pw 0.0.0 → 0.0.1

data/lib/cell/cell.rb

@@ -0,0 +1,31 @@
+require_relative "./lib/atom.rb"
+require_relative "../helper/numeric"
+require_relative "./lib/write"
+require_relative "./lib/boundary"
+require_relative "./lib/private"
+require_relative "./lib/redef"
+class Cell < Array
+  attr_reader :min, :max, :celldm, :units
+  def initialize params = {}
+    add_to_atoms params[:atoms] unless params[:atoms].nil?
+    params[:units].lowercase! if params[:units].is_a? String
+    @units = params[:units] || :crystal
+    @celldm = (@units == :crystal ? [1,1,1] : params[:celldm].dup) rescue @celldm = []
+    @realcelldm = (@units == :bohr ? params[:celldm].map{|v| v*0.52918} : params[:celldm]) rescue @realcelldm = []
+    @min = []
+    @max = []
+  end
+  def celldm= *args
+    arr = args.flatten
+    @celldm = (@units == :crystal ? [1,1,1] : arr)
+    @realcelldm = (@units == :bohr ? arr.map{|v| v*0.52918} : arr)
+    update_atoms_celldm
+  end
+  def units= unit
+    unit.lowercase! if unit.is_a? String
+    unit = unit.to_sym
+    return self if unit == @units
+    change_units unit
+    @units = unit
+  end
+end

data/lib/cell/lib/atom.rb

@@ -0,0 +1,54 @@
+class Atom
+  attr_accessor :uid, :fixed, :celldm
+  attr_reader :coor
+  def initialize params = {}
+    @name = params[:name].to_sym rescue @name = :X
+    @coor = params[:coor].dup rescue @coor = []
+    @uid = params[:uid] || nil
+    @fixed = params[:fixed]||false
+    @celldm = params[:celldm] || nil
+    # element = params[:element] ||  #TODO element constants. dont forget fixing dup
+  end
+  def coor= *c; @coor = c.flatten;end
+  def name= nm; @name = nm.to_sym; end
+  def name; @name.to_s; end
+  def x; @coor[0]; end
+  def y; @coor[1]; end
+  def z; @coor[2]; end
+  def x= num; @coor[0] = num; end
+  def y= num; @coor[1] = num; end
+  def z= num; @coor[2] = num; end
+  def move! *args
+    args.flatten!
+    args = args * 3 if args.length == 1
+    for i in 0..2;coor[i]+=args[i];end
+    return self
+  end
+  def move *args
+    a = self.dup
+    return a.move!(*args)
+  end
+  def to_s
+    l = (@fixed ? "  0  0  0" : "")
+    output = "%-4s%14.9f%14.9f%14.9f%s" % [@name, coor[0], coor[1], coor[2], l]
+    return output
+  end
+  def dup
+    Atom.new(:name => @name, :coor => @coor, :uid => @uid, :fixed => @fixed, :celldm => @celldm)
+  end
+  def dist other
+    if other.is_a? Atom
+      arr = other.coor
+    elsif other.is_a? Array and other.length = 3
+      arr = other
+    else
+      return nil
+    end
+    d = [] 
+    for i in 0..2
+      d.push (@coor[i] - arr[i]).abs
+      d[i] = @celldm[i] - d[i] if (!@celldm.nil? and d[i] > @celldm[i]/2) 
+    end
+    return (d[0]**2+d[1]**2+d[2]**2).sqrt
+  end
+end

data/lib/cell/lib/boundary.rb

@@ -0,0 +1,40 @@
+class Cell < Array
+  def dist x, y
+    $stderr.puts "Distance in crystal units is usually not meaningful!" if @units == :crystal
+    arr = wrap(0)
+    return arr[x].dist arr[y]
+  end
+  def wrap! tol = 0.5
+    self.each do |atom|
+      (0..2).each {|i| atom.coor[i] -= @celldm[i] while atom.coor[i] - @celldm[i] > tol}
+      (0..2).each {|i| atom.coor[i] += @celldm[i] while atom.coor[i] < -tol}
+    end
+    scan_mins_maxes
+    return self
+  end
+  def wrap tol = 0.5
+    arr = self.dup
+    return arr.wrap!(tol)
+  end
+  def move! *args
+    args.flatten!
+    args*=3 if args.length == 1
+    self.each do |atom|
+      atom.move! args
+    end
+    for i in 0..2;@max[i]+=args[i];@min[i]+=args[i];end
+    return self
+  end
+  def move *args
+    arr = self.dup
+    return arr.move! *args
+  end
+  def reset_order!
+    self.old_sort!{|x,y| x.uid <=> y.uid}
+    return self
+  end
+  def reset_order
+    arr = self.dup
+    return arr.reset_order!
+  end
+end

