crystalcell 0.0.3 → 0.0.4

data/lib/crystalcell/element.rb

@@ -1,148 +1,57 @@
-#
-# 元素(原子種)に関する情報を集めたクラス
-# 基本理念として、原子番号を最もネイティブなデータとして ID 付けをする。
-# 原子番号は人間がいなかったとしてもそれで区分できるが、
-# 原子記号は人間がつけたものだから。
+# Class for elements and their information.
 #
 class CrystalCell::Element
-    # 全データを生成しておく。
-    def initialize
-        #原子記号, 原子番号, 周期, 族, 質量数(平均), イオン半径
-        @symbol = Array.new #; @mass = Array.new @radius = Array.new
-        #i =     1; @symbol[i], @mass[i], @radius[i] = 'H', 1.008, nil
-        i =     0; @symbol[i] = nil
-        i =     1; @symbol[i] = 'H'
-        i =     2; @symbol[i] = 'He'
-        i =     3; @symbol[i] = 'Li'
-        i =     4; @symbol[i] = 'Be'
-        i =     5; @symbol[i] = 'B'
-        i =     6; @symbol[i] = 'C'
-        i =     7; @symbol[i] = 'N'
-        i =     8; @symbol[i] = 'O'
-        i =     9; @symbol[i] = 'F'
-        i =  10; @symbol[i] = 'Ne'
-        i =  11; @symbol[i] = 'Na'
-        i =  12; @symbol[i] = 'Mg'
-        i =  13; @symbol[i] = 'Al'
-        i =  14; @symbol[i] = 'Si'
-        i =  15; @symbol[i] = 'P'
-        i =  16; @symbol[i] = 'S'
-        i =  17; @symbol[i] = 'Cl'
-        i =  18; @symbol[i] = 'Ar'
-        i =  19; @symbol[i] = 'K'
-        i =  20; @symbol[i] = 'Ca'
-        i =  21; @symbol[i] = 'Sc'
-        i =  22; @symbol[i] = 'Ti'
-        i =  23; @symbol[i] = 'V'
-        i =  24; @symbol[i] = 'Cr'
-        i =  25; @symbol[i] = 'Mn'
-        i =  26; @symbol[i] = 'Fe'
-        i =  27; @symbol[i] = 'Co'
-        i =  28; @symbol[i] = 'Ni'
-        i =  29; @symbol[i] = 'Cu'
-        i =  30; @symbol[i] = 'Zn'
-        i =  31; @symbol[i] = 'Ga'
-        i =  32; @symbol[i] = 'Ge'
-        i =  33; @symbol[i] = 'As'
-        i =  34; @symbol[i] = 'Se'
-        i =  35; @symbol[i] = 'Br'
-        i =  36; @symbol[i] = 'Kr'
-        i =  37; @symbol[i] = 'Rb'
-        i =  38; @symbol[i] = 'Sr'
-        i =  39; @symbol[i] = 'Y'
-        i =  40; @symbol[i] = 'Zr'
-        i =  41; @symbol[i] = 'Nb'
-        i =  42; @symbol[i] = 'Mo'
-        i =  43; @symbol[i] = 'Tc'
-        i =  44; @symbol[i] = 'Ru'
-        i =  45; @symbol[i] = 'Rh'
-        i =  46; @symbol[i] = 'Pd'
-        i =  47; @symbol[i] = 'Ag'
-        i =  48; @symbol[i] = 'Cd'
-        i =  49; @symbol[i] = 'In'
-        i =  50; @symbol[i] = 'Sn'
-        i =  51; @symbol[i] = 'Sb'
-        i =  52; @symbol[i] = 'Te'
-        i =  53; @symbol[i] = 'I'
-        i =  54; @symbol[i] = 'Xe'
-        i =  55; @symbol[i] = 'Cs'
-        i =  56; @symbol[i] = 'Ba'
-        i =  57; @symbol[i] = 'La'
-        i =  58; @symbol[i] = 'Ce'
-        i =  59; @symbol[i] = 'Pr'
-        i =  60; @symbol[i] = 'Nd'
-        i =  61; @symbol[i] = 'Pm'
-        i =  62; @symbol[i] = 'Sm'
-        i =  63; @symbol[i] = 'Eu'
-        i =  64; @symbol[i] = 'Gd'
-        i =  65; @symbol[i] = 'Tb'
-        i =  66; @symbol[i] = 'Dy'
-        i =  67; @symbol[i] = 'Ho'
-        i =  68; @symbol[i] = 'Er'
-        i =  69; @symbol[i] = 'Tm'
-        i =  70; @symbol[i] = 'Yb'
-        i =  71; @symbol[i] = 'Lu'
-        i =  72; @symbol[i] = 'Hf'
-        i =  73; @symbol[i] = 'Ta'
-        i =  74; @symbol[i] = 'W'
-        i =  75; @symbol[i] = 'Re'
-        i =  76; @symbol[i] = 'Os'
-        i =  77; @symbol[i] = 'Ir'
-        i =  78; @symbol[i] = 'Pt'
-        i =  79; @symbol[i] = 'Au'
-        i =  80; @symbol[i] = 'Hg'
-        i =  81; @symbol[i] = 'Tl'
-        i =  82; @symbol[i] = 'Pb'
-        i =  83; @symbol[i] = 'Bi'
-        i =  84; @symbol[i] = 'Po'
-        i =  85; @symbol[i] = 'At'
-        i =  86; @symbol[i] = 'Rn'
-        i =  87; @symbol[i] = 'Fr'
-        i =  88; @symbol[i] = 'Ra'
-        i =  89; @symbol[i] = 'Ac'
-        i =  90; @symbol[i] = 'Th'
-        i =  91; @symbol[i] = 'Pa'
-        i =  92; @symbol[i] = 'U'
-        i =  93; @symbol[i] = 'Np'
-        i =  94; @symbol[i] = 'Pu'
-        i =  95; @symbol[i] = 'Am'
-        i =  96; @symbol[i] = 'Cm'
-        i =  97; @symbol[i] = 'Bk'
-        i =  98; @symbol[i] = 'Cf'
-        i =  99; @symbol[i] = 'Es'
-        i = 100; @symbol[i] = 'Fm'
-        i = 101; @symbol[i] = 'Md'
-        i = 102; @symbol[i] = 'No'
-        i = 103; @symbol[i] = 'Lr'
-    end
 
