vasputils 0.0.3 → 0.0.4

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", ">= 0.0.4"
+  gem "comana", ">= 0.0.5"
   gem "builtinextension", ">= 0.0.3"
 end

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.4

data/bin/lsvasp

@@ -0,0 +1,90 @@
+#! /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|
+  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

@@ -1,17 +1,24 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
+
+SCRIPT_FILE = "pbs.sh"
+PBS_LOG = "pbs.log"
+
+
 require "optparse"
+require "yaml"
+require "pp"
 
 ## option analysis
 OPTS = {}
 op = OptionParser.new
-op.on("-e", "--economy"  , "Prior efficiency."){OPTS[:e] = true}
+#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("-n", "--nebm"     , "Nudged Elastic Band method."){OPTS[:n] = true}
+#op.on("-c", "--cond-find", "Condition Finding.")         {OPTS[:c] = true}
 
 op.parse!(ARGV)
 
@@ -20,11 +27,40 @@ cluster = ARGV[0]
 #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."
+#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
+
+if File.exits?(SCRIPT_FILE)
+  puts "#{SCRIPT_FILE} already exist. Exit."
   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 "vaspgeomopt"
+  #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

@@ -0,0 +1,35 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+
+require "rubygems"
+gem "vasputils"
+require "vasputils/vaspdir.rb"
+require "vasputils/vaspgeomopt.rb"
+
+require "optparse"
+
+## option analysis
+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]
+  calc_dir = VaspGeomOpt.new(dir)
+else
+  calc_dir = VaspDir.new(dir)
+end
+
+#pp calc_dir
+
+begin
+  calc_dir.start
+rescue Comana::AlreadyStartedError
+  puts "Already started. Exit."
+  exit
+end

data/lib/vasputils/calcinspector.rb

@@ -3,22 +3,22 @@
 
 # 計算の状態を解析するクラス。
 class CalcInspector
-	#
-	#def initialize
-	#end
+  #
+  #def initialize
+  #end
 
-	# 引数 calc で渡された計算の状態を返す。
-	# calc は以下のメソッドを持つ必要がある。
-	#   - started?
-	#   - normal_ended?
-	#   - to_be_continued?
-	def self.inspect(calc)
-		return "YET"       unless calc.started?
-		return "STARTED"   unless calc.normal_ended?
-		return "NEXT"      if     calc.to_be_continued?
-		return "FINISHED"
-		#raise "must not occur"
-	end
+  # 引数 calc で渡された計算の状態を返す。
+  # calc は以下のメソッドを持つ必要がある。
+  #   - started?
+  #   - normal_ended?
+  #   - to_be_continued?
+  def self.inspect(calc)
+    return "YET"       unless calc.started?
+    return "STARTED"   unless calc.normal_ended?
+    return "NEXT"      if     calc.to_be_continued?
+    return "FINISHED"
+    #raise "must not occur"
+  end
 
 end
 

data/lib/vasputils/incar.rb

@@ -18,38 +18,38 @@
 # まず、自分で使う範囲だけ作る。
 # あとで余力があれば精密化する。
 module Incar
-	#
-	#def initialize()
-	#end
-	
-	# 与えられた IO を読み込み、INCAR として解析したハッシュを返す。
-	def self.parse(io)
-		results = {}
-		io.each_line do |line|
-			line.sub!(/\#.*/, "") # コメント文字以降を削除
-			next unless /=/ =~ line
-			if /(.*)=(.*)/ =~ line
-				key = $1.strip
-				val = $2.strip
-				val.sub!(/\s.*$/, "")
-				next if key.empty?
-				results[key] = val
-			end
-		end
-		return results
-	end
+  #
+  #def initialize()
+  #end
+  
+  # 与えられた IO を読み込み、INCAR として解析したハッシュを返す。
+  def self.parse(io)
+    results = {}
+    io.each_line do |line|
+      line.sub!(/\#.*/, "") # コメント文字以降を削除
+      next unless /=/ =~ line
+      if /(.*)=(.*)/ =~ line
+        key = $1.strip
+        val = $2.strip
+        val.sub!(/\s.*$/, "")
+        next if key.empty?
+        results[key] = val
+      end
+    end
+    return results
+  end
 
-	# 与えられた名前のファイルを INCAR として解析したハッシュを返す。
-	def self.load_file(file)
-		io = File.open(file, "r")
-		return self.parse(io)
-	end
+  # 与えられた名前のファイルを INCAR として解析したハッシュを返す。
+  def self.load_file(file)
+    io = File.open(file, "r")
+    return self.parse(io)
+  end
 
-	## 与えられたデータ対(ハッシュ)を io に書き出す。
-	## io が nil の場合は INCAR 形式文字列を返す。
-	## (改行文字を埋め込んでおり、配列化していない)
-	#def dump(pairs, io = nil)
-	#end
+  ## 与えられたデータ対(ハッシュ)を io に書き出す。
+  ## io が nil の場合は INCAR 形式文字列を返す。
+  ## (改行文字を埋め込んでおり、配列化していない)
+  #def dump(pairs, io = nil)
+  #end
 
