crystalcell 0.0.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.1.3"
+  gem "jeweler", "~> 1.8.3"
+  gem "simplecov", ">= 0"
+  gem "mageo", ">= 0.0.0"
+  gem "malge", ">= 0.0.1"
+  gem "maset", ">= 0.0.0"
+  gem "builtinextension", ">= 0.0.3"
+end

data/LICENSE.txt

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+Copyright (c) 2012 ippei94da
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= crystalcell
+
+Description goes here.
+
+== Contributing to crystalcell
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2012 ippei94da. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "crystalcell"
+  gem.homepage = "http://github.com/ippei94da/crystalcell"
+  gem.license = "MIT"
+  gem.summary = %Q{Classes around a cell in crystallography}
+  gem.description = %Q{This gem provides Cell, LatticeAxes, Atom classes, and so on.
+    And this provides simple treatment of a periodic boundary condition.
+  }
+  gem.email = "ippei94da@gmail.com"
+  gem.authors = ["ippei94da"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |test|
+#  test.libs << 'test'
+#  test.pattern = 'test/**/test_*.rb'
+#  test.verbose = true
+#  test.rcov_opts << '--exclude "gems/*"'
+#end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "crystalcell #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.0

data/lib/crystalcell/atom.rb

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+
+raise "Atom class need ruby version later than 1.9." if RUBY_VERSION.to_f < 1.9
+
+
+require "rubygems"
+gem "mageo"
+require "mageo/vector3dinternal.rb"
+
+# Class for an atom in a cell.
+# This class doesn't have lattice information.
+# Forbid changes in internal information. When you want to change, you can make a new instance.
+# This class is not assumeed in a periodic condition.
+class Atom
+	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
+	end
+
+end
+