vasputils 0.0.3 → 0.0.4

data/vasputils.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = "vasputils"
-  s.version = "0.0.3"
+  s.version = "0.0.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-04-30"
+  s.date = "2012-05-07"
   s.description = "This gem provides parsers for some of input and output files for VASP.\n    This will provide support command for computations."
   s.email = "ippei94da@gmail.com"
-  s.executables = ["addVolumeToten.rb", "latticeconstants", "lsvaspdir", "lsvaspseries", "qsubvasp", "repeatvasp", "symposcar"]
+  s.executables = ["addVolumeToten.rb", "latticeconstants", "lsvasp", "lsvaspdir", "lsvaspseries", "qsubvasp", "runvasp", "symposcar"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -26,21 +26,22 @@ Gem::Specification.new do |s|
     "VERSION",
     "bin/addVolumeToten.rb",
     "bin/latticeconstants",
+    "bin/lsvasp",
     "bin/lsvaspdir",
     "bin/lsvaspseries",
     "bin/qsubvasp",
-    "bin/repeatvasp",
+    "bin/runvasp",
     "bin/symposcar",
     "lib/vasputils.rb",
     "lib/vasputils/calcinspector.rb",
-    "lib/vasputils/calcrepeater.rb",
-    "lib/vasputils/calcseries.rb",
     "lib/vasputils/incar.rb",
     "lib/vasputils/kpoints.rb",
     "lib/vasputils/outcar.rb",
     "lib/vasputils/poscar.rb",
     "lib/vasputils/potcar.rb",
     "lib/vasputils/vaspdir.rb",
+    "lib/vasputils/vaspgeomopt.rb",
+    "memo.txt",
     "test/calcseries/dup_finished/try00/CONTCAR",
     "test/calcseries/dup_finished/try00/INCAR",
     "test/calcseries/dup_finished/try00/KPOINTS",
@@ -100,21 +101,19 @@ Gem::Specification.new do |s|
     "test/repeatVasp/Iter2-Nsw2.00/POTCAR",
     "test/repeatVasp/test.sh",
     "test/test_calcinspector.rb",
-    "test/test_calcrepeater.rb",
-    "test/test_calcseries.rb",
     "test/test_incar.rb",
     "test/test_kpoints.rb",
     "test/test_outcar.rb",
     "test/test_poscar.rb",
     "test/test_potcar.rb",
     "test/test_vaspdir.rb",
+    "test/test_vaspgeomopt.rb",
     "test/vaspdir/finished/CONTCAR",
     "test/vaspdir/finished/INCAR",
     "test/vaspdir/finished/KPOINTS",
     "test/vaspdir/finished/OUTCAR",
     "test/vaspdir/finished/POSCAR",
     "test/vaspdir/finished/POTCAR",
-    "test/vaspdir/finished/lock",
     "test/vaspdir/lack-INCAR/KPOINTS",
     "test/vaspdir/lack-INCAR/POSCAR",
     "test/vaspdir/lack-INCAR/POTCAR",
@@ -131,7 +130,6 @@ Gem::Specification.new do |s|
     "test/vaspdir/locked/KPOINTS",
     "test/vaspdir/locked/POSCAR",
     "test/vaspdir/locked/POTCAR",
-    "test/vaspdir/locked/lock",
     "test/vaspdir/not-yet/INCAR",
     "test/vaspdir/not-yet/KPOINTS",
     "test/vaspdir/not-yet/POSCAR",
@@ -142,7 +140,61 @@ Gem::Specification.new do |s|
     "test/vaspdir/started/OUTCAR",
     "test/vaspdir/started/POSCAR",
     "test/vaspdir/started/POTCAR",
-    "test/vaspdir/started/lock",
+    "test/vaspgeomopt/ended-Iter1/try00/CONTCAR",
+    "test/vaspgeomopt/ended-Iter1/try00/INCAR",
+    "test/vaspgeomopt/ended-Iter1/try00/KPOINTS",
+    "test/vaspgeomopt/ended-Iter1/try00/OUTCAR",
+    "test/vaspgeomopt/ended-Iter1/try00/POSCAR",
+    "test/vaspgeomopt/ended-Iter1/try00/POTCAR",
+    "test/vaspgeomopt/ended-Iter1/try01/INCAR",
+    "test/vaspgeomopt/ended-Iter1/try01/KPOINTS",
