vasputils 0.0.1 → 0.0.2

data/test/test_vaspdir.rb

@@ -3,9 +3,9 @@
 
 $TEST = true
 
-class VaspDir
-  attr_reader :mode
-end
+require "rubygems"
+gem "comana"
+require "comana.rb"
 
 require "test/unit"
 require "vasputils/vaspdir.rb"
@@ -14,62 +14,42 @@ require "vasputils/vaspdir.rb"
 # assert_in_delta( cor, data, $tolerance )
 # assert_raise( RuntimeError ){}
 
+class VaspDir < Comana
+  attr_reader :mode
+  public :finished?
+end
+
 
 class TC_VaspDir < Test::Unit::TestCase
 
-  GENERATED_FILES_VD00 = 
-  [
-    "test/vaspdir/not-yet-ISIF2/CHG",
-    "test/vaspdir/not-yet-ISIF2/CHGCAR",
-    "test/vaspdir/not-yet-ISIF2/CONTCAR",
-    "test/vaspdir/not-yet-ISIF2/DOSCAR",
-    "test/vaspdir/not-yet-ISIF2/EIGENVAL",
-    "test/vaspdir/not-yet-ISIF2/IBZKPT",
-    "test/vaspdir/not-yet-ISIF2/OSZICAR",
-    "test/vaspdir/not-yet-ISIF2/OUTCAR",
-    "test/vaspdir/not-yet-ISIF2/PCDAT",
-    "test/vaspdir/not-yet-ISIF2/WAVECAR",
-    "test/vaspdir/not-yet-ISIF2/XDATCAR",
-    "test/vaspdir/not-yet-ISIF2/machines",
-    "test/vaspdir/not-yet-ISIF2/vasprun.xml",
-    "test/vaspdir/not-yet-ISIF2/lock",
+  GENERATED_FILES_VD00 = [
+    "test/vaspdir/not-yet/CHG",
+    "test/vaspdir/not-yet/CHGCAR",
+    "test/vaspdir/not-yet/CONTCAR",
+    "test/vaspdir/not-yet/DOSCAR",
+    "test/vaspdir/not-yet/EIGENVAL",
+    "test/vaspdir/not-yet/IBZKPT",
+    "test/vaspdir/not-yet/OSZICAR",
+    "test/vaspdir/not-yet/OUTCAR",
+    "test/vaspdir/not-yet/PCDAT",
+    "test/vaspdir/not-yet/WAVECAR",
+    "test/vaspdir/not-yet/XDATCAR",
+    "test/vaspdir/not-yet/machines",
+    "test/vaspdir/not-yet/vasprun.xml",
   ]
 
   def setup
-    @vd00 = VaspDir.new("test/vaspdir/not-yet-ISIF2")
-    @vd01 = VaspDir.new("test/vaspdir/not-yet-ISIF3")
-    @vd02 = VaspDir.new("test/vaspdir/ISIF3-NSW100-OUTCAR-Iter1-INT")
-    @vd03 = VaspDir.new("test/vaspdir/ISIF2-NSW100-OUTCAR-Iter1")
-    @vd04 = VaspDir.new("test/vaspdir/ISIF3-NSW002-OUTCAR-Iter2")
-    @vd05 = VaspDir.new("test/vaspdir/ISIF3-NSW100-OUTCAR-Iter3")
-    @vd06 = VaspDir.new("test/vaspdir/PI")
-    @vd07 = VaspDir.new("test/vaspdir/lock")
-    @vd08 = VaspDir.new("test/vaspdir/lock-PI")
-    @vd09 = VaspDir.new("test/vaspdir/ISIF2-NSW100-OUTCAR-Iter3")
-    @vd10 = VaspDir.new("test/vaspdir/next-try00")
-    @vd11 = VaspDir.new("test/vaspdir/ISIF2-NSW000-OUTCAR-Iter1")
-    @vd12 = VaspDir.new("test/vaspdir/ISIF2-NSW001-OUTCAR-Iter1")
-    @vd13 = VaspDir.new("test/vaspdir/ISIF3-NSW000-OUTCAR-Iter1")
-    @vd14 = VaspDir.new("test/vaspdir/ISIF3-NSW001-OUTCAR-Iter1")
-    @vd15 = VaspDir.new("test/vaspdir/IBRION-1-NSW000-OUTCAR-Iter1")
+    @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")
 
