crystalcell 0.0.6 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGES

@@ -1,6 +1,12 @@
 = crystalcell Changelog
 
-== Master (for 0.0.7)
+<!-- Master -->
+
+== Version 0.1.0 [2016-07-12] released
+
+* Add Cell.to_povcell
+* Add CrystalCell::Povray::Tetrahedron
+* Add LatticeAxes.to_a
 
 == Version 0.0.6 [2016-05-31] released
 

data/Gemfile

@@ -6,13 +6,13 @@ source "http://rubygems.org"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "test-unit", "~> 3.1"
+  gem "test-unit", "~> 3.2"
   gem "rdoc", "~> 4.2"
   gem "bundler", "~> 1.11"
   gem "jeweler", "~> 2.0"
   gem "simplecov", "~> 0.11"
   gem "malge", "~> 0.0"
-  gem "mageo", "~> 0.0"
+  gem "mageo", "~> 0.1"
   gem "maset", "~> 0.0"
   gem "builtinextension", "~> 0.1"
 end

data/VERSION

@@ -1 +1 @@
-0.0.6
+0.1.0

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 0.0.6 ruby lib
+# stub: crystalcell 0.1.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "crystalcell"
-  s.version = "0.0.6"
+  s.version = "0.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["ippei94da"]
-  s.date = "2016-05-31"
+  s.date = "2016-07-12"
   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 = [
@@ -36,20 +36,27 @@ Gem::Specification.new do |s|
     "lib/crystalcell/povray.rb",
     "lib/crystalcell/povray/camera.rb",
     "lib/crystalcell/povray/cell.rb",
+    "lib/crystalcell/povray/color.rb",
     "lib/crystalcell/povray/cylinder.rb",
     "lib/crystalcell/povray/element.rb",
     "lib/crystalcell/povray/sphere.rb",
+    "lib/crystalcell/povray/tetrahedron.rb",
     "lib/crystalcell/povray/triangle.rb",
     "test/cif/ZrO2-25C.cif",
     "test/helper.rb",
     "test/povray/test_camera.rb",
     "test/povray/test_cell.rb",
+    "test/povray/test_colors.rb",
+    "test/povray/test_cylinder.rb",
     "test/povray/test_element.rb",
+    "test/povray/test_tetrahedron.rb",
+    "test/povray/test_triangle.rb",
     "test/test_atom.rb",
     "test/test_cell.rb",
     "test/test_element.rb",
     "test/test_latticeaxes.rb",
-    "test/test_periodiccell.rb"
+    "test/test_periodiccell.rb",
+    "test/test_povray.rb"
   ]
   s.homepage = "http://github.com/ippei94da/crystalcell"
   s.licenses = ["MIT"]
@@ -60,34 +67,34 @@ Gem::Specification.new do |s|
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<test-unit>, ["~> 3.1"])
+      s.add_development_dependency(%q<test-unit>, ["~> 3.2"])
       s.add_development_dependency(%q<rdoc>, ["~> 4.2"])
       s.add_development_dependency(%q<bundler>, ["~> 1.11"])
       s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
       s.add_development_dependency(%q<simplecov>, ["~> 0.11"])
       s.add_development_dependency(%q<malge>, ["~> 0.0"])
-      s.add_development_dependency(%q<mageo>, ["~> 0.0"])
+      s.add_development_dependency(%q<mageo>, ["~> 0.1"])
       s.add_development_dependency(%q<maset>, ["~> 0.0"])
       s.add_development_dependency(%q<builtinextension>, ["~> 0.1"])
     else
-      s.add_dependency(%q<test-unit>, ["~> 3.1"])
+      s.add_dependency(%q<test-unit>, ["~> 3.2"])
       s.add_dependency(%q<rdoc>, ["~> 4.2"])
       s.add_dependency(%q<bundler>, ["~> 1.11"])
       s.add_dependency(%q<jeweler>, ["~> 2.0"])
       s.add_dependency(%q<simplecov>, ["~> 0.11"])
       s.add_dependency(%q<malge>, ["~> 0.0"])
-      s.add_dependency(%q<mageo>, ["~> 0.0"])
+      s.add_dependency(%q<mageo>, ["~> 0.1"])
       s.add_dependency(%q<maset>, ["~> 0.0"])
       s.add_dependency(%q<builtinextension>, ["~> 0.1"])
     end
   else
-    s.add_dependency(%q<test-unit>, ["~> 3.1"])
+    s.add_dependency(%q<test-unit>, ["~> 3.2"])
     s.add_dependency(%q<rdoc>, ["~> 4.2"])
     s.add_dependency(%q<bundler>, ["~> 1.11"])
     s.add_dependency(%q<jeweler>, ["~> 2.0"])
     s.add_dependency(%q<simplecov>, ["~> 0.11"])
     s.add_dependency(%q<malge>, ["~> 0.0"])
-    s.add_dependency(%q<mageo>, ["~> 0.0"])
+    s.add_dependency(%q<mageo>, ["~> 0.1"])
     s.add_dependency(%q<maset>, ["~> 0.0"])
     s.add_dependency(%q<builtinextension>, ["~> 0.1"])
   end

