crysna 0.0.4

data/lib/crysna.rb

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+require "rubygems"
+require "mageo"
+require "crystalcell"
+require "vasputils"
+require "progressbar"
+
+module Crysna; end
+
+require "crysna/frameatom"
+require "crysna/frameinterstitialcell"
+require "crysna/interstitialatom"
+require "crysna/site"
+require "crysna/atom"
+require "crysna/sitewithposition"
+require "crysna/siteconfiguration"
+require "crysna/modelstructure"
+require "crysna/cell"
+require "crysna/optionmanager"
+require "crysna/sitenamelabeledcell"
+require "crysna/siteoperation"
+require "crysna/transitionfinder"
+require "crysna/transitionfinder/cell"
+require "crysna/transitionfinder/cellmanager"
+require "crysna/transitionfinder/edge"
+#require "crysna/transitionfinder/edgemanager"
+#require "crysna/uniquesitesgenerator"

data/lib/crysna/atom.rb

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+#! /usr/bin/env ruby
+# coding: utf-8
+
+#Site with element info.
+#This doesn't have coordinates.
+#
+class Crysna::Atom
+  attr_reader :element
+  attr_reader :site
+
+  #
+  def initialize(element, sitename, global_vector)
+    @element = element
+    @site = Crysna::Site.new(sitename, global_vector)
+  end
+
+  def ==(other)
+    return false unless self.element == other.element
+    return false unless self.site == other.site
+    return true
+  end
+
+  def migrate!(site_name, global_vector)
+    new_gvec = @site.global_vector + global_vector.to_v3di
+    @site = Crysna::Site.new(site_name, new_gvec)
+  end
+
+  def migrate(site_name, global_vector)
+    result = Marshal.load(Marshal.dump(self))
+    result.migrate!(site_name, global_vector)
+    result
+  end
+
+  # Return center-migrate atom.
+  # Therefore, global_vector becomes [0,0,0]
+  def centering
+    result = Marshal.load(Marshal.dump(self))
+    result.centering!
+    result
+  end
+
+  # Destructive migrate to center cell.
+  # Therefore, global_vector becomes [0,0,0]
+  def centering!
+    self.migrate!(@site.name, @site.global_vector * (-1))
+  end
+
+
+  #Mainly for sort
+  def <=>(other)
+    flag = @element <=> other.element
+    return flag unless flag == 0
+
+    flag = @site.name <=> other.site.name
+    return flag unless flag == 0
+
+    flag = @site.global_vector[0] <=> other.site.global_vector[0]
+    return flag unless flag == 0
+
+    flag = @site.global_vector[1] <=> other.site.global_vector[1]
+    return flag unless flag == 0
+
+    flag = @site.global_vector[2] <=> other.site.global_vector[2]
+    return flag
+  end
+
+  ##Not-destructive method for site migration.
+  #def migrate(name, g_vector)
+  #    result = Marshal.load(Marshal.dump(self))
+  #    result.migrate!(name, g_vector)
+  #    return result
+  #end
+
+  ##Destructive method for site migration.
+  #def migrate!(name, g_vector)
+  #    @name = name
+  #    @global_vector.size.times do |i|
+  #        @global_vector[i] += g_vector[i]
+  #    end
+  #end
+
+  #Return site name. E.g., "B"
+  def sitename
+    @site.name
+  end
+
+  #Return site name with suffix as global vector with the manner of cif.
+  #E.g., "B555"
+  def full_sitename
+    result = sitename
+    @site.global_vector.each do |i|
+      result += (i+5).to_i.to_s
+    end
+    result
+  end
+end
+

