crysna 0.0.4

data/bin/siteoperation

@@ -0,0 +1,109 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "pp"
+require "yaml"
+require "optparse"
+require "rubygems"
+require "progressbar"
+require "crysna"
+
+TOLERANCE = 1E-10
+
+## option analysis
+om = Crysna::OptionManager.new([:model, :operation, :symmetry])
+om.parser.banner += "\n" + <<HERE
+Output yaml which includes from_site and to_site with symmetry operations.
+HERE
+#結晶中のサイトに全て名前がつけられていることを前提とする。
+#内部座標 i に対して、対称操作の rotation R と translation T を作用させる。
+#x = Ri + T
+
+om.parser.parse!(ARGV)
+options = om.options
+
+unless ARGV.size == 0
+  puts om.parser.banner, "Exit."
+  exit
+end
+
+
+
+mcell = Crysna::ModelStructure.load_file(options[:model])
+f_sites = mcell.frame_sites
+i_sites = mcell.ideal_interstitial_sites
+s_sites = mcell.scatter_sites
+
+log_io = File.open("siteoperations.log", "w")
+result_io = File.open(options[:operation], "w")
+results = []
+
+if options[:symmetry]
+  operations = YAML.load_file(options[:symmetry])
+else
+  operations = mcell.symmetry_operations
+end
+
+
+pbar = ProgressBar.new(
+  "siteoperations",
+  operations.size
+)
+
+operations.size.times do |i|
+  pbar.inc
+  ope = operations[i]
+  log_io.puts "Operation[#{i}]: #{ope["rotation"]}, #{ope["translation"]}"
+
+  ##finding
+  operation_id   = ope["operation_id"]
+  rotation = Matrix[* ope["rotation"]]
+  translation = Mageo::Vector3D[* ope["translation"]]
+
+  operation = {}
+  f_sites.each do |name, coordinates|
+    log_io.puts "Frame site: #{name}, #{coordinates}"
+
+    new_coord = rotation * coordinates + translation
+    new_site = mcell.find_nearest_frame_site(new_coord)
+    log_io.puts "    new_coord = #{new_coord}"
+    log_io.puts "    new_site = #{new_site.inspect}"
+
+    #operation[name] = [new_site[0], new_site[1].to_a]
+    operation[name] = [new_site[0], new_site[1].to_a, rotation.to_a]
+  end
+
+  i_sites.each do |name, coordinates|
+    log_io.puts "Interstitial site: #{name}, #{coordinates}"
+
+    new_coord = rotation * coordinates + translation
+    new_site =
+      mcell.select_interstitial_sites27(new_coord, TOLERANCE, log_io)[0]
+    log_io.puts "    new_coord = #{new_coord}"
+    log_io.puts "    new_site = #{new_site.inspect}"
+    operation[name] =
+      #[new_site.name, new_site.global_vector.to_a]
+      [new_site.name, new_site.global_vector.to_a, rotation.to_a]
+  end
+
+  s_sites.each do |name, coordinates|
+    log_io.puts "Scatter site: #{name}, #{coordinates}"
+
+    new_coord = rotation * coordinates + translation
+    new_site = mcell.find_site(new_coord, s_sites)
+    log_io.puts "    new_coord = #{new_coord}"
+    log_io.puts "    new_site = #{new_site.inspect}"
+
+    #operation[name] = [new_site[0], new_site[1].to_a]
+    operation[name] = [new_site[0], new_site[1].to_a, rotation.to_a]
+  end
+
+  item = {
+    "operation_id" => operation_id,
+    "operation" => operation
+  }
+  results << item
+end
+YAML.dump(results, result_io)
+
+log_io.close

data/bin/sitesingle

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+#! /usr/bin/env ruby
+# coding: utf-8
+
+## Output cells of not duplicated occupied site.
+
+require "pp"
+require "yaml"
+require "crysna"
+
+## option analysis
+om = Crysna::OptionManager.new([:combination, :single])
+om.parser.banner += "\n" +
+<<HERE
+  Default input  #{Crysna::OptionManager::DEFAULT_SITE_COMBINATION_FILE}
+  Default output #{Crysna::OptionManager::DEFAULT_SITE_SINGLE_FILE}
+HERE
+om.parser.parse!(ARGV)
+options = om.options
+
+
+cells = YAML.load_file(options[:combination])
+
+results = {}
+cells.each do |name, elems_sites|
+  cell = Crysna::Cell.new(elems_sites)
+  sitenames = cell.sites.values.flatten
+  num_sites = sitenames.size
+  next unless sitenames.uniq.size == num_sites
+  results[name] = elems_sites
+end
+pp results
+
+File.open(options[:single], "w") do |io|
+  YAML.dump(results, io)
+end
+

