vasputils 0.0.8 → 0.0.9

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vasputils
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-29 00:00:00.000000000 Z
+date: 2012-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &80740170 !ruby/object:Gem::Requirement
+  requirement: &83019100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *80740170
+  version_requirements: *83019100
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &80739710 !ruby/object:Gem::Requirement
+  requirement: &83018860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *80739710
+  version_requirements: *83018860
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &80739300 !ruby/object:Gem::Requirement
+  requirement: &83018620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *80739300
+  version_requirements: *83018620
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &80739060 !ruby/object:Gem::Requirement
+  requirement: &83018380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *80739060
+  version_requirements: *83018380
 - !ruby/object:Gem::Dependency
   name: crystalcell
-  requirement: &80738780 !ruby/object:Gem::Requirement
+  requirement: &83018140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *80738780
+  version_requirements: *83018140
 - !ruby/object:Gem::Dependency
   name: mageo
-  requirement: &80738530 !ruby/object:Gem::Requirement
+  requirement: &83017900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *80738530
+  version_requirements: *83017900
 - !ruby/object:Gem::Dependency
   name: malge
-  requirement: &80738290 !ruby/object:Gem::Requirement
+  requirement: &83017660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: 0.0.1
   type: :development
   prerelease: false
-  version_requirements: *80738290
+  version_requirements: *83017660
 - !ruby/object:Gem::Dependency
   name: maset
-  requirement: &80738050 !ruby/object:Gem::Requirement
+  requirement: &83017420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *80738050
+  version_requirements: *83017420
 - !ruby/object:Gem::Dependency
   name: comana
-  requirement: &80737740 !ruby/object:Gem::Requirement
+  requirement: &83017180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 0.0.9
   type: :development
   prerelease: false
-  version_requirements: *80737740
+  version_requirements: *83017180
 - !ruby/object:Gem::Dependency
   name: builtinextension
-  requirement: &80737270 !ruby/object:Gem::Requirement
+  requirement: &83016940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,16 +120,14 @@ dependencies:
         version: 0.0.3
   type: :development
   prerelease: false
-  version_requirements: *80737270
+  version_requirements: *83016940
 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
 executables:
 - addVolumeToten.rb
+- checkvasp
 - latticeconstants
-- lsvasp
-- lsvaspdir
-- lsvaspseries
 - qsubvasp
 - runvasp
 - symposcar
@@ -145,10 +143,8 @@ files:
 - Rakefile
 - VERSION
 - bin/addVolumeToten.rb
+- bin/checkvasp
 - bin/latticeconstants
-- bin/lsvasp
-- bin/lsvaspdir
-- bin/lsvaspseries
 - bin/qsubvasp
 - bin/runvasp
 - bin/symposcar
@@ -161,6 +157,7 @@ files:
 - lib/vasputils/potcar.rb
 - lib/vasputils/vaspdir.rb
 - lib/vasputils/vaspgeomopt.rb
+- lib/vasputils/vaspkpointsfinder.rb
 - memo.txt
 - test/calcseries/dup_finished/try00/CONTCAR
 - test/calcseries/dup_finished/try00/INCAR
@@ -228,6 +225,7 @@ files:
 - test/test_potcar.rb
 - test/test_vaspdir.rb
 - test/test_vaspgeomopt.rb
+- test/test_vaspkpointsfinder.rb
 - test/vaspdir/finished/CONTCAR
 - test/vaspdir/finished/INCAR
 - test/vaspdir/finished/KPOINTS
@@ -315,6 +313,10 @@ files:
 - test/vaspgeomopt/till01/try01/KPOINTS
 - test/vaspgeomopt/till01/try01/POSCAR
 - test/vaspgeomopt/till01/try01/POTCAR
+- test/vaspkpointsfinder/01-01-01/try00/INCAR
+- test/vaspkpointsfinder/01-01-01/try00/KPOINTS
+- test/vaspkpointsfinder/01-01-01/try00/POSCAR
+- test/vaspkpointsfinder/01-01-01/try00/POTCAR
 - vasputils.gemspec
 homepage: http://github.com/ippei94da/vasputils
 licenses:
@@ -331,7 +333,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -929575121
+      hash: 434831473
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/bin/lsvasp

@@ -1,95 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-# Show state of vasp geometry optimization calculations.
-
-#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)
-
-dirs = ARGV
-dirs = Dir.glob("*").sort if ARGV.empty?
-
-## generate headline
-#items  = []
-#OPTIONS.each do |key, val|
-#  case key
-#  when :cutoff    then items << sprintf("%6s", "ENCUT")
-#  when :k_mesh    then items << sprintf("%2s, %2s, %2s, %8s, %8s, %8s",
-#    "ka", "kb", "kc", "ka_shift", "kb_shift", "kc_shift")
-#  when :irr_k     then items << sprintf("%4s", "ir_k")
-#  when :lattice   then
-#    items << sprintf("%9s, %9s, %9s, %9s, %9s, %9s",
-#      "a", "b", "c", "alpha", "beta", "gamma")
-#  when :e_steps   then items << sprintf("%4s", "el_s")
-#  when :i_steps   then items << sprintf("%4s", "io_s")
-#  when :time      then items << sprintf("%8s", "time")
-#  when :time_e    then items << sprintf("%8s", "time/ele")
-#  when :toten     then items << sprintf("%16s", "TOTEN")
-#  end
-#end
-#items << "calc_name"
-#puts "#" + items.join(", ")
-
-dirs.each do |dir|
-  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/lsvaspdir

