vasputils 0.1.3 → 0.1.4
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- checksums.yaml +4 -4
- data/CHANGES +6 -2
- data/VERSION +1 -1
- data/lib/vasputils/poscar.rb +7 -9
- data/lib/vasputils/potcar.rb +1 -1
- data/lib/vasputils/vaspgeometryoptimizer.rb +1 -1
- data/lib/vasputils/vasprunxml.rb +6 -0
- data/lib/vasputils/xdatcar.rb +1 -1
- data/test/test_poscar.rb +9 -4
- data/test/test_vaspgeometryoptimizer.rb +1 -1
- data/test/test_vasprunxml.rb +11 -0
- data/vasputils.gemspec +3 -3
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: 01cd9553715d4619bb01ce5b2d31978c447cc03a
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4
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data.tar.gz: 45590fabd8de6c5f4bc669399d334c22f3c12936
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: a934034c6cccf101adcc139a939b24585bf09ea6fd8b26cb8e67fe7788649012804ee2e0c82fef5c9585e7b4f9d79c13284c219a7ca6b1955404607553ed6042
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7
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data.tar.gz: b224b574ef436f651330ccb6eea3c9ef2b11b9b0649513552bd8adb9c2f12634cff73dbcd7418eb35d2eb1e26e54cde847c87e0b1ed82cff2c321f4759b73aad
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data/CHANGES
CHANGED
@@ -1,6 +1,10 @@
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= vasputils changelog
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-
== Master (for 0.1.
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== Master (for 0.1.5)
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5
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== Version 0.1.4 [2016-05-09] released
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* Refactoring of unused variables
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7
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* Add VasprunXml::calculation_energies
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8
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9
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== Version 0.1.3 [2016-04-20] released
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* Add 'incar generate --overwrite'
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@@ -47,7 +51,7 @@
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* Add bin/poscar
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* Add bin/potcar
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* Add vaspspcond including subcommand 'vary', instead of varycondition.
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50
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-
* Add VaspUtils::
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54
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+
* Add VaspUtils::VasprunXml
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* Add bin/geomoptposcar
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* Add subcommand `povray' to bin/poscar
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* Add element order to Poscar.dump
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.4
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data/lib/vasputils/poscar.rb
CHANGED
@@ -46,7 +46,7 @@ class VaspUtils::Poscar
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axes = []
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3.times do |i| #each axis of a, b, c.
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vec = io.readline.strip.split(/\s+/) #in x,y,z directions
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49
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-
axes << vec.collect! { |
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+
axes << vec.collect! { |j| j.to_f * scale } #multiply scaling factor
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end
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51
51
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# Element symbol (vasp 5). Nothing in vasp 4.
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@@ -220,7 +220,7 @@ class VaspUtils::Poscar
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end
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end
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-
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klass.new(axes, atoms)
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end
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# selective_dynamics は常に on にする。
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@@ -270,8 +270,8 @@ class VaspUtils::Poscar
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:direct => true,
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:positions => new_positions
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}
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-
correct = VaspUtils::Poscar.new(hash)
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+
VaspUtils::Poscar.new(hash)
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end
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#
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@@ -379,13 +379,11 @@ class VaspUtils::Poscar
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def sprint_position(i)
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str = sprintf(" % 18.15f % 18.15f % 18.15f", * @positions[i])
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if @selective_dynamics
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-
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-
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-
(flag == true) ? str += " T" : str += " F"
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-
end
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-
else
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-
str += " T T T"
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@selective_dynamics[i].each do |flag|
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(flag == true) ? str += " T" : str += " F"
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end
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else
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#str += " T T T"
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end
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str
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end
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data/lib/vasputils/potcar.rb
CHANGED
@@ -79,7 +79,7 @@ class VaspUtils::VaspGeometryOptimizer < Comana::ComputationManager
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#Keep 'geomopt00/{POSCAR,POTCAR,INCAR,POTCAR}', remove others.
