vasputils 0.0.11 → 0.0.12

data/CHANGES

@@ -1,48 +1,69 @@
 = vasputils changelog
 
-== Master (for 0.0.12)
+== Master (for 0.0.13)
+
+== Version 0.0.12 [2014-08-30] released
+  - Update bin/symposcar .
+  - Add options to bin/checkvasp and modified output format.
+  - Rename VaspGeomOpt to VaspGeometryOptimizer
+  - Add VaspGeometryOptimizer::reset_init
+  - Add VaspGeometryOptimizer::reset_next
+  - Add VaspGeometryOptimizer::reset_reincarnation
+  - Add bin/resetvaspgeompot
+  - Remove bin/nextvasp. Use bin/resetvaspgeomopt -n.
+  - Rename bin/setvaspdir to bin/resetvaspdir
+  - Remove optiions from bin/resetvaspdir
+  - Change prefix for subdir of VaspGeomOpt from "try" to "geomopt"
+  - Change indent width from 2 to 4.
+  - Add bin/varycondition and related libraries.
+  - Raise InitializeError when VaspGeometryOptimizer.new is failed.
+  - Divide bin/checkvasp to bin/showvaspdir and bin/showvaspgeomopt.
+  - Divide bin/runvasp to bin/runvaspdir and bin/runvaspgeomopt.
+  - Add some options to bin/showvaspdir
+  - Update dependency on other gems.
 
 == Version 0.0.11
-  Modify bin/qsubvasp
-  Add VaspUtils::generate_kmeshes
-  Add example/dot.vasputils
-  Add Setting class
-  Add Potcar::Concatenater
-  Add Incar.dump
-  Modify vasputils/poscar.rb to adjust vasp 5.2 style.
+  - Modify bin/qsubvasp
+  - Add VaspUtils::generate_kmeshes
+  - Add example/dot.vasputils
+  - Add Setting class
+  - Add Potcar::Concatenater
+  - Add Incar.dump
+  - Modify vasputils/poscar.rb to adjust vasp 5.2 style
+  - Renamed and modified bin/rmvaspout to bin/redovasp
+  - Add bin/nextvasp
 
 == Version 0.0.10
-  Delete Outcar.volume
-  Delete Outcar.irreducible_kpoints
-  Accelerate Outcar, using UNIX commands: grep, tail, and head
-  Modify bin/symposcar
-  Add bin/rmvaspout
-  Change name space for classes
+  - Delete Outcar.volume
+  - Delete Outcar.irreducible_kpoints
+  - Accelerate Outcar, using UNIX commands: grep, tail, and head
+  - Modify bin/symposcar
+  - Add bin/rmvaspout
+  - Change name space for classes
 
 == Version 0.0.9
-  Add VaspDir.poscar
-  Add bin/checkvasp
-  Delete bin/lsvasp, bin/lsvaspdir, bin/lsvaspseries
+  - Add VaspDir.poscar
+  - Add bin/checkvasp
+  - Delete bin/lsvasp, bin/lsvaspdir, bin/lsvaspseries
 
 == Version 0.0.8
-  Modified bin/qsubvasp, add -g option
+  - Modified bin/qsubvasp, add -g option
 
 == Version 0.0.7
-  Modified bin/qsubvasp
+  - Modified bin/qsubvasp
 
 == Version 0.0.6
-  bin/qsubvasp is added
-  lib/vaspdir is modified to raise ExecuteError when vasp failed
+  - bin/qsubvasp is added
+  - lib/vaspdir is modified to raise ExecuteError when vasp failed
 
 == Version 0.0.5
-  Modifiy error process in VaspDir.calculate
-  Add runvasp
-  Add qsubvasp
+  - Modifiy error process in VaspDir.calculate
+  - Add qsubvasp
 
 == Version 0.0.4
-  Modified to use Comana
-  bin/runvasp is added
-  VaspDir is modified
-  VaspGeomOpt is added
+  - Modified to use Comana
+  - bin/runvasp is added
+  - VaspDir is modified
+  - VaspGeomOpt is added
 
