crystalcell 0.1.0 → 0.1.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4a6d81b3b2df5aebe2d59092c8af9a06a86de351
-  data.tar.gz: 5956faf1dcd9aba246f3738ec238dd99d10bf0f6
+  metadata.gz: f9397d63b61597552c608dbef090bd1648bb5685
+  data.tar.gz: 7b10b0f30d8552a5e6be3481e3735cad5d595ed2
 SHA512:
-  metadata.gz: 93d44dd90fcc58571b9db57aa3cf1f072ab2469743d2d190bd17bf0b046f38f1ad3b2e5fd59d05fc7e3ef9efd75b706d834031830375b4d1fbf1f3c2d70b426b
-  data.tar.gz: 7b07a0e21b1972342ef2b647f215b4ec66c02aedeafead6de6c72d076250fc44d05366da87df2ff7a2f236b0ca0ff02d183250787cc7c2c623d2372922101a28
+  metadata.gz: 9392b319f43e8b50921e1fe25b4b4a4037d6c21d24f729290620b71be337f9b5631d2e1e3552ad7dbd42f1edc5ef0e1dfbb64f94b4233103c47cf0055b09e3ce
+  data.tar.gz: b8deedf28f6e4a0420f3a7873119998ca0a6557ab9769a10e6e56e8b733ab8213d564883f050a4127ded7b133958a033c30e43f015106d4117b5df9c35e2a8a0

data/CHANGES

@@ -2,6 +2,12 @@
 
 <!-- Master -->
 
+== Version 0.1.1 [2017-05-23] released
+
+* Add CrystalCell::Povray::Cell.bond
+* Add CrystalCell::atoms_of_element
+* Add name in CrystalCell::Cell.atoms_in_supercell
+
 == Version 0.1.0 [2016-07-12] released
 
 * Add Cell.to_povcell

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/crystalcell.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: crystalcell 0.1.0 ruby lib
+# stub: crystalcell 0.1.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "crystalcell"
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["ippei94da"]
-  s.date = "2016-07-12"
+  s.date = "2017-05-23"
   s.description = "This gem provides Cell, LatticeAxes, Atom classes, and so on.\n    And this provides simple treatment of a periodic boundary condition.\n  "
   s.email = "ippei94da@gmail.com"
   s.extra_rdoc_files = [

data/lib/crystalcell/cell.rb

@@ -99,13 +99,19 @@ class CrystalCell::Cell
     @atoms.collect{ |i| i.position }
   end
 
-  #元素情報が elem の原子の index を配列にまとめて返す。
-  #index は原子の永続的な id ではない。
+  # ブロックの評価が真になった原子の index を配列にして返す。
   #Array#select は index ではなく要素そのものを配列にして返すので、少し違う。
+  #index は原子の永続的な id ではない。
   def select_indices( &block )
     return @atoms.select_indices( &block )
   end
 
+  #元素情報が elem の原子を配列にまとめて返す。(not indices)
+  def atoms_of_element(str)
+    @atoms.select{ |i| i.element == str }
+  end
+
+
   #Set element name to each atom in self.
   #Argument 'elems' is a list of new names, which has [] method. e.g.,
   #    1. Array, [ 'Li', 'O' ]
@@ -139,10 +145,22 @@ class CrystalCell::Cell
   def atoms_in_supercell( a_min, a_max, b_min, b_max, c_min, c_max )
     results = []
     @atoms.each do |atom|
+      #pp atom; exit
       a_min.upto( a_max ) do |a|
         b_min.upto( b_max ) do |b|
           c_min.upto( c_max ) do |c|
-            results << CrystalCell::Atom.new( atom.element, (atom.position.to_v3di + [ a, b, c ].to_v3di).to_a )
+            new_name = sprintf("%s-%d%d%d",
+                               atom.name,
+                               a + 5,
+                               b + 5,
+                               c + 5
+                              )
+            results << CrystalCell::Atom.new(
+              atom.element,
+              (atom.position.to_v3di + [ a, b, c ].to_v3di).to_a,
+              new_name
+            )
+
           end
         end
       end

data/lib/crystalcell/povray.rb

@@ -10,13 +10,14 @@ require 'crystalcell/povray/tetrahedron.rb'
 require 'crystalcell/povray/color.rb'
 
 
-DEFAULT_ENVIRONMENTS = [
-  'background {color rgb<1,1,1>}',
-  'light_source{ < 4, 1, 4 > color <1,1,1> parallel point_at 0 }',
-  'default{ texture{ finish{ ambient 0.4 phong 1.0 phong_size 10 } } }',
-]
-
 class CrystalCell::Povray
+
+  DEFAULT_ENVIRONMENTS = [
+    'background {color rgb<1,1,1>}',
+    'light_source{ < 4, 1, 4 > color <1,1,1> parallel point_at 0 }',
+    'default{ texture{ finish{ ambient 0.4 phong 1.0 phong_size 10 } } }',
+  ]
+
   attr_reader :camera, :environments, :cell, :axes
   
   # camera_info indicates hash with the keys of camera info,
@@ -60,7 +61,7 @@ class CrystalCell::Povray
     File.open(povfile, 'w') do |io|
       dump(io)
     end
-    system "povray -D #{povfile}"
+    system "povray -D #{povfile} > /dev/null"
   end
 
