vasputils 0.0.9 → 0.0.10

data/lib/vasputils/potcar.rb

@@ -1,7 +1,9 @@
+require "vasputils.rb"
+
 #
 # Class for dealing with POTCAR.
 #
-module Potcar
+module VaspUtils::Potcar
   def self.load_file(file)
     results = {}
     results[:name] = file

data/lib/vasputils/vaspdir.rb

@@ -11,15 +11,12 @@ gem "comana"
 require "comana/computationmanager.rb"
 require "comana/machineinfo.rb"
 
-require "vasputils/incar.rb"
-require "vasputils/outcar.rb"
-require "vasputils/poscar.rb"
-require "vasputils/kpoints.rb"
+require "vasputils.rb"
 
 # Class for VASP executable directory,
 # including input and output files.
 #
-class VaspDir < ComputationManager
+class VaspUtils::VaspDir < ComputationManager
   class InitializeError < Exception; end
   class NoVaspBinaryError < Exception; end
   class PrepareNextError < Exception; end
@@ -37,19 +34,19 @@ class VaspDir < ComputationManager
   # 配下の OUTCAR を Outcar 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 outcar
-    Outcar.load_file("#{@dir}/OUTCAR")
+    VaspUtils::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")
+    VaspUtils::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
-    Poscar.load_file("#{@dir}/CONTCAR")
+    VaspUtils::Poscar.load_file("#{@dir}/CONTCAR")
   end
 
   # 配下の KPOINTS を読み込んだ結果をハッシュにして返す。
@@ -57,12 +54,12 @@ class VaspDir < ComputationManager
   # 存在しなければ例外 Errno::ENOENT を返す筈だが、
   # vasp dir の判定を incar でやっているので置こる筈がない。
   def incar
-    Incar.load_file("#{@dir}/INCAR")
+    VaspUtils::Incar.load_file("#{@dir}/INCAR")
   end
 
   # 配下の KPOINTS を読み込んだ結果をハッシュにして返す。
   def kpoints
-    Kpoints.load_file("#{@dir}/KPOINTS")
+    VaspUtils::Kpoints.load_file("#{@dir}/KPOINTS")
   end
 
   # 正常に終了していれば true を返す。
@@ -72,7 +69,7 @@ class VaspDir < ComputationManager
   # PI12345 ファイルは実行中のみ存在し、終了後 vasp (mpi？) に自動的に削除される。
   def finished?
     begin
-      return Outcar.load_file("#{@dir}/OUTCAR")[:normal_ended]
+      return VaspUtils::Outcar.load_file("#{@dir}/OUTCAR")[:normal_ended]
     rescue Errno::ENOENT
       return false
     end

data/lib/vasputils/{vaspgeomopt.rb → vaspgeometryoptimizer.rb}

@@ -8,12 +8,13 @@ require "rubygems"
 gem "comana"
 require "comana/computationmanager.rb"
 
-require "vasputils/vaspdir.rb"
+require "vasputils.rb"
+#require "vasputils/vaspdir.rb"
 
 #
 #
 #
-class VaspGeomOpt < ComputationManager
+class VaspUtils::VaspGeometryOptimizer < ComputationManager
   class NoVaspDirError < Exception; end
   class LatestDirStartedError < Exception; end
   class NoIntegerEndedNameError < Exception; end
@@ -80,9 +81,9 @@ class VaspGeomOpt < ComputationManager
   def latest_dir
     Dir.glob("#{@dir}/*").sort.reverse.find do |dir|
       begin
-        vd = VaspDir.new(dir)
+        vd = VaspUtils::VaspDir.new(dir)
         return vd
-      rescue VaspDir::InitializeError
+      rescue VaspUtils::VaspDir::InitializeError
         next
       end
     end
@@ -108,7 +109,7 @@ class VaspGeomOpt < ComputationManager
     FileUtils.cp("#{latest_dir.dir}/XDATCAR" , "#{new_dir}/XDATCAR" )
     FileUtils.cp("#{latest_dir.dir}/CONTCAR" , "#{new_dir}/POSCAR"  ) # change name
     # without POSCAR, OUTCAR, vasprun.xml
-    VaspDir.new(new_dir)
+    VaspUtils::VaspDir.new(new_dir)
   end
 
 end

data/memo.txt

@@ -1,12 +1,20 @@
 #
 
+0.0.10 release
+  Delete Outcar.volume
+  Delete Outcar.irreducible_kpoints
+  Accelerate Outcar, using UNIX commands: grep, tail and head
+  Modify bin/symposcar
+  Add bin/rmvaspout
+  Change name space for classes
+
 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.
+  Modified bin/qsubvasp, add -g option
 
