crystalcell 0.0.3 → 0.0.4

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: db6d8120f97d6fa22fe9fe5095bb3f848a75e8ba
+  data.tar.gz: 9aee254b92a6c89df45b3459bc30f35297a3c4b5
+SHA512:
+  metadata.gz: 3a5158acc279b9f2bfd7bca995e0584e9afb34ddbab6aa9e48ea9c1d3b4a868589b0c502679900d1f2869730b4b1cc2d0a2414ff81e24a683d689462ca8896b3
+  data.tar.gz: 68a56c0ea4bf4eb2ee5f58a40727b4df5c9697ea0aad93cecf6a71c65193adcd5cff4713c9eaa0ff00f16409bd8f8fc81fa2e4ad22d868e0fc0b256a4ed5e3b9

data/CHANGES

@@ -1,6 +1,28 @@
 = crystalcell Changelog
 
-== Master (for 0.0.3)
+== Master (for 0.0.5)
+
+== Version 0.0.4 [2016-03-11] released
+* LatticeAxes.axes is added.
+* LatticeAxes.* is added.
+* LatticeAxes.to_a is added.
+
+* CrystalCell::Povray::Cell      is added
+* CrystalCell::Povray::Cylinder  is added
+* CrystalCell::Povray::Element   is added
+* CrystalCell::Povray::Sphere    is added
+* CrystalCell::Povray::Triangle  is added
+
+* CrystalCell::Element
+    * remove get*() methods.
+    * remove include? methods.
+    * add symbol_to_num method
+    * add num_to_symbol method
+    * rename radius to atomic_radius
+
+* CrystalCell::PeriodicCell.find_bonds returns preserved order of elements
+
+== Version 0.0.3 [2015-02-05] released
 * Add CrystalCell::LatticeAxes.new_lc
 
 == Version 0.0.2 [2014-08-30] 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 "rdoc", "~> 4.1.1"
-  gem "bundler", "~> 1.7.2"
-  gem "jeweler", "~> 2.0.1"
-  gem "simplecov", ">= 0.9.0"
-  gem "malge", ">= 0.0.8"
-  gem "mageo", ">= 0.0.3"
-  gem "maset", ">= 0.0.0"
-  gem "builtinextension", ">= 0.1.2"
-  #gem "psych", ">= 0"
+  gem "test-unit", "~> 3.1"
+  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 "maset", "~> 0.0"
+  gem "builtinextension", "~> 0.1"
 end

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.4

data/crystalcell.gemspec

@@ -2,14 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: crystalcell 0.0.4 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "crystalcell"
-  s.version = "0.0.3"
+  s.version = "0.0.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["ippei94da"]
-  s.date = "2015-02-05"
+  s.date = "2016-03-10"
   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 = [
@@ -31,8 +33,16 @@ Gem::Specification.new do |s|
     "lib/crystalcell/element.rb",
     "lib/crystalcell/latticeaxes.rb",
     "lib/crystalcell/periodiccell.rb",
+    "lib/crystalcell/povray.rb",
+    "lib/crystalcell/povray/cell.rb",
+    "lib/crystalcell/povray/cylinder.rb",
+    "lib/crystalcell/povray/element.rb",
+    "lib/crystalcell/povray/sphere.rb",
+    "lib/crystalcell/povray/triangle.rb",
     "test/cif/ZrO2-25C.cif",
     "test/helper.rb",
+    "test/povray/test_cell.rb",
+    "test/povray/test_element.rb",
     "test/test_atom.rb",
     "test/test_cell.rb",
     "test/test_element.rb",
@@ -41,41 +51,43 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/ippei94da/crystalcell"
   s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "2.5.1"
   s.summary = "Classes around a cell in crystallography"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<rdoc>, ["~> 4.1.1"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.7.2"])
-      s.add_development_dependency(%q<jeweler>, ["~> 2.0.1"])
-      s.add_development_dependency(%q<simplecov>, [">= 0.9.0"])
-      s.add_development_dependency(%q<malge>, [">= 0.0.8"])
-      s.add_development_dependency(%q<mageo>, [">= 0.0.3"])
-      s.add_development_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_development_dependency(%q<builtinextension>, [">= 0.1.2"])
+      s.add_development_dependency(%q<test-unit>, ["~> 3.1"])
+      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<maset>, ["~> 0.0"])
+      s.add_development_dependency(%q<builtinextension>, ["~> 0.1"])
     else
-      s.add_dependency(%q<rdoc>, ["~> 4.1.1"])
-      s.add_dependency(%q<bundler>, ["~> 1.7.2"])
-      s.add_dependency(%q<jeweler>, ["~> 2.0.1"])
-      s.add_dependency(%q<simplecov>, [">= 0.9.0"])
-      s.add_dependency(%q<malge>, [">= 0.0.8"])
-      s.add_dependency(%q<mageo>, [">= 0.0.3"])
-      s.add_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_dependency(%q<builtinextension>, [">= 0.1.2"])
+      s.add_dependency(%q<test-unit>, ["~> 3.1"])
+      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<maset>, ["~> 0.0"])
+      s.add_dependency(%q<builtinextension>, ["~> 0.1"])
     end
   else
-    s.add_dependency(%q<rdoc>, ["~> 4.1.1"])
-    s.add_dependency(%q<bundler>, ["~> 1.7.2"])
-    s.add_dependency(%q<jeweler>, ["~> 2.0.1"])
-    s.add_dependency(%q<simplecov>, [">= 0.9.0"])
-    s.add_dependency(%q<malge>, [">= 0.0.8"])
-    s.add_dependency(%q<mageo>, [">= 0.0.3"])
-    s.add_dependency(%q<maset>, [">= 0.0.0"])
-    s.add_dependency(%q<builtinextension>, [">= 0.1.2"])
+    s.add_dependency(%q<test-unit>, ["~> 3.1"])
+    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<maset>, ["~> 0.0"])
+    s.add_dependency(%q<builtinextension>, ["~> 0.1"])
   end
 end
 

