crystalcell 0.0.3 → 0.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/CHANGES +23 -1
- data/Gemfile +9 -9
- data/VERSION +1 -1
- data/crystalcell.gemspec +41 -29
- data/lib/crystalcell/atom.rb +116 -118
- data/lib/crystalcell/cell.rb +542 -586
- data/lib/crystalcell/element.rb +49 -140
- data/lib/crystalcell/latticeaxes.rb +198 -185
- data/lib/crystalcell/periodiccell.rb +246 -244
- data/lib/crystalcell/povray/cell.rb +110 -0
- data/lib/crystalcell/povray/cylinder.rb +12 -0
- data/lib/crystalcell/povray/element.rb +284 -0
- data/lib/crystalcell/povray/sphere.rb +12 -0
- data/lib/crystalcell/povray/triangle.rb +17 -0
- data/lib/crystalcell/povray.rb +7 -0
- data/lib/crystalcell.rb +5 -1
- data/test/povray/test_cell.rb +179 -0
- data/test/povray/test_element.rb +230 -0
- data/test/test_atom.rb +198 -198
- data/test/test_cell.rb +1481 -1464
- data/test/test_element.rb +422 -642
- data/test/test_latticeaxes.rb +299 -283
- data/test/test_periodiccell.rb +928 -953
- metadata +63 -62
data/test/test_cell.rb
CHANGED
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#! /usr/bin/env ruby
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#! /usr/bin/ruby1.9 -W
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require "helper"
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require 'stringio'
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class CrystalCell::Cell
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public :symmetry_operations
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end
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class FooCell < CrystalCell::Cell; end
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class TC_Cell < Test::Unit::TestCase
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$tolerance = 10 ** (-10)
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$symprec = 1.0e-05
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$angle_tolerance = -1.0
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def setup
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# 原子のないセル。
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vectors00 = [[2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]
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axes00 = CrystalCell::LatticeAxes.new([[2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]])
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@c00 = CrystalCell::Cell.new(axes00)
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@c00.comment = 'c00'
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# 元素の識別子を数字にしたもの。
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ),
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CrystalCell::Atom.new( 1, [0.1, 0.2, 0.3] ),
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]
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@c01 = CrystalCell::Cell.new(axes00, atoms)
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@c01.comment = 'c01'
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# Li と O を1つずつ入れたセル。
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# @c02 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] )
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atoms = [
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CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ),
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CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ),
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]
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@c02 = CrystalCell::Cell.new(vectors00, atoms)
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@c02.comment = 'c02'
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# 原子の順序を逆にしたもの。
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atoms = [
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CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ),
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CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ),
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]
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@c03 = CrystalCell::Cell.new(vectors00, atoms)
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@c03.comment = 'c03'
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# 原子の順序がいりまじったもの
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atoms = [
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CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ),
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CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ),
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CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] ),
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]
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@c04 = CrystalCell::Cell.new(vectors00, atoms)
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@c04.comment = 'c04'
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# 原子が不足しているもの。
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atoms = [
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CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ),
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]
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@c05 = CrystalCell::Cell.new(vectors00, atoms)
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@c05.comment = 'c05'
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# Selective dynamics をいれたもの。
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atoms = [
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CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0], nil, [true, false, false ] ),
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CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ),
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]
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@c06 = CrystalCell::Cell.new(vectors00, atoms)
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@c06.comment = 'c06'
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# 元素の識別子を数字にしたもの。
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atoms = [
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CrystalCell::Atom.new( 0, Mageo::Vector3DInternal[0.0, 0.0, 0.0] ),
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CrystalCell::Atom.new( 1, Mageo::Vector3DInternal[0.2, 0.2, 0.2] ),
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]
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@c07 = CrystalCell::Cell.new(vectors00, atoms)
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@c07.comment = 'c07'
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# セル外の座標の原子を追加。
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atoms = [
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CrystalCell::Atom.new( 'Li', [ 1.2, 3.4, 5.6], "atom0", [ false, false, true] ),
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CrystalCell::Atom.new( 'O', [-1.2, -3.4, -5.6] ),
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]
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@c08 = CrystalCell::Cell.new(vectors00, atoms)
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@c08.comment = 'c08'
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#cubic
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axes = CrystalCell::LatticeAxes.new(
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[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
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)
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] )
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]
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@c10 = CrystalCell::Cell.new( axes, atoms)
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@c10.comment = 'cubic'
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#hexagonal
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axes = CrystalCell::LatticeAxes.new(
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[
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[0.86602540378443864676, 0.5, 0.0],
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[0.0, 1.0, 0.0],
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[0.0, 0.0, 1.0],
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]
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)
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] )
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]
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@c11 = CrystalCell::Cell.new( axes, atoms)
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@c11.comment = 'hexagonal'
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#monoclinic
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axes = CrystalCell::LatticeAxes.new(
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[ [1.5, 1.4, 0.0],
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[0.0, 1.2, 0.0],
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[0.0, 0.0, 1.0],
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]
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)
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0]),
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#CrystalCell::Atom.new( 0, [0.1, 0.2, 0.3]),
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#CrystalCell::Atom.new( 0, [0.2, 0.3, 0.4]),
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]
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@c12 = CrystalCell::Cell.new( axes, atoms)
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@c12.comment = 'monoclinic'
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#orthorhombic
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axes = CrystalCell::LatticeAxes.new(
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[
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[3.0, 0.0, 0.0],
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[0.0, 2.0, 0.0],
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[0.0, 0.0, 1.0],
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]
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)
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0])
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]
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@c13 = CrystalCell::Cell.new( axes, atoms)
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@c13.comment = 'orthorhombic'
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#tetragonal
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axes = CrystalCell::LatticeAxes.new(
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[
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[2.0, 0.0, 0.0],
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[0.0, 2.0, 0.0],
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[0.0, 0.0, 1.0],
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]
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)
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0], )
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]
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@c14 = CrystalCell::Cell.new( axes, atoms)
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@c14.comment = 'tetragonal'
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#tetragonal-b
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axes = CrystalCell::LatticeAxes.new(
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[
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[2.0, 0.0, 0.0],
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[0.0, 1.0, 0.0],
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[0.0, 0.0, 2.0],
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]
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)
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atoms = [
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CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0], )
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]
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@c14b = CrystalCell::Cell.new( axes, atoms)
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@c14b.comment = 'tetragonal-b'
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#triclinic
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axes = CrystalCell::LatticeAxes.new(
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[
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[1.5, 1.4, 1.3],
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[0.0, 1.2, 1.1],
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176
|
+
[0.0, 0.0, 1.0],
|
|
177
|
+
]
|
|
178
|
+
)
|
|
179
|
+
atoms = [
|
|
180
|
+
CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ),
|
|
181
|
+
CrystalCell::Atom.new( 0, [0.1, 0.2, 0.3] ),
|
|
182
|
+
CrystalCell::Atom.new( 0, [0.2, 0.3, 0.4] ),
|
|
183
|
+
]
|
|
184
|
+
@c15 = CrystalCell::Cell.new( axes, atoms)
|
|
185
|
+
@c15.comment = 'triclinic'
|
|
186
|
+
|
|
187
|
+
#trigonal
|
|
188
|
+
axes = CrystalCell::LatticeAxes.new(
|
|
189
|
+
[
|
|
190
|
+
[0.86602540378443864676, 0.5, 0.0],
|
|
191
|
+
[0.0, 1.0, 0.0],
|
|
192
|
+
[0.0, 0.0, 1.0],
|
|
193
|
+
]
|
|
194
|
+
)
|
|
195
|
+
atoms = [
|
|
196
|
+
CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0]),
|
|
197
|
+
CrystalCell::Atom.new( 0, [0.333333333333333, 0.333333333333333, 0.333333333333333] ),
|
|
198
|
+
]
|
|
199
|
+
@c16 = CrystalCell::Cell.new( axes, atoms)
|
|
200
|
+
@c16.comment = 'trigonal'
|
|
201
|
+
end
|
|
202
|
+
|
|
203
|
+
def test_initialize
|
|
204
|
+
la = CrystalCell::LatticeAxes.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] )
|
|
205
|
+
c10 = CrystalCell::Cell.new( la )
|
|
206
|
+
c10.comment = 'c00'
|
|
207
|
+
assert_equal( CrystalCell::Cell, c10.class )
|
|
208
|
+
assert_in_delta( 2.0, c10.axes[0][0], $tolerance )
|
|
209
|
+
assert_in_delta( 2.0, c10.axes[0][1], $tolerance )
|
|
210
|
+
assert_in_delta( 2.0, c10.axes[0][2], $tolerance )
|
|
211
|
+
assert_in_delta( 0.0, c10.axes[1][0], $tolerance )
|
|
212
|
+
assert_in_delta( 2.0, c10.axes[1][1], $tolerance )
|
|
213
|
+
assert_in_delta( 2.0, c10.axes[1][2], $tolerance )
|
|
214
|
+
assert_in_delta( 0.0, c10.axes[2][0], $tolerance )
|
|
215
|
+
assert_in_delta( 0.0, c10.axes[2][1], $tolerance )
|
|
216
|
+
assert_in_delta( 2.0, c10.axes[2][2], $tolerance )
|
|
217
|
+
|
|
218
|
+
|
|
219
|
+
end
|
|
220
|
+
|
|
221
|
+
def test_positions
|
|
222
|
+
assert_equal( [], @c00.positions)
|
|
223
|
+
assert_equal( [ Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.2, 0.2, 0.2] ], @c02.positions )
|
|
224
|
+
assert_equal( [ Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.1, 0.2, 0.3] ], @c01.positions )
|
|
225
|
+
end
|
|
226
|
+
|
|
227
|
+
def test_select_indices
|
|
228
|
+
assert_equal( [], @c00.select_indices{ |i| i.element == "" } )
|
|
229
|
+
assert_equal( [], @c00.select_indices{ |i| i.element == "Li" } )
|
|
230
|
+
|
|
231
|
+
assert_equal( [] , @c01.select_indices{ |i| i.element == "" } )
|
|
232
|
+
assert_equal( [] , @c01.select_indices{ |i| i.element == "Li" } )
|
|
233
|
+
#@c01.select_indices{ |i| p i.element }
|
|
234
|
+
assert_equal( [0], @c01.select_indices{ |i| i.element == 0 } )
|
|
235
|
+
|
|
236
|
+
assert_equal( [1], @c01.select_indices{ |i| i.element == 1 } )
|
|
237
|
+
|
|
238
|
+
assert_equal( [] , @c04.select_indices{ |i| i.element == "" } )
|
|
239
|
+
assert_equal( [0, 2], @c04.select_indices{ |i| i.element == "Li" } )
|
|
240
|
+
assert_equal( [1], @c04.select_indices{ |i| i.element == "O" } )
|
|
241
|
+
assert_equal( [ ], @c04.select_indices{ |i| i.element == 0 } )
|
|
242
|
+
assert_equal( [ ], @c04.select_indices{ |i| i.element == 1 } )
|
|
243
|
+
|
|
244
|
+
assert_equal( [1, 2], @c04.select_indices{ |i| i.position[0] > 0.05 } )
|
|
245
|
+
end
|
|
246
|
+
|
|
247
|
+
def test_atoms_in_supercell
|
|
248
|
+
t = @c02.atoms_in_supercell( 0, 0, 0, 0, 0, 1 )
|
|
249
|
+
assert_equal( 'Li', t[0].element )
|
|
250
|
+
assert_equal( 'Li', t[1].element )
|
|
251
|
+
assert_equal( 'O' , t[2].element )
|
|
252
|
+
assert_equal( 'O' , t[3].element )
|
|
253
|
+
|
|
254
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t[0].position )
|
|
255
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 1.0], t[1].position )
|
|
256
|
+
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t[2].position )
|
|
257
|
+
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 1.2], t[3].position )
|
|
258
|
+
|
|
259
|
+
t = @c02.atoms_in_supercell(-1, 1,-1, 1,-1, 1 )
|
|
260
|
+
assert_equal( ['Li']*27 + ['O'] * 27 , t.map{|i| i.element} )
|
|
261
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, -1.0], t[ 0].position )
|
|
262
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, 0.0], t[ 1].position )
|
|
263
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, 1.0], t[ 2].position )
|
|
264
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, -1.0], t[ 3].position )
|
|
265
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, 0.0], t[ 4].position )
|
|
266
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, 1.0], t[ 5].position )
|
|
267
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, -1.0], t[ 6].position )
|
|
268
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, 0.0], t[ 7].position )
|
|
269
|
+
assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, 1.0], t[ 8].position )
|
|
270
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, -1.0], t[ 9].position )
|
|
271
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, 0.0], t[10].position )
|
|
272
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, 1.0], t[11].position )
|
|
273
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, -1.0], t[12].position )
|
|
274
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, 0.0], t[13].position )
|
|
275
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, 1.0], t[14].position )
|
|
276
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, -1.0], t[15].position )
|
|
277
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, 0.0], t[16].position )
|
|
278
|
+
assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, 1.0], t[17].position )
|
|
279
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, -1.0], t[18].position )
|
|
280
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, 0.0], t[19].position )
|
|
281
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, 1.0], t[20].position )
|
|
282
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, -1.0], t[21].position )
|
|
283
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, 0.0], t[22].position )
|
|
284
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, 1.0], t[23].position )
|
|
285
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, -1.0], t[24].position )
|
|
286
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, 0.0], t[25].position )
|
|
287
|
+
assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, 1.0], t[26].position )
|
|
288
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, -0.8], t[27].position )
|
|
289
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, 0.2], t[28].position )
|
|
290
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, 1.2], t[29].position )
|
|
291
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, -0.8], t[30].position )
|
|
292
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, 0.2], t[31].position )
|
|
293
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, 1.2], t[32].position )
|
|
294
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, -0.8], t[33].position )
|
|
295
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, 0.2], t[34].position )
|
|
296
|
+
assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, 1.2], t[35].position )
|
|
297
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, -0.8], t[36].position )
|
|
298
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, 0.2], t[37].position )
|
|
299
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, 1.2], t[38].position )
|
|
300
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, -0.8], t[39].position )
|
|
301
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], t[40].position )
|
|
302
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 1.2], t[41].position )
|
|
303
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, -0.8], t[42].position )
|
|
304
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, 0.2], t[43].position )
|
|
305
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, 1.2], t[44].position )
|
|
306
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, -0.8], t[45].position )
|
|
307
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, 0.2], t[46].position )
|
|
308
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, 1.2], t[47].position )
|
|
309
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, -0.8], t[48].position )
|
|
310
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, 0.2], t[49].position )
|
|
311
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, 1.2], t[50].position )
|
|
312
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, -0.8], t[51].position )
|
|
313
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, 0.2], t[52].position )
|
|
314
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, 1.2], t[53].position )
|
|
315
|
+
end
|
|
316
|
+
|
|
317
|
+
def test_elements
|
|
318
|
+
assert_equal( [], @c00.elements)
|
|
319
|
+
assert_equal( [ 'Li', 'O' ], @c02.elements )
|
|
320
|
+
assert_equal( [ 0, 1 ], @c01.elements )
|
|
321
|
+
end
|
|
322
|
+
|
|
323
|
+
def test_add_atom
|
|
324
|
+
assert_raise(ArgumentError){
|
|
325
|
+
@c00.add_atom('Li', [0.5, 0.5, 0.5] )
|
|
326
|
+
}
|
|
327
|
+
|
|
328
|
+
@c00.add_atom(CrystalCell::Atom.new( 'Li', [0.5, 0.5, 0.5] ))
|
|
329
|
+
assert_equal( 1 , @c00.atoms.size)
|
|
330
|
+
assert_equal( 'Li' , @c00.atoms[0].element)
|
|
331
|
+
assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c00.atoms[0].position)
|
|
332
|
+
assert_equal( nil , @c00.atoms[0].name )
|
|
333
|
+
|
|
334
|
+
@c00.add_atom(CrystalCell::Atom.new( nil , [0.5, 0.5, 0.5], 'A' ))
|
|
335
|
+
assert_equal( 2 , @c00.atoms.size)
|
|
336
|
+
assert_equal( nil , @c00.atoms[1].element)
|
|
337
|
+
assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c00.atoms[1].position)
|
|
338
|
+
assert_equal( 'A' , @c00.atoms[1].name )
|
|
339
|
+
|
|
340
|
+
@c02.add_atom(CrystalCell::Atom.new( 'Li', [0.5, 0.5, 0.5] ))
|
|
341
|
+
assert_equal( 3 , @c02.atoms.size)
|
|
342
|
+
assert_equal( 'Li' , @c02.atoms[0].element)
|
|
343
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position)
|
|
344
|
+
assert_equal( 'O' , @c02.atoms[1].element)
|
|
345
|
+
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], @c02.atoms[1].position)
|
|
346
|
+
assert_equal( 'Li' , @c02.atoms[2].element)
|
|
347
|
+
assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c02.atoms[2].position)
|
|
348
|
+
|
|
349
|
+
@c01.add_atom(CrystalCell::Atom.new( 'Li', [0.5, 0.5, 0.5] ))
|
|
350
|
+
assert_equal( 3 , @c01.atoms.size)
|
|
351
|
+
assert_equal( 0 , @c01.atoms[0].element)
|
|
352
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c01.atoms[0].position)
|
|
353
|
+
assert_equal( 1 , @c01.atoms[1].element)
|
|
354
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], @c01.atoms[1].position)
|
|
355
|
+
assert_equal( 'Li' , @c01.atoms[2].element)
|
|
356
|
+
assert_equal( Mageo::Vector3DInternal[0.5, 0.5, 0.5], @c01.atoms[2].position)
|
|
357
|
+
|
|
358
|
+
end
|
|
359
|
+
|
|
360
|
+
def test_delete_atom
|
|
361
|
+
# assert_raise(RuntimeError ) {@c00.delete_atom( 0 ) }
|
|
362
|
+
assert_equal(nil, @c00.delete_atom( 0 ) )
|
|
363
|
+
assert_equal([], @c00.positions )
|
|
364
|
+
assert_equal([], @c00.elements )
|
|
365
|
+
|
|
366
|
+
@c02.delete_atom( 0 )
|
|
367
|
+
assert_equal( [ Mageo::Vector3DInternal[0.2, 0.2, 0.2] ], @c02.positions)
|
|
368
|
+
assert_equal( [ 'O' ], @c02.elements )
|
|
369
|
+
@c02.delete_atom( 0 )
|
|
370
|
+
assert_equal( [], @c02.positions)
|
|
371
|
+
assert_equal( [], @c02.elements )
|
|
372
|
+
|
|
373
|
+
@c01.delete_atom( 0 )
|
|
374
|
+
assert_equal( [ Mageo::Vector3DInternal[0.1, 0.2, 0.3] ], @c01.positions)
|
|
375
|
+
assert_equal( [ 1 ], @c01.elements )
|
|
376
|
+
end
|
|
377
|
+
|
|
378
|
+
def test_set_elements
|
|
379
|
+
# 原子がないので変更されない。
|
|
380
|
+
@c00.set_elements( [] )
|
|
381
|
+
assert_equal( [], @c00.atoms )
|
|
382
|
+
|
|
383
|
+
# 0 -> 'Li、 1 -> 'O' に変更。
|
|
384
|
+
tmp = Marshal.load( Marshal.dump( @c01 ))
|
|
385
|
+
tmp.set_elements( [ 'Li', 'O' ] )
|
|
386
|
+
assert_equal( 'Li', tmp.atoms[0].element )
|
|
387
|
+
assert_equal( 'O', tmp.atoms[1].element )
|
|
388
|
+
|
|
389
|
+
# 0 -> 'Li, 片方だけ変更。
|
|
390
|
+
tmp = Marshal.load( Marshal.dump( @c01 ))
|
|
391
|
+
tmp.set_elements( [ 'Li' ] )
|
|
392
|
+
assert_equal( 'Li', tmp.atoms[0].element )
|
|
393
|
+
assert_equal( 1, tmp.atoms[1].element )
|
|
394
|
+
|
|
395
|
+
# 元々整数値以外にセットされているのでマッチせず変更されない。
|
|
396
|
+
tmp = Marshal.load( Marshal.dump( @c02 ))
|
|
397
|
+
tmp.set_elements( [ 'O', 'Li' ] )
|
|
398
|
+
assert_equal( 'Li', tmp.atoms[0].element )
|
|
399
|
+
assert_equal( 'O', tmp.atoms[1].element )
