crysna 0.0.4

data/test/test_optionmanager.rb

@@ -0,0 +1,172 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "helper"
+#require "test/unit"
+#require "pkg/klass.rb"
+
+class TC_OptionManager < Test::Unit::TestCase
+  def setup
+    @o00 = Crysna::OptionManager.new
+  end
+
+  def test_parse_all
+    ary = []
+    @o00.parser.parse!(ary)
+    corrects = {
+      :cells=>"cells.yaml",
+      :fitted=>"fittedstructure.yaml",
+      :occupied=>"occupiedsite.yaml",
+      :model=>"model.yaml",
+      :symid=>"symidsite.yaml",
+      :migration=>"sitemigration.yaml",
+      :operation=>"siteoperation.yaml",
+      :symmetry=>"symoperation.yaml",
+      :unique  =>"siteunique.yaml",
+      :single=>"sitesingle.yaml",
+      :combination=> 'sitecombination.yaml',
+      :candidate=> 'sitecandidate.yaml',
+      :quiet=>false,
+    }
+    assert_equal(corrects, @o00.options)
+
+    setup
+    ary = %w(-m test.yaml)
+    @o00.parser.parse!(ary)
+    corrects = {
+      :cells=>"cells.yaml",
+      :fitted=>"fittedstructure.yaml",
+      :occupied=>"occupiedsite.yaml",
+      :model=>"test.yaml",
+      :symid=>"symidsite.yaml",
+      :migration=>"sitemigration.yaml",
+      :operation=>"siteoperation.yaml",
+      :symmetry=>"symoperation.yaml",
+      :unique  =>"siteunique.yaml",
+      :single=>"sitesingle.yaml",
+      :combination=> 'sitecombination.yaml',
+      :candidate=> 'sitecandidate.yaml',
+      :quiet=>false,
+    }
+    assert_equal(corrects, @o00.options)
+
+    setup
+    ary = %w(-f test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:fitted])
+
+    setup
+    ary = %w(-M test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:migration])
+
+    setup
+    ary = %w(-o test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:operation])
+
+    setup
+    ary = %w(-c test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:cells])
+
+    setup
+    ary = %w(-i test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:symid])
+
+    setup
+    ary = %w(-y test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:symmetry])
+
+    #### --model=-
+    setup
+    ary = %w(--model=-)
+    @o00.parser.parse!(ary)
+    assert_equal('-', @o00.options[:model])
+
+    setup
+    ary = %w(-m -)
+    @o00.parser.parse!(ary)
+    assert_equal('-', @o00.options[:model])
+
+    setup
+    ary = %w(-b test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:combination])
+
+    setup
+    ary = %w(-d test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:candidate])
+
+    setup
+    ary = %w(-s test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:single])
+
+    setup
+    ary = %w(-u test.yaml)
+    @o00.parser.parse!(ary)
+    assert_equal('test.yaml', @o00.options[:unique])
+
+  end
+
+  def test_init
+    ary = []
+    @o00.parser.parse!(ary)
+    corrects = {
+      :cells=>"cells.yaml",
+      :fitted=>"fittedstructure.yaml",
+      :occupied=>"occupiedsite.yaml",
+      :model=>"model.yaml",
+      :symid=>"symidsite.yaml",
+      :migration=>"sitemigration.yaml",
+      :operation=>"siteoperation.yaml",
+      :symmetry=>"symoperation.yaml",
+      :unique  =>"siteunique.yaml",
+      :single=>"sitesingle.yaml",
+      :combination=> 'sitecombination.yaml',
+      :candidate=> 'sitecandidate.yaml',
+      :quiet=>false,
+    }
+    assert_equal(corrects, @o00.options)
+
+    o10 = Crysna::OptionManager.new([:model])
+    ary = []
+    o10.parser.parse!(ary)
+    corrects = {
+      :model=>"model.yaml",
+    }
+    assert_equal(corrects, o10.options)
+
+    assert_raise(Crysna::OptionManager::INVARID_OPTION){
+      Crysna::OptionManager.new([:cells, :unknown])
+    }
+  end
+
+  def test_parse
+    setup
+    ary = %w(-m test.yaml abc)
+    @o00.parse!(ary)
+    corrects = {
+      :cells=>"cells.yaml",
+      :fitted=>"fittedstructure.yaml",
+      :occupied=>"occupiedsite.yaml",
+      :model=>"test.yaml",
+      :symid=>"symidsite.yaml",
+      :migration=>"sitemigration.yaml",
+      :operation=>"siteoperation.yaml",
+      :symmetry=>"symoperation.yaml",
+      :unique  =>"siteunique.yaml",
+      :single=>"sitesingle.yaml",
+      :combination=> 'sitecombination.yaml',
+      :candidate=> 'sitecandidate.yaml',
+      :quiet=>false,
+    }
+    assert_equal(corrects, @o00.options)
+    assert_equal(['abc'], ary)
+  end
+end
+

data/test/test_site.rb

@@ -0,0 +1,40 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "helper"
+#require "test/unit"
+#require "pkg/klass.rb"
+
+class TC_Site < Test::Unit::TestCase
+  def setup
+    @cs_S00_m01 = Crysna::Site.new("S00", [-1, 0, 1])
+    @cs_S00_101 = Crysna::Site.new("S00", [ 0, 0, 1])
+    @cs_S00_m11 = Crysna::Site.new("S00", [-1, 1, 1])
+    @cs_S00_m00 = Crysna::Site.new("S00", [-1, 0, 0])
+    @cs_S01_m01 = Crysna::Site.new("S01", [-1, 0, 1])
+  end
+
+  def test_equal?
