vasputils 0.0.11 → 0.0.12

data/lib/vasputils/poscar.rb

@@ -1,10 +1,8 @@
 #! /usr/bin/ruby
 
 require "rubygems"
-gem "crystalcell"
-require "crystalcell/cell.rb"
-
-require "vasputils.rb"
+#gem "crystalcell"
+require "crystalcell"
 
 # Class to manage POSCAR format of VASP.
 # 
@@ -20,165 +18,165 @@ require "vasputils.rb"
 # VASP 5 系を使うようになれば事情が変わるだろう。
 class VaspUtils::Poscar
 
-  class ElementMismatchError < Exception; end
-  class ParseError < Exception; end
-
-  # io を読み込んで Cell クラスインスタンスを返す。
-  # 構文解析できなければ例外 Poscar::ParseError を投げる。
-  def self.parse(io)
-    # analyze POSCAR.
-
-    begin
-      #line 1: comment (string)
-      comment = io.readline.chomp
-
-      #line 2: universal scaling factor (float)
-      scale = io.readline.to_f
-      raise "Poscar.load_file cannot use negative scaling factor.\n" if scale < 0
-
-      #line 3-5: axes (3x3 Array of float)
-      axes = []
-      3.times do |i| #each axis of a, b, c.
-        vec = io.readline.strip.split(/\s+/) #in x,y,z directions
-        axes << vec.collect! { |i| i.to_f * scale } #multiply scaling factor
-      end
-
-      # Element symbol (vasp 5). Nothing in vasp 4.
-      #elements = io.readline.strip.split(/\s+/).map{|i| i.to_i}
-      vals = io.readline.strip.split(/\s+/)
-      if vals[0].to_i == 0
-        elements = vals
-        nums_elements = io.readline.strip.split(/\s+/).map{|i| i.to_i}
-      else
-        elements = []
-        vals.size.times { |i| elements << i }
-        nums_elements = vals.map{|i| i.to_i}
-      end
-
-      # 'Selective dynamics' or not (bool)
-      line = io.readline
-      if line =~ /^\s*s/i
-        selective_dynamics = true
-        line = io.readline    # when this situation, reading one more line is nessesarry
-      end
-
-      if (line =~ /^\s*d/i) # allow only 'Direct' now
-        direct = true
-      else
-        raise "Not 'direct' indication."
-      end
-
-      # atom positions
-      # e.g., positions_of_elements
-      # e.g., movable_flags_of_elements
-
-      atoms = []
-      nums_elements.size.times do |elem_index|
-        nums_elements[elem_index].times do |index|
-        items = io.readline.strip.split(/\s+/)
-        pos = items[0..2].map {|coord| coord.to_f}
-
-        mov_flags = []
-        if items.size >= 6 then
-          items[3..5].each do |i|
-            (i =~ /^t/i) ? mov_flags << true : mov_flags << false
-          end
-          atoms << Atom.new(elements[elem_index], pos, mov_flags)
-        else
-          atoms << Atom.new(elements[elem_index], pos)
-        end
+    class ElementMismatchError < Exception; end
+    class ParseError < Exception; end
+
+    # io を読み込んで Cell クラスインスタンスを返す。
+    # 構文解析できなければ例外 Poscar::ParseError を投げる。
+    def self.parse(io)
+        # analyze POSCAR.
+
+        begin
+            #line 1: comment (string)
+            comment = io.readline.chomp
+
+            #line 2: universal scaling factor (float)
+            scale = io.readline.to_f
+            raise "Poscar.load_file cannot use negative scaling factor.\n" if scale < 0
+
+            #line 3-5: axes (3x3 Array of float)
+            axes = []
+            3.times do |i| #each axis of a, b, c.
+                vec = io.readline.strip.split(/\s+/) #in x,y,z directions
+                axes << vec.collect! { |i| i.to_f * scale } #multiply scaling factor
+            end
+
+            # Element symbol (vasp 5). Nothing in vasp 4.
+            #elements = io.readline.strip.split(/\s+/).map{|i| i.to_i}
+            vals = io.readline.strip.split(/\s+/)
+            if vals[0].to_i == 0
+                elements = vals
+                nums_elements = io.readline.strip.split(/\s+/).map{|i| i.to_i}
+            else
+                elements = []
+                vals.size.times { |i| elements << i }
+                nums_elements = vals.map{|i| i.to_i}
+            end
+
+            # 'Selective dynamics' or not (bool)
+            line = io.readline
+            if line =~ /^\s*s/i
+                selective_dynamics = true
+                line = io.readline      # when this situation, reading one more line is nessesarry
+            end
+
+            if (line =~ /^\s*d/i) # allow only 'Direct' now
+                direct = true
+            else
+                raise "Not 'direct' indication."
+            end
+
+            # atom positions
+            # e.g., positions_of_elements
+            # e.g., movable_flags_of_elements
+
+            atoms = []
+            nums_elements.size.times do |elem_index|
+                nums_elements[elem_index].times do |index|
+                items = io.readline.strip.split(/\s+/)
+                pos = items[0..2].map {|coord| coord.to_f}
+
+                mov_flags = []
+                if items.size >= 6 then
+                    items[3..5].each do |i|
+                        (i =~ /^t/i) ? mov_flags << true : mov_flags << false
+                    end
+                    atoms << CrystalCell::Atom.new(elements[elem_index], pos, mov_flags)
+                else
+                    atoms << CrystalCell::Atom.new(elements[elem_index], pos)
+                end
+                end
+            end
+        rescue EOFError
+            raise ParseError, "end of file reached"
         end
-      end
-    rescue EOFError
-      raise ParseError, "end of file reached"
-    end
 