|
|
400
|
+
|
|
401
|
+
# Hash argument.
|
|
402
|
+
# 0 -> 'Li、 1 -> 'O' に変更。
|
|
403
|
+
tmp = Marshal.load( Marshal.dump( @c01 ))
|
|
404
|
+
tmp.set_elements( { 0 => 'Li', 1 => 'O' } )
|
|
405
|
+
assert_equal( 'Li', tmp.atoms[0].element )
|
|
406
|
+
assert_equal( 'O', tmp.atoms[1].element )
|
|
407
|
+
|
|
408
|
+
# 'Li' -> 'Na', 'O' -> 'S' に変更。
|
|
409
|
+
tmp = Marshal.load( Marshal.dump( @c02 ))
|
|
410
|
+
tmp.set_elements( { 'Li' => 'Na', 'O' => 'S' } )
|
|
411
|
+
assert_equal( 'Na', tmp.atoms[0].element )
|
|
412
|
+
assert_equal( 'S', tmp.atoms[1].element )
|
|
413
|
+
|
|
414
|
+
# 'Li' -> 'Na'、 片方だけ変更。
|
|
415
|
+
tmp = Marshal.load( Marshal.dump( @c02 ))
|
|
416
|
+
tmp.set_elements( { 'Li' => 'Na' } )
|
|
417
|
+
assert_equal( 'Na', tmp.atoms[0].element )
|
|
418
|
+
assert_equal( 'O', tmp.atoms[1].element )
|
|
419
|
+
end
|
|
420
|
+
|
|
421
|
+
def test_equal_lattice_in_delta?
|
|
422
|
+
assert_equal( true , @c00.equal_lattice_in_delta?(@c00, 0.001, 0.1) )
|
|
423
|
+
assert_equal( true , @c00.equal_lattice_in_delta?(@c02, 0.001, 0.1) )
|
|
424
|
+
assert_equal( true , @c00.equal_lattice_in_delta?(@c01, 0.001, 0.1) )
|
|
425
|
+
assert_equal( true , @c02.equal_lattice_in_delta?(@c00, 0.001, 0.1) )
|
|
426
|
+
assert_equal( true , @c02.equal_lattice_in_delta?(@c02, 0.001, 0.1) )
|
|
427
|
+
assert_equal( true , @c02.equal_lattice_in_delta?(@c01, 0.001, 0.1) )
|
|
428
|
+
assert_equal( true , @c01.equal_lattice_in_delta?(@c00, 0.001, 0.1) )
|
|
429
|
+
assert_equal( true , @c01.equal_lattice_in_delta?(@c02, 0.001, 0.1) )
|
|
430
|
+
assert_equal( true , @c01.equal_lattice_in_delta?(@c01, 0.001, 0.1) )
|
|
431
|
+
|
|
432
|
+
end
|
|
433
|
+
|
|
434
|
+
def test_equal_atoms_in_delta?
|
|
435
|
+
assert_equal( true , @c00.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
436
|
+
assert_equal( false, @c00.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
437
|
+
assert_equal( false, @c00.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
438
|
+
assert_equal( false, @c00.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
439
|
+
assert_equal( false, @c00.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
440
|
+
assert_equal( false, @c00.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
441
|
+
assert_equal( false, @c02.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
442
|
+
assert_equal( true , @c02.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
443
|
+
assert_equal( false, @c02.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
444
|
+
assert_equal( true , @c02.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
445
|
+
assert_equal( false, @c02.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
446
|
+
assert_equal( false, @c02.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
447
|
+
assert_equal( false, @c01.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
448
|
+
assert_equal( false, @c01.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
449
|
+
assert_equal( true , @c01.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
450
|
+
assert_equal( false, @c01.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
451
|
+
assert_equal( false, @c01.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
452
|
+
assert_equal( false, @c01.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
453
|
+
assert_equal( false, @c03.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
454
|
+
assert_equal( true , @c03.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
455
|
+
assert_equal( false, @c03.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
456
|
+
assert_equal( true , @c03.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
457
|
+
assert_equal( false, @c03.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
458
|
+
assert_equal( false, @c03.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
459
|
+
assert_equal( false, @c04.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
460
|
+
assert_equal( false, @c04.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
461
|
+
assert_equal( false, @c04.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
462
|
+
assert_equal( false, @c04.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
463
|
+
assert_equal( true , @c04.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
464
|
+
assert_equal( false, @c04.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
465
|
+
assert_equal( false, @c05.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
466
|
+
assert_equal( false, @c05.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
467
|
+
assert_equal( false, @c05.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
468
|
+
assert_equal( false, @c05.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
469
|
+
assert_equal( false, @c05.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
470
|
+
assert_equal( true , @c05.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
471
|
+
end
|
|
472
|
+
|
|
473
|
+
def test_equal_in_delta?
|
|
474
|
+
assert_equal(true , @c00.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
475
|
+
assert_equal(false, @c00.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
476
|
+
assert_equal(false, @c00.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
477
|
+
assert_equal(false, @c00.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
478
|
+
assert_equal(false, @c00.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
479
|
+
assert_equal(false, @c00.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
480
|
+
|
|
481
|
+
assert_equal(false, @c02.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
482
|
+
assert_equal(false, @c02.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
483
|
+
assert_equal(true , @c02.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
484
|
+
assert_equal(true , @c02.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
485
|
+
assert_equal(false, @c02.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
486
|
+
assert_equal(false, @c02.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
487
|
+
|
|
488
|
+
assert_equal(false, @c01.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
489
|
+
assert_equal(true , @c01.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
490
|
+
assert_equal(false, @c01.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
491
|
+
assert_equal(false, @c01.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
492
|
+
assert_equal(false, @c01.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
493
|
+
assert_equal(false, @c01.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
494
|
+
|
|
495
|
+
assert_equal(false, @c03.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
496
|
+
assert_equal(false, @c03.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
497
|
+
assert_equal(true , @c03.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
498
|
+
assert_equal(true , @c03.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
499
|
+
assert_equal(false, @c03.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
500
|
+
assert_equal(false, @c03.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
501
|
+
|
|
502
|
+
assert_equal(false, @c04.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
503
|
+
assert_equal(false, @c04.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
504
|
+
assert_equal(false, @c04.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
505
|
+
assert_equal(false, @c04.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
506
|
+
assert_equal(true , @c04.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
507
|
+
assert_equal(false, @c04.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
508
|
+
|
|
509
|
+
assert_equal(false, @c05.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
510
|
+
assert_equal(false, @c05.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
511
|
+
assert_equal(false, @c05.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
512
|
+
assert_equal(false, @c05.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
513
|
+
assert_equal(false, @c05.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
514
|
+
assert_equal(true , @c05.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
515
|
+
end
|
|
516
|
+
|
|
517
|
+
def test_equal
|
|
518
|
+
cell = CrystalCell::Cell.new( CrystalCell::LatticeAxes.new([ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]))
|
|
519
|
+
assert_equal( true , @c00 == cell )
|
|
520
|
+
assert_equal( false, @c01 == cell )
|
|
521
|
+
|
|
522
|
+
cell = CrystalCell::Cell.new( CrystalCell::LatticeAxes.new([ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]))
|
|
523
|
+
cell.add_atom(CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ))
|
|
524
|
+
cell.add_atom(CrystalCell::Atom.new( 1, [0.1, 0.2, 0.3] ))
|
|
525
|
+
assert_equal( false, @c00 == cell )
|
|
526
|
+
assert_equal( true , @c01 == cell )
|
|
527
|
+
end
|
|
528
|
+
|
|
529
|
+
def test_distance
|
|
530
|
+
assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], [1,1,1])}
|
|
531
|
+
assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], Mageo::Vector3DInternal[1,1,1])}
|
|
532
|
+
assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], Mageo::Vector3D[1,1,1])}
|
|
533
|
+
|
|
534
|
+
assert_in_delta(
|
|
535
|
+
Math::sqrt(0.56),
|
|
536
|
+
@c00.distance(Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.1, 0.1, 0.1] ),
|
|
537
|
+
$tolerance
|
|
538
|
+
)
|
|
539
|
+
assert_in_delta( Math::sqrt( 1.6**2 + 3.4**2 + 5.4**2),
|
|
540
|
+
@c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.8, 0.9, 1.0] ), $tolerance
|
|
541
|
+
)
|
|
542
|
+
|
|
543
|
+
assert_in_delta( Math::sqrt(0.56), @c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.1, 0.1, 0.1] ), $tolerance )
|
|
544
|
+
assert_in_delta( Math::sqrt( 1.6**2 + 3.4**2 + 5.4**2),
|
|
545
|
+
@c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.8, 0.9, 1.0] ), $tolerance
|
|
546
|
+
)
|
|
547
|
+
end
|
|
548
|
+
|
|
549
|
+
#def test_dump_poscar
|
|
550
|
+
# c00_str = [
|
|
551
|
+
# 'c00',
|
|
552
|
+
# '1.0',
|
|
553
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
554
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
555
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
556
|
+
# ' ',
|
|
557
|
+
# '',
|
|
558
|
+
# 'Direct'
|
|
559
|
+
# ].join("\n")
|
|
560
|
+
|
|
561
|
+
# c01_str = [
|
|
562
|
+
# 'c01',
|
|
563
|
+
# '1.0',
|
|
564
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
565
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
566
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
567
|
+
# ' 0 1',
|
|
568
|
+
# ' 1 1',
|
|
569
|
+
# 'Direct',
|
|
570
|
+
# ' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
571
|
+
# ' 0.10000000000000 0.20000000000000 0.30000000000000'
|
|
572
|
+
# ].join("\n")
|
|
573
|
+
|
|
574
|
+
# c02_str = [
|
|
575
|
+
# 'c02',
|
|
576
|
+
# '1.0',
|
|
577
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
578
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
579
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
580
|
+
# ' Li O',
|
|
581
|
+
# ' 1 1',
|
|
582
|
+
# 'Direct',
|
|
583
|
+
# ' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
584
|
+
# ' 0.20000000000000 0.20000000000000 0.20000000000000'
|
|
585
|
+
# ].join("\n")
|
|
586
|
+
|
|
587
|
+
# c03_str = [
|
|
588
|
+
# 'c03',
|
|
589
|
+
# '1.0',
|
|
590
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
591
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
592
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
593
|
+
# ' Li O',
|
|
594
|
+
# ' 1 1',
|
|
595
|
+
# 'Direct',
|
|
596
|
+
# ' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
597
|
+
# ' 0.20000000000000 0.20000000000000 0.20000000000000'
|
|
598
|
+
# ].join("\n")
|
|
599
|
+
|
|
600
|
+
# c04_str = [
|
|
601
|
+
# 'c04',
|
|
602
|
+
# '1.0',
|
|
603
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
604
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
605
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
606
|
+
# ' Li O',
|
|
607
|
+
# ' 2 1',
|
|
608
|
+
# 'Direct',
|
|
609
|
+
# ' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
610
|
+
# ' 0.10000000000000 0.20000000000000 0.30000000000000',
|
|
611
|
+
# ' 0.20000000000000 0.20000000000000 0.20000000000000'
|
|
612
|
+
# ].join("\n")
|
|
613
|
+
|
|
614
|
+
# c05_str = [
|
|
615
|
+
# 'c05',
|
|
616
|
+
# '1.0',
|
|
617
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
618
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
619
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
620
|
+
# ' Li',
|
|
621
|
+
# ' 1',
|
|
622
|
+
# 'Direct',
|
|
623
|
+
# ' 0.00000000000000 0.00000000000000 0.00000000000000'
|
|
624
|
+
# ].join("\n")
|
|
625
|
+
|
|
626
|
+
# c06_str = [
|
|
627
|
+
# 'c06',
|
|
628
|
+
# '1.0',
|
|
629
|
+
# ' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
630
|
+
# ' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
631
|
+
# ' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
632
|
+
# ' Li O',
|
|
633
|
+
# ' 1 1',
|
|
634
|
+
# 'Selective dynamics',
|
|
635
|
+
# 'Direct',
|
|
636
|
+
# ' 0.00000000000000 0.00000000000000 0.00000000000000 T F F',
|
|
637
|
+
# ' 0.20000000000000 0.20000000000000 0.20000000000000 T T T'
|
|
638
|
+
# ].join("\n")
|
|
639
|
+
|
|
640
|
+
# # Raise exception
|
|
641
|
+
# # assert_raise( RuntimeError ){ @c00.dump_poscar( [], io ) }
|
|
642
|
+
# assert_raise( RuntimeError ){ @c00.dump_poscar( [0] ) }
|
|
643
|
+
# assert_raise( RuntimeError ){ @c00.dump_poscar( [0, 1] ) }
|
|
644
|
+
# assert_raise( RuntimeError ){ @c00.dump_poscar( ['Li'] ) }
|
|
645
|
+
# assert_raise( RuntimeError ){ @c00.dump_poscar( ['Li', 'O'] ) }
|
|
646
|
+
# assert_raise( RuntimeError ){ @c02.dump_poscar( [] ) }
|
|
647
|
+
# assert_raise( RuntimeError ){ @c02.dump_poscar( [0] ) }
|
|
648
|
+
# assert_raise( RuntimeError ){ @c02.dump_poscar( [0, 1] ) }
|
|
649
|
+
# assert_raise( RuntimeError ){ @c02.dump_poscar( ['Li'] ) }
|
|
650
|
+
# assert_raise( RuntimeError ){ @c01.dump_poscar( [] ) }
|
|
651
|
+
# assert_raise( RuntimeError ){ @c01.dump_poscar( [0] ) }
|
|
652
|
+
# assert_raise( RuntimeError ){ @c01.dump_poscar( ['Li'] ) }
|
|
653
|
+
# assert_raise( RuntimeError ){ @c01.dump_poscar( ['Li', 'O'] ) }
|
|
654
|
+
# assert_raise( RuntimeError ){ @c04.dump_poscar( [] ) }
|
|
655
|
+
# assert_raise( RuntimeError ){ @c04.dump_poscar( [0] ) }
|
|
656
|
+
# assert_raise( RuntimeError ){ @c04.dump_poscar( [0, 1] ) }
|
|
657
|
+
# assert_raise( RuntimeError ){ @c04.dump_poscar( ['Li'] ) }
|
|
658
|
+
# assert_raise( RuntimeError ){ @c05.dump_poscar( [] ) }
|
|
659
|
+
# assert_raise( RuntimeError ){ @c05.dump_poscar( [0] ) }
|
|
660
|
+
# assert_raise( RuntimeError ){ @c05.dump_poscar( [0, 1] ) }
|
|
661
|
+
# assert_raise( RuntimeError ){ @c05.dump_poscar( ['Li', 'O'] ) }
|
|
662
|
+
# assert_raise( RuntimeError ){ @c03.dump_poscar( [] ) }
|
|
663
|
+
# assert_raise( RuntimeError ){ @c03.dump_poscar( [0] ) }
|
|
664
|
+
# assert_raise( RuntimeError ){ @c03.dump_poscar( [0, 1] ) }
|
|
665
|
+
# assert_raise( RuntimeError ){ @c03.dump_poscar( ['Li'] ) }
|
|
666
|
+
|
|
667
|
+
# #
|
|
668
|
+
# StringIO.new do |io|
|
|
669
|
+
# @c00.dump_poscar( [], io )
|
|
670
|
+
# assert_equal( c00_str, io.read )
|
|
671
|
+
# end
|
|
672
|
+
|
|
673
|
+
# StringIO.new do |io|
|
|
674
|
+
# @c01.dump_poscar( [ 0, 1 ], io )
|
|
675
|
+
# assert_equal( c01, io.read )
|
|
676
|
+
# end
|
|
677
|
+
|
|
678
|
+
# StringIO.new do |io|
|
|
679
|
+
# @c02.dump_poscar( [ 'Li', 'O' ], io )
|
|
680
|
+
# assert_equal( c02, io.read )
|
|
681
|
+
# end
|
|
682
|
+
|
|
683
|
+
# StringIO.new do |io|
|
|
684
|
+
# @c03.dump_poscar( [ 'Li', 'O' ], io )
|
|
685
|
+
# assert_equal( c03, io.read )
|
|
686
|
+
# end
|
|
687
|
+
|
|
688
|
+
# StringIO.new do |io|
|
|
689
|
+
# @c04.dump_poscar( [ 'Li', 'O' ], io )
|
|
690
|
+
# assert_equal( c04, io.read )
|
|
691
|
+
# end
|
|
692
|
+
|
|
693
|
+
# StringIO.new do |io|
|
|
694
|
+
# @c05.dump_poscar( [ 'Li', 'O' ], io )
|
|
695
|
+
# assert_equal( c05, io.read )
|
|
696
|
+
# end
|
|
697
|
+
|
|
698
|
+
# assert_equal( c00_str, @c00.dump_poscar( [ ], nil ) )
|
|
699
|
+
# assert_equal( c01_str, @c01.dump_poscar( [ 0 , 1 ], nil ) )
|
|
700
|
+
# assert_equal( c02_str, @c02.dump_poscar( [ 'Li', 'O' ], nil ) )
|
|
701
|
+
# assert_equal( c03_str, @c03.dump_poscar( [ 'Li', 'O' ], nil ) )
|
|
702
|
+
# assert_equal( c04_str, @c04.dump_poscar( [ 'Li', 'O' ], nil ) )
|
|
703
|
+
# assert_equal( c05_str, @c05.dump_poscar( [ 'Li' ], nil ) )
|
|
704
|
+
|
|
705
|
+
# assert_equal( c00_str, @c00.dump_poscar( [ ] ) )
|
|
706
|
+
# assert_equal( c01_str, @c01.dump_poscar( [ 0 , 1 ] ) )
|
|
707
|
+
# assert_equal( c02_str, @c02.dump_poscar( [ 'Li', 'O' ] ) )
|
|
708
|
+
# assert_equal( c03_str, @c03.dump_poscar( [ 'Li', 'O' ] ) )
|
|
709
|
+
# assert_equal( c04_str, @c04.dump_poscar( [ 'Li', 'O' ] ) )
|
|
710
|
+
# assert_equal( c05_str, @c05.dump_poscar( [ 'Li' ] ) )
|
|
711
|
+
|
|
712
|
+
# assert_equal( c06_str, @c06 .dump_poscar( [ 'Li', 'O' ] ) )
|
|
713
|
+
|
|
714
|
+
#end
|
|
715
|
+
|
|
716
|
+
def test_rotate
|
|
717
|
+
@c02.add_atom(CrystalCell::Atom.new( 'Li', [1.1, 1.2, 1.3] ))
|
|
718
|
+
assert_equal(
|
|
719
|
+
[ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ],
|
|
720
|
+
Mageo::Vector3DInternal[ -0.2, -0.2, -0.2 ],
|
|
721
|
+
Mageo::Vector3DInternal[ -1.1, -1.2, -1.3 ]
|
|
722
|
+
],
|
|
723
|
+
@c02.rotate( [[-1, 0, 0],[0, -1, 0],[0, 0, -1]] ).positions
|
|
724
|
+
)