 0.0.7 release
   Modified bin/qsubvasp

data/test/test_incar.rb

@@ -2,6 +2,7 @@
 # coding: utf-8
 
 require "test/unit"
+require "vasputils.rb"
 require "vasputils/incar.rb"
 require "stringio"
 
@@ -74,12 +75,12 @@ class TC_Incar < Test::Unit::TestCase
     io.puts "     NGY = 36"
     io.puts "     NGZ = 42"
     io.rewind
-    pairs = Incar.parse(io)
+    pairs = VaspUtils::Incar.parse(io)
     assert_equal(SAMPLE_PAIRS, pairs)
   end
 
   def test_self_load_file
-    pairs = Incar.load_file "test/incar/INCAR.00"
+    pairs = VaspUtils::Incar.load_file "test/incar/INCAR.00"
     assert_equal(SAMPLE_PAIRS, pairs)
 
     corrects = {
@@ -109,11 +110,11 @@ class TC_Incar < Test::Unit::TestCase
       "NGY"     => "36",
       "NGZ"     => "42",
     }
-    pairs = Incar.load_file "test/incar/INCAR.01"
+    pairs = VaspUtils::Incar.load_file "test/incar/INCAR.01"
     assert_equal(corrects, pairs)
 
     # not exist
-    assert_raise(Errno::ENOENT){Incar.load_file("")}
+    assert_raise(Errno::ENOENT){VaspUtils::Incar.load_file("")}
   end
 
   #def test_dump

data/test/test_kpoints.rb

@@ -3,6 +3,7 @@
 
 require "test/unit"
 require "stringio"
+require "vasputils.rb"
 require "vasputils/kpoints.rb"
 
 class TC_Kpoints < Test::Unit::TestCase
@@ -17,7 +18,7 @@ class TC_Kpoints < Test::Unit::TestCase
     io.puts "  1  2  3"
     io.puts "  0.4  0.5  0.6"
     io.rewind
-    k00 = Kpoints.parse(io)
+    k00 = VaspUtils::Kpoints.parse(io)
     assert_equal("Automatic mesh", k00[:comment])
     assert_equal(:monkhorst, k00[:type])
     assert_equal([1, 2, 3], k00[:mesh])
@@ -33,7 +34,7 @@ class TC_Kpoints < Test::Unit::TestCase
     io.puts "  1  2  3"
     io.puts "  0.4  0.5  0.6"
     io.rewind
-    k01 = Kpoints.parse(io)
+    k01 = VaspUtils::Kpoints.parse(io)
     assert_equal("Automatic mesh", k01[:comment])
     assert_equal(:gamma_center, k01[:type])
     assert_equal([1, 2, 3], k01[:mesh])
@@ -43,7 +44,7 @@ class TC_Kpoints < Test::Unit::TestCase
   end
 
   def test_self_load_file
-    k00 = Kpoints.load_file("test/kpoints/m123-456")
+    k00 = VaspUtils::Kpoints.load_file("test/kpoints/m123-456")
     assert_equal("Automatic mesh", k00[:comment])
     assert_equal(:monkhorst, k00[:type])
     assert_equal([1, 2, 3], k00[:mesh])
@@ -51,7 +52,7 @@ class TC_Kpoints < Test::Unit::TestCase
     assert_in_delta(0.5, k00[:shift][1])
     assert_in_delta(0.6, k00[:shift][2])
 
-    k01 = Kpoints.load_file("test/kpoints/g123-456")
+    k01 = VaspUtils::Kpoints.load_file("test/kpoints/g123-456")
     assert_equal("Automatic mesh", k01[:comment])
     assert_equal(:gamma_center, k01[:type])
     assert_equal([1, 2, 3], k01[:mesh])
@@ -68,7 +69,7 @@ class TC_Kpoints < Test::Unit::TestCase
       :shift => [0.4, 0.5, 0.6],
     }
     io = StringIO.new
-    Kpoints.dump(hash, io)
+    VaspUtils::Kpoints.dump(hash, io)
     io.rewind
     results = io.readlines
     corrects = [
@@ -90,7 +91,7 @@ class TC_Kpoints < Test::Unit::TestCase
       :shift => [0.4, 0.5, 0.6],
     }
     io = StringIO.new
-    Kpoints.dump(hash, io)
+    VaspUtils::Kpoints.dump(hash, io)
     io.rewind
     results = io.readlines
     corrects = [