-    cell = Cell.new(axes, atoms)
-    cell.comment = comment
-    cell
-  end
-
-  # file で与えられた名前のファイルを読み込んで Cell クラスインスタンスを返す。
-  # 構文解析できなければ例外 Poscar::ParseError を投げる。
-  def self.load_file(file)
-    io = File.open(file, "r")
-    self.parse(io)
-  end
-
-  # POSCAR 形式で書き出す。
-  # cell は Cell クラスインスタンスと同等のメソッドを持つもの。
-  # elems は書き出す元素の順番。
-  #   elems が cell の持つ元素リストとマッチしなければ
-  #   例外 Poscar::ElementMismatchError を投げる。
-  # io は書き出すファイルハンドル。
-  # 'version' indicates a poscar style for vasp 4 or 5.
-  def self.dump(cell, elems, io, version = 5)
-    unless (Mapping::map?(cell.elements.uniq, elems){ |i, j| i == j })
-      raise ElementMismatchError,
-      "elems [#{elems.join(",")}] mismatches to cell.elements [#{cell.elements.join(",")}."
+        cell = CrystalCell::Cell.new(axes, atoms)
+        cell.comment = comment
+        cell
     end
 
-    io.puts cell.comment
-    io.puts "1.0" #scale
-    3.times do |i|
-      io.printf("  % 18.15f  % 18.15f  % 18.15f\n", cell.axes[i][0], cell.axes[i][1], cell.axes[i][2]
-      )
+    # file で与えられた名前のファイルを読み込んで CrystalCell::Cell クラスインスタンスを返す。
+    # 構文解析できなければ例外 Poscar::ParseError を投げる。
+    def self.load_file(file)
+        io = File.open(file, "r")
+        self.parse(io)
     end
 