-    # 原子記号から原子番号を取得。e.g., H から 1
-    # 与えられたものが原子番号ならそのまま返す、ようにしたいがまだできてない。
-    # リストに存在しなければ raise する。
-    def getAtomicNumber( name )
-        symbol = @symbol.index( name )
-        raise "Symbol #{name} not found." if (symbol == nil || symbol == 0)
-        symbol
-    end
+  class NotExistError < Exception; end
+
+  SYMBOLS = [nil] + %w(
+    H He
+    Li Be B  C  N O F  Ne
+    Na Mg Al Si P S Cl Ar
+    K  Ca Sc Ti V  Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
+    Rb Sr Y  Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I  Xe
+    Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
+      Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
+    Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
+  )
+
+  #https://www.hulinks.co.jp/support/c-maker/qa_05.html
+  ATOMIC_RADII = [nil,
+    0.53, 0.31,
+    1.67, 1.12, 0.87, 0.67, 0.56, 0.48, 0.42, 0.38,
+    1.90, 1.45, 1.18, 1.11, 0.98, 0.88, 0.79, 0.71,
+    2.43, 1.94, 1.84, 1.76, 1.71, 1.66, 1.61, 1.56,
+      1.52, 1.49, 1.45, 1.42, 1.36, 1.25, 1.14, 1.03, 0.94, 0.88,
+    2.65, 2.19, 2.12, 2.06, 1.98, 1.90, 1.83, 1.78,
+      1.73, 1.69, 1.65, 1.61, 1.56, 1.45, 1.33, 1.23, 1.15, 1.08,
+    2.98, 2.53, 1.95, 1.85, 2.47, 2.06, 2.05, 2.38,
+      2.31, 2.33, 2.25, 2.28, 2.26, 2.26, 2.22, 2.22, 2.17, 2.08, 2.00,
+      1.93, 1.88, 1.85, 1.80, 1.77, 1.74, 1.71, 1.56, 1.54, 1.43, 1.35, 1.27, 1.20,
+    nil, nil, 1.95, 1.80, 1.80, 1.75, 1.75, 1.75, 1.75
+  ]
+
 
