vasputils 0.0.9 → 0.0.10

data/VERSION

@@ -1 +1 @@
-0.0.9
+0.0.10

data/bin/checkvasp

@@ -6,14 +6,15 @@
 #require "vasputils/calcseries.rb"
 require "rubygems"
 gem "vasputils"
+require "vasputils.rb"
 
-require "vasputils/vaspgeomopt.rb"
-require "vasputils/vaspdir.rb"
+#require "vasputils/vaspgeomopt.rb"
+#require "vasputils/vaspdir.rb"
 require "pp"
 #require "optparse"
 
 LONGEST_STATE = :terminated.size
-KLASSES = [VaspDir, VaspGeomOpt]
+KLASSES = [VaspUtils::VaspDir, VaspUtils::VaspGeometryOptimizer]
 
 dirs = ARGV
 dirs = Dir.glob("*").sort if ARGV.empty?
@@ -42,7 +43,7 @@ dirs.each do |dir|
   printf "%-11s ", klass_name
 
   case klass_name
-  when "VaspDir"
+  when "VaspUtils::VaspDir"
     calc = klass.new(dir)
     printf "%-10s ", calc.state
     #pp calc.outcar
@@ -55,7 +56,7 @@ dirs.each do |dir|
       printf "%8s %3s (%3s) ", " "*8, " "*3, " "*3
     end
 
-  when "VaspGeomOpt"
+  when "VaspUtils::VaspGeometryOptimizer"
     calc = klass.new(dir)
     printf "%-10s ", calc.state
 

data/bin/latticeconstants

@@ -1,14 +1,19 @@
 #! /usr/bin/env ruby
 
-require "vasputils/poscar.rb"
-require "crystal/latticeaxes.rb"
-require "crystal/cell2.rb"
+require "rubygems"
+
+gem "vasputils"
+require "vasputils.rb"
+
+gem "crystalcell"
+require "crystalcell/latticeaxes.rb"
+require "crystalcell/cell.rb"
 
 puts "       a,        b,        c,  alpha,   beta,  gamma,     volume, file"
 ARGV.each do |file|
-	axes = Poscar.load_file(file).axes
-	printf("%8.5f, %8.5f, %8.5f, %6.2f, %6.2f, %6.2f, ",
-		*(axes.get_lattice_constants))
-	printf("%10.5f, ", Cell2.new(axes).calc_volume) # show volume
-	puts file
+  axes = VaspUtils::Poscar.load_file(file).axes
+  printf("%8.5f, %8.5f, %8.5f, %6.2f, %6.2f, %6.2f, ",
+    *(axes.get_lattice_constants))
+  printf("%10.5f, ", Cell.new(axes).calc_volume) # show volume
+  puts file
 end

data/bin/qsubvasp

@@ -25,8 +25,8 @@ gem "comana"
 require "comana/queuesubmitter.rb"
 require "comana/machineinfo.rb"
 
-require "vasputils/vaspdir.rb"
-require "vasputils/vaspgeomopt.rb"
+gem "vasputils"
+require "vasputils.rb"
 
 opts = {}
 
@@ -61,15 +61,15 @@ def condition_check(opts)
     begin
       conds["target"] = VaspGeomOpt.new(File.expand_path(ARGV[0]))
       conds["command"] = "runvasp -g"
-    rescue VaspGeomOpt::NoVaspDirError
+    rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
       puts "Seem not to be a directory for VaspGeomOpt #{ARGV}"
       exit
     end
   else
     begin
-      conds["target"] = VaspDir.new(File.expand_path(ARGV[0]))
+      conds["target"] = VaspUtils::VaspDir.new(File.expand_path(ARGV[0]))
       conds["command"] = "runvasp"
-    rescue VaspDir::InitializeError
+    rescue VaspUtils::VaspDir::InitializeError
       puts "Seem not to be a directory for VaspDir #{ARGV}"
       exit
     end