   # shoot 4 angles and unite.

data/lib/crystalcell/povray/cell.rb

@@ -6,7 +6,11 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
   LATTICE_RADIUS = 0.02
   LATTICE_COLOR  = [0.50, 0.50, 0.50]
   BOND_RADIUS    = 0.05
-  BOND_COLOR     = [0.75, 0.75, 0.75]
+  #BOND_COLOR     = [0.75, 0.75, 0.75]
+
+
+  class SizeError < StandardError; end
+  class AtomNotFoundError < StandardError; end
 
   # povray 形式の文字列を返す。
   def to_pov
@@ -22,43 +26,89 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
 
   # 原子を描画するための pov 形式文字列を返す。
   # 周期境界近傍の原子が tolerance 未満ならば、反対側のセル境界にも描画する。
-  def atoms_to_povs(tolerance = 0.0)
+  def atoms_to_povs(tolerance: 0.0, transmit: nil)
     results = []
     atoms.each do |atom|
       periodic_translations(atom.position, tolerance).each do |translation|
-        results << atom_to_pov(atom.translate(translation))
+        results << atom_to_pov(atom: atom.translate(translation), transmit: transmit)
+        #results << atom_to_pov(atom.translate(translation))
       end
     end
     results
   end
 
-  ## 原子間の連結棒を描画するための pov 形式文字列を返す。
-  ## E.g.,
-  ##   elem0 = 'O'
-  ##   elem1 = 'Li'
-  ##   min_distance = 0.0
-  ##   max_distance = 1.0
-  ## 上記の指定の場合、O-O 間かつ距離が 0.0〜1.0 の原子間のみ
-  ## bond を出力する。
-  #def bonds_to_povs(elem0, elem1, min_distance, max_distance)
-  #  results = []
-  #  cell = self.to_pcell
-  #  cell.find_bonds(elem0, elem1, min_distance, max_distance).each do |pair|
-  #    cart0 = pair[0].to_v3d(self.axes)
-  #    cart1 = pair[1].to_v3d(self.axes)
-  #    midpoint = Mageo::Vector3D.midpoint(cart0, cart1)
-  #    results << Mageo::Cylinder.new(
-  #      [cart0, midpoint], BOND_RADIUS).to_pov(
-  #        CrystalCell::Povray::Element.color(elem0)) + "\n"
-  #    results << Mageo::Cylinder.new(
-  #      [cart1, midpoint], BOND_RADIUS).to_pov(
-  #        CrystalCell::Povray::Element.color(elem1)) + "\n"
-  #  end
-  #  results
-  #end
+  # Return povray format string to draw bond between two atoms.
+  # contents should be like ['Na1', 'Cl2'] # (element + number)
+  def bond(atomids)
+    #pp atomids
+    if atomids.size != 2
+      raise SizeError
+    end
+    atoms = []
+    atomids.each do |atomid|
+      atom = atom_by_id(atomid)
+      raise AtomNotFoundError, atomid unless atom
+      atoms << atom
+    end
+    intermediate =
+      (( atoms[0].position +  atoms[1].position )/ 2.0) .to_v3d(self.axes)
+    results = []
+    atoms.each do |atom|
+      cyl = CrystalCell::Povray::Cylinder.new(
+        atom.position.to_v3d(self.axes),
+        intermediate,
+        BOND_RADIUS,
+        CrystalCell::Povray::Element.color( atom.element)
+      )
+      results << cyl.to_pov
+    end
+    results.join("\n")
+  end
+
+  # Return povray format string to draw triangle among three atoms.
+  # contents should be like ['Na1', 'Cl2', 'Cl3'] # (element + number from 1)
+  # Color is set as 0th item in atomids
+  def triangle(atomids)
+    if atomids.size != 3
+      raise SizeError
+    end
+    atoms = []
+    atomids.each do |atomid|
+      atom = atom_by_id(atomid)
+      raise AtomNotFoundError, atomid unless atom
+      atoms << atom
+    end
+    #pp atoms
+    tri  = CrystalCell::Povray::Triangle.new(
+      *atoms.map { |atom| atom.position.to_v3d(self.axes)},
+      CrystalCell::Povray::Element.color( atoms[0].element)
+    )
+    tri.to_pov
+  end
+
+  # Return povray format string to draw tetrahedron among four atoms.
+  # contents should be like ['Na1', 'Cl2', 'Cl3', 'Cl4'] # (element + number from 1)
+  # Color is set as 0th item in atomids
+  def tetrahedron(atomids)
+    if atomids.size != 4
+      raise SizeError
+    end
+    atoms = []
+    atomids.each do |atomid|
+      atom = atom_by_id(atomid)
+      raise AtomNotFoundError, atomid unless atom
+      atoms << atom
+    end
+    #pp atoms
+    tetra  = CrystalCell::Povray::Tetrahedron.new(
+      *atoms.map { |atom| atom.position.to_v3d(self.axes)},
+      CrystalCell::Povray::Element.color( atoms[0].element)
+    )
+    tetra.to_pov
+  end
 
