vasputils 0.0.11 → 0.0.12

data/bin/resetvaspgeomopt

@@ -0,0 +1,73 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+USAGE = <<HERE
+    USAGE: setvaspgeomopt <-i|-n|-r> [-Y|-N] target_dirs ...
+HERE
+
+require "optparse"
+require "fileutils"
+require "rubygems"
+require "comana"
+require "vasputils"
+
+## option analysis
+OPTIONS = {}
+op = OptionParser.new
+op.on("-i", "--reset-init", "Remain only 'geomopt00/{INCAR,KPOINTS,POSCAR,POTCAR}'."){OPTIONS[:init] = true}
+op.on("-n", "--next" , "Next vasp for geometry optimization."){OPTIONS[:next] = true}
+op.on("-r", "--reincarnate", "Like reset, but generate 'geomopt00' using final CONTCAR."){OPTIONS[:reincarnate] = 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)
+
+def check_options(opts)
+    modes = [opts[:init], opts[:next], opts[:reincarnate]]
+    return false unless modes.select{|t| t ==true}.size == 1
+
+    #return false if (opts[:yes] && opts[:no])
+    return true
+end
+
+unless check_options(OPTIONS)
+    puts USAGE
+    exit
+end
+
+tgts = ARGV
+tgts = [ENV['PWD']] if tgts.size == 0
+
+#pp OPTIONS; exit
+#pp tgts; exit
+#
+tgts.each do |tgt_dir|
+    puts "Directory: #{tgt_dir}"
+
+    # Check tgt_dir is VaspDir?
+    begin
+        tgt = VaspUtils::VaspGeometryOptimizer.new(tgt_dir)
+    rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
+        puts "  Not VaspGeometryOptimizer: #{tgt_dir}"
+        next
+    end
+
+    if OPTIONS[:init]
+        puts "  Back to init: #{tgt_dir}"
+        tgt.reset_init
+    end
+
+    if OPTIONS[:next]
+        puts "  Generate next: #{tgt_dir}"
+        #begin
+            tgt.reset_next
+        #rescue VaspUtils::VaspGeometryOptimizer::NoContcarError
+            #puts "  CONTCAR not exist in latest_dir: #{tgt_dir}"
+        #end
+    end
+
+    if OPTIONS[:reincarnate]
+        puts "  Reincarnate(generate dir as new calc): #{tgt_dir}"
+        tgt.reset_reincarnate
+    end
+end

data/bin/runvasp

@@ -1,52 +1,45 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
-require "rubygems"
-gem "comana"
-require "comana/computationmanager.rb"
-
-#gem "vasputils"
-require "vasputils.rb"
-
-require "optparse"
-
-## option analysis
-opts = {}
-op = OptionParser.new
-op.on("-g"    , "--geom-opt",  "Geometry optimization"){opts[:geom] = true}
-op.on("-c"    , "--cond-find", "Condition finding"    ){opts[:cond] = true}
-op.parse!(ARGV)
-
-dir = ARGV[0] || "."
-
-if opts[:geom] && opts[:cond]
-  puts "-g and -c must not be duplicated."
-  exit
-end
-
-if opts[:geom]
-  begin
-    calc_dir = VaspUtils::VaspGeometryOptimizer.new(dir)
-  rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
-    puts "Not suitable for VaspGeometryOptimizer: #{dir}"
-    exit
-  end
-elsif opts[:cond]
-  TODO
-else
-  begin
-    calc_dir = VaspUtils::VaspDir.new(dir)
-  rescue VaspUtils::VaspDir::InitializeError
-    puts "Not VaspDir: #{dir}"
-    exit
-  end
-end
-
-#pp calc_dir.class.ancestors
-
-begin
-  calc_dir.start
-rescue ComputationManager::AlreadyStartedError
-  puts "Already started. Exit."
-  exit
-end
+puts "'runvasp' is obsoleted. Use 'runvaspdir' or 'runvaspgeomopt'."
+
+#require "rubygems"
+##require "comana"
+##gem "comana"
+##require "comana/computationmanager.rb"
+#
+##gem "vasputils"
+#require "vasputils"
+#
+#require "optparse"
+#
+### option analysis
+#opts = {}
+#op = OptionParser.new
+#op.on("-g"      , "--geom-opt",    "Geometry optimization"){opts[:geom] = true}
+#op.parse!(ARGV)
+#
+#dir = ARGV[0] || "."
+#
+#if opts[:geom]
+#    begin
+#        calc_dir = VaspUtils::VaspGeometryOptimizer.new(dir)
+#    rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
+#        puts "Not suitable for VaspGeometryOptimizer: #{dir}"
+#        exit
+#    end
+#else
+#    begin
+#        calc_dir = VaspUtils::VaspDir.new(dir)
+#    rescue VaspUtils::VaspDir::InitializeError
+#        puts "Not VaspDir: #{dir}"
+#        exit
+#    end
+#end
+#
+#begin
+#    calc_dir.start
+#rescue Comana::ComputationManager::AlreadyStartedError
+#    puts "Already started. Exit."
+#    exit
+#end