data/bin/rmvaspout

@@ -0,0 +1,40 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "optparse"
+
+require "fileutils"
+#require "rubygems"
+#gem "vasputils"
+require "vasputils"
+
+## option analysis
+OPTIONS = {}
+op = OptionParser.new
+op.on("-f"    , "--force"    , "Force to remove finished calc."){ OPTIONS[:force] = true}
+op.parse!(ARGV)
+
+ARGV.each do |tgt|
+  # Checking directory for normal VASP.
+  begin
+    vd = VaspUtils::VaspDir.new(tgt)
+  rescue VaspUtils::VaspDir.InitializeError
+    puts "Not VaspDir: #{tgt}"
+    next
+  end
+
+  # Delete
+  if OPTIONS[:force] || (! vd.finished?)
+    Dir.glob(tgt + "/*").each do |file|
+      next if file == tgt + "/INCAR"
+      next if file == tgt + "/KPOINTS"
+      next if file == tgt + "/POSCAR"
+      next if file == tgt + "/POTCAR"
+      puts "Deleting #{file}"
+      FileUtils.remove_entry_secure file
+    end
+  else
+    puts "Leave finished calc: #{tgt}"
+    next
+  end
+end

data/bin/runvasp

@@ -6,8 +6,7 @@ gem "comana"
 require "comana/computationmanager.rb"
 
 #gem "vasputils"
-require "vasputils/vaspdir.rb"
-require "vasputils/vaspgeomopt.rb"
+require "vasputils.rb"
 
 require "optparse"
 
@@ -27,8 +26,8 @@ end
 
 if opts[:geom]
   begin
-    calc_dir = VaspGeomOpt.new(dir)
-  rescue VaspGeomOpt::NoVaspDirError
+    calc_dir = VaspUtils::VaspGeomOpt.new(dir)
+  rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
     puts "Not suitable for VaspGeomOpt: #{dir}"
     exit
   end
@@ -36,8 +35,8 @@ elsif opts[:cond]
   TODO
 else
   begin
-    calc_dir = VaspDir.new(dir)
-  rescue VaspDir::InitializeError
+    calc_dir = VaspUtils::VaspDir.new(dir)
+  rescue VaspUtils::VaspDir::InitializeError
     puts "Not VaspDir: #{dir}"
     exit
   end

data/bin/symposcar

@@ -1,35 +1,39 @@
 #!/usr/bin/env ruby
-#   Copyright (C) 2008 Atsushi Togo
-#   togo.atsushi@gmail.com
+# Original version, Copyright (C) 2008 Atsushi Togo, togo.atsushi@gmail.com
+# Little modified by Ippei Kishida. [2012-06-12]
 #
-#   Little modified by Ippei Kishida. [2012-02-19]
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
 # 
-#   This program is free software; you can redistribute it and/or
-#   modify it under the terms of the GNU General Public License
-#   as published by the Free Software Foundation; either version 2
-#   of the License, or (at your option) any later version.
-#   
-#   This program is distributed in the hope that it will be useful,
-#   but WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#   GNU General Public License for more details.
-#   
-#   You should have received a copy of the GNU General Public License
-#   along with this program; if not, write to
-#   the Free Software Foundation, Inc., 51 Franklin Street,
-#   Fifth Floor, Boston, MA 02110-1301, USA, or see
-#   http://www.gnu.org/copyleft/gpl.html
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to
+# the Free Software Foundation, Inc., 51 Franklin Street,
+# Fifth Floor, Boston, MA 02110-1301, USA, or see
+# http://www.gnu.org/copyleft/gpl.html
 #
 # Usage: symPoscar.rb [OPTION] [structure]
 # OPTION: -s, --symprec= : Symmetry check precision
 
+require 'pp'
 require 'optparse'
 require 'getspg.so'
-require 'poscar'
-require 'pp'
 include Getspg
 
