crystalcell 0.0.1 → 0.0.2

data/CHANGES

@@ -1,13 +1,19 @@
 = crystalcell Changelog
 
-== Master (for 0.0.1)
+== Master (for 0.0.3)
+
+== Version 0.0.2 [2014-08-30] released
+* Change cell.dump_poscar for vasp 5.
+* Update dependency on other gems.
+
+== Version 0.0.1 [2013-04-18] released
 * Change indent char from tab char to two spaces.
 * Introduce module CrystalCell as new namespace.
 * Add Cell#symmetry_operations and Cell#axis_independencies.
   They depends on spglib.
 * Getspg loading is changed.
 * Adjust to mageo-0.0.2.
-* Adjust to builtinextension-0.1.0
+* Adjust to builtinextension-0.1.0.
 
 == Version 0.0.0
 * Initial release.

data/Gemfile

@@ -6,13 +6,13 @@ 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", "~> 1.3.5"
-  gem "jeweler", "~> 1.8.3"
-  gem "simplecov", ">= 0"
-  gem "malge", ">= 0.0.6"
-  gem "mageo", ">= 0.0.2"
+  gem "rdoc", "~> 4.1.1"
+  gem "bundler", "~> 1.7.2"
+  gem "jeweler", "~> 2.0.1"
+  gem "simplecov", ">= 0.9.0"
+  gem "malge", ">= 0.0.8"
+  gem "mageo", ">= 0.0.3"
   gem "maset", ">= 0.0.0"
-  gem "builtinextension", ">= 0.1.0"
+  gem "builtinextension", ">= 0.1.2"
   #gem "psych", ">= 0"
 end

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.0.2

data/lib/crystalcell/cell.rb

@@ -574,6 +574,9 @@ class CrystalCell::Cell
       elem_list[ elem ] = @atoms.select{ |atom| atom.element == elem }
     end
 
+    ##element symbols
+    results << "  " + element_order.join("  ")
+
     ##numbers of element atoms
     tmp = ''
     element_order.each do |elem|

data/test/cif/ZrO2-25C.cif

@@ -0,0 +1,40 @@
+#======================================================================
+
+# CRYSTAL DATA
+# obtained from
+# http://staff.aist.go.jp/nomura-k/japanese/itscgallary.htm
+# Reference: M. Yashima, T. Hirose, S. Katano, Y. Suzuki, M. Kakihana,
+# and M. Yoshimura, Physical Review B - Condensed Matter and Materials
+# Physics, 51, 8018 (1995).
+
+#----------------------------------------------------------------------
+
+_pd_phase_name                         'ZrO2'
+_cell_length_a                         5.1501(2)
+_cell_length_b                         5.2077(2)
+_cell_length_c                         5.3171(2)
+_cell_angle_alpha                      90
+_cell_angle_beta                       99.224(2)
+_cell_angle_gamma                      90
+_symmetry_space_group_name_H-M         'P 21/c  '
+_symmetry_Int_Tables_number            14
+
+loop_
+_symmetry_equiv_pos_as_xyz
+   'x, y, z'
+   '-x, -y, -z'
+   '-x, y+1/2, -z+1/2'
+   'x, -y+1/2, z+1/2'
+
+loop_
+   _atom_site_label
+   _atom_site_occupancy
+   _atom_site_fract_x
+   _atom_site_fract_y
+   _atom_site_fract_z
+   _atom_site_thermal_displace_type
+   _atom_site_B_iso_or_equiv
+   _atom_site_type_symbol
+   Zr       1    0.2746(3)    0.0407(3)    0.2078(2)   Biso 0.313   Zr
+   O1       1    0.0705(3)    0.3327(3)    0.3447(3)   Biso 0.328   O
+   O2       1    0.4499(3)    0.7588(3)    0.4793(3)   Biso 0.151   O

data/test/test_cell.rb

@@ -552,32 +552,35 @@ class TC_Cell < Test::Unit::TestCase
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  ',
       '',
       'Direct'
     ].join("\n")
 
-    c02_str = [
-      'c02',
+    c01_str = [
+      'c01',
       '1.0',
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  0  1',
       '  1  1',
       'Direct',
       '    0.00000000000000      0.00000000000000      0.00000000000000',
-      '    0.20000000000000      0.20000000000000      0.20000000000000'
+      '    0.10000000000000      0.20000000000000      0.30000000000000'
     ].join("\n")
 
-    c01_str = [
-      'c01',
+    c02_str = [
+      'c02',
       '1.0',
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  Li  O',
       '  1  1',
       'Direct',
       '    0.00000000000000      0.00000000000000      0.00000000000000',
-      '    0.10000000000000      0.20000000000000      0.30000000000000'
+      '    0.20000000000000      0.20000000000000      0.20000000000000'
     ].join("\n")
 
     c03_str = [
@@ -586,6 +589,7 @@ class TC_Cell < Test::Unit::TestCase
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  Li  O',
       '  1  1',
       'Direct',
       '    0.00000000000000      0.00000000000000      0.00000000000000',
@@ -598,6 +602,7 @@ class TC_Cell < Test::Unit::TestCase
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  Li  O',
       '  2  1',
       'Direct',
       '    0.00000000000000      0.00000000000000      0.00000000000000',
@@ -611,6 +616,7 @@ class TC_Cell < Test::Unit::TestCase
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  Li',
       '  1',
       'Direct',
       '    0.00000000000000      0.00000000000000      0.00000000000000'
@@ -622,6 +628,7 @@ class TC_Cell < Test::Unit::TestCase
       '    2.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      2.00000000000000      2.00000000000000',
       '    0.00000000000000      0.00000000000000      2.00000000000000',
+      '  Li  O',
       '  1  1',
       'Selective dynamics',
       'Direct',
@@ -663,13 +670,13 @@ class TC_Cell < Test::Unit::TestCase
     end
 