-    # Element symbols for vasp 5.
-    if version >= 5
-      io.puts cell.atoms.map {|atom| atom.element}.uniq.join(" ")
-    end
+    # POSCAR 形式で書き出す。
+    # cell は CrystalCell::Cell クラスインスタンスと同等のメソッドを持つもの。
+    # elems は書き出す元素の順番。
+    #       elems が cell の持つ元素リストとマッチしなければ
+    #       例外 Poscar::ElementMismatchError を投げる。
+    # io は書き出すファイルハンドル。
+    # 'version' indicates a poscar style for vasp 4 or 5.
+    def self.dump(cell, elems, io, version = 5)
+        unless (Mapping::map?(cell.elements.uniq, elems){ |i, j| i == j })
+            raise ElementMismatchError,
+            "elems [#{elems.join(",")}] mismatches to cell.elements [#{cell.elements.join(",")}."
+        end
 
-    # Atom numbers.
-    elem_list = Hash.new
-    elems.each do |elem|
-      elem_list[ elem ] = cell.atoms.select{ |atom| atom.element == elem }
-    end
-    io.puts(elems.map { |elem| elem_list[elem].size }.join(" "))
-
-    # Selective dynamics
-    # どれか1つでも getMovableFlag が真であれば Selective dynamics をオンにする
-    selective_dynamics = false
-    cell.atoms.each do |atom|
-      if atom.movable_flags
-        selective_dynamics = true
-        io.puts "Selective dynamics"
-        break
-      end
-    end
+        io.puts cell.comment
+        io.puts "1.0" #scale
+        3.times do |i|
+            io.printf("  % 18.15f    % 18.15f    % 18.15f\n", cell.axes[i][0], cell.axes[i][1], cell.axes[i][2]
+            )
+        end
 
-    elems.each do |elem|
-      elem_list[ elem ].each do |atom|
-        if atom.movable_flags
-          selective_dynamics = true
-          break
+        # Element symbols for vasp 5.
+        if version >= 5
+            io.puts cell.atoms.map {|atom| atom.element}.uniq.join(" ")
+        end
+
+        # Atom numbers.
+        elem_list = Hash.new
+        elems.each do |elem|
+            elem_list[ elem ] = cell.atoms.select{ |atom| atom.element == elem }
+        end
+        io.puts(elems.map { |elem| elem_list[elem].size }.join(" "))
+
+        # Selective dynamics
+        # どれか1つでも getMovableFlag が真であれば Selective dynamics をオンにする
+        selective_dynamics = false
+        cell.atoms.each do |atom|
+            if atom.movable_flags
+                selective_dynamics = true
+                io.puts "Selective dynamics"
+                break
+            end
+        end
+
+        elems.each do |elem|
+            elem_list[ elem ].each do |atom|
+                if atom.movable_flags
+                    selective_dynamics = true
+                    break
+                end
+            end
+            break if selective_dynamics
         end
-      end
-      break if selective_dynamics
-    end
 
-    io.puts "Direct"
-
-    # positions of atoms
-    elems.each do |elem|
-      elem_list[ elem ].each do |atom|
-        tmp =  sprintf(
-          "  % 18.15f  % 18.15f  % 18.15f",
-          * atom.position)
-        if selective_dynamics
-          if atom.movable_flags == nil
-            tmp += " T T T"
-          else
-            atom.movable_flags.each do |mov|
-              (mov == true) ?  tmp += " T" : tmp += " F"
+        io.puts "Direct"
+
+        # positions of atoms
+        elems.each do |elem|
+            elem_list[ elem ].each do |atom|
+                tmp =    sprintf(
+                    "    % 18.15f    % 18.15f    % 18.15f",
+                    * atom.position)
+                if selective_dynamics
+                    if atom.movable_flags == nil
+                        tmp += " T T T"
+                    else
+                        atom.movable_flags.each do |mov|
+                            (mov == true) ?  tmp += " T" : tmp += " F"
+                        end
+                    end
+                end
+                io.puts tmp
             end
-          end
         end
-        io.puts tmp
-      end
     end
-  end
 
 end
 

data/lib/vasputils/potcar/concatenater.rb

@@ -7,31 +7,31 @@ require "pp"
 #
 #
 class VaspUtils::Potcar::Concatenater
-  class NoPotcarError < Exception; end
+    class NoPotcarError < Exception; end
 