+    "test/vaspgeomopt/ended-Iter1/try01/OUTCAR",
+    "test/vaspgeomopt/ended-Iter1/try01/POSCAR",
+    "test/vaspgeomopt/ended-Iter1/try01/POTCAR",
+    "test/vaspgeomopt/ended-Iter2/try00/CONTCAR",
+    "test/vaspgeomopt/ended-Iter2/try00/INCAR",
+    "test/vaspgeomopt/ended-Iter2/try00/KPOINTS",
+    "test/vaspgeomopt/ended-Iter2/try00/OUTCAR",
+    "test/vaspgeomopt/ended-Iter2/try00/POSCAR",
+    "test/vaspgeomopt/ended-Iter2/try00/POTCAR",
+    "test/vaspgeomopt/ended-Iter2/try01/INCAR",
+    "test/vaspgeomopt/ended-Iter2/try01/KPOINTS",
+    "test/vaspgeomopt/ended-Iter2/try01/OUTCAR",
+    "test/vaspgeomopt/ended-Iter2/try01/POSCAR",
+    "test/vaspgeomopt/ended-Iter2/try01/POTCAR",
+    "test/vaspgeomopt/not-yet/try00/INCAR",
+    "test/vaspgeomopt/not-yet/try00/KPOINTS",
+    "test/vaspgeomopt/not-yet/try00/POSCAR",
+    "test/vaspgeomopt/not-yet/try00/POTCAR",
+    "test/vaspgeomopt/prepare_next/try00/CHG",
+    "test/vaspgeomopt/prepare_next/try00/CHGCAR",
+    "test/vaspgeomopt/prepare_next/try00/CONTCAR",
+    "test/vaspgeomopt/prepare_next/try00/DOSCAR",
+    "test/vaspgeomopt/prepare_next/try00/EIGENVAL",
+    "test/vaspgeomopt/prepare_next/try00/INCAR",
+    "test/vaspgeomopt/prepare_next/try00/KPOINTS",
+    "test/vaspgeomopt/prepare_next/try00/OSZICAR",
+    "test/vaspgeomopt/prepare_next/try00/OUTCAR",
+    "test/vaspgeomopt/prepare_next/try00/PCDAT",
+    "test/vaspgeomopt/prepare_next/try00/POSCAR",
+    "test/vaspgeomopt/prepare_next/try00/POTCAR",
+    "test/vaspgeomopt/prepare_next/try00/WAVECAR",
+    "test/vaspgeomopt/prepare_next/try00/XDATCAR",
+    "test/vaspgeomopt/prepare_next/try00/vasprun.xml",
+    "test/vaspgeomopt/started/try00/INCAR",
+    "test/vaspgeomopt/started/try00/KPOINTS",
+    "test/vaspgeomopt/started/try00/POSCAR",
+    "test/vaspgeomopt/started/try00/POTCAR",
+    "test/vaspgeomopt/till01/try00/CONTCAR",
+    "test/vaspgeomopt/till01/try00/INCAR",
+    "test/vaspgeomopt/till01/try00/KPOINTS",
+    "test/vaspgeomopt/till01/try00/OUTCAR",
+    "test/vaspgeomopt/till01/try00/POSCAR",
+    "test/vaspgeomopt/till01/try00/POTCAR",
+    "test/vaspgeomopt/till01/try01/INCAR",
+    "test/vaspgeomopt/till01/try01/KPOINTS",
+    "test/vaspgeomopt/till01/try01/POSCAR",
+    "test/vaspgeomopt/till01/try01/POTCAR",
     "vasputils.gemspec"
   ]
   s.homepage = "http://github.com/ippei94da/vasputils"
@@ -163,7 +215,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<mageo>, [">= 0.0.0"])
       s.add_development_dependency(%q<malge>, [">= 0.0.1"])
       s.add_development_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_development_dependency(%q<comana>, [">= 0.0.4"])
+      s.add_development_dependency(%q<comana>, [">= 0.0.5"])
       s.add_development_dependency(%q<builtinextension>, [">= 0.0.3"])
     else
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
@@ -174,7 +226,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<mageo>, [">= 0.0.0"])
       s.add_dependency(%q<malge>, [">= 0.0.1"])
       s.add_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_dependency(%q<comana>, [">= 0.0.4"])
+      s.add_dependency(%q<comana>, [">= 0.0.5"])
       s.add_dependency(%q<builtinextension>, [">= 0.0.3"])
     end
   else
