vasputils 0.0.11 → 0.0.12

data/test/test_vaspgeometryoptimizer.rb

@@ -2,96 +2,195 @@
 # coding: utf-8
 
 require "fileutils"
+require "stringio"
 require "test/unit"
 
 require "vasputils.rb"
 #require "vasputils/vaspgeometryoptimizer.rb"
 
 
-class VaspUtils::VaspGeometryOptimizer < ComputationManager
-  public :latest_dir, :prepare_next
+class VaspUtils::VaspGeometryOptimizer < Comana::ComputationManager
+    public :latest_dir, :prepare_next
 end
 
 class TC_VaspGeometryOptimizer < Test::Unit::TestCase
-  TEST_DIR = "test/vaspgeometryoptimizer"
-  def setup
-    @vgo00 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/not-yet")
-    @vgo01 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/started")
-    @vgo02 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/till01")
-    @vgo03 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/ended-Iter1")
-    @vgo04 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/ended-Iter2")
-  end
-
-  def test_initialize
-    assert_raise(VaspUtils::VaspGeometryOptimizer::NoVaspDirError){
-      VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/not-geomopt")
-    }
-  end
-
-  def test_latest_dir
-    assert_equal("#{@vgo00.dir}/try00", @vgo00.latest_dir.dir)
-    assert_equal("#{@vgo01.dir}/try00", @vgo01.latest_dir.dir)
-    assert_equal("#{@vgo02.dir}/try01", @vgo02.latest_dir.dir)
-    assert_equal("#{@vgo03.dir}/try01", @vgo03.latest_dir.dir)
-  end
-
-  def test_finished?
-    assert_equal(false, @vgo00.finished?)
-    assert_equal(false, @vgo01.finished?)
-    assert_equal(false, @vgo02.finished?)
-    assert_equal(true , @vgo03.finished?)
-    assert_equal(false, @vgo04.finished?)
-  end
-
-  def test_next_name
-    assert_equal( "try01" , VaspUtils::VaspGeometryOptimizer.next_name("try00"))
-    assert_equal( "try01" , VaspUtils::VaspGeometryOptimizer.next_name("try0"))
-    assert_equal( "try10" , VaspUtils::VaspGeometryOptimizer.next_name("try09"))
-    assert_equal( "try11" , VaspUtils::VaspGeometryOptimizer.next_name("try10"))
-    assert_equal( "try100", VaspUtils::VaspGeometryOptimizer.next_name("try99"))
-    assert_equal( "01"    , VaspUtils::VaspGeometryOptimizer.next_name("00"))
-    assert_equal( "try01" , VaspUtils::VaspGeometryOptimizer.next_name("try"))
-    #assert_raise(VaspUtils::VaspGeometryOptimizer::NoIntegerEndedNameError){VaspUtils::VaspGeometryOptimizer.next_name("try")}
-  end
-
-  def test_prepare_next
-    dir = TEST_DIR + "/prepare_next"
-    old_number_dir = dir + "/try00"
-    new_number_dir = dir + "/try01"
-
-    if Dir.exist?(new_number_dir)
-      Dir.glob(new_number_dir + "/*").each do |file|
-        FileUtils.rm file
-      end
-      Dir.rmdir new_number_dir
+    TEST_DIR = "test/vaspgeometryoptimizer"
+    def setup
+        @vgo00 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/not-yet")
+        @vgo01 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/started")
+        @vgo02 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/till01")
+        @vgo03 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/ended-Iter1")
+        @vgo04 = VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/ended-Iter2")
     end
 
