vasputils 0.0.8 → 0.0.9

data/VERSION

@@ -1 +1 @@
-0.0.8
+0.0.9

data/bin/checkvasp

@@ -0,0 +1,79 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+# Show state of vasp geometry optimization calculations.
+
+#require "vasputils/calcseries.rb"
+require "rubygems"
+gem "vasputils"
+
+require "vasputils/vaspgeomopt.rb"
+require "vasputils/vaspdir.rb"
+require "pp"
+#require "optparse"
+
+LONGEST_STATE = :terminated.size
+KLASSES = [VaspDir, VaspGeomOpt]
+
+dirs = ARGV
+dirs = Dir.glob("*").sort if ARGV.empty?
+
+def guess(dir)
+  KLASSES.each do |klass|
+    begin
+      vd = klass.new(dir)
+      return klass
+    rescue klass::InitializeError
+    end
+  end
+  raise "Cannot identify class for directory #{dir}."
+end
+
+dirs.each do |dir|
+  next unless File.directory? dir
+
+  begin
+    klass = guess(dir)
+    klass_name = klass.to_s
+  rescue 
+    klass_name = "UnknownDir"
+  end
+
+  printf "%-11s ", klass_name
+
+  case klass_name
+  when "VaspDir"
+    calc = klass.new(dir)
+    printf "%-10s ", calc.state
+    #pp calc.outcar
+    printf "%5s ", ""
+    begin
+      outcar = calc.outcar
+      printf "%8.3f %3d (%3d) ",
+        outcar[:totens][-1], outcar[:ionic_steps], outcar[:electronic_steps]
+    rescue
+      printf "%8s %3s (%3s) ", " "*8, " "*3, " "*3
+    end
+
+  when "VaspGeomOpt"
+    calc = klass.new(dir)
+    printf "%-10s ", calc.state
+
+    ld = calc.latest_dir
+    printf "%5s ", ld.dir.sub(/.*try/, "try")
+    begin
+      outcar = ld.outcar
+      printf "%8.3f %3d (%3d) ",
+        outcar[:totens][-1], outcar[:ionic_steps], outcar[:electronic_steps]
+    rescue
+      printf "%8s %3s (%3s) ", " "*8, " "*3, " "*3
+    end
+
+  when "UnknownDir"
+    printf "-" * 35
+    printf " "
+
+  end
+  puts dir
+
+end

data/bin/runvasp

@@ -12,17 +12,35 @@ require "vasputils/vaspgeomopt.rb"
 require "optparse"
 
 ## option analysis
-OPTIONS = {}
+opts = {}
 op = OptionParser.new
-op.on("-g"    , "--geom-opt", "Geometry optimization"){OPTIONS[:g] = true}
+op.on("-g"    , "--geom-opt",  "Geometry optimization"){opts[:geom] = true}
+op.on("-c"    , "--cond-find", "Condition finding"    ){opts[:cond] = true}
 op.parse!(ARGV)
 
 dir = ARGV[0] || "."
 
-if OPTIONS[:g]
-  calc_dir = VaspGeomOpt.new(dir)
+if opts[:geom] && opts[:cond]
+  puts "-g and -c must not be duplicated."
+  exit
+end
+
+if opts[:geom]
+  begin
+    calc_dir = VaspGeomOpt.new(dir)
+  rescue VaspGeomOpt::NoVaspDirError
+    puts "Not suitable for VaspGeomOpt: #{dir}"
+    exit
+  end
+elsif opts[:cond]
+  TODO
 else
-  calc_dir = VaspDir.new(dir)
+  begin
+    calc_dir = VaspDir.new(dir)
+  rescue VaspDir::InitializeError
+    puts "Not VaspDir: #{dir}"
+    exit
+  end
 end
 
 #pp calc_dir.class.ancestors

data/lib/vasputils/vaspdir.rb

@@ -40,6 +40,12 @@ class VaspDir < ComputationManager
     Outcar.load_file("#{@dir}/OUTCAR")
   end
 