|
|
725
|
+
|
|
726
|
+
# Check not destructed.
|
|
727
|
+
assert_equal(
|
|
728
|
+
[ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ],
|
|
729
|
+
Mageo::Vector3DInternal[ 0.2, 0.2, 0.2 ],
|
|
730
|
+
Mageo::Vector3DInternal[ 1.1, 1.2, 1.3 ]
|
|
731
|
+
],
|
|
732
|
+
@c02.positions
|
|
733
|
+
)
|
|
734
|
+
end
|
|
735
|
+
|
|
736
|
+
def test_rotate!
|
|
737
|
+
@c02.add_atom(CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] ))
|
|
738
|
+
@c02.rotate!( [[-1, 0, 0],[0, -1, 0],[0, 0, -1]] )
|
|
739
|
+
assert_equal(
|
|
740
|
+
[ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ],
|
|
741
|
+
Mageo::Vector3DInternal[ -0.2, -0.2, -0.2 ],
|
|
742
|
+
Mageo::Vector3DInternal[ -0.1, -0.2, -0.3 ]
|
|
743
|
+
],
|
|
744
|
+
@c02.positions
|
|
745
|
+
)
|
|
746
|
+
end
|
|
747
|
+
|
|
748
|
+
def test_translate
|
|
749
|
+
poss = @c02.translate( [1.1, 1.2, 1.3] ).positions
|
|
750
|
+
assert_in_delta( 1.1, poss[0][0], $tolerance )
|
|
751
|
+
assert_in_delta( 1.2, poss[0][1], $tolerance )
|
|
752
|
+
assert_in_delta( 1.3, poss[0][2], $tolerance )
|
|
753
|
+
assert_in_delta( 1.3, poss[1][0], $tolerance )
|
|
754
|
+
assert_in_delta( 1.4, poss[1][1], $tolerance )
|
|
755
|
+
assert_in_delta( 1.5, poss[1][2], $tolerance )
|
|
756
|
+
|
|
757
|
+
poss = @c02.translate( [-0.3,-0.3,-0.3] ).positions
|
|
758
|
+
assert_in_delta( -0.3, poss[0][0], $tolerance )
|
|
759
|
+
assert_in_delta( -0.3, poss[0][1], $tolerance )
|
|
760
|
+
assert_in_delta( -0.3, poss[0][2], $tolerance )
|
|
761
|
+
assert_in_delta( -0.1, poss[1][0], $tolerance )
|
|
762
|
+
assert_in_delta( -0.1, poss[1][1], $tolerance )
|
|
763
|
+
assert_in_delta( -0.1, poss[1][2], $tolerance )
|
|
764
|
+
|
|
765
|
+
# Check not destructed.
|
|
766
|
+
assert_equal(
|
|
767
|
+
[ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ],
|
|
768
|
+
Mageo::Vector3DInternal[ 0.2, 0.2, 0.2 ]
|
|
769
|
+
],
|
|
770
|
+
@c02.positions
|
|
771
|
+
)
|
|
772
|
+
end
|
|
773
|
+
|
|
774
|
+
def test_translate!
|
|
775
|
+
@c02.translate!( [1.1, 1.2, 1.3] )
|
|
776
|
+
poss = @c02.positions
|
|
777
|
+
|
|
778
|
+
assert_in_delta( 1.1, poss[0][0], $tolerance )
|
|
779
|
+
assert_in_delta( 1.2, poss[0][1], $tolerance )
|
|
780
|
+
assert_in_delta( 1.3, poss[0][2], $tolerance )
|
|
781
|
+
assert_in_delta( 1.3, poss[1][0], $tolerance )
|
|
782
|
+
assert_in_delta( 1.4, poss[1][1], $tolerance )
|
|
783
|
+
assert_in_delta( 1.5, poss[1][2], $tolerance )
|
|
784
|
+
end
|
|
785
|
+
|
|
786
|
+
def test_center_of_atoms
|
|
787
|
+
# No atom in the cell.
|
|
788
|
+
assert_raise( CrystalCell::Cell::NoAtomError ){ @c00.center_of_atoms }
|
|
789
|
+
|
|
790
|
+
assert_equal( Mageo::Vector3DInternal[0.05, 0.1, 0.15], @c01.center_of_atoms )
|
|
791
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c02.center_of_atoms )
|
|
792
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c03.center_of_atoms )
|
|
793
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 4.0/30.0, 5.0/30.0], @c04.center_of_atoms )
|
|
794
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c05.center_of_atoms )
|
|
795
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c06.center_of_atoms )
|
|
796
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c07.center_of_atoms )
|
|
797
|
+
end
|
|
798
|
+
|
|
799
|
+
def test_calc_volume
|
|
800
|
+
# @c00 = CrystalCell::Cell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] )
|
|
801
|
+
assert_in_delta( 8.00, @c00.calc_volume, $tolerance)
|
|
802
|
+
|
|
803
|
+
c10 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] )
|
|
804
|
+
c11 = CrystalCell::Cell.new( [ [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5] ] )
|
|
805
|
+
assert_in_delta( 1.00, c10.calc_volume, $tolerance)
|
|
806
|
+
assert_in_delta( 0.25, c11.calc_volume, $tolerance)
|
|
807
|
+
end
|
|
808
|
+
|
|
809
|
+
def test_cell_of_elements
|
|
810
|
+
t = @c04.cell_of_elements( [ 'Li' ] )
|
|
811
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
812
|
+
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
813
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
814
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
815
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
816
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
817
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
818
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
819
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
820
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
821
|
+
assert_equal( 2, t.atoms.size )
|
|
822
|
+
# checking atom 0
|
|
823
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
824
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
825
|
+
assert_equal( nil , t.atoms[0].name )
|
|
826
|
+
# checking atom 1
|
|
827
|
+
assert_equal( 'Li' , t.atoms[1].element)
|
|
828
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position)
|
|
829
|
+
assert_equal( nil , t.atoms[1].name )
|
|
830
|
+
|
|
831
|
+
t = @c04.cell_of_elements( [ 'Li', 'O' ] )
|
|
832
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
833
|
+
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
834
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
835
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
836
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
837
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
838
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
839
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
840
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
841
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
842
|
+
assert_equal( 3, t.atoms.size )
|
|
843
|
+
# checking atom 0
|
|
844
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
845
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
846
|
+
assert_equal( nil , t.atoms[0].name )
|
|
847
|
+
# checking atom 1
|
|
848
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
849
|
+
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[1].position)
|
|
850
|
+
assert_equal( nil , t.atoms[1].name )
|
|
851
|
+
# checking atom 2
|
|
852
|
+
assert_equal( 'Li' , t.atoms[2].element)
|
|
853
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[2].position)
|
|
854
|
+
assert_equal( nil , t.atoms[2].name )
|
|
855
|
+
|
|
856
|
+
t = @c04.cell_of_elements( [ 'O' ] )
|
|
857
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
858
|
+
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
859
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
860
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
861
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
862
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
863
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
864
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
865
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
866
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
867
|
+
assert_equal( 1, t.atoms.size )
|
|
868
|
+
# checking atom 0
|
|
869
|
+
assert_equal( 'O' , t.atoms[0].element)
|
|
870
|
+
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[0].position)
|
|
871
|
+
assert_equal( nil , t.atoms[0].name )
|
|
872
|
+
|
|
873
|
+
t = @c04.cell_of_elements( [ 'F' ] )
|
|
874
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
875
|
+
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
876
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
877
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
878
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
879
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
880
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
881
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
882
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
883
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
884
|
+
assert_equal( 0, t.atoms.size )
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
# サブクラスで使用したときに、サブクラスで作られるか？
|
|
888
|
+
fc04 = FooCell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] )
|
|
889
|
+
fc04.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ))
|
|
890
|
+
fc04.add_atom(CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ))
|
|
891
|
+
fc04.add_atom(CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] ))
|
|
892
|
+
fc04.comment = 'fc04'
|
|
893
|
+
t = fc04.cell_of_elements( [ 'Li' ] )
|
|
894
|
+
assert_equal( FooCell, t.class )
|
|
895
|
+
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
896
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
897
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
898
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
899
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
900
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
901
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
902
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
903
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
904
|
+
assert_equal( 2, t.atoms.size )
|
|
905
|
+
# checking atom 0
|
|
906
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
907
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
908
|
+
assert_equal( nil , t.atoms[0].name )
|
|
909
|
+
# checking atom 1
|
|
910
|
+
assert_equal( 'Li' , t.atoms[1].element)
|
|
911
|
+
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position)
|
|
912
|
+
assert_equal( nil , t.atoms[1].name )
|
|
913
|
+
end
|
|
914
|
+
|
|
915
|
+
def test_unite
|
|
916
|
+
## 格子定数が違えば例外。将来的な feature.
|
|
917
|
+
#t = CrystalCell::Cell.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ] )
|
|
918
|
+
#t.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ))
|
|
919
|
+
#t.comment = 't'
|
|
920
|
+
#assert_raise( CrystalCell::Cell::AxesMismatchError ){ @c05.unite( t ) }
|
|
921
|
+
t = CrystalCell::Cell.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ] )
|
|
922
|
+
t.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ))
|
|
923
|
+
t.comment = 't'
|
|
924
|
+
assert_nothing_raised{ @c05.unite( t ) }
|
|
925
|
+
|
|
926
|
+
# unite
|
|
927
|
+
# 同じ座標のものがあっても気にせず統合する。
|
|
928
|
+
t = @c05.unite( @c06 )
|
|
929
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
930
|
+
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
931
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
932
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
933
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
934
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
935
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
936
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
937
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
938
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
939
|
+
assert_equal( 3, t.atoms.size )
|
|
940
|
+
# checking atom 0
|
|
941
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
942
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
943
|
+
assert_equal( nil , t.atoms[0].name )
|
|
944
|
+
# checking atom 1
|
|
945
|
+
assert_equal( 'Li' , t.atoms[1].element)
|
|
946
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[1].position)
|
|
947
|
+
assert_equal( nil , t.atoms[1].name )
|
|
948
|
+
# checking atom 2
|
|
949
|
+
assert_equal( 'O' , t.atoms[2].element)
|
|
950
|
+
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[2].position)
|
|
951
|
+
assert_equal( nil , t.atoms[2].name )
|
|
952
|
+
end
|
|
953
|
+
|
|
954
|
+
def test_inverse_axis!
|
|
955
|
+
@c02.inverse_axis!( 0 )
|
|
956
|
+
t = @c02
|
|
957
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
958
|
+
assert_in_delta(-2.0, t.axes[0][0], $tolerance )
|
|
959
|
+
assert_in_delta(-2.0, t.axes[0][1], $tolerance )
|
|
960
|
+
assert_in_delta(-2.0, t.axes[0][2], $tolerance )
|
|
961
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
962
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
963
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
964
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
965
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
966
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
967
|
+
assert_equal( 2, t.atoms.size )
|
|
968
|
+
# checking atom 0
|
|
969
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
970
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
971
|
+
assert_equal( nil , t.atoms[0].name )
|
|
972
|
+
# checking atom 1
|
|
973
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
974
|
+
assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
|
|
975
|
+
assert_equal( nil , t.atoms[1].name )
|
|
976
|
+
end
|
|
977
|
+
|
|
978
|
+
def test_inverse_axis
|
|
979
|
+
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.inverse_axis( -1 ) }
|
|
980
|
+
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.inverse_axis( 3 ) }
|
|
981
|
+
|
|
982
|
+
# x 軸反転
|
|
983
|
+
t = @c02.inverse_axis( 0 )
|
|
984
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
985
|
+
assert_in_delta( -2.0, t.axes[0][0], $tolerance )
|
|
986
|
+
assert_in_delta( -2.0, t.axes[0][1], $tolerance )
|
|
987
|
+
assert_in_delta( -2.0, t.axes[0][2], $tolerance )
|
|
988
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
989
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
990
|
+
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
991
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
992
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
993
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
994
|
+
assert_equal( 2, t.atoms.size )
|
|
995
|
+
# checking atom 0
|
|
996
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
997
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
998
|
+
assert_equal( nil , t.atoms[0].name )
|
|
999
|
+
# checking atom 1
|
|
1000
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1001
|
+
assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
|
|
1002
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1003
|
+
# checking non-destructive
|
|
1004
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1005
|
+
assert_in_delta( 2.0, @c02.axes[0][0], $tolerance )
|
|
1006
|
+
assert_in_delta( 2.0, @c02.axes[0][1], $tolerance )
|
|
1007
|
+
assert_in_delta( 2.0, @c02.axes[0][2], $tolerance )
|
|
1008
|
+
assert_in_delta( 0.0, @c02.axes[1][0], $tolerance )
|
|
1009
|
+
assert_in_delta( 2.0, @c02.axes[1][1], $tolerance )
|
|
1010
|
+
assert_in_delta( 2.0, @c02.axes[1][2], $tolerance )
|
|
1011
|
+
assert_in_delta( 0.0, @c02.axes[2][0], $tolerance )
|
|
1012
|
+
assert_in_delta( 0.0, @c02.axes[2][1], $tolerance )
|
|
1013
|
+
assert_in_delta( 2.0, @c02.axes[2][2], $tolerance )
|
|
1014
|
+
assert_equal( 2, @c02.atoms.size )
|
|
1015
|
+
# checking atom 0
|
|
1016
|
+
assert_equal( 'Li' , @c02.atoms[0].element)
|
|
1017
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position)
|
|
1018
|
+
assert_equal( nil , @c02.atoms[0].name )
|
|
1019
|
+
# checking atom 1
|
|
1020
|
+
assert_equal( 'O' , @c02.atoms[1].element)
|
|
1021
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], @c02.atoms[1].position)
|
|
1022
|
+
assert_equal( nil , @c02.atoms[1].name )
|
|
1023
|
+
|
|
1024
|
+
# y 軸反転
|
|
1025
|
+
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ]
|
|
1026
|
+
# ↓ y 軸反転
|
|
1027
|
+
# [ [ ax, ay, az], [ 0,-by,-bz], [ 0, 0, cz] ]
|
|
1028
|
+
# ↓ b vector の y 成分が正になるようにする。
|
|
1029
|
+
# すなわち z 軸回りに半回転し、全ての x, y 成分が反転する。
|
|
1030
|
+
# [ [-ax,-ay, az], [ 0, by,-bz], [ 0, 0, cz] ]
|
|
1031
|
+
t = @c02.inverse_axis( 1 )
|
|
1032
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1033
|
+
assert_in_delta( -2.0, t.axes[0][0], $tolerance )
|
|
1034
|
+
assert_in_delta( -2.0, t.axes[0][1], $tolerance )
|
|
1035
|
+
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
1036
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
1037
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
1038
|
+
assert_in_delta( -2.0, t.axes[1][2], $tolerance )
|
|
1039
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
1040
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
1041
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
1042
|
+
assert_equal( 2, t.atoms.size )
|
|
1043
|
+
# checking atom 0
|
|
1044
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1045
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
1046
|
+
assert_equal( nil , t.atoms[0].name )
|
|
1047
|
+
# checking atom 1
|
|
1048
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1049
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2,-0.2, 0.2], t.atoms[1].position)
|
|
1050
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1051
|
+
|
|
1052
|
+
# z 軸反転
|
|
1053
|
+
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ]
|
|
1054
|
+
# ↓ z 軸反転
|
|
1055
|
+
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0,-cz] ]
|
|
1056
|
+
# ↓ c vector の z 成分が正になるようにする。
|
|
1057
|
+
# b vector の y 成分も正であることを保存する回転は、
|
|
1058
|
+
# y 軸回りに半回転し、全ての x, z 成分が反転する。
|
|
1059
|
+
# [ [-ax, ay,-az], [ 0, by,-bz], [ 0, 0, cz] ]
|
|
1060
|
+
t = @c02.inverse_axis( 2 )
|
|
1061
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1062
|
+
assert_in_delta(-2.0, t.axes[0][0], $tolerance )
|
|
1063
|
+
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
1064
|
+
assert_in_delta(-2.0, t.axes[0][2], $tolerance )
|
|
1065
|
+
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
1066
|
+
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
1067
|
+
assert_in_delta(-2.0, t.axes[1][2], $tolerance )
|
|
1068
|
+
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
1069
|
+
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
1070
|
+
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
1071
|
+
assert_equal( 2, t.atoms.size )
|
|
1072
|
+
# checking atom 0
|
|
1073
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1074
|
+
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
1075
|
+
assert_equal( nil , t.atoms[0].name )
|
|
1076
|
+
# checking atom 1
|
|
1077
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1078
|
+
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2,-0.2], t.atoms[1].position)
|
|
1079
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1080
|
+
|
|
1081
|
+
end
|
|
1082
|
+
|
|
1083
|
+
def test_exchange_axes!