-    vgo = VaspUtils::VaspGeometryOptimizer.new(dir)
-    vgo.prepare_next
-    assert(Dir.exist?(new_number_dir))
-    assert(File.exist?(new_number_dir + "/CHG"     ))
-    assert(File.exist?(new_number_dir + "/CHGCAR"  ))
-    assert(File.exist?(new_number_dir + "/DOSCAR"  ))
-    assert(File.exist?(new_number_dir + "/EIGENVAL"))
-    assert(File.exist?(new_number_dir + "/INCAR"   ))
-    assert(File.exist?(new_number_dir + "/KPOINTS" ))
-    assert(File.exist?(new_number_dir + "/OSZICAR" ))
-    assert(File.exist?(new_number_dir + "/PCDAT"   ))
-    assert(File.exist?(new_number_dir + "/POTCAR"  ))
-    assert(File.exist?(new_number_dir + "/WAVECAR" ))
-    assert(File.exist?(new_number_dir + "/XDATCAR" ))
-    assert(File.exist?(new_number_dir + "/POSCAR"  ))
-    assert(! File.exist?(new_number_dir + "/CONTCAR" ))
-    assert(! File.exist?(new_number_dir + "/OUTCAR" ))
-    assert(! File.exist?(new_number_dir + "/vasprun.xml" ))
-
-    if Dir.exist?(new_number_dir)
-      Dir.glob(new_number_dir + "/*").each do |file|
-        FileUtils.rm file
-      end
-      Dir.rmdir new_number_dir
+    def test_initialize
+        assert_raise(VaspUtils::VaspGeometryOptimizer::InitializeError){
+            VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/not-geomopt/nothing")
+        }
+
+        assert_raise(VaspUtils::VaspGeometryOptimizer::InitializeError){
+            VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "/not-geomopt/not-geomopt-subdir")
+        }
+
+        #assert_raise(VaspUtils::VaspGeometryOptimizer::InitializeError){
+        assert_raise(VaspUtils::VaspGeometryOptimizer::InitializeError){
+            VaspUtils::VaspGeometryOptimizer.new( TEST_DIR + "test/vaspgeometryoptimizer/multiple_vaspdir")
+        }
+    end
+
+    def test_latest_dir
+        assert_equal("#{@vgo00.dir}/geomopt00", @vgo00.latest_dir.dir)
+        assert_equal("#{@vgo01.dir}/geomopt00", @vgo01.latest_dir.dir)
+        assert_equal("#{@vgo02.dir}/geomopt01", @vgo02.latest_dir.dir)
+        assert_equal("#{@vgo03.dir}/geomopt01", @vgo03.latest_dir.dir)
+    end
+
+    def test_finished?
+        assert_equal(false, @vgo00.finished?)
+        assert_equal(false, @vgo01.finished?)
+        assert_equal(false, @vgo02.finished?)
+        assert_equal(true , @vgo03.finished?)
+        assert_equal(false, @vgo04.finished?)
+    end
+
+    def test_next_name
+        assert_equal( "geomopt01" , VaspUtils::VaspGeometryOptimizer.next_name("geomopt00"))
+        assert_equal( "geomopt01" , VaspUtils::VaspGeometryOptimizer.next_name("geomopt0"))
+        assert_equal( "geomopt10" , VaspUtils::VaspGeometryOptimizer.next_name("geomopt09"))
+        assert_equal( "geomopt11" , VaspUtils::VaspGeometryOptimizer.next_name("geomopt10"))
+        assert_equal( "geomopt100", VaspUtils::VaspGeometryOptimizer.next_name("geomopt99"))
+        assert_equal( "01"      , VaspUtils::VaspGeometryOptimizer.next_name("00"))
+        assert_equal( "geomopt01" , VaspUtils::VaspGeometryOptimizer.next_name("geomopt"))