data/lib/cell/lib/private.rb

@@ -0,0 +1,80 @@
+class Cell < Array
+  private
+  def cell_bindings arg, i = self.length
+      arg.uid = i
+      arg.celldm = @celldm
+      return arg
+  end
+  def add_to_atoms args
+    args.each do |atom|
+      unless self << atom.dup
+        $stderr.puts "#{atom} is not an Atom"
+      end
+    end
+  end
+  def update_mins_maxes arg
+    for i in 0..2 
+      (@min[i] = arg[i] if @min[i] > arg[i]) rescue @min[i] = arg[i]
+      (@max[i] = arg[i] if @max[i] < arg[i]) rescue @max[i] = arg[i]
+    end
+  end
+  def update_atoms_celldm
+    self.each do |atom|
+      atom.celldm = @celldm
+    end
+  end
+  def scan_mins_maxes
+    @min = self[0].coor.dup
+    @max = self[0].coor.dup
+    self.each do |atom|
+      for i in 0..2 
+        (@min[i] = atom.coor[i] if @min[i] > atom.coor[i]) rescue @min[i] = atom.coor[i]
+        (@max[i] = atom.coor[i] if @max[i] < atom.coor[i]) rescue @max[i] = atom.coor[i]
+      end
+    end
+  end
+  def change_units unit
+    if unit == :crystal
+      self.map!{|atom| atom.coor = toCry(atom.coor);atom}
+      @max = toCry @max
+      @min = toCry @min
+      @celldm = [1,1,1]
+    elsif unit == :angstrom
+      @celldm = @realcelldm
+      if @units == :crystal
+        self.map!{|atom| atom.coor = fromCry(atom.coor);atom}
+        @max = fromCry @max
+        @min = fromCry @min
+      elsif @units == :bohr
+        self.map!{|atom| atom.coor = bhr2ang(atom.coor);atom}
+        @max = bhr2ang @max
+        @min = bhr2ang @min
+      end
+    elsif unit == :bohr
+      @celldm = @realcelldm.map{|v| v/0.52918}
+      if @units == :crystal
+        self.map!{|atom| atom.coor = fromCry(atom.coor);atom}
+        @max = fromCry @max
+        @min = fromCry @min
+      elsif @units == :angstrom
+        self.map!{|atom| atom.coor = ang2bhr(atom.coor);atom}
+        @max = ang2bhr @max
+        @min = ang2bhr @min
+      end
+    end
+  end
+  def toCry args
+    for i in 0..2; args[i]/=@celldm[i]; end rescue nil
+    return args
+  end
+  def fromCry args
+    for i in 0..2; args[i]*=@celldm[i]; end rescue nil
+    return args
+  end
+  def ang2bhr args
+    return args.map{|v| v / 0.52918}
+  end
+  def bhr2ang args
+    return args.map{|v| v * 0.52918}
+  end
+end