data/lib/crysna/cell.rb

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+#! /usr/bin/env ruby
+# coding: utf-8
+
+#require "yaml"
+#require "crystal/cell2.rb"
+#require "crystal/atom2.rb"
+
+#
+# 常にソートされたものを返す。
+#
+class Crysna::Cell
+  include Comparable
+
+  #attr_reader :energy
+  #attr_reader :atoms
+  #alias to_hash sites
+
+  class DuplicateSiteError < Exception; end
+  class TypeError < Exception; end
+  class NoEntryError < Exception; end
+
+  # sites は element を鍵、サイト名リストを値としたハッシュ。
+  # e.g., sites = { 0 => ["S00", "S01"], 1 => ["S02", "S03"], }
+  #def initialize(sites, energy = nil)
+  def initialize(sites)
+    @atoms = []
+    sites.each do |elem, names|
+      names.each do |name|
+        @atoms << Crysna::Atom.new(elem, name, [0,0,0])
+      end
+    end
+  end
+
+  def self.load_file(file)
+    self.new(YAML.load_file(file))
+  end
+
+  # Generate new instance by POCAR style indication.
+  # elems is like {'Ag'=>2, 'I'=>2}$
+  # sitenames is like ['2A', '2B', 'IA', 'IA']
+  def self.new_elems_sitenames(elems, sitenames)
+    sites = {}
+    elems.each do |elem, num|
+      site_elem = []
+      num.times { site_elem << sitenames.shift}
+      sites[elem] = site_elem
+    end
+    sites
+    self.new(sites)
+  end
+
+  #Return sorted @atoms
+  def atoms
+    @atoms.sort!
+    @atoms
+  end
+
+  #Return internal data with format at initialize
+  # e.g., { 0 => ["S00", "S01"], 1 => ["S02", "S03"]}
+  def sites
+    results = {}
+    @atoms.each do |atom|
+      elem = atom.element
+      sitename = atom.site.name
+      results[elem] = [] unless results.has_key? elem
+      results[elem] << sitename
+    end
+    results
+  end
+
+
+  # element が占有するサイト site_name を追加する。
+  # dup_check を true にすると、
+  # サイト名が重複したときに例外 Crysna::Cell::DuplicateSiteError
+  # を生じる。
+  # dup_check を false にすると、このチェックが行われない。
+  def add_atom(element, site_name, global_vector, dup_check = false)
+    if dup_check
+      @atoms.each do |atom|
+        if atom.site.name == site_name
+          raise DuplicateSiteError,
+            "#{site_name} is already occupied in #{@sites.inspect}"
+        end
+      end
+    end
+
+    @atoms << Crysna::Atom.new(element, site_name, global_vector)
+    @atoms.sort!
+  end
+
+
+  # Execute symmetry operation.
+  # site_operation is a hash;
+  #       the key is old name,
+  #       and the value is an array of
+  #       [new_name, global_vector, rotation]
+  # matrix indicates operation to global vector.
+  def operate(site_operation)
+    #pp site_operation
+    @atoms.each do |atom|
+      #pp site_operation;exit
+      unless site_operation.keys.include?(atom.site.name)
+        raise NoEntryError, "#{atom.site.name} is not in #{site_operation.inspect}"
+      end
+    end
+
+    #result = Crysna::Cell.new({})
+    result = self.class.new({})
+    atoms.each do |atom|
+      op = site_operation[atom.site.name]
+      new_name, shift_vector, rotation = *op
+      pos =
+        Matrix[* rotation] * atom.site.global_vector +
+        Mageo::Vector3DInternal[* shift_vector]
+      new_vector = Mageo::Vector3DInternal[* pos] 
+
+      result.add_atom(atom.element, new_name, new_vector)
+    end
+
+    return result
+  end
+
+  def ==(other)
+    return false unless atoms.sort == other.atoms.sort
+    return true
+  end
+
+  # self に対して1つ原子を追加したときにありうる
+  # 全ての Crysna::Cell を配列にして返す。
+  # site_candidates は元素名を鍵、サイトリストを値としたハッシュ。
+  #
+  # dup_check は重複サイトチェック。
+  # 重複サイトに複数の原子が入る場合を判定する。
+  # dup_check が true    だと返される結果に該当項目が含まれない。
+  # dup_check が false だと返される結果に該当項目が含まれる。
+  # 
+  # site_candidates に含まれていないサイトが self に含まれていても
+  # エラーにはせず含まれたまま処理する。
+  def added_sites(site_candidates, dup_check = false)
+    results = []
+    site_candidates.each do |element, added_sites|
+      added_sites.each do |added_site|
+        site_config = Marshal.load(Marshal.dump(self))
+        begin
+          site_config.add_atom(element, added_site, [0, 0, 0], dup_check)
+        rescue DuplicateSiteError
+          next
+        end
+        results << site_config
+      end
+    end
+    return results
+  end
+
+  ## Return element list, which is unique and sorted.
+  def elements
+    @atoms.map{|atom| atom.element}.sort.uniq
+  end
+
+  def atoms_of_element(element)
+    results = []
+    atoms.each do |atom|
+      results << atom if atom.element == element
+    end
+    results.sort
+  end
+
+  # Destructive migrate all atoms to center cell.