-    # 原子番号から原子記号を取得。e.g., 1 から H
-    # 与えられたものが原子記号ならそのまま返す、ようにしたいがまだできてない。
-    # リストに存在しなければ raise する。
-    def getSymbol( num )
-        raise "getSymbol(num) requires Fixnum, but #{num}" if (num.class != Fixnum)
-        raise "Atomic number is out of range." if (num <= 0 || @symbol.size <= num)
-        @symbol[num]
-    end
+  # Return atomic number from element symbol, e.g., H to 1.
+  # If not found, raise CrystalCell::Element::NotExistError.
+  def self.symbol_to_num(str)
+    symbol = SYMBOLS.index( str )
+    raise NotExistError, "Symbol #{str} not found." if (symbol == nil || symbol == 0)
+    symbol
+  end
 
-    # 引数 id がリストに含まれているか？
-    # id は原子番号でも原子記号でも可にしたいが、とりあえず symbol だけ。
-    def include?( symbol )
-        return false if symbol == nil
-        @symbol.include?( symbol )
-    end
+  # Return element symbols from atomic number 'num', e.g., 1 to H
+  # If not found, raise CrystalCell::Element::NotExistError.
+  def self.num_to_symbol(num)
+      raise NotExistError, "#{num} is not Fixnum." if (num.class != Fixnum)
+      raise NotExistError, "#{num} is out of range." if (num <= 0 || SYMBOLS.size <= num)
+      SYMBOLS[num]
+  end
 
-    ##
-    #def getRadius
-    #end
+  # Return atomic radius.
+  # 'id' can be indicated by number and elemet symbol.
+  def self.atomic_radius(id)
+    id = self.symbol_to_num(id) if id.class == String
+    ATOMIC_RADII[id]
+  end
 
 end

data/lib/crystalcell/latticeaxes.rb

@@ -19,195 +19,208 @@ require "malge/simultaneousequations.rb"
 #               [0.00000, 0.00000, 0.70710]]
 class CrystalCell::LatticeAxes < Mageo::Axes
 