-  # 'potcar_path' indicates a storage directory of POTCARs.
-  # 'elem_potcar' indicates a correspondence
-  # between element symbol and prior POTCAR as Hash.
-  def initialize(potcar_path, elem_potcar)
-    @potcar_path = potcar_path
-    @elem_potcar = elem_potcar
-  end
+    # 'potcar_path' indicates a storage directory of POTCARs.
+    # 'elem_potcar' indicates a correspondence
+    # between element symbol and prior POTCAR as Hash.
+    def initialize(potcar_path, elem_potcar)
+        @potcar_path = potcar_path
+        @elem_potcar = elem_potcar
+    end
 
-  # Concatenate POTCARs.
-  # Write to io if defined
-  # Return string if io is nil.
-  def dump(elements, io = nil)
-    result = elements.map { |elem|
-      raise NoPotcarError unless @elem_potcar.include? elem
-      filename = @potcar_path + "/" + @elem_potcar[elem] + "/POTCAR"
-      File.read filename
-    }.join("")
+    # Concatenate POTCARs.
+    # Write to io if defined
+    # Return string if io is nil.
+    def dump(elements, io = nil)
+        result = elements.map { |elem|
+            raise NoPotcarError unless @elem_potcar.include? elem
+            filename = @potcar_path + "/" + @elem_potcar[elem] + "/POTCAR"
+            File.read filename
+        }.join("")
 
-    if io # is defined
-      io.print result
-    else
-      return result
+        if io # is defined
+            io.print result
+        else
+            return result
+        end
     end
-  end
 end
 

data/lib/vasputils/potcar.rb

@@ -1,20 +1,20 @@
-require "vasputils.rb"
+#require "vasputils.rb"
 
 #
 # Class for dealing with POTCAR.
 #
 module VaspUtils::Potcar
-  def self.load_file(file)
-    results = {}
-    results[:name] = file
+    def self.load_file(file)
+        results = {}
+        results[:name] = file
 
-    elements = Array.new
-    File.open( file, "r" ).each do |line|
-      if line =~ /VRHFIN\s*=\s*([A-Za-z]*)/
-        elements << $1
-      end
+        elements = Array.new
+        File.open( file, "r" ).each do |line|
+            if line =~ /VRHFIN\s*=\s*([A-Za-z]*)/
+                elements << $1
+            end
+        end
+        results[:elements] = elements
+        results
     end
-    results[:elements] = elements
-    results
-  end
 end

data/lib/vasputils/setting.rb

@@ -2,33 +2,33 @@
 # coding: utf-8
 
 require 'yaml'
-require 'vasputils'
+#require 'vasputils'
 
 
 # Class to deal with private settings for VaspUtils.
 
 class VaspUtils::Setting
-  class NoEntryError < Exception; end
-
-  #
-  def initialize(file = ENV["HOME"] + "/.vasputils")
-    @data = YAML.load_file(file)
-  end
-
-  # Return value corresponding to a key.
-  # Raise VaspUtils::Setting::NoEntryError if the key is not exist.
-  def [](key)
-    unless @data.include? key 
-      raise NoEntryError, key
+    class NoEntryError < Exception; end
+
+    #
+    def initialize(file = ENV["HOME"] + "/.vasputils")
+        @data = YAML.load_file(file)
+    end
+
+    # Return value corresponding to a key.
+    # Raise VaspUtils::Setting::NoEntryError if the key is not exist.
+    def [](key)
+        unless @data.include? key 
+            raise NoEntryError, key
+        end
+        @data[key]
     end
-    @data[key]
-  end
-
-  #def get(key)
-  #  unless @data.include? key 
-  #    raise NoEntryError, key
-  #  end
-  #  @data[key]
-  #end
+
+    #def get(key)
+    #    unless @data.include? key 
+    #        raise NoEntryError, key
+    #    end
+    #    @data[key]
+    #end
 end