   # 格子の棒を描画するための pov 形式文字列を返す。
-  def lattice_to_povs
+  def lattice_to_povs # should be changed to 'lattice'
     v000 = Vector3DInternal[ 0.0, 0.0, 0.0 ].to_v3d(self.axes)
     v001 = Vector3DInternal[ 0.0, 0.0, 1.0 ].to_v3d(self.axes)
     v010 = Vector3DInternal[ 0.0, 1.0, 0.0 ].to_v3d(self.axes)
@@ -87,12 +137,25 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
     results
   end
 
+  # Return atom from 'atom_id' like 'Na1' or 'Na1-556'.
+  def atom_by_id(atom_id)
+    elem_num, perio = atom_id.split('-')
+    /^(\D+)(\d+)/ =~ elem_num
+    elem = $1
+    num = $2
+    perio ||= '555'
+    atom = atoms_of_element(elem)[num.to_i - 1]
+    vec = perio.split(//).map { |figure| figure.to_i - 5 }
+    atom.translate(vec.to_v3di)
+  end
+
   private
 
-  def atom_to_pov(atom)
+  def atom_to_pov(atom:, transmit: nil)
+  #def atom_to_pov(atom)
     color  = CrystalCell::Povray::Element.color( atom.element)
     radius = CrystalCell::Povray::Element.draw_radius(atom.element) * RADIUS_RATIO
-    Mageo::Sphere.new(atom.position.to_v3d(axes), radius).to_pov(color) +
+    Mageo::Sphere.new(atom.position.to_v3d(axes), radius).to_pov(color: color, transmit: transmit) +
     " // #{atom.element}" + "\n"
   end
 

data/lib/crystalcell/povray/sphere.rb

@@ -3,9 +3,16 @@
 class Mageo::Sphere
   # povray 形式の文字列を返す。
   # color は Float による配列。通常、0〜1の範囲。
-  def to_pov(color)
-    sprintf( "object { sphere{<% 7.4f, % 7.4f, % 7.4f>, %7.4f} pigment {color rgb <%4.2f, %4.2f, %4.2f>} }",
-      *position, radius, *color)
+  def to_pov(color: , transmit: nil)
+    result = sprintf("object { sphere{<% 7.4f, % 7.4f, % 7.4f>, %7.4f} ", *position, radius)
+    #sprintf( "object { sphere{<% 7.4f, % 7.4f, % 7.4f>, %7.4f} pigment {color rgb <%4.2f, %4.2f, %4.2f>} }",
+    #  *position, radius, *color)
+
+    if transmit
+      result += sprintf("pigment {color rgbt <%4.2f, %4.2f, %4.2f, %4.2f>} }", *color, transmit)
+    else
+      result += sprintf("pigment {color rgb <%4.2f, %4.2f, %4.2f>} }", *color)
+    end
   end
 
   def dump(io)

data/lib/crystalcell/povray/triangle.rb

@@ -13,16 +13,13 @@ class CrystalCell::Povray::Triangle < Mageo::Triangle
   # povray 形式の文字列を返す。
   # color は Float による配列。通常、0〜1の範囲。
   def to_pov
-    v = self.vertices
-    result = sprintf("triangle{<%f,%f,%f>,<%f,%f,%f>,<%f,%f,%f>",
+    #v = self.vertices
+    #sprintf( "object { cylinder{ <% 7.4f, % 7.4f, % 7.4f>, <% 7.4f, % 7.4f, % 7.4f>, %7.4f } pigment { color rgb <%4.2f, %4.2f, %4.2f> } }",
+    result = sprintf("triangle{ < % 7.4f, % 7.4f, % 7.4f>,<% 7.4f,% 7.4f,% 7.4f>,<% 7.4f,% 7.4f,% 7.4f>",
       *@vertices[0], *@vertices[1], *@vertices[2])
-    result +=  sprintf(" pigment {color rgb<%f,%f,%f>", *@color)
-    result +=  sprintf(" transmit %f", @transmit) if @transmit
+    result +=  sprintf(" pigment {color rgb<% 7.4f,% 7.4f,% 7.4f>", *@color)
+    result +=  sprintf(" transmit % 7.4f", @transmit) if @transmit
     result +=  "}}"
-    #result = sprintf("triangle{<%f,%f,%f>,<%f,%f,%f>,<%f,%f,%f> " +
-    #  "pigment {color rgb<%f,%f,%f>}}",
-    #  *@vertices[0], *@vertices[1], *@vertices[2], *@color)
-    #
     return result
   end
 

data/test/povray/test_cell.rb

@@ -2,6 +2,7 @@
 # coding: utf-8
 
 require "helper"
+require "pp"
 
 class TC_Povray_Sphere < Test::Unit::TestCase
   def setup
@@ -11,7 +12,11 @@ class TC_Povray_Sphere < Test::Unit::TestCase
   def test_to_pov
     assert_equal( 
       "object { sphere{< 1.0000,  2.0000,  3.0000>,  2.0000} pigment {color rgb <0.30, 0.60, 0.90>} }",
-      @s00.to_pov([0.3, 0.6, 0.9]) )
+      @s00.to_pov(color: [0.3, 0.6, 0.9]) )
+
+    assert_equal( 
+      "object { sphere{< 1.0000,  2.0000,  3.0000>,  2.0000} pigment {color rgbt <0.30, 0.60, 0.90, 0.50>} }",
+      @s00.to_pov(color: [0.3, 0.6, 0.9], transmit: 0.5) )
   end
 end
 