+  # 配下の POSCAR を Cell2 インスタンスにして返す。
+  # 存在しなければ例外 Errno::ENOENT を返す。
+  def poscar
+    Poscar.load_file("#{@dir}/POSCAR")
+  end
+
   # 配下の CONTCAR を Cell2 インスタンスにして返す。
   # 存在しなければ例外 Errno::ENOENT を返す。
   def contcar

data/lib/vasputils/vaspgeomopt.rb

@@ -70,6 +70,25 @@ class VaspGeomOpt < ComputationManager
     return true
   end
 
+  # Find latest VaspDir.
+  # Return a last VaspDir which has the name by name sort
+  # and which can be made as a VaspDir instance.
+  # Note: in a series of geometry optimization,
+  #   the directory names should have a rule of naming
+  #   which can define a method <=>.
+  #   Usually, it is simple sort of String.
+  def latest_dir
+    Dir.glob("#{@dir}/*").sort.reverse.find do |dir|
+      begin
+        vd = VaspDir.new(dir)
+        return vd
+      rescue VaspDir::InitializeError
+        next
+      end
+    end
+    raise NoVaspDirError, @dir
+  end
+
   private
 
   # Generate next directory of latest_dir.
@@ -92,24 +111,5 @@ class VaspGeomOpt < ComputationManager
     VaspDir.new(new_dir)
   end
 
-  # Find latest VaspDir.
-  # Return a last VaspDir which has the name by name sort
-  # and which can be made as a VaspDir instance.
-  # Note: in a series of geometry optimization,
-  #   the directory names should have a rule of naming
-  #   which can define a method <=>.
-  #   Usually, it is simple sort of String.
-  def latest_dir
-    Dir.glob("#{@dir}/*").sort.reverse.find do |dir|
-      begin
-        vd = VaspDir.new(dir)
-        return vd
-      rescue VaspDir::InitializeError
-        next
-      end
-    end
-    raise NoVaspDirError, @dir
-  end
-
 end
 

data/lib/vasputils/vaspkpointsfinder.rb

@@ -0,0 +1,72 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "vasputils/vaspdir.rb"
+
+# 
+# 
+# 
+class VaspKpointsFinder
+
+
+  def initialize(dir)
+    @dir = dir # redefine in subclass. 
+    @lockdir    = "lock_vaspkfind"
+    @alive_time = 3600
+
+    @previous_kpoints = nil
+    @kpoints = [ 0, 0, 0 ] #indicate ka, kb, kc
+
+    @kpoint_candidates = list_kpoints
+  end
+
+  private
+
+  def calculate
+    @previous_kpoints = Marshal.load(Marshal.dump(@kpoints))
+
+    #@kpoints を起点として、
+    #ka の最適化し、精度以下となる最低の条件を @kpoints に登録。
+    #kb の最適化し、精度以下となる最低の条件を @kpoints に登録。
+    #kc の最適化し、精度以下となる最低の条件を @kpoints に登録。
+    3.times do |i| # each three k axis.
+      
+    end
+
+    #k の gamma center / hexagonal
+    #k の shift
+    #spin の有無。当面は有りを前提。INCAR で ISPIN をチェックする。
+  end
+
+  # Do nothing.
+  def prepare_next
+  end
+
+  def finished?
+    @previous_kpoints == @kpoints
+  end
+
+  # Using lattice constants of POSCAR, which is an initial value.
+  #
+  def list_kpoints
+    #vd = VaspDir.new(Dir.glob(@dir + "/*/try00")[0])
+    #results = []
+    #vd.poscar.axes.get_lattice_constants[0..2].map do |length|
+    #end
+  end
+end
+
+
+  #def lowest_encut
+  #  min_dir = Dir.glob(@dir + "/*/*").min_by { |dir| VaspDir.new(dir).incar["ENCUT"] }
+  #  VaspDir.new(min_dir).incar["ENCUT"].to_i
+  #end
+
+  #def list_encuts
+  #  results = []
+  #  (lowest_encut/100).upto 10 do |i|
+  #    results << i * 100
+  #  end
+  #  results
+  #end
+

data/memo.txt

@@ -1,5 +1,10 @@
 #
 
+0.0.9 release
+  Add VaspDir.poscar
+  Add bin/checkvasp
+  Delete bin/lsvasp, bin/lsvaspdir, bin/lsvaspseries
+
 0.0.8 release
   Modified bin/qsubvasp, add -g option.
 