+    assert_equal(true , @cs_S00_m01.equal?(Crysna::Site.new("S00", [-1, 0, 1] )))
+    assert_equal(false, @cs_S00_m01.equal?(@cs_S00_101))
+    assert_equal(false, @cs_S00_m01.equal?(@cs_S00_m11))
+    assert_equal(false, @cs_S00_m01.equal?(@cs_S00_m00))
+    assert_equal(false, @cs_S00_m01.equal?(@cs_S01_m01))
+
+    assert_equal(true , @cs_S00_m01 == Crysna::Site.new("S00", [-1, 0, 1] ))
+    assert_equal(false, @cs_S00_m01 == @cs_S00_101)
+    assert_equal(false, @cs_S00_m01 == @cs_S00_m11)
+    assert_equal(false, @cs_S00_m01 == @cs_S00_m00)
+    assert_equal(false, @cs_S00_m01 == @cs_S01_m01)
+  end
+
+  def test_same_globla_vector?
+    assert_equal(true , @cs_S00_m01.same_globla_vector?(Crysna::Site.new("S00", [-1, 0, 1])))
+    assert_equal(false, @cs_S00_m01.same_globla_vector?(@cs_S00_101))
+    assert_equal(false, @cs_S00_m01.same_globla_vector?(@cs_S00_m11))
+    assert_equal(false, @cs_S00_m01.same_globla_vector?(@cs_S00_m00))
+    assert_equal(true , @cs_S00_m01.same_globla_vector?(@cs_S01_m01))
+  end
+
+end
+

data/test/test_siteconfiguration.rb

@@ -0,0 +1,29 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require 'helper'
+#require 'test/unit'
+#require 'pkg/klass.rb'
+
+class SiteConfiguration
+end
+
+class TC_SiteConfiguration < Test::Unit::TestCase
+  def setup
+    hash = {
+      'Ag' => ['1A', '2A'],
+      'I'  => ['IA', 'IB'],
+    }
+    @sc = Crysna::SiteConfiguration.new(hash)
+  end
+
+  def test_initalize
+    hash = {
+      'Ag' => ['1A', '2A'],
+      'I'  => ['IA', 'IB'],
+    }
+    assert_equal(hash, @sc.elem_sites)
+  end
+
+end
+

data/test/test_sitenamelabeledcell.rb

@@ -0,0 +1,528 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "helper"
+#require "test/unit"
+#require "mathextension/vector3dinternal.rb"
+#require "crystal/atom2.rb"
+#require "crysna/sitenamelabeledcell.rb"
+
+# assert_equal( cor, data)
+# assert_in_delta( cor, data, $tolerance )
+# assert_raise( RuntimeError ){}
+
+class SiteNameLabeledCell
+  public :nearest_atom_index
+  public_class_method :nearest_site
+  public_class_method :unique_sitenames?