|
|
1084
|
+
# b, c の交換。
|
|
1085
|
+
@c08.exchange_axes!( [ 1, 2 ] )
|
|
1086
|
+
t = @c08
|
|
1087
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1088
|
+
lc = t.axes.get_lattice_constants
|
|
1089
|
+
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1090
|
+
assert_in_delta( 2.0 , lc[1], $tolerance )
|
|
1091
|
+
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[2], $tolerance )
|
|
1092
|
+
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1093
|
+
assert_in_delta( 35.2643896827547, lc[4], $tolerance )
|
|
1094
|
+
assert_in_delta( 54.7356103172453, lc[5], $tolerance )
|
|
1095
|
+
assert_equal( true, t.axes.lefthand? )
|
|
1096
|
+
assert_equal( 2, t.atoms.size )
|
|
1097
|
+
# checking atom 0
|
|
1098
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1099
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 5.6, 3.4], t.atoms[0].position)
|
|
1100
|
+
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1101
|
+
assert_equal( [ false, false, true] , t.atoms[0].movable_flags )
|
|
1102
|
+
# checking atom 1
|
|
1103
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1104
|
+
assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position)
|
|
1105
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1106
|
+
end
|
|
1107
|
+
|
|
1108
|
+
def test_exchange_axes
|
|
1109
|
+
assert_raise( CrystalCell::Cell::ArgumentError ){ @c02.exchange_axes( [ 0 ] ) }
|
|
1110
|
+
assert_raise( CrystalCell::Cell::ArgumentError ){ @c02.exchange_axes( [ 0, 1, 2] ) }
|
|
1111
|
+
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.exchange_axes( [0, 3] ) }
|
|
1112
|
+
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.exchange_axes( [-1, 2] ) }
|
|
1113
|
+
assert_raise( CrystalCell::Cell::SameAxesError ){ @c02.exchange_axes( [ 1,1] ) }
|
|
1114
|
+
|
|
1115
|
+
# b, c の交換。
|
|
1116
|
+
t = @c08.exchange_axes( [ 1, 2 ] )
|
|
1117
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1118
|
+
lc = t.axes.get_lattice_constants
|
|
1119
|
+
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1120
|
+
assert_in_delta( 2.0 , lc[1], $tolerance )
|
|
1121
|
+
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[2], $tolerance )
|
|
1122
|
+
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1123
|
+
assert_in_delta( 35.2643896827547, lc[4], $tolerance )
|
|
1124
|
+
assert_in_delta( 54.7356103172453, lc[5], $tolerance )
|
|
1125
|
+
assert_equal( true, t.axes.lefthand? )
|
|
1126
|
+
assert_equal( 2, t.atoms.size )
|
|
1127
|
+
# checking atom 0
|
|
1128
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1129
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 5.6, 3.4], t.atoms[0].position)
|
|
1130
|
+
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1131
|
+
# checking atom 1
|
|
1132
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1133
|
+
assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position)
|
|
1134
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1135
|
+
|
|
1136
|
+
# b, c の交換によって非破壊であることを確認。
|
|
1137
|
+
t = @c08
|
|
1138
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1139
|
+
lc = t.axes.get_lattice_constants
|
|
1140
|
+
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1141
|
+
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1142
|
+
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1143
|
+
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1144
|
+
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1145
|
+
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1146
|
+
assert_equal( true, t.axes.righthand? )
|
|
1147
|
+
assert_equal( 2, t.atoms.size )
|
|
1148
|
+
# checking atom 0
|
|
1149
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1150
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1151
|
+
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1152
|
+
# checking atom 1
|
|
1153
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1154
|
+
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1155
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1156
|
+
|
|
1157
|
+
end
|
|
1158
|
+
|
|
1159
|
+
def test_reflect!
|
|
1160
|
+
@c08.reflect!
|
|
1161
|
+
t = @c08
|
|
1162
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1163
|
+
lc = t.axes.get_lattice_constants
|
|
1164
|
+
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1165
|
+
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1166
|
+
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1167
|
+
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1168
|
+
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1169
|
+
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1170
|
+
assert_equal( true, t.axes.lefthand? )
|
|
1171
|
+
assert_equal( 2, t.atoms.size )
|
|
1172
|
+
# checking atom 0
|
|
1173
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1174
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1175
|
+
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1176
|
+
# checking atom 1
|
|
1177
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1178
|
+
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1179
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1180
|
+
end
|
|
1181
|
+
|
|
1182
|
+
def test_reflect
|
|
1183
|
+
t = @c08.reflect
|
|
1184
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1185
|
+
lc = t.axes.get_lattice_constants
|
|
1186
|
+
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1187
|
+
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1188
|
+
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1189
|
+
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1190
|
+
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1191
|
+
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1192
|
+
assert_equal( true, t.axes.lefthand? )
|
|
1193
|
+
assert_equal( 2, t.atoms.size )
|
|
1194
|
+
# checking atom 0
|
|
1195
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1196
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1197
|
+
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1198
|
+
# checking atom 1
|
|
1199
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1200
|
+
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1201
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1202
|
+
|
|
1203
|
+
# 非破壊であることを確認。
|
|
1204
|
+
t = @c08
|
|
1205
|
+
assert_equal( CrystalCell::Cell, t.class )
|
|
1206
|
+
lc = t.axes.get_lattice_constants
|
|
1207
|
+
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1208
|
+
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1209
|
+
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1210
|
+
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1211
|
+
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1212
|
+
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1213
|
+
assert_equal( true, t.axes.righthand? )
|
|
1214
|
+
assert_equal( 2, t.atoms.size )
|
|
1215
|
+
# checking atom 0
|
|
1216
|
+
assert_equal( 'Li' , t.atoms[0].element)
|
|
1217
|
+
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1218
|
+
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1219
|
+
# checking atom 1
|
|
1220
|
+
assert_equal( 'O' , t.atoms[1].element)
|
|
1221
|
+
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1222
|
+
assert_equal( nil , t.atoms[1].name )
|
|
1223
|
+
end
|
|
1224
|
+
|
|
1225
|
+
def test_operate
|
|
1226
|
+
# identity operation
|
|
1227
|
+
rotation = [
|
|
1228
|
+
[1, 0, 0],
|
|
1229
|
+
[0, 1, 0],
|
|
1230
|
+
[0, 0, 1],
|
|
1231
|
+
]
|
|
1232
|
+
translation = [0.0, 0.0, 0.0]
|
|
1233
|
+
result = @c01.operate(rotation, translation)
|
|
1234
|
+
assert_in_delta( 0.0, result.atoms[0].position[0], $tolerance)
|
|
1235
|
+
assert_in_delta( 0.0, result.atoms[0].position[1], $tolerance)
|
|
1236
|
+
assert_in_delta( 0.0, result.atoms[0].position[2], $tolerance)
|
|
1237
|
+
assert_in_delta( 0.1, result.atoms[1].position[0], $tolerance)
|
|
1238
|
+
assert_in_delta( 0.2, result.atoms[1].position[1], $tolerance)
|
|
1239
|
+
assert_in_delta( 0.3, result.atoms[1].position[2], $tolerance)
|
|
1240
|
+
|
|
1241
|
+
# rotation
|
|
1242
|
+
rotation = [
|
|
1243
|
+
[1, 0, 0],
|
|
1244
|
+
[0, 1, 0],
|
|
1245
|
+
[0, 0,-1],
|
|
1246
|
+
]
|
|
1247
|
+
translation = [0.0, 0.0, 0.0]
|
|
1248
|
+
result = @c01.operate(rotation, translation)
|
|
1249
|
+
assert_in_delta( 0.0, result.atoms[0].position[0], $tolerance)
|
|
1250
|
+
assert_in_delta( 0.0, result.atoms[0].position[1], $tolerance)
|
|
1251
|
+
assert_in_delta( 0.0, result.atoms[0].position[2], $tolerance)
|
|
1252
|
+
assert_in_delta( 0.1, result.atoms[1].position[0], $tolerance)
|
|
1253
|
+
assert_in_delta( 0.2, result.atoms[1].position[1], $tolerance)
|
|
1254
|
+
assert_in_delta(-0.3, result.atoms[1].position[2], $tolerance)
|
|
1255
|
+
|
|
1256
|
+
# translation
|
|
1257
|
+
rotation = [
|
|
1258
|
+
[1, 0, 0],
|
|
1259
|
+
[0, 1, 0],
|
|
1260
|
+
[0, 0, 1],
|
|
1261
|
+
]
|
|
1262
|
+
translation = [0.1, 0.2, 0.3]
|
|
1263
|
+
result = @c01.operate(rotation, translation)
|
|
1264
|
+
assert_in_delta(0.1, result.atoms[0].position[0], $tolerance)
|
|
1265
|
+
assert_in_delta(0.2, result.atoms[0].position[1], $tolerance)
|
|
1266
|
+
assert_in_delta(0.3, result.atoms[0].position[2], $tolerance)
|
|
1267
|
+
assert_in_delta(0.2, result.atoms[1].position[0], $tolerance)
|
|
1268
|
+
assert_in_delta(0.4, result.atoms[1].position[1], $tolerance)
|
|
1269
|
+
assert_in_delta(0.6, result.atoms[1].position[2], $tolerance)
|
|
1270
|
+
|
|
1271
|
+
# rotation & translation
|
|
1272
|
+
rotation = [
|
|
1273
|
+
[1, 0, 0],
|
|
1274
|
+
[0, 1, 0],
|
|
1275
|
+
[0, 0,-1],
|
|
1276
|
+
]
|
|
1277
|
+
translation = [0.1, 0.2, 0.3]
|
|
1278
|
+
result = @c01.operate(rotation, translation)
|
|
1279
|
+
assert_in_delta(0.1, result.atoms[0].position[0], $tolerance)
|
|
1280
|
+
assert_in_delta(0.2, result.atoms[0].position[1], $tolerance)
|
|
1281
|
+
assert_in_delta(0.3, result.atoms[0].position[2], $tolerance)
|
|
1282
|
+
assert_in_delta(0.2, result.atoms[1].position[0], $tolerance)
|
|
1283
|
+
assert_in_delta(0.4, result.atoms[1].position[1], $tolerance)
|
|
1284
|
+
assert_in_delta(0.0, result.atoms[1].position[2], $tolerance)
|
|
1285
|
+
end
|
|
1286
|
+
|
|
1287
|
+
def test_axis_independencies
|
|
1288
|
+
unless defined? Getspg
|
|
1289
|
+
puts
|
|
1290
|
+
puts "test_axis_independencies() is ignored because spglib is not installed."
|
|
1291
|
+
return
|
|
200
1292
|
end
|
|
201
1293
|
|
|
202
|
-
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
|
|
206
|
-
|
|
207
|
-
|
|
208
|
-
|
|
209
|
-
|
|
210
|
-
|
|
211
|
-
|
|
212
|
-
|
|
213
|
-
|
|
214
|
-
|
|
215
|
-
|
|
216
|
-
|
|
217
|
-
|
|
218
|
-
|
|
219
|
-
|
|
220
|
-
|
|
221
|
-
|
|
222
|
-
|
|
223
|
-
|
|
224
|
-
|
|
225
|
-
|
|
226
|
-
def test_select_indices
|
|
227
|
-
assert_equal( [], @c00.select_indices{ |i| i.element == "" } )
|
|
228
|
-
assert_equal( [], @c00.select_indices{ |i| i.element == "Li" } )
|
|
229
|
-
|
|
230
|
-
assert_equal( [] , @c01.select_indices{ |i| i.element == "" } )
|
|
231
|
-
assert_equal( [] , @c01.select_indices{ |i| i.element == "Li" } )
|
|
232
|
-
#@c01.select_indices{ |i| p i.element }
|
|
233
|
-
assert_equal( [0], @c01.select_indices{ |i| i.element == 0 } )
|
|
234
|
-
|
|
235
|
-
assert_equal( [1], @c01.select_indices{ |i| i.element == 1 } )
|
|
236
|
-
|
|
237
|
-
assert_equal( [] , @c04.select_indices{ |i| i.element == "" } )
|
|
238
|
-
assert_equal( [0, 2], @c04.select_indices{ |i| i.element == "Li" } )
|
|
239
|
-
assert_equal( [1], @c04.select_indices{ |i| i.element == "O" } )
|
|
240
|
-
assert_equal( [ ], @c04.select_indices{ |i| i.element == 0 } )
|
|
241
|
-
assert_equal( [ ], @c04.select_indices{ |i| i.element == 1 } )
|
|
242
|
-
|
|
243
|
-
assert_equal( [1, 2], @c04.select_indices{ |i| i.position[0] > 0.05 } )
|
|
244
|
-
end
|
|
245
|
-
|
|
246
|
-
def test_atoms_in_supercell
|
|
247
|
-
t = @c02.atoms_in_supercell( 0, 0, 0, 0, 0, 1 )
|
|
248
|
-
assert_equal( 'Li', t[0].element )
|
|
249
|
-
assert_equal( 'Li', t[1].element )
|
|
250
|
-
assert_equal( 'O' , t[2].element )
|
|
251
|
-
assert_equal( 'O' , t[3].element )
|
|
252
|
-
|
|
253
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t[0].position )
|
|
254
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 1.0], t[1].position )
|
|
255
|
-
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t[2].position )
|
|
256
|
-
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 1.2], t[3].position )
|
|
257
|
-
|
|
258
|
-
t = @c02.atoms_in_supercell(-1, 1,-1, 1,-1, 1 )
|
|
259
|
-
assert_equal( ['Li']*27 + ['O'] * 27 , t.map{|i| i.element} )
|
|
260
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, -1.0], t[ 0].position )
|
|
261
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, 0.0], t[ 1].position )
|
|
262
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, -1.0, 1.0], t[ 2].position )
|
|
263
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, -1.0], t[ 3].position )
|
|
264
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, 0.0], t[ 4].position )
|
|
265
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, 0.0, 1.0], t[ 5].position )
|
|
266
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, -1.0], t[ 6].position )
|
|
267
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, 0.0], t[ 7].position )
|
|
268
|
-
assert_equal( Mageo::Vector3DInternal[-1.0, 1.0, 1.0], t[ 8].position )
|
|
269
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, -1.0], t[ 9].position )
|
|
270
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, 0.0], t[10].position )
|
|
271
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, -1.0, 1.0], t[11].position )
|
|
272
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, -1.0], t[12].position )
|
|
273
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, 0.0], t[13].position )
|
|
274
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, 0.0, 1.0], t[14].position )
|
|
275
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, -1.0], t[15].position )
|
|
276
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, 0.0], t[16].position )
|
|
277
|
-
assert_equal( Mageo::Vector3DInternal[ 0.0, 1.0, 1.0], t[17].position )
|
|
278
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, -1.0], t[18].position )
|
|
279
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, 0.0], t[19].position )
|
|
280
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, -1.0, 1.0], t[20].position )
|
|
281
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, -1.0], t[21].position )
|
|
282
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, 0.0], t[22].position )
|
|
283
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, 0.0, 1.0], t[23].position )
|
|
284
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, -1.0], t[24].position )
|
|
285
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, 0.0], t[25].position )
|
|
286
|
-
assert_equal( Mageo::Vector3DInternal[ 1.0, 1.0, 1.0], t[26].position )
|
|
287
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, -0.8], t[27].position )
|
|
288
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, 0.2], t[28].position )
|
|
289
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, -0.8, 1.2], t[29].position )
|
|
290
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, -0.8], t[30].position )
|
|
291
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, 0.2], t[31].position )
|
|
292
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, 0.2, 1.2], t[32].position )
|
|
293
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, -0.8], t[33].position )
|
|
294
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, 0.2], t[34].position )
|
|
295
|
-
assert_equal( Mageo::Vector3DInternal[-0.8, 1.2, 1.2], t[35].position )
|
|
296
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, -0.8], t[36].position )
|
|
297
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, 0.2], t[37].position )
|
|
298
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, -0.8, 1.2], t[38].position )
|
|
299
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, -0.8], t[39].position )
|
|
300
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], t[40].position )
|
|
301
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 1.2], t[41].position )
|
|
302
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, -0.8], t[42].position )
|
|
303
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, 0.2], t[43].position )
|
|
304
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 1.2, 1.2], t[44].position )
|
|
305
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, -0.8], t[45].position )
|
|
306
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, 0.2], t[46].position )
|
|
307
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, -0.8, 1.2], t[47].position )
|
|
308
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, -0.8], t[48].position )
|
|
309
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, 0.2], t[49].position )
|
|
310
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 0.2, 1.2], t[50].position )
|
|
311
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, -0.8], t[51].position )
|
|
312
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, 0.2], t[52].position )
|
|
313
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 1.2, 1.2], t[53].position )
|
|
1294
|
+
assert_equal([false, false, false],
|
|
1295
|
+
@c10 .axis_independencies($symprec, $angle_tolerance))
|
|
1296
|
+
assert_equal([false, false, true ],
|
|
1297
|
+
@c11 .axis_independencies($symprec, $angle_tolerance))
|
|
1298
|
+
assert_equal([true , true , true ],
|
|
1299
|
+
@c12 .axis_independencies($symprec, $angle_tolerance))
|
|
1300
|
+
assert_equal([true , true , true ],
|
|
1301
|
+
@c13 .axis_independencies($symprec, $angle_tolerance))
|
|
1302
|
+
assert_equal([false, false, true ],
|
|
1303
|
+
@c14 .axis_independencies($symprec, $angle_tolerance))
|
|
1304
|
+
assert_equal([false, true , false],
|
|
1305
|
+
@c14b.axis_independencies($symprec, $angle_tolerance))
|
|
1306
|
+
assert_equal([true , true , true ],
|
|
1307
|
+
@c15 .axis_independencies($symprec, $angle_tolerance))
|
|
1308
|
+
assert_equal([false, false, true ],
|
|
1309
|
+
@c16 .axis_independencies($symprec, $angle_tolerance))
|
|
1310
|
+
end
|
|
1311
|
+
|
|
1312
|
+
def test_symmetry_operations
|
|
1313
|
+
unless defined? Getspg
|
|
1314
|
+
puts
|
|
1315
|
+
puts "test_symmetry_operations() is ignored because spglib is not installed."