@@ -83,37 +88,95 @@ class TC_Povray_Cell < Test::Unit::TestCase
       "object { sphere{< 2.0000,  2.0000,  2.0000>,  0.1770} pigment {color rgb <0.53, 0.88, 0.45>} } // Li\n",
       "object { sphere{< 0.4000,  0.6000,  0.8000>,  0.4200} pigment {color rgb <1.00, 0.01, 0.00>} } // O\n",
     ]
-    t = @c00.atoms_to_povs(0.01)
+    t = @c00.atoms_to_povs(tolerance: 0.01)
     corrects.each_with_index do |correct, index|
       assert_equal(correct, t[index], "line #{index.to_s}")
     end
     assert_equal(corrects.size, t.size)
+
+    # with transmit
+    results = @c00.atoms_to_povs(transmit: 0.5)
+    corrects = [ "object { sphere{< 0.0000,  0.0000,  0.0000>,  0.1770} pigment {color rgbt <0.53, 0.88, 0.45, 0.50>} } // Li\n",
+        "object { sphere{< 0.4000,  0.6000,  0.8000>,  0.4200} pigment {color rgbt <1.00, 0.01, 0.00, 0.50>} } // O\n"
+      ]
+    assert_equal(corrects, results)
+
   end
 
-  def test_bonds_to_povs
-    ## PeriodicCell.find_bonds に依存しており、
-    ## これがなんか不安な動作。 -0.0000 になるとか、誤差だろうなあ。
-    ## このためテストは頑張って作らない。
-    ## PeriodicCell.find_bonds をリファクタリングとかしてから
-    ## テストをするかもしれん。
-    
-    #assert_equal( [
-    #	"object { cylinder{ < 0.0000,  0.0000,  0.0000>, < 0.4000,  0.6000,  0.8000>,  0.0500 } pigment { color rgb <0.75, 0.75, 0.75> } }"
-    #	],
-    #	@c00.bonds_to_povs(["Li", "O"], 0.0, 1.1)
-    #)
-
-    #assert_equal( [
-    #	"object { cylinder{ < 0.0000,  0.0000,  0.0000>, < 0.4000,  0.6000,  0.8000>,  0.0500 } pigment { color rgb <0.75, 0.75, 0.75> } }"
-    #	],
-    #	@c00.bonds_to_povs(["O", "Li"], 0, 1.1 )
-    #)
-
-    #assert_equal([
-    #	"object { cylinder{ < 0.0000,  0.0000,  0.0000>, < 0.0000,  0.0000,  0.0000>,  0.0500 } pigment { color rgb <0.75, 0.75, 0.75> } }"
-    #	],
-    #	@c00.bonds_to_povs(["Li", "Li"], 0, 2.0 )
-    #)
+  def test_bond
+    axes = [
+      [2.0, 0.0, 0.0],
+      [0.0, 2.0, 0.0],
+      [0.0, 0.0, 2.0],
+    ]
+    atoms = [
+      CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0]),
+      CrystalCell::Atom.new("O", [0.2, 0.3, 0.4]),
+      CrystalCell::Atom.new("O", [0.3, 0.3, 0.4]),
+    ]
+    c00 = CrystalCell::Povray::Cell.new(axes, atoms)
+    result =  c00.bond(['Li1', 'O2'])
+    correct = [
+      "object { cylinder{ < 0.0000,  0.0000,  0.0000>, < 0.3000,  0.3000,  0.4000>,  0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
+      "object { cylinder{ < 0.6000,  0.6000,  0.8000>, < 0.3000,  0.3000,  0.4000>,  0.0500 } pigment { color rgb <1.00, 0.01, 0.00> } }",
+    ].join("\n")
+    assert_equal( correct, result)
+
+    result =  c00.bond(['Li1-555', 'O2-555'])
+    correct = [
+      "object { cylinder{ < 0.0000,  0.0000,  0.0000>, < 0.3000,  0.3000,  0.4000>,  0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
+      "object { cylinder{ < 0.6000,  0.6000,  0.8000>, < 0.3000,  0.3000,  0.4000>,  0.0500 } pigment { color rgb <1.00, 0.01, 0.00> } }",
+    ].join("\n")
+    assert_equal( correct, result)
+
+    result =  c00.bond(['Li1-555', 'Li1-556'])
+    correct = [
+      "object { cylinder{ < 0.0000,  0.0000,  0.0000>, < 0.0000,  0.0000,  1.0000>,  0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
+      "object { cylinder{ < 0.0000,  0.0000,  2.0000>, < 0.0000,  0.0000,  1.0000>,  0.0500 } pigment { color rgb <0.53, 0.88, 0.45> } }",
+    ].join("\n")
+    assert_equal( correct, result)
+  end
+
+  def test_triangle
+    axes = [
+      [2.0, 0.0, 0.0],
+      [0.0, 2.0, 0.0],
+      [0.0, 0.0, 2.0],
+    ]
+    atoms = [
+      CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0]),
+      CrystalCell::Atom.new("O", [0.2, 0.3, 0.4]),
+      CrystalCell::Atom.new("O", [0.3, 0.3, 0.4]),
+    ]
+    c00 = CrystalCell::Povray::Cell.new(axes, atoms)
+    result =  c00.triangle(['Li1', 'O1', 'O2'])
+    correct = [
+      "triangle{ <  0.0000,  0.0000,  0.0000>,< 0.4000, 0.6000, 0.8000>,< 0.6000, 0.6000, 0.8000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
+    ].join('')
+    assert_equal( correct, result)
+  end
+
+  def test_tetrahedron
+    axes = [
+      [2.0, 0.0, 0.0],
+      [0.0, 2.0, 0.0],
+      [0.0, 0.0, 2.0],
+    ]
+    atoms = [
+      CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0]),
+      CrystalCell::Atom.new("Li", [0.5, 0.5, 0.5]),
+      CrystalCell::Atom.new("O", [0.2, 0.3, 0.4]),
+      CrystalCell::Atom.new("O", [0.3, 0.3, 0.4]),
+    ]
+    c00 = CrystalCell::Povray::Cell.new(axes, atoms)
+    result =  c00.tetrahedron(['Li1', 'Li2', 'O1', 'O2'])
+    correct = [
+      "triangle{ <  0.0000,  0.0000,  0.0000>,< 1.0000, 1.0000, 1.0000>,< 0.4000, 0.6000, 0.8000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
+      "triangle{ <  1.0000,  1.0000,  1.0000>,< 0.4000, 0.6000, 0.8000>,< 0.6000, 0.6000, 0.8000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
+      "triangle{ <  0.4000,  0.6000,  0.8000>,< 0.6000, 0.6000, 0.8000>,< 0.0000, 0.0000, 0.0000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}",
+      "triangle{ <  0.6000,  0.6000,  0.8000>,< 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 1.0000> pigment {color rgb< 0.5255, 0.8784, 0.4549>}}"
+    ].join("\n")
+    assert_equal( correct, result)
   end
 