+end
+
+class TC_SiteNameLabeledCell < Test::Unit::TestCase
+  $tolerance = 1.0 * (10 **(-10))
+
+  def setup
+    @sites00 = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    @atoms00 = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ]),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ])
+    ]
+    @c00 = SiteNameLabeledCell.new(
+      [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ], @atoms00, @sites00
+    )
+    @c00.comment = "c00"
+
+    @sites01 = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    @atoms01 = [
+      CrystalCell::Atom.new( 0, [ 0.99, 0.99, 0.99 ]),
+      CrystalCell::Atom.new( 0, [ 0.90, 0.20, 0.30 ])
+    ]
+    @c01 = SiteNameLabeledCell.new(
+      [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ], @atoms01, @sites01
+    )
+  end
+
+  def test_initialize
+    # サイト数と原子数が一致しないときに例外。
+    assert_raise( SiteNameLabeledCell::InitializeError ){
+      SiteNameLabeledCell.new(
+        [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ],
+        @atoms00,
+        {}
+      )
+    }
+
+    # 同上
+    sites = Hash.new
+    sites["site00"] = Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ]
+    sites["site01"] = Mageo::Vector3DInternal[ 0.20, 0.20, 0.20 ]
+    sites["site02"] = Mageo::Vector3DInternal[ 0.80, 0.80, 0.80 ]
+    assert_raise( SiteNameLabeledCell::InitializeError ){
+      SiteNameLabeledCell.new(
+        [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ],
+        @atoms00,
+        sites
+      )
+    }
+
+    # 最近接の原子とサイト名が一対一対応しないときに例外。
+    sites = Hash.new
+    sites["site00"] = Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ]
+    sites["site01"] = Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ]
+    assert_raise( SiteNameLabeledCell::InitializeError ){
+      SiteNameLabeledCell.new(
+        [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ],
+        @atoms00,
+        sites
+      )
+    }
+
+    # 同上、ただし周期境界を考慮していることを確認。
+    sites = Hash.new
+    sites["site00"] = Mageo::Vector3DInternal[ 0.0, 0.0, 0.8 ]
+    sites["site01"] = Mageo::Vector3DInternal[ 0.0, 0.0, 0.1 ]
+    atoms = []
+    atoms << CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.05 ])
+    atoms << CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.99 ])
+    assert_raise( SiteNameLabeledCell::InitializeError ){
+      SiteNameLabeledCell.new(
+        [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ],
+        atoms,
+        sites
+      )
+    }
+
+    axes = [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ]
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.99, 0.99, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.90, 0.99, 0.01 ]
+    }
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.90, 0.01, 0.01 ]),
+      CrystalCell::Atom.new( 0, [ 0.99, 0.01, 0.01 ])
+    ]
+    #
+    assert_nothing_raised{ SiteNameLabeledCell.new(axes, atoms, sites) }
+  end
+
+  def test_nearest_atom_index
+    assert_raise(SiteNameLabeledCell::TypeError){
+      @c00.nearest_atom_index( Mageo::Vector3DInternal[0.0, 0.0, 0.0] )
+    }
+
+    assert_equal(0 , @c00.nearest_atom_index("site00"))
+    assert_equal(1 , @c00.nearest_atom_index("site01"))
+  end
+
+  def test_sum_square_distances
+    # 破壊的でないことを確認。
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+    }
+    atoms = [
+      CrystalCell::Atom.new( 0, [-0.01,-0.01,-0.01 ], "site00"),
+    ]
+    cell = SiteNameLabeledCell.new(
+      [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ], atoms, sites
+    )
+    #pp cell
+    assert_in_delta( 0.0012, cell.sum_square_distances, $tolerance)
+    assert_in_delta(-0.01, cell.atoms[0].position[0], $tolerance)
+    assert_in_delta(-0.01, cell.atoms[0].position[1], $tolerance)
+    assert_in_delta(-0.01, cell.atoms[0].position[2], $tolerance)
+
+    # 機能テスト
+    assert_in_delta(0.0112 , @c00.sum_square_distances, $tolerance)
+
+  end
+
+  def test_to_cell
+    t = @c00.to_cell
+    assert_equal(CrystalCell::Cell, t.class)
+    assert_equal(2, t.atoms.size)
+    assert_equal(0, t.atoms[0].element)
+    assert_equal("site00", t.atoms[0].name)
+    assert_equal(Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
+    assert_equal(0, t.atoms[1].element)
+    assert_equal("site01", t.atoms[1].name)
+    assert_equal(Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position)
+    assert_equal("c00", t.comment)
+  end
+
+  def test_center_of_sites
+    vec = @c00.center_of_sites
+    assert_equal(Mageo::Vector3DInternal, vec.class)