|
|
1316
|
+
return
|
|
314
1317
|
end
|
|
315
1318
|
|
|
316
|
-
|
|
317
|
-
|
|
318
|
-
|
|
319
|
-
|
|
1319
|
+
f13 = 1.0/3.0
|
|
1320
|
+
|
|
1321
|
+
#cubic/POSCAR #Pm-3m (221) / m-3m / -P 4 2 3 (517)
|
|
1322
|
+
corrects = [
|
|
1323
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1324
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1325
|
+
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1326
|
+
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1327
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1328
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1329
|
+
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1330
|
+
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1331
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----09----
|
|
1332
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----10----
|
|
1333
|
+
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----11----
|
|
1334
|
+
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----12----
|
|
1335
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13----
|
|
1336
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14----
|
|
1337
|
+
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15----
|
|
1338
|
+
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16----
|
|
1339
|
+
{:rotation => [[ 0, 0, 1], [ 1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----17----
|
|
1340
|
+
{:rotation => [[ 0, 0, -1], [-1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----18----
|
|
1341
|
+
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----19----
|
|
1342
|
+
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----20----
|
|
1343
|
+
{:rotation => [[ 0, 0, 1], [-1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----21----
|
|
1344
|
+
{:rotation => [[ 0, 0, -1], [ 1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----22----
|
|
1345
|
+
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----23----
|
|
1346
|
+
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----24----
|
|
1347
|
+
{:rotation => [[ 0, 0, -1], [ 1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----25----
|
|
1348
|
+
{:rotation => [[ 0, 0, 1], [-1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----26----
|
|
1349
|
+
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----27----
|
|
1350
|
+
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----28----
|
|
1351
|
+
{:rotation => [[ 0, 0, -1], [-1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----29----
|
|
1352
|
+
{:rotation => [[ 0, 0, 1], [ 1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----30----
|
|
1353
|
+
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----31----
|
|
1354
|
+
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----32----
|
|
1355
|
+
{:rotation => [[ 0, 1, 0], [ 0, 0, 1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----33----
|
|
1356
|
+
{:rotation => [[ 0, -1, 0], [ 0, 0, -1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----34----
|
|
1357
|
+
{:rotation => [[ 1, 0, 0], [ 0, 0, 1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----35----
|
|
1358
|
+
{:rotation => [[-1, 0, 0], [ 0, 0, -1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----36----
|
|
1359
|
+
{:rotation => [[ 0, -1, 0], [ 0, 0, 1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----37----
|
|
1360
|
+
{:rotation => [[ 0, 1, 0], [ 0, 0, -1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----38----
|
|
1361
|
+
{:rotation => [[-1, 0, 0], [ 0, 0, 1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----39----
|
|
1362
|
+
{:rotation => [[ 1, 0, 0], [ 0, 0, -1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----40----
|
|
1363
|
+
{:rotation => [[ 0, -1, 0], [ 0, 0, -1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----41----
|
|
1364
|
+
{:rotation => [[ 0, 1, 0], [ 0, 0, 1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----42----
|
|
1365
|
+
{:rotation => [[-1, 0, 0], [ 0, 0, -1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----43----
|
|
1366
|
+
{:rotation => [[ 1, 0, 0], [ 0, 0, 1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----44----
|
|
1367
|
+
{:rotation => [[ 0, 1, 0], [ 0, 0, -1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----45----
|
|
1368
|
+
{:rotation => [[ 0, -1, 0], [ 0, 0, 1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----46----
|
|
1369
|
+
{:rotation => [[ 1, 0, 0], [ 0, 0, -1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----47----
|
|
1370
|
+
{:rotation => [[-1, 0, 0], [ 0, 0, 1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----48----
|
|
1371
|
+
]
|
|
1372
|
+
|
|
1373
|
+
results = @c10 .symmetry_operations($symprec, $angle_tolerance)
|
|
1374
|
+
assert_equal(corrects.size, results.size)
|
|
1375
|
+
corrects.size.times do |index|
|
|
1376
|
+
assert_equal(corrects[index], results[index])
|
|
320
1377
|
end
|
|
321
1378
|
|
|
322
|
-
|
|
323
|
-
|
|
324
|
-
|
|
325
|
-
|
|
326
|
-
|
|
327
|
-
|
|
328
|
-
|
|
329
|
-
|
|
330
|
-
|
|
331
|
-
|
|
332
|
-
|
|
333
|
-
|
|
334
|
-
|
|
335
|
-
|
|
336
|
-
|
|
337
|
-
|
|
338
|
-
|
|
339
|
-
|
|
340
|
-
|
|
341
|
-
|
|
342
|
-
|
|
343
|
-
|
|
344
|
-
|
|
345
|
-
|
|
346
|
-
|
|
347
|
-
|
|
348
|
-
|
|
349
|
-
|
|
350
|
-
|
|
351
|
-
|
|
352
|
-
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
|
|
356
|
-
|
|
357
|
-
|
|
358
|
-
|
|
359
|
-
|
|
360
|
-
|
|
361
|
-
|
|
362
|
-
|
|
363
|
-
|
|
364
|
-
|
|
365
|
-
|
|
366
|
-
|
|
367
|
-
|
|
368
|
-
|
|
369
|
-
|
|
370
|
-
|
|
371
|
-
|
|
372
|
-
|
|
373
|
-
|
|
374
|
-
|
|
375
|
-
|
|
376
|
-
|
|
377
|
-
|
|
378
|
-
|
|
379
|
-
|
|
380
|
-
|
|
381
|
-
|
|
382
|
-
|
|
383
|
-
|
|
384
|
-
|
|
385
|
-
|
|
386
|
-
|
|
387
|
-
|
|
388
|
-
|
|
389
|
-
|
|
390
|
-
|
|
391
|
-
|
|
392
|
-
|
|
393
|
-
|
|
394
|
-
|
|
395
|
-
|
|
396
|
-
|
|
397
|
-
|
|
398
|
-
|
|
399
|
-
|
|
400
|
-
|
|
401
|
-
|
|
402
|
-
|
|
403
|
-
|
|
404
|
-
|
|
405
|
-
|
|
406
|
-
|
|
407
|
-
|
|
408
|
-
|
|
409
|
-
|
|
410
|
-
|
|
411
|
-
|
|
412
|
-
|
|
413
|
-
# 'Li' -> 'Na'、 片方だけ変更。
|
|
414
|
-
tmp = Marshal.load( Marshal.dump( @c02 ))
|
|
415
|
-
tmp.set_elements( { 'Li' => 'Na' } )
|
|
416
|
-
assert_equal( 'Na', tmp.atoms[0].element )
|
|
417
|
-
assert_equal( 'O', tmp.atoms[1].element )
|
|
418
|
-
end
|
|
419
|
-
|
|
420
|
-
def test_equal_lattice_in_delta?
|
|
421
|
-
assert_equal( true , @c00.equal_lattice_in_delta?(@c00, 0.001, 0.1) )
|
|
422
|
-
assert_equal( true , @c00.equal_lattice_in_delta?(@c02, 0.001, 0.1) )
|
|
423
|
-
assert_equal( true , @c00.equal_lattice_in_delta?(@c01, 0.001, 0.1) )
|
|
424
|
-
assert_equal( true , @c02.equal_lattice_in_delta?(@c00, 0.001, 0.1) )
|
|
425
|
-
assert_equal( true , @c02.equal_lattice_in_delta?(@c02, 0.001, 0.1) )
|
|
426
|
-
assert_equal( true , @c02.equal_lattice_in_delta?(@c01, 0.001, 0.1) )
|
|
427
|
-
assert_equal( true , @c01.equal_lattice_in_delta?(@c00, 0.001, 0.1) )
|
|
428
|
-
assert_equal( true , @c01.equal_lattice_in_delta?(@c02, 0.001, 0.1) )
|
|
429
|
-
assert_equal( true , @c01.equal_lattice_in_delta?(@c01, 0.001, 0.1) )
|
|
430
|
-
|
|
431
|
-
end
|
|
432
|
-
|
|
433
|
-
def test_equal_atoms_in_delta?
|
|
434
|
-
assert_equal( true , @c00.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
435
|
-
assert_equal( false, @c00.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
436
|
-
assert_equal( false, @c00.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
437
|
-
assert_equal( false, @c00.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
438
|
-
assert_equal( false, @c00.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
439
|
-
assert_equal( false, @c00.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
440
|
-
assert_equal( false, @c02.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
441
|
-
assert_equal( true , @c02.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
442
|
-
assert_equal( false, @c02.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
443
|
-
assert_equal( true , @c02.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
444
|
-
assert_equal( false, @c02.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
445
|
-
assert_equal( false, @c02.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
446
|
-
assert_equal( false, @c01.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
447
|
-
assert_equal( false, @c01.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
448
|
-
assert_equal( true , @c01.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
449
|
-
assert_equal( false, @c01.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
450
|
-
assert_equal( false, @c01.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
451
|
-
assert_equal( false, @c01.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
452
|
-
assert_equal( false, @c03.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
453
|
-
assert_equal( true , @c03.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
454
|
-
assert_equal( false, @c03.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
455
|
-
assert_equal( true , @c03.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
456
|
-
assert_equal( false, @c03.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
457
|
-
assert_equal( false, @c03.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
458
|
-
assert_equal( false, @c04.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
459
|
-
assert_equal( false, @c04.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
460
|
-
assert_equal( false, @c04.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
461
|
-
assert_equal( false, @c04.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
462
|
-
assert_equal( true , @c04.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
463
|
-
assert_equal( false, @c04.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
464
|
-
assert_equal( false, @c05.equal_atoms_in_delta?( @c00, 0.01 ) )
|
|
465
|
-
assert_equal( false, @c05.equal_atoms_in_delta?( @c02, 0.01 ) )
|
|
466
|
-
assert_equal( false, @c05.equal_atoms_in_delta?( @c01, 0.01 ) )
|
|
467
|
-
assert_equal( false, @c05.equal_atoms_in_delta?( @c03, 0.01 ) )
|
|
468
|
-
assert_equal( false, @c05.equal_atoms_in_delta?( @c04, 0.01 ) )
|
|
469
|
-
assert_equal( true , @c05.equal_atoms_in_delta?( @c05, 0.01 ) )
|
|
470
|
-
end
|
|
471
|
-
|
|
472
|
-
def test_equal_in_delta?
|
|
473
|
-
assert_equal(true , @c00.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
474
|
-
assert_equal(false, @c00.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
475
|
-
assert_equal(false, @c00.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
476
|
-
assert_equal(false, @c00.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
477
|
-
assert_equal(false, @c00.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
478
|
-
assert_equal(false, @c00.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
479
|
-
|
|
480
|
-
assert_equal(false, @c02.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
481
|
-
assert_equal(false, @c02.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
482
|
-
assert_equal(true , @c02.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
483
|
-
assert_equal(true , @c02.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
484
|
-
assert_equal(false, @c02.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
485
|
-
assert_equal(false, @c02.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
486
|
-
|
|
487
|
-
assert_equal(false, @c01.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
488
|
-
assert_equal(true , @c01.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
489
|
-
assert_equal(false, @c01.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
490
|
-
assert_equal(false, @c01.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
491
|
-
assert_equal(false, @c01.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
492
|
-
assert_equal(false, @c01.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
493
|
-
|
|
494
|
-
assert_equal(false, @c03.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
495
|
-
assert_equal(false, @c03.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
496
|
-
assert_equal(true , @c03.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
497
|
-
assert_equal(true , @c03.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
498
|
-
assert_equal(false, @c03.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
499
|
-
assert_equal(false, @c03.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
500
|
-
|
|
501
|
-
assert_equal(false, @c04.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
502
|
-
assert_equal(false, @c04.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
503
|
-
assert_equal(false, @c04.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
504
|
-
assert_equal(false, @c04.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
505
|
-
assert_equal(true , @c04.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
506
|
-
assert_equal(false, @c04.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
507
|
-
|
|
508
|
-
assert_equal(false, @c05.equal_in_delta?( @c00, 0.001, 0.1, 0.01 ) )
|
|
509
|
-
assert_equal(false, @c05.equal_in_delta?( @c01, 0.001, 0.1, 0.01 ) )
|
|
510
|
-
assert_equal(false, @c05.equal_in_delta?( @c02, 0.001, 0.1, 0.01 ) )
|
|
511
|
-
assert_equal(false, @c05.equal_in_delta?( @c03, 0.001, 0.1, 0.01 ) )
|
|
512
|
-
assert_equal(false, @c05.equal_in_delta?( @c04, 0.001, 0.1, 0.01 ) )
|
|
513
|
-
assert_equal(true , @c05.equal_in_delta?( @c05, 0.001, 0.1, 0.01 ) )
|
|
514
|
-
end
|
|
515
|
-
|
|
516
|
-
def test_equal
|
|
517
|
-
cell = CrystalCell::Cell.new( CrystalCell::LatticeAxes.new([ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]))
|
|
518
|
-
assert_equal( true , @c00 == cell )
|
|
519
|
-
assert_equal( false, @c01 == cell )
|
|
520
|
-
|
|
521
|
-
cell = CrystalCell::Cell.new( CrystalCell::LatticeAxes.new([ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0]]))
|
|
522
|
-
cell.add_atom(CrystalCell::Atom.new( 0, [0.0, 0.0, 0.0] ))
|
|
523
|
-
cell.add_atom(CrystalCell::Atom.new( 1, [0.1, 0.2, 0.3] ))
|
|
524
|
-
assert_equal( false, @c00 == cell )
|
|
525
|
-
assert_equal( true , @c01 == cell )
|
|
526
|
-
end
|
|
527
|
-
|
|
528
|
-
def test_distance
|
|
529
|
-
assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], [1,1,1])}
|
|
530
|
-
assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], Mageo::Vector3DInternal[1,1,1])}
|
|
531
|
-
assert_raise(CrystalCell::Cell::TypeError){@c00.distance([0,0,0], Mageo::Vector3D[1,1,1])}
|
|
532
|
-
|
|
533
|
-
assert_in_delta(
|
|
534
|
-
Math::sqrt(0.56),
|
|
535
|
-
@c00.distance(Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.1, 0.1, 0.1] ),
|
|
536
|
-
$tolerance
|
|
537
|
-
)
|
|
538
|
-
assert_in_delta( Math::sqrt( 1.6**2 + 3.4**2 + 5.4**2),
|
|
539
|
-
@c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.8, 0.9, 1.0] ), $tolerance
|
|
540
|
-
)
|
|
541
|
-
|
|
542
|
-
assert_in_delta( Math::sqrt(0.56), @c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.1, 0.1, 0.1] ), $tolerance )