 == Version 0.0.3

data/Gemfile

@@ -6,14 +6,15 @@ source "http://rubygems.org"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rdoc", ">= 3.12"
-  gem "bundler", ">= 1.1.3"
-  gem "jeweler", ">= 1.8.3"
-  gem "simplecov", ">= 0"
-  gem "crystalcell", ">= 0.0.0"
-  gem "mageo", ">= 0.0.0"
-  gem "malge", ">= 0.0.1"
+  gem "rdoc", "~> 4.1.1"
+  gem "bundler", "~> 1.7.2"
+  gem "jeweler", "~> 2.0.1"
+  gem "simplecov", ">= 0.9.0"
+  gem "mageo", ">= 0.0.3"
+  gem "malge", ">= 0.0.8"
   gem "maset", ">= 0.0.0"
-  gem "comana", ">= 0.0.9"
-  gem "builtinextension", ">= 0.0.3"
+  gem "comana", ">= 0.0.10"
+  gem "builtinextension", ">= 0.1.2"
+  gem "crystalcell", ">= 0.0.2"
+  #gem "psych", ">= 0"
 end

data/VERSION

@@ -1 +1 @@
-0.0.11
+0.0.12

data/bin/checkvasp

@@ -1,80 +1,111 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
-# Show state of vasp geometry optimization calculations.
+puts "'checkvasp' is obsoleted. Use showvaspdir and showvaspgeomopt."
+exit
 
-#require "vasputils/calcseries.rb"
-require "rubygems"
-gem "vasputils"
-require "vasputils.rb"
-
-#require "vasputils/vaspgeomopt.rb"
-#require "vasputils/vaspdir.rb"
-require "pp"
+## Show state of vasp geometry optimization calculations.
+#
+##require "vasputils/calcseries.rb"
+#require "rubygems"
+#gem "vasputils"
+#require "vasputils.rb"
+#
+#require "pp"
 #require "optparse"
-
-LONGEST_STATE = :terminated.size
-KLASSES = [VaspUtils::VaspDir, VaspUtils::VaspGeometryOptimizer]
-
-dirs = ARGV
-dirs = Dir.glob("*").sort if ARGV.empty?
-
-def guess(dir)
-  KLASSES.each do |klass|
-    begin
-      vd = klass.new(dir)
-      return klass
-    rescue klass::InitializeError
-    end
-  end
-  raise "Cannot identify class for directory #{dir}."
-end
-
-dirs.each do |dir|
-  next unless File.directory? dir
-
-  begin
-    klass = guess(dir)
-    klass_name = klass.to_s
-  rescue 
-    klass_name = "UnknownDir"
-  end
-
-  printf "%-11s ", klass_name
-
-  case klass_name
-  when "VaspUtils::VaspDir"
-    calc = klass.new(dir)
-    printf "%-10s ", calc.state
-    #pp calc.outcar
-    printf "%5s ", ""
-    begin
-      outcar = calc.outcar
-      printf "%8.3f %3d (%3d) ",
-        outcar[:totens][-1], outcar[:ionic_steps], outcar[:electronic_steps]
-    rescue
-      printf "%8s %3s (%3s) ", " "*8, " "*3, " "*3
-    end
-
-  when "VaspUtils::VaspGeometryOptimizer"
-    calc = klass.new(dir)
-    printf "%-10s ", calc.state
-
-    ld = calc.latest_dir
-    printf "%5s ", ld.dir.sub(/.*try/, "try")
-    begin
-      outcar = ld.outcar
-      printf "%8.3f %3d (%3d) ",
-        outcar[:totens][-1], outcar[:ionic_steps], outcar[:electronic_steps]
-    rescue
-      printf "%8s %3s (%3s) ", " "*8, " "*3, " "*3
-    end
-
-  when "UnknownDir"
-    printf "-" * 35
-    printf " "
-
-  end
-  puts dir
-
-end
+#
+### option analysis
+#OPTIONS = {}
+#op = OptionParser.new
+#OPTIONS[:show_state] = []
+#op.on("-f", "--finished"    , "Show finished. -a is ignored."){OPTIONS[:show_state] << :finished}
+#op.on("-y", "--yet"             , "Show yet."                                      ){OPTIONS[:show_state] << :yet}
+#op.on("-t", "--terminated", "Show terminated."                         ){OPTIONS[:show_state] << :terminated}
+#op.on("-s", "--started"     , "Show sarted."                                   ){OPTIONS[:show_state] << :started}
+#op.on("-l", "--files-with-matches", "Show filename only."  ){OPTIONS[:filename  ] = true}
+#op.parse!(ARGV)
+#
+### if all select are not set, all are set.
+#if OPTIONS[:show_state].size == 0
+#    OPTIONS[:all]   = true
+#end
+##pp OPTIONS; exit
+#
+#LONGEST_STATE = :terminated.size
+#KLASSES = [VaspUtils::VaspDir, VaspUtils::VaspGeometryOptimizer]
+#
+#dirs = ARGV
+#dirs = Dir.glob("*").sort if ARGV.empty?
+#
+#def guess(dir)
+#    KLASSES.each do |klass|
+#        begin
+#            vd = klass.new(dir)
+#            return klass
+#        rescue klass::InitializeError
+#        end
+#    end
+#    raise "Cannot identify class for directory #{dir}."
+#end
+#
+#def show(klass_name, state, try, toten, i_step, e_step, dir)
+#    if (OPTIONS[:all]) || (OPTIONS[:show_state].include? state)
+#        unless OPTIONS[:filename]
+#            printf "%-11s ", klass_name
+#            printf "%-10s ", state
+#            printf "%5s ", try
+#            printf "%17s %3s (%3s) ", toten, i_step, e_step
+#        end
+#        print  dir
+#        puts
+#    end
+#end
+#
+#dirs.each do |dir|
+#    next unless File.directory? dir
+#
+#    begin
+#        klass = guess(dir)
+#        klass_name = klass.to_s
+#    rescue 
+#        klass_name = "UnknownDir"
+#    end
+#
+#    case klass_name
+#    when "VaspUtils::VaspDir"
+#        klass_name = "VaspDir"
+#        calc = klass.new(dir)
+#        state = calc.state
+#        try = ""
+#        begin
+#            outcar = calc.outcar
+#            toten  = sprintf("%17.6f", outcar[:totens][-1].to_f)
+#            i_step = outcar[:ionic_steps]
+#            e_step = outcar[:electronic_steps]
+#        rescue
+#            toten  = i_step = e_step = ""
+#        end
+#
+#    when "VaspUtils::VaspGeometryOptimizer"
+#        klass_name = "VaspGeomOpt"
+#        calc = klass.new(dir)
+#        state = calc.state
+#
+#        ld = calc.latest_dir
+#        try = sprintf "%5s", ld.dir.sub(/.*try/, "try")
+#        begin
+#            outcar = ld.outcar
+#            toten  = sprintf("%15.6f ", outcar[:totens][-1].to_f)
+#            i_step = outcar[:ionic_steps]
+#            e_step = outcar[:electronic_steps]
+#        rescue
+#            toten  = i_step = e_step = ""
+#        end
+#
+#    when "UnknownDir"
+#        klass_name = "UnknownDir"
+#        state = try = toten = i_step = e_step = ""
+#    end
+#    show(klass_name, state, try, toten, i_step, e_step, dir)
+#
+#end

