crysna 0.0.4

data/bin/occupiedpolyhedralsite

@@ -0,0 +1,96 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "rubygems"
+require "crysna"
+require "yaml"
+require "pp"
+require "optparse"
+
+TOLERANCE = 1.0E-10
+PROGRAM_NAME = File.basename __FILE__
+LOG_FILE = "#{PROGRAM_NAME}.log"
+
+## option analysis
+om = Crysna::OptionManager.new([:model, :fitted, :occupied])
+om.parser.banner += "\n" + <<HERE
+Find site names of occupied interstitial sites.
+Default output: #{Crysna::OptionManager::DEFAULT_OCCUPIED_SITES_FILE}
+HERE
+om.parser.parse!(ARGV)
+options = om.options
+
+unless ARGV.size == 2
+  puts om.parser.banner, "Exit."
+  exit
+end
+
+
+model_cell_00 = Crysna::ModelStructure.load_file(ARGV[0])
+optimized_ficell = YAML.load_file(ARGV[1])
+
+## If not identified structure
+if optimized_ficell.class == String
+  results = optimized_ficell
+  result_io = File.open(options[:occupied], "w")
+  YAML.dump(results, result_io)
+  exit
+end
+
+## Normal process.
+results = {}
+optimized_ficell["frame_atoms"].each do |name, atom|
+  elem = atom["element"]
+  results[elem] ||= []
+  results[elem] << name
+end
+
+frame_sites = {}
+optimized_ficell["frame_atoms"].each do |name, atom|
+  frame_sites[name] = Mageo::Vector3DInternal[*atom["coordinates"]]
+end
+
+hash = {
+  "frame_elements" => model_cell_00.frame_elements,
+  "symmetry_operations" => model_cell_00.symmetry_operations,
+  "octahedral_sites" => model_cell_00.octahedral_sites,
+  "tetrahedral_sites" => model_cell_00.tetrahedral_sites,
+  "frame_sites" => frame_sites
+}
+
+begin
+  model_cell = Crysna::ModelStructure.new(hash)
+rescue Crysna::ModelStructure::SiteVolumeError
+  results = "Volume mismatch."
+  result_io = File.open(options[:occupied], "w")
+  YAML.dump(results, result_io)
+  exit
+end
+
+log_io = File.open(LOG_FILE, "w")
+i_atoms = optimized_ficell["interstitials"]
+
+pbar = ProgressBar.new( __FILE__, i_atoms.size)
+i_atoms.each_with_index do |atom, index|
+  log_io.puts "    atom #{index}; element #{atom["element"]}, coordinates #{atom["coordinates"].to_s}"
+  pbar.inc
+
+  elem = atom["element"]
+  coord = atom["coordinates"]
+  results[elem] ||= []
+  begin
+    results[elem] << model_cell.find_interstitial_site(coord, TOLERANCE, log_io)
+  rescue Crysna::ModelStructure::SiteDetectionError
+    results = "Interstitial site detection error."
+    result_io = File.open(options[:occupied], "w")
+    YAML.dump(results, result_io)
+    exit
+  end
+end
+pbar.finish
+log_io.close
+
+results.each { |elem, sites| sites.sort! }
+
+result_io = File.open(options[:occupied], "w")
+YAML.dump(results, result_io)

