poscar.rb in vasputils-0.0.12

- old
+ new

@@ -1,13 +1,11 @@
 #! /usr/bin/ruby
 
 require "rubygems"
-gem "crystalcell"
-require "crystalcell/cell.rb"
+#gem "crystalcell"
+require "crystalcell"
 
-require "vasputils.rb"
-
 # Class to manage POSCAR format of VASP.
 # 
 # parse と dump のどちらかだけでなく、両方を統括して扱うクラス。
 #
 # MEMO
@@ -18,167 +16,167 @@
 # こうしておくことで POTCAR がない環境でも POSCAR を扱うことができる。
 #
 # 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
+    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.
+    # 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
+        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 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
+            #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
+            # 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
+            # '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
+            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
+            # 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}
+            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)
+                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
-      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(" "))
+        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
 
-    # 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
+        # Element symbols for vasp 5.
+        if version >= 5
+            io.puts cell.atoms.map {|atom| atom.element}.uniq.join(" ")
+        end
 
-    elems.each do |elem|
-      elem_list[ elem ].each do |atom|
-        if atom.movable_flags
-          selective_dynamics = true
-          break
+        # Atom numbers.
+        elem_list = Hash.new
+        elems.each do |elem|
+            elem_list[ elem ] = cell.atoms.select{ |atom| atom.element == elem }
         end
-      end
-      break if selective_dynamics
-    end
+        io.puts(elems.map { |elem| elem_list[elem].size }.join(" "))
 
-    io.puts "Direct"
+        # 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
 
-    # 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"
+        elems.each do |elem|
+            elem_list[ elem ].each do |atom|
+                if atom.movable_flags
+                    selective_dynamics = true
+                    break
+                end
             end
-          end
+            break if selective_dynamics
         end
-        io.puts tmp
-      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"
+                        end
+                    end
+                end
+                io.puts tmp
+            end
+        end
     end
-  end
 
 end
 