data/lib/crystalcell/atom.rb

@@ -6,125 +6,123 @@ raise "Atom class need ruby version later than 1.9." if RUBY_VERSION.to_f < 1.9
 # This class is not assumeed in a periodic condition.
 class CrystalCell::Atom
 
-    include Mageo
-
-    class TypeError < Exception ; end
-
-    # Do not change :position to attr_accessor.
-    # This must be Vector3DInternal instance.
-    attr_reader :movable_flags
-    attr_accessor :element, :name, :position
-
-    # Arguments:
-    #       elements:
-    #           Identifier of a element.
-    #           This may be String like "Li", Integer like 0, or other class instances.
-    #           Why doesn't this class have concrete name of elements?
-    #           The reason is below:
-    #               - This class is assumed to be used in Cell class instances.
-    #                   When we treat symmetry of the cell, the elements of atoms are not necessary information.
-    #                   This specification enable highly abstract level of treatment of cells.
-    #               - POSCAR file of VASP (before ver.4 series) don't have element information.
-    #                   This specification enable to use POSCAR directly without POTCAR or element indication.
-    #       position:
-    #           Coordinates of an atom.
-    #           This argument 'position' is mainly assumed as a internal coordinate.
-    #       name:
-    #           Identifier of an atom, e.g., "Li1" or "O23".
-    #       movable_flags: 
-    #           Movable flags of an atom in each of three directions as a Array of three items.
-    def initialize(element, position, name = nil, movable_flags = nil)
-        #p position
-        #p position.methods.sort
-        raise TypeError, "Position doesn't have []: (#{position.inspect})" unless position.methods.include?(:[])
-        raise TypeError, "Number of items in position is not 3: (#{position})" if position.size != 3
-        raise TypeError, "Coordinate is not a Float: (#{position})" if position[0].class != Float
-        raise TypeError, "Coordinate is not a Float: (#{position})" if position[1].class != Float
-        raise TypeError, "Coordinate is not a Float: (#{position})" if position[2].class != Float
-
-        @element = element
-        set_position(position)
-        @name = name
-        @movable_flags = movable_flags
-    end
-
-    ## Class methods
-
-    # Equivalence checking (class method version).
-    # Return true when all the condition below are satisfied:
-    #       - same element identifier.
-    #       - difference of coordinates is within tolerance.
-    # Note that distance cannot be used since this class doesn't have a lattice axes.
-    # Imagine the shape of tolerant zone is a hexahedron.
-    def self.equal_in_delta?(atom0, atom1, tol = 0.0)
-        return false if atom0.element != atom1.element
-        3.times do |i|
-            return false if ((atom0.position[i] - atom1.position[i]).abs > tol)
-        end
-        return true
-    end
-
-    ## Instance methods
-
-    # Restricted equivalence checking.
-    # Return true when all the condition below are satisfied:
-    #       - same element identifier.
-    #       - difference of coordinates is the same.
-    # This method should be used after well-consideration.
-    # Arbitrary coordinates are not generally the same like Float instances.
-    # It is a good idea to use in test scripts.
-    def ==(other)
-        #pp self
-        #pp other
-        self.class.equal_in_delta?(self, other, 0.0)
-    end
-
-    # Equivalence checking (instance method version) .
-    # Return true when all the condition below are satisfied:
-    #       - same element identifier.
-    #       - difference of coordinates is within tolerance.
-    def equal_in_delta?(other, tol = 0.0)
-        self.class.equal_in_delta?(self, other, tol)
-    end
-
-    #Return Vector3DInternal instance consist of coordinates between 0 and 1.
-    def internal_coordinates
-        result = @position.map{ |coord| coord - coord.floor }
-        return Vector3DInternal[ *result ]
-    end
-
-    # Return Vector3DInternal instance consist of integers,
-    # by which self.internal_coordinates translate to self.position.
-    def translation_symmetry_operation
-        result = @position.map{ |coord| coord.floor }
-        return Vector3DInternal[ *result ]
-    end
-
-    # Overwrite position.
-    def set_position(position)
-        #pp position
-        #pp position.class
-        raise TypeError, "#{position.class}" if position.class == Vector3D
-        @position = position.to_v3di
-    end
-
-    # Translate atom position (destructive).
-    # Argument 'vec' should be given as internal vector,
-    # which is an Array or Vector3DInternal instance but Vector3D instance.
-    def translate!(vec)
-        raise TypeError if vec.class == Vector3D
-        raise TypeError if vec.size != 3
-        self.set_position(@position + Vector3DInternal[ *vec ])
-    end
-
-    # Translate atom position (nondestructive).