     GENERATED_FILES_VD00.each do |file|
       FileUtils.rm file if File.exist? file
     end
-  end
 
-  def teardown
-    ["test/vaspdir/next-try01/POSCAR" ,
-      "test/vaspdir/next-try01/POTCAR" ,
-      "test/vaspdir/next-try01/INCAR"  ,
-      "test/vaspdir/next-try01/KPOINTS"].each do |filename|
-      FileUtils.rm(filename) if File.exist?(filename)
-    end
-    Dir.rmdir("test/vaspdir/next-try01") if File.exist?("test/vaspdir/next-try01")
-
-    GENERATED_FILES_VD00.each do |file|
-      FileUtils.rm file if File.exist? file
-    end
+    #lock_dir = "test/vaspdir/not-yet/lock"
+    #Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
   end
 
   def test_initialize
@@ -77,177 +57,67 @@ class TC_VaspDir < Test::Unit::TestCase
     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_equal(:geom_opt_atoms,   @vd00.mode)
-    assert_equal(:geom_opt_lattice, @vd01.mode)
-    assert_equal(:geom_opt_lattice, @vd02.mode)
-    assert_equal(:geom_opt_atoms,   @vd03.mode)
-  end
-
-  def test_name
-    assert_equal("test/vaspdir/not-yet-ISIF2"                , @vd00.name)
-    assert_equal("test/vaspdir/not-yet-ISIF3"                , @vd01.name)
-    assert_equal("test/vaspdir/ISIF3-NSW100-OUTCAR-Iter1-INT", @vd02.name)
-    assert_equal("test/vaspdir/ISIF2-NSW100-OUTCAR-Iter1"    , @vd03.name)
-    assert_equal("test/vaspdir/ISIF3-NSW002-OUTCAR-Iter2"    , @vd04.name)
-    assert_equal("test/vaspdir/ISIF3-NSW100-OUTCAR-Iter3"    , @vd05.name)
-    assert_equal("test/vaspdir/PI"                           , @vd06.name)
-    assert_equal("test/vaspdir/lock"                         , @vd07.name)
-    assert_equal("test/vaspdir/lock-PI"                      , @vd08.name)
-    assert_equal("test/vaspdir/ISIF2-NSW100-OUTCAR-Iter3"    , @vd09.name)
-    assert_equal("test/vaspdir/next-try00"                   , @vd10.name)
-    assert_equal("test/vaspdir/ISIF2-NSW000-OUTCAR-Iter1"    , @vd11.name)
-    assert_equal("test/vaspdir/ISIF2-NSW001-OUTCAR-Iter1"    , @vd12.name)
-    assert_equal("test/vaspdir/ISIF3-NSW000-OUTCAR-Iter1"    , @vd13.name)
-    assert_equal("test/vaspdir/ISIF3-NSW001-OUTCAR-Iter1"    , @vd14.name)
-    assert_equal("test/vaspdir/IBRION-1-NSW000-OUTCAR-Iter1" , @vd15.name)
-  end
-
-  def test_started?
-    assert_equal(false, @vd00.started?)
-    assert_equal(false, @vd01.started?)
-    assert_equal(true , @vd02.started?)
-    assert_equal(true , @vd03.started?)
-    assert_equal(true , @vd04.started?)
-    assert_equal(true , @vd05.started?)
-    assert_equal(false, @vd06.started?)
-    assert_equal(true , @vd07.started?)
-    assert_equal(true , @vd08.started?)
-    assert_equal(true , @vd09.started?)
-    assert_equal(true , @vd10.started?)
-    assert_equal(true , @vd11.started?)
-    assert_equal(true , @vd12.started?)
-    assert_equal(true , @vd13.started?)
-    assert_equal(true , @vd14.started?)
-    assert_equal(true , @vd15.started?)
-  end
-
-  def test_normal_ended?
-    assert_equal(false, @vd00.normal_ended?)
-    assert_equal(false, @vd01.normal_ended?)
-    assert_equal(false, @vd02.normal_ended?)
-    assert_equal(true , @vd03.normal_ended?)
-    assert_equal(true , @vd04.normal_ended?)
-    assert_equal(true , @vd05.normal_ended?)
-    assert_equal(false, @vd06.normal_ended?)
-    assert_equal(false, @vd07.normal_ended?)
-    assert_equal(false, @vd08.normal_ended?)
-    assert_equal(true , @vd09.normal_ended?)
   end
 