+        #assert_raise(VaspUtils::VaspGeometryOptimizer::NoIntegerEndedNameError){VaspUtils::VaspGeometryOptimizer.next_name("try")}
+    end
+
+    def test_prepare_next
+        dir = TEST_DIR + "/prepare_next/normal"
+        old_number_dir = dir + "/geomopt00"
+        new_number_dir = dir + "/geomopt01"
+
+        if Dir.exist?(new_number_dir)
+            Dir.glob(new_number_dir + "/*").each do |file|
+                FileUtils.rm file
+            end
+            Dir.rmdir new_number_dir
+        end
+
+        vgo = VaspUtils::VaspGeometryOptimizer.new(dir)
+        vgo.prepare_next
+        assert_equal(true ,Dir.exist?(new_number_dir))
+        assert_equal(true , File.exist?(new_number_dir + "/CHG"         ))
+        assert_equal(true , File.exist?(new_number_dir + "/CHGCAR"  ))
+        assert_equal(true , File.exist?(new_number_dir + "/DOSCAR"  ))
+        assert_equal(true , File.exist?(new_number_dir + "/EIGENVAL"))
+        assert_equal(true , File.exist?(new_number_dir + "/INCAR"       ))
+        assert_equal(true , File.exist?(new_number_dir + "/KPOINTS" ))
+        assert_equal(true , File.exist?(new_number_dir + "/OSZICAR" ))
+        assert_equal(true , File.exist?(new_number_dir + "/PCDAT"       ))
+        assert_equal(true , File.exist?(new_number_dir + "/POTCAR"  ))
+        assert_equal(true , File.exist?(new_number_dir + "/WAVECAR" ))
+        assert_equal(true , File.exist?(new_number_dir + "/XDATCAR" ))
+        assert_equal(true , File.exist?(new_number_dir + "/POSCAR"  ))
+        assert_equal(false, File.exist?(new_number_dir + "/CONTCAR" ))
+        assert_equal(false, File.exist?(new_number_dir + "/OUTCAR" ))
+        assert_equal(false, File.exist?(new_number_dir + "/vasprun.xml" ))
+
+        if Dir.exist?(new_number_dir)
+            Dir.glob(new_number_dir + "/*").each do |file|
+                FileUtils.rm file
+            end
+            Dir.rmdir new_number_dir
+        end
+
+        dir = TEST_DIR + "/prepare_next/no-contcar"
+        vgo = VaspUtils::VaspGeometryOptimizer.new(dir)
+        assert_raise(VaspUtils::VaspGeometryOptimizer::NoContcarError){
+            vgo.prepare_next
+        }
+    end
+
+
+    def test_reset_init
+        orig = TEST_DIR + "/reset_init/orig"
+        tmp  = TEST_DIR + "/reset_init/tmp"
+        FileUtils.rm_r tmp if FileTest.exist? tmp
+        FileUtils.cp_r(orig, tmp)
+        vgo = VaspUtils::VaspGeometryOptimizer.new(tmp)
+        vgo.reset_init
+        assert_equal(true,  File.exist?("#{tmp}/geomopt00"))
+        assert_equal(false, File.exist?("#{tmp}/geomopt01"))
+        assert_equal(4,         Dir.glob("#{tmp}/geomopt00/*").size)
+        assert_equal("POSCAR_00\n", File.open("#{tmp}/geomopt00/POSCAR", "r").readline)
+        FileUtils.rm_rf tmp if FileTest.exist? tmp
+    end
+
+    def test_reset_next
+        #with correct POSCAR and CONTCAR
+        orig = TEST_DIR + "/reset_next/poscar-contcar/orig"
+        tmp  = TEST_DIR + "/reset_next/poscar-contcar/tmp"