data/lib/crystalcell/cell.rb

@@ -135,7 +135,7 @@ class CrystalCell::Cell
   #b_max : b 軸方向のセルの方向を整数で示したときの最大値
   #c_min : c 軸方向のセルの方向を整数で示したときの最小値
   #c_max : c 軸方向のセルの方向を整数で示したときの最大値
-  #-1, 1, -1, 1, -1, 1 と指定すれば 3x3x3 の 27倍体積の構造になる。
+  #-1, 1, -1, 1, -1, 1 と指定すれば 3x3x3 の 27倍の原子数になる。
   def atoms_in_supercell( a_min, a_max, b_min, b_max, c_min, c_max )
     results = []
     @atoms.each do |atom|
@@ -291,7 +291,7 @@ class CrystalCell::Cell
   #Generate a new cell with the same lattice consants,
   #containing atoms of indicated elements.
   #Argument 'elems' must be an array of element names.
-  #含まれる @atoms の順序は、保存される。元素ごとに並び換えたりしない。
+  #含まれる @atoms の順序は保存される。元素ごとに並び換えたりしない。
   #CrystalCell::Atom.element が elems の要素のどれかと完全一致しているもののみ対象となる。
   #サブクラスのインスタンスで実行した場合には、
   #サブクラスのインスタンスとして生成する。
@@ -519,6 +519,11 @@ class CrystalCell::Cell
 
   #ptg_symbol, ptg_num, trans_mat = getptg(rotations)
 
+  def to_povcell
+    #pp @axes
+    CrystalCell::Povray::Cell.new(@axes, @atoms)
+  end
+
   private
 
   def get_spg_dataset
@@ -530,7 +535,7 @@ class CrystalCell::Cell
       table[elem]
     end
     hall_num= 0
-    dataset = get_dataset(axes_t, poss, types, hall_num, @symprec, @angle_tolerance)
+    get_dataset(axes_t, poss, types, hall_num, @symprec, @angle_tolerance)
   end
 
   #POSCAR の内容の文字列を生成。

data/lib/crystalcell/povray/camera.rb

@@ -19,39 +19,63 @@ class CrystalCell::Povray::Camera
     #@location = [   3.0, 3.0, 3.0 ]
     #@look_at  = [   0.0, 0.0, 0.0 ]
     #@sky      = [   0.0, 0.0, 1.0 ]
-    #@right    = [ -1.00, 0.0, 0.0 ]
+    #@right    =
     #@up       = [   0.0, 1.0, 0.0 ]
     #@angle    = 68
 
-  attr_accessor :orthographic, :location, :look_at, :sky, :right, :up, :angle
+  attr_accessor :camera_type, :location, :right, :up, :direction,
+    :sky, :angle, :look_at
 
-  def initialize(orthographic:, location:, look_at:, sky:, right:, up:, angle:,
-                 additions: [])
-    @orthographic = orthographic
-    @location     = location    
-    @look_at      = look_at     
-    @sky          = sky         
-    @right        = right       
-    @up           = up          
-    @angle        = angle       
-    @additions    = additions       
+  # camera_type: perspectice, orthographic, etc.
+  # Note: default values of some setting is modified from original povray
+  #   because of left-handed coordinate system.
+  #   This library provide only on right-handed system in crystallography.
+  #
+  #   ---------------------------------------------
+  #   setting       default_orig  default_this
+  #   camera_type   perspective   
+  #   location      <0,0,0>       
+  #   direction     <0,0,1>       
+  #   right         <1.33,0,0>    [-1.33, 0.0, 0.0],
+  #   sky           <0,1,0>       [  0.0, 0.0, 1.0],
+  #   up            <0,1,0>       
+  #   look_at       <0,0,1>
+  def initialize(camera_type:      nil, # perspective
+                 location:         nil, # <0,0,0>
+                 right:            [-1.33, 0.0, 0.0],
+                 up:               nil,
+                 direction:        nil,
+                 sky:              [0.0, 0.0, 1.0],
+                 angle:            nil,
+                 #camera_modifiers: nil,
+                 look_at:          nil
+                 )
+    @camera_type  = camera_type
+    @location     = location
+    @right        = right
+    @up           = up
+    @direction    = direction
+    @sky          = sky
+    @angle        = angle
+    #@camera_modifiers    = camera_modifiers
+    @look_at      = look_at
   end
 