+#require 'rubygems'
+#gem 'vasputils'
+#require 'vasputils/poscar'
+require 'vasputils.rb'
+
+
 symprec = 1e-5
+angle_tolerance = -1.0
 nonewline = false
 pos_shift = [0,0,0]
 shift_string = false
@@ -38,6 +42,7 @@ is_operations = false
 is_dataset = false
 opt = OptionParser.new
 opt.on('-s', '--symprec=', 'Symmetry check precision') {|tmp| symprec = tmp.to_f}
+opt.on('-a', '--angle_tolerance=', 'Symmetry check precision for angle between lattice vectors in degrees') {|tmp| angle_tolerance = tmp.to_f}
 opt.on('-d', '--shift=', 'uniform shift of internal atomic positions') {|shift_string|}
 opt.on('-n', '--nonewline', 'Do not output the trailing newline') {nonewline = true}
 opt.on('-l', '--long', 'Long output') {is_long_output = true}
@@ -46,16 +51,18 @@ opt.on('-d', '--dataset', 'Dataset') {is_dataset = true}
 opt.parse!(ARGV)
 
 unless ARGV.size == 1
-	puts "Indicate only 1 POSCAR or CONTCAR. Exit."
-	exit
+  puts "Indicate only 1 POSCAR or CONTCAR. Exit."
+  exit
 end
 
 if shift_string
   pos_shift = []
   shift_string.split.each {|val| pos_shift << val.to_f }
 end
-cell = Vasp::Poscar.new(ARGV.shift).cell
-lattice = cell.axis.transpose
+
+cell = VaspUtils::Poscar.load_file(ARGV.shift)
+lattice = cell.axes.to_a.transpose
+
 names = (cell.atoms.collect {|atom| atom.name}).uniq
 position = []
 types = []
@@ -73,14 +80,16 @@ end
 
 if is_long_output
   spg, brv_lattice, brv_positions, brv_types, spgnum = 
-    refine_cell(types.size, lattice, position, types, symprec)
+    refine_cell(types.size, lattice, position, types, symprec, angle_tolerance)
 end
 
 spgnum, spg, hall_symbol, t_mat, o_shift,
 rotations, translations, wyckoffs = get_dataset( lattice,
                                                  position,
                                                  types,
-                                                 symprec )
+                                                 symprec,
+                                                 angle_tolerance)
+ptg_symbol, ptg_num, trans_mat = getptg(rotations)
 
 if spgnum > 0
   if nonewline
@@ -136,11 +145,12 @@ if is_operations
                                             lattice,
                                             position,
                                             types,
-                                            symprec )
+                                            symprec,
+                                            angle_tolerance)
 end
 
 
-if is_operations
+if is_operations or is_dataset
   rotations.size.times do |i|
     puts "- # ----#{i+1}----"
     puts "  rotation:"

data/lib/vasputils.rb

@@ -0,0 +1,11 @@
+module VaspUtils; end
+
+require "vasputils/incar.rb"
+require "vasputils/kpoints.rb"
+require "vasputils/outcar.rb"
+require "vasputils/poscar.rb"
+require "vasputils/potcar.rb"
+require "vasputils/vaspdir.rb"
+require "vasputils/vaspgeometryoptimizer.rb"
+require "vasputils/vaspkpointsfinder.rb"
+

data/lib/vasputils/incar.rb

@@ -1,6 +1,8 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
+require "vasputils.rb"
+
 # see http://cms.mpi.univie.ac.at/vasp/vasp/INCAR_File.html
 #
 # INCAR のフォーマット
@@ -17,7 +19,7 @@
 # Class to utilize INCAR file of VASP.
 # まず、自分で使う範囲だけ作る。
 # あとで余力があれば精密化する。
-module Incar
+module VaspUtils::Incar
   #
   #def initialize()
   #end

data/lib/vasputils/kpoints.rb

@@ -1,8 +1,10 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
+require "vasputils.rb"
+
 # Module dearing with KPOINTS.
-module Kpoints
+module VaspUtils::Kpoints
   def self.parse(io)
     results = {}
     results[:comment] = io.readline.chomp

data/lib/vasputils/outcar.rb

@@ -1,3 +1,5 @@
+require "vasputils.rb"
+
 # OUTCAR をパースする。
 # 精確には行わず、必要な情報だけをピックアップする感じ。
 #
@@ -9,50 +11,63 @@
 #
 # 基本的に終了した計算から情報を取り出すには vasprun.xml を読む。
 # OUTCAR は終了する前も含めてなんか簡単に見るために使う、という位置付けで。
-
-module Outcar
+module VaspUtils::Outcar
   #toten は全 electronic and ionic steps のを flat に並べただけのもの。
   #必要なら構造化するが、現状その予定はない。
   #attr_reader :name
   #attr_reader :ionic_steps, :electronic_steps, :totens, :volumes, :elapsed_time
 