data/bin/occupiedscattersite

@@ -0,0 +1,77 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "rubygems"
+require "crysna"
+require "yaml"
+require "pp"
+require "optparse"
+
+TOLERANCE = 1.0E-10
+PROGRAM_NAME = File.basename __FILE__
+LOG_FILE = "#{PROGRAM_NAME}.log"
+
+## option analysis
+om = Crysna::OptionManager.new([:model, :fitted, :occupied])
+om.parser.banner += "\n    Identify occupied interstitial sites in fitted_structure using model_structure."
+om.parser.parse!(ARGV)
+options = om.options
+
+unless ARGV.size == 0
+  puts om.parser.banner, "Exit."
+  exit
+end
+
+model_cell_00 = Crysna::ModelStructure.load_file(options[:model])
+optimized_ficell = YAML.load_file(options[:fitted])
+
+## Normal process.
+results = {}
+optimized_ficell["frame_atoms"].each do |name, atom|
+  elem = atom["element"]
+  results[elem] ||= []
+  results[elem] << name
+end
+
+frame_sites = {}
+optimized_ficell["frame_atoms"].each do |name, atom|
+  frame_sites[name] = Mageo::Vector3DInternal[*atom["coordinates"]]
+end
+
+hash = {
+  "frame_elements" => model_cell_00.frame_elements,
+  "symmetry_operations" => model_cell_00.symmetry_operations,
+  "scatter_sites" => model_cell_00.scatter_sites,
+  "frame_sites" => frame_sites
+}
+
+begin
+  model_cell = Crysna::ModelStructure.new(hash)
+rescue Crysna::ModelStructure::SiteVolumeError
+  results = "Volume mismatch."
+  result_io = File.open(options[:occupied], "w")
+  YAML.dump(results, result_io)
+  exit
+end
+
+log_io = File.open(LOG_FILE, "w")
+i_atoms = optimized_ficell["interstitials"]
+s_sites = model_cell.scatter_sites
+
+pbar = ProgressBar.new( PROGRAM_NAME, i_atoms.size)
+i_atoms.each_with_index do |atom, index|
+  log_io.puts "    atom #{index}; element #{atom["element"]}, coordinates #{atom["coordinates"].to_s}"
+  pbar.inc
+
+  elem = atom["element"]
+  coord = atom["coordinates"]
+  results[elem] ||= []
+  results[elem] << model_cell.find_site(coord, s_sites)[0]
+end
+pbar.finish
+log_io.close
+
+results.each { |elem, sites| sites.sort! }
+
+result_io = File.open(options[:occupied], "w")
+YAML.dump(results, result_io)

data/bin/site2poscar

@@ -0,0 +1,66 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+# Generate POSCAR from sitename info and coordinates.
+#
+require "optparse"
+require "pp"
+require "crysna"
+require "vasputils"
+
+## option analysis
+om = Crysna::OptionManager.new([:cells, :model])
+om.parser.banner = <<HERE
+#{om.parser.banner}
+Example: #{File.basename("#{__FILE__}")} --model=model.yaml --lattice='4.0,5.0,6.0,90.0,90.0,120.0' --cells=cells.yaml",
+--model, --lattice, and --cells options are necessary.",
+string parts in --lattice option correspond to 'a,b,c,alpha,beta,gama'.",
+HERE
+
+om.parser.on("-m val", "--model=val", "model.yaml"){|str|
+  om.options[:model] = Crysna::ModelStructure.load_file(str)
+}
+om.parser.on("-l val", "--lattice=val", "Lattice constants of 6 values."){|str|
+  lc = str.split(",").map{|digit| digit.to_f}
+  om.options[:axes] = CrystalCell::LatticeAxes.lc_to_axes( lc )
+}
+om.parser.parse!(ARGV)
+options = om.options
+
+unless options[:model] && options[:axes] && options[:cells]
+  # if any is empty
+  puts om.parser.banner
+  exit
+end
+
+mc = options[:model]
+sitenames_coordinates =mc.frame_sites.merge(mc.ideal_interstitial_sites).merge(mc.scatter_sites)
+
+dirs_confs = YAML.load_file options[:cells]
+
+dirs_confs.each do |key, sites|
+  hash = {}
+  hash[:comment           ] = key
+  hash[:scale             ] = 1.0
+  hash[:axes              ] = options[:axes]
+  hash[:direct            ] = true
+  hash[:selective_dynamics] = false
+  hash[:elements          ] = sites.keys
+  hash[:nums_elements     ] = sites.values.map{|i| i.size}
+  hash[:positions         ] = sites.values.flatten.map do |site|
+    sitenames_coordinates[site]
+  end
+  poscar = VaspUtils::Poscar.new(hash)
+
+  if File.exist? key
+    puts "Already exist: #{key}"
+    next
+  else
+    Dir.mkdir key
+    File.open("#{key}/POSCAR", "w") do |io|
+      poscar.dump(io)
+    end
+  end
+
+end
+