data/test/test_outcar.rb

@@ -1,21 +1,22 @@
 #! /usr/bin/ruby
 
 require 'test/unit'
+require "vasputils.rb"
 require 'vasputils/outcar.rb'
 
 class TC_Outcar < Test::Unit::TestCase
   $tolerance = 10**(-10)
 
   def setup
-    @o01    = Outcar.load_file( "test/outcar/01-13-FIN.OUTCAR" )
-    @o01int = Outcar.load_file( "test/outcar/01-03-INT.OUTCAR" )
-    @o02    = Outcar.load_file( "test/outcar/02-05-FIN.OUTCAR" )
-    @o03    = Outcar.load_file( "test/outcar/03-05-FIN.OUTCAR" )
-    @o04    = Outcar.load_file( "test/outcar/10-01-FIN.OUTCAR" )
+    @o01    = VaspUtils::Outcar.load_file( "test/outcar/01-13-FIN.OUTCAR" )
+    @o01int = VaspUtils::Outcar.load_file( "test/outcar/01-03-INT.OUTCAR" )
+    @o02    = VaspUtils::Outcar.load_file( "test/outcar/02-05-FIN.OUTCAR" )
+    @o03    = VaspUtils::Outcar.load_file( "test/outcar/03-05-FIN.OUTCAR" )
+    @o04    = VaspUtils::Outcar.load_file( "test/outcar/10-01-FIN.OUTCAR" )
   end
 
   def test_self_load_file
-    assert_raise(Errno::ENOENT){Outcar.load_file( "" )}
+    assert_raise(Errno::ENOENT){VaspUtils::Outcar.load_file( "" )}
   end
 
   #def test_nsw
@@ -133,30 +134,30 @@ class TC_Outcar < Test::Unit::TestCase
     #assert_in_delta( Iter1-Nsw0/OUTCAR:1463:  free  energy   TOTEN  =    -53232.707599
   end
 
-  def test_volume
-    assert_in_delta( 44.88, @o01   [:volumes][0], $tolerance )
-    assert_in_delta( 44.88, @o01   [:volumes][1], $tolerance )
-    assert_in_delta( 44.88, @o01int[:volumes][0], $tolerance )
-    assert_in_delta( 44.88, @o02   [:volumes][0], $tolerance )
-    assert_in_delta( 44.88, @o02   [:volumes][1], $tolerance )
-    assert_in_delta( 44.16, @o02   [:volumes][2], $tolerance )
-    assert_in_delta( 44.88, @o03   [:volumes][0], $tolerance )
-    assert_in_delta( 44.88, @o03   [:volumes][1], $tolerance )
-    assert_in_delta( 44.16, @o03   [:volumes][2], $tolerance )
-    assert_in_delta( 43.84, @o03   [:volumes][3], $tolerance )
-
-    #assert_in_delta( Iter1-Nsw0/OUTCAR:343:  volume of cell :     1258.66
-    #assert_in_delta( Iter1-Nsw0/OUTCAR:1488:  volume of cell :     1258.66
+  #def test_volume
+  #  assert_in_delta( 44.88, @o01   [:volumes][0], $tolerance )
+  #  assert_in_delta( 44.88, @o01   [:volumes][1], $tolerance )
+  #  assert_in_delta( 44.88, @o01int[:volumes][0], $tolerance )
+  #  assert_in_delta( 44.88, @o02   [:volumes][0], $tolerance )
+  #  assert_in_delta( 44.88, @o02   [:volumes][1], $tolerance )
+  #  assert_in_delta( 44.16, @o02   [:volumes][2], $tolerance )
+  #  assert_in_delta( 44.88, @o03   [:volumes][0], $tolerance )
+  #  assert_in_delta( 44.88, @o03   [:volumes][1], $tolerance )
+  #  assert_in_delta( 44.16, @o03   [:volumes][2], $tolerance )
+  #  assert_in_delta( 43.84, @o03   [:volumes][3], $tolerance )
+
+  #  #assert_in_delta( Iter1-Nsw0/OUTCAR:343:  volume of cell :     1258.66
+  #  #assert_in_delta( Iter1-Nsw0/OUTCAR:1488:  volume of cell :     1258.66
 
-  end
+  #end
 
   def test_elapsed_time
     assert_equal(nil, @o01int[:elapsed_time])
     assert_in_delta(164.134, @o04[:elapsed_time], $tolerance )
   end
 