-    class InitializeError < Exception; end
-    class ArgumentError < Exception; end
-    class TypeError < Exception; end
-
-    include Math
-    include Mageo
-
-    # Argument 'vectors' is three vectors with the order of a, b, c.
-    # If you want to make LatticeAxes instances from lattice constants,
-    # you should convert to axes with LatticeAxes.lc_to_axes
-    # 任意の向きのベクトルを渡しても、必ず triangulate する。
-    def initialize(vectors)
-        raise InitializeError, "#{vectors.inspect}" unless vectors.size == 3
-
-        if vectors.class == CrystalCell::LatticeAxes
-            @axes = vectors
-        else
-            begin
-                vectors = self.class.triangulate(vectors)
-            rescue Vector3D::RangeError
-                raise InitializeError, "#{vectors.inspect}"
-            end
-
-            super(vectors)
-        end
+  attr_reader :axes
+
+  class InitializeError < Exception; end
+  class ArgumentError < Exception; end
+  class TypeError < Exception; end
+
+  include Math
+  include Mageo
+
+  # Argument 'vectors' is three vectors with the order of a, b, c.
+  # If you want to make LatticeAxes instances from lattice constants,
+  # you should convert to axes with LatticeAxes.lc_to_axes
+  # 任意の向きのベクトルを渡しても、必ず triangulate する。
+  def initialize(vectors)
+    raise InitializeError, "#{vectors.inspect}" unless vectors.size == 3
+
+    if vectors.class == CrystalCell::LatticeAxes
+      @axes = vectors
+    else
+      begin
+        vectors = self.class.triangulate(vectors)
+      rescue Vector3D::RangeError
+        raise InitializeError, "#{vectors.inspect}"
+      end
+
+      super(vectors)
     end
-
-
-    ## Class methods
-
-    # Generate new instance from lattice constants.
-    def self.new_lc(lc)
-        vec = CrystalCell::LatticeAxes.lc_to_axes(lc)
-        CrystalCell::LatticeAxes.new(vec)
-    end
-
-    # Convert six lattice constants to three axes.
-    # Set true to the argument of 'righthand' if a assumed lattice has righthand axis system.
-    def self.lc_to_axes(lc, righthand = true)
-        raise ArgumentError if (lc.size != 6)
-
-        a = lc[0]
-        b = lc[1]
-        c = lc[2]
-        alpha = (2.0*PI) * lc[3] / 360.0 # radian
-        beta    = (2.0*PI) * lc[4] / 360.0 # radian
-        gamma = (2.0*PI) * lc[5] / 360.0 # radian
-
-        v_c = Vector3D[0.0, 0.0, c]
-        v_b = Vector3D[0.0, b * Math::sin(alpha), b * Math::cos(alpha)]
-        v_a_z = a * Math::cos(beta)
-        v_a_y = (a * (Math::cos(gamma) - Math::cos(alpha) * Math::cos(beta)))/ Math::sin(alpha)
-        v_a_x = Math::sqrt(a**2 - v_a_y**2 - v_a_z**2)
-        v_a_x *= -1.0 if righthand == false
-        v_a = Vector3D[v_a_x, v_a_y, v_a_z]
-        return [v_a, v_b, v_c]
-    end
-
-    # Convert three axes to six lattice constants.
-    def self.axes_to_lc(axes)
-        axes.collect!{|i| Vector3D[*i] }
-        a = axes[0].r
-        b = axes[1].r
-        c = axes[2].r
-        alpha = axes[1].angle_degree(axes[2])
-        beta    = axes[2].angle_degree(axes[0])
-        gamma = axes[0].angle_degree(axes[1])
-        return [ a, b, c, alpha, beta, gamma ]
+  end
+
+
+  ## Class methods
+
+  # Generate new instance from lattice constants.
+  def self.new_lc(lc)
+    vec = CrystalCell::LatticeAxes.lc_to_axes(lc)
+    CrystalCell::LatticeAxes.new(vec)
+  end
+
+  # Convert six lattice constants to three axes.
+  # Set true to the argument of 'righthand' if a assumed lattice has righthand axis system.
+  def self.lc_to_axes(lc, righthand = true)