+  # Therefore, global_vector becomes [0,0,0]
+  def centering!
+    @atoms.map! do |atom|
+      atom.centering
+    end
+    return self
+  end
+
+  # Return center-migrateed cell with  all atoms.
+  # Therefore, global_vector becomes [0,0,0]
+  def centering
+    result = Marshal.load(Marshal.dump(self))
+    result.centering!
+    result
+  end
+
+
+  # compare
+  # configuration_string で比較する。
+  ### old
+  ### 元素名ソートで若いものから優先して比較する。
+  ### Enumerable の min もしくは max メソッドで一意のものが導き出さ
+  ### れさえすれば良いので、大小の物理的な意味はあまり深く考えない。
+  ### 当面の基準は、以下:
+  ###       - 含まれる元素リストをソートした配列で比較し、
+  ###           違えばこれを返す。
+  ###           このチェックを通過したら含まれる元素は
+  ###           同じということになる。
+  ###       - 元素名でソートして番号の若いものから優先的に
+  ###           サイト名の配列で比較。
+  ###           違えばこれを返す。
+  ###           全ての元素について行う。
+  ###       - これらのチェックを通過すれば等しい。
+  def <=>(other)
+    self.configuration_string <=> other.configuration_string
+
+    ###self_tmp = self.centering
+    ###other_tmp = other.centering
+    ###raise TypeError unless other_tmp.is_a? Crysna::Cell
+    ###
+    ####pp self_tmp.configuration_string_full
+    ####pp other_tmp.configuration_string_full
+    ###
+    ###elems = (self_tmp.elements + other_tmp.elements).sort.uniq
+    ###
+    ###elems.each do |element|
+    ###    self_tmp_atoms = atoms_of_element(element)
+    ###    other_tmp_atoms = other_tmp.atoms_of_element(element)
+    ###
+    ###    flag = self_tmp_atoms.size <=> other_tmp_atoms.size
+    ###    #pp self_tmp_atoms.size
+    ###    #pp other_tmp_atoms.size
+    ###    return flag unless flag == 0
+    ###
+    ###    flag = self_tmp_atoms <=> other_tmp_atoms
+    ###
+    ###    return flag unless flag == 0
+    ###    self_tmp_atoms.size.times do |i|
+    ###        #pp self_tmp_atoms[i]
+    ###        #pp other_tmp_atoms[i]
+    ###        flag = self_tmp_atoms[i] <=> other_tmp_atoms[i]
+    ###        return flag unless flag == 0
+    ###    end
+    ###end
+    ###
+    ###return 0
+  end
+
+  #Return the cell which is the first in sort.
+  def minimize(operations, io = File.open(File::NULL, "w"))
+    min = self
+    io.puts "in Cell::minimize()"
+    operations.each do |ope|
+      id = ope['operation_id']
+      operation = ope['operation']
+
+      io.puts "operation_id: " + id.to_s
+      new = self.operate(operation)
+      new.atoms.each do |atom|
+        io.puts "#{atom.site.name}#{atom.site.global_vector.to_a}"
+      end
+      if new < min
+        min = new
+        io.puts "min is updated"
+      end
+
+      io.puts
+    end
+    return min
+  end
+
+  #Output yaml format.
+  #Note that global_vector is discarded.
+  def to_yaml
+    results = {}
+    atoms.each do |atom|
+      results[atom.element] ||= []
+      results[atom.element] << atom.site.name
+    end
+    YAML.dump(results)
+  end
+
+  # CrystalCell::Cell クラスインスタンスを返す。
+  # 引数 axes は格子ベクトルを絶対座標で表したもの。
+  # 引数 sites_coordinates はサイト名を鍵、内部座標を値とするハッシュ。
+  def to_cell(axes, sites_coordinates)
+    la = CrystalCell::LatticeAxes.new(axes)
+    cc_atoms = []
+    atoms.each do |atom|
+      cc_atoms << CrystalCell::Atom.new(atom.element, sites_coordinates[atom.site.name])
+    end
+    CrystalCell::Cell.new(la, cc_atoms)
+  end
+
+  def [](index)
+    atoms[index]
+  end
+
+  #Return string to which sitenames of atoms are joined.
+  #Ignoreing their elements.
+  #For example, "ABCD"
+  def configuration_string
+    #atoms.map do |atom|
+    #    atom.sitename
+    #end . join("")
+    result = elements.map do |elem|
+      "#{elem}:" +
+        atoms_of_element(elem).map {|atom| atom.sitename}.join("-")
+    end .join(",")
+    result
+  end
+
+  #Return string to which configuration_string_full of atoms are joined.
+  #Ignoreing their elements.
+  #For example, "A555-B455-C556-D555"
+  #Note: suffix of arabic number is the same manner of CIF indices.
+  def configuration_string_full
+    result = elements.map do |elem|
+      "#{elem}:" +
+        atoms_of_element(elem).map {|atom| atom.full_sitename}.join("-")
+    end .join(",")
+    result
+  end
+
+end
+

data/lib/crysna/frameatom.rb

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+#! /usr/bin/env ruby
+# coding: utf-8
+
+#require "crystal/atom2.rb"
+
+#
+# Class for frame atom.
+# This class is the same as CrystalCell::Atom, except for the class name.
+# This class is assumed to be used in FrameInterstitialCell.
+#
+class FrameAtom < CrystalCell::Atom
+end
+