   def test_lattice_to_povs
@@ -141,7 +204,12 @@ class TC_Povray_Cell < Test::Unit::TestCase
   def test_atom_to_pov
     assert_equal(
       "object { sphere{< 0.2000,  0.4000,  0.6000>,  0.1770} pigment {color rgb <0.53, 0.88, 0.45>} } // Li\n",
-      @c00.atom_to_pov( CrystalCell::Atom.new("Li", [0.1, 0.2, 0.3]))
+      @c00.atom_to_pov(atom: CrystalCell::Atom.new("Li", [0.1, 0.2, 0.3]))
+    )
+
+    assert_equal(
+      "object { sphere{< 0.2000,  0.4000,  0.6000>,  0.1770} pigment {color rgbt <0.53, 0.88, 0.45, 0.50>} } // Li\n",
+      @c00.atom_to_pov(atom: CrystalCell::Atom.new("Li", [0.1, 0.2, 0.3]), transmit: 0.5)
     )
   end
 
@@ -175,5 +243,28 @@ class TC_Povray_Cell < Test::Unit::TestCase
     assert_equal(corrects, t)
   end
 
+  def test_atom_by_id
+    result = @c00.atom_by_id('Li1-555')
+    correct = CrystalCell::Atom.new("Li", [0.0, 0.0, 0.0])
+    assert_equal(correct, result)
+
+    result = @c00.atom_by_id('Li1-556')
+    correct = CrystalCell::Atom.new("Li", [0.0, 0.0, 1.0])
+    assert_equal(correct, result)
+
+    result = @c00.atom_by_id('Li1-565')
+    correct = CrystalCell::Atom.new("Li", [0.0, 1.0, 0.0])
+    assert_equal(correct, result)
+
+    result = @c00.atom_by_id('Li1-655')
+    correct = CrystalCell::Atom.new("Li", [1.0, 0.0, 0.0])
+    assert_equal(correct, result)
+
+    result = @c00.atom_by_id('Li1-455')
+    correct = CrystalCell::Atom.new("Li", [-1.0, 0.0, 0.0])
+    assert_equal(correct, result)
+
+  end
+
 end
 

data/test/povray/test_tetrahedron.rb

@@ -19,10 +19,10 @@ class TC_Tetrahedron < Test::Unit::TestCase
   def test_to_pov
     #VERTEX_INDICES_OF_TRIANGLES = [ [ 0, 1, 2 ], [ 1, 2, 3 ], [ 2, 3, 0 ], [ 3, 0, 1 ] ]
     correct = [
-      "triangle{<0.000000,0.000000,0.000000>,<1.000000,1.000000,0.000000>,<0.000000,1.000000,1.000000> pigment {color rgb<0.250000,0.500000,0.750000>}}",
-      "triangle{<1.000000,1.000000,0.000000>,<0.000000,1.000000,1.000000>,<1.000000,0.000000,1.000000> pigment {color rgb<0.250000,0.500000,0.750000>}}",
-      "triangle{<0.000000,1.000000,1.000000>,<1.000000,0.000000,1.000000>,<0.000000,0.000000,0.000000> pigment {color rgb<0.250000,0.500000,0.750000>}}",
-      "triangle{<1.000000,0.000000,1.000000>,<0.000000,0.000000,0.000000>,<1.000000,1.000000,0.000000> pigment {color rgb<0.250000,0.500000,0.750000>}}",
+      "triangle{ <  0.0000,  0.0000,  0.0000>,< 1.0000, 1.0000, 0.0000>,< 0.0000, 1.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
+      "triangle{ <  1.0000,  1.0000,  0.0000>,< 0.0000, 1.0000, 1.0000>,< 1.0000, 0.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
+      "triangle{ <  0.0000,  1.0000,  1.0000>,< 1.0000, 0.0000, 1.0000>,< 0.0000, 0.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
+      "triangle{ <  1.0000,  0.0000,  1.0000>,< 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
     ].join("\n")
     assert_equal(
       correct,
@@ -31,10 +31,10 @@ class TC_Tetrahedron < Test::Unit::TestCase
 