+        FileUtils.rm_r tmp if FileTest.exist? tmp
+        FileUtils.cp_r(orig, tmp)
+        vgo = VaspUtils::VaspGeometryOptimizer.new(tmp)
+        io = StringIO.new
+        vgo.reset_next(io)
+        assert_equal(true,  File.exist?("#{tmp}/geomopt00"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt01"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt02"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt03"))
+        assert_equal(4,         Dir.glob("#{tmp}/geomopt03/*").size)
+        assert_equal("CONTCAR_02\n", File.open("#{tmp}/geomopt03/POSCAR", "r").readline)
+        FileUtils.rm_rf tmp if FileTest.exist? tmp
+
+        #with correct POSCAR and empty CONTCAR
+        orig = TEST_DIR + "/reset_next/empty-contcar/orig"
+        tmp  = TEST_DIR + "/reset_next/empty-contcar/tmp"
+        FileUtils.rm_r tmp if FileTest.exist? tmp
+        FileUtils.cp_r(orig, tmp)
+        vgo = VaspUtils::VaspGeometryOptimizer.new(tmp)
+        vgo.reset_next(io)
+        assert_equal(true,  File.exist?("#{tmp}/geomopt00"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt01"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt02"))
+        assert_equal(false,  File.exist?("#{tmp}/geomopt03"))
+        assert_equal(4,         Dir.glob("#{tmp}/geomopt02/*").size)
+        assert_equal("POSCAR_02\n", File.open("#{tmp}/geomopt02/POSCAR", "r").readline)
+        FileUtils.rm_rf tmp if FileTest.exist? tmp
+
+        #with correct POSCAR and no CONTCAR
+        orig = TEST_DIR + "/reset_next/no-contcar/orig"
+        tmp  = TEST_DIR + "/reset_next/no-contcar/tmp"
+        FileUtils.rm_r tmp if FileTest.exist? tmp
+        FileUtils.cp_r(orig, tmp)
+        vgo = VaspUtils::VaspGeometryOptimizer.new(tmp)
+        vgo.reset_next(io)
+        assert_equal(true,  File.exist?("#{tmp}/geomopt00"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt01"))
+        assert_equal(true,  File.exist?("#{tmp}/geomopt02"))
+        assert_equal(false,  File.exist?("#{tmp}/geomopt03"))
+        assert_equal(4,         Dir.glob("#{tmp}/geomopt02/*").size)
+        assert_equal("POSCAR_02\n", File.open("#{tmp}/geomopt02/POSCAR", "r").readline)
+        FileUtils.rm_rf tmp if FileTest.exist? tmp
+    end
+
+    def test_reset_reincarnation
+        orig = TEST_DIR + "/reset_reincarnation/orig"
+        tmp  = TEST_DIR + "/reset_reincarnation/tmp"
+
+        FileUtils.rm_r tmp if FileTest.exist? tmp
+
+        FileUtils.cp_r(orig, tmp)
+        vgo = VaspUtils::VaspGeometryOptimizer.new(tmp)
+        vgo.reset_reincarnate
+
+        assert_equal(true,  File.exist?("#{tmp}/geomopt00"))
+        assert_equal(false, File.exist?("#{tmp}/geomopt01"))
+        #assert_equal(1,         Dir.glob("#{tmp}/*").size)
+            #This test may rail in NFS environment due to nfs lock; geomopt02/.nfs*.
+        assert_equal(4,         Dir.glob("#{tmp}/geomopt00/*").size)
+        assert_equal("CONTCAR_01\n", File.open("#{tmp}/geomopt00/POSCAR", "r").readline)
+
+        FileUtils.rm_rf tmp if FileTest.exist? tmp
     end
-  end
 