   def dump(io)
     io.puts "camera {"
-    io.puts "  orthographic" if @orthographic
-    io.printf("  location <%f, %f, %f >\n", *@location)
-    io.printf("  look_at  <%f, %f, %f >\n", *@look_at)
-    io.printf("  sky      <%f, %f, %f >\n", *@sky)
-    io.printf("  right    <%f, %f, %f >\n", *@right)
-    io.printf("  up       <%f, %f, %f >\n", *@up)
-    io.printf("  angle    %f\n"           , @angle)
+    io.printf("  %s\n", @camera_type) if @camera_type
+    io.printf("  location  <%f, %f, %f >\n", *@location)  if @location
+    io.printf("  right     <%f, %f, %f >\n", *@right)     if @right
+    io.printf("  up        <%f, %f, %f >\n", *@up)        if @up
+    io.printf("  direction <%f, %f, %f >\n", *@direction) if @direction
+    io.printf("  sky       <%f, %f, %f >\n", *@sky)       if @sky
+    io.printf("  angle     %f\n"           , @angle)      if @angle
+    #@camera_modifiers.each do |i|
+    #  io.puts i
+    #end
+    io.printf("  look_at   <%f, %f, %f >\n", *@look_at) if @look_at
     io.puts "}"
-    @additions.each do |i|
-      io.puts i
-    end
   end
 
 end
 
-

data/lib/crystalcell/povray/cell.rb

@@ -3,17 +3,22 @@
 class CrystalCell::Povray::Cell < CrystalCell::Cell
   RADIUS_RATIO = 0.3
   
-  LATTICE_RADIUS = 0.1
+  LATTICE_RADIUS = 0.02
   LATTICE_COLOR  = [0.50, 0.50, 0.50]
   BOND_RADIUS    = 0.05
   BOND_COLOR     = [0.75, 0.75, 0.75]
 
   # povray 形式の文字列を返す。
   def to_pov
-   return atoms_to_pov + bonds_to_pov + lattice_to_pov
+    #return atoms_to_povs + bonds_to_povs + lattice_to_povs
+    return atoms_to_povs + lattice_to_povs
   end
 
-  #private
+  def dump(io)
+    self.to_pov.each do |line|
+      io.print line
+    end
+  end
 
   # 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。
@@ -27,30 +32,30 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
     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
+  ## 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
 
   # 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
@@ -64,18 +69,21 @@ class CrystalCell::Povray::Cell < CrystalCell::Cell
     v111 = Vector3DInternal[ 1.0, 1.0, 1.0 ].to_v3d(self.axes)
 
     results = []
-    results << Mageo::Cylinder.new([v000, v001], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v010, v011], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v100, v101], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v110, v111], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v000, v010], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v100, v110], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v001, v011], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v101, v111], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v000, v100], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v001, v101], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v010, v110], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
-    results << Mageo::Cylinder.new([v011, v111], LATTICE_RADIUS).to_pov(LATTICE_COLOR).to_s + "\n"
+    cy = CrystalCell::Povray::Cylinder
+    r = LATTICE_RADIUS
+    c = LATTICE_COLOR
+    results << cy.new(v000, v001, r, c).to_pov.to_s + "\n"
+    results << cy.new(v010, v011, r, c).to_pov.to_s + "\n"
+    results << cy.new(v100, v101, r, c).to_pov.to_s + "\n"
+    results << cy.new(v110, v111, r, c).to_pov.to_s + "\n"
+    results << cy.new(v000, v010, r, c).to_pov.to_s + "\n"
+    results << cy.new(v100, v110, r, c).to_pov.to_s + "\n"
+    results << cy.new(v001, v011, r, c).to_pov.to_s + "\n"
+    results << cy.new(v101, v111, r, c).to_pov.to_s + "\n"
+    results << cy.new(v000, v100, r, c).to_pov.to_s + "\n"
+    results << cy.new(v001, v101, r, c).to_pov.to_s + "\n"
+    results << cy.new(v010, v110, r, c).to_pov.to_s + "\n"
+    results << cy.new(v011, v111, r, c).to_pov.to_s + "\n"
     results
   end
 