|
|
543
|
-
assert_in_delta( Math::sqrt( 1.6**2 + 3.4**2 + 5.4**2),
|
|
544
|
-
@c00.distance( Mageo::Vector3DInternal[0.0, 0.0, 0.0], Mageo::Vector3DInternal[0.8, 0.9, 1.0] ), $tolerance
|
|
545
|
-
)
|
|
546
|
-
end
|
|
547
|
-
|
|
548
|
-
def test_dump_poscar
|
|
549
|
-
c00_str = [
|
|
550
|
-
'c00',
|
|
551
|
-
'1.0',
|
|
552
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
553
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
554
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
555
|
-
' ',
|
|
556
|
-
'',
|
|
557
|
-
'Direct'
|
|
558
|
-
].join("\n")
|
|
559
|
-
|
|
560
|
-
c01_str = [
|
|
561
|
-
'c01',
|
|
562
|
-
'1.0',
|
|
563
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
564
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
565
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
566
|
-
' 0 1',
|
|
567
|
-
' 1 1',
|
|
568
|
-
'Direct',
|
|
569
|
-
' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
570
|
-
' 0.10000000000000 0.20000000000000 0.30000000000000'
|
|
571
|
-
].join("\n")
|
|
572
|
-
|
|
573
|
-
c02_str = [
|
|
574
|
-
'c02',
|
|
575
|
-
'1.0',
|
|
576
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
577
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
578
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
579
|
-
' Li O',
|
|
580
|
-
' 1 1',
|
|
581
|
-
'Direct',
|
|
582
|
-
' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
583
|
-
' 0.20000000000000 0.20000000000000 0.20000000000000'
|
|
584
|
-
].join("\n")
|
|
585
|
-
|
|
586
|
-
c03_str = [
|
|
587
|
-
'c03',
|
|
588
|
-
'1.0',
|
|
589
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
590
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
591
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
592
|
-
' Li O',
|
|
593
|
-
' 1 1',
|
|
594
|
-
'Direct',
|
|
595
|
-
' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
596
|
-
' 0.20000000000000 0.20000000000000 0.20000000000000'
|
|
597
|
-
].join("\n")
|
|
598
|
-
|
|
599
|
-
c04_str = [
|
|
600
|
-
'c04',
|
|
601
|
-
'1.0',
|
|
602
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
603
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
604
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
605
|
-
' Li O',
|
|
606
|
-
' 2 1',
|
|
607
|
-
'Direct',
|
|
608
|
-
' 0.00000000000000 0.00000000000000 0.00000000000000',
|
|
609
|
-
' 0.10000000000000 0.20000000000000 0.30000000000000',
|
|
610
|
-
' 0.20000000000000 0.20000000000000 0.20000000000000'
|
|
611
|
-
].join("\n")
|
|
612
|
-
|
|
613
|
-
c05_str = [
|
|
614
|
-
'c05',
|
|
615
|
-
'1.0',
|
|
616
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
617
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
618
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
619
|
-
' Li',
|
|
620
|
-
' 1',
|
|
621
|
-
'Direct',
|
|
622
|
-
' 0.00000000000000 0.00000000000000 0.00000000000000'
|
|
623
|
-
].join("\n")
|
|
624
|
-
|
|
625
|
-
c06_str = [
|
|
626
|
-
'c06',
|
|
627
|
-
'1.0',
|
|
628
|
-
' 2.00000000000000 2.00000000000000 2.00000000000000',
|
|
629
|
-
' 0.00000000000000 2.00000000000000 2.00000000000000',
|
|
630
|
-
' 0.00000000000000 0.00000000000000 2.00000000000000',
|
|
631
|
-
' Li O',
|
|
632
|
-
' 1 1',
|
|
633
|
-
'Selective dynamics',
|
|
634
|
-
'Direct',
|
|
635
|
-
' 0.00000000000000 0.00000000000000 0.00000000000000 T F F',
|
|
636
|
-
' 0.20000000000000 0.20000000000000 0.20000000000000 T T T'
|
|
637
|
-
].join("\n")
|
|
638
|
-
|
|
639
|
-
# Raise exception
|
|
640
|
-
# assert_raise( RuntimeError ){ @c00.dump_poscar( [], io ) }
|
|
641
|
-
assert_raise( RuntimeError ){ @c00.dump_poscar( [0] ) }
|
|
642
|
-
assert_raise( RuntimeError ){ @c00.dump_poscar( [0, 1] ) }
|
|
643
|
-
assert_raise( RuntimeError ){ @c00.dump_poscar( ['Li'] ) }
|
|
644
|
-
assert_raise( RuntimeError ){ @c00.dump_poscar( ['Li', 'O'] ) }
|
|
645
|
-
assert_raise( RuntimeError ){ @c02.dump_poscar( [] ) }
|
|
646
|
-
assert_raise( RuntimeError ){ @c02.dump_poscar( [0] ) }
|
|
647
|
-
assert_raise( RuntimeError ){ @c02.dump_poscar( [0, 1] ) }
|
|
648
|
-
assert_raise( RuntimeError ){ @c02.dump_poscar( ['Li'] ) }
|
|
649
|
-
assert_raise( RuntimeError ){ @c01.dump_poscar( [] ) }
|
|
650
|
-
assert_raise( RuntimeError ){ @c01.dump_poscar( [0] ) }
|
|
651
|
-
assert_raise( RuntimeError ){ @c01.dump_poscar( ['Li'] ) }
|
|
652
|
-
assert_raise( RuntimeError ){ @c01.dump_poscar( ['Li', 'O'] ) }
|
|
653
|
-
assert_raise( RuntimeError ){ @c04.dump_poscar( [] ) }
|
|
654
|
-
assert_raise( RuntimeError ){ @c04.dump_poscar( [0] ) }
|
|
655
|
-
assert_raise( RuntimeError ){ @c04.dump_poscar( [0, 1] ) }
|
|
656
|
-
assert_raise( RuntimeError ){ @c04.dump_poscar( ['Li'] ) }
|
|
657
|
-
assert_raise( RuntimeError ){ @c05.dump_poscar( [] ) }
|
|
658
|
-
assert_raise( RuntimeError ){ @c05.dump_poscar( [0] ) }
|
|
659
|
-
assert_raise( RuntimeError ){ @c05.dump_poscar( [0, 1] ) }
|
|
660
|
-
assert_raise( RuntimeError ){ @c05.dump_poscar( ['Li', 'O'] ) }
|
|
661
|
-
assert_raise( RuntimeError ){ @c03.dump_poscar( [] ) }
|
|
662
|
-
assert_raise( RuntimeError ){ @c03.dump_poscar( [0] ) }
|
|
663
|
-
assert_raise( RuntimeError ){ @c03.dump_poscar( [0, 1] ) }
|
|
664
|
-
assert_raise( RuntimeError ){ @c03.dump_poscar( ['Li'] ) }
|
|
665
|
-
|
|
666
|
-
#
|
|
667
|
-
StringIO.new do |io|
|
|
668
|
-
@c00.dump_poscar( [], io )
|
|
669
|
-
assert_equal( c00_str, io.read )
|
|
670
|
-
end
|
|
671
|
-
|
|
672
|
-
StringIO.new do |io|
|
|
673
|
-
@c01.dump_poscar( [ 0, 1 ], io )
|
|
674
|
-
assert_equal( c01, io.read )
|
|
675
|
-
end
|
|
676
|
-
|
|
677
|
-
StringIO.new do |io|
|
|
678
|
-
@c02.dump_poscar( [ 'Li', 'O' ], io )
|
|
679
|
-
assert_equal( c02, io.read )
|
|
680
|
-
end
|
|
681
|
-
|
|
682
|
-
StringIO.new do |io|
|
|
683
|
-
@c03.dump_poscar( [ 'Li', 'O' ], io )
|
|
684
|
-
assert_equal( c03, io.read )
|
|
1379
|
+
#monoclinic/POSCAR #P2/m (10) / 2/m / -P 2y (57)
|
|
1380
|
+
corrects = [
|
|
1381
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1382
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1383
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1384
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1385
|
+
]
|
|
1386
|
+
#pp @c12
|
|
1387
|
+
assert_equal(corrects, @c12 .symmetry_operations($symprec, $angle_tolerance)) #monoclinic
|
|
1388
|
+
|
|
1389
|
+
#orthorhombic/POSCAR #Pmmm (47) / mmm / -P 2 2 (227)
|
|
1390
|
+
corrects = [
|
|
1391
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1392
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1393
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1394
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1395
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1396
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1397
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1398
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1399
|
+
]
|
|
1400
|
+
assert_equal(corrects, @c13 .symmetry_operations($symprec, $angle_tolerance)) #orthorhombic
|
|
1401
|
+
|
|
1402
|
+
#tetragonal-b/POSCAR #P4/mmm (123) / 4/mmm/ -P 4 2 (400)
|
|
1403
|
+
corrects = [
|
|
1404
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1405
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1406
|
+
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1407
|
+
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1408
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1409
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1410
|
+
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1411
|
+
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1412
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----09----
|
|
1413
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----10----
|
|
1414
|
+
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----11----
|
|
1415
|
+
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----12----
|
|
1416
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13----
|
|
1417
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14----
|
|
1418
|
+
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----15----
|
|
1419
|
+
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----16----
|
|
1420
|
+
]
|
|
1421
|
+
assert_equal(corrects, @c14b .symmetry_operations($symprec, $angle_tolerance)) #tetragonal
|
|
1422
|
+
|
|
1423
|
+
#tetragonal/POSCAR #P4/mmm (123) / 4/mmm/ -P 4 2 (400)
|
|
1424
|
+
corrects = [
|
|
1425
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1426
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1427
|
+
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1428
|
+
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1429
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1430
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1431
|
+
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1432
|
+
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1433
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----09----
|
|
1434
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----10----
|
|
1435
|
+
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----11----
|
|
1436
|
+
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----12----
|
|
1437
|
+
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13----
|
|
1438
|
+
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14----
|
|
1439
|
+
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15----
|
|
1440
|
+
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16----
|
|
1441
|
+
]
|
|
1442
|
+
assert_equal(corrects, @c14.symmetry_operations($symprec, $angle_tolerance)) #tetragonal-b
|
|
1443
|
+
|
|
1444
|
+
#triclinic/POSCAR #P1 (1) / 1 / P 1 (1)
|
|
1445
|
+
corrects = [
|
|
1446
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1447
|
+
]
|
|
1448
|
+
assert_equal(corrects, @c15 .symmetry_operations($symprec, $angle_tolerance)) #triclinic
|
|
1449
|
+
|
|
1450
|
+
#trigonal/POSCAR #P-3m1 (164) / -3m / -P 3 2= (456)
|
|
1451
|
+
corrects = [
|
|
1452
|
+
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1453
|
+
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----02----
|
|
1454
|
+
{:rotation => [[-1, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----03----
|
|
1455
|
+
{:rotation => [[ 1, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----04----
|
|
1456
|
+
{:rotation => [[ 0, 1, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [1.0, 0.0, 1.0]}, #----05----
|
|
1457
|
+
{:rotation => [[ 0, -1, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----06----
|
|
1458
|
+
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----07----
|
|
1459
|
+
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [1.0, 0.0, 1.0]}, #----08----
|
|
1460
|
+
{:rotation => [[-1, 0, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----09----
|
|
1461
|
+
{:rotation => [[ 1, 0, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----10----
|
|
1462
|
+
{:rotation => [[ 1, 1, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----11----
|
|
1463
|
+
{:rotation => [[-1, -1, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----12----
|
|
1464
|
+
]
|
|
1465
|
+
results = @c16.symmetry_operations($symprec, $angle_tolerance)
|
|
1466
|
+
corrects.size.times do |i|
|
|
1467
|
+
3.times do |x|
|
|
1468
|
+
3.times do |y|
|
|
1469
|
+
assert_in_delta(corrects[i][:rotation][x][y], results[i][:rotation][x][y], $tolerance)
|
|
685
1470
|
end
|
|
686
|
-
|
|
687
|
-
|
|
688
|
-
|
|
689
|
-
|
|
690
|
-
end
|
|
691
|
-
|
|
692
|
-
StringIO.new do |io|
|
|
693
|
-
@c05.dump_poscar( [ 'Li', 'O' ], io )
|
|
694
|
-
assert_equal( c05, io.read )
|
|
695
|
-
end
|
|
696
|
-
|
|
697
|
-
assert_equal( c00_str, @c00.dump_poscar( [ ], nil ) )
|
|
698
|
-
assert_equal( c01_str, @c01.dump_poscar( [ 0 , 1 ], nil ) )
|
|
699
|
-
assert_equal( c02_str, @c02.dump_poscar( [ 'Li', 'O' ], nil ) )
|
|
700
|
-
assert_equal( c03_str, @c03.dump_poscar( [ 'Li', 'O' ], nil ) )
|
|
701
|
-
assert_equal( c04_str, @c04.dump_poscar( [ 'Li', 'O' ], nil ) )
|
|
702
|
-
assert_equal( c05_str, @c05.dump_poscar( [ 'Li' ], nil ) )
|
|
703
|
-
|
|
704
|
-
assert_equal( c00_str, @c00.dump_poscar( [ ] ) )
|
|
705
|
-
assert_equal( c01_str, @c01.dump_poscar( [ 0 , 1 ] ) )
|
|
706
|
-
assert_equal( c02_str, @c02.dump_poscar( [ 'Li', 'O' ] ) )
|
|
707
|
-
assert_equal( c03_str, @c03.dump_poscar( [ 'Li', 'O' ] ) )
|
|
708
|
-
assert_equal( c04_str, @c04.dump_poscar( [ 'Li', 'O' ] ) )
|
|
709
|
-
assert_equal( c05_str, @c05.dump_poscar( [ 'Li' ] ) )
|
|
710
|
-
|
|
711
|
-
assert_equal( c06_str, @c06 .dump_poscar( [ 'Li', 'O' ] ) )
|
|
712
|
-
|
|
1471
|
+
end
|
|
1472
|
+
3.times do |xyz|
|
|
1473
|
+
assert_in_delta(corrects[i][:translation][xyz], results[i][:translation][xyz], $tolerance)
|
|
1474
|
+
end
|
|
713
1475
|
end
|
|
714
1476
|
|
|
715
|
-
|
|
716
|
-
|
|
717
|
-
|
|
718
|
-
|
|
719
|
-
|
|
720
|
-
|
|
721
|
-
|
|
722
|
-
|
|
723
|
-
|
|
724
|
-
|
|
725
|
-
|
|
726
|
-
|
|
727
|
-
|
|
728
|
-
|
|
729
|
-
|
|
730
|
-
|
|
731
|
-
|
|
732
|
-
|
|
733
|
-
end
|
|
734
|
-
|
|
735
|
-
|
|
736
|
-
|
|
737
|
-
|
|
738
|
-
|
|
739
|
-
|
|
740
|
-
Mageo::Vector3DInternal[ -0.2, -0.2, -0.2 ],
|
|
741
|
-
Mageo::Vector3DInternal[ -0.1, -0.2, -0.3 ]
|
|
742
|
-
],
|
|
743
|
-
@c02.positions
|
|
744
|
-
)
|
|
745
|
-
end
|
|
746
|
-
|
|
747
|
-
def test_translate
|
|
748
|
-
poss = @c02.translate( [1.1, 1.2, 1.3] ).positions
|
|
749
|
-
assert_in_delta( 1.1, poss[0][0], $tolerance )
|
|
750
|
-
assert_in_delta( 1.2, poss[0][1], $tolerance )
|
|
751
|
-
assert_in_delta( 1.3, poss[0][2], $tolerance )
|
|
752
|
-
assert_in_delta( 1.3, poss[1][0], $tolerance )
|
|
753
|
-
assert_in_delta( 1.4, poss[1][1], $tolerance )
|
|
754
|
-
assert_in_delta( 1.5, poss[1][2], $tolerance )
|
|
755
|
-
|
|
756
|
-
poss = @c02.translate( [-0.3,-0.3,-0.3] ).positions
|
|
757
|
-
assert_in_delta( -0.3, poss[0][0], $tolerance )
|
|
758
|
-
assert_in_delta( -0.3, poss[0][1], $tolerance )
|
|
759
|
-
assert_in_delta( -0.3, poss[0][2], $tolerance )
|
|
760
|
-
assert_in_delta( -0.1, poss[1][0], $tolerance )
|
|
761
|
-
assert_in_delta( -0.1, poss[1][1], $tolerance )
|
|
762
|
-
assert_in_delta( -0.1, poss[1][2], $tolerance )
|
|
763
|
-
|
|
764
|
-
# Check not destructed.
|
|
765
|
-
assert_equal(
|
|
766
|
-
[ Mageo::Vector3DInternal[ 0.0, 0.0, 0.0 ],
|
|
767
|
-
Mageo::Vector3DInternal[ 0.2, 0.2, 0.2 ]
|
|
768
|
-
],
|
|
769
|
-
@c02.positions
|
|
770
|
-
)
|
|
771
|
-
end
|
|
772
|
-
|
|
773
|
-
def test_translate!
|
|
774
|
-
@c02.translate!( [1.1, 1.2, 1.3] )
|
|
775
|
-
poss = @c02.positions
|
|
776
|
-
|
|
777
|
-
assert_in_delta( 1.1, poss[0][0], $tolerance )
|
|
778
|
-
assert_in_delta( 1.2, poss[0][1], $tolerance )
|
|
779
|
-
assert_in_delta( 1.3, poss[0][2], $tolerance )
|
|
780
|
-
assert_in_delta( 1.3, poss[1][0], $tolerance )
|
|
781
|
-
assert_in_delta( 1.4, poss[1][1], $tolerance )
|
|
782
|
-
assert_in_delta( 1.5, poss[1][2], $tolerance )