data/test/test_calcinspector.rb

@@ -5,47 +5,47 @@ require "test/unit"
 require "vasputils/calcinspector.rb"
 
 class YetCalc
-	def started?        ; return false; end
-	def normal_ended?   ; return false; end
-	def to_be_continued?; return false; end
-	def finished?       ; return false; end
+  def started?        ; return false; end
+  def normal_ended?   ; return false; end
+  def to_be_continued?; return false; end
+  def finished?       ; return false; end
 end
 
 class StartedCalc
-	def started?        ; return true ; end
-	def normal_ended?   ; return false; end
-	def to_be_continued?; return false; end
-	def finished?       ; return false; end
+  def started?        ; return true ; end
+  def normal_ended?   ; return false; end
+  def to_be_continued?; return false; end
+  def finished?       ; return false; end
 end
 
 class NextCalc
-	def started?        ; return true ; end
-	def normal_ended?   ; return true ; end
-	def to_be_continued?; return true ; end
-	def finished?       ; return false; end
+  def started?        ; return true ; end
+  def normal_ended?   ; return true ; end
+  def to_be_continued?; return true ; end
+  def finished?       ; return false; end
 end
 
 class FinishedCalc
-	def started?        ; return true ; end
-	def normal_ended?   ; return true ; end
-	def to_be_continued?; return false; end
-	def finished?       ; return true ; end
+  def started?        ; return true ; end
+  def normal_ended?   ; return true ; end
+  def to_be_continued?; return false; end
+  def finished?       ; return true ; end
 end
 
 class TC_ListCalculation < Test::Unit::TestCase
-	def setup
-		@dc00 = YetCalc.new
-		@dc01 = StartedCalc.new
-		@dc02 = NextCalc.new
-		@dc03 = FinishedCalc.new
-	end
-
-	def test_self_inspect
-		assert_equal("YET",      CalcInspector.inspect(@dc00))
-		assert_equal("STARTED",  CalcInspector.inspect(@dc01))
-		assert_equal("NEXT",     CalcInspector.inspect(@dc02))
-		assert_equal("FINISHED", CalcInspector.inspect(@dc03))
-	end
+  def setup
+    @dc00 = YetCalc.new
+    @dc01 = StartedCalc.new
+    @dc02 = NextCalc.new
+    @dc03 = FinishedCalc.new
+  end
+
+  def test_self_inspect
+    assert_equal("YET",      CalcInspector.inspect(@dc00))
+    assert_equal("STARTED",  CalcInspector.inspect(@dc01))
+    assert_equal("NEXT",     CalcInspector.inspect(@dc02))
+    assert_equal("FINISHED", CalcInspector.inspect(@dc03))
+  end
 
 
 

data/test/test_incar.rb

@@ -5,122 +5,122 @@ require "test/unit"
 require "vasputils/incar.rb"
 require "stringio"
 
-#	assert_equal( cor, data)
-#	assert_in_delta( cor, data, $tolerance )
-#	assert_raise( RuntimeError ){}
+# assert_equal( cor, data)
+# assert_in_delta( cor, data, $tolerance )
+# assert_raise( RuntimeError ){}
 