data/bin/siteuniq

@@ -0,0 +1,32 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "pp"
+require "yaml"
+require "crysna"
+
+## option analysis
+om = Crysna::OptionManager.new([:symid, :unique])
+om.parser.banner += "\n    Output minimum expression in occupied site names among symmetry operations"
+om.parser.on("-c"    , "--collective-yaml"    , "Deal input file as collective data."){    options[:collective] = true}
+
+om.parser.parse!(ARGV)
+options = om.options
+
+cells = YAML.load_file(options[:symid])
+
+results = {}
+uniq_cells = []
+cells.each do |name, elems_sites|
+  cell = Crysna::Cell.new(elems_sites)
+  next if uniq_cells.include? cell
+  uniq_cells << cell
+  results[name] = elems_sites
+end
+pp results
+
+#pp options[:unique]
+File.open(options[:unique], "w") do |io|
+  YAML.dump(results, io)
+end
+

data/bin/symidsite

@@ -0,0 +1,65 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+#
+require "rubygems"
+require "crysna"
+require "optparse"
+require "pp"
+
+
+PROGRAM_NAME = File.basename __FILE__
+LOG_FILE = "#{PROGRAM_NAME}.log"
+
+## option analysis
+om = Crysna::OptionManager.new([:occupied, :operation, :symid])
+om.parser.banner += "\n    Output minimum expression in occupied site names among symmetry operations"
+om.parser.on("-c"    , "--collective-yaml"    , "Deal input file as collective data."){    om.options[:collective] = true}
+om.parser.on("-q"    , "--quiet"    , "Supress verbose output."){    om.options[:quiet] = true}
+
+om.parser.parse!(ARGV)
+options = om.options
+
+#pp options; exit
+
+
+#unless ARGV.size == 2
+#    puts om.parser.banner, "Exit."
+#    exit
+#end
+
+yaml = YAML.load_file(options[:occupied])
+log_io = File.open(LOG_FILE, "w")
+
+if options[:collective]
+  configurations = yaml
+else
+  configurations = {"." => yaml}
+end
+
+#pp configurations
+
+## Normal process
+results = {}
+configurations.each do |name, conf|
+  log_io.puts "-"*60
+  log_io.puts name
+  log_io.puts conf
+  cell = Crysna::Cell.new(conf)
+  operations = YAML.load_file(options[:operation])
+
+  min_cell = cell.minimize(operations, log_io)
+  item = {}
+  min_cell.atoms.each do |atom|
+    item[atom.element] ||= []
+    item[atom.element] << atom.site.name
+  end
+  results[name] = item
+end
+
+#pp options[:symid]
+#pp results
+
+pp results unless options[:quiet]
+File.open(options[:symid], "w") do |io|
+  YAML.dump(results, io)
+end

data/bin/transitcell

@@ -0,0 +1,46 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "optparse"
+require "rubygems"
+require "crysna"
+require "yaml"
+
+## option analysis
+om = Crysna::OptionManager.new([:cells, :migration, :operation])
+om.parser.banner = <<HERE
+  Usage: #{File.basename("#{__FILE__}")} [options] start_cell_id
+HERE
+om.parser.parse!(ARGV)
+options = om.options
+
+# option analysis
+
+unless ARGV.size == 1
+  puts om.parser.banner
+  exit
+end
+
+raw_cells = YAML.load_file(options[:cells])
+migrations = YAML.load_file(options[:migration])
+operations = YAML.load_file(options[:operation])
+start = ARGV[0]
+
+dot_io    = File.open("transitcell.dot", "w")
+result_io = File.open("transitcell.out", "w")
+$log_io   = File.open("transitcell.log", "w")
+
+cells = []
+raw_cells.each do |name, cell|
+  cells << Crysna::TransitionFinder::Cell.new(cell["sites"], cell["toten"], name)
+end
+
+finder = Crysna::TransitionFinder.new(cells,
+                   migrations,
+                   operations)
+#現状では、2要素からなる配列を返すことを想定。
+#要素0、1 はそれぞれ起点から global_vector の異なる等価な状態に
+#到達するパスを表現する配列。
+#パスは Cell を要素とし、それぞれの previous でそこに至る操作を記録してる。
+#将来的には Path クラスかなんか用意するかもしれん。
+finder.find_path(start, nil, result_io, dot_io)

