show time per elec. steps."){ OPTIONS[:time_e] = true }
+#op.on("-E", "--toten"           , "Show toten."            ){ OPTIONS[:toten  ] = true }
+#op.on("-a", "--all"             , "Show all information."  ){
+#  # -a で出力される順序はここで決まる。
+#  OPTIONS[:cutoff    ] = true
+#  OPTIONS[:irr_k     ] = true
+#  OPTIONS[:k_mesh    ] = true
+#  OPTIONS[:i_steps   ] = true
+#  OPTIONS[:e_steps   ] = true
+#  OPTIONS[:time      ] = true
+#  OPTIONS[:time_e    ] = true
+#  OPTIONS[:lattice   ] = true
+#  OPTIONS[:toten     ] = true
+#}
+#
+#op.parse!(ARGV)
 
 dirs = ARGV
 dirs = Dir.glob("*").sort if ARGV.empty?
@@ -59,32 +59,37 @@ dirs = Dir.glob("*").sort if ARGV.empty?
 #puts "#" + items.join(", ")
 
 dirs.each do |dir|
-  begin
-    ldir = VaspGeomOpt.new(dir).latest_dir
-    results = []
-    names = []
-    OPTIONS.each do |key, val|
-      case key
-      when :cutoff
-        results << sprintf("%6s", ldir.finished_calc.incar["ENCUT"])
-      when :k_mesh    then results << sprintf("%2d, %2d, %2d, %8.5f, %8.5f, %8.5f",
-        * ldir.finished_calc.kpoints[:mesh], * ldir.finished_calc.kpoints[:shift])
-      when :irr_k     then results << sprintf("%4d", ldir.finished_calc.outcar[:irreducible_kpoints])
-      when :lattice   then
-        results << sprintf("%9.5f, %9.5f, %9.5f, %9.5f, %9.5f, %9.5f",
-          * ldir.finished_calc.contcar.axes.get_lattice_constants)
-      when :e_steps   then results << sprintf("%4d", ldir.internal_steps)
-      when :i_steps   then results << sprintf("%4d", ldir.external_steps)
-      when :time      then results << sprintf("%8d", ldir.elapsed_time)
-      when :time_e    then results << sprintf("%8d", ldir.elapsed_time/ldir.internal_steps)
-      when :toten     then results << sprintf("%16.4f", ldir.finished_calc.outcar[:totens][-1])
-      end
-    end
-    results << dir
-    puts " " + results.join(", ")
-  rescue
-    puts "Something wrong: #{dir}"
-    next
-  end
+  state = VaspGeomOpt.new(dir).state
+  longest = :terminated.size
+  state = state.to_s + (" " * (longest - state.size ))
+
+  puts 
+  #begin
+  #  ldir = VaspGeomOpt.new(dir).latest_dir
+  #  results = []
+  #  names = []
+  #  OPTIONS.each do |key, val|
+  #    case key
+  #    when :cutoff
+  #      results << sprintf("%6s", ldir.finished_calc.incar["ENCUT"])
+  #    when :k_mesh    then results << sprintf("%2d, %2d, %2d, %8.5f, %8.5f, %8.5f",
+  #      * ldir.finished_calc.kpoints[:mesh], * ldir.finished_calc.kpoints[:shift])
+  #    when :irr_k     then results << sprintf("%4d", ldir.finished_calc.outcar[:irreducible_kpoints])
+  #    when :lattice   then
+  #      results << sprintf("%9.5f, %9.5f, %9.5f, %9.5f, %9.5f, %9.5f",
+  #        * ldir.finished_calc.contcar.axes.get_lattice_constants)
+  #    when :e_steps   then results << sprintf("%4d", ldir.internal_steps)
+  #    when :i_steps   then results << sprintf("%4d", ldir.external_steps)
+  #    when :time      then results << sprintf("%8d", ldir.elapsed_time)
+  #    when :time_e    then results << sprintf("%8d", ldir.elapsed_time/ldir.internal_steps)
+  #    when :toten     then results << sprintf("%16.4f", ldir.finished_calc.outcar[:totens][-1])
+  #    end
+  #  end
+  #  results << dir
+  #  puts " " + results.join(", ")
+  #rescue
+  #  puts "Something wrong: #{dir}"
+  #  next
+  #end
 
 end

data/bin/qsubvasp

@@ -12,30 +12,89 @@
 #     the INDICATOR in ~/.machineinfo
 #     Default value is 1.
 #
-#   calc_dir must be a vasp geometry optimization directory.
+#   calc_dir is a vasp directory as usual,
+#   when with -g option, VaspGeomOpt directory.
 