     @t00.transmit = 0.5
     correct = [
-      "triangle{<0.000000,0.000000,0.000000>,<1.000000,1.000000,0.000000>,<0.000000,1.000000,1.000000> pigment {color rgb<0.250000,0.500000,0.750000> transmit 0.500000}}",
-      "triangle{<1.000000,1.000000,0.000000>,<0.000000,1.000000,1.000000>,<1.000000,0.000000,1.000000> pigment {color rgb<0.250000,0.500000,0.750000> transmit 0.500000}}",
-      "triangle{<0.000000,1.000000,1.000000>,<1.000000,0.000000,1.000000>,<0.000000,0.000000,0.000000> pigment {color rgb<0.250000,0.500000,0.750000> transmit 0.500000}}",
-      "triangle{<1.000000,0.000000,1.000000>,<0.000000,0.000000,0.000000>,<1.000000,1.000000,0.000000> pigment {color rgb<0.250000,0.500000,0.750000> transmit 0.500000}}",
+      "triangle{ <  0.0000,  0.0000,  0.0000>,< 1.0000, 1.0000, 0.0000>,< 0.0000, 1.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit  0.5000}}",
+      "triangle{ <  1.0000,  1.0000,  0.0000>,< 0.0000, 1.0000, 1.0000>,< 1.0000, 0.0000, 1.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit  0.5000}}",
+      "triangle{ <  0.0000,  1.0000,  1.0000>,< 1.0000, 0.0000, 1.0000>,< 0.0000, 0.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit  0.5000}}",
+      "triangle{ <  1.0000,  0.0000,  1.0000>,< 0.0000, 0.0000, 0.0000>,< 1.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit  0.5000}}",
     ].join("\n")
     assert_equal(
       correct,

data/test/povray/test_triangle.rb

@@ -25,13 +25,13 @@ class TC_Triangle < Test::Unit::TestCase
 
   def test_to_pov
     assert_equal(
-      "triangle{<0.000000,0.000000,0.000000>,<1.000000,0.000000,0.000000>,<0.000000,1.000000,0.000000> pigment {color rgb<0.250000,0.500000,0.750000>}}",
+      "triangle{ <  0.0000,  0.0000,  0.0000>,< 1.0000, 0.0000, 0.0000>,< 0.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500>}}",
       @t00.to_pov
     )
 
     @t00.transmit = 0.5
     assert_equal(
-      "triangle{<0.000000,0.000000,0.000000>,<1.000000,0.000000,0.000000>,<0.000000,1.000000,0.000000> pigment {color rgb<0.250000,0.500000,0.750000> transmit 0.500000}}",
+      "triangle{ <  0.0000,  0.0000,  0.0000>,< 1.0000, 0.0000, 0.0000>,< 0.0000, 1.0000, 0.0000> pigment {color rgb< 0.2500, 0.5000, 0.7500> transmit  0.5000}}",
       @t00.to_pov
     )
   end

data/test/test_cell.rb

@@ -3,6 +3,7 @@
 
 require "helper"
 require 'stringio'
+require 'pp'
 
 #class CrystalCell::Cell
 #  public :symmetry_operations
@@ -33,8 +34,8 @@ class TC_Cell < Test::Unit::TestCase
     # Li と O を1つずつ入れたセル。
     # @c02 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] )
     atoms = [
-      CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ),
-      CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ),
+      CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0], 'Li1' ),
+      CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2], 'O1' ),
     ]
     @c02 = CrystalCell::Cell.new(vectors00, atoms)
     @c02.comment = 'c02'
@@ -214,8 +215,6 @@ class TC_Cell < Test::Unit::TestCase
     assert_in_delta( 0.0, c10.axes[2][0], $tolerance )
     assert_in_delta( 0.0, c10.axes[2][1], $tolerance )
     assert_in_delta( 2.0, c10.axes[2][2], $tolerance )
-
-
   end
 
   def test_positions
@@ -244,6 +243,25 @@ class TC_Cell < Test::Unit::TestCase
     assert_equal( [1, 2], @c04.select_indices{ |i| i.position[0] > 0.05 } )
   end
 