@@ -186,7 +238,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<mageo>, [">= 0.0.0"])
     s.add_dependency(%q<malge>, [">= 0.0.1"])
     s.add_dependency(%q<maset>, [">= 0.0.0"])
-    s.add_dependency(%q<comana>, [">= 0.0.4"])
+    s.add_dependency(%q<comana>, [">= 0.0.5"])
     s.add_dependency(%q<builtinextension>, [">= 0.0.3"])
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vasputils
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-30 00:00:00.000000000 Z
+date: 2012-05-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &79594890 !ruby/object:Gem::Requirement
+  requirement: &86738910 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *79594890
+  version_requirements: *86738910
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &79594490 !ruby/object:Gem::Requirement
+  requirement: &86737820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *79594490
+  version_requirements: *86737820
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &79593170 !ruby/object:Gem::Requirement
+  requirement: &86753150 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *79593170
+  version_requirements: *86753150
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &78632520 !ruby/object:Gem::Requirement
+  requirement: &86752350 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *78632520
+  version_requirements: *86752350
 - !ruby/object:Gem::Dependency
   name: crystalcell
-  requirement: &78630690 !ruby/object:Gem::Requirement
+  requirement: &86751370 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *78630690
+  version_requirements: *86751370
 - !ruby/object:Gem::Dependency
   name: mageo
-  requirement: &78629680 !ruby/object:Gem::Requirement
+  requirement: &86749640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *78629680
+  version_requirements: *86749640
 - !ruby/object:Gem::Dependency
   name: malge
-  requirement: &78628750 !ruby/object:Gem::Requirement
+  requirement: &86748730 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: 0.0.1
   type: :development
   prerelease: false
-  version_requirements: *78628750
+  version_requirements: *86748730
 - !ruby/object:Gem::Dependency
   name: maset
-  requirement: &78628020 !ruby/object:Gem::Requirement
+  requirement: &86745950 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,21 +98,21 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *78628020
+  version_requirements: *86745950
 - !ruby/object:Gem::Dependency
   name: comana
-  requirement: &78627530 !ruby/object:Gem::Requirement
+  requirement: &86584290 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.4
+        version: 0.0.5
   type: :development
   prerelease: false
-  version_requirements: *78627530
+  version_requirements: *86584290
 - !ruby/object:Gem::Dependency
   name: builtinextension
-  requirement: &78626870 !ruby/object:Gem::Requirement
+  requirement: &86583340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,17 +120,18 @@ dependencies:
         version: 0.0.3
   type: :development
   prerelease: false
-  version_requirements: *78626870
+  version_requirements: *86583340
 description: ! "This gem provides parsers for some of input and output files for VASP.\n
   \   This will provide support command for computations."