+    raise ArgumentError if (lc.size != 6)
+
+    a = lc[0]
+    b = lc[1]
+    c = lc[2]
+    alpha = (2.0*PI) * lc[3] / 360.0 # radian
+    beta    = (2.0*PI) * lc[4] / 360.0 # radian
+    gamma = (2.0*PI) * lc[5] / 360.0 # radian
+
+    v_c = Vector3D[0.0, 0.0, c]
+    v_b = Vector3D[0.0, b * Math::sin(alpha), b * Math::cos(alpha)]
+    v_a_z = a * Math::cos(beta)
+    v_a_y = (a * (Math::cos(gamma) - Math::cos(alpha) * Math::cos(beta)))/ Math::sin(alpha)
+    v_a_x = Math::sqrt(a**2 - v_a_y**2 - v_a_z**2)
+    v_a_x *= -1.0 if righthand == false
+    v_a = Vector3D[v_a_x, v_a_y, v_a_z]
+    return [v_a, v_b, v_c]
+  end
+
+  # Convert three axes to six lattice constants.
+  def self.axes_to_lc(axes)
+    axes.collect!{|i| Vector3D[*i] }
+    a = axes[0].r
+    b = axes[1].r
+    c = axes[2].r
+    alpha = axes[1].angle_degree(axes[2])
+    beta    = axes[2].angle_degree(axes[0])
+    gamma = axes[0].angle_degree(axes[1])
+    return [ a, b, c, alpha, beta, gamma ]
+  end
+
+  # Return true if the relation of vector order is righthand system.
+  def self.righthand?(axes)
+    axes.map! { |i| Vector3D[*i] }
+    return true if Vector3D.scalar_triple_product(*axes) > 0.0
+    return false
+  end
+
+  # Return true if the relation of vector order is lefthand system.
+  def self.lefthand?(axes)
+    axes.map! { |i| Vector3D[*i] }
+    return true if Vector3D.scalar_triple_product(*axes) < 0.0
+    return false
+  end
+
+  # Convert three axes to three axes with rules below:
+  #       c axis is along z axis in cartesian system.
+  #       b axis is on y-z plane in cartesian system.
+  # Return an array of three Vector3D instances.
+  # This class does not convert righthand to lefthand system.
+  # The name of this method 'triangulate' originates from the
+  # matrix indicating the vectors being triangular matrix.
+  #
+  # クラスメソッドは廃止の方向で。
+  # vectors の数をチェックするのは initialize でやるべきことだろうし、
+  # LatticeAxes クラスインスタンス以外で triangulate を使う場面が想像できない。
+  #
+  def self.triangulate(vectors)
+    vectors.map! { |i| Vector3D[*i] }
+    raise InitializeError if self.dependent?(vectors)
+    lc = self.axes_to_lc(vectors)
+    righthand = self.righthand?(vectors)
+    return self.lc_to_axes(lc, righthand)
+  end
+
+  ## Instance methods.
+
+  # Get lattice constants in six values.
+  def get_lattice_constants
+    return CrystalCell::LatticeAxes.axes_to_lc(@axes)
+  end
+
+  def righthand?
+    self.class.righthand?(@axes)
+  end
+
+  def lefthand?
+    self.class.lefthand?(@axes)
+  end
+
+  # This class is obsoleted. [2011-12-22]
+  ## Convert internal coordinates to cartesian coordinates.
+  ## Return a Vector3DInternal class instance, which is not a cartesian vector.
+  #def internal2cartesian(internal_coord)
+  # Vector3DInternal[ *internal_coord ].to_v3d(axes)
+  #end
+
+  # This class is obsoleted. [2011-12-22]
+  ## Convert cartesian coordinates to internal coordinates.
+  ## Return a Vector3D class instance, which is a cartesian vector.
+  #def cartesian2internal(cartesian_coord)
+  # #pp cartesian_coord
+  # Vector3D[ *cartesian_coord ].to_v3di(axes)
+  #end
+
+  # Compare <other> CrystalCell::LatticeAxes instance.
+  # <length_ratio> is tolerance of ratio in length of axes.
+  # <angle_tolerance> is tolerance of value in angle between axes.
+  def equal_in_delta?(other, length_ratio, angle_tolerance)
+    length_a = self .get_lattice_constants[0..2]
+    length_b = other.get_lattice_constants[0..2]
+    3.times do |i|
+      return false unless ((length_a[i] - length_b[i]).abs <= length_ratio)
     end
 