+    assert_in_delta(0.06, vec[0], $tolerance)
+    assert_in_delta(0.11, vec[1], $tolerance)
+    assert_in_delta(0.16, vec[2], $tolerance)
+  end
+
+  def test_center_of_atoms
+    vec = @c00.center_of_atoms
+    assert_equal(Mageo::Vector3DInternal, vec.class)
+    assert_in_delta(0.05, vec[0], $tolerance)
+    assert_in_delta(0.10, vec[1], $tolerance)
+    assert_in_delta(0.15, vec[2], $tolerance)
+  end
+
+  def test_sitenames_positions
+    t = @c00.sitenames_positions
+    assert_equal(2, t.size)
+    assert_equal(Mageo::Vector3DInternal, t["site00"].class)
+    assert_in_delta(0.00, t["site00"][0], $tolerance)
+    assert_in_delta(0.00, t["site00"][1], $tolerance)
+    assert_in_delta(0.00, t["site00"][2], $tolerance)
+    #
+    assert_equal(Mageo::Vector3DInternal, t["site01"].class)
+    assert_in_delta(0.10, t["site01"][0], $tolerance)
+    assert_in_delta(0.20, t["site01"][1], $tolerance)
+    assert_in_delta(0.30, t["site01"][2], $tolerance)
+
+    t = @c01.sitenames_positions
+    assert_equal(2, t.size)
+    assert_equal(Mageo::Vector3DInternal, t["site00"].class)
+    assert_in_delta(-0.01, t["site00"][0], $tolerance)
+    assert_in_delta(-0.01, t["site00"][1], $tolerance)
+    assert_in_delta(-0.01, t["site00"][2], $tolerance)
+    #
+    assert_equal(Mageo::Vector3DInternal, t["site01"].class)
+    assert_in_delta(-0.10, t["site01"][0], $tolerance)
+    assert_in_delta( 0.20, t["site01"][1], $tolerance)
+    assert_in_delta( 0.30, t["site01"][2], $tolerance)
+  end
+
+  def test_sitenames_elements
+    assert_equal(
+      { "site00" => 0,
+        "site01" => 0
+      },
+      @c00.sitenames_elements
+    )
+    assert_equal(
+      { "site00" => 0,
+        "site01" => 0
+      },
+      @c01.sitenames_elements
+    )
+  end
+end
+
+class TC_SiteNameLabeledCellClassMethods < Test::Unit::TestCase
+  def setup
+    @sites00 = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    @atoms00 = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ]),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ])
+    ]
+
+    @sites01 = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    @atoms01 = [
+      CrystalCell::Atom.new( 0, [ 0.99, 0.99, 0.99 ]),
+      CrystalCell::Atom.new( 0, [ 0.90, 0.20, 0.30 ])
+    ]
+  end
+
+  def test_self_unique_sitenames?
+    atoms01 = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site01")
+    ]
+    assert_equal(true , SiteNameLabeledCell.unique_sitenames?(atoms01))
+    
+    atoms01 = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00")
+    ]
+    assert_equal(false, SiteNameLabeledCell.unique_sitenames?(atoms01))
+    
+    atoms01 = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], nil)
+    ]
+    assert_equal(false, SiteNameLabeledCell.unique_sitenames?(atoms01))
+  end
+
+  def test_label_sitenames
+    axes = [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ]
+    sites = @sites00
+    atoms = @atoms00
+    t = SiteNameLabeledCell.label_sitenames(axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_equal("site00", t[0].name)
+    assert_in_delta(0.00, t[0].position[0])
+    assert_in_delta(0.00, t[0].position[1])
+    assert_in_delta(0.00, t[0].position[2])
+    #
+    assert_equal("site01", t[1].name)
+    assert_in_delta(0.10, t[1].position[0])
+    assert_in_delta(0.20, t[1].position[1])
+    assert_in_delta(0.30, t[1].position[2])
+
+    axes = [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ]
+    sites = @sites01
+    atoms = @atoms01
+    t = SiteNameLabeledCell.label_sitenames(axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_equal("site00", t[0].name)
+    assert_in_delta( 0.99, t[0].position[0])
+    assert_in_delta( 0.99, t[0].position[1])
+    assert_in_delta( 0.99, t[0].position[2])
+    #
+    assert_equal("site01", t[1].name)
+    assert_in_delta( 0.90, t[1].position[0])
+    assert_in_delta( 0.20, t[1].position[1])
+    assert_in_delta( 0.30, t[1].position[2])
+
+    axes = [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ]
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.99, 0.99, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.90, 0.99, 0.01 ]
+    }
+    #
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.90, 0.01, 0.01 ]),
+      CrystalCell::Atom.new( 0, [ 0.99, 0.01, 0.01 ])
+    ]
+    #
+    t = SiteNameLabeledCell.label_sitenames(axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_in_delta( 0.90, t[0].position[0])
+    assert_in_delta( 0.01, t[0].position[1])
+    assert_in_delta( 0.01, t[0].position[2])