data/lib/cell/lib/redef.rb

@@ -0,0 +1,83 @@
+class Cell < Array
+  alias :old_sort! :sort!
+  def sort! fields, tol = 0.5
+    tol = [tol, tol, tol] unless tol.is_a? Array
+    self.old_sort! do |a, b|
+      g = fields.to_s.split(//)
+      t = a.name <=> b.name
+      x = a.x.approx_sort(b.x, tol[0])
+      y = a.y.approx_sort(b.y, tol[1])
+      z = a.z.approx_sort(b.z, tol[2])
+      result = 0
+      while result == 0 and g.length > 0
+        result = eval(g.shift)
+      end
+      result
+    end 
+    return self
+  end
+  def sort *args
+    arr = self.dup
+    return arr.sort!(*args)
+  end
+  alias :old_p :<<
+  def << arg
+    if arg.is_a?(Atom)
+      cell_bindings arg
+      update_mins_maxes arg.coor
+      self.old_p(arg.dup)
+    else false
+    end
+  end
+  alias :old_unshift :unshift
+  def unshift arg
+    if arg.is_a?(Atom)
+      cell_bindings arg, 0
+      self.each{|atom| atom.uid+=1}
+      update_mins_maxes arg.coor
+      self.old_unshift(arg.dup)
+    else false
+    end
+  end
+  alias :old_push :push
+  def push arg
+    if arg.is_a?(Atom)
+      cell_bindings arg
+      update_mins_maxes arg.coor
+      self.old_push(arg.dup)
+    else false
+    end
+  end
+  alias :old_insert :insert
+  def insert arg, index
+    if arg.is_a?(Atom)
+      cell_bindings arg, index
+      update_mins_maxes arg.coor
+      self.each do |atom|
+        atom.uid+=1 if atom uid >= index
+      end
+      self.old_insert(arg.dup, index)
+    else false
+    end
+  end
+  alias :old_plus :+
+  def + arg 
+      if arg.is_a?(Cell)
+        update_mins_maxes arg.min
+        update_mins_maxes arg.max
+        self.old_plus(arg)
+      else false
+      end
+  end
+  def dup
+    if @units ==  :bohr 
+      arr = Cell.new(:units => @units, :celldm => @celldm)
+    else
+      arr = Cell.new(:units => @units, :celldm => @realcelldm)
+    end
+    self.each do |atom|
+      arr << atom.dup
+    end
+    return arr 
+  end
+end

data/lib/cell/lib/write.rb

@@ -0,0 +1,31 @@
+class Cell < Array
+  def to_s
+    output = ""
+    self.each do |atom|
+      output += "%s\n" % atom.to_s
+    end
+    return output
+  end
+  def to_pdb
+    arr = (@units == :angstrom ? self : self.dup)
+    arr.units = :angstrom
+    output = "CRYST1%9.3f%9.3f%9.3f  90.00  90.00  90.00 P             1\n" % arr.celldm
+    i = 0
+    arr.each do |atom|
+      i += 1
+      output += "ATOM  %5d %-4s     X   1    %8.3f%8.3f%8.3f  1.00  1.00          %-2s\n" % ([i, atom.name] + atom.coor + [atom.name])
+    end
+    return output
+  end
+  def to_xyz
+    arr = (@units == :angstrom ? self : self.dup)
+    arr.units = :angstrom
+    output = "%d\n" % arr.length
+    output += "Cell Dimensions %10.6f %10.6f %10.6f\n" % arr.celldm
+    arr.each do |atom|
+      output += "%-2s  %10.6f %10.6f %10.6f\n" % ([atom.name] + atom.coor)
+    end
+    return output
+  end
+  # def to_cif
+end

data/lib/helper/array.rb

@@ -0,0 +1,24 @@
+class Array
+  def numbers!
+    i = length - 1
+    self.reverse_each do |elem|
+      if elem.is_a? Array
+        self[i] = elem.numbers!
+      else
+        elem.numeric? ? self[i] = Float(elem):self.delete_at(i)
+      end
+      i -= 1
+    end
+    return self
+  end
+  def numerify!
+    self.each_index do |i|
+      if self[i].is_a? Array
+        self[i] = self[i].numerify!
+      else
+        self[i] = Float(self[i]) if self[i].numeric?
+      end
+    end
+    return self
+  end
+end

data/lib/helper/numeric.rb

@@ -0,0 +1,30 @@
+class Numeric
+  (Math.methods - Module.methods - ["hypot", "ldexp"]).each do |method|
+    define_method method do
+      Math.send method, self
+    end
+  end
+  def approx_sort other, tol = self.to_f/10
+    d = self - other
+    if d > tol
+      return 1
+    elsif -d > tol
+      return -1
+    else 
+      return 0
+    end
+  end
+  def numeric?
+    true
+  end
+end
+class Object
+  def numeric?
+    false
+  end
+end
+class String
+  def numeric? 
+    Float(self) != nil rescue false
+  end
+end

