crystalcell 0.0.1 → 0.0.2
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- data/CHANGES +8 -2
- data/Gemfile +7 -7
- data/VERSION +1 -1
- data/lib/crystalcell/cell.rb +3 -0
- data/test/cif/ZrO2-25C.cif +40 -0
- data/test/test_cell.rb +17 -10
- metadata +68 -28
- data/crystalcell.gemspec +0 -80
data/CHANGES
CHANGED
@@ -1,13 +1,19 @@
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1
1
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= crystalcell Changelog
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2
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-
== Master (for 0.0.
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+
== Master (for 0.0.3)
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4
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+
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5
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+
== Version 0.0.2 [2014-08-30] released
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* Change cell.dump_poscar for vasp 5.
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7
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* Update dependency on other gems.
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8
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+
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9
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== Version 0.0.1 [2013-04-18] released
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* Change indent char from tab char to two spaces.
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5
11
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* Introduce module CrystalCell as new namespace.
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12
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* Add Cell#symmetry_operations and Cell#axis_independencies.
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They depends on spglib.
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8
14
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* Getspg loading is changed.
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9
15
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* Adjust to mageo-0.0.2.
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10
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-
* Adjust to builtinextension-0.1.0
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+
* Adjust to builtinextension-0.1.0.
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17
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== Version 0.0.0
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* Initial release.
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data/Gemfile
CHANGED
@@ -6,13 +6,13 @@ 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
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# Include everything needed to run rake, tests, features, etc.
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8
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group :development do
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9
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-
gem "rdoc", "~>
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10
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-
gem "bundler", "~> 1.
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11
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-
gem "jeweler", "~>
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12
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-
gem "simplecov", ">= 0"
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13
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-
gem "malge", ">= 0.0.
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14
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-
gem "mageo", ">= 0.0.
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9
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+
gem "rdoc", "~> 4.1.1"
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10
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+
gem "bundler", "~> 1.7.2"
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11
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+
gem "jeweler", "~> 2.0.1"
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12
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+
gem "simplecov", ">= 0.9.0"
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13
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+
gem "malge", ">= 0.0.8"
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14
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+
gem "mageo", ">= 0.0.3"
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gem "maset", ">= 0.0.0"
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-
gem "builtinextension", ">= 0.1.
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+
gem "builtinextension", ">= 0.1.2"
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#gem "psych", ">= 0"
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18
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end
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.0.
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1
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+
0.0.2
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data/lib/crystalcell/cell.rb
CHANGED
@@ -574,6 +574,9 @@ class CrystalCell::Cell
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|
574
574
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elem_list[ elem ] = @atoms.select{ |atom| atom.element == elem }
|
575
575
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end
|
576
576
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|
577
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+
##element symbols
|
578
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+
results << " " + element_order.join(" ")
|
579
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+
|
577
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##numbers of element atoms
|
578
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tmp = ''
|
579
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element_order.each do |elem|
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@@ -0,0 +1,40 @@
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1
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+
#======================================================================
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+
|
3
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+
# CRYSTAL DATA
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# obtained from
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# http://staff.aist.go.jp/nomura-k/japanese/itscgallary.htm
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6
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+
# Reference: M. Yashima, T. Hirose, S. Katano, Y. Suzuki, M. Kakihana,
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7
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+
# and M. Yoshimura, Physical Review B - Condensed Matter and Materials
|
8
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+
# Physics, 51, 8018 (1995).
|
9
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+
|
10
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+
#----------------------------------------------------------------------
|
11
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+
|
12
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+
_pd_phase_name 'ZrO2'
|
13
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+
_cell_length_a 5.1501(2)
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14
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+
_cell_length_b 5.2077(2)
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15
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+
_cell_length_c 5.3171(2)
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16
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+
_cell_angle_alpha 90
|
17
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+
_cell_angle_beta 99.224(2)
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18
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+
_cell_angle_gamma 90
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19
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+
_symmetry_space_group_name_H-M 'P 21/c '
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20
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_symmetry_Int_Tables_number 14
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21
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+
|
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+
loop_
|
23
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_symmetry_equiv_pos_as_xyz
|
24
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+
'x, y, z'
|
25
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+
'-x, -y, -z'
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26
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'-x, y+1/2, -z+1/2'
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'x, -y+1/2, z+1/2'
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+
|
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+
loop_
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+
_atom_site_label
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_atom_site_occupancy
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_atom_site_fract_x
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+
_atom_site_fract_y
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_atom_site_fract_z
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+
_atom_site_thermal_displace_type
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_atom_site_B_iso_or_equiv
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_atom_site_type_symbol
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+
Zr 1 0.2746(3) 0.0407(3) 0.2078(2) Biso 0.313 Zr
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39
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+
O1 1 0.0705(3) 0.3327(3) 0.3447(3) Biso 0.328 O
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40
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+
O2 1 0.4499(3) 0.7588(3) 0.4793(3) Biso 0.151 O
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data/test/test_cell.rb
CHANGED
@@ -552,32 +552,35 @@ class TC_Cell < Test::Unit::TestCase
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552
552
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' 2.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 0.00000000000000 2.00000000000000',
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+
' ',
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'',
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'Direct'
|
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].join("\n")
|
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|
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-
|
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-
'
|
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+
c01_str = [
|
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'c01',
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'1.0',
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' 2.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 0.00000000000000 2.00000000000000',
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' 0 1',
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' 1 1',
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'Direct',
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' 0.00000000000000 0.00000000000000 0.00000000000000',
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-
' 0.
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+
' 0.10000000000000 0.20000000000000 0.30000000000000'
|
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].join("\n")
|
570
572
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|
571
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-
|
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-
'
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+
c02_str = [
|
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'c02',
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575
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'1.0',
|
574
576
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' 2.00000000000000 2.00000000000000 2.00000000000000',
|
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577
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' 0.00000000000000 2.00000000000000 2.00000000000000',
|
576
578
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' 0.00000000000000 0.00000000000000 2.00000000000000',
|
579
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+
' Li O',
|
577
580
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' 1 1',
|
578
581
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'Direct',
|
579
582
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' 0.00000000000000 0.00000000000000 0.00000000000000',
|
580
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-
' 0.
|
583
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+
' 0.20000000000000 0.20000000000000 0.20000000000000'
|
581
584
|
].join("\n")
|
582
585
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|
583
586
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c03_str = [
|
@@ -586,6 +589,7 @@ class TC_Cell < Test::Unit::TestCase
|
|
586
589
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' 2.00000000000000 2.00000000000000 2.00000000000000',
|
587
590
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' 0.00000000000000 2.00000000000000 2.00000000000000',
|
588
591
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' 0.00000000000000 0.00000000000000 2.00000000000000',
|
592
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+
' Li O',
|
589
593
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' 1 1',
|
590
594
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'Direct',
|
591
595
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' 0.00000000000000 0.00000000000000 0.00000000000000',
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@@ -598,6 +602,7 @@ class TC_Cell < Test::Unit::TestCase
|
|
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602
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' 2.00000000000000 2.00000000000000 2.00000000000000',
|
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603
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' 0.00000000000000 2.00000000000000 2.00000000000000',
|
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604
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' 0.00000000000000 0.00000000000000 2.00000000000000',
|
605
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+
' Li O',
|
601
606
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' 2 1',
|
602
607
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'Direct',
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603
608
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' 0.00000000000000 0.00000000000000 0.00000000000000',
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@@ -611,6 +616,7 @@ class TC_Cell < Test::Unit::TestCase
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611
616
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' 2.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 2.00000000000000 2.00000000000000',
|
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' 0.00000000000000 0.00000000000000 2.00000000000000',
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+
' Li',
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' 1',
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621
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'Direct',
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' 0.00000000000000 0.00000000000000 0.00000000000000'
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@@ -622,6 +628,7 @@ class TC_Cell < Test::Unit::TestCase
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' 2.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 2.00000000000000 2.00000000000000',
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' 0.00000000000000 0.00000000000000 2.00000000000000',
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631
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+
' Li O',
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' 1 1',
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'Selective dynamics',
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'Direct',
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@@ -663,13 +670,13 @@ class TC_Cell < Test::Unit::TestCase
|
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670
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end
|
664
671
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|
665
672
|
StringIO.new do |io|
|
666
|
-
@
|
667
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-
assert_equal(
|
673
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+
@c01.dump_poscar( [ 0, 1 ], io )
|
674
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+
assert_equal( c01, io.read )
|
668
675
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end
|
669
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StringIO.new do |io|
|
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-
@
|
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-
assert_equal(
|
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+
@c02.dump_poscar( [ 'Li', 'O' ], io )
|
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+
assert_equal( c02, io.read )
|
673
680
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end
|
674
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StringIO.new do |io|
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: crystalcell
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3
3
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version: !ruby/object:Gem::Version
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-
version: 0.0.
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+
version: 0.0.2
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prerelease:
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platform: ruby
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authors:
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@@ -9,77 +9,107 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date:
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date: 2014-08-30 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rdoc
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version:
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version: 4.1.1
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type: :development
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 4.1.1
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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-
version: 1.
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+
version: 1.7.2
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type: :development
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prerelease: false
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-
version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.7.2
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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-
version:
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version: 2.0.1
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type: :development
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prerelease: false
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-
version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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+
- - ~>
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- !ruby/object:Gem::Version
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version: 2.0.1
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- !ruby/object:Gem::Dependency
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name: simplecov
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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-
version:
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version: 0.9.0
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type: :development
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prerelease: false
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version_requirements:
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: 0.9.0
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- !ruby/object:Gem::Dependency
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name: malge
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requirement:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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- - ! '>='
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- !ruby/object:Gem::Version
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-
version: 0.0.
|
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+
version: 0.0.8
|
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type: :development
|
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prerelease: false
|
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-
version_requirements:
|
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+
version_requirements: !ruby/object:Gem::Requirement
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+
none: false
|
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+
requirements:
|
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+
- - ! '>='
|
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+
- !ruby/object:Gem::Version
|
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version: 0.0.8
|
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- !ruby/object:Gem::Dependency
|
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name: mageo
|
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-
requirement:
|
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+
requirement: !ruby/object:Gem::Requirement
|
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none: false
|
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requirements:
|
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|
- - ! '>='
|
75
100
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- !ruby/object:Gem::Version
|
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|
-
version: 0.0.
|
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+
version: 0.0.3
|
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102
|
type: :development
|
78
103
|
prerelease: false
|
79
|
-
version_requirements:
|
104
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
|
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+
requirements:
|
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+
- - ! '>='
|
108
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+
- !ruby/object:Gem::Version
|
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version: 0.0.3
|
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110
|
- !ruby/object:Gem::Dependency
|
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|
name: maset
|
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-
requirement:
|
112
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+
requirement: !ruby/object:Gem::Requirement
|
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|
none: false
|
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requirements:
|
85
115
|
- - ! '>='
|
@@ -87,18 +117,28 @@ dependencies:
|
|
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version: 0.0.0
|
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type: :development
|
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|
prerelease: false
|
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|
-
version_requirements:
|
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
|
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+
requirements:
|
123
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+
- - ! '>='
|
124
|
+
- !ruby/object:Gem::Version
|
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|
+
version: 0.0.0
|
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|
- !ruby/object:Gem::Dependency
|
92
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|
name: builtinextension
|
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-
requirement:
|
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|
+
requirement: !ruby/object:Gem::Requirement
|
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|
none: false
|
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requirements:
|
96
131
|
- - ! '>='
|
97
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|
- !ruby/object:Gem::Version
|
98
|
-
version: 0.1.
|
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|
+
version: 0.1.2
|
99
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|
type: :development
|
100
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|
prerelease: false
|
101
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-
version_requirements:
|
136
|
+
version_requirements: !ruby/object:Gem::Requirement
|
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+
none: false
|
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+
requirements:
|
139
|
+
- - ! '>='
|
140
|
+
- !ruby/object:Gem::Version
|
141
|
+
version: 0.1.2
|
102
142
|
description: ! "This gem provides Cell, LatticeAxes, Atom classes, and so on.\n And
|
103
143
|
this provides simple treatment of a periodic boundary condition.\n "
|
104
144
|
email: ippei94da@gmail.com
|
@@ -115,13 +155,13 @@ files:
|
|
115
155
|
- README.rdoc
|
116
156
|
- Rakefile
|
117
157
|
- VERSION
|
118
|
-
- crystalcell.gemspec
|
119
158
|
- lib/crystalcell.rb
|
120
159
|
- lib/crystalcell/atom.rb
|
121
160
|
- lib/crystalcell/cell.rb
|
122
161
|
- lib/crystalcell/element.rb
|
123
162
|
- lib/crystalcell/latticeaxes.rb
|
124
163
|
- lib/crystalcell/periodiccell.rb
|
164
|
+
- test/cif/ZrO2-25C.cif
|
125
165
|
- test/helper.rb
|
126
166
|
- test/test_atom.rb
|
127
167
|
- test/test_cell.rb
|
@@ -143,7 +183,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
143
183
|
version: '0'
|
144
184
|
segments:
|
145
185
|
- 0
|
146
|
-
hash: -
|
186
|
+
hash: -2738925869661308590
|
147
187
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
148
188
|
none: false
|
149
189
|
requirements:
|
@@ -152,7 +192,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
152
192
|
version: '0'
|
153
193
|
requirements: []
|
154
194
|
rubyforge_project:
|
155
|
-
rubygems_version: 1.8.