-  def test_irreducible_kpoints
-    assert_equal(15, @o01[:irreducible_kpoints])
-  end
+  #def test_irreducible_kpoints
+  #  assert_equal(15, @o01[:irreducible_kpoints])
+  #end
 
 end

data/test/test_poscar.rb

@@ -2,6 +2,7 @@
 
 require "test/unit"
 require "stringio"
+require "vasputils.rb"
 require "vasputils/poscar.rb"
 
 require "rubygems"
@@ -28,8 +29,8 @@ class TC_Poscar < Test::Unit::TestCase
     cell = Cell.new(axes, atoms)
     cell.comment = "test"
     io = StringIO.new
-    assert_raises(Poscar::ElementMismatchError){
-      Poscar.dump(cell, [0,1,2], io)}
+    assert_raises(VaspUtils::Poscar::ElementMismatchError){
+      VaspUtils::Poscar.dump(cell, [0,1,2], io)}
 
     # 生成
     axes = LatticeAxes.new( [
@@ -45,7 +46,7 @@ class TC_Poscar < Test::Unit::TestCase
     cell = Cell.new(axes, atoms)
     cell.comment = "test"
     io = StringIO.new
-    Poscar.dump(cell, [0,1], io)
+    VaspUtils::Poscar.dump(cell, [0,1], io)
     io.rewind
     corrects = [
       "test\n",
@@ -73,7 +74,7 @@ class TC_Poscar < Test::Unit::TestCase
     cell = Cell.new(axes, atoms)
     cell.comment = "test"
     io = StringIO.new
-    Poscar.dump(cell, [0,1], io)
+    VaspUtils::Poscar.dump(cell, [0,1], io)
     io.rewind
     corrects = [
       "test\n",
@@ -97,7 +98,7 @@ class TC_Poscar < Test::Unit::TestCase
 
   def test_parse
     io = StringIO.new
-    assert_raises(Poscar::ParseError){ Poscar.parse(io) }
+    assert_raises(VaspUtils::Poscar::ParseError){ VaspUtils::Poscar.parse(io) }
 
     io = StringIO.new
     io.puts "sample0"
@@ -111,7 +112,7 @@ class TC_Poscar < Test::Unit::TestCase
     io.puts "    0.5  0.0  0.0  #Ge-002"
     io.puts "    0.5  0.5  0.0  #O--003"
     io.rewind
-    cell = Poscar.parse(io)
+    cell = VaspUtils::Poscar.parse(io)
     assert_equal("sample0", cell.comment)
     assert_equal(
       LatticeAxes.new( [
@@ -142,7 +143,7 @@ class TC_Poscar < Test::Unit::TestCase
     io.puts "    0.5  0.5  0.0  T T T #O--003"
     io.puts "    0.5  0.5  0.5  T T T #O--004"
     io.rewind
-    cell = Poscar.parse(io)
+    cell = VaspUtils::Poscar.parse(io)
     assert_equal("sample1", cell.comment)
     assert_equal(
       LatticeAxes.new( [
@@ -167,7 +168,7 @@ class TC_Poscar < Test::Unit::TestCase
   end
 
   def test_load_file
-    cell = Poscar.load_file("test/poscar/POSCAR.00")
+    cell = VaspUtils::Poscar.load_file("test/poscar/POSCAR.00")
     assert_equal("sample0", cell.comment)
     assert_equal(
       LatticeAxes.new( [
@@ -184,7 +185,7 @@ class TC_Poscar < Test::Unit::TestCase
     assert_equal(
       Atom.new(2, [0.5, 0.5, 0.0], "#O--003"), cell.atoms[2])
 
-    #cell = Poscar.load_file("test/poscar/POSCAR.02")
+    #cell = VaspUtils::Poscar.load_file("test/poscar/POSCAR.02")
     #assert_equal("sample0", cell.comment)
     #assert_in_delta( 7.1028554188641708, cell.axes[0][0], $tolerance)
     #assert_in_delta(-0.0000000169534433, cell.axes[0][1], $tolerance)
@@ -203,7 +204,7 @@ class TC_Poscar < Test::Unit::TestCase
   end
 