 #require "optparse"
-require "yaml"
 require "pp"
+require "yaml"
+require "optparse"
 
 require "rubygems"
 gem "comana"
 require "comana/queuesubmitter.rb"
-#require "comana/machineinfo.rb"
+require "comana/machineinfo.rb"
 
 require "vasputils/vaspdir.rb"
 require "vasputils/vaspgeomopt.rb"
 
+opts = {}
+
+op = OptionParser.new
+op.on("-c cluster", "--cluster" , "Cluster name."){|v| opts["cluster"] = v }
+op.on("-n number", "--number", "Indicate node number, or key in ~/.machineinfo."){|v|
+  opts["number"] = v
+}
+op.on("-g", "--geom-opt", "Geometry optimization."){ opts["geomopt"] = true}
+op.parse!(ARGV)
+
+def condition_check(opts)
+  # Condition Check
+  mi = MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo")
+  conds = {}
+  # cluster
+  name = opts["cluster"]
+  #pp mi.get_info(name)
+  if name
+    conds["cluster"] = name
+  else
+    puts "-c CLUSTER_NAME is necessary."
+    exit
+  end
 
-OPTS = QueueSubmitter.parse_options(
-  ARGV, MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo")
-)
-OPTS[:directory] = VaspGeomOpt.new(File.expand_path(ARGV[0]))
-OPTS[:command] = "runvasp -g"
-#pp OPTS; exit
+  # target and command
+  unless ARGV.size == 1
+    puts "Indicate only one directory for vasp. Argument: #{ARGV}"
+    exit
+  end
+  if opts["geomopt"]
+    begin
+      conds["target"] = VaspGeomOpt.new(File.expand_path(ARGV[0]))
+      conds["command"] = "runvasp -g"
+    rescue VaspGeomOpt::NoVaspDirError
+      puts "Seem not to be a directory for VaspGeomOpt #{ARGV}"
+      exit
+    end
+  else
+    begin
+      conds["target"] = VaspDir.new(File.expand_path(ARGV[0]))
+      conds["command"] = "runvasp"
+    rescue VaspDir::InitializeError
+      puts "Seem not to be a directory for VaspDir #{ARGV}"
+      exit
+    end
+  end
 
-qs = QueueSubmitter.new(OPTS)
+  # number
+  str = opts["number"]
+  num = str.to_i
+  if num > 0
+    conds["number"] = num
+  else
+    if mi.get_info(name).has_key?(str)
+      conds["number"] = mi.get_info(name)[str]
+    else
+      puts "-n argument must be a positive integer or key in ~/machineinfo."
+      exit
+    end
+  end
+  conds
+end
+opts = condition_check(opts)
+
+qs = QueueSubmitter.new(opts)
 #pp qs; exit
+
 begin
   qs.start
   puts "Submitted. Exit."

data/memo.txt

@@ -1,9 +1,12 @@
 #
 
+0.0.8 release
+  Modified bin/qsubvasp, add -g option.
+
 0.0.7 release
   Modified bin/qsubvasp
 
-0.0.6 release [2012-05-10]
+0.0.6 release
   bin/qsubvasp is added.
   lib/vaspdir is modified to raise ExecuteError when vasp failed.
 

data/vasputils.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "vasputils"
-  s.version = "0.0.7"
+  s.version = "0.0.8"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-05-18"
+  s.date = "2012-05-29"
   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>, [">= 0.0.8"])
+      s.add_development_dependency(%q<comana>, [">= 0.0.9"])
       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>, [">= 0.0.8"])
+      s.add_dependency(%q<comana>, [">= 0.0.9"])
       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>, [">= 0.0.8"])
+    s.add_dependency(%q<comana>, [">= 0.0.9"])
     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: 0.0.7
+  version: 0.0.8
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-18 00:00:00.000000000 Z
+date: 2012-05-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &85401430 !ruby/object:Gem::Requirement
+  requirement: &80740170 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *85401430
+  version_requirements: *80740170
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &85401110 !ruby/object:Gem::Requirement
+  requirement: &80739710 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *85401110
+  version_requirements: *80739710
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &85400730 !ruby/object:Gem::Requirement
+  requirement: &80739300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *85400730
+  version_requirements: *80739300
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &85400380 !ruby/object:Gem::Requirement
+  requirement: &80739060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *85400380
+  version_requirements: *80739060
 - !ruby/object:Gem::Dependency
   name: crystalcell
-  requirement: &85400010 !ruby/object:Gem::Requirement
+  requirement: &80738780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *85400010
+  version_requirements: *80738780
 - !ruby/object:Gem::Dependency
   name: mageo
-  requirement: &85399650 !ruby/object:Gem::Requirement
+  requirement: &80738530 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *85399650
+  version_requirements: *80738530
 - !ruby/object:Gem::Dependency
   name: malge
-  requirement: &85399320 !ruby/object:Gem::Requirement
+  requirement: &80738290 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: 0.0.1
   type: :development
   prerelease: false
-  version_requirements: *85399320
+  version_requirements: *80738290
 - !ruby/object:Gem::Dependency
   name: maset
-  requirement: &85398980 !ruby/object:Gem::Requirement
+  requirement: &80738050 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,21 +98,21 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *85398980
+  version_requirements: *80738050
 - !ruby/object:Gem::Dependency
   name: comana
-  requirement: &85830120 !ruby/object:Gem::Requirement
+  requirement: &80737740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.8
+        version: 0.0.9
   type: :development
   prerelease: false
-  version_requirements: *85830120
+  version_requirements: *80737740
 - !ruby/object:Gem::Dependency
   name: builtinextension
-  requirement: &85829250 !ruby/object:Gem::Requirement
+  requirement: &80737270 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,7 +120,7 @@ dependencies:
         version: 0.0.3
   type: :development
   prerelease: false
-  version_requirements: *85829250
+  version_requirements: *80737270
 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: -1045014531
+      hash: -929575121
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: