vasputils 0.0.4 → 0.0.5
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- data/Gemfile +3 -3
- data/VERSION +1 -1
- data/bin/qsubvasp +1 -1
- data/bin/runvasp +5 -3
- data/lib/vasputils/vaspdir.rb +11 -37
- data/lib/vasputils/vaspgeomopt.rb +4 -3
- data/memo.txt +5 -0
- data/test/test_vaspdir.rb +4 -4
- data/test/test_vaspgeomopt.rb +2 -1
- data/vasputils.gemspec +11 -11
- metadata +26 -26
data/Gemfile
CHANGED
@@ -6,9 +6,9 @@ source "http://rubygems.org"
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|
6
6
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# Add dependencies to develop your gem here.
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7
7
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# Include everything needed to run rake, tests, features, etc.
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8
8
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group :development do
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9
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-
gem "rdoc", "
|
10
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-
gem "bundler", "
|
11
|
-
gem "jeweler", "
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9
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+
gem "rdoc", ">= 3.12"
|
10
|
+
gem "bundler", ">= 1.1.3"
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11
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+
gem "jeweler", ">= 1.8.3"
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12
12
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gem "simplecov", ">= 0"
|
13
13
|
gem "crystalcell", ">= 0.0.0"
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14
14
|
gem "mageo", ">= 0.0.0"
|
data/VERSION
CHANGED
@@ -1 +1 @@
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|
1
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-
0.0.
|
1
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+
0.0.5
|
data/bin/qsubvasp
CHANGED
@@ -45,7 +45,7 @@ File.open(SCRIPT_FILE, "w") do |io|
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|
45
45
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io.puts "#PBS -N task"
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46
46
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io.puts "#PBS -l nodes=4:ppn=1:Ga"
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47
47
|
io.puts "cd $PBS_O_WORKDIR"
|
48
|
-
io.puts "
|
48
|
+
io.puts "runvasp"
|
49
49
|
#io.puts "#/usr/local/bin/mpiexec /usr/local/bin/vasp5212mpi-ifc11-fast"
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50
50
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#io.puts "#/home/ippei/local/mpi/mpiexec-0.84/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
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51
51
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#io.puts "#/usr/local/calc/mpiexec/bin/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
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data/bin/runvasp
CHANGED
@@ -1,8 +1,10 @@
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|
1
1
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#! /usr/bin/env ruby
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2
2
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# coding: utf-8
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3
3
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|
4
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-
|
5
4
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require "rubygems"
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5
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+
gem "comana"
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6
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+
require "comana/computationmanager.rb"
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7
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+
|
6
8
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gem "vasputils"
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7
9
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require "vasputils/vaspdir.rb"
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8
10
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require "vasputils/vaspgeomopt.rb"
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@@ -25,11 +27,11 @@ else
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|
25
27
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calc_dir = VaspDir.new(dir)
|
26
28
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end
|
27
29
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|
28
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-
#pp calc_dir
|
30
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+
#pp calc_dir.class.ancestors
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29
31
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|
30
32
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begin
|
31
33
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calc_dir.start
|
32
|
-
rescue
|
34
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+
rescue ComputationManager::AlreadyStartedError
|
33
35
|
puts "Already started. Exit."
|
34
36
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exit
|
35
37
|
end
|
data/lib/vasputils/vaspdir.rb
CHANGED
@@ -28,8 +28,10 @@ require "vasputils/kpoints.rb"
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|
28
28
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# try00 形式の postfix がついていることを前提とする。
|
29
29
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# 00 の部分には CONTCAR を POSCAR にする手続きで連続して行う計算の番号を示す。
|
30
30
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#
|
31
|
-
class VaspDir <
|
31
|
+
class VaspDir < ComputationManager
|
32
32
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class InitializeError < Exception; end
|
33
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+
class NoVaspBinaryError < Exception; end
|
34
|
+
class PrepareNextError < Exception; end
|
33
35
|
|
34
36
|
#INCAR 解析とかして、モードを調べる。
|
35
37
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#- 格子定数の構造最適化モード(ISIF = 3)
|
@@ -37,6 +39,7 @@ class VaspDir < Comana
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|
37
39
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##- k 点探索モードは無理だろう。
|
38
40
|
def initialize(dir)
|
39
41
|
super(dir)
|
42
|
+
@lockdir = "lock_vaspdir"
|
40
43
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%w(INCAR KPOINTS POSCAR POTCAR).each do |file|
|
41
44
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infile = "#{@dir}/#{file}"
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42
45
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raise InitializeError, infile unless FileTest.exist? infile
|
@@ -96,58 +99,29 @@ class VaspDir < Comana
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|
96
99
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# そのうち mpiexec from torque に対応するが、
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97
100
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# まずは mpirun で動くように作る。
|
98
101
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def calculate
|
99
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-
#File.open(lock_file, "w") do |lock_io|
|
100
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-
# lock_io.puts "HOST: #{ENV["HOST"]}"
|
101
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-
# lock_io.puts "START: #{Time.now.to_s}"
|
102
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-
# lock_io.flush
|
103
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-
|
104
|
-
# num_cores = 4 if /^Se\d\d/ =~ ENV["HOST"]
|
105
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-
# num_cores = 4 if /^Ge\d\d/ =~ ENV["HOST"]
|
106
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-
# num_cores = 4 if /^Ga\d\d/ =~ ENV["HOST"]
|
107
|
-
# num_cores = 4 if /^At$/ =~ ENV["HOST"]
|
108
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-
# num_cores = 2 if /^yggdrasil$/ =~ ENV["HOST"]
|
109
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-
|
110
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-
# # machines を生成
|
111
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-
# File.open("#{@dir}/machines", "w") do |io|
|
112
|
-
# io.puts "localhost:#{num_cores}"
|
113
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-
# end
|
114
|
-
#end
|
115
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-
#num_cores = 4
|
116
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-
|
117
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-
#settings = YAML.load_file("#{ENV["HOME"]}/.machineinfo")
|
118
|
-
#setting = settings[ENV["HOST"]]
|
119
102
|
begin
|
120
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-
|
121
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-
|
103
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+
info =
|
104
|
+
MachineInfo.load_file("#{ENV["HOME"]}/.machineinfo").get_info(ENV["HOST"])
|
105
|
+
vasp = info["vasp"]
|
122
106
|
rescue
|
123
|
-
vasp = "vasp"
|
107
|
+
#vasp = "vasp"
|
108
|
+
raise NoVaspBinaryError, "No vasp path in #{ENV["HOME"]}/.machineinfo"
|
124
109
|
end
|
125
110
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command = "cd #{@dir};"
|
126
111
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command += vasp
|
127
112
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command += "> stdout"
|
128
113
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|
129
|
-
#if ENV["PBS_JOBID"]
|
130
|
-
# command += "/usr/local/calc/mpiexec/bin/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
|
131
|
-
#else
|
132
|
-
# /usr/local/calc/bin/vasp5212-mpich2"
|
133
|
-
## command = "cd #{@dir};" +
|
134
|
-
## "/usr/local/calc/mpich-1.2.7-ifc7/bin/mpirun " +
|
135
|
-
## "-np #{num_cores} " +
|
136
|
-
## "-machinefile machines " +
|
137
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-
## "/usr/local/calc/vasp/vasp4631mpi" +
|
138
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-
## "> stdout"
|
139
|
-
#end
|
140
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-
|
141
114
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system command
|
142
115
|
end
|
143
116
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|
144
117
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def prepare_next
|
145
118
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#do_nothing
|
119
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+
raise PrepareNextError, "VaspDir doesn't need next."
|
146
120
|
end
|
147
121
|
|
148
122
|
end
|
149
123
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|
150
|
-
#class VaspGeometryOptimization <
|
124
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+
#class VaspGeometryOptimization < ComputationManager
|
151
125
|
# # 次の計算ディレクトリを作成し、
|
152
126
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# # その VaspDir クラスで self を置き換える。
|
153
127
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# # 計算が正常終了していなければ、例外 VaspDirNotEndedError を生じる。
|
@@ -6,20 +6,21 @@ require "fileutils"
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|
6
6
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|
7
7
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require "rubygems"
|
8
8
|
gem "comana"
|
9
|
-
require "comana"
|
9
|
+
require "comana/computationmanager.rb"
|
10
10
|
|
11
|
-
require "vasputils/vaspdir"
|
11
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+
require "vasputils/vaspdir.rb"
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12
12
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|
13
13
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#
|
14
14
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#
|
15
15
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#
|
16
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-
class VaspGeomOpt <
|
16
|
+
class VaspGeomOpt < ComputationManager
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17
17
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class NoVaspDirError < Exception; end
|
18
18
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class LatestDirStartedError < Exception; end
|
19
19
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class NoIntegerEndedNameError < Exception; end
|
20
20
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|
21
21
|
def initialize(dir)
|
22
22
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super(dir)
|
23
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+
@lockdir = "lock_vaspgeomopt"
|
23
24
|
latest_dir # to check.
|
24
25
|
end
|
25
26
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|
data/memo.txt
CHANGED
data/test/test_vaspdir.rb
CHANGED
@@ -5,7 +5,7 @@ $TEST = true
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|
5
5
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|
6
6
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require "rubygems"
|
7
7
|
gem "comana"
|
8
|
-
require "comana.rb"
|
8
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+
require "comana/computationmanager.rb"
|
9
9
|
|
10
10
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require "test/unit"
|
11
11
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require "vasputils/vaspdir.rb"
|
@@ -14,7 +14,7 @@ require "vasputils/vaspdir.rb"
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|
14
14
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# assert_in_delta( cor, data, $tolerance )
|
15
15
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# assert_raise( RuntimeError ){}
|
16
16
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|
17
|
-
class VaspDir <
|
17
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+
class VaspDir < ComputationManager
|
18
18
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attr_reader :mode
|
19
19
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|
20
20
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def calculate
|
@@ -88,7 +88,7 @@ class TC_VaspDir < Test::Unit::TestCase
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|
88
88
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end
|
89
89
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|
90
90
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def test_calculate
|
91
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-
lock_dir = "test/vaspdir/not-yet/
|
91
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+
lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
|
92
92
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Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
|
93
93
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#pp @vd00;exit
|
94
94
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#@vd00.calculate
|
@@ -102,7 +102,7 @@ class TC_VaspDir < Test::Unit::TestCase
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|
102
102
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assert(FileTest.exist? "test/vaspdir/not-yet/POSCAR")
|
103
103
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assert(FileTest.exist? "test/vaspdir/not-yet/POTCAR")
|
104
104
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|
105
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-
lock_dir = "test/vaspdir/not-yet/
|
105
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+
lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
|
106
106
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Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
|
107
107
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end
|
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108
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|
data/test/test_vaspgeomopt.rb
CHANGED
data/vasputils.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
|
7
7
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s.name = "vasputils"
|
8
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-
s.version = "0.0.
|
8
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+
s.version = "0.0.5"
|
9
9
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|
10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["ippei94da"]
|
12
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-
s.date = "2012-05-
|
12
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+
s.date = "2012-05-08"
|
13
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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."
|
14
14
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s.email = "ippei94da@gmail.com"
|
15
15
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s.executables = ["addVolumeToten.rb", "latticeconstants", "lsvasp", "lsvaspdir", "lsvaspseries", "qsubvasp", "runvasp", "symposcar"]
|
@@ -207,9 +207,9 @@ Gem::Specification.new do |s|
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|
207
207
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s.specification_version = 3
|
208
208
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|
209
209
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
210
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-
s.add_development_dependency(%q<rdoc>, ["
|
211
|
-
s.add_development_dependency(%q<bundler>, ["
|
212
|
-
s.add_development_dependency(%q<jeweler>, ["
|
210
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+
s.add_development_dependency(%q<rdoc>, [">= 3.12"])
|
211
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+
s.add_development_dependency(%q<bundler>, [">= 1.1.3"])
|
212
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+
s.add_development_dependency(%q<jeweler>, [">= 1.8.3"])
|
213
213
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s.add_development_dependency(%q<simplecov>, [">= 0"])
|
214
214
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s.add_development_dependency(%q<crystalcell>, [">= 0.0.0"])
|
215
215
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s.add_development_dependency(%q<mageo>, [">= 0.0.0"])
|
@@ -218,9 +218,9 @@ Gem::Specification.new do |s|
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|
218
218
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s.add_development_dependency(%q<comana>, [">= 0.0.5"])
|
219
219
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s.add_development_dependency(%q<builtinextension>, [">= 0.0.3"])
|
220
220
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else
|
221
|
-
s.add_dependency(%q<rdoc>, ["
|
222
|
-
s.add_dependency(%q<bundler>, ["
|
223
|
-
s.add_dependency(%q<jeweler>, ["
|
221
|
+
s.add_dependency(%q<rdoc>, [">= 3.12"])
|
222
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+
s.add_dependency(%q<bundler>, [">= 1.1.3"])
|
223
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+
s.add_dependency(%q<jeweler>, [">= 1.8.3"])
|
224
224
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s.add_dependency(%q<simplecov>, [">= 0"])
|
225
225
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s.add_dependency(%q<crystalcell>, [">= 0.0.0"])
|
226
226
|
s.add_dependency(%q<mageo>, [">= 0.0.0"])
|
@@ -230,9 +230,9 @@ Gem::Specification.new do |s|
|
|
230
230
|
s.add_dependency(%q<builtinextension>, [">= 0.0.3"])
|
231
231
|
end
|
232
232
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else
|
233
|
-
s.add_dependency(%q<rdoc>, ["
|
234
|
-
s.add_dependency(%q<bundler>, ["
|
235
|
-
s.add_dependency(%q<jeweler>, ["
|
233
|
+
s.add_dependency(%q<rdoc>, [">= 3.12"])
|
234
|
+
s.add_dependency(%q<bundler>, [">= 1.1.3"])
|
235
|
+
s.add_dependency(%q<jeweler>, [">= 1.8.3"])
|
236
236
|
s.add_dependency(%q<simplecov>, [">= 0"])
|
237
237
|
s.add_dependency(%q<crystalcell>, [">= 0.0.0"])
|
238
238
|
s.add_dependency(%q<mageo>, [">= 0.0.0"])
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: vasputils
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.5
|
5
5
|
prerelease:
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
@@ -9,44 +9,44 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2012-05-
|
12
|
+
date: 2012-05-08 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: rdoc
|
16
|
-
requirement: &
|
16
|
+
requirement: &82143140 !ruby/object:Gem::Requirement
|
17
17
|
none: false
|
18
18
|
requirements:
|
19
|
-
- -
|
19
|
+
- - ! '>='
|
20
20
|
- !ruby/object:Gem::Version
|
21
21
|
version: '3.12'
|
22
22
|
type: :development
|
23
23
|
prerelease: false
|
24
|
-
version_requirements: *
|
24
|
+
version_requirements: *82143140
|
25
25
|
- !ruby/object:Gem::Dependency
|
26
26
|
name: bundler
|
27
|
-
requirement: &
|
27
|
+
requirement: &82141240 !ruby/object:Gem::Requirement
|
28
28
|
none: false
|
29
29
|
requirements:
|
30
|
-
- -
|
30
|
+
- - ! '>='
|
31
31
|
- !ruby/object:Gem::Version
|
32
32
|
version: 1.1.3
|
33
33
|
type: :development
|
34
34
|
prerelease: false
|
35
|
-
version_requirements: *
|
35
|
+
version_requirements: *82141240
|
36
36
|
- !ruby/object:Gem::Dependency
|
37
37
|
name: jeweler
|
38
|
-
requirement: &
|
38
|
+
requirement: &82139430 !ruby/object:Gem::Requirement
|
39
39
|
none: false
|
40
40
|
requirements:
|
41
|
-
- -
|
41
|
+
- - ! '>='
|
42
42
|
- !ruby/object:Gem::Version
|
43
43
|
version: 1.8.3
|
44
44
|
type: :development
|
45
45
|
prerelease: false
|
46
|
-
version_requirements: *
|
46
|
+
version_requirements: *82139430
|
47
47
|
- !ruby/object:Gem::Dependency
|
48
48
|
name: simplecov
|
49
|
-
requirement: &
|
49
|
+
requirement: &82155010 !ruby/object:Gem::Requirement
|
50
50
|
none: false
|
51
51
|
requirements:
|
52
52
|
- - ! '>='
|
@@ -54,10 +54,10 @@ dependencies:
|
|
54
54
|
version: '0'
|
55
55
|
type: :development
|
56
56
|
prerelease: false
|
57
|
-
version_requirements: *
|
57
|
+
version_requirements: *82155010
|
58
58
|
- !ruby/object:Gem::Dependency
|
59
59
|
name: crystalcell
|
60
|
-
requirement: &
|
60
|
+
requirement: &82154520 !ruby/object:Gem::Requirement
|
61
61
|
none: false
|
62
62
|
requirements:
|
63
63
|
- - ! '>='
|
@@ -65,10 +65,10 @@ dependencies:
|
|
65
65
|
version: 0.0.0
|
66
66
|
type: :development
|
67
67
|
prerelease: false
|
68
|
-
version_requirements: *
|
68
|
+
version_requirements: *82154520
|
69
69
|
- !ruby/object:Gem::Dependency
|
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|
name: mageo
|
71
|
-
requirement: &
|
71
|
+
requirement: &82153850 !ruby/object:Gem::Requirement
|
72
72
|
none: false
|
73
73
|
requirements:
|
74
74
|
- - ! '>='
|
@@ -76,10 +76,10 @@ dependencies:
|
|
76
76
|
version: 0.0.0
|
77
77
|
type: :development
|
78
78
|
prerelease: false
|
79
|
-
version_requirements: *
|
79
|
+
version_requirements: *82153850
|
80
80
|
- !ruby/object:Gem::Dependency
|
81
81
|
name: malge
|
82
|
-
requirement: &
|
82
|
+
requirement: &82153190 !ruby/object:Gem::Requirement
|
83
83
|
none: false
|
84
84
|
requirements:
|
85
85
|
- - ! '>='
|
@@ -87,10 +87,10 @@ dependencies:
|
|
87
87
|
version: 0.0.1
|
88
88
|
type: :development
|
89
89
|
prerelease: false
|
90
|
-
version_requirements: *
|
90
|
+
version_requirements: *82153190
|
91
91
|
- !ruby/object:Gem::Dependency
|
92
92
|
name: maset
|
93
|
-
requirement: &
|
93
|
+
requirement: &82152310 !ruby/object:Gem::Requirement
|
94
94
|
none: false
|
95
95
|
requirements:
|
96
96
|
- - ! '>='
|
@@ -98,10 +98,10 @@ dependencies:
|
|
98
98
|
version: 0.0.0
|
99
99
|
type: :development
|
100
100
|
prerelease: false
|
101
|
-
version_requirements: *
|
101
|
+
version_requirements: *82152310
|
102
102
|
- !ruby/object:Gem::Dependency
|
103
103
|
name: comana
|
104
|
-
requirement: &
|
104
|
+
requirement: &82150690 !ruby/object:Gem::Requirement
|
105
105
|
none: false
|
106
106
|
requirements:
|
107
107
|
- - ! '>='
|
@@ -109,10 +109,10 @@ dependencies:
|
|
109
109
|
version: 0.0.5
|
110
110
|
type: :development
|
111
111
|
prerelease: false
|
112
|
-
version_requirements: *
|
112
|
+
version_requirements: *82150690
|
113
113
|
- !ruby/object:Gem::Dependency
|
114
114
|
name: builtinextension
|
115
|
-
requirement: &
|
115
|
+
requirement: &82149970 !ruby/object:Gem::Requirement
|
116
116
|
none: false
|
117
117
|
requirements:
|
118
118
|
- - ! '>='
|
@@ -120,7 +120,7 @@ dependencies:
|
|
120
120
|
version: 0.0.3
|
121
121
|
type: :development
|
122
122
|
prerelease: false
|
123
|
-
version_requirements: *
|
123
|
+
version_requirements: *82149970
|
124
124
|
description: ! "This gem provides parsers for some of input and output files for VASP.\n
|
125
125
|
\ This will provide support command for computations."
|
126
126
|
email: ippei94da@gmail.com
|
@@ -331,7 +331,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
331
331
|
version: '0'
|
332
332
|
segments:
|
333
333
|
- 0
|
334
|
-
hash: -
|
334
|
+
hash: -917063793
|
335
335
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
336
336
|
none: false
|
337
337
|
requirements:
|