+  def test_atoms_of_element
+    vectors00 = [[2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]
+    atom0 = CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] )
+    atom1 = CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] )
+    atom2 = CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] )
+    atoms = [ atom0, atom1, atom2] 
+    c04 = CrystalCell::Cell.new(vectors00, atoms)
+    c04.comment = 'c04'
+
+    assert_equal([atom0, atom1], c04.atoms_of_element('Li'))
+    assert_equal([atom2]       , c04.atoms_of_element('O'))
+    assert_equal([]            , c04.atoms_of_element('S'))
+  end
+
+  #def test_supercell
+  #  @c02.supercell(
+
+  #end
+
   def test_atoms_in_supercell
     t = @c02.atoms_in_supercell( 0, 0, 0, 0, 0, 1 )
     assert_equal( 'Li', t[0].element )
@@ -257,61 +275,63 @@ class TC_Cell < Test::Unit::TestCase
     assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 1.2], t[3].position )
 
     t = @c02.atoms_in_supercell(-1, 1,-1, 1,-1, 1 )
-    assert_equal( ['Li']*27 + ['O'] * 27 , t.map{|i| i.element} )
-    assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, -1.0], t[ 0].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0, -1.0,    0.0], t[ 1].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0, -1.0,    1.0], t[ 2].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0,  0.0, -1.0], t[ 3].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0,  0.0,    0.0], t[ 4].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0,  0.0,    1.0], t[ 5].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0,  1.0, -1.0], t[ 6].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0,  1.0,    0.0], t[ 7].position )
-    assert_equal( Mageo::Vector3DInternal[-1.0,  1.0,    1.0], t[ 8].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, -1.0], t[ 9].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0,    0.0], t[10].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0,    1.0], t[11].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0,  0.0, -1.0], t[12].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0,  0.0,    0.0], t[13].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0,  0.0,    1.0], t[14].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0,  1.0, -1.0], t[15].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0,  1.0,    0.0], t[16].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.0,  1.0,    1.0], t[17].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, -1.0], t[18].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0,    0.0], t[19].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0,    1.0], t[20].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0,  0.0, -1.0], t[21].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0,  0.0,    0.0], t[22].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0,  0.0,    1.0], t[23].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0,  1.0, -1.0], t[24].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0,  1.0,    0.0], t[25].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.0,  1.0,    1.0], t[26].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, -0.8], t[27].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8, -0.8,    0.2], t[28].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8, -0.8,    1.2], t[29].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8,  0.2, -0.8], t[30].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8,  0.2,    0.2], t[31].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8,  0.2,    1.2], t[32].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8,  1.2, -0.8], t[33].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8,  1.2,    0.2], t[34].position )
-    assert_equal( Mageo::Vector3DInternal[-0.8,  1.2,    1.2], t[35].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, -0.8], t[36].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8,    0.2], t[37].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8,    1.2], t[38].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2,  0.2, -0.8], t[39].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2,  0.2,    0.2], t[40].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2,  0.2,    1.2], t[41].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2,  1.2, -0.8], t[42].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2,  1.2,    0.2], t[43].position )
-    assert_equal( Mageo::Vector3DInternal[ 0.2,  1.2,    1.2], t[44].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, -0.8], t[45].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8,    0.2], t[46].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8,    1.2], t[47].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2,  0.2, -0.8], t[48].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2,  0.2,    0.2], t[49].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2,  0.2,    1.2], t[50].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2,  1.2, -0.8], t[51].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2,  1.2,    0.2], t[52].position )
-    assert_equal( Mageo::Vector3DInternal[ 1.2,  1.2,    1.2], t[53].position )
+    assert_equal(['Li']*27 + ['O'] * 27 , t.map{|i| i.element} )
+    assert_equal(Mageo::Vector3DInternal[-1.0,-1.0,-1.0],t[ 0].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0,-1.0, 0.0],t[ 1].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0,-1.0, 1.0],t[ 2].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0, 0.0,-1.0],t[ 3].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0, 0.0, 0.0],t[ 4].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0, 0.0, 1.0],t[ 5].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0, 1.0,-1.0],t[ 6].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0, 1.0, 0.0],t[ 7].position)
+    assert_equal(Mageo::Vector3DInternal[-1.0, 1.0, 1.0],t[ 8].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0,-1.0,-1.0],t[ 9].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0,-1.0, 0.0],t[10].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0,-1.0, 1.0],t[11].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0, 0.0,-1.0],t[12].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0, 0.0, 0.0],t[13].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0, 0.0, 1.0],t[14].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0, 1.0,-1.0],t[15].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0, 1.0, 0.0],t[16].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.0, 1.0, 1.0],t[17].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0,-1.0,-1.0],t[18].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0,-1.0, 0.0],t[19].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0,-1.0, 1.0],t[20].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0, 0.0,-1.0],t[21].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0, 0.0, 0.0],t[22].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0, 0.0, 1.0],t[23].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0, 1.0,-1.0],t[24].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0, 1.0, 0.0],t[25].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.0, 1.0, 1.0],t[26].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8,-0.8,-0.8],t[27].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8,-0.8, 0.2],t[28].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8,-0.8, 1.2],t[29].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8, 0.2,-0.8],t[30].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8, 0.2, 0.2],t[31].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8, 0.2, 1.2],t[32].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8, 1.2,-0.8],t[33].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8, 1.2, 0.2],t[34].position)
+    assert_equal(Mageo::Vector3DInternal[-0.8, 1.2, 1.2],t[35].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2,-0.8,-0.8],t[36].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2,-0.8, 0.2],t[37].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2,-0.8, 1.2],t[38].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2, 0.2,-0.8],t[39].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2, 0.2, 0.2],t[40].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2, 0.2, 1.2],t[41].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2, 1.2,-0.8],t[42].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2, 1.2, 0.2],t[43].position)
+    assert_equal(Mageo::Vector3DInternal[ 0.2, 1.2, 1.2],t[44].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2,-0.8,-0.8],t[45].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2,-0.8, 0.2],t[46].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2,-0.8, 1.2],t[47].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2, 0.2,-0.8],t[48].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2, 0.2, 0.2],t[49].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2, 0.2, 1.2],t[50].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2, 1.2,-0.8],t[51].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2, 1.2, 0.2],t[52].position)
+    assert_equal(Mageo::Vector3DInternal[ 1.2, 1.2, 1.2],t[53].position)
+
+    assert_equal('Li1-444',t[ 0].name)
   end
 