     StringIO.new do |io|
-      @c02.dump_poscar( [ 'Li', 'O' ], io )
-      assert_equal( c02, io.read )
+      @c01.dump_poscar( [ 0, 1 ], io )
+      assert_equal( c01, io.read )
     end
 
     StringIO.new do |io|
-      @c01.dump_poscar( [ 0, 1 ], io )
-      assert_equal( c01, io.read )
+      @c02.dump_poscar( [ 'Li', 'O' ], io )
+      assert_equal( c02, io.read )
     end
 
     StringIO.new do |io|

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crystalcell
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,77 +9,107 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-18 00:00:00.000000000 Z
+date: 2014-08-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &80677790 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: 4.1.1
   type: :development
   prerelease: false
-  version_requirements: *80677790
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.1.1
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &80676850 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.3.5
+        version: 1.7.2
   type: :development
   prerelease: false
-  version_requirements: *80676850
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.7.2
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &80676610 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.8.3
+        version: 2.0.1
   type: :development
   prerelease: false
-  version_requirements: *80676610
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.0.1
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &80676370 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.9.0
   type: :development
   prerelease: false
-  version_requirements: *80676370
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.0
 - !ruby/object:Gem::Dependency
   name: malge
-  requirement: &80676130 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.6
+        version: 0.0.8
   type: :development
   prerelease: false
-  version_requirements: *80676130
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.8
 - !ruby/object:Gem::Dependency
   name: mageo
-  requirement: &80675560 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.0.2
+        version: 0.0.3
   type: :development
   prerelease: false
-  version_requirements: *80675560
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.3
 - !ruby/object:Gem::Dependency
   name: maset
-  requirement: &80674860 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,18 +117,28 @@ dependencies:
         version: 0.0.0
   type: :development
   prerelease: false
-  version_requirements: *80674860
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.0
 - !ruby/object:Gem::Dependency
   name: builtinextension
-  requirement: &80674320 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.2
   type: :development
   prerelease: false
-  version_requirements: *80674320
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
 description: ! "This gem provides Cell, LatticeAxes, Atom classes, and so on.\n    And
   this provides simple treatment of a periodic boundary condition.\n  "
 email: ippei94da@gmail.com
@@ -115,13 +155,13 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
-- crystalcell.gemspec
 - lib/crystalcell.rb
 - lib/crystalcell/atom.rb
 - lib/crystalcell/cell.rb
 - lib/crystalcell/element.rb
 - lib/crystalcell/latticeaxes.rb
 - lib/crystalcell/periodiccell.rb
+- test/cif/ZrO2-25C.cif
 - test/helper.rb
 - test/test_atom.rb
 - test/test_cell.rb
@@ -143,7 +183,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -251979683
+      hash: -2738925869661308590
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -152,7 +192,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Classes around a cell in crystallography

data/crystalcell.gemspec

@@ -1,80 +0,0 @@
-# Generated by jeweler
-# DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
-# -*- encoding: utf-8 -*-
-
-Gem::Specification.new do |s|
-  s.name = "crystalcell"
-  s.version = "0.0.1"
-
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["ippei94da"]
-  s.date = "2013-04-18"
-  s.description = "This gem provides Cell, LatticeAxes, Atom classes, and so on.\n    And this provides simple treatment of a periodic boundary condition.\n  "
-  s.email = "ippei94da@gmail.com"
-  s.extra_rdoc_files = [
-    "LICENSE.txt",
-    "README.rdoc"
-  ]
-  s.files = [
-    ".document",
-    "CHANGES",
-    "Gemfile",
-    "LICENSE.txt",
-    "README.rdoc",
-    "Rakefile",
-    "VERSION",
-    "crystalcell.gemspec",
-    "lib/crystalcell.rb",
-    "lib/crystalcell/atom.rb",
-    "lib/crystalcell/cell.rb",
-    "lib/crystalcell/element.rb",
-    "lib/crystalcell/latticeaxes.rb",
-    "lib/crystalcell/periodiccell.rb",
-    "test/helper.rb",
-    "test/test_atom.rb",
-    "test/test_cell.rb",
-    "test/test_element.rb",
-    "test/test_latticeaxes.rb",
-    "test/test_periodiccell.rb"
-  ]
-  s.homepage = "http://github.com/ippei94da/crystalcell"
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.11"
-  s.summary = "Classes around a cell in crystallography"
-
-  if s.respond_to? :specification_version then
-    s.specification_version = 3
-
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.3.5"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_development_dependency(%q<simplecov>, [">= 0"])
-      s.add_development_dependency(%q<malge>, [">= 0.0.6"])
-      s.add_development_dependency(%q<mageo>, [">= 0.0.2"])
-      s.add_development_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_development_dependency(%q<builtinextension>, [">= 0.1.0"])
-    else
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["~> 1.3.5"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_dependency(%q<simplecov>, [">= 0"])
-      s.add_dependency(%q<malge>, [">= 0.0.6"])
-      s.add_dependency(%q<mageo>, [">= 0.0.2"])
-      s.add_dependency(%q<maset>, [">= 0.0.0"])
-      s.add_dependency(%q<builtinextension>, [">= 0.1.0"])
-    end
-  else
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["~> 1.3.5"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-    s.add_dependency(%q<simplecov>, [">= 0"])
-    s.add_dependency(%q<malge>, [">= 0.0.6"])
-    s.add_dependency(%q<mageo>, [">= 0.0.2"])
-    s.add_dependency(%q<maset>, [">= 0.0.0"])
-    s.add_dependency(%q<builtinextension>, [">= 0.1.0"])
-  end
-end
-