 class TC_Incar < Test::Unit::TestCase
-	#def setup
-	#	@k = Incar.new
-	#end
-	
-	SAMPLE_PAIRS = {
-		"SYSTEM"  => "Untitled",
-		"PREC"    => "High",
-		"IBRION"  => "2",
-		"NSW"     => "100",
-		"ISIF"    => "2",
-		"ENCUT"   => "400",
-		"NELM"    => "60",
-		"NELMIN"  => "2",
-		"EDIFF"   => "1.0e-05",
-		"EDIFFG"  => "-0.02",
-		"VOSKOWN" => "1",
-		"NBLOCK"  => "1",
-		"ISPIN"   => "1",
-		"INIWAV"  => "1",
-		"ISTART"  => "1",
-		"ICHARG"  => "1",
-		"LWAVE"   => ".TRUE.",
-		"LCHARG"  => ".TRUE.",
-		"ISMEAR"  => "0",
-		"SIGMA"   => "0.1",
-		"IALGO"   => "38",
-		"LREAL"   => "Auto",
-		"NGX"     => "36",
-		"NGY"     => "36",
-		"NGZ"     => "42",
-	}
+  #def setup
+  # @k = Incar.new
+  #end
+  
+  SAMPLE_PAIRS = {
+    "SYSTEM"  => "Untitled",
+    "PREC"    => "High",
+    "IBRION"  => "2",
+    "NSW"     => "100",
+    "ISIF"    => "2",
+    "ENCUT"   => "400",
+    "NELM"    => "60",
+    "NELMIN"  => "2",
+    "EDIFF"   => "1.0e-05",
+    "EDIFFG"  => "-0.02",
+    "VOSKOWN" => "1",
+    "NBLOCK"  => "1",
+    "ISPIN"   => "1",
+    "INIWAV"  => "1",
+    "ISTART"  => "1",
+    "ICHARG"  => "1",
+    "LWAVE"   => ".TRUE.",
+    "LCHARG"  => ".TRUE.",
+    "ISMEAR"  => "0",
+    "SIGMA"   => "0.1",
+    "IALGO"   => "38",
+    "LREAL"   => "Auto",
+    "NGX"     => "36",
+    "NGY"     => "36",
+    "NGZ"     => "42",
+  }
 
-	def test_self_parse
-		io = StringIO.new
-		io.puts "# SCF input for VASP"
-		io.puts "# Note that VASP uses the FIRST occurence of a keyword"
-		io.puts "# if single point calc, IBRION = -1, NSW = 0, and comment out ISIF"
-		io.puts ""
-		io.puts "SYSTEM = Untitled (VASP)"
-		io.puts "    PREC = High"
-		io.puts "  IBRION = 2        #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient"
-		io.puts "     NSW = 100      #maximum number of ionic steps"
-		io.puts "    ISIF = 2"
-		io.puts "   ENCUT = 400"
-		io.puts "    NELM = 60       #maximum number of electronic steps"
-		io.puts "  NELMIN = 2        #minimum number of electronic steps"
-		io.puts "   EDIFF = 1.0e-05"
-		io.puts "  EDIFFG = -0.02"
-		io.puts " VOSKOWN = 1"
-		io.puts "  NBLOCK = 1"
-		io.puts "   ISPIN = 1        #1:non spin polarized, 2:spin polarized"
-		io.puts "  INIWAV = 1"
-		io.puts "  ISTART = 1"
-		io.puts "  ICHARG = 1"
-		io.puts "   LWAVE = .TRUE."
-		io.puts "  LCHARG = .TRUE."
-		io.puts "  ISMEAR = 0"
-		io.puts "   SIGMA = 0.1"
-		io.puts "   IALGO = 38       #38:KosugiAlgorithm, 48:RMM-DIIS"
-		io.puts "   LREAL = Auto     #fast & not accurate"
-		io.puts "     NGX = 36"
-		io.puts "     NGY = 36"
-		io.puts "     NGZ = 42"
-		io.rewind
-		pairs = Incar.parse(io)
-		assert_equal(SAMPLE_PAIRS, pairs)
-	end
+  def test_self_parse
+    io = StringIO.new
+    io.puts "# SCF input for VASP"
+    io.puts "# Note that VASP uses the FIRST occurence of a keyword"
+    io.puts "# if single point calc, IBRION = -1, NSW = 0, and comment out ISIF"
+    io.puts ""
+    io.puts "SYSTEM = Untitled (VASP)"
+    io.puts "    PREC = High"
+    io.puts "  IBRION = 2        #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient"
+    io.puts "     NSW = 100      #maximum number of ionic steps"
+    io.puts "    ISIF = 2"
+    io.puts "   ENCUT = 400"
+    io.puts "    NELM = 60       #maximum number of electronic steps"
+    io.puts "  NELMIN = 2        #minimum number of electronic steps"
+    io.puts "   EDIFF = 1.0e-05"
+    io.puts "  EDIFFG = -0.02"
+    io.puts " VOSKOWN = 1"
+    io.puts "  NBLOCK = 1"
+    io.puts "   ISPIN = 1        #1:non spin polarized, 2:spin polarized"
+    io.puts "  INIWAV = 1"
+    io.puts "  ISTART = 1"
+    io.puts "  ICHARG = 1"
+    io.puts "   LWAVE = .TRUE."
+    io.puts "  LCHARG = .TRUE."
+    io.puts "  ISMEAR = 0"
+    io.puts "   SIGMA = 0.1"
+    io.puts "   IALGO = 38       #38:KosugiAlgorithm, 48:RMM-DIIS"
+    io.puts "   LREAL = Auto     #fast & not accurate"
+    io.puts "     NGX = 36"
+    io.puts "     NGY = 36"
+    io.puts "     NGZ = 42"
+    io.rewind
+    pairs = Incar.parse(io)
+    assert_equal(SAMPLE_PAIRS, pairs)
+  end
 