data/bin/genincar

@@ -21,8 +21,8 @@ op.parse!(ARGV)
 
 encut = ARGV[0].to_i
 if encut == 0
-  puts "ENCUT must be indicated as an argument."
-  exit
+    puts "ENCUT must be indicated as an argument."
+    exit
 end
 
 setting = VaspUtils::Setting.new
@@ -32,8 +32,8 @@ items = setting["incar_default"]
 items["ENCUT"] = encut
 
 VaspUtils::Incar.dump(items, STDOUT)
-#  setting['potcar_dir'],
-#  setting['element_potcar']
+#    setting['potcar_dir'],
+#    setting['element_potcar']
 #)
 #vpc.dump(elements, STDOUT)
 

data/bin/genkpoints

@@ -15,28 +15,28 @@ require "vasputils.rb"
 #op.parse!(ARGV)
 
 unless ARGV.size == 4
-  puts "USAGE: genkpoints style kx ky kz"
-  puts "  where style is m or g, indicating Monkhorst or GammaCenter, respectively."
-  puts "  kx, ky, kz indicate mesh points for each direction."
-  exit
+    puts "USAGE: genkpoints style kx ky kz"
+    puts "  where style is m or g, indicating Monkhorst or GammaCenter, respectively."
+    puts "  kx, ky, kz indicate mesh points for each direction."
+    exit
 end
 
 data = {}
 if ARGV[0] =~ /^m/i
-  data[:type] = :monkhorst
+    data[:type] = :monkhorst
 elsif ARGV[0] =~ /^g/i
-  data[:type] = :gamma_center
+    data[:type] = :gamma_center
 else
-  puts "Unknown type. Exit."
-  exit
+    puts "Unknown type. Exit."
+    exit
 end
 
 data[:mesh] = ARGV[1..3].map do |i|
-  unless i.to_i 
-    puts "Mesh divisions must be larger than 0. Exit"
-    exit
-  end
-  i.to_i
+    unless i.to_i 
+        puts "Mesh divisions must be larger than 0. Exit"
+        exit
+    end
+    i.to_i
 end
 
