crystalcell 0.0.2 → 0.0.3
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- data/CHANGES +1 -0
- data/VERSION +1 -1
- data/crystalcell.gemspec +81 -0
- data/lib/crystalcell/atom.rb +118 -118
- data/lib/crystalcell/cell.rb +584 -584
- data/lib/crystalcell/element.rb +135 -135
- data/lib/crystalcell/latticeaxes.rb +194 -188
- data/lib/crystalcell/periodiccell.rb +244 -244
- data/test/test_atom.rb +198 -198
- data/test/test_cell.rb +1450 -1478
- data/test/test_element.rb +642 -642
- data/test/test_latticeaxes.rb +283 -278
- data/test/test_periodiccell.rb +948 -948
- metadata +4 -3
data/test/test_latticeaxes.rb
CHANGED
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@@ -4,287 +4,292 @@ require "helper"
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require "rubygems"
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class CrystalCell::LatticeAxes
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#public :triangulate, :rotate
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#public :rotate
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end
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class TC_LatticeAxes < Test::Unit::TestCase
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assert_in_delta(
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$tolerance = 10 ** (-10)
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include Math
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def setup
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@axes1 = [ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ]
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@lc1 = CrystalCell::LatticeAxes.new([ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ])
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@lc2 = CrystalCell::LatticeAxes.new([ [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5] ])
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@lc3 = CrystalCell::LatticeAxes.new(CrystalCell::LatticeAxes.lc_to_axes([1.0, 1.0, 1.0, 90.0, 90.0, 90.0]))
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@lc4 = CrystalCell::LatticeAxes.new(
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CrystalCell::LatticeAxes.lc_to_axes(
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[ Math::sqrt(0.5), Math::sqrt(0.5), Math::sqrt(0.5),
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60.0, 60.0, 60.0]) # Math::sqrt(0.5) == 0.5* Math::sqrt(2.0)
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)
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@lc5 = CrystalCell::LatticeAxes.new([ [1.0, 1.0, 1.0], [0.0, 1.0, 1.0], [0.0, 0.0, 1.0] ])
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@lc6 = CrystalCell::LatticeAxes.new([ [1.0, 1.0, 1.0], [0.0,-1.0,-1.0], [0.0, 0.0, 1.0] ])
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@vec_x = Mageo::Vector3D[ 1.0, 0.0, 0.0 ]
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@vec_y = Mageo::Vector3D[ 0.0, 1.0, 0.0 ]
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@vec_z = Mageo::Vector3D[ 0.0, 0.0, 1.0 ]
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@vec_0 = Mageo::Vector3D[ 0.0, 0.0, 0.0 ]
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@vec_1 = Mageo::Vector3D[ 1.0, 1.0, 0.0 ]
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end
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def test_initialize
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assert_raise(ArgumentError) { CrystalCell::LatticeAxes.new }
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assert_raise(CrystalCell::LatticeAxes::InitializeError) { CrystalCell::LatticeAxes.new([]) }
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assert_raise(CrystalCell::LatticeAxes::InitializeError) {
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CrystalCell::LatticeAxes.new([1.0, 1.0, 1.0, 90.0, 90.0, 90.0])
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}
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assert_raise(CrystalCell::LatticeAxes::InitializeError) {CrystalCell::LatticeAxes.new([0,1])}
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assert_raise(CrystalCell::LatticeAxes::InitializeError) {CrystalCell::LatticeAxes.new([0,1,2,3])}
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assert_nothing_raised {CrystalCell::LatticeAxes.new([ @vec_x, @vec_y, @vec_z ]) }
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assert_raise(CrystalCell::LatticeAxes::InitializeError) {CrystalCell::LatticeAxes.new([ @vec_x, @vec_y, @vec_0 ]) }
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assert_raise(CrystalCell::LatticeAxes::InitializeError) {CrystalCell::LatticeAxes.new([ @vec_x, @vec_y, [1, 2, 3, 4] ]) }
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assert_in_delta(1.0, @lc1.axes[0][0], $tolerance)
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assert_in_delta(0.0, @lc1.axes[0][1], $tolerance)
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assert_in_delta(0.0, @lc1.axes[0][2], $tolerance)
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assert_in_delta(0.0, @lc1.axes[1][0], $tolerance)
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assert_in_delta(1.0, @lc1.axes[1][1], $tolerance)
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assert_in_delta(0.0, @lc1.axes[1][2], $tolerance)
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assert_in_delta(0.0, @lc1.axes[2][0], $tolerance)
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assert_in_delta(0.0, @lc1.axes[2][1], $tolerance)
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assert_in_delta(1.0, @lc1.axes[2][2], $tolerance)
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assert_in_delta(- 0.577350269189626, @lc2.axes[0][0], $tolerance)
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assert_in_delta( 0.204124145231932, @lc2.axes[0][1], $tolerance)
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assert_in_delta( 0.353553390593274, @lc2.axes[0][2], $tolerance)
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assert_in_delta( 0.000000000000000, @lc2.axes[1][0], $tolerance)
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assert_in_delta( 0.612372435695795, @lc2.axes[1][1], $tolerance)
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assert_in_delta( 0.353553390593274, @lc2.axes[1][2], $tolerance)
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assert_in_delta( 0.000000000000000, @lc2.axes[2][0], $tolerance)
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assert_in_delta( 0.000000000000000, @lc2.axes[2][1], $tolerance)
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assert_in_delta( 0.707106781186548, @lc2.axes[2][2], $tolerance)
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assert_in_delta(1.0, @lc3.axes[0][0], $tolerance)
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assert_in_delta(0.0, @lc3.axes[0][1], $tolerance)
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assert_in_delta(0.0, @lc3.axes[0][2], $tolerance)
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assert_in_delta(0.0, @lc3.axes[1][0], $tolerance)
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assert_in_delta(1.0, @lc3.axes[1][1], $tolerance)
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assert_in_delta(0.0, @lc3.axes[1][2], $tolerance)
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assert_in_delta(0.0, @lc3.axes[2][0], $tolerance)
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assert_in_delta(0.0, @lc3.axes[2][1], $tolerance)
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assert_in_delta(1.0, @lc3.axes[2][2], $tolerance)
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assert_in_delta(0.577350269189626, @lc4.axes[0][0], $tolerance)
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assert_in_delta(0.204124145231932, @lc4.axes[0][1], $tolerance)
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assert_in_delta(0.353553390593274, @lc4.axes[0][2], $tolerance)
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assert_in_delta(0.000000000000000, @lc4.axes[1][0], $tolerance)
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assert_in_delta(0.612372435695795, @lc4.axes[1][1], $tolerance)
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assert_in_delta(0.353553390593274, @lc4.axes[1][2], $tolerance)
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assert_in_delta(0.000000000000000, @lc4.axes[2][0], $tolerance)
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assert_in_delta(0.000000000000000, @lc4.axes[2][1], $tolerance)
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assert_in_delta(0.707106781186548, @lc4.axes[2][2], $tolerance)
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# triangulate の結果、b 軸の y 成分は 正方向であるべき。
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assert_in_delta(-1.0, @lc6.axes[0][0], $tolerance)
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assert_in_delta(-1.0, @lc6.axes[0][1], $tolerance)
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assert_in_delta(1.0, @lc6.axes[0][2], $tolerance)
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assert_in_delta(0.0, @lc6.axes[1][0], $tolerance)
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assert_in_delta(1.0, @lc6.axes[1][1], $tolerance)
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assert_in_delta(-1.0, @lc6.axes[1][2], $tolerance)
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assert_in_delta(0.0, @lc6.axes[2][0], $tolerance)
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assert_in_delta(0.0, @lc6.axes[2][1], $tolerance)
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assert_in_delta(1.0, @lc6.axes[2][2], $tolerance)