|
|
783
|
-
end
|
|
784
|
-
|
|
785
|
-
def test_center_of_atoms
|
|
786
|
-
# No atom in the cell.
|
|
787
|
-
assert_raise( CrystalCell::Cell::NoAtomError ){ @c00.center_of_atoms }
|
|
788
|
-
|
|
789
|
-
assert_equal( Mageo::Vector3DInternal[0.05, 0.1, 0.15], @c01.center_of_atoms )
|
|
790
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c02.center_of_atoms )
|
|
791
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c03.center_of_atoms )
|
|
792
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 4.0/30.0, 5.0/30.0], @c04.center_of_atoms )
|
|
793
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c05.center_of_atoms )
|
|
794
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c06.center_of_atoms )
|
|
795
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.1, 0.1], @c07.center_of_atoms )
|
|
796
|
-
end
|
|
797
|
-
|
|
798
|
-
def test_calc_volume
|
|
799
|
-
# @c00 = CrystalCell::Cell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] )
|
|
800
|
-
assert_in_delta( 8.00, @c00.calc_volume, $tolerance)
|
|
801
|
-
|
|
802
|
-
c10 = CrystalCell::Cell.new( [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ] )
|
|
803
|
-
c11 = CrystalCell::Cell.new( [ [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5] ] )
|
|
804
|
-
assert_in_delta( 1.00, c10.calc_volume, $tolerance)
|
|
805
|
-
assert_in_delta( 0.25, c11.calc_volume, $tolerance)
|
|
806
|
-
end
|
|
807
|
-
|
|
808
|
-
def test_cell_of_elements
|
|
809
|
-
t = @c04.cell_of_elements( [ 'Li' ] )
|
|
810
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
811
|
-
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
812
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
813
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
814
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
815
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
816
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
817
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
818
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
819
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
820
|
-
assert_equal( 2, t.atoms.size )
|
|
821
|
-
# checking atom 0
|
|
822
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
823
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
824
|
-
assert_equal( nil , t.atoms[0].name )
|
|
825
|
-
# checking atom 1
|
|
826
|
-
assert_equal( 'Li' , t.atoms[1].element)
|
|
827
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position)
|
|
828
|
-
assert_equal( nil , t.atoms[1].name )
|
|
829
|
-
|
|
830
|
-
t = @c04.cell_of_elements( [ 'Li', 'O' ] )
|
|
831
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
832
|
-
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
833
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
834
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
835
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
836
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
837
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
838
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
839
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
840
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
841
|
-
assert_equal( 3, t.atoms.size )
|
|
842
|
-
# checking atom 0
|
|
843
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
844
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
845
|
-
assert_equal( nil , t.atoms[0].name )
|
|
846
|
-
# checking atom 1
|
|
847
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
848
|
-
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[1].position)
|
|
849
|
-
assert_equal( nil , t.atoms[1].name )
|
|
850
|
-
# checking atom 2
|
|
851
|
-
assert_equal( 'Li' , t.atoms[2].element)
|
|
852
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[2].position)
|
|
853
|
-
assert_equal( nil , t.atoms[2].name )
|
|
854
|
-
|
|
855
|
-
t = @c04.cell_of_elements( [ 'O' ] )
|
|
856
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
857
|
-
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
858
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
859
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
860
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
861
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
862
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
863
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
864
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
865
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
866
|
-
assert_equal( 1, t.atoms.size )
|
|
867
|
-
# checking atom 0
|
|
868
|
-
assert_equal( 'O' , t.atoms[0].element)
|
|
869
|
-
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[0].position)
|
|
870
|
-
assert_equal( nil , t.atoms[0].name )
|
|
871
|
-
|
|
872
|
-
t = @c04.cell_of_elements( [ 'F' ] )
|
|
873
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
874
|
-
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
875
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
876
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
877
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
878
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
879
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
880
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
881
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
882
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
883
|
-
assert_equal( 0, t.atoms.size )
|
|
884
|
-
|
|
885
|
-
|
|
886
|
-
# サブクラスで使用したときに、サブクラスで作られるか？
|
|
887
|
-
fc04 = FooCell.new( [ [2.0, 2.0, 2.0], [0.0, 2.0, 2.0], [0.0, 0.0, 2.0] ] )
|
|
888
|
-
fc04.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ))
|
|
889
|
-
fc04.add_atom(CrystalCell::Atom.new( 'O' , [0.2, 0.2, 0.2] ))
|
|
890
|
-
fc04.add_atom(CrystalCell::Atom.new( 'Li', [0.1, 0.2, 0.3] ))
|
|
891
|
-
fc04.comment = 'fc04'
|
|
892
|
-
t = fc04.cell_of_elements( [ 'Li' ] )
|
|
893
|
-
assert_equal( FooCell, t.class )
|
|
894
|
-
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
895
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
896
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
897
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
898
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
899
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
900
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
901
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
902
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
903
|
-
assert_equal( 2, t.atoms.size )
|
|
904
|
-
# checking atom 0
|
|
905
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
906
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
907
|
-
assert_equal( nil , t.atoms[0].name )
|
|
908
|
-
# checking atom 1
|
|
909
|
-
assert_equal( 'Li' , t.atoms[1].element)
|
|
910
|
-
assert_equal( Mageo::Vector3DInternal[0.1, 0.2, 0.3], t.atoms[1].position)
|
|
911
|
-
assert_equal( nil , t.atoms[1].name )
|
|
912
|
-
end
|
|
913
|
-
|
|
914
|
-
def test_unite
|
|
915
|
-
## 格子定数が違えば例外。将来的な feature.
|
|
916
|
-
#t = CrystalCell::Cell.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ] )
|
|
917
|
-
#t.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ))
|
|
918
|
-
#t.comment = 't'
|
|
919
|
-
#assert_raise( CrystalCell::Cell::AxesMismatchError ){ @c05.unite( t ) }
|
|
920
|
-
t = CrystalCell::Cell.new( [ [2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0] ] )
|
|
921
|
-
t.add_atom(CrystalCell::Atom.new( 'Li', [0.0, 0.0, 0.0] ))
|
|
922
|
-
t.comment = 't'
|
|
923
|
-
assert_nothing_raised{ @c05.unite( t ) }
|
|
924
|
-
|
|
925
|
-
# unite
|
|
926
|
-
# 同じ座標のものがあっても気にせず統合する。
|
|
927
|
-
t = @c05.unite( @c06 )
|
|
928
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
929
|
-
assert_in_delta( 2.0, t.axes[0][0], $tolerance )
|
|
930
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
931
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
932
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
933
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
934
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
935
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
936
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
937
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
938
|
-
assert_equal( 3, t.atoms.size )
|
|
939
|
-
# checking atom 0
|
|
940
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
941
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
942
|
-
assert_equal( nil , t.atoms[0].name )
|
|
943
|
-
# checking atom 1
|
|
944
|
-
assert_equal( 'Li' , t.atoms[1].element)
|
|
945
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[1].position)
|
|
946
|
-
assert_equal( nil , t.atoms[1].name )
|
|
947
|
-
# checking atom 2
|
|
948
|
-
assert_equal( 'O' , t.atoms[2].element)
|
|
949
|
-
assert_equal( Mageo::Vector3DInternal[0.2, 0.2, 0.2], t.atoms[2].position)
|
|
950
|
-
assert_equal( nil , t.atoms[2].name )
|
|
951
|
-
end
|
|
952
|
-
|
|
953
|
-
def test_inverse_axis!
|
|
954
|
-
@c02.inverse_axis!( 0 )
|
|
955
|
-
t = @c02
|
|
956
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
957
|
-
assert_in_delta(-2.0, t.axes[0][0], $tolerance )
|
|
958
|
-
assert_in_delta(-2.0, t.axes[0][1], $tolerance )
|
|
959
|
-
assert_in_delta(-2.0, t.axes[0][2], $tolerance )
|
|
960
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
961
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
962
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
963
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
964
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
965
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
966
|
-
assert_equal( 2, t.atoms.size )
|
|
967
|
-
# checking atom 0
|
|
968
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
969
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
970
|
-
assert_equal( nil , t.atoms[0].name )
|
|
971
|
-
# checking atom 1
|
|
972
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
973
|
-
assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
|
|
974
|
-
assert_equal( nil , t.atoms[1].name )
|
|
975
|
-
end
|
|
976
|
-
|
|
977
|
-
def test_inverse_axis
|
|
978
|
-
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.inverse_axis( -1 ) }
|
|
979
|
-
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.inverse_axis( 3 ) }
|
|
980
|
-
|
|
981
|
-
# x 軸反転
|
|
982
|
-
t = @c02.inverse_axis( 0 )
|
|
983
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
984
|
-
assert_in_delta( -2.0, t.axes[0][0], $tolerance )
|
|
985
|
-
assert_in_delta( -2.0, t.axes[0][1], $tolerance )
|
|
986
|
-
assert_in_delta( -2.0, t.axes[0][2], $tolerance )
|
|
987
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
988
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
989
|
-
assert_in_delta( 2.0, t.axes[1][2], $tolerance )
|
|
990
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
991
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
992
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
993
|
-
assert_equal( 2, t.atoms.size )
|
|
994
|
-
# checking atom 0
|
|
995
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
996
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
997
|
-
assert_equal( nil , t.atoms[0].name )
|
|
998
|
-
# checking atom 1
|
|
999
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1000
|
-
assert_equal( Mageo::Vector3DInternal[-0.2, 0.2, 0.2], t.atoms[1].position)
|
|
1001
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1002
|
-
# checking non-destructive
|
|
1003
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1004
|
-
assert_in_delta( 2.0, @c02.axes[0][0], $tolerance )
|
|
1005
|
-
assert_in_delta( 2.0, @c02.axes[0][1], $tolerance )
|
|
1006
|
-
assert_in_delta( 2.0, @c02.axes[0][2], $tolerance )
|
|
1007
|
-
assert_in_delta( 0.0, @c02.axes[1][0], $tolerance )
|
|
1008
|
-
assert_in_delta( 2.0, @c02.axes[1][1], $tolerance )
|
|
1009
|
-
assert_in_delta( 2.0, @c02.axes[1][2], $tolerance )
|
|
1010
|
-
assert_in_delta( 0.0, @c02.axes[2][0], $tolerance )
|
|
1011
|
-
assert_in_delta( 0.0, @c02.axes[2][1], $tolerance )
|
|
1012
|
-
assert_in_delta( 2.0, @c02.axes[2][2], $tolerance )
|
|
1013
|
-
assert_equal( 2, @c02.atoms.size )
|
|
1014
|
-
# checking atom 0
|
|
1015
|
-
assert_equal( 'Li' , @c02.atoms[0].element)
|
|
1016
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], @c02.atoms[0].position)
|
|
1017
|
-
assert_equal( nil , @c02.atoms[0].name )
|
|
1018
|
-
# checking atom 1
|
|
1019
|
-
assert_equal( 'O' , @c02.atoms[1].element)
|
|
1020
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2, 0.2], @c02.atoms[1].position)
|
|
1021
|
-
assert_equal( nil , @c02.atoms[1].name )
|
|
1022
|
-
|
|
1023
|
-
# y 軸反転
|
|
1024
|
-
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ]
|
|
1025
|
-
# ↓ y 軸反転
|
|
1026
|
-
# [ [ ax, ay, az], [ 0,-by,-bz], [ 0, 0, cz] ]
|
|
1027
|
-
# ↓ b vector の y 成分が正になるようにする。
|
|
1028
|
-
# すなわち z 軸回りに半回転し、全ての x, y 成分が反転する。
|
|
1029
|
-
# [ [-ax,-ay, az], [ 0, by,-bz], [ 0, 0, cz] ]
|
|
1030
|
-
t = @c02.inverse_axis( 1 )
|
|
1031
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1032
|
-
assert_in_delta( -2.0, t.axes[0][0], $tolerance )
|
|
1033
|
-
assert_in_delta( -2.0, t.axes[0][1], $tolerance )
|
|
1034
|
-
assert_in_delta( 2.0, t.axes[0][2], $tolerance )
|
|
1035
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
1036
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
1037
|
-
assert_in_delta( -2.0, t.axes[1][2], $tolerance )
|
|
1038
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
1039
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
1040
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
1041
|
-
assert_equal( 2, t.atoms.size )
|
|
1042
|
-
# checking atom 0
|
|
1043
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1044
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
1045
|
-
assert_equal( nil , t.atoms[0].name )
|
|
1046
|
-
# checking atom 1
|
|
1047
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1048
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2,-0.2, 0.2], t.atoms[1].position)
|
|
1049
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1050
|
-
|
|
1051
|
-
# z 軸反転
|
|
1052
|
-
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0, cz] ]
|
|
1053
|
-
# ↓ z 軸反転
|
|
1054
|
-
# [ [ ax, ay, az], [ 0, by, bz], [ 0, 0,-cz] ]
|
|
1055
|
-
# ↓ c vector の z 成分が正になるようにする。
|
|
1056
|
-
# b vector の y 成分も正であることを保存する回転は、
|
|
1057
|
-
# y 軸回りに半回転し、全ての x, z 成分が反転する。
|
|
1058
|
-
# [ [-ax, ay,-az], [ 0, by,-bz], [ 0, 0, cz] ]
|
|
1059
|
-
t = @c02.inverse_axis( 2 )
|
|
1060
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1061
|
-
assert_in_delta(-2.0, t.axes[0][0], $tolerance )
|
|
1062
|
-
assert_in_delta( 2.0, t.axes[0][1], $tolerance )
|
|
1063
|
-
assert_in_delta(-2.0, t.axes[0][2], $tolerance )
|
|
1064
|
-
assert_in_delta( 0.0, t.axes[1][0], $tolerance )
|
|
1065
|
-
assert_in_delta( 2.0, t.axes[1][1], $tolerance )
|
|
1066
|
-
assert_in_delta(-2.0, t.axes[1][2], $tolerance )
|
|
1067
|
-
assert_in_delta( 0.0, t.axes[2][0], $tolerance )
|
|
1068
|
-
assert_in_delta( 0.0, t.axes[2][1], $tolerance )
|
|
1069
|
-
assert_in_delta( 2.0, t.axes[2][2], $tolerance )
|
|
1070
|
-
assert_equal( 2, t.atoms.size )
|
|
1071
|
-
# checking atom 0
|
|
1072
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1073
|
-
assert_equal( Mageo::Vector3DInternal[0.0, 0.0, 0.0], t.atoms[0].position)
|
|
1074
|
-
assert_equal( nil , t.atoms[0].name )
|
|
1075
|
-
# checking atom 1
|
|
1076
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1077
|
-
assert_equal( Mageo::Vector3DInternal[ 0.2, 0.2,-0.2], t.atoms[1].position)
|
|
1078
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1079
|
-
|
|
1080
|
-
end
|
|
1081
|
-
|
|
1082
|
-
def test_exchange_axes!
|
|
1083
|
-
# b, c の交換。
|
|
1084
|
-
@c08.exchange_axes!( [ 1, 2 ] )
|
|
1085
|
-
t = @c08
|
|
1086
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1087
|
-
lc = t.axes.get_lattice_constants
|
|
1088
|
-
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1089
|
-
assert_in_delta( 2.0 , lc[1], $tolerance )
|
|
1090
|
-
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[2], $tolerance )
|
|
1091
|
-
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1092
|
-
assert_in_delta( 35.2643896827547, lc[4], $tolerance )
|
|
1093
|
-
assert_in_delta( 54.7356103172453, lc[5], $tolerance )
|
|
1094
|
-
assert_equal( true, t.axes.lefthand? )
|
|
1095
|
-
assert_equal( 2, t.atoms.size )
|
|
1096
|
-
# checking atom 0
|
|
1097
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1098
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 5.6, 3.4], t.atoms[0].position)
|
|
1099
|
-
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1100
|
-
assert_equal( [ false, false, true] , t.atoms[0].movable_flags )
|
|
1101
|
-
# checking atom 1
|
|
1102
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1103
|
-
assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position)
|
|
1104
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1105
|
-
end
|
|
1106
|
-
|
|
1107
|
-
def test_exchange_axes
|
|
1108
|
-
assert_raise( CrystalCell::Cell::ArgumentError ){ @c02.exchange_axes( [ 0 ] ) }
|
|
1109
|
-
assert_raise( CrystalCell::Cell::ArgumentError ){ @c02.exchange_axes( [ 0, 1, 2] ) }
|
|
1110
|
-
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.exchange_axes( [0, 3] ) }
|
|
1111
|
-
assert_raise( CrystalCell::Cell::AxesRangeError ){ @c02.exchange_axes( [-1, 2] ) }
|
|
1112
|
-
assert_raise( CrystalCell::Cell::SameAxesError ){ @c02.exchange_axes( [ 1,1] ) }
|
|
1113
|
-
|
|
1114
|
-
# b, c の交換。
|
|
1115
|
-
t = @c08.exchange_axes( [ 1, 2 ] )
|
|
1116
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1117
|
-
lc = t.axes.get_lattice_constants
|
|
1118
|
-
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1119
|
-
assert_in_delta( 2.0 , lc[1], $tolerance )
|
|
1120
|
-
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[2], $tolerance )
|
|
1121
|
-
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1122
|
-
assert_in_delta( 35.2643896827547, lc[4], $tolerance )
|
|
1123
|
-
assert_in_delta( 54.7356103172453, lc[5], $tolerance )
|
|
1124
|
-
assert_equal( true, t.axes.lefthand? )
|
|
1125
|
-
assert_equal( 2, t.atoms.size )
|
|
1126
|
-
# checking atom 0
|
|
1127
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1128
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 5.6, 3.4], t.atoms[0].position)
|
|
1129
|
-
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1130
|
-
# checking atom 1
|
|
1131
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1132
|
-
assert_equal( Mageo::Vector3DInternal[-1.2, -5.6, -3.4], t.atoms[1].position)
|
|
1133
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1134
|
-
|
|
1135
|
-
# b, c の交換によって非破壊であることを確認。
|
|
1136
|
-
t = @c08
|
|
1137
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1138
|
-
lc = t.axes.get_lattice_constants
|
|
1139
|
-
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1140
|
-
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1141
|
-
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1142
|
-
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1143
|
-
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1144
|
-
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1145
|
-
assert_equal( true, t.axes.righthand? )
|
|
1146
|
-
assert_equal( 2, t.atoms.size )
|
|
1147
|
-
# checking atom 0
|
|
1148
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1149
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1150
|
-
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1151
|
-
# checking atom 1
|
|
1152
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1153
|
-
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1154
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1155
|
-
|
|
1156
|
-
end
|
|
1157
|
-
|
|
1158
|
-
def test_reflect!
|
|
1159
|
-
@c08.reflect!