|
195
|
+
rubygems_version: 1.8.23
|
156
196
|
signing_key:
|
157
197
|
specification_version: 3
|
158
198
|
summary: Classes around a cell in crystallography
|
data/crystalcell.gemspec
DELETED
@@ -1,80 +0,0 @@
|
|
1
|
-
# Generated by jeweler
|
2
|
-
# DO NOT EDIT THIS FILE DIRECTLY
|
3
|
-
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
4
|
-
# -*- encoding: utf-8 -*-
|
5
|
-
|
6
|
-
Gem::Specification.new do |s|
|
7
|
-
s.name = "crystalcell"
|
8
|
-
s.version = "0.0.1"
|
9
|
-
|
10
|
-
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
|
-
s.authors = ["ippei94da"]
|
12
|
-
s.date = "2013-04-18"
|
13
|
-
s.description = "This gem provides Cell, LatticeAxes, Atom classes, and so on.\n And this provides simple treatment of a periodic boundary condition.\n "
|
14
|
-
s.email = "ippei94da@gmail.com"
|
15
|
-
s.extra_rdoc_files = [
|
16
|
-
"LICENSE.txt",
|
17
|
-
"README.rdoc"
|
18
|
-
]
|
19
|
-
s.files = [
|
20
|
-
".document",
|
21
|
-
"CHANGES",
|
22
|
-
"Gemfile",
|
23
|
-
"LICENSE.txt",
|
24
|
-
"README.rdoc",
|
25
|
-
"Rakefile",
|
26
|
-
"VERSION",
|
27
|
-
"crystalcell.gemspec",
|
28
|
-
"lib/crystalcell.rb",
|
29
|
-
"lib/crystalcell/atom.rb",
|
30
|
-
"lib/crystalcell/cell.rb",
|
31
|
-
"lib/crystalcell/element.rb",
|
32
|
-
"lib/crystalcell/latticeaxes.rb",
|
33
|
-
"lib/crystalcell/periodiccell.rb",
|
34
|
-
"test/helper.rb",
|
35
|
-
"test/test_atom.rb",
|
36
|
-
"test/test_cell.rb",
|
37
|
-
"test/test_element.rb",
|
38
|
-
"test/test_latticeaxes.rb",
|
39
|
-
"test/test_periodiccell.rb"
|
40
|
-
]
|
41
|
-
s.homepage = "http://github.com/ippei94da/crystalcell"
|
42
|
-
s.licenses = ["MIT"]
|
43
|
-
s.require_paths = ["lib"]
|
44
|
-
s.rubygems_version = "1.8.11"
|
45
|
-
s.summary = "Classes around a cell in crystallography"
|
46
|
-
|
47
|
-
if s.respond_to? :specification_version then
|
48
|
-
s.specification_version = 3
|
49
|
-
|
50
|
-
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
51
|
-
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
|
52
|
-
s.add_development_dependency(%q<bundler>, ["~> 1.3.5"])
|
53
|
-
s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
|
54
|
-
s.add_development_dependency(%q<simplecov>, [">= 0"])
|
55
|
-
s.add_development_dependency(%q<malge>, [">= 0.0.6"])
|
56
|
-
s.add_development_dependency(%q<mageo>, [">= 0.0.2"])
|
57
|
-
s.add_development_dependency(%q<maset>, [">= 0.0.0"])
|
58
|
-
s.add_development_dependency(%q<builtinextension>, [">= 0.1.0"])
|
59
|
-
else
|
60
|
-
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
61
|
-
s.add_dependency(%q<bundler>, ["~> 1.3.5"])
|
62
|
-
s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
|
63
|
-
s.add_dependency(%q<simplecov>, [">= 0"])
|
64
|
-
s.add_dependency(%q<malge>, [">= 0.0.6"])
|
65
|
-
s.add_dependency(%q<mageo>, [">= 0.0.2"])
|
66
|
-
s.add_dependency(%q<maset>, [">= 0.0.0"])
|
67
|
-
s.add_dependency(%q<builtinextension>, [">= 0.1.0"])
|
68
|
-
end
|
69
|
-
else
|
70
|
-
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
71
|
-
s.add_dependency(%q<bundler>, ["~> 1.3.5"])
|
72
|
-
s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
|
73
|
-
s.add_dependency(%q<simplecov>, [">= 0"])
|
74
|
-
s.add_dependency(%q<malge>, [">= 0.0.6"])
|
75
|
-
s.add_dependency(%q<mageo>, [">= 0.0.2"])
|
76
|
-
s.add_dependency(%q<maset>, [">= 0.0.0"])
|
77
|
-
s.add_dependency(%q<builtinextension>, [">= 0.1.0"])
|
78
|
-
end
|
79
|
-
end
|
80
|
-
|