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end
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+
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102
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+
## Class methods.
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103
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+
#
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104
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+
def test_new_lc
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105
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+
result = CrystalCell::LatticeAxes.new_lc([1.0, 1.0, 1.0, 90.0, 90.0, 90.0])
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106
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+
assert_equal(@lc3, result)
|
|
107
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+
end
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|
108
|
+
|
|
109
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+
#def test_self_triangulate
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110
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+
# result = CrystalCell::LatticeAxes.triangulate([ [0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5] ])
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111
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+
# assert_in_delta(0.577350269189626, result[0][0], $tolerance)
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112
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+
# assert_in_delta(0.204124145231932, result[0][1], $tolerance)
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113
|
+
# assert_in_delta(0.353553390593274, result[0][2], $tolerance)
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114
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+
# assert_in_delta(0.000000000000000, result[1][0], $tolerance)
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115
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+
# assert_in_delta(0.612372435695795, result[1][1], $tolerance)
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116
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+
# assert_in_delta(0.353553390593274, result[1][2], $tolerance)
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117
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+
# assert_in_delta(0.000000000000000, result[2][0], $tolerance)
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118
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+
# assert_in_delta(0.000000000000000, result[2][1], $tolerance)
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119
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+
# assert_in_delta(0.707106781186548, result[2][2], $tolerance)
|
|
120
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+
#end
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121
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+
|
|
122
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+
def test_self_lc_to_axes
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123
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+
axes = CrystalCell::LatticeAxes.lc_to_axes([ 1.0, 1.0, 1.0, 90.0, 90.0, 90.0 ])
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124
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+
assert_in_delta(@axes1[0][0], axes[0][0], $tolerance)
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|
125
|
+
assert_in_delta(@axes1[0][1], axes[0][1], $tolerance)
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|
126
|
+
assert_in_delta(@axes1[0][2], axes[0][2], $tolerance)
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|
127
|
+
assert_in_delta(@axes1[1][0], axes[1][0], $tolerance)
|
|
128
|
+
assert_in_delta(@axes1[1][1], axes[1][1], $tolerance)
|
|
129
|
+
assert_in_delta(@axes1[1][2], axes[1][2], $tolerance)
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|
130
|
+
assert_in_delta(@axes1[2][0], axes[2][0], $tolerance)
|
|
131
|
+
assert_in_delta(@axes1[2][1], axes[2][1], $tolerance)
|
|
132
|
+
assert_in_delta(@axes1[2][2], axes[2][2], $tolerance)
|
|
133
|
+
|
|
134
|
+
axes = CrystalCell::LatticeAxes.lc_to_axes([ 1.0, 1.0, 1.0, 90.0, 90.0, 90.0 ], false)
|
|
135
|
+
assert_in_delta(- @axes1[0][0], axes[0][0], $tolerance)
|
|
136
|
+
assert_in_delta( @axes1[0][1], axes[0][1], $tolerance)
|
|
137
|
+
assert_in_delta( @axes1[0][2], axes[0][2], $tolerance)
|
|
138
|
+
assert_in_delta( @axes1[1][0], axes[1][0], $tolerance)
|
|
139
|
+
assert_in_delta( @axes1[1][1], axes[1][1], $tolerance)
|
|
140
|
+
assert_in_delta( @axes1[1][2], axes[1][2], $tolerance)
|
|
141
|
+
assert_in_delta( @axes1[2][0], axes[2][0], $tolerance)
|
|
142
|
+
assert_in_delta( @axes1[2][1], axes[2][1], $tolerance)
|
|
143
|
+
assert_in_delta( @axes1[2][2], axes[2][2], $tolerance)
|
|
144
|
+
end
|
|
145
|
+
|
|
146
|
+
def test_self_axes_to_lc
|
|
147
|
+
correct = [ 1.0, 1.0, 1.0, 90.0, 90.0, 90.0 ]
|
|
148
|
+
assert_equal(correct, CrystalCell::LatticeAxes.axes_to_lc(@axes1))
|
|
149
|
+
|
|
150
|
+
#correct = [ 1.0, 1.0, 1.0, 90.0, 90.0, 90.0 ]
|
|
151
|
+
#assert_equal(correct, CrystalCell::LatticeAxes.axes_to_lc(@axes1))
|
|
152
|
+
end
|
|
153
|
+
|
|
154
|
+
def test_equal_in_delta?
|
|
155
|
+
assert_equal(true , @lc1.equal_in_delta?(@lc1, 0.01, 1.0))
|
|
156
|
+
assert_equal(false, @lc1.equal_in_delta?(@lc2, 0.01, 1.0))
|
|
157
|
+
assert_equal(false, @lc1.equal_in_delta?(@lc4, 0.01, 1.0))
|
|
158
|
+
assert_equal(false, @lc2.equal_in_delta?(@lc1, 0.01, 1.0))
|
|
159
|
+
assert_equal(true , @lc2.equal_in_delta?(@lc2, 0.01, 1.0))
|
|
160
|
+
assert_equal(true , @lc2.equal_in_delta?(@lc4, 0.01, 1.0))
|
|
161
|
+
assert_equal(false, @lc4.equal_in_delta?(@lc1, 0.01, 1.0))
|
|
162
|
+
assert_equal(true , @lc4.equal_in_delta?(@lc2, 0.01, 1.0))
|
|
163
|
+
assert_equal(true , @lc4.equal_in_delta?(@lc4, 0.01, 1.0))
|
|
164
|
+
end
|
|
165
|
+
|
|
166
|
+
def test_self_righthand?
|
|
167
|
+
# Righthand
|
|
168
|
+
assert_equal(true , CrystalCell::LatticeAxes.righthand?([ @vec_x, @vec_y, @vec_z ]))
|
|
169
|
+
assert_equal(true , CrystalCell::LatticeAxes.righthand?([ @vec_y, @vec_z, @vec_x ]))
|
|
170
|
+
assert_equal(true , CrystalCell::LatticeAxes.righthand?([ @vec_z, @vec_x, @vec_y ]))
|
|
171
|
+
|
|
172
|
+
# Lefthand
|
|
173
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_z, @vec_y, @vec_x ]))
|
|
174
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_x, @vec_z, @vec_y ]))
|
|
175
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_y, @vec_x, @vec_z ]))
|
|
176
|
+
|
|
177
|
+
# Including zero vector.
|
|
178
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_0, @vec_y, @vec_z ]))
|
|
179
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_0, @vec_z, @vec_x ]))
|
|
180
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_0, @vec_x, @vec_y ]))
|
|
181
|
+
|
|
182
|
+
# One vector is on the plane of residual two vectors.
|
|
183
|
+
assert_equal(false, CrystalCell::LatticeAxes.righthand?([ @vec_x, @vec_y, @vec_1 ]))
|
|
184
|
+
end
|
|
185
|
+
|
|
186
|
+
def test_self_lefthand?
|
|
187
|
+
# Righthand
|
|
188
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_x, @vec_y, @vec_z ]))
|
|
189
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_y, @vec_z, @vec_x ]))
|
|
190
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_z, @vec_x, @vec_y ]))
|
|
191
|
+
|
|
192
|
+
# Lefthand
|
|
193
|
+
assert_equal(true , CrystalCell::LatticeAxes.lefthand?([ @vec_z, @vec_y, @vec_x ]))
|
|
194
|
+
assert_equal(true , CrystalCell::LatticeAxes.lefthand?([ @vec_x, @vec_z, @vec_y ]))
|
|
195
|
+
assert_equal(true , CrystalCell::LatticeAxes.lefthand?([ @vec_y, @vec_x, @vec_z ]))
|
|
196
|
+
|
|
197
|
+
# Including zero vector.
|
|
198
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_0, @vec_y, @vec_z ]))
|
|
199
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_0, @vec_z, @vec_x ]))
|
|
200
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_0, @vec_x, @vec_y ]))
|
|
201
|
+
|
|
202
|
+
# One vector is on the plane of residual two vectors.
|
|
203
|
+
assert_equal(false, CrystalCell::LatticeAxes.lefthand?([ @vec_x, @vec_y, @vec_1 ]))
|
|
204
|
+
end
|
|
205
|
+
|
|
206
|
+
## Instance methods.
|
|
207
|
+
|
|
208
|
+
def test_get_lattice_constants
|
|
209
|
+
assert_in_delta( 1.0, @lc1.get_lattice_constants[0], $tolerance)
|
|
210
|
+
assert_in_delta( 1.0, @lc1.get_lattice_constants[1], $tolerance)
|
|
211
|
+
assert_in_delta( 1.0, @lc1.get_lattice_constants[2], $tolerance)
|
|
212
|
+
assert_in_delta(90.0, @lc1.get_lattice_constants[3], $tolerance)
|
|
213
|
+
assert_in_delta(90.0, @lc1.get_lattice_constants[4], $tolerance)
|
|
214
|
+
assert_in_delta(90.0, @lc1.get_lattice_constants[5], $tolerance)
|
|
215
|
+
assert_in_delta(Math::sqrt(0.5), @lc2.get_lattice_constants[0], $tolerance)
|
|
216
|
+
assert_in_delta(Math::sqrt(0.5), @lc2.get_lattice_constants[1], $tolerance)
|
|
217
|
+
assert_in_delta(Math::sqrt(0.5), @lc2.get_lattice_constants[2], $tolerance)
|
|
218
|
+
assert_in_delta(60.0, @lc2.get_lattice_constants[3], $tolerance)
|
|
219
|
+
assert_in_delta(60.0, @lc2.get_lattice_constants[4], $tolerance)
|
|
220
|
+
assert_in_delta(60.0, @lc2.get_lattice_constants[5], $tolerance)
|
|
221
|
+
assert_in_delta( 1.0, @lc3.get_lattice_constants[0], $tolerance)
|
|
222
|
+
assert_in_delta( 1.0, @lc3.get_lattice_constants[1], $tolerance)
|
|
223
|
+
assert_in_delta( 1.0, @lc3.get_lattice_constants[2], $tolerance)
|
|
224
|
+
assert_in_delta(90.0, @lc3.get_lattice_constants[3], $tolerance)
|
|
225
|
+
assert_in_delta(90.0, @lc3.get_lattice_constants[4], $tolerance)
|
|
226
|
+
assert_in_delta(90.0, @lc3.get_lattice_constants[5], $tolerance)
|
|
227
|
+
assert_in_delta(Math::sqrt(0.5), @lc4.get_lattice_constants[0], $tolerance)
|
|
228
|
+
assert_in_delta(Math::sqrt(0.5), @lc4.get_lattice_constants[1], $tolerance)
|
|
229
|
+
assert_in_delta(Math::sqrt(0.5), @lc4.get_lattice_constants[2], $tolerance)
|
|
230
|
+
assert_in_delta(60.0, @lc4.get_lattice_constants[3], $tolerance)
|
|
231
|
+
assert_in_delta(60.0, @lc4.get_lattice_constants[4], $tolerance)
|
|
232
|
+
assert_in_delta(60.0, @lc4.get_lattice_constants[5], $tolerance)
|
|
233
|
+
end
|
|
234
|
+
|
|
235
|
+
def test_righthand?
|
|
236
|
+
assert_equal(true , @lc1.righthand?)
|
|
237
|
+
assert_equal(false, @lc2.righthand?)
|
|
238
|
+
end
|
|
239
|
+
|
|
240
|
+
def test_lefthand?
|
|
241
|
+
assert_equal(false, @lc1.lefthand?)
|
|
242
|
+
assert_equal(true , @lc2.lefthand?)
|
|
243
|
+
end
|
|
244
|
+
|
|
245
|
+
#def test_internal2cartesian
|
|
246
|
+
# assert_raise(CrystalCell::LatticeAxes::TypeError){
|
|
247
|
+
# @lc5.internal2cartesian([ 2.0, 3.0, 4.0 ])
|
|
248
|
+
# }
|
|
249
|
+
# assert_in_delta(2.0, @lc5.internal2cartesian([ 2.0, 3.0, 4.0 ])[0], $tolerance)
|
|
250
|
+
# assert_in_delta(5.0, @lc5.internal2cartesian([ 2.0, 3.0, 4.0 ])[1], $tolerance)
|
|
251
|
+
# assert_in_delta(9.0, @lc5.internal2cartesian([ 2.0, 3.0, 4.0 ])[2], $tolerance)
|
|
252
|
+
#end
|
|
253
|
+
|
|
254
|
+
#def test_cartesian2internal
|
|
255
|
+
# assert_in_delta(2.0, @lc5.cartesian2internal([ 2.0, 5.0, 9.0 ])[0], $tolerance)
|
|
256
|
+
# assert_in_delta(3.0, @lc5.cartesian2internal([ 2.0, 5.0, 9.0 ])[1], $tolerance)
|
|
257
|
+
# assert_in_delta(4.0, @lc5.cartesian2internal([ 2.0, 5.0, 9.0 ])[2], $tolerance)
|
|
258
|
+
#end
|
|
259
|
+
|
|
260
|
+
def test_equal
|
|
261
|
+
assert_equal(true , @lc1 == @lc1)
|
|
262
|
+
assert_equal(true , @lc2 == @lc2)
|
|
263
|
+
assert_equal(true , @lc3 == @lc3)
|
|
264
|
+
|
|
265
|
+
assert_equal(false, @lc1 == @lc2)
|
|
266
|
+
assert_equal(false, @lc2 == @lc3)
|
|
267
|
+
assert_equal(true , @lc3 == @lc1)
|
|
268
|
+
|
|
269
|
+
assert_equal(true , @lc1 == @lc3)
|
|
270
|
+
assert_equal(false, @lc2 == @lc1)
|
|
271
|
+
assert_equal(false, @lc3 == @lc2)
|
|
272
|
+
end
|
|
273
|
+
|
|
274
|
+
def test_triangulate
|
|
275
|
+
t = CrystalCell::LatticeAxes.new([ [0.5, 0.5, 0.0], [0.0, 0.5, 0.5], [0.5, 0.0, 0.5] ])
|
|
276
|
+
assert_in_delta(0.577350269189626, t[0][0], $tolerance)
|
|
277
|
+
assert_in_delta(0.204124145231932, t[0][1], $tolerance)
|
|
278
|
+
assert_in_delta(0.353553390593274, t[0][2], $tolerance)
|
|
279
|
+
assert_in_delta(0.000000000000000, t[1][0], $tolerance)
|
|
280
|
+
assert_in_delta(0.612372435695795, t[1][1], $tolerance)
|
|
281
|
+
assert_in_delta(0.353553390593274, t[1][2], $tolerance)
|
|
282
|
+
assert_in_delta(0.000000000000000, t[2][0], $tolerance)
|
|
283
|
+
assert_in_delta(0.000000000000000, t[2][1], $tolerance)
|
|
284
|
+
assert_in_delta(0.707106781186548, t[2][2], $tolerance)
|
|
285
|
+
end
|
|
286
|
+
|
|
287
|
+
#def test_rotate
|
|
288
|
+
# #@lc1 = CrystalCell::LatticeAxes.new([ [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0] ])
|
|
289
|
+
# @lc1.rotate(0, 1, 2)
|
|
290
|
+
#
|
|
291
|
+
# TODO
|
|
292
|
+
#end
|
|
288
293
|
|
|
289
294
|
|
|
290
295
|
end
|