lib/vasputils/poscar.rb in vasputils-0.0.10 vs lib/vasputils/poscar.rb in vasputils-0.0.11

@@ -41,53 +41,61 @@
       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 6: numbers of elements. e.g.,[1, 1, 2]
-      nums_elements = io.readline.strip.split( /\s+/ ).map{|i| i.to_i}
+      # 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
 
-      #line 7-(8): 'Selective dynamics' or not (bool)
+      # '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
+      if (line =~ /^\s*d/i) # allow only 'Direct' now
         direct = true
       else
         raise "Not 'direct' indication."
       end
 
-      #line 9(8): position
-      #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+/ )
+        items = io.readline.strip.split(/\s+/)
         pos = items[0..2].map {|coord| coord.to_f}
-        #pp pos
 
         mov_flags = []
         if items.size >= 6 then
           items[3..5].each do |i|
-            ( i =~ /^t/i ) ? mov_flags << true : mov_flags << false
+            (i =~ /^t/i) ? mov_flags << true : mov_flags << false
           end
-          atoms << Atom.new(elem_index, pos, mov_flags)
+          atoms << Atom.new(elements[elem_index], pos, mov_flags)
         else
-          atoms << Atom.new(elem_index, pos)
+          atoms << Atom.new(elements[elem_index], pos)
         end
         end
       end
     rescue EOFError
       raise ParseError, "end of file reached"
     end
 
-    cell = Cell.new(axes, atoms )
+    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。
@@ -101,24 +109,30 @@
   # 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。
-  def self.dump(cell, elems, io)
+  # '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
 
     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]
+      io.printf("  % 18.15f  % 18.15f  % 18.15f\n", cell.axes[i][0], cell.axes[i][1], cell.axes[i][2]
       )
     end
 
-    # collect information
+    # 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(" "))
@@ -149,16 +163,16 @@
     # positions of atoms
     elems.each do |elem|
       elem_list[ elem ].each do |atom|
         tmp =  sprintf(
           "  % 18.15f  % 18.15f  % 18.15f",
-          * atom.position )
+          * 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"
+              (mov == true) ?  tmp += " T" : tmp += " F"
             end
           end
         end
         io.puts tmp
       end