-    # Argument 'vec' should be given as internal vector,
-    # which is an Array or Vector3DInternal instance but Vector3D instance.
-    def translate(vec)
-        tmp = Marshal.load(Marshal.dump(self))
-        tmp.translate!(vec)
-        return tmp
+  include Mageo
+
+  class TypeError < StandardError ; end
+
+  # Do not change :position to attr_accessor.
+  # This must be Vector3DInternal instance.
+  attr_reader :movable_flags
+  attr_accessor :element, :name, :position
+
+  # Arguments:
+  #       elements:
+  #           Identifier of a element.
+  #           This may be String like "Li", Integer like 0, or other class instances.
+  #           Why doesn't this class have concrete name of elements?
+  #           The reason is below:
+  #               - This class is assumed to be used in Cell class instances.
+  #                   When we treat symmetry of the cell, the elements of atoms are not necessary information.
+  #                   This specification enable highly abstract level of treatment of cells.
+  #               - POSCAR file of VASP (before ver.4 series) don't have element information.
+  #                   This specification enable to use POSCAR directly without POTCAR or element indication.
+  #       position:
+  #           Coordinates of an atom.
+  #           This argument 'position' is mainly assumed as a internal coordinate.
+  #       name:
+  #           Identifier of an atom, e.g., "Li1" or "O23".
+  #       movable_flags: 
+  #           Movable flags of an atom in each of three directions as a Array of three items.
+  def initialize(element, position, name = nil, movable_flags = nil)
+    raise TypeError, "Position doesn't have []: (#{position.inspect})" unless position.methods.include?(:[])
+    raise TypeError, "Number of items in position is not 3: (#{position})" if position.size != 3
+    raise TypeError, "Coordinate is not a Float: (#{position})" if position[0].class != Float
+    raise TypeError, "Coordinate is not a Float: (#{position})" if position[1].class != Float
+    raise TypeError, "Coordinate is not a Float: (#{position})" if position[2].class != Float
+
+    @element = element
+    set_position(position)
+    @name = name
+    @movable_flags = movable_flags
+  end
+
+  ## Class methods
+
+  # Equivalence checking (class method version).
+  # Return true when all the condition below are satisfied:
+  #       - same element identifier.
+  #       - difference of coordinates is within tolerance.
+  # Note that distance cannot be used since this class doesn't have a lattice axes.
+  # Imagine the shape of tolerant zone is a hexahedron.
+  def self.equal_in_delta?(atom0, atom1, tol = 0.0)
+    return false if atom0.element != atom1.element
+    3.times do |i|
+      return false if ((atom0.position[i] - atom1.position[i]).abs > tol)
     end
+    return true
+  end
+
+  ## Instance methods
+
+  # Restricted equivalence checking.
+  # Return true when all the condition below are satisfied:
+  #       - same element identifier.
+  #       - difference of coordinates is the same.
+  # This method should be used after well-consideration.
+  # Arbitrary coordinates are not generally the same like Float instances.
+  # It is a good idea to use in test scripts.
+  def ==(other)
+    #pp self
+    #pp other
+    self.class.equal_in_delta?(self, other, 0.0)
+  end
+
+  # Equivalence checking (instance method version) .
+  # Return true when all the condition below are satisfied:
+  #       - same element identifier.
+  #       - difference of coordinates is within tolerance.
+  def equal_in_delta?(other, tol = 0.0)
+    self.class.equal_in_delta?(self, other, tol)
+  end
+
+  #Return Vector3DInternal instance consist of coordinates between 0 and 1.
+  def internal_coordinates
+    result = @position.map{ |coord| coord - coord.floor }
+    return Vector3DInternal[ *result ]
+  end
+
+  # Return Vector3DInternal instance consist of integers,
+  # by which self.internal_coordinates translate to self.position.
+  def translation_symmetry_operation
+    result = @position.map{ |coord| coord.floor }
+    return Vector3DInternal[ *result ]
+  end
+
+  # Overwrite position.
+  def set_position(position)
+    #pp position
+    #pp position.class
+    raise TypeError, "#{position.class}" if position.class == Vector3D
+    @position = position.to_v3di
+  end
+
+  # Translate atom position (destructive).
+  # Argument 'vec' should be given as internal vector,
+  # which is an Array or Vector3DInternal instance but Vector3D instance.
+  def translate!(vec)
+    raise TypeError if vec.class == Vector3D
+    raise TypeError if vec.size != 3
+    self.set_position(@position + Vector3DInternal[ *vec ])
+  end
+
+  # Translate atom position (nondestructive).
+  # Argument 'vec' should be given as internal vector,
+  # which is an Array or Vector3DInternal instance but Vector3D instance.
+  def translate(vec)
+    tmp = Marshal.load(Marshal.dump(self))
+    tmp.translate!(vec)
+    return tmp
+  end
 
 end