 email: ippei94da@gmail.com
 executables:
 - addVolumeToten.rb
 - latticeconstants
+- lsvasp
 - lsvaspdir
 - lsvaspseries
 - qsubvasp
-- repeatvasp
+- runvasp
 - symposcar
 extensions: []
 extra_rdoc_files:
@@ -145,21 +146,22 @@ files:
 - VERSION
 - bin/addVolumeToten.rb
 - bin/latticeconstants
+- bin/lsvasp
 - bin/lsvaspdir
 - bin/lsvaspseries
 - bin/qsubvasp
-- bin/repeatvasp
+- bin/runvasp
 - bin/symposcar
 - lib/vasputils.rb
 - lib/vasputils/calcinspector.rb
-- lib/vasputils/calcrepeater.rb
-- lib/vasputils/calcseries.rb
 - lib/vasputils/incar.rb
 - lib/vasputils/kpoints.rb
 - lib/vasputils/outcar.rb
 - lib/vasputils/poscar.rb
 - lib/vasputils/potcar.rb
 - lib/vasputils/vaspdir.rb
+- lib/vasputils/vaspgeomopt.rb
+- memo.txt
 - test/calcseries/dup_finished/try00/CONTCAR
 - test/calcseries/dup_finished/try00/INCAR
 - test/calcseries/dup_finished/try00/KPOINTS
@@ -219,21 +221,19 @@ files:
 - test/repeatVasp/Iter2-Nsw2.00/POTCAR
 - test/repeatVasp/test.sh
 - test/test_calcinspector.rb
-- test/test_calcrepeater.rb
-- test/test_calcseries.rb
 - test/test_incar.rb
 - test/test_kpoints.rb
 - test/test_outcar.rb
 - test/test_poscar.rb
 - test/test_potcar.rb
 - test/test_vaspdir.rb
+- test/test_vaspgeomopt.rb
 - test/vaspdir/finished/CONTCAR
 - test/vaspdir/finished/INCAR
 - test/vaspdir/finished/KPOINTS
 - test/vaspdir/finished/OUTCAR
 - test/vaspdir/finished/POSCAR
 - test/vaspdir/finished/POTCAR
-- test/vaspdir/finished/lock
 - test/vaspdir/lack-INCAR/KPOINTS
 - test/vaspdir/lack-INCAR/POSCAR
 - test/vaspdir/lack-INCAR/POTCAR
@@ -250,7 +250,6 @@ files:
 - test/vaspdir/locked/KPOINTS
 - test/vaspdir/locked/POSCAR
 - test/vaspdir/locked/POTCAR
-- test/vaspdir/locked/lock
 - test/vaspdir/not-yet/INCAR
 - test/vaspdir/not-yet/KPOINTS
 - test/vaspdir/not-yet/POSCAR
@@ -261,7 +260,61 @@ files:
 - test/vaspdir/started/OUTCAR
 - test/vaspdir/started/POSCAR
 - test/vaspdir/started/POTCAR
-- test/vaspdir/started/lock
+- test/vaspgeomopt/ended-Iter1/try00/CONTCAR
+- test/vaspgeomopt/ended-Iter1/try00/INCAR
+- test/vaspgeomopt/ended-Iter1/try00/KPOINTS
+- test/vaspgeomopt/ended-Iter1/try00/OUTCAR
+- test/vaspgeomopt/ended-Iter1/try00/POSCAR
+- test/vaspgeomopt/ended-Iter1/try00/POTCAR
+- test/vaspgeomopt/ended-Iter1/try01/INCAR
+- test/vaspgeomopt/ended-Iter1/try01/KPOINTS
+- test/vaspgeomopt/ended-Iter1/try01/OUTCAR
+- test/vaspgeomopt/ended-Iter1/try01/POSCAR
+- test/vaspgeomopt/ended-Iter1/try01/POTCAR
+- test/vaspgeomopt/ended-Iter2/try00/CONTCAR
+- test/vaspgeomopt/ended-Iter2/try00/INCAR
+- test/vaspgeomopt/ended-Iter2/try00/KPOINTS
+- test/vaspgeomopt/ended-Iter2/try00/OUTCAR
+- test/vaspgeomopt/ended-Iter2/try00/POSCAR
+- test/vaspgeomopt/ended-Iter2/try00/POTCAR
+- test/vaspgeomopt/ended-Iter2/try01/INCAR
+- test/vaspgeomopt/ended-Iter2/try01/KPOINTS