data/bin/runvaspdir

@@ -0,0 +1,19 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "rubygems" #require "comana"
+require "vasputils"
+require "optparse"
+
+dir = ARGV[0] || "."
+
+begin
+    calc_dir = VaspUtils::VaspDir.new(dir)
+    calc_dir.start
+rescue VaspUtils::VaspDir::InitializeError
+    puts "Not VaspDir: #{dir}"
+    exit
+rescue Comana::ComputationManager::AlreadyStartedError
+    puts "Already started. Exit."
+    exit
+end

data/bin/runvaspgeomopt

@@ -0,0 +1,19 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "rubygems"
+require "vasputils"
+require "optparse"
+
+dir = ARGV[0] || "."
+
+begin
+    calc_dir = VaspUtils::VaspGeometryOptimizer.new(dir)
+    calc_dir.start
+rescue VaspUtils::VaspGeometryOptimizer::NoVaspDirError
+    puts "Not suitable for VaspGeometryOptimizer: #{dir}"
+    exit
+rescue Comana::ComputationManager::AlreadyStartedError
+    puts "Already started. Exit."
+    exit
+end

data/bin/showvaspdir

@@ -0,0 +1,171 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+# Show state of vasp geometry optimization calculations.
+
+#require "vasputils/calcseries.rb"
+require "rubygems"
+gem "vasputils"
+require "vasputils.rb"
+
+require "pp"
+require "csv"
+require "optparse"
+
+DEFAULT_ITEMS = [
+    :klass_name,
+    :state,
+    :toten,
+    :dir,
+]
+ALL_ITEMS = [
+    :ka,
+    :kb,
+    :kc,
+    :encut,
+    :i_step,
+    :e_step,
+    :time,
+] + DEFAULT_ITEMS
+
+# for printf option. minus value indicate left shifted printing.
+WIDTH = {
+    :dir         => "-20",
+    :e_step      => "3",
+    :i_step      => "3",
+    :klass_name  => "11",
+    :ka          => "2",
+    :kb          => "2",
+    :kc          => "2",
+    :encut       => "6",
+    :state       => "10",
+    :time        => "15",
+    :toten       => "17",
+}
+
+ALL_DIR_STATES = [
+    :finished,
+    :yet,
+    :terminated,
+    :started,
+]
+
+## option analysis
+show_items = []
+show_dir_states = []
+OPTIONS = {}
+op = OptionParser.new
+OPTIONS[:show_dir] = []
+op.on("-f", "--finished"  , "Show finished dir."   ){show_dir_states << :finished}
+op.on("-y", "--yet"       , "Show yet dir."        ){show_dir_states << :yet}
+op.on("-t", "--terminated", "Show terminated dir." ){show_dir_states << :terminated}
+op.on("-s", "--started"   , "Show sarted dir."     ){show_dir_states << :started}
+op.on("-l", "--dirs-with-matches", "Show dir name only."){OPTIONS[:dirnameonly  ] = true}
+
+op.on("-a", "--all-items"   , "Show all items."         ){OPTIONS[:all_items] = true}
+op.on("-S", "--state"       , "Show STATE."             ){show_items << :state    }
+op.on("-e", "--toten"       , "Show TOTEN."             ){show_items << :toten    }
+op.on("-i", "--ionic-steps" , "Show ionic steps as I_S."){show_items << :ionic_steps}
+op.on("-L", "--last-update" , "Show LAST-UPDATE."       ){show_items << :last_update}
+op.on("-k", "--kpoints" , "Show KPOINTS."               ){
+    show_items << :ka
+    show_items << :kb
+    show_items << :kc
+}
+op.on("-c", "--encut" , "Show ENCUT."                   ){show_items << :encut    }
+op.on("-C", "--csv" , "CSV format"                   ){OPTIONS[:csv] = true}
+op.parse!(ARGV)
+
+if OPTIONS[:all_items]
+    SHOW_ITEMS = ALL_ITEMS
+elsif OPTIONS[:dirnameonly]
+    SHOW_ITEMS = [:dir]
+elsif show_items.empty?
+    SHOW_ITEMS = DEFAULT_ITEMS
+else 
+    SHOW_ITEMS = show_items.push :dir
+end
+
+if show_dir_states.empty?
+    show_dir_states = ALL_DIR_STATES
+else 
+    show_dir_states # do nothing
+end
+
+dirs = ARGV
+dirs = Dir.glob("*").sort if ARGV.empty?
+
+def show(hash)
+    items = SHOW_ITEMS.map do |item|
+        val = sprintf("%#{WIDTH[item]}s", hash[item])
+        val = hash[item] if OPTIONS[:csv]
+        val
+    end
+    separator = " "
+    separator = "," if OPTIONS[:csv]
+
+    puts items.join(separator)
+end
+
+#I_S is ionic steps
+#E_S is electronic steps
+unless OPTIONS[:dirnameonly]
+    results = {
+        :klass_name => "TYPE",
+        :ka         => "KA",
+        :kb         => "KB",
+        :kc         => "KC",
+        :encut      => "ENCUT",
+        :state      => "STATE",
+        :toten      => "TOTEN",
+        :i_step     => "I_S",
+        :e_step     => "E_S",
+        :time       => "LAST_UPDATE",
+        :dir        => "DIR"
+    }
+    show(results)
+end
+
+dirs.each do |dir|
+    next unless File.directory? dir
+    #pp dir
+
+    begin
+        klass_name = "VaspDir"
+        calc = VaspUtils::VaspDir.new(dir)
+        state = calc.state
+        begin
+            outcar = calc.outcar
+            toten    = outcar[:totens][-1].to_f
+            i_step = outcar[:ionic_steps]
+            e_step = outcar[:electronic_steps]
+            #time = calc.latest_modified_time.to_s
+            time = calc.latest_modified_time.strftime("%Y%m%d-%H%M%S")
+            ka, kb, kc = calc.kpoints[:mesh]
+            encut = calc.incar["ENCUT"]
+        rescue
+            toten = i_step = e_step = time = ka = kb = kc = encut = ""
+        end
+
+    rescue VaspUtils::VaspDir::InitializeError
+        klass_name = "-------"
+        #state = toten = i_step = e_step = "---"
+    end
+    results = {
+        :klass_name => klass_name,
+        :ka         => ka,
+        :kb         => kb,
+        :kc         => kc,
+        :encut      => encut,
+        :state      => state,
+        :toten      => toten,
+        :i_step     => i_step,
+        :e_step     => e_step,
+        :time       => time,
+        :dir        => dir,
+    }
+
+    show(results) if show_dir_states.include? results[:state]
+
+end
+