   #def setup
-  # #@pp02 = Poscar.new("test/poscar/POSCAR.shirai")
+  # #@pp02 = VaspUtils::Poscar.new("test/poscar/POSCAR.shirai")
   #end
 
 end

data/test/test_potcar.rb

@@ -1,14 +1,15 @@
 #! /usr/bin/ruby
 
 require "test/unit"
+require "vasputils.rb"
 require "vasputils/potcar.rb"
 
 class TC_Potcar < Test::Unit::TestCase
 
   def setup
-    @p0 = Potcar.load_file("test/potcar/POTCAR"           )
-    @p1 = Potcar.load_file("test/potcar/POTCAR.dummy"     )
-    @p2 = Potcar.load_file("test/potcar/POTCAR.allElement")
+    @p0 = VaspUtils::Potcar.load_file("test/potcar/POTCAR"           )
+    @p1 = VaspUtils::Potcar.load_file("test/potcar/POTCAR.dummy"     )
+    @p2 = VaspUtils::Potcar.load_file("test/potcar/POTCAR.allElement")
   end
 
   def test_get_filename
@@ -40,8 +41,8 @@ class TC_Potcar < Test::Unit::TestCase
   end
 
   #def test_self_elements
-  # assert_equal([ "Li", "Ge", "O" ], Potcar.elements( @p0 ))
-  # assert_equal([ "Li", "Ge", "O" ], Potcar.elements( @p1 ))
+  # assert_equal([ "Li", "Ge", "O" ], VaspUtils::Potcar.elements( @p0 ))
+  # assert_equal([ "Li", "Ge", "O" ], VaspUtils::Potcar.elements( @p1 ))
   # correct = [
   #   "Ac", "Ac", "Ag", "Al", "Al", "Ar", "As", "Au", "B", "B", "B", "Ba",
   #   "Be", "Be", "Bi", "Bi", "Br", "C", "C", "C", "Ca", "Ca", "Cd", "Ce",
@@ -58,7 +59,7 @@ class TC_Potcar < Test::Unit::TestCase
   #   "Ta", "Ta", "Tb", "Tc", "Tc", "Te", "Th", "Th", "Ti", "Ti", "Ti",
   #   "Tl", "Tl", "Tm", "Tm", "U", "U", "V", "V", "V", "W", "W", "X", "Y",
   #   "Yb", "Yb", "Zn", "Zr", "Zr"]
-  # assert_equal( correct, Potcar.elements( @p2 ))
+  # assert_equal( correct, VaspUtils::Potcar.elements( @p2 ))
   #end
 
 end

data/test/test_vaspdir.rb

@@ -8,13 +8,13 @@ gem "comana"
 require "comana/computationmanager.rb"
 
 require "test/unit"
-require "vasputils/vaspdir.rb"
+require "vasputils.rb"
 
 # assert_equal( cor, data)
 # assert_in_delta( cor, data, $tolerance )
 # assert_raise( RuntimeError ){}
 
-class VaspDir < ComputationManager
+class VaspUtils::VaspDir < ComputationManager
   attr_reader :mode
 
   def calculate
@@ -60,10 +60,10 @@ class TC_VaspDir < Test::Unit::TestCase
   ]
 
   def setup
-    @vd00 = VaspDir.new("test/vaspdir/not-yet")
-    @vd01 = VaspDir.new("test/vaspdir/locked")
-    @vd02 = VaspDir.new("test/vaspdir/started")
-    @vd03 = VaspDir.new("test/vaspdir/finished")
+    @vd00 = VaspUtils::VaspDir.new("test/vaspdir/not-yet")
+    @vd01 = VaspUtils::VaspDir.new("test/vaspdir/locked")
+    @vd02 = VaspUtils::VaspDir.new("test/vaspdir/started")
+    @vd03 = VaspUtils::VaspDir.new("test/vaspdir/finished")
 
     GENERATED_FILES_VD00.each do |file|
       FileUtils.rm file if File.exist? file
@@ -74,10 +74,10 @@ class TC_VaspDir < Test::Unit::TestCase
   end
 
   def test_initialize
-    assert_raise(VaspDir::InitializeError){VaspDir.new("test/vaspdir/lack-INCAR"  )}
-    assert_raise(VaspDir::InitializeError){VaspDir.new("test/vaspdir/lack-KPOINTS")}
-    assert_raise(VaspDir::InitializeError){VaspDir.new("test/vaspdir/lack-POSCAR" )}
-    assert_raise(VaspDir::InitializeError){VaspDir.new("test/vaspdir/lack-POTCAR" )}
+    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-INCAR"  )}
+    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-KPOINTS")}
+    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-POSCAR" )}
+    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-POTCAR" )}
   end
 
   def test_finished?