data/crysna.gemspec

@@ -0,0 +1,219 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: crysna 0.0.4 ruby lib
+
+Gem::Specification.new do |s|
+  s.name = "crysna"
+  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 = "2016-04-20"
+  s.description = "This gem provide a site analysis for crystal cell."
+  s.email = "ippei94da@gmail.com"
+  s.executables = ["checkmodel", "collectcell", "fitframe", "occupiedpolyhedralsite", "occupiedscattersite", "site2poscar", "site2pov", "sitecombination", "sitemigration", "sitemigrationdistance", "siteoperation", "sitesingle", "siteuniq", "symidsite", "transitcell"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "CHANGES",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/checkmodel",
+    "bin/collectcell",
+    "bin/fitframe",
+    "bin/occupiedpolyhedralsite",
+    "bin/occupiedscattersite",
+    "bin/site2poscar",
+    "bin/site2pov",
+    "bin/sitecombination",
+    "bin/sitemigration",
+    "bin/sitemigrationdistance",
+    "bin/siteoperation",
+    "bin/sitesingle",
+    "bin/siteuniq",
+    "bin/symidsite",
+    "bin/transitcell",
+    "crysna.gemspec",
+    "lib/crysna.rb",
+    "lib/crysna/atom.rb",
+    "lib/crysna/cell.rb",
+    "lib/crysna/frameatom.rb",
+    "lib/crysna/frameinterstitialcell.rb",
+    "lib/crysna/interstitialatom.rb",
+    "lib/crysna/modelstructure.rb",
+    "lib/crysna/optionmanager.rb",
+    "lib/crysna/site.rb",
+    "lib/crysna/siteconfiguration.rb",
+    "lib/crysna/sitenamelabeledcell.rb",
+    "lib/crysna/siteoperation.rb",
+    "lib/crysna/sitewithposition.rb",
+    "lib/crysna/transitionfinder.rb",
+    "lib/crysna/transitionfinder/cell.rb",
+    "lib/crysna/transitionfinder/cellmanager.rb",
+    "lib/crysna/transitionfinder/edge.rb",
+    "test/.gitignore",
+    "test/cell_orig/POSCAR",
+    "test/cell_orig/model.yaml",
+    "test/collectcells/.gitignore",
+    "test/collectcells/model.yaml",
+    "test/collectcells/nooutcar/minexpconfiguration.yaml",
+    "test/collectcells/normal-higher/OUTCAR",
+    "test/collectcells/normal-higher/minexpconfiguration.yaml",
+    "test/collectcells/normal-lower/OUTCAR",
+    "test/collectcells/normal-lower/minexpconfiguration.yaml",
+    "test/collectcells/normal/OUTCAR",
+    "test/collectcells/normal/minexpconfiguration.yaml",
+    "test/collectcells/normalB/OUTCAR",
+    "test/collectcells/normalB/minexpconfiguration.yaml",
+    "test/collectcells/unfinished/OUTCAR",
+    "test/collectcells/unfinished/minexpconfiguration.yaml",
+    "test/collectcells/unidentified/OUTCAR",
+    "test/collectcells/unidentified/minexpconfiguration.yaml",
+    "test/fitmodelstructure/.gitignore",
+    "test/fitmodelstructure/AgI/CONTCAR",
+    "test/fitmodelstructure/AgI/fitmodelstructure.log",
+    "test/fitmodelstructure/AgI/model.yaml",
+    "test/fitmodelstructure/normal/CONTCAR",
+    "test/fitmodelstructure/normal/fitmodelstructure.log",
+    "test/fitmodelstructure/normal/model.yaml",
+    "test/fitmodelstructure/unidentified/CONTCAR",
+    "test/fitmodelstructure/unidentified/fitmodelstructure.log",
+    "test/fitmodelstructure/unidentified/model.yaml",
+    "test/helper.rb",
+    "test/identifypolyhedralsites/.gitignore",
+    "test/identifypolyhedralsites/identifyatomsites.log",
+    "test/identifypolyhedralsites/normal/fitmodelstructure.yaml",
+    "test/identifypolyhedralsites/normal/model.yaml",
+    "test/identifypolyhedralsites/unidentified/fitmodelstructure.yaml",
+    "test/identifypolyhedralsites/unidentified/model.yaml",
+    "test/identifypolyhedralsites/volumemismatch/fitmodelstructure.yaml",
+    "test/identifypolyhedralsites/volumemismatch/model.yaml",
+    "test/identifyscattersites/CONTCAR",
+    "test/identifyscattersites/POSCAR",
+    "test/identifyscattersites/fitmodelstructure.log",
+    "test/identifyscattersites/fitmodelstructure.yaml",
+    "test/identifyscattersites/identifyscattersites.yaml",
+    "test/identifyscattersites/model.yaml",
+    "test/minexpconfiguration/.gitignore",
+    "test/minexpconfiguration/collective/AgI/.gitignore",
+    "test/minexpconfiguration/collective/AgI/siteoperations.yaml",
+    "test/minexpconfiguration/collective/AgI/sitesingle.yaml",