 end
 

data/test/test_vasputils.rb

@@ -5,61 +5,61 @@ require "test/unit"
 require "vasputils.rb"
 
 class TC_VaspUtils < Test::Unit::TestCase
-  #def setup
-  #  @k = VaspUtils.new
-  #end
+    #def setup
+    #    @k = VaspUtils.new
+    #end
 
-  #def test_generate_kmeshes
-  #  results = VaspUtils::generate_kmeshes([1.0, 1.0, 1.0], 5.0)
-  #  corrects = [
-  #    [1,1,1],
-  #    [2,2,2],
-  #    [4,4,4],
-  #    [8,8,8],
-  #  ]
-  #  assert_equal(corrects, results)
+    #def test_generate_kmeshes
+    #    results = VaspUtils::generate_kmeshes([1.0, 1.0, 1.0], 5.0)
+    #    corrects = [
+    #        [1,1,1],
+    #        [2,2,2],
+    #        [4,4,4],
+    #        [8,8,8],
+    #    ]
+    #    assert_equal(corrects, results)
 
-  #  results = VaspUtils::generate_kmeshes([1.0, 1.0, 2.0], 5.0)
-  #  corrects = [
-  #    [1,1,1],
-  #    [2,2,1],
-  #    [4,4,2],
-  #    [8,8,4],
-  #  ]
-  #  assert_equal(corrects, results)
+    #    results = VaspUtils::generate_kmeshes([1.0, 1.0, 2.0], 5.0)
+    #    corrects = [
+    #        [1,1,1],
+    #        [2,2,1],
+    #        [4,4,2],
+    #        [8,8,4],
+    #    ]
+    #    assert_equal(corrects, results)
 
-  #  results = VaspUtils::generate_kmeshes([1.0, 1.0, 3.0], 5.0)
-  #  corrects = [
-  #    [1,1,1], #1.0, 1.0, 3.0
-  #    [2,2,1], #2.0, 2.0, 3.0
-  #    [4,4,1], #4.0, 4.0, 3.0
-  #    [4,4,2], #4.0, 4.0, 6.0
-  #    [8,8,2], #8.0, 8.0, 6.0
-  #  ]
-  #  assert_equal(corrects, results)
+    #    results = VaspUtils::generate_kmeshes([1.0, 1.0, 3.0], 5.0)
+    #    corrects = [
+    #        [1,1,1], #1.0, 1.0, 3.0
+    #        [2,2,1], #2.0, 2.0, 3.0
+    #        [4,4,1], #4.0, 4.0, 3.0
+    #        [4,4,2], #4.0, 4.0, 6.0
+    #        [8,8,2], #8.0, 8.0, 6.0
+    #    ]
+    #    assert_equal(corrects, results)
 
-  #  # check condition of equal
-  #  results = VaspUtils::generate_kmeshes([1.0, 1.0, 1.0], 2.0)
-  #  corrects = [
-  #    [1,1,1],
-  #    [2,2,2],
-  #  ]
-  #  assert_equal(corrects, results)
+    #    # check condition of equal
+    #    results = VaspUtils::generate_kmeshes([1.0, 1.0, 1.0], 2.0)
+    #    corrects = [
+    #        [1,1,1],
+    #        [2,2,2],
+    #    ]
+    #    assert_equal(corrects, results)
 
-  #  assert_raise(VaspUtils::ArgumentError,
-  #    VaspUtils::generate_kmeshes([1.0, 2.0, 2.0, 0.0], 5.0)
-  #  )
-  #end
+    #    assert_raise(VaspUtils::ArgumentError,
+    #        VaspUtils::generate_kmeshes([1.0, 2.0, 2.0, 0.0], 5.0)
+    #    )
+    #end
 
-  #def test_generate_wavelengths
-  #  results = VaspUtils::generate_wavelengths([2.0, 2.0, 3.0], 5.0)
-  #  corrects = [2.0, 3.0, 4.0, 6.0]
-  #  assert_equal(corrects, results)
+    #def test_generate_wavelengths
+    #    results = VaspUtils::generate_wavelengths([2.0, 2.0, 3.0], 5.0)
+    #    corrects = [2.0, 3.0, 4.0, 6.0]
+    #    assert_equal(corrects, results)
 
-  #  results = VaspUtils::generate_wavelengths([1.0, 1.0, 1.0], 2.0)
-  #  corrects = [1.0, 2.0]
-  #  assert_equal(corrects, results)
-  #end
+    #    results = VaspUtils::generate_wavelengths([1.0, 1.0, 1.0], 2.0)
+    #    corrects = [1.0, 2.0]
+    #    assert_equal(corrects, results)
+    #end
 
 end
 

data/test/vaspdir/reset_init/finished/orig/CONTCAR

@@ -0,0 +1,17 @@
+CONTCAR
+   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/reset_init/finished/orig/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/reset_init/finished/orig/KPOINTS

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