data/lib/crystalcell/povray/color.rb

@@ -0,0 +1,42 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+#
+#
+#
+class CrystalCell::Povray::Color
+
+  PI = Math::PI
+  #
+  def initialize()
+  end
+
+  # 色相環(color circle) 上での色を、与えられた角度に対して返す。
+  # 強度は [r, g, b] の配列で、0.0<=x<=1.0 の実数。
+  def self.circle_color(theta)
+    theta = theta % (2*PI); #-2*pi 〜 +2*pi の範囲に入る
+
+    r = self.trapezoidal_wave(theta, (4.0/6.0) * 2.0 * PI)
+    g = self.trapezoidal_wave(theta, (0.0/6.0) * 2.0 * PI)
+    b = self.trapezoidal_wave(theta, (2.0/6.0) * 2.0 * PI)
+    [r, g, b]
+  end
+
+  # 台形波
+  def self.trapezoidal_wave(theta, phase)
+    x = (theta - phase)/ (2.0*PI)
+    x = x -  x.floor
+    if (0.0/6.0) <= x && x < (1.0/6.0)
+      return x * 6.0
+    elsif (1.0/6.0) <= x && x < (3.0/6.0)
+      return 1.0
+    elsif (3.0/6.0) <= x && x < (4.0/6.0)
+      return 4.0 - x * 6.0
+    elsif (4.0/6.0) <= x && x < (6.0/6.0)
+      return 0.0
+    end
+  end
+
+end
+
+  #      thetaBase: その色が上がり始める点を基準とする。R ならば 4π/3

data/lib/crystalcell/povray/cylinder.rb

@@ -1,12 +1,22 @@
 #! /usr/bin/env ruby # coding: utf-8
 
-class Mageo::Cylinder
+class CrystalCell::Povray::Cylinder < Mageo::Cylinder
+  attr_reader :positions, :color
+
+  def initialize(position0, position1, radius, color)
+    super(position0, position1, radius)
+    @color = color
+  end
+
   # 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)
+  def to_pov
     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> } }",
-      *positions[0], *positions[1], radius, *color)
+    *positions[0], *positions[1], radius, *color)
+    #*@positions[0], *@positions[1], radius, @color)
   end
-end
-
 
+  def dump(io)
+    io.puts self.to_pov
+  end
+end

data/lib/crystalcell/povray/sphere.rb

@@ -7,6 +7,10 @@ class Mageo::Sphere
     sprintf( "object { sphere{<% 7.4f, % 7.4f, % 7.4f>, %7.4f} pigment {color rgb <%4.2f, %4.2f, %4.2f>} }",
       *position, radius, *color)
   end
+
+  def dump(io)
+    io.puts self.to_pov
+  end
 end
 
 

data/lib/crystalcell/povray/tetrahedron.rb

@@ -0,0 +1,34 @@
+#! /usr/bin/env ruby # coding: utf-8
+
+class CrystalCell::Povray::Tetrahedron < Mageo::Tetrahedron
+  
+  attr_accessor :color, :transmit
+  
+  # color should be Array like [r, g, b]. Float from 0.0 to 1.0.
+  def initialize(v0, v1, v2, v3, color, transmit = nil)
+    super(v0, v1, v2, v3)
+    @color =  color
+    @transmit =  transmit
+  end
+
+  # 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
+    triangles.map { |triangle| triangle.to_pov }.join("\n")
+  end
+
+  def dump(io)
+    io.puts self.to_pov
+  end
+
+  def triangles
+    results = VERTEX_INDICES_OF_TRIANGLES.map do |indices|
+    CrystalCell::Povray::Triangle.new( *(indices.map{|i| @vertices[i] }), @color, @transmit )
+    end
+    return results
+  end
+
+  private
+
+end
+

data/lib/crystalcell/povray/triangle.rb

@@ -1,17 +1,33 @@
 #! /usr/bin/env ruby # coding: utf-8
 
-class Mageo::Triangle
+class CrystalCell::Povray::Triangle < Mageo::Triangle
+
+  attr_accessor :color, :transmit
+  
+  def initialize(vec0, vec1, vec2, color, transmit = nil)
+    super(vec0, vec1, vec2)
+    @color = color
+    @transmit = transmit
+  end
+
   # 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)
+  def to_pov
     v = self.vertices
-    result = "polygon { 4, " + sprintf("<%7.4f, %7.4f, %7.4f>, ", v[0][0], v[0][1], v[0][2]) +
-      sprintf("<%7.4f, %7.4f, %7.4f>, ", v[1][0], v[1][1], v[1][2]) +
-      sprintf("<%7.4f, %7.4f, %7.4f>, ", v[2][0], v[2][1], v[2][2]) +
-      sprintf("<%7.4f, %7.4f, %7.4f> " , v[0][0], v[0][1], v[0][2]) +
-      "pigment { color rgb <1, 0, 0> } }"
+    result = sprintf("triangle{<%f,%f,%f>,<%f,%f,%f>,<%f,%f,%f>",
+      *@vertices[0], *@vertices[1], *@vertices[2])
+    result +=  sprintf(" pigment {color rgb<%f,%f,%f>", *@color)
+    result +=  sprintf(" transmit %f", @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
-end
 
+  def dump(io)
+    io.puts self.to_pov
+  end
+end