 data[:shift] = [0.0, 0.0, 0.0]

data/bin/genpotcar

@@ -21,7 +21,7 @@ elements = ARGV
 setting = VaspUtils::Setting.new
 
 vpc = VaspUtils::Potcar::Concatenater.new(
-  setting['potcar_dir'],
-  setting['element_potcar']
+    setting['potcar_dir'],
+    setting['default_potcar']
 )
 vpc.dump(elements, STDOUT)

data/bin/latticeconstants

@@ -1,19 +1,17 @@
 #! /usr/bin/env ruby
 
 require "rubygems"
+require "vasputils"
 
-gem "vasputils"
-require "vasputils.rb"
+#gem "crystalcell"
+#require "crystalcell/latticeaxes.rb"
+#require "crystalcell/cell.rb"
 
-gem "crystalcell"
-require "crystalcell/latticeaxes.rb"
-require "crystalcell/cell.rb"
-
-puts "       a,        b,        c,  alpha,   beta,  gamma,     volume, file"
+puts "           a,              b,              c,  alpha,     beta,    gamma,         volume, file"
 ARGV.each do |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
+    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, ", CrystalCell::Cell.new(axes).calc_volume) # show volume
+    puts file
 end

data/bin/qsubvasp

@@ -1,19 +1,20 @@
 #! /usr/bin/env ruby
 # coding: utf-8
-#
-# USAGE:
-# qsubvasp [-n num] -c CLUSTER_NAME calc_dir
-#
-#   [-n INDICATOR]
-#     Integer can be uused as INDICATOR.
-#     If INDICATOR cannot be evaluated as positive integer,
-#     try to find tue hostname of localhost and
-#     key of
-#     the INDICATOR in ~/.machineinfo
-#     Default value is 1.
-#
-#   calc_dir is a vasp directory as usual,
-#   when with -g option, VaspGeometryOptimizer directory.
+
+USAGE = <<HERE
+    USAGE: qsubvasp [-c CLUSTER_NAME] [-n num] calc_dir
+
+     [-n INDICATOR]
+         Integer can be uused as INDICATOR.
+         If INDICATOR cannot be evaluated as positive integer,
+         try to find tue hostname of localhost and
+         key of
+         the INDICATOR in ~/.clustersetting
+         Default value is 1.
+
+     calc_dir is a vasp directory as usual,
+     when with -g option, VaspGeometryOptimizer directory.
+HERE
 
 #require "optparse"
 require "pp"
@@ -21,88 +22,70 @@ require "yaml"
 require "optparse"
 
 require "rubygems"
-gem "comana"
-require "comana/queuesubmitter.rb"
-require "comana/machineinfo.rb"
+require "comana"
 
 gem "vasputils"
 require "vasputils.rb"
 
-opts = {}
+OPTIONS = {}
 
 op = OptionParser.new
-op.on("-c cluster", "--cluster" , "Cluster name."){|v| opts["cluster"] = v }
-op.on("-n number", "--number", "Indicate node number, or key in ~/.machineinfo."){|v|
-  opts["number"] = v
+op.on("-c cluster", "--cluster=name" , "Cluster name."){|v| OPTIONS[:cluster] = v }
+op.on("-n number", "--nodes=num", "Indicate node number, or key in ~/.clustersetting."){|v|
+    OPTIONS[:num_nodes] = v
 }
-op.on("-g", "--geom-opt", "Geometry optimization."){ opts["geomopt"] = true}
+op.on("-g", "--geom-opt", "Geometry optimization."){ OPTIONS[:geomopt] = true}
+op.on("-p num", "--priority=num", "Set priority of job."){|v| OPTIONS[:priority] = v }
 op.parse!(ARGV)
 
 def condition_check(opts)
-  # Condition Check
-  mi = MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo")
-  conds = {}
-  # cluster
-  name = opts["cluster"]
-  #pp mi.get_info(name)
-  if name
-    conds["cluster"] = name
-  else
-    puts "-c CLUSTER_NAME is necessary."
-    exit
-  end
+    # Condition Check
+    mi = Comana::ClusterSetting.load_file("#{ENV["HOME"]}/.clustersetting")
+    conds = {}
 