   def self.load_file(file)
+    raise Errno::ENOENT unless File.exist?(file)
+
     results = {}
     results[:name] = file
-    results[:irreducible_kpoints] = nil
-    results[:electronic_steps   ] = 0
-    results[:ionic_steps        ] = 0
-    results[:totens             ] = []
-    results[:volumes            ] = []
+    #results[:irreducible_kpoints] = nil
+    #results[:electronic_steps   ] = 0
+    #results[:ionic_steps        ] = 0
+    #results[:totens             ] = []
+    #results[:volumes            ] = []
     results[:elapsed_time       ] = nil
     results[:normal_ended       ] = false
 
-    lines = File.readlines(file)
-    lines.each do |line|
-      if /Found\s+(\d+)\s+irreducible k-points/i =~ line
-        results[:irreducible_kpoints] = $1.to_i
-      end
-
-      if /^-* Iteration\s+(\d+)/ =~ line
-        results[:ionic_steps     ] = $1.to_i
-        results[:electronic_steps] += 1
-      end
-
-      #if /free\s+energy\s+TOTEN\s+=\s(.*)\s+eV/ =~ line
-      if /TOTEN\s+=\s(.*)\s+eV/ =~ line
-        results[:totens] << $1.to_f
-      end
-
-      if /volume of cell :\s+(\d+\.\d+)$/ =~ line
-        results[:volumes] << $1.to_f
-      end
-
-      if (/Elapsed time \(sec\):\s+(\d+\.\d+)/ =~ line)
-        results[:elapsed_time] = $1.to_f
-      end
+    #lines = File.readlines(file)
+    #lines.each do |line|
+    #  #if /Found\s+(\d+)\s+irreducible k-points/i =~ line
+    #  #  results[:irreducible_kpoints] = $1.to_i
+    #  #end
+
+    #  #if /^-* Iteration\s+(\d+)/ =~ line
+    #  #  results[:ionic_steps     ] = $1.to_i
+    #  #  results[:electronic_steps] += 1
+    #  #end
+
+    #  ##if /free\s+energy\s+TOTEN\s+=\s(.*)\s+eV/ =~ line
+    #  #if /TOTEN\s+=\s(.*)\s+eV/ =~ line
+    #  #  results[:totens] << $1.to_f
+    #  #end
+
+    #  #if /volume of cell :\s+(\d+\.\d+)$/ =~ line
+    #  #  results[:volumes] << $1.to_f
+    #  #end
+    #end
+
+    lines = `grep Iteration #{file}`.split("\n")
+    results[:electronic_steps] = lines.size
+    /^-* Iteration\s+(\d+)/ =~ lines[-1]
+    results[:ionic_steps     ] = $1.to_i
+
+    results[:totens] = `grep TOTEN #{file}`.split("\n").map do |line|
+      /TOTEN\s+=\s(.*)\s+eV/ =~ line
+      $1.to_f
+    end
+
+    line = `tail -q -n 8 #{file}| head -n 1`
+    if (/Elapsed time \(sec\):\s+(\d+\.\d+)/ =~ line)
+      results[:elapsed_time] = $1.to_f
     end
 
-    results[:normal_ended] = true if (/Voluntary context switches:/ =~ lines[-1])
+    line = `tail -q -n 1 #{file}`
+    results[:normal_ended] = true if (/Voluntary context switches:/ =~ line)
 
     results
   end

data/lib/vasputils/poscar.rb

@@ -4,6 +4,8 @@ require "rubygems"
 gem "crystalcell"
 require "crystalcell/cell.rb"
 
+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。
@@ -16,7 +18,7 @@ require "crystalcell/cell.rb"
 # 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 Poscar
+class VaspUtils::Poscar
 
   class ElementMismatchError < Exception; end
   class ParseError < Exception; end