+- test/vaspgeomopt/ended-Iter2/try01/OUTCAR
+- test/vaspgeomopt/ended-Iter2/try01/POSCAR
+- test/vaspgeomopt/ended-Iter2/try01/POTCAR
+- test/vaspgeomopt/not-yet/try00/INCAR
+- test/vaspgeomopt/not-yet/try00/KPOINTS
+- test/vaspgeomopt/not-yet/try00/POSCAR
+- test/vaspgeomopt/not-yet/try00/POTCAR
+- test/vaspgeomopt/prepare_next/try00/CHG
+- test/vaspgeomopt/prepare_next/try00/CHGCAR
+- test/vaspgeomopt/prepare_next/try00/CONTCAR
+- test/vaspgeomopt/prepare_next/try00/DOSCAR
+- test/vaspgeomopt/prepare_next/try00/EIGENVAL
+- test/vaspgeomopt/prepare_next/try00/INCAR
+- test/vaspgeomopt/prepare_next/try00/KPOINTS
+- test/vaspgeomopt/prepare_next/try00/OSZICAR
+- test/vaspgeomopt/prepare_next/try00/OUTCAR
+- test/vaspgeomopt/prepare_next/try00/PCDAT
+- test/vaspgeomopt/prepare_next/try00/POSCAR
+- test/vaspgeomopt/prepare_next/try00/POTCAR
+- test/vaspgeomopt/prepare_next/try00/WAVECAR
+- test/vaspgeomopt/prepare_next/try00/XDATCAR
+- test/vaspgeomopt/prepare_next/try00/vasprun.xml
+- test/vaspgeomopt/started/try00/INCAR
+- test/vaspgeomopt/started/try00/KPOINTS
+- test/vaspgeomopt/started/try00/POSCAR
+- test/vaspgeomopt/started/try00/POTCAR
+- test/vaspgeomopt/till01/try00/CONTCAR
+- test/vaspgeomopt/till01/try00/INCAR
+- test/vaspgeomopt/till01/try00/KPOINTS
+- test/vaspgeomopt/till01/try00/OUTCAR
+- test/vaspgeomopt/till01/try00/POSCAR
+- test/vaspgeomopt/till01/try00/POTCAR
+- test/vaspgeomopt/till01/try01/INCAR
+- test/vaspgeomopt/till01/try01/KPOINTS
+- test/vaspgeomopt/till01/try01/POSCAR
+- test/vaspgeomopt/till01/try01/POTCAR
 - vasputils.gemspec
 homepage: http://github.com/ippei94da/vasputils
 licenses:
@@ -278,7 +331,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 754558063
+      hash: -619006479
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/bin/repeatvasp

@@ -1,47 +0,0 @@
-#! /usr/bin/ruby
-
-# Usage:
-#   repeatvasp calc_dir
-#   引数は計算ディレクトリで、1つのみ許可。
-#
-# 引数のディレクトリで計算を実行する。
-# 他所には投げず、localhost で実行する。
-#
-# 以下の条件を満たすとき、計算を繰り返す。
-# - cell shape, volume を含めた構造最適化で ionic step が 2以上。
-# - 構造最適化で ionic step が nsw と同じ。
-# - NEBM
-#
-# 計算の状態に応じたディレクトリ名をつける。
-# これらの名前は人間が分かり易くするためのものであって、
-# プログラムが計算の状態を把握するのはあくまで
-# 中のファイルを見て行うものとする。
-#
-# 状態を表す文字列をディレクトリ末尾に着ける機能はなし。
-# これをやると面倒。
-# この辺の確認は専用コマンドを用意することにする。
-#
-# 次の計算になるときに、
-# 元のディレクトリは末尾に 00 を付加する？
-# 次のディレクトリは末尾に 01 以降、インクリメント。
-# 01 からスタートしたときは、適当に 02 とか。
-#
-# 当面、計算ディレクトリは -try00 と末尾についていることを前提とする。
-
-require "vasputils/calcrepeater"
-require "vasputils/vaspdir"
-
-if ARGV.size != 1
-	puts "Number of arguments must be 1."
-	exit
-end
-
-vd = VaspDir.new(ARGV[0])
-cr = CalcRepeater.new
-begin
-	cr.repeat(vd)
-rescue VaspDir::PostfixMismatchError
-	puts "Postfix mismatches to #{VaspDir::POSTFIX}. Exit."
-rescue VaspDir::LockedError
-	puts "Lock file exist. Exit."
-end