-  # target and command
-  unless ARGV.size == 1
-    puts "Indicate only one directory for vasp. Argument: #{ARGV}"
-    exit
-  end
-  if opts["geomopt"]
-    begin
-      conds["target"] = VaspUtils::VaspGeometryOptimizer.new(File.expand_path(ARGV[0]))
-      conds["command"] = "runvasp -g"
-    rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
-      puts "Seem not to be a directory for VaspGeometryOptimizer #{ARGV}"
-      exit
-    end
-  else
-    begin
-      conds["target"] = VaspUtils::VaspDir.new(File.expand_path(ARGV[0]))
-      conds["command"] = "runvasp"
-    rescue VaspUtils::VaspDir::InitializeError
-      puts "Seem not to be a directory for VaspDir #{ARGV}"
-      exit
-    end
-  end
+    conds[:cluster] = opts[:cluster]
+    conds[:num_nodes]       = opts[:num_nodes].to_i if opts[:num_nodes]
 
-  # number
-  str = opts["number"]
-  num = str.to_i
-  if num > 0
-    conds["number"] = num
-  else
-    if mi.get_info(name).has_key?(str)
-      conds["number"] = mi.get_info(name)[str]
+    # target and command
+    unless ARGV.size == 1
+        puts "Indicate only one directory for vasp. Argument: #{ARGV}"
+        exit
+    end
+    if opts[:geomopt]
+        begin
+            conds[:target] = VaspUtils::VaspGeometryOptimizer.new(File.expand_path(ARGV[0]))
+            conds[:command] = "runvasp -g"
+        rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
+            puts "Seem not to be a directory for VaspGeometryOptimizer #{ARGV}"
+            exit
+        end
     else
-      puts "-n argument must be a positive integer or key in ~/machineinfo."
-      exit
+        begin
+            conds[:target] = VaspUtils::VaspDir.new(File.expand_path(ARGV[0]))
+            conds[:command] = "runvasp"
+        rescue VaspUtils::VaspDir::InitializeError
+            puts "Seem not to be a directory for VaspDir #{ARGV}"
+            exit
+        end
     end
-  end
-  conds
+
+    conds[:priority] = opts[:priority].to_i
+    conds
 end
-opts = condition_check(opts)
+opts = condition_check(OPTIONS)
+#pp opts; exit
 
-qs = QueueSubmitter.new(opts)
-#pp qs; exit
+print ARGV[0] + ", "
+qs = Comana::QueueSubmitter.new(opts)
 
 begin
-  qs.start
-  puts "Submitted. Exit."
-  exit
-rescue QueueSubmitter::AlreadyStartedError
-  puts "Already started. Exit."
-  exit
-rescue QueueSubmitter::PrepareNextError
-  puts "Must not happen."
-  exit
+    qs.start
+    puts "Submitted. Exit."
+    exit
+rescue Comana::QueueSubmitter::AlreadyStartedError
+    puts "Already started. Exit."
+    exit
+#rescue Comana::QueueSubmitter::PrepareNextError
+#    puts "Must not happen."
+#    exit
 end

data/bin/resetvaspdir

@@ -0,0 +1,51 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "optparse"
+require "fileutils"
+require "rubygems"
+require "comana"
+require "vasputils"
+
+## option analysis
+#OPTIONS = {}
+#op = OptionParser.new
+#op.on("-r", "--reset", "Reset to initial state, remove except for 4 files."){OPTIONS[:reset] = true}
+#op.on("-y", "--yes"    , "Answer yes to all questions."                ){OPTIONS[:yes]  = true}
+#op.on("-n", "--no"     , "Answer no    to all questions."              ){OPTIONS[:no ]  = true}
+#op.parse!(ARGV)
+
+tgts = ARGV
+tgts = [ENV['PWD']] if tgts.size == 0
+
+#pp tgts; exit
+
+#def ask
+#    print "    Execute? [y/n]: "
+#    if OPTIONS[:yes]
+#        puts "-y option is indicated."
+#        return true
+#    end
+#
+#    if OPTIONS[:no]
+#        puts "-n option is indicated."
+#        return false
+#    end
+#
+#    /^y/i =~ $stdin.readline
+#end
+
+tgts.each do |tgt_dir|
+    puts "Directory: #{tgt_dir}"
+
+    # Check tgt_dir is VaspDir?
+    begin
+        vd = VaspUtils::VaspDir.new(tgt_dir)
+    rescue VaspUtils::VaspDir::InitializeError
+        puts "  Not VaspDir: #{tgt_dir}"
+        next
+    end
+
+    vd.reset_init
+
+end