@@ -1,63 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-# vasp の計算ディレクトリの状態を表示する。
-# 
-#  - YET       未計算(lock がない)
-#  - STARTED   計算中 or 計算が終了したが、何らかのエラーが生じた。
-#              (lock があるが、normal_ended ではない)
-#              計算が中断されたか、計算中かの判断は原理上つけられない。
-#  - NEXT      計算が正常に終了し、収束していない。次の計算が生成された。
-#  - FINISHED  計算が正常に終了し、収束した。
-#  
-#  引数でディレクトリを指定できる。
-#  引数なしだとカレントディレクトリの全てのディレクトリ。
-#
-#  オプションをつけると、指定の状態のディレクトリを出力。
-#    -y : YET
-#    -s : STARTED
-#    -n : NEXT
-#    -f : FINISHED
-#   -c -n のように複数指定できる。
-#  
-#  デフォルトでは引数のディレクトリまたは
-#  -S オプションで状態を出力せず、ディレクトリ名だけを出力する。
-#    このオプションはシェルの backquote `` 機能から使うことを想定している。
-
-require "optparse"
-
-require "rubygems"
-gem "vasputils"
-require "vasputils/calcinspector.rb"
-require "vasputils/vaspdir.rb"
-
-OPTIONS = {}
-OPTIONS[:target_status] = ["YET", "STARTED", "NEXT", "FINISHED"]
-tmp = []
-op = OptionParser.new
-op.on("-y", "--yet"      , "Show calcs of YET."     ){tmp << "YET"      }
-op.on("-s", "--started"  , "Show calcs of STARTED." ){tmp << "STARTED"  }
-op.on("-n", "--next"     , "Show calcs of NEXT."    ){tmp << "NEXT"     }
-op.on("-f", "--finished" , "Show calcs of FINISHED."){tmp << "FINISHED"}
-op.on("-S", "--no-status", "Not output status."     ){OPTIONS[:nostatus] = true}
-op.parse!(ARGV)
-OPTIONS[:target_status] = tmp unless tmp.empty?
-
-#pp OPTIONS
-
-dirs = ARGV
-dirs = Dir.glob("*").sort if ARGV.empty?
-dirs.each do |dir|
-	begin
-		vd = VaspDir.new(dir)
-		status = CalcInspector.inspect(vd)
-		#pp status
-		if OPTIONS[:target_status].include?(status)
-			printf("%10s ", status) unless OPTIONS[:nostatus]
-			printf("%s\n", dir)
-		end
-	rescue VaspDir::InitializeError
-		#pp "Something wrong."
-		next
-	end
-end

data/bin/lsvaspseries

@@ -1,95 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-# vasp の計算シリーズの状態を表示する。
-#   - total ionic steps
-#   - total electronic steps
-#   - total elapsed time
-#   - final TOTEN
-#   - final cell parameter
-
-require "vasputils/calcseries.rb"
-require "vasputils/vaspdir.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)
-
-dirs = ARGV
-dirs = Dir.glob("*").sort if ARGV.empty?
-
-# generate headline
-items  = []
-OPTIONS.each do |key, val|
-	case key
-	when :cutoff    then items << sprintf("%6s", "ENCUT")
-	when :k_mesh    then items << sprintf("%2s, %2s, %2s, %8s, %8s, %8s",
-		"ka", "kb", "kc", "ka_shift", "kb_shift", "kc_shift")
-	when :irr_k     then items << sprintf("%4s", "ir_k")
-	when :lattice   then
-		items << sprintf("%9s, %9s, %9s, %9s, %9s, %9s",
-			"a", "b", "c", "alpha", "beta", "gamma")
-	when :e_steps   then items << sprintf("%4s", "el_s")
-	when :i_steps   then items << sprintf("%4s", "io_s")
-	when :time      then items << sprintf("%8s", "time")
-	when :time_e    then items << sprintf("%8s", "time/ele")
-	when :toten     then items << sprintf("%16s", "TOTEN")
-	end
-end
-items << "calc_name"
-puts "#" + items.join(", ")
-
-dirs.each do |dir|
-	begin
-		cs = CalcSeries.new(dir)
-		results = []
-		names = []
-		OPTIONS.each do |key, val|
-			case key
-			when :cutoff
-				results << sprintf("%6s", cs.finished_calc.incar["ENCUT"])
-			when :k_mesh    then results << sprintf("%2d, %2d, %2d, %8.5f, %8.5f, %8.5f",
-				* cs.finished_calc.kpoints[:mesh], * cs.finished_calc.kpoints[:shift])
-			when :irr_k     then results << sprintf("%4d", cs.finished_calc.outcar[:irreducible_kpoints])
-			when :lattice   then
-				results << sprintf("%9.5f, %9.5f, %9.5f, %9.5f, %9.5f, %9.5f",
-					* cs.finished_calc.contcar.axes.get_lattice_constants)
-			when :e_steps   then results << sprintf("%4d", cs.internal_steps)
-			when :i_steps   then results << sprintf("%4d", cs.external_steps)
-			when :time      then results << sprintf("%8d", cs.elapsed_time)
-			when :time_e    then results << sprintf("%8d", cs.elapsed_time/cs.internal_steps)
-			when :toten     then results << sprintf("%16.4f", cs.finished_calc.outcar[:totens][-1])
-			end
-		end
-		results << dir
-		puts " " + results.join(", ")
-	rescue
-		puts "Something wrong: #{dir}"
-		next
-	end
-
-end