data/bin/showvaspgeomopt

@@ -0,0 +1,83 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+# Show state of vasp geometry optimization calculations.
+
+#require "vasputils/calcseries.rb"
+require "rubygems"
+gem "vasputils"
+require "vasputils.rb"
+
+require "pp"
+require "optparse"
+
+## 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
+
+dirs = ARGV
+dirs = Dir.glob("*").sort if ARGV.empty?
+
+def show(klass_name, state, toten, i_step, e_step, time, dir)
+    if (OPTIONS[:all]) || (OPTIONS[:show_state].include? state)
+        unless OPTIONS[:filename]
+            printf "%-11s ", klass_name
+            printf "%-10s ", state
+            printf "%17s " , toten
+            printf "%3s "    , i_step
+            printf "(%3s) ", e_step
+            printf "%15s ", time
+        end
+        print    dir
+        puts
+    end
+end
+
+
+#I_S is ionic steps
+#E_S is electronic steps
+unless OPTIONS[:filename]
+    show("TYPE", "STATE", "TOTEN", "I_S", "E_S", "MODIFIED_TIME", "DIR")
+    puts "======================================================================"
+end
+dirs.each do |dir|
+    next unless File.directory? dir
+
+    begin
+        klass_name = "VaspGeomOpt"
+        calc = VaspUtils::VaspGeometryOptimizer.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]
+            time = calc.latest_modified_time.strftime("%Y%m%d-%H%M%S")
+        rescue
+            toten    = i_step = e_step = time = ""
+        end
+
+    rescue VaspUtils::VaspGeometryOptimizer::InitializeError
+        klass_name = "-------"
+        state = toten = i_step = e_step = "---"
+    end
+
+    show(klass_name, state, toten, i_step, e_step, time, dir)
+end
+
+