+    "test/minexpconfiguration/collective/AgI/test.sh",
+    "test/minexpconfiguration/normal/identifysites.yaml",
+    "test/minexpconfiguration/normal/minexpconfiguration.log",
+    "test/minexpconfiguration/normal/siteoperations.yaml",
+    "test/minexpconfiguration/unidentified/identifysites.yaml",
+    "test/minexpconfiguration/unidentified/siteoperations.yaml",
+    "test/sitecombination/initsites.yaml",
+    "test/sitecombination/initsites_test2.yaml",
+    "test/sitecombination/sitecombination.yaml",
+    "test/siteconfiguration/elements-sitenames.yaml",
+    "test/siteconfiguration/latticeaxes.yaml",
+    "test/siteconfiguration/sitenames-coordinates.yaml",
+    "test/sitemigrationsdistance/model.yaml",
+    "test/siteoperations/.gitignore",
+    "test/siteoperations/model.yaml",
+    "test/siteoperations/symmetryoperations.yaml",
+    "test/sitesingle/.gitignore",
+    "test/sitesingle/sitecombination.yaml",
+    "test/siteuniq/minexpconfiguration.yaml",
+    "test/siteuniq/siteuniq.yaml",
+    "test/test_atom.rb",
+    "test/test_cell.rb",
+    "test/test_commands.rb",
+    "test/test_crystana.rb",
+    "test/test_frameatom.rb",
+    "test/test_frameinterstitialcell.rb",
+    "test/test_interstitialatom.rb",
+    "test/test_modelstructure.rb",
+    "test/test_optionmanager.rb",
+    "test/test_site.rb",
+    "test/test_siteconfiguration.rb",
+    "test/test_sitenamelabeledcell.rb",
+    "test/test_siteoperation.rb",
+    "test/test_sitewithposition.rb",
+    "test/test_transitionfinder.rb",
+    "test/transitcell/.gitignore",
+    "test/transitcell/collectcells.yaml",
+    "test/transitcell/sitemigrations.yaml",
+    "test/transitcell/siteoperations.yaml",
+    "test/transitcell/transitcell.log",
+    "test/transitionfinder/collectcells.yaml",
+    "test/transitionfinder/sitemigrations.yaml",
+    "test/transitionfinder/siteoperations.yaml",
+    "test/transitionfinder/test_cell.rb",
+    "test/transitionfinder/test_cellmanager.rb",
+    "test/transitionfinder/test_edge.rb",
+    "test/uniquesitesgenerator/elements-sitenames.yaml",
+    "test/uniquesitesgenerator/siteoperations.yaml"
+  ]
+  s.homepage = "http://github.com/ippei94da/crysna"
+  s.licenses = ["MIT"]
+  s.rubygems_version = "2.5.1"
+  s.summary = "CRYstal Site aNAlyzser."
+
+  if s.respond_to? :specification_version then
+    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<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<progressbar>, ["~> 0.21"])
+      s.add_development_dependency(%q<ruby-graphviz>, ["~> 1.2"])
+      s.add_development_dependency(%q<mageo>, ["~> 0.0"])
+      s.add_development_dependency(%q<malge>, ["~> 0.0"])
+      s.add_development_dependency(%q<crystalcell>, ["~> 0.0"])
+      s.add_development_dependency(%q<builtinextension>, ["~> 0.1"])
+      s.add_development_dependency(%q<maset>, ["~> 0.0"])
+      s.add_development_dependency(%q<comana>, ["~> 0.0"])
+      s.add_development_dependency(%q<gnuplot>, ["~> 2.6"])
+      s.add_development_dependency(%q<vasputils>, ["~> 0.1"])
+    else
+      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<progressbar>, ["~> 0.21"])
+      s.add_dependency(%q<ruby-graphviz>, ["~> 1.2"])
+      s.add_dependency(%q<mageo>, ["~> 0.0"])
+      s.add_dependency(%q<malge>, ["~> 0.0"])
+      s.add_dependency(%q<crystalcell>, ["~> 0.0"])
+      s.add_dependency(%q<builtinextension>, ["~> 0.1"])
+      s.add_dependency(%q<maset>, ["~> 0.0"])
+      s.add_dependency(%q<comana>, ["~> 0.0"])
+      s.add_dependency(%q<gnuplot>, ["~> 2.6"])
+      s.add_dependency(%q<vasputils>, ["~> 0.1"])
+    end
+  else
+    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<progressbar>, ["~> 0.21"])
+    s.add_dependency(%q<ruby-graphviz>, ["~> 1.2"])
+    s.add_dependency(%q<mageo>, ["~> 0.0"])
+    s.add_dependency(%q<malge>, ["~> 0.0"])
+    s.add_dependency(%q<crystalcell>, ["~> 0.0"])
+    s.add_dependency(%q<builtinextension>, ["~> 0.1"])
+    s.add_dependency(%q<maset>, ["~> 0.0"])
+    s.add_dependency(%q<comana>, ["~> 0.0"])
+    s.add_dependency(%q<gnuplot>, ["~> 2.6"])
+    s.add_dependency(%q<vasputils>, ["~> 0.1"])
+  end
+end
+