data/bin/site2pov

@@ -0,0 +1,30 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+# サイトを描画するための pov 形式を標準出力に書き出す。
+# オプション以外の最初の引数は POSCAR/CONTCAR
+# それ以外の引数は書き出すサイト名。
+
+
+#require "pp"
+#require "yaml"
+#require "optparse"
+#require "crysna/modelcell.rb"
+#require "povrayutils/povrayobject.rb"
+
+unless ARGV.size >= 2
+  puts "Usage: site2pov model.yaml SITE_A [SITE_B...]"
+  exit
+end
+
+model_cell_file = ARGV.shift
+site_names = ARGV
+
+model_cell = ModelStructure::Cell.load_file(model_cell_file, false)
+model_cell.polyhedra.each do |name, polyhedron|
+  if site_names.include?(name)
+    polyhedron.triangles.each do |triangle|
+      puts triangle.to_pov([1.0, 0.0, 0.0])
+    end
+  end
+end

data/bin/sitecombination

@@ -0,0 +1,69 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "pp"
+require "yaml"
+require "crysna"
+
+#IN_FILE  = Crysna::OptionManager::DEFAULT_SITE_CANDIDATE_FILE
+#OUT_FILE = Crysna::OptionManager::DEFAULT_SITE_COMBINATION_FILE
+
+## option analysis
+om = Crysna::OptionManager.new([:candidate, :combination])
+om.parser.banner += "\n" +
+<<HERE
+  Default input  #{Crysna::OptionManager::DEFAULT_SITE_CANDIDATE_FILE}
+  Default output #{Crysna::OptionManager::DEFAULT_SITE_COMBINATION_FILE}
+HERE
+om.parser.parse!(ARGV)
+options = om.options
+
+def combination_array(ary)
+  if ary.size == 1
+    return ary[0].map{|item| [item]}
+  end
+
+  item_1st = ary.shift
+  sub_ary = combination_array(ary)
+  result = []
+  item_1st.each do |item|
+    sub_ary.each do |sub_item|
+      result << [item, *sub_item]
+    end
+  end
+  return result
+end
+
+elem_sites = YAML.load_file(options[:candidate])   # パース
+
+elems = {}
+elem_sites.each do |elem, atoms|
+  elems[elem] = atoms.size
+end
+
+sites_combinations = []
+elem_sites.each do |elem, combinations|
+  combinations.each do |combi|
+    sites_combinations << combi
+  end
+end
+# [[["1A", "2A"], ["1B", "2B"], ["1C", "2C"]], [["IA"], ["IB", "2X"]]]
+
+combinations = combination_array( sites_combinations )
+
+max = combinations.size
+num_figure = max.to_s.size
+
+results = {}
+combinations.size.times do |i|
+  name = sprintf("%0#{num_figure}d", i )
+  combi = combinations[i]
+  elems_sitenames = Crysna::Cell.new_elems_sitenames(elems, combi).sites
+  results[name] = elems_sitenames
+end
+pp results
+
+File.open(options[:combination], "w") do |io|
+  YAML.dump(results, io)
+end
+

data/bin/sitemigration

@@ -0,0 +1,80 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+# 結晶中のサイト同士の位置関係を解析し、
+# 移動可能な組を yaml 形式で出力する。
+
+require "optparse"
+require "rubygems"
+require "progressbar"
+require "crysna"
+
+
+TOLERANCE = 1.0E-10
+
+## option analysis
+om = Crysna::OptionManager.new([:model, :fitted, :migration])
+om.parser.banner += "\n" +
+<<HERE
+    Default output sitemigration.yaml and sitemigration.dot .
+HERE
+om.parser.on("-n val", "--number=val", "Indicate the least number of shared vertices."){|v| om.options[:number] = v.to_i}
+om.parser.parse!(ARGV)
+options = om.options
+
+unless options[:number]
+  puts om.parser.banner
+  exit
+end
+
+unless ARGV.size == 0
+  puts om.parser.banner
+  exit
+end
+
+model_cell = Crysna::ModelStructure.load_file(options[:model])
+polyhedra = model_cell.polyhedra
+names = polyhedra.keys
+
+dot_io = File.open("sitemigration.dot", "w")
+dot_io.puts "graph sample {"
+bi_results = {}
+
+pbar = ProgressBar.new("sitemigration", names.size * (names.size - 1) / 2)
+
+names.combination(2).each do |name0, name1|
+  pbar.inc
+
+  ## finding
+  (-1).upto(1) do |a|
+    (-1).upto(1) do |b|
+      (-1).upto(1) do |c|
+        p0 = polyhedra[name0]
+        p1 = polyhedra[name1].translate(Mageo::Vector3D[-a, -b, -c])
+        if p0.shared_vertices(p1, TOLERANCE).size >= options[:number]
+          #for yaml
+          bi_results[name0] ||= []
+          bi_results[name0] << [name1, [a,b,c]]
+          bi_results[name1] ||= []
+          bi_results[name1] << [name0, [-a,-b,-c]]
+
+          #for dot
+          g_vec = [a, b, c].to_s
+          #g_vec = "" if [a, b, c] == [0, 0, 0]
+
+          #dot_io.puts "  #{name0} -- #{name1}[headlabel = \"#{g_vec}\"];"
+          dot_io.print "  #{name0} -- #{name1}"
+          dot_io.print " [headlabel = \"#{g_vec}\"];" unless [a, b, c] == [0, 0, 0]
+          dot_io.puts
+        end
+      end
+    end
+  end
+end
+dot_io.puts "}"
+
+File.open(options[:migration], "w") do |io|
+  YAML.dump(bi_results, io)
+end
+
+puts