   def test_elements
@@ -968,11 +988,11 @@ class TC_Cell < Test::Unit::TestCase
     # checking atom 0
     assert_equal( 'Li'                   , t.atoms[0].element)
     assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
-    assert_equal( nil                        , t.atoms[0].name )
+    assert_equal( 'Li1'                       , t.atoms[0].name )
     # checking atom 1
     assert_equal( 'O'                        , t.atoms[1].element)
     assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
-    assert_equal( nil                        , t.atoms[1].name )
+    assert_equal( 'O1'                       , t.atoms[1].name )
   end
 
   def test_inverse_axis
@@ -995,11 +1015,11 @@ class TC_Cell < Test::Unit::TestCase
     # checking atom 0
     assert_equal( 'Li'                   , t.atoms[0].element)
     assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
-    assert_equal( nil                        , t.atoms[0].name )
+    assert_equal( 'Li1'                      , t.atoms[0].name )
     # checking atom 1
     assert_equal( 'O'                        , t.atoms[1].element)
     assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
-    assert_equal( nil                        , t.atoms[1].name )
+    assert_equal( 'O1'                       , t.atoms[1].name )
     # checking non-destructive
     assert_equal( CrystalCell::Cell, t.class )
     assert_in_delta( 2.0, @c02.axes[0][0], $tolerance )
@@ -1015,11 +1035,11 @@ class TC_Cell < Test::Unit::TestCase
     # checking atom 0
     assert_equal( 'Li'                   , @c02.atoms[0].element)
     assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position)
-    assert_equal( nil                        , @c02.atoms[0].name )
+    assert_equal( 'Li1'                      , @c02.atoms[0].name )
     # checking atom 1
     assert_equal( 'O'                        , @c02.atoms[1].element)
     assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], @c02.atoms[1].position)
-    assert_equal( nil                        , @c02.atoms[1].name )
+    assert_equal( 'O1'                       , @c02.atoms[1].name )
 
     # y 軸反転
     # [ [ ax, ay, az], [    0, by, bz], [    0,  0, cz] ]
@@ -1043,11 +1063,11 @@ class TC_Cell < Test::Unit::TestCase
     # checking atom 0
     assert_equal( 'Li'                   , t.atoms[0].element)
     assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
-    assert_equal( nil                        , t.atoms[0].name )
+    assert_equal( 'Li1'                      , t.atoms[0].name )
     # checking atom 1
     assert_equal( 'O'                        , t.atoms[1].element)
     assert_equal( Mageo::Vector3DInternal[ 0.2,-0.2, 0.2], t.atoms[1].position)
-    assert_equal( nil                        , t.atoms[1].name )
+    assert_equal( 'O1'                       , t.atoms[1].name )
 
     # z 軸反転
     # [ [ ax, ay, az], [    0, by, bz], [    0,  0, cz] ]
@@ -1072,11 +1092,11 @@ class TC_Cell < Test::Unit::TestCase
     # checking atom 0
     assert_equal( 'Li'                   , t.atoms[0].element)
     assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
-    assert_equal( nil                        , t.atoms[0].name )
+    assert_equal( 'Li1'                      , t.atoms[0].name )
     # checking atom 1
     assert_equal( 'O'                        , t.atoms[1].element)
     assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2,-0.2], t.atoms[1].position)
-    assert_equal( nil                        , t.atoms[1].name )
+    assert_equal( 'O1'                       , t.atoms[1].name )
 
   end
 
@@ -1102,7 +1122,7 @@ class TC_Cell < Test::Unit::TestCase
     # checking atom 1
     assert_equal( 'O'                        , t.atoms[1].element)
     assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position)
-    assert_equal( nil                        , t.atoms[1].name )
+    assert_equal( nil                       , t.atoms[1].name )
   end
 
   def test_exchange_axes
@@ -1285,7 +1305,6 @@ class TC_Cell < Test::Unit::TestCase
   end
 
   def test_symmetry_operations
-    f13 = 1.0/3.0
 
     #cubic/POSCAR #Pm-3m (221) / m-3m / -P 4 2 3 (517)
     corrects = [
@@ -1416,6 +1435,7 @@ class TC_Cell < Test::Unit::TestCase
     #]
     #assert_equal(corrects, @c15 .symmetry_operations) #triclinic
 
+    #f13 = 1.0/3.0
     ##trigonal/POSCAR #P-3m1 (164) / -3m  / -P 3 2= (456)
     #corrects = [
     #  {:rotation => [[ 1.0,  0.0,  0], [ 0.0,  1.0,  0], [ 0.0, 0.0,  1.0]], :translation => [0.0, 0.0, 0.0]}, #----01----

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: crystalcell
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
 platform: ruby
 authors:
 - ippei94da
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-07-12 00:00:00.000000000 Z
+date: 2017-05-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: test-unit