-	def test_self_load_file
-		pairs = Incar.load_file "test/incar/INCAR.00"
-		assert_equal(SAMPLE_PAIRS, pairs)
+  def test_self_load_file
+    pairs = Incar.load_file "test/incar/INCAR.00"
+    assert_equal(SAMPLE_PAIRS, pairs)
 
-		corrects = {
-			"SYSTEM"  => "Untitled",
-			"PREC"    => "High",
-			"IBRION"  => "2",
-			"NSW"     => "0",
-			"ISIF"    => "2",
-			"ENCUT"   => "400",
-			"NELM"    => "60",
-			"NELMIN"  => "2",
-			"EDIFF"   => "1.0e-05",
-			"EDIFFG"  => "-0.02",
-			"VOSKOWN" => "1",
-			"NBLOCK"  => "1",
-			"ISPIN"   => "1",
-			"INIWAV"  => "1",
-			"ISTART"  => "1",
-			"ICHARG"  => "1",
-			"LWAVE"   => ".TRUE.",
-			"LCHARG"  => ".TRUE.",
-			"ISMEAR"  => "0",
-			"SIGMA"   => "0.1",
-			"IALGO"   => "38",
-			"LREAL"   => "Auto",
-			"NGX"     => "36",
-			"NGY"     => "36",
-			"NGZ"     => "42",
-		}
-		pairs = Incar.load_file "test/incar/INCAR.01"
-		assert_equal(corrects, pairs)
+    corrects = {
+      "SYSTEM"  => "Untitled",
+      "PREC"    => "High",
+      "IBRION"  => "2",
+      "NSW"     => "0",
+      "ISIF"    => "2",
+      "ENCUT"   => "400",
+      "NELM"    => "60",
+      "NELMIN"  => "2",
+      "EDIFF"   => "1.0e-05",
+      "EDIFFG"  => "-0.02",
+      "VOSKOWN" => "1",
+      "NBLOCK"  => "1",
+      "ISPIN"   => "1",
+      "INIWAV"  => "1",
+      "ISTART"  => "1",
+      "ICHARG"  => "1",
+      "LWAVE"   => ".TRUE.",
+      "LCHARG"  => ".TRUE.",
+      "ISMEAR"  => "0",
+      "SIGMA"   => "0.1",
+      "IALGO"   => "38",
+      "LREAL"   => "Auto",
+      "NGX"     => "36",
+      "NGY"     => "36",
+      "NGZ"     => "42",
+    }
+    pairs = Incar.load_file "test/incar/INCAR.01"
+    assert_equal(corrects, pairs)
 
-		# not exist
-		assert_raise(Errno::ENOENT){Incar.load_file("")}
-	end
+    # not exist
+    assert_raise(Errno::ENOENT){Incar.load_file("")}
+  end
 
-	#def test_dump
-	#	
-	#	
-	#	TODO
-	#end
+  #def test_dump
+  # 
+  # 
+  # TODO
+  #end
 
 end