 end
 

data/lib/vasputils/kpoints.rb

@@ -3,39 +3,39 @@
 
 # Module dearing with KPOINTS.
 module Kpoints
-	def self.parse(io)
-		results = {}
-		results[:comment] = io.readline.chomp
-
-		raise "Not automatic generating KPOINTS! 2nd line must be 0." unless io.readline == "0\n"
-
-		line = io.readline
-		case line
-		when /^m/i; then; results[:type] = :monkhorst
-		when /^g/i; then; results[:type] = :gamma_center
-		else
-			raise "Kpoints module can deal with only monkhorst and gamma-center."
-		end
-
-		#pp io.readline.strip.split(/\s+/).map{|i| i.to_i}
-		results[:mesh] = io.readline.strip.split(/\s+/).map{|i| i.to_i}
-		#pp io.readline.strip.split(/\s+/).map{|i| i.to_f}
-		results[:shift] = io.readline.strip.split(/\s+/).map{|i| i.to_f}
-
-		return results
-	end
-
-	# 
-	def self.load_file(file)
-		self.parse(File.open(file, "r"))
-	end
-
-	def self.dump(data, io)
-		io.puts "Automatic mesh"
-		io.puts "0"
-		io.puts data[:type].to_s.capitalize
-		io.puts data[:mesh].join(" ")
-		io.puts data[:shift].join(" ")
-	end
+  def self.parse(io)
+    results = {}
+    results[:comment] = io.readline.chomp
+
+    raise "Not automatic generating KPOINTS! 2nd line must be 0." unless io.readline == "0\n"
+
+    line = io.readline
+    case line
+    when /^m/i; then; results[:type] = :monkhorst
+    when /^g/i; then; results[:type] = :gamma_center
+    else
+      raise "Kpoints module can deal with only monkhorst and gamma-center."
+    end
+
+    #pp io.readline.strip.split(/\s+/).map{|i| i.to_i}
+    results[:mesh] = io.readline.strip.split(/\s+/).map{|i| i.to_i}
+    #pp io.readline.strip.split(/\s+/).map{|i| i.to_f}
+    results[:shift] = io.readline.strip.split(/\s+/).map{|i| i.to_f}
+
+    return results
+  end
+
+  # 
+  def self.load_file(file)
+    self.parse(File.open(file, "r"))
+  end
+
+  def self.dump(data, io)
+    io.puts "Automatic mesh"
+    io.puts "0"
+    io.puts data[:type].to_s.capitalize
+    io.puts data[:mesh].join(" ")
+    io.puts data[:shift].join(" ")
+  end
 end
 

data/lib/vasputils/outcar.rb

@@ -11,49 +11,49 @@
 # OUTCAR は終了する前も含めてなんか簡単に見るために使う、という位置付けで。
 
 module Outcar
-	#toten は全 electronic and ionic steps のを flat に並べただけのもの。
-	#必要なら構造化するが、現状その予定はない。
-	#attr_reader :name
-	#attr_reader :ionic_steps, :electronic_steps, :totens, :volumes, :elapsed_time
-
-	def self.load_file(file)
-		results = {}
-		results[:name] = file
-		results[:irreducible_kpoints] = nil
-		results[:electronic_steps   ] = 0
-		results[:ionic_steps        ] = 0
-		results[:totens             ] = []
-		results[:volumes            ] = []
-		results[:elapsed_time       ] = nil
-		results[:normal_ended       ] = false
-
-		lines = File.readlines(file)
-		lines.each do |line|
-			if /Found\s+(\d+)\s+irreducible k-points/i =~ line
-				results[:irreducible_kpoints] = $1.to_i
-			end
-
-			if /^-* Iteration\s+(\d+)/ =~ line
-				results[:ionic_steps     ] = $1.to_i
-				results[:electronic_steps] += 1
-			end
-
-			#if /free\s+energy\s+TOTEN\s+=\s(.*)\s+eV/ =~ line
-			if /TOTEN\s+=\s(.*)\s+eV/ =~ line
-				results[:totens] << $1.to_f
-			end
-
-			if /volume of cell :\s+(\d+\.\d+)$/ =~ line
-				results[:volumes] << $1.to_f
-			end
-
-			if (/Elapsed time \(sec\):\s+(\d+\.\d+)/ =~ line)
-				results[:elapsed_time] = $1.to_f
-			end
-		end
-
-		results[:normal_ended] = true if (/Voluntary context switches:/ =~ lines[-1])
-
-		results
-	end
+  #toten は全 electronic and ionic steps のを flat に並べただけのもの。
+  #必要なら構造化するが、現状その予定はない。
+  #attr_reader :name
+  #attr_reader :ionic_steps, :electronic_steps, :totens, :volumes, :elapsed_time
+
+  def self.load_file(file)
+    results = {}
+    results[:name] = file
+    results[:irreducible_kpoints] = nil
+    results[:electronic_steps   ] = 0
+    results[:ionic_steps        ] = 0
+    results[:totens             ] = []
+    results[:volumes            ] = []
+    results[:elapsed_time       ] = nil
+    results[:normal_ended       ] = false
+
+    lines = File.readlines(file)
+    lines.each do |line|
+      if /Found\s+(\d+)\s+irreducible k-points/i =~ line
+        results[:irreducible_kpoints] = $1.to_i
+      end
+
+      if /^-* Iteration\s+(\d+)/ =~ line
+        results[:ionic_steps     ] = $1.to_i
+        results[:electronic_steps] += 1
+      end
+
+      #if /free\s+energy\s+TOTEN\s+=\s(.*)\s+eV/ =~ line
+      if /TOTEN\s+=\s(.*)\s+eV/ =~ line
+        results[:totens] << $1.to_f
+      end
+
+      if /volume of cell :\s+(\d+\.\d+)$/ =~ line
+        results[:volumes] << $1.to_f
+      end
+
+      if (/Elapsed time \(sec\):\s+(\d+\.\d+)/ =~ line)
+        results[:elapsed_time] = $1.to_f
+      end
+    end
+
+    results[:normal_ended] = true if (/Voluntary context switches:/ =~ lines[-1])
+
+    results
+  end
 end