+    assert_equal("site01", t[0].name)
+    #
+    assert_in_delta( 0.99, t[1].position[0])
+    assert_in_delta( 0.01, t[1].position[1])
+    assert_in_delta( 0.01, t[1].position[2])
+    assert_equal("site00", t[1].name)
+
+    axes = [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ]
+    #
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.01, 0.01, 0.01 ]),
+      CrystalCell::Atom.new( 0, [-0.89,-0.79,-0.69 ])
+    ]
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    t = SiteNameLabeledCell.label_sitenames(axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_in_delta( 0.01, t[0].position[0])
+    assert_in_delta( 0.01, t[0].position[1])
+    assert_in_delta( 0.01, t[0].position[2])
+    assert_equal("site00", t[0].name)
+    #
+    assert_in_delta(-0.89, t[1].position[0])
+    assert_in_delta(-0.79, t[1].position[1])
+    assert_in_delta(-0.69, t[1].position[2])
+    assert_equal("site01", t[1].name)
+  end
+
+  def test_periodically_translate_atoms_to_nearest_site
+    axes = [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ]
+    sites = @sites00
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ], "site01")
+    ]
+    t = SiteNameLabeledCell.periodically_translate_atoms_to_nearest_site(
+      axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_equal("site00", t[0].name)
+    assert_in_delta(0.00, t[0].position[0])
+    assert_in_delta(0.00, t[0].position[1])
+    assert_in_delta(0.00, t[0].position[2])
+    #
+    assert_equal("site01", t[1].name)
+    assert_in_delta(0.10, t[1].position[0])
+    assert_in_delta(0.20, t[1].position[1])
+    assert_in_delta(0.30, t[1].position[2])
+
+    axes = [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ]
+    sites = @sites01
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.99, 0.99, 0.99 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.90, 0.20, 0.30 ], "site01")
+    ]
+    t = SiteNameLabeledCell.periodically_translate_atoms_to_nearest_site(
+      axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_equal("site00", t[0].name)
+    assert_in_delta(-0.01, t[0].position[0])
+    assert_in_delta(-0.01, t[0].position[1])
+    assert_in_delta(-0.01, t[0].position[2])
+    #
+    assert_equal("site01", t[1].name)
+    assert_in_delta(-0.10, t[1].position[0])
+    assert_in_delta( 0.20, t[1].position[1])
+    assert_in_delta( 0.30, t[1].position[2])
+
+    axes = [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ]
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.99, 0.99, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.90, 0.99, 0.01 ]
+    }
+    #
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.90, 0.01, 0.01 ], "site01"),
+      CrystalCell::Atom.new( 0, [ 0.99, 0.01, 0.01 ], "site00")
+    ]
+    #
+    t = SiteNameLabeledCell.periodically_translate_atoms_to_nearest_site(
+      axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_in_delta( 0.90, t[0].position[0])
+    assert_in_delta( 1.01, t[0].position[1])
+    assert_in_delta( 0.01, t[0].position[2])
+    assert_equal("site01", t[0].name)
+    #
+    assert_in_delta( 0.99, t[1].position[0])
+    assert_in_delta( 1.01, t[1].position[1])
+    assert_in_delta( 0.01, t[1].position[2])
+    assert_equal("site00", t[1].name)
+
+    axes = [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ]
+    #
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.01, 0.01, 0.01 ], "site00"),
+      CrystalCell::Atom.new( 0, [-0.89,-0.79,-0.69 ], "site01")
+    ]
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    #
+    t = SiteNameLabeledCell.periodically_translate_atoms_to_nearest_site(
+      axes, atoms, sites)
+    assert_equal(2, t.size)
+    assert_in_delta( 0.01, t[0].position[0])
+    assert_in_delta( 0.01, t[0].position[1])
+    assert_in_delta( 0.01, t[0].position[2])
+    assert_equal("site00", t[0].name)
+    #
+    assert_in_delta( 0.11, t[1].position[0])
+    assert_in_delta( 0.21, t[1].position[1])
+    assert_in_delta( 0.31, t[1].position[2])
+    assert_equal("site01", t[1].name)
+
+  end
+
+  def test_self_nearest_site
+    la = CrystalCell::LatticeAxes.new([ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ])
+    pos = Mageo::Vector3DInternal[0.0, 0.0, 0.0]
+    t = SiteNameLabeledCell.nearest_site(la, pos, @sites00)
+    assert_equal("site00" , t)
+
+    pos = Mageo::Vector3DInternal[0.1, 0.2, 0.3]
+    t = SiteNameLabeledCell.nearest_site(la, pos, @sites00)
+    assert_equal("site01" , t)
+  end
+
+  def test_labeled_all_atoms?