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def reset_initialize
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poscars = Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort
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-
poscar = nil
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#poscar = nil
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path = nil
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# Find the first geometory optimization
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data/lib/vasputils/vasprunxml.rb
CHANGED
@@ -34,6 +34,7 @@ class VaspUtils::VasprunXml
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axis.text.strip.split.map {|i| i.to_f}
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end
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end
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+
results
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end
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def positions_list
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@@ -105,5 +106,10 @@ class VaspUtils::VasprunXml
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def num_spins
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@data.xpath("/modeling/parameters/separator[@name='electronic']/separator[@name='electronic spin']/i[@name='ISPIN']").children.to_s.to_i
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end
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# energies of each ionic step
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def calculation_energies
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@data.xpath("/modeling/calculation/energy/i[@name='e_fr_energy']").children.to_a.map{|i| i.to_s.to_f}
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end
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end
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data/lib/vasputils/xdatcar.rb
CHANGED
@@ -43,7 +43,7 @@ class VaspUtils::Xdatcar
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axes = []
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3.times do |i| #each axis of a, b, c.
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vec = io.readline.strip.split(/\s+/) #in x,y,z directions
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46
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-
axes << vec.collect! { |
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+
axes << vec.collect! { |j| j.to_f * scale } #multiply scaling factor
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end
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vals = io.readline.strip.split(/\s+/)
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data/test/test_poscar.rb
CHANGED
@@ -255,7 +255,12 @@ class TC_Poscar < Test::Unit::TestCase
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],
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:elements => %w(Li Ge O),
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:nums_elements => [1,1,2],
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-
:selective_dynamics =>
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:selective_dynamics => [
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[true , true , true ],
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[true , true , false],
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[true , false, false],
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[false, false, false],
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],
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:direct => true,
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:positions => [
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[0.0, 0.0, 0.0],
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@@ -277,9 +282,9 @@ class TC_Poscar < Test::Unit::TestCase
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"Selective dynamics\n",
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"Direct\n",
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" 0.000000000000000 0.000000000000000 0.000000000000000 T T T\n",
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" 0.500000000000000 0.000000000000000 0.000000000000000 T T
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" 0.500000000000000 0.500000000000000 0.000000000000000 T
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" 0.500000000000000 0.500000000000000 0.500000000000000
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" 0.500000000000000 0.000000000000000 0.000000000000000 T T F\n",
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" 0.500000000000000 0.500000000000000 0.000000000000000 T F F\n",
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" 0.500000000000000 0.500000000000000 0.500000000000000 F F F\n",
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]
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lines = io.readlines
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corrects.each_with_index do |cor, index|
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@@ -59,7 +59,7 @@ class TC_VaspGeometryOptimizer < Test::Unit::TestCase
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def test_prepare_next
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dir = TEST_DIR + "/prepare_next/normal"
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-
old_number_dir = dir + "/geomopt00"
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#old_number_dir = dir + "/geomopt00"
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new_number_dir = dir + "/geomopt01"
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if Dir.exist?(new_number_dir)
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data/test/test_vasprunxml.rb
CHANGED
@@ -133,6 +133,17 @@ class TC_VasprunXml < Test::Unit::TestCase
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assert_raise(error){ @v00.partial_dos(5, 1)}
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end
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def test_calculation_energies
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results = @v01.calculation_energies
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assert_equal(5 , results.size)
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assert_equal(-4.21361453, results[0])
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assert_equal(-4.31607186, results[1])
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assert_equal(-4.39832854, results[2])
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assert_equal(-4.40043741, results[3])
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assert_equal(-4.40063677, results[4])
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end
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end
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data/vasputils.gemspec
CHANGED
@@ -2,16 +2,16 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: vasputils 0.1.
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# stub: vasputils 0.1.4 ruby lib
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Gem::Specification.new do |s|
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s.name = "vasputils"
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s.version = "0.1.
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s.version = "0.1.4"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib"]
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s.authors = ["ippei94da"]
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s.date = "2016-
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s.date = "2016-05-09"
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s.description = "This gem provides parsers for some of input and output files for VASP.\n This will provide support command for computations."
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s.email = "ippei94da@gmail.com"
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s.executables = ["incar", "kpoints", "poscar", "potcar", "vaspdir", "vaspgeomopt", "vasprunxml"]
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metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: vasputils
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version: !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.4
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platform: ruby
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authors:
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- ippei94da
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2016-
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date: 2016-05-09 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
|
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name: test-unit
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