lib/vasputils/poscar.rb in vasputils-0.1.6 vs lib/vasputils/poscar.rb in vasputils-0.1.7

@@ -3,11 +3,11 @@
 
 require "rubygems"
 require "crystalcell"
 
 # 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。
 class VaspUtils::Poscar
 
   class ElementMismatchError < Exception; end
   class ParseError < Exception; end
@@ -128,24 +128,26 @@
       nums_elements[atom.element] += 1
     end
     nums_elements = elements.map{|elem| nums_elements[elem]}
 
     positions = []
-    movable_flags = []
+    #movable_flags = []
     selective_dynamics = false
     atoms.each do |atom|
       positions << atom.position
-      movable_flags << atom.movable_flags
-      selective_dynamics = true if movable_flags
+      #movable_flags << atom.movable_flags
+      #selective_dynamics = true if movable_flags
     end
 
-    selective_dynamics = movable_flags if movable_flags
+    #selective_dynamics = movable_flags if movable_flags
+    selective_dynamics = false
 
     options = {
       :comment            => cell.comment           ,
       :scale              => 1.0               ,
-      :axes               => cell.axes.to_a,
+      #:axes               => cell.axes.to_a,
+      :axes               => cell.axes,
       :elements           => elements          ,
       :nums_elements      => nums_elements     ,
       :selective_dynamics => selective_dynamics,
       :direct             => true,
       :positions          => positions             ,
@@ -162,11 +164,10 @@
   #
   # 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 dump(io, elements = nil, version = 5)
   def dump(io, version = 5)
-    elements = @elements unless elements
     elem_indices = elements.map {|elem| @elements.find_index(elem)}
     unless (Mapping::map?(@elements.uniq, elements){ |i, j| i == j })
         raise ElementMismatchError,
         "elements [#{elements.join(",")}] mismatches to cell.elements [#{cell.elements.join(",")}."
     end
@@ -210,11 +211,11 @@
         movable_flags = nil
         if @selective_dynamics
           movable_flags = @selective_dynamics[total_id]
         end
         atoms << CrystalCell::Atom.new(
-          element, 
+          element,
           @positions[total_id],
           movable_flags
         )
         total_id += 1
       end
@@ -272,21 +273,21 @@
     }
 
     VaspUtils::Poscar.new(hash)
   end
 
-  # 
+  #
   def ==(other)
     result = true
-    result = false unless @comment             == other.comment            
-    result = false unless @scale               == other.scale              
-    result = false unless @axes                == other.axes               
-    result = false unless @elements            == other.elements           
-    result = false unless @nums_elements       == other.nums_elements      
-    result = false unless @selective_dynamics  == other.selective_dynamics 
-    result = false unless @direct              == other.direct             
-    result = false unless @positions           == other.positions          
+    result = false unless @comment             == other.comment
+    result = false unless @scale               == other.scale
+    result = false unless @axes                == other.axes
+    result = false unless @elements            == other.elements
+    result = false unless @nums_elements       == other.nums_elements
+    result = false unless @selective_dynamics  == other.selective_dynamics
+    result = false unless @direct              == other.direct
+    result = false unless @positions           == other.positions
     result
   end
 
   def substitute(elem1, elem2)
     result = Marshal.load(Marshal.dump(self))
@@ -294,11 +295,11 @@
     result
   end
 
   def substitute!(elem1, elem2)
     @elements.map! do |elem|
-      if elem == elem1 
+      if elem == elem1
         elem2
       else
         elem
       end
     end
@@ -324,20 +325,19 @@
       val.each do |pos|
         @positions << pos
       end
     end
   end
-  
+
   def periodic_nearest(coord0, coord1)
     pcell = CrystalCell::PeriodicCell.new( [
       [1.0, 0.0, 0.0],
       [0.0, 1.0, 0.0],
       [0.0, 0.0, 1.0],
     ])
     result = coord1.to_v3di + pcell.nearest_direction( coord0.to_v3di, coord1.to_v3di)
     result.to_a
   end
-
 
   def interpolate_coords(coord0, coord1, ratio)
     ((coord0.to_v3d * (1-ratio) + coord1.to_v3d * ratio)).to_a
   end