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ], "site01")
+    ]
+    assert_equal(true, SiteNameLabeledCell.labeled_all_atoms?(atoms, @sites00))
+
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ], "site00")
+    ]
+    assert_equal(true, SiteNameLabeledCell.labeled_all_atoms?(atoms, @sites00))
+
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ], "site00"),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ])
+    ]
+    assert_equal(false, SiteNameLabeledCell.labeled_all_atoms?(atoms, @sites00))
+
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ]),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ], "site00")
+    ]
+    assert_equal(false, SiteNameLabeledCell.labeled_all_atoms?(atoms, @sites00))
+
+    atoms = [
+      CrystalCell::Atom.new( 0, [ 0.00, 0.00, 0.00 ]),
+      CrystalCell::Atom.new( 0, [ 0.10, 0.20, 0.30 ])
+    ]
+    assert_equal(false, SiteNameLabeledCell.labeled_all_atoms?(atoms, @sites00))
+
+  end
+
+  def test_self_check_inside_all_sites
+    assert_nothing_raised{SiteNameLabeledCell.check_inside_all_sites(@sites00)}
+    assert_nothing_raised{SiteNameLabeledCell.check_inside_all_sites(@sites01)}
+
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.00, 0.00, 0.00 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    assert_nothing_raised{SiteNameLabeledCell.check_inside_all_sites(sites)}
+
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 1.01, 0.00, 0.00 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    assert_raise(SiteNameLabeledCell::OutOfCellError){
+      SiteNameLabeledCell.check_inside_all_sites(sites)}
+
+    sites = {
+      "site00" => Mageo::Vector3DInternal[-0.01, 0.00, 0.00 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+    assert_raise(SiteNameLabeledCell::OutOfCellError){
+      SiteNameLabeledCell.check_inside_all_sites(sites)}
+  end
+
+  #def test_site_name
+  # assert_equal("site00", @c00.site_name(Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ]))
+  # assert_equal("site00", @c00.site_name(Mageo::Vector3DInternal[ 0.00, 0.00, 0.00 ]))
+  # assert_equal("site01", @c00.site_name(Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]))
+  # assert_equal("site01", @c00.site_name(Mageo::Vector3DInternal[ 0.10, 0.20, 0.30 ]))
+
+  # assert_raise(SiteNameLabeledCell::TypeError){
+  #       @c00.site_name(Mageo::Vector3D[ 0.10, 0.20, 0.30 ]))
+  # }
+  #end
+
+end
+
+class TC_Crystalcell_Cell < Test::Unit::TestCase
+  def setup
+    # 元素の識別子を数字にしたもの。
+    atoms = [
+      CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ),
+      CrystalCell::Atom.new( 1, [0.1, 0.2, 0.3] ),
+    ]
+    @c00 = CrystalCell::Cell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ], atoms )
+    @c00.comment = "c01"
+  end
+
+  def test_to_snlcell
+    sites = {
+      "site00" => Mageo::Vector3DInternal[ 0.01, 0.01, 0.01 ],
+      "site01" => Mageo::Vector3DInternal[ 0.11, 0.21, 0.31 ]
+    }
+
+    t = @c00.to_snlcell( sites )
+    assert_equal(SiteNameLabeledCell, t.class)
+    assert_equal( 2, t.atoms.size)
+    assert_equal( "site00", t.atoms[0].name)
+    assert_equal( "site01", t.atoms[1].name)
+    assert_equal( "c01", t.comment)
+  end
+end