-  def test_to_be_continued?
-    assert_equal(false, @vd00.to_be_continued?)
-    assert_equal(false, @vd01.to_be_continued?)
-    assert_equal(false, @vd02.to_be_continued?)
-    assert_equal(false, @vd03.to_be_continued?)
-    assert_equal(true , @vd04.to_be_continued?)
-    assert_equal(true , @vd05.to_be_continued?)
-    assert_equal(false, @vd06.to_be_continued?)
-    assert_equal(false, @vd07.to_be_continued?)
-    assert_equal(false, @vd08.to_be_continued?)
-    assert_equal(false, @vd09.to_be_continued?)
-    assert_equal(true , @vd10.to_be_continued?)
-    assert_equal(false, @vd11.to_be_continued?)
-    assert_equal(false, @vd12.to_be_continued?)
-    assert_equal(false, @vd13.to_be_continued?)
-    assert_equal(false, @vd14.to_be_continued?)
-    assert_equal(false, @vd15.to_be_continued?)
+  def test_finished?
+    assert_equal(false, @vd00.finished?)
+    assert_equal(false, @vd01.finished?)
+    assert_equal(false, @vd02.finished?)
+    assert_equal(true , @vd03.finished?)
   end
 
   def test_calculate
-    assert_raise(VaspDir::LockedError){@vd07.calculate}
-    assert_raise(VaspDir::LockedError){@vd08.calculate}
-
-    #
+    lock_dir = "test/vaspdir/not-yet/lock"
+    Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
+    #pp @vd00;exit
+    #@vd00.calculate
     assert_nothing_raised{@vd00.calculate}
+
     GENERATED_FILES_VD00.each do |file|
       assert(FileTest.exist?(file), "#{file} not found.")
     end
-    assert(FileTest.exist? "test/vaspdir/not-yet-ISIF2/INCAR")
-    assert(FileTest.exist? "test/vaspdir/not-yet-ISIF2/KPOINTS")
-    assert(FileTest.exist? "test/vaspdir/not-yet-ISIF2/POSCAR")
-    assert(FileTest.exist? "test/vaspdir/not-yet-ISIF2/POTCAR")
-    #
-    io = File.open("test/vaspdir/not-yet-ISIF2/lock", "r")
-    lines = io.readlines
-    assert_equal("HOST: #{ENV["HOST"]}\n", lines[0])
-    assert(/^START: / =~ lines[1])
-    assert_equal("STATUS: normal ended.\n", lines[2])
-
-    io.close
-    # あとかたづけは teardown にまかせる。
-  end
-
-  def test_next
-    assert_raise(VaspDir::NotEndedError){@vd00.next}
-    assert_raise(VaspDir::NotEndedError){@vd01.next}
-    assert_raise(VaspDir::NotEndedError){@vd02.next}
-    assert_raise(VaspDir::ConvergedError){@vd03.next}
-    assert_raise(VaspDir::NotEndedError){@vd06.next}
-    assert_raise(VaspDir::NotEndedError){@vd07.next}
-    assert_raise(VaspDir::NotEndedError){@vd08.next}
-    assert_raise(VaspDir::ConvergedError){@vd09.next}
-
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try00"))
-    assert_equal(false, FileTest.exist?("test/vaspdir/next-try01"))
-    @vd10.next
-    assert_equal("test/vaspdir/next-try01", @vd10.name)
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try00"))
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try01"))
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try01/POSCAR"))
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try01/POTCAR"))
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try01/INCAR"))
-    assert_equal(true , FileTest.exist?("test/vaspdir/next-try01/KPOINTS"))
-    assert_equal(4 , Dir.glob("test/vaspdir/next-try01/*").size)
-    #
-    poscar_00  = File.open("test/vaspdir/next-try00/POSCAR" ).readlines
-    contcar_00 = File.open("test/vaspdir/next-try00/CONTCAR").readlines
-    poscar_01  = File.open("test/vaspdir/next-try01/POSCAR" ).readlines
-    assert_equal(false, poscar_00  == contcar_00)
-    assert_equal(true,  contcar_00 == poscar_01)
-    assert_equal(false, poscar_01  == poscar_00)
-    # あとかたづけは teardown にまかせる。
-  end
-
-  def test_teardown
-    # NO TEST
-  end
-
-  def test_internal_steps
-    assert_equal(18, @vd10.internal_steps)
-  end
+    assert(FileTest.exist? "test/vaspdir/not-yet/INCAR")
+    assert(FileTest.exist? "test/vaspdir/not-yet/KPOINTS")
+    assert(FileTest.exist? "test/vaspdir/not-yet/POSCAR")
+    assert(FileTest.exist? "test/vaspdir/not-yet/POTCAR")
 