data/lib/helper/object.rb

@@ -0,0 +1,24 @@
+class Object
+  def deep_clone
+    return @deep_cloning_obj if @deep_cloning
+    @deep_cloning_obj = clone
+    @deep_cloning_obj.instance_variables.each do |var|
+      val = @deep_cloning_obj.instance_variable_get(var)
+      begin
+        @deep_cloning = true
+        val = val.deep_clone
+      rescue TypeError
+        next
+      ensure
+        @deep_cloning = false
+      end
+      @deep_cloning_obj.instance_variable_set(var, val)
+    end
+    deep_cloning_obj = @deep_cloning_obj
+    @deep_cloning_obj = nil
+    deep_cloning_obj
+  end
+  def to_sym
+    self.to_s.to_sym
+  end
+end

data/lib/pw.rb

@@ -1,2 +1,50 @@
-module QE
+require_relative "./cell/cell"
+require "fileutil"
+require_relative "./helper/array.rb"
+
+class PW
+  def self.input ifile
+    cell = nil
+    File.open(ifile, 'r') do |f|
+      nat = f.ff(/nat/).readline.split(/[ ,]/).numbers![0]
+      celldm = []
+      while f.ff(/celldm/)
+        celldm.push f.readline.split(/[ ,]/).numbers!
+      end
+      celldm.map!{|v| v == celldm[0] ? v * 0.52918 : v * celldm[0]}
+      f.ff(/ATOMIC_POSITIONS/)
+      unit = unit? f.readline
+      cell = Cell.new(:celldm => celldm, :units => unit)
+      f.head(nat, true).map{|v| v.split.numerify!}.each do |atom|
+        cell << Atom.new(:name => atom[0], :coor => atom[1,4], :fixed => !atom[4].nil?)
+      end
+    end
+    return cell
+  end
+  def self.output ofile
+    cell = nil
+    File.open(ofile, 'r') do |f|
+      nat = f.ff(/number of atoms/).readline.split.numbers![0]
+      celldm = f.ff(/celldm/).readline.split.numbers!
+      celldm.map!{|v| v == celldm[0] ? v * 0.52918 : v * celldm[0]}
+      f.seek f.size
+      unit = unit? f.rew(/ATOMIC_POSITIONS/).readline
+      cell = Cell.new(:celldm => celldm, :units => unit)
+      f.head(nat, true).map{|v| v.split.numerify!}.each do |atom|
+        cell << Atom.new(:name => atom[0], :coor => atom[1,3], :fixed => !atom[4].nil?)
+      end
+    end
+    return cell
+  end
+  private
+  def self.unit? h
+    if /crystal/i =~ h
+      unit = :crystal
+    elsif /angstrom/i =~ h
+      unit = :angstrom
+    elsif /bohr/i =~ h
+      unit = :bohr
+    end
+    return unit
+  end
 end

metadata

@@ -1,15 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: pw
 version: !ruby/object:Gem::Version
-  version: 0.0.0
   prerelease: 
+  version: 0.0.1
 platform: ruby
 authors:
 - Sencer Selcuk
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-12 00:00:00.000000000 Z
+date: 2013-02-04 00:00:00.000000000 Z
 dependencies: []
 description: Quantum Espresso
 email: sencerselcuk@twitter
@@ -17,7 +17,16 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- lib/cell/lib/private.rb
+- lib/cell/lib/redef.rb
+- lib/cell/lib/boundary.rb
+- lib/cell/lib/write.rb
+- lib/cell/lib/atom.rb
+- lib/cell/cell.rb
 - lib/pw.rb
+- lib/helper/object.rb
+- lib/helper/numeric.rb
+- lib/helper/array.rb
 homepage: 
 licenses: []
 post_install_message: 
@@ -25,17 +34,17 @@ rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
+required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+  none: false
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.23
@@ -43,3 +52,4 @@ signing_key:
 specification_version: 3
 summary: will be implemented
 test_files: []
+has_rdoc: