crystalcell 0.0.0
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- data/.document +5 -0
- data/Gemfile +17 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +19 -0
- data/Rakefile +55 -0
- data/VERSION +1 -0
- data/lib/crystalcell/atom.rb +133 -0
- data/lib/crystalcell/cell.rb +547 -0
- data/lib/crystalcell/element.rb +148 -0
- data/lib/crystalcell/latticeaxes.rb +210 -0
- data/lib/crystalcell/periodiccell.rb +277 -0
- data/lib/crystalcell.rb +0 -0
- data/test/helper.rb +17 -0
- data/test/test_atom.rb +210 -0
- data/test/test_cell.rb +1167 -0
- data/test/test_element.rb +656 -0
- data/test/test_latticeaxes.rb +294 -0
- data/test/test_periodiccell.rb +965 -0
- metadata +197 -0
data/test/test_atom.rb
ADDED
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#! /usr/bin/ruby
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require "test/unit"
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4
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require "crystalcell/atom.rb"
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require "rubygems"
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6
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gem "mageo"
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require "mageo/vector3d.rb"
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8
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9
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class TC_Atom < Test::Unit::TestCase
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$tolerance = 10.0 ** (-10)
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11
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def setup
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@a0 = Atom.new("Li", [ 0.0, 0.0, 0.0 ])
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14
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@a1 = Atom.new("Li", [ 1.0, 1.0, 1.0 ])
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15
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@a2 = Atom.new("Li", [ 0.0, 0.0, 0.0 ])
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16
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@a3 = Atom.new("Be", [ 0.0, 0.0, 0.0 ])
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@a4 = Atom.new("Li", [ 1.0, 2.3, 4.5 ])
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@a5 = Atom.new("Li", [-1.0,-2.3,-4.5 ])
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19
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@a6 = Atom.new( 3, [-1.0,-2.3,-4.5 ])
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end
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def test_initialize
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assert_raise(Atom::TypeError){ Atom.new(nil, nil, nil) }
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assert_raise(Atom::TypeError){ Atom.new(nil, nil, "A") }
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assert_raise(Atom::TypeError){ Atom.new(nil, [0.0, 0.0], "A") }
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assert_raise(Atom::TypeError){ Atom.new(nil, [0.0, 0.0, 0.0, 0.0], "A") }
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a0 = Atom.new(nil, [ 0.0, 0.0, 0.0], nil)
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a1 = Atom.new(nil, [ 0.0, 0.0, 0.0], "A")
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assert_equal(nil, a0.name)
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assert_equal("A", a1.name)
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end
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33
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def test_equal_in_delta?
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assert_equal(true , Atom.equal_in_delta?(@a0, @a0))
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assert_equal(false, Atom.equal_in_delta?(@a0, @a1))
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assert_equal(true , Atom.equal_in_delta?(@a0, @a2))
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assert_equal(false, Atom.equal_in_delta?(@a0, @a3))
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assert_equal(false, Atom.equal_in_delta?(@a1, @a0))
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assert_equal(true , Atom.equal_in_delta?(@a1, @a1))
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assert_equal(false, Atom.equal_in_delta?(@a1, @a2))
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assert_equal(false, Atom.equal_in_delta?(@a1, @a3))
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assert_equal(true , Atom.equal_in_delta?(@a2, @a0))
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assert_equal(false, Atom.equal_in_delta?(@a2, @a1))
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assert_equal(true , Atom.equal_in_delta?(@a2, @a2))
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assert_equal(false, Atom.equal_in_delta?(@a2, @a3))
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assert_equal(false, Atom.equal_in_delta?(@a3, @a0))
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assert_equal(false, Atom.equal_in_delta?(@a3, @a1))
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assert_equal(false, Atom.equal_in_delta?(@a3, @a2))
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assert_equal(true , Atom.equal_in_delta?(@a3, @a3))
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51
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assert_equal(true , Atom.equal_in_delta?(@a0, @a0, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a0, @a1, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a0, @a2, 2.0))
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assert_equal(false, Atom.equal_in_delta?(@a0, @a3, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a1, @a0, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a1, @a1, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a1, @a2, 2.0))
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assert_equal(false, Atom.equal_in_delta?(@a1, @a3, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a2, @a0, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a2, @a1, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a2, @a2, 2.0))
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assert_equal(false, Atom.equal_in_delta?(@a2, @a3, 2.0))
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63
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assert_equal(false, Atom.equal_in_delta?(@a3, @a0, 2.0))
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assert_equal(false, Atom.equal_in_delta?(@a3, @a1, 2.0))
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assert_equal(false, Atom.equal_in_delta?(@a3, @a2, 2.0))
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assert_equal(true , Atom.equal_in_delta?(@a3, @a3, 2.0))
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assert_equal(true , @a0.equal_in_delta?(@a0))
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assert_equal(false, @a0.equal_in_delta?(@a1))
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assert_equal(true , @a0.equal_in_delta?(@a2))
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assert_equal(false, @a0.equal_in_delta?(@a3))
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assert_equal(false, @a1.equal_in_delta?(@a0))
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assert_equal(true , @a1.equal_in_delta?(@a1))
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assert_equal(false, @a1.equal_in_delta?(@a2))
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assert_equal(false, @a1.equal_in_delta?(@a3))
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assert_equal(true , @a2.equal_in_delta?(@a0))
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assert_equal(false, @a2.equal_in_delta?(@a1))
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assert_equal(true , @a2.equal_in_delta?(@a2))
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assert_equal(false, @a2.equal_in_delta?(@a3))
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assert_equal(false, @a3.equal_in_delta?(@a0))
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assert_equal(false, @a3.equal_in_delta?(@a1))
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assert_equal(false, @a3.equal_in_delta?(@a2))
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assert_equal(true , @a3.equal_in_delta?(@a3))
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assert_equal(true , @a0.equal_in_delta?(@a0, 2.0))
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assert_equal(true , @a0.equal_in_delta?(@a1, 2.0))
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assert_equal(true , @a0.equal_in_delta?(@a2, 2.0))
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assert_equal(false, @a0.equal_in_delta?(@a3, 2.0))
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assert_equal(true , @a1.equal_in_delta?(@a0, 2.0))
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assert_equal(true , @a1.equal_in_delta?(@a1, 2.0))
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assert_equal(true , @a1.equal_in_delta?(@a2, 2.0))
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assert_equal(false, @a1.equal_in_delta?(@a3, 2.0))
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assert_equal(true , @a2.equal_in_delta?(@a0, 2.0))
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assert_equal(true , @a2.equal_in_delta?(@a1, 2.0))
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assert_equal(true , @a2.equal_in_delta?(@a2, 2.0))
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assert_equal(false, @a2.equal_in_delta?(@a3, 2.0))
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assert_equal(false, @a3.equal_in_delta?(@a0, 2.0))
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assert_equal(false, @a3.equal_in_delta?(@a1, 2.0))
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assert_equal(false, @a3.equal_in_delta?(@a2, 2.0))
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assert_equal(true , @a3.equal_in_delta?(@a3, 2.0))
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end
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def test_equal
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assert_equal(true, @a0 == Atom.new("Li", [0.0, 0.0, 0.0]))
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assert_equal(true, @a1 == Atom.new("Li", [1.0, 1.0, 1.0]))
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assert_equal(true, @a2 == Atom.new("Li", [0.0, 0.0, 0.0]))
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assert_equal(true, @a3 == Atom.new("Be", [0.0, 0.0, 0.0]))
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assert_equal(false, @a0 == Atom.new("Li", [0.9, 0.0, 0.0]))
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assert_equal(false, @a1 == Atom.new("Li", [1.1, 1.0, 1.0]))
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assert_equal(false, @a2 == Atom.new("Li", [0.9, 0.0, 0.0]))
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assert_equal(false, @a3 == Atom.new("Be", [0.9, 0.0, 0.0]))
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end
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def test_internal_coordinates
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assert_equal(Vector3DInternal[ 0.0, 0.0, 0.0 ], @a0.internal_coordinates)
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assert_equal(Vector3DInternal[ 0.0, 0.0, 0.0 ], @a1.internal_coordinates)
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assert_equal(Vector3DInternal[ 0.0, 0.0, 0.0 ], @a2.internal_coordinates)
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assert_equal(Vector3DInternal[ 0.0, 0.0, 0.0 ], @a3.internal_coordinates)
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121
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assert_equal(Vector3DInternal, @a4.internal_coordinates.class)
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assert_in_delta(0.0, @a4.internal_coordinates[0], $tolerance)
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assert_in_delta(0.3, @a4.internal_coordinates[1], $tolerance)
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assert_in_delta(0.5, @a4.internal_coordinates[2], $tolerance)
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assert_equal(Vector3DInternal, @a5.internal_coordinates.class)
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assert_in_delta(0.0, @a5.internal_coordinates[0], $tolerance)
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assert_in_delta(0.7, @a5.internal_coordinates[1], $tolerance)
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assert_in_delta(0.5, @a5.internal_coordinates[2], $tolerance)
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end
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def test_translation_symmetry_operation
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assert_equal(Vector3DInternal[ 0, 0, 0 ], @a0.translation_symmetry_operation)
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assert_equal(Vector3DInternal[ 1, 1, 1 ], @a1.translation_symmetry_operation)
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assert_equal(Vector3DInternal[ 0, 0, 0 ], @a2.translation_symmetry_operation)
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assert_equal(Vector3DInternal[ 0, 0, 0 ], @a3.translation_symmetry_operation)
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assert_equal(Vector3DInternal[ 1, 2, 4 ], @a4.translation_symmetry_operation)
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assert_equal(Vector3DInternal[-1,-3,-5 ], @a5.translation_symmetry_operation)
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end
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140
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141
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def test_set_position
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assert_equal(Vector3DInternal[ 1.2, 2.3, 3.4 ], @a3.set_position([ 1.2, 2.3, 3.4 ]))
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143
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assert_equal(Vector3DInternal[ 2.3, 3.4, 4.5 ], @a4.set_position([ 2.3, 3.4, 4.5 ]))
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assert_raise(Atom::TypeError){
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@a4.set_position(Vector3D[ 2.3, 3.4, 4.5 ])
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}
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end
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148
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149
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def test_element
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@a6.element = "Li"
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assert_equal(@a5, @a6)
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end
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153
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154
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def test_translate!
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@a0.translate!([ 1.2, 3.4, 5.6 ])
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156
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assert_equal("Li", @a0.element)
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157
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assert_in_delta(1.2 , @a0.position[0], $tolerance)
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158
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assert_in_delta(3.4 , @a0.position[1], $tolerance)
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159
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assert_in_delta(5.6 , @a0.position[2], $tolerance)
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160
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161
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@a3.translate!([ 1.2, 3.4, 5.6 ])
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162
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assert_equal("Be", @a3.element)
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163
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assert_in_delta(1.2 , @a3.position[0], $tolerance)
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164
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assert_in_delta(3.4 , @a3.position[1], $tolerance)
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165
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assert_in_delta(5.6 , @a3.position[2], $tolerance)
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166
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167
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168
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@a5.translate!([ 1.0, 1.0, 1.0 ])
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169
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assert_equal("Li", @a5.element)
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170
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assert_in_delta(0.0 , @a5.position[0], $tolerance)
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assert_in_delta(-1.3 , @a5.position[1], $tolerance)
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assert_in_delta(-3.5 , @a5.position[2], $tolerance)
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173
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174
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# Vector3D なら例外
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assert_raise(Atom::TypeError){ @a0.translate!(Vector3D[ 0.0, 0.0, 0.0 ]) }
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177
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# 3次元でなければ例外
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178
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assert_raise(Atom::TypeError){ @a0.translate!([ 0.0, 0.0 ]) }
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179
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assert_raise(Atom::TypeError){ @a0.translate!([ 0.0, 0.0, 0.0, 0.0 ]) }
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180
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end
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181
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182
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def test_translate
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183
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t = @a0.translate([ 1.2, 3.4, 5.6 ])
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184
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assert_equal("Li", t.element)
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185
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assert_in_delta(1.2, t.position[0], $tolerance)
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186
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assert_in_delta(3.4, t.position[1], $tolerance)
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187
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assert_in_delta(5.6, t.position[2], $tolerance)
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188
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189
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t = @a3.translate([ 1.2, 3.4, 5.6 ])
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190
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assert_equal("Be", t.element)
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191
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assert_in_delta(1.2, t.position[0], $tolerance)
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192
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assert_in_delta(3.4, t.position[1], $tolerance)
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193
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assert_in_delta(5.6, t.position[2], $tolerance)
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194
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195
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t = @a5.translate([ 1.0, 1.0, 1.0 ])
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196
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assert_equal("Li", t.element)
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197
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assert_in_delta(0.0, t.position[0], $tolerance)
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198
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assert_in_delta(-1.3, t.position[1], $tolerance)
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199
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assert_in_delta(-3.5, t.position[2], $tolerance)
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200
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+
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201
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# Vector3D なら例外
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202
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assert_raise(Atom::TypeError){ @a0.translate(Vector3D[ 0.0, 0.0, 0.0 ]) }
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203
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+
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204
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# 3次元でなければ例外
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205
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assert_raise(Atom::TypeError){ @a0.translate([ 0.0, 0.0 ]) }
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206
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assert_raise(Atom::TypeError){ @a0.translate([ 0.0, 0.0, 0.0, 0.0 ]) }
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207
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end
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208
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209
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end
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210
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