-  def test_external_steps
-    assert_equal(2, @vd10.external_steps)
-  end
-
-  def test_elapsed_time
-    assert_in_delta(126.383, @vd10.elapsed_time)
+    lock_dir = "test/vaspdir/not-yet/lock"
+    Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
   end
 
   def test_outcar
-    assert_equal("test/vaspdir/next-try00/OUTCAR", @vd10.outcar[:name])
+    assert_equal("test/vaspdir/started/OUTCAR", @vd02.outcar[:name])
+    assert_equal("test/vaspdir/finished/OUTCAR", @vd03.outcar[:name])
   end
 
   def test_contcar
-    t = @vd10.contcar
+    t = @vd03.contcar
     assert_equal(Cell, t.class)
-    assert_in_delta(3.8678456093562040, t.axes[2][2])
+    assert_in_delta(3.8879999999999999, t.axes[2][2])
     
     assert_raise(Errno::ENOENT){@vd00.contcar}
   end
 
   def test_incar
-    t = @vd10.incar
+    t = @vd00.incar
     assert_equal("400", t["ENCUT"])
   end
 
   def test_kpoints
-    t = @vd10.kpoints
+    t = @vd00.kpoints
     assert_equal("Automatic mesh", t[:comment])
   end
 
   #undef test_next
 
+  def teardown
+    GENERATED_FILES_VD00.each do |file|
+      FileUtils.rm file if File.exist? file
+    end
+
+    #lock_dir = "test/vaspdir/not-yet/lock"
+    #Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
+  end
+
 end
 

data/test/vaspdir/finished/CONTCAR

@@ -0,0 +1,17 @@
+Untitled (VASP)                         
+   1.00000000000000     
+     3.6509999999999998    0.0000000000000000    0.0000000000000000
+    -1.8254999999999919    3.1618587492169889    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    3.8879999999999999
+   3   1
+Selective dynamics
+Direct
+  0.0000000000000000  0.0000000000000000  0.5000000000000000   T   T   T
+  0.3333333333333357  0.6666666666666642  0.0000000000000000   T   T   T
+  0.6666666666666642  0.3333333333333357  0.0000000000000000   T   T   T
+  0.0000000000000000  0.0000000000000000  0.0000000000000000   F   F   F
+ 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00

data/test/vaspdir/finished/INCAR

@@ -0,0 +1,27 @@
+# SCF input for VASP
+
+SYSTEM = Untitled (VASP)
+    PREC = High
+  IBRION = -1     #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
+     NSW = 0      #maximum number of ionic steps
+   ENCUT = 400
+    NELM = 60       #maximum number of electronic steps
+  NELMIN = 2        #minimum number of electronic steps
+   EDIFF = 1.0e-05
+  EDIFFG = -0.02
+ VOSKOWN = 1
+  NBLOCK = 1
+   ISPIN = 1        #1:non spin polarized, 2:spin polarized
+  INIWAV = 1
+  ISTART = 1
+  ICHARG = 1
+   LWAVE = .TRUE.
+  LCHARG = .TRUE.
+  ISMEAR = 0
+   SIGMA = 0.1
+   IALGO = 38       #38:KosugiAlgorithm, 48:RMM-DIIS
+   #LREAL = .FALSE.
+   LREAL = Auto     #fast & not accurate
+     NGX = 36
+     NGY = 36
+     NGZ = 42

data/test/vaspdir/finished/KPOINTS

@@ -0,0 +1,6 @@
+Automatic mesh
+0
+Monkhorst Pack
+  5  5  5
+  0.  0.  0.
+