data/bin/sitemigrationdistance

@@ -0,0 +1,87 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "optparse"
+require "rubygems"
+require "progressbar"
+#require "mageo"
+require "crysna"
+
+
+
+#TOLERANCE = 1.0E-10
+
+## option analysis
+#om = Crysna::OptionManager.new([:model, :fitted, :migration])
+om = Crysna::OptionManager.new([:model, :migration])
+om.parser.banner += "\n" + <<HERE
+Analyse relationship between sites in crystal,
+and output combination of movable sites with yaml format.
+HERE
+
+om.parser.on("-d val", "--distance=val", "Maximum distance."){|v| om.options[:distance] = v.to_f}
+om.parser.on("-l val", "--lattice=val", "Lattice constants."){|v| om.options[:lattice] = v}
+om.parser.parse!(ARGV)
+options = om.options
+
+if options[:lattice]
+  latticeconstants = options[:lattice].split(",").map{|str| str.to_f}
+  #pp latticeconstants
+  axes = CrystalCell::LatticeAxes.new_lc(latticeconstants)
+else
+  puts "No lattice constants."
+  puts "Indicate, e.g., --lattice='1.0,2.0,3.0,90.0,90.0,90.0'"
+  exit
+end
+
+if ARGV.size != 0 || (! options[:distance])
+  puts om.parser.banner
+  exit
+end
+
+model_cell = Crysna::ModelStructure.load_file(options[:model])
+s_sites = model_cell.scatter_sites
+
+names = s_sites.keys
+
+dot_io = File.open("sitemigration.dot", "w")
+dot_io.puts "graph sample {"
+bi_results = {}
+
+pbar = ProgressBar.new("sitemigration", names.size * (names.size - 1) / 2)
+
+names.combination(2).each do |name0, name1|
+  pbar.inc
+  ## finding
+  (-1).upto(1) do |a|
+    (-1).upto(1) do |b|
+      (-1).upto(1) do |c|
+        p0 = s_sites[name0].to_v3di.to_v3d(axes)
+        p1 = (s_sites[name1].to_v3di + (Mageo::Vector3DInternal[a, b, c])).to_v3d( axes)
+
+        distance = (p0 - p1).r
+        if distance < options[:distance]
+          bi_results[name0] ||= []
+          bi_results[name0] << [name1, [a,b,c]]
+          bi_results[name1] ||= []
+          bi_results[name1] << [name0, [-a,-b,-c]]
+          #for dot
+          g_vec = [a, b, c].to_s
+          #g_vec = "" if [a, b, c] == [0, 0, 0]
+
+          #dot_io.puts "  #{name0} -- #{name1}[headlabel = \"#{g_vec}\"];"
+          dot_io.print "  #{name0} -- #{name1}"
+          dot_io.print " [headlabel = \"#{g_vec}\"];" unless [a, b, c] == [0, 0, 0]
+          dot_io.puts
+        end
+      end
+    end
+  end
+end
+dot_io.puts "}"
+
+File.open(options[:migration], "w") do |io|
+  YAML.dump(bi_results, io)
+end
+
+puts