|
|
1160
|
-
t = @c08
|
|
1161
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1162
|
-
lc = t.axes.get_lattice_constants
|
|
1163
|
-
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1164
|
-
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1165
|
-
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1166
|
-
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1167
|
-
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1168
|
-
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1169
|
-
assert_equal( true, t.axes.lefthand? )
|
|
1170
|
-
assert_equal( 2, t.atoms.size )
|
|
1171
|
-
# checking atom 0
|
|
1172
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1173
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1174
|
-
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1175
|
-
# checking atom 1
|
|
1176
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1177
|
-
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1178
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1179
|
-
end
|
|
1180
|
-
|
|
1181
|
-
def test_reflect
|
|
1182
|
-
t = @c08.reflect
|
|
1183
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1184
|
-
lc = t.axes.get_lattice_constants
|
|
1185
|
-
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1186
|
-
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1187
|
-
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1188
|
-
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1189
|
-
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1190
|
-
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1191
|
-
assert_equal( true, t.axes.lefthand? )
|
|
1192
|
-
assert_equal( 2, t.atoms.size )
|
|
1193
|
-
# checking atom 0
|
|
1194
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1195
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1196
|
-
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1197
|
-
# checking atom 1
|
|
1198
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1199
|
-
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1200
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1201
|
-
|
|
1202
|
-
# 非破壊であることを確認。
|
|
1203
|
-
t = @c08
|
|
1204
|
-
assert_equal( CrystalCell::Cell, t.class )
|
|
1205
|
-
lc = t.axes.get_lattice_constants
|
|
1206
|
-
assert_in_delta( 2.0 * Math::sqrt( 3.0 ) , lc[0], $tolerance )
|
|
1207
|
-
assert_in_delta( 2.0 * Math::sqrt( 2.0 ) , lc[1], $tolerance )
|
|
1208
|
-
assert_in_delta( 2.0 , lc[2], $tolerance )
|
|
1209
|
-
assert_in_delta( 45.0000000000000, lc[3], $tolerance )
|
|
1210
|
-
assert_in_delta( 54.7356103172453, lc[4], $tolerance )
|
|
1211
|
-
assert_in_delta( 35.2643896827547, lc[5], $tolerance )
|
|
1212
|
-
assert_equal( true, t.axes.righthand? )
|
|
1213
|
-
assert_equal( 2, t.atoms.size )
|
|
1214
|
-
# checking atom 0
|
|
1215
|
-
assert_equal( 'Li' , t.atoms[0].element)
|
|
1216
|
-
assert_equal( Mageo::Vector3DInternal[ 1.2, 3.4, 5.6], t.atoms[0].position)
|
|
1217
|
-
assert_equal( 'atom0' , t.atoms[0].name )
|
|
1218
|
-
# checking atom 1
|
|
1219
|
-
assert_equal( 'O' , t.atoms[1].element)
|
|
1220
|
-
assert_equal( Mageo::Vector3DInternal[-1.2, -3.4, -5.6], t.atoms[1].position)
|
|
1221
|
-
assert_equal( nil , t.atoms[1].name )
|
|
1222
|
-
end
|
|
1223
|
-
|
|
1224
|
-
def test_operate
|
|
1225
|
-
# identity operation
|
|
1226
|
-
rotation = [
|
|
1227
|
-
[1, 0, 0],
|
|
1228
|
-
[0, 1, 0],
|
|
1229
|
-
[0, 0, 1],
|
|
1230
|
-
]
|
|
1231
|
-
translation = [0.0, 0.0, 0.0]
|
|
1232
|
-
result = @c01.operate(rotation, translation)
|
|
1233
|
-
assert_in_delta( 0.0, result.atoms[0].position[0], $tolerance)
|
|
1234
|
-
assert_in_delta( 0.0, result.atoms[0].position[1], $tolerance)
|
|
1235
|
-
assert_in_delta( 0.0, result.atoms[0].position[2], $tolerance)
|
|
1236
|
-
assert_in_delta( 0.1, result.atoms[1].position[0], $tolerance)
|
|
1237
|
-
assert_in_delta( 0.2, result.atoms[1].position[1], $tolerance)
|
|
1238
|
-
assert_in_delta( 0.3, result.atoms[1].position[2], $tolerance)
|
|
1239
|
-
|
|
1240
|
-
# rotation
|
|
1241
|
-
rotation = [
|
|
1242
|
-
[1, 0, 0],
|
|
1243
|
-
[0, 1, 0],
|
|
1244
|
-
[0, 0,-1],
|
|
1245
|
-
]
|
|
1246
|
-
translation = [0.0, 0.0, 0.0]
|
|
1247
|
-
result = @c01.operate(rotation, translation)
|
|
1248
|
-
assert_in_delta( 0.0, result.atoms[0].position[0], $tolerance)
|
|
1249
|
-
assert_in_delta( 0.0, result.atoms[0].position[1], $tolerance)
|
|
1250
|
-
assert_in_delta( 0.0, result.atoms[0].position[2], $tolerance)
|
|
1251
|
-
assert_in_delta( 0.1, result.atoms[1].position[0], $tolerance)
|
|
1252
|
-
assert_in_delta( 0.2, result.atoms[1].position[1], $tolerance)
|
|
1253
|
-
assert_in_delta(-0.3, result.atoms[1].position[2], $tolerance)
|
|
1254
|
-
|
|
1255
|
-
# translation
|
|
1256
|
-
rotation = [
|
|
1257
|
-
[1, 0, 0],
|
|
1258
|
-
[0, 1, 0],
|
|
1259
|
-
[0, 0, 1],
|
|
1260
|
-
]
|
|
1261
|
-
translation = [0.1, 0.2, 0.3]
|
|
1262
|
-
result = @c01.operate(rotation, translation)
|
|
1263
|
-
assert_in_delta(0.1, result.atoms[0].position[0], $tolerance)
|
|
1264
|
-
assert_in_delta(0.2, result.atoms[0].position[1], $tolerance)
|
|
1265
|
-
assert_in_delta(0.3, result.atoms[0].position[2], $tolerance)
|
|
1266
|
-
assert_in_delta(0.2, result.atoms[1].position[0], $tolerance)
|
|
1267
|
-
assert_in_delta(0.4, result.atoms[1].position[1], $tolerance)
|
|
1268
|
-
assert_in_delta(0.6, result.atoms[1].position[2], $tolerance)
|
|
1269
|
-
|
|
1270
|
-
# rotation & translation
|
|
1271
|
-
rotation = [
|
|
1272
|
-
[1, 0, 0],
|
|
1273
|
-
[0, 1, 0],
|
|
1274
|
-
[0, 0,-1],
|
|
1275
|
-
]
|
|
1276
|
-
translation = [0.1, 0.2, 0.3]
|
|
1277
|
-
result = @c01.operate(rotation, translation)
|
|
1278
|
-
assert_in_delta(0.1, result.atoms[0].position[0], $tolerance)
|
|
1279
|
-
assert_in_delta(0.2, result.atoms[0].position[1], $tolerance)
|
|
1280
|
-
assert_in_delta(0.3, result.atoms[0].position[2], $tolerance)
|
|
1281
|
-
assert_in_delta(0.2, result.atoms[1].position[0], $tolerance)
|
|
1282
|
-
assert_in_delta(0.4, result.atoms[1].position[1], $tolerance)
|
|
1283
|
-
assert_in_delta(0.0, result.atoms[1].position[2], $tolerance)
|
|
1284
|
-
end
|
|
1285
|
-
|
|
1286
|
-
def test_axis_independencies
|
|
1287
|
-
unless defined? Getspg
|
|
1288
|
-
puts
|
|
1289
|
-
puts "test_axis_independencies() is ignored because spglib is not installed."
|
|
1290
|
-
return
|
|
1291
|
-
end
|
|
1292
|
-
|
|
1293
|
-
assert_equal([false, false, false],
|
|
1294
|
-
@c10 .axis_independencies($symprec, $angle_tolerance))
|
|
1295
|
-
assert_equal([false, false, true ],
|
|
1296
|
-
@c11 .axis_independencies($symprec, $angle_tolerance))
|
|
1297
|
-
assert_equal([true , true , true ],
|
|
1298
|
-
@c12 .axis_independencies($symprec, $angle_tolerance))
|
|
1299
|
-
assert_equal([true , true , true ],
|
|
1300
|
-
@c13 .axis_independencies($symprec, $angle_tolerance))
|
|
1301
|
-
assert_equal([false, false, true ],
|
|
1302
|
-
@c14 .axis_independencies($symprec, $angle_tolerance))
|
|
1303
|
-
assert_equal([false, true , false],
|
|
1304
|
-
@c14b.axis_independencies($symprec, $angle_tolerance))
|
|
1305
|
-
assert_equal([true , true , true ],
|
|
1306
|
-
@c15 .axis_independencies($symprec, $angle_tolerance))
|
|
1307
|
-
assert_equal([false, false, true ],
|
|
1308
|
-
@c16 .axis_independencies($symprec, $angle_tolerance))
|
|
1309
|
-
end
|
|
1310
|
-
|
|
1311
|
-
def test_symmetry_operations
|
|
1312
|
-
unless defined? Getspg
|
|
1313
|
-
puts
|
|
1314
|
-
puts "test_symmetry_operations() is ignored because spglib is not installed."
|
|
1315
|
-
return
|
|
1316
|
-
end
|
|
1317
|
-
|
|
1318
|
-
f13 = 1.0/3.0
|
|
1319
|
-
|
|
1320
|
-
#cubic/POSCAR #Pm-3m (221) / m-3m / -P 4 2 3 (517)
|
|
1321
|
-
corrects = [
|
|
1322
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1323
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1324
|
-
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1325
|
-
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1326
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1327
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1328
|
-
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1329
|
-
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1330
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----09----
|
|
1331
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----10----
|
|
1332
|
-
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----11----
|
|
1333
|
-
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----12----
|
|
1334
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13----
|
|
1335
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14----
|
|
1336
|
-
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15----
|
|
1337
|
-
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16----
|
|
1338
|
-
{:rotation => [[ 0, 0, 1], [ 1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----17----
|
|
1339
|
-
{:rotation => [[ 0, 0, -1], [-1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----18----
|
|
1340
|
-
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----19----
|
|
1341
|
-
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----20----
|
|
1342
|
-
{:rotation => [[ 0, 0, 1], [-1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----21----
|
|
1343
|
-
{:rotation => [[ 0, 0, -1], [ 1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----22----
|
|
1344
|
-
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----23----
|
|
1345
|
-
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----24----
|
|
1346
|
-
{:rotation => [[ 0, 0, -1], [ 1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----25----
|
|
1347
|
-
{:rotation => [[ 0, 0, 1], [-1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----26----
|
|
1348
|
-
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----27----
|
|
1349
|
-
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----28----
|
|
1350
|
-
{:rotation => [[ 0, 0, -1], [-1, 0, 0], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----29----
|
|
1351
|
-
{:rotation => [[ 0, 0, 1], [ 1, 0, 0], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----30----
|
|
1352
|
-
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----31----
|
|
1353
|
-
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----32----
|
|
1354
|
-
{:rotation => [[ 0, 1, 0], [ 0, 0, 1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----33----
|
|
1355
|
-
{:rotation => [[ 0, -1, 0], [ 0, 0, -1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----34----
|
|
1356
|
-
{:rotation => [[ 1, 0, 0], [ 0, 0, 1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----35----
|
|
1357
|
-
{:rotation => [[-1, 0, 0], [ 0, 0, -1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----36----
|
|
1358
|
-
{:rotation => [[ 0, -1, 0], [ 0, 0, 1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----37----
|
|
1359
|
-
{:rotation => [[ 0, 1, 0], [ 0, 0, -1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----38----
|
|
1360
|
-
{:rotation => [[-1, 0, 0], [ 0, 0, 1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----39----
|
|
1361
|
-
{:rotation => [[ 1, 0, 0], [ 0, 0, -1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----40----
|
|
1362
|
-
{:rotation => [[ 0, -1, 0], [ 0, 0, -1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----41----
|
|
1363
|
-
{:rotation => [[ 0, 1, 0], [ 0, 0, 1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----42----
|
|
1364
|
-
{:rotation => [[-1, 0, 0], [ 0, 0, -1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----43----
|
|
1365
|
-
{:rotation => [[ 1, 0, 0], [ 0, 0, 1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----44----
|
|
1366
|
-
{:rotation => [[ 0, 1, 0], [ 0, 0, -1], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----45----
|
|
1367
|
-
{:rotation => [[ 0, -1, 0], [ 0, 0, 1], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----46----
|
|
1368
|
-
{:rotation => [[ 1, 0, 0], [ 0, 0, -1], [ 0, 1, 0]], :translation => [0.0, 0.0, 0.0]}, #----47----
|
|
1369
|
-
{:rotation => [[-1, 0, 0], [ 0, 0, 1], [ 0, -1, 0]], :translation => [0.0, 0.0, 0.0]}, #----48----
|
|
1370
|
-
]
|
|
1371
|
-
|
|
1372
|
-
results = @c10 .symmetry_operations($symprec, $angle_tolerance)
|
|
1373
|
-
assert_equal(corrects.size, results.size)
|
|
1374
|
-
corrects.size.times do |index|
|
|
1375
|
-
assert_equal(corrects[index], results[index])
|
|
1376
|
-
end
|
|
1377
|
-
|
|
1378
|
-
#monoclinic/POSCAR #P2/m (10) / 2/m / -P 2y (57)
|
|
1379
|
-
corrects = [
|
|
1380
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1381
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1382
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1383
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1384
|
-
]
|
|
1385
|
-
#pp @c12
|
|
1386
|
-
assert_equal(corrects, @c12 .symmetry_operations($symprec, $angle_tolerance)) #monoclinic
|
|
1387
|
-
|
|
1388
|
-
#orthorhombic/POSCAR #Pmmm (47) / mmm / -P 2 2 (227)
|
|
1389
|
-
corrects = [
|
|
1390
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1391
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1392
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1393
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1394
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1395
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1396
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1397
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1398
|
-
]
|
|
1399
|
-
assert_equal(corrects, @c13 .symmetry_operations($symprec, $angle_tolerance)) #orthorhombic
|
|
1400
|
-
|
|
1401
|
-
#tetragonal-b/POSCAR #P4/mmm (123) / 4/mmm/ -P 4 2 (400)
|
|
1402
|
-
corrects = [
|
|
1403
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1404
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1405
|
-
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1406
|
-
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1407
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1408
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1409
|
-
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1410
|
-
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1411
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----09----
|
|
1412
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----10----
|
|
1413
|
-
{:rotation => [[ 0, 0, -1], [ 0, -1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----11----
|
|
1414
|
-
{:rotation => [[ 0, 0, 1], [ 0, 1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----12----
|
|
1415
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13----
|
|
1416
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14----
|
|
1417
|
-
{:rotation => [[ 0, 0, 1], [ 0, -1, 0], [ 1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----15----
|
|
1418
|
-
{:rotation => [[ 0, 0, -1], [ 0, 1, 0], [-1, 0, 0]], :translation => [0.0, 0.0, 0.0]}, #----16----
|
|
1419
|
-
]
|
|
1420
|
-
assert_equal(corrects, @c14b .symmetry_operations($symprec, $angle_tolerance)) #tetragonal
|
|
1421
|
-
|
|
1422
|
-
#tetragonal/POSCAR #P4/mmm (123) / 4/mmm/ -P 4 2 (400)
|
|
1423
|
-
corrects = [
|
|
1424
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1425
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----02----
|
|
1426
|
-
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----03----
|
|
1427
|
-
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----04----
|
|
1428
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----05----
|
|
1429
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----06----
|
|
1430
|
-
{:rotation => [[ 0, 1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----07----
|
|
1431
|
-
{:rotation => [[ 0, -1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----08----
|
|
1432
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----09----
|
|
1433
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----10----
|
|
1434
|
-
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----11----
|
|
1435
|
-
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----12----
|
|
1436
|
-
{:rotation => [[-1, 0, 0], [ 0, 1, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----13----
|
|
1437
|
-
{:rotation => [[ 1, 0, 0], [ 0, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----14----
|
|
1438
|
-
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, -1]], :translation => [0.0, 0.0, 0.0]}, #----15----
|
|
1439
|
-
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----16----
|
|
1440
|
-
]
|
|
1441
|
-
assert_equal(corrects, @c14.symmetry_operations($symprec, $angle_tolerance)) #tetragonal-b
|
|
1442
|
-
|
|
1443
|
-
#triclinic/POSCAR #P1 (1) / 1 / P 1 (1)
|
|
1444
|
-
corrects = [
|
|
1445
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1446
|
-
]
|
|
1447
|
-
assert_equal(corrects, @c15 .symmetry_operations($symprec, $angle_tolerance)) #triclinic
|
|
1448
|
-
|
|
1449
|
-
#trigonal/POSCAR #P-3m1 (164) / -3m / -P 3 2= (456)
|
|
1450
|
-
corrects = [
|
|
1451
|
-
{:rotation => [[ 1, 0, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 0.0]}, #----01----
|
|
1452
|
-
{:rotation => [[-1, 0, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----02----
|
|
1453
|
-
{:rotation => [[-1, -1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----03----
|
|
1454
|
-
{:rotation => [[ 1, 1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----04----
|
|
1455
|
-
{:rotation => [[ 0, 1, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [1.0, 0.0, 1.0]}, #----05----
|
|
1456
|
-
{:rotation => [[ 0, -1, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----06----
|
|
1457
|
-
{:rotation => [[ 0, -1, 0], [-1, 0, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----07----
|
|
1458
|
-
{:rotation => [[ 0, 1, 0], [ 1, 0, 0], [ 0, 0, 1]], :translation => [1.0, 0.0, 1.0]}, #----08----
|
|
1459
|
-
{:rotation => [[-1, 0, 0], [ 1, 1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----09----
|
|
1460
|
-
{:rotation => [[ 1, 0, 0], [-1, -1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----10----
|
|
1461
|
-
{:rotation => [[ 1, 1, 0], [ 0, -1, 0], [ 0, 0, -1]], :translation => [f13, f13, f13]}, #----11----
|
|
1462
|
-
{:rotation => [[-1, -1, 0], [ 0, 1, 0], [ 0, 0, 1]], :translation => [0.0, 0.0, 1.0]}, #----12----
|
|
1463
|
-
]
|
|
1464
|
-
results = @c16.symmetry_operations($symprec, $angle_tolerance)
|
|
1465
|
-
corrects.size.times do |index|
|
|
1466
|
-
3.times do |i|
|
|
1467
|
-
3.times do |j|
|
|
1468
|
-
assert_in_delta(
|
|
1469
|
-
corrects[index][:rotation][i][j] %1.0,
|
|
1470
|
-
results[index][:rotation][i][j] %1.0,
|
|
1471
|
-
$tolerance
|
|
1472
|
-
)
|
|
1473
|
-
end
|
|
1474
|
-
end
|
|
1475
|
-
|
|
1476
|
-
3.times do |i|
|
|
1477
|
-
assert_in_delta(
|
|
1478
|
-
corrects[index][:translation][i] % 1.0,
|
|
1479
|
-
results[index][:translation][i] %1.0,
|
|
1480
|
-
$tolerance
|
|
1481
|
-
)
|
|
1482
|
-
end
|
|
1483
|
-
end
|
|
1484
|
-
end
|
|
1477
|
+
#corrects.size.times do |index|
|
|
1478
|
+
# 3.times do |i|
|
|
1479
|
+
# 3.times do |j|
|
|
1480
|
+
# assert_in_delta(
|
|
1481
|
+
# corrects[index][:rotation][i][j] %1.0,
|
|
1482
|
+
# results[index][:rotation][i][j] %1.0,
|
|
1483
|
+
# $tolerance
|
|
1484
|
+
# )
|
|
1485
|
+
# end
|
|
1486
|
+
# end
|
|
1487
|
+
|
|
1488
|
+
# 3.times do |i|
|
|
1489
|
+
# assert_in_delta(
|
|
1490
|
+
# corrects[index][:translation][i] % 1.0,
|
|
1491
|
+
# results[index][:translation][i] %1.0,
|
|
1492
|
+
# $tolerance
|
|
1493
|
+
# )
|
|
1494
|
+
# end
|
|
1495
|
+
#end
|
|
1496
|
+
end
|
|
1497
|
+
|
|
1498
|
+
def dump_povray
|
|
1499
|
+
#pp @c01
|
|
1500
|
+
##TODO
|
|
1501
|
+
end
|
|
1485
1502
|
|
|
1486
1503
|
end
|