-    # Return true if the relation of vector order is righthand system.
-    def self.righthand?(axes)
-        axes.map! { |i| Vector3D[*i] }
-        return true if Vector3D.scalar_triple_product(*axes) > 0.0
-        return false
+    angle_a  = self .get_lattice_constants[3..5]
+    angle_b  = other.get_lattice_constants[3..5]
+    3.times do |i|
+      return false unless ((angle_a[i] - angle_b[i]).abs <=    angle_tolerance)
     end
-
-    # Return true if the relation of vector order is lefthand system.
-    def self.lefthand?(axes)
-        axes.map! { |i| Vector3D[*i] }
-        return true if Vector3D.scalar_triple_product(*axes) < 0.0
-        return false
-    end
-
-    # Convert three axes to three axes with rules below:
-    #       c axis is along z axis in cartesian system.
-    #       b axis is on y-z plane in cartesian system.
-    # Return an array of three Vector3D instances.
-    # This class does not convert righthand to lefthand system.
-    # The name of this method 'triangulate' originates from the
-    # matrix indicating the vectors being triangular matrix.
-    #
-    # クラスメソッドは廃止の方向で。
-    # vectors の数をチェックするのは initialize でやるべきことだろうし、
-    # LatticeAxes クラスインスタンス以外で triangulate を使う場面が想像できない。
-    #
-    def self.triangulate(vectors)
-        vectors.map! { |i| Vector3D[*i] }
-        raise InitializeError if self.dependent?(vectors)
-        lc = self.axes_to_lc(vectors)
-        righthand = self.righthand?(vectors)
-        return self.lc_to_axes(lc, righthand)
-    end
-
-    ## Instance methods.
-
-    # Get lattice constants in six values.
-    def get_lattice_constants
-        return CrystalCell::LatticeAxes.axes_to_lc(@axes)
+    return true
+  end
+
+  def ==(other)
+    3.times do |i|
+      3.times do |j|
+        return false if self[i][j] != other[i][j]
+      end
     end
-
-    def righthand?
-        self.class.righthand?(@axes)
-    end
-
-    def lefthand?
-        self.class.lefthand?(@axes)
-    end
-
-    # This class is obsoleted. [2011-12-22]
-    ## Convert internal coordinates to cartesian coordinates.
-    ## Return a Vector3DInternal class instance, which is not a cartesian vector.
-    #def internal2cartesian(internal_coord)
-    # Vector3DInternal[ *internal_coord ].to_v3d(axes)
-    #end
-
-    # This class is obsoleted. [2011-12-22]
-    ## Convert cartesian coordinates to internal coordinates.
-    ## Return a Vector3D class instance, which is a cartesian vector.
-    #def cartesian2internal(cartesian_coord)
-    # #pp cartesian_coord
-    # Vector3D[ *cartesian_coord ].to_v3di(axes)
-    #end
-
-    # Compare <other> CrystalCell::LatticeAxes instance.
-    # <length_ratio> is tolerance of ratio in length of axes.
-    # <angle_tolerance> is tolerance of value in angle between axes.
-    def equal_in_delta?(other, length_ratio, angle_tolerance)
-        length_a = self .get_lattice_constants[0..2]
-        length_b = other.get_lattice_constants[0..2]
-        3.times do |i|
-            return false unless ((length_a[i] - length_b[i]).abs <= length_ratio)
-        end
-
-        angle_a  = self .get_lattice_constants[3..5]
-        angle_b  = other.get_lattice_constants[3..5]
-        3.times do |i|
-            return false unless ((angle_a[i] - angle_b[i]).abs <=    angle_tolerance)
-        end
-        return true
-    end
-
-    def ==(other)
-        3.times do |i|
-            3.times do |j|
-                return false if self[i][j] != other[i][j]
-            end
-        end
-        return true
-    end
-
-    private
-
-    def triangulate
-        #self.class.triangulate(@axes)
-    # rotate(2, 2, 1)
-    # rotate(2, 0, 2)
-    # rotate(1, 2, 1)
-    end
-
-    #private
-
-    ## 保持する全ての軸を回転する。
-    ## 以下の index は Axes クラス保持している配列における index。
-    ## target_index          回転の際の角度を決めるベクトルの
-    ##  self が保持する内部座標軸の index。
-    ## center_axis_index 回転の中心軸のベクトルの index in x, y, z。
-    ## plane_axis_index) 回転の目的地となる平面を、中心軸と共に構成するベクトルの index
-    ##  in x, y, z。
-    #def rotate(target_index, center_axis_index, plane_axis_index)
-    # theta = 
-
-    # axes[target_index]
-    # 
-    # HERE
-
-    # self.each do |vector|
-    #       vector
-    # end
-    #end
+    return true
+  end
+
+  ## Multiply all vectors. Not destructive.
+  def *(val)
+    #result = Marshal.load(Marshal.dump(self))
+
+    self.class.new(@axes.map{|vec| vec * val})
+  end
+
+  def to_a
+    @axes.map{|v| v.to_a}
+  end
+
+  private
+
+  def triangulate
+    #self.class.triangulate(@axes)
+  # rotate(2, 2, 1)
+  # rotate(2, 0, 2)
+  # rotate(1, 2, 1)
+  end
+
+  #private
+
+  ## 保持する全ての軸を回転する。
+  ## 以下の index は Axes クラス保持している配列における index。
+  ## target_index          回転の際の角度を決めるベクトルの
+  ##  self が保持する内部座標軸の index。
+  ## center_axis_index 回転の中心軸のベクトルの index in x, y, z。
+  ## plane_axis_index) 回転の目的地となる平面を、中心軸と共に構成するベクトルの index
+  ##  in x, y, z。
+  #def rotate(target_index, center_axis_index, plane_axis_index)
+  # theta = 
+
+  # axes[target_index]
+  # 
+  # HERE
+
+  # self.each do